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Conserved domains on  [gi|133327|sp|P08775|]
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RecName: Full=DNA-directed RNA polymerase II subunit RPB1; Short=RNA polymerase II subunit B1; AltName: Full=3'-5' exoribonuclease; AltName: Full=DNA-directed RNA polymerase II subunit A; AltName: Full=DNA-directed RNA polymerase III largest subunit; AltName: Full=RNA-directed RNA polymerase II subunit RPB1

Protein Classification

DNA-directed RNA polymerase II subunit RPB1( domain architecture ID 11553359)

DNA-directed RNA polymerase II subunit RPB1, together with RPB2, forms the active site, DNA entry channel and RNA exit channel of RNAP II, a large multi-subunit complex responsible for the synthesis of mRNA

EC:  2.7.7.6
Gene Ontology:  GO:0006351|GO:0001055|GO:0003677|GO:0005665|GO:0046872
PubMed:  22365827

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNAP_II_RPB1_N cd02733
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
 19-876 0e+00

Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.


:

Pssm-ID: 259848 [Multi-domain]  Cd Length: 751  Bit Score: 1611.06  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     19 KRVQFGVLSPDELKRMSVTEggIKYPETTE-GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHV 97
Cdd:cd02733    1 KRVQFGILSPDEIRAMSVAE--IEHPETYEnGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     98 GFLVKTMKVLRCVCffcskllvdsnnpkikdilakskgqpkkrlthvydlckgkniceggeemdnkfgveqpegdedltk 177
Cdd:cd02733   79 GFLTKILKILRCVC------------------------------------------------------------------ 92

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    178 ekghggcgryqprirrsglelyaewkhvnedsqekKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPP 257
Cdd:cd02733   93 -----------------------------------KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPP 137

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    258 LSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLK 337
Cdd:cd02733  138 PAVRPSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLK 217

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    338 SLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAK 417
Cdd:cd02733  218 SIRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAK 297

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    418 YIIRDNGDRIDLRFHPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFD 497
Cdd:cd02733  298 YIIRDDGERIDLRYLKKASDLHLQYGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFD 377

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    498 GDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQP 577
Cdd:cd02733  378 GDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMWLPDWDGKIPQP 457

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    578 AILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPddedsGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISY 657
Cdd:cd02733  458 AILKPKPLWTGKQIFSLIIPKINNLIRSSSHHD-----GDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIW 532

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    658 LEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTF 737
Cdd:cd02733  533 LEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIGDTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESF 612

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    738 ENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGP 817
Cdd:cd02733  613 ENKVNRILNKARDKAGKSAQKSLSEDNNFKAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGP 692

                        810       820       830       840       850
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 133327    818 ESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD 876
Cdd:cd02733  693 ESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
RNAP_II_Rpb1_C cd02584
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
 1058-1476 0e+00

Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.


:

Pssm-ID: 132720 [Multi-domain]  Cd Length: 410  Bit Score: 821.84  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1058 FRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTP 1137
Cdd:cd02584    1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1138 SLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVA--RISPWLLRVE 1215
Cdd:cd02584   81 SLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEqdRLSPWLLRIE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1216 LDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKMQEeeevvdkMDDDVFLRCIESNMLTD 1295
Cdd:cd02584  161 LDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEED-------SEDDVFLKKIESNMLSD 233

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1296 MTLQGIEQISKVYMhlpQTDNKKKIIItEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVR 1375
Cdd:cd02584  234 MTLKGIEGIRKVFI---REENKKKVDI-ETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAAR 309

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1376 KALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVS 1455
Cdd:cd02584  310 KALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVS 389

                        410       420
                 ....*....|....*....|.
gi 133327   1456 ENIMLGQLAPAGTGCFDLLLD 1476
Cdd:cd02584  390 ENIMLGQLAPIGTGCFDLLLD 410
RNA_pol_Rpb1_6 pfam04992
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 896-1079 3.06e-96

RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.


:

Pssm-ID: 461511  Cd Length: 188  Bit Score: 308.27  E-value: 3.06e-96
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      896 LAGESVEFQNLATLKPSNKAFEKKFRFDYTNERA--LRRTLQEDLVKDVLSNAHIQNELEREFERMREDREVLR-VIFPT 972
Cdd:pfam04992    1 LDGAFIEKQKIDTLKLSDAAFEKRYRLDVMDEKSgfLPGYLEEGVIKEIAGDPEVQQLLDEEYEQLLEDRELLReIIFPT 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      973 GDSKVV-LPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLLFNIHLRSTLCS 1051
Cdd:pfam04992   81 GDSKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVVVRGDDPLSKEAQENATLLFKILLRSRLAS 160

                          170       180
                   ....*....|....*....|....*...
gi 133327     1052 RRMAEEFRLSGEAFDWLLGEIESKFNQA 1079
Cdd:pfam04992  161 KRVLEEYRLNKEAFDWVLGEIESRFLQA 188
Herpes_BLLF1 super family cl37540
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 1857-1961 1.96e-14

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


The actual alignment was detected with superfamily member pfam05109:

Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 79.19  E-value: 1.96e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1857 SPKYSPTSPKYSPTSPKYSP------------TSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYS 1924
Cdd:pfam05109  475 SPTPAGTTSGASPVTPSPSPrdngteskapdmTSPTSAVTTPTPNATSPTPAVTTPTPNATSPTLGKTSPTSAVTTPTPN 554

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 133327     1925 PTSPTYSPTSPKGSTYSP----TSPGYSPTSPTYSLTSPAI 1961
Cdd:pfam05109  555 ATSPTPAVTTPTPNATIPtlgkTSPTSAVTTPTPNATSPTV 595
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 1491-1610 3.16e-10

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


:

Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 59.46  E-value: 3.16e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      1491 PGLGAAGPTGMFFGSAPSPMGgiSPAMTP-WNQ--GATPAYGAWSPSVGSgmTP----GAAGFSPSAASDASGFSPGYSP 1563
Cdd:smart01104   15 PAWGSRTPGTAAGGAPTARGG--SGSRTPaWGGagSRTPAWGGAGPTGSR--TPawggASAWGNKSSEGSASSWAAGPGG 90

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 133327      1564 AWsptpgspgspgpsspyipspgGAMSPSYSPTSPAYEPRSPGGYTP 1610
Cdd:smart01104   91 AY---------------------GAPTPGYGGTPSAYGPATPGGGAM 116
 
Name Accession Description Interval E-value
RNAP_II_RPB1_N cd02733
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
 19-876 0e+00

Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.


Pssm-ID: 259848 [Multi-domain]  Cd Length: 751  Bit Score: 1611.06  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     19 KRVQFGVLSPDELKRMSVTEggIKYPETTE-GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHV 97
Cdd:cd02733    1 KRVQFGILSPDEIRAMSVAE--IEHPETYEnGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     98 GFLVKTMKVLRCVCffcskllvdsnnpkikdilakskgqpkkrlthvydlckgkniceggeemdnkfgveqpegdedltk 177
Cdd:cd02733   79 GFLTKILKILRCVC------------------------------------------------------------------ 92

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    178 ekghggcgryqprirrsglelyaewkhvnedsqekKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPP 257
Cdd:cd02733   93 -----------------------------------KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPP 137

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    258 LSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLK 337
Cdd:cd02733  138 PAVRPSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLK 217

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    338 SLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAK 417
Cdd:cd02733  218 SIRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAK 297

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    418 YIIRDNGDRIDLRFHPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFD 497
Cdd:cd02733  298 YIIRDDGERIDLRYLKKASDLHLQYGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFD 377

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    498 GDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQP 577
Cdd:cd02733  378 GDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMWLPDWDGKIPQP 457

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    578 AILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPddedsGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISY 657
Cdd:cd02733  458 AILKPKPLWTGKQIFSLIIPKINNLIRSSSHHD-----GDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIW 532

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    658 LEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTF 737
Cdd:cd02733  533 LEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIGDTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESF 612

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    738 ENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGP 817
Cdd:cd02733  613 ENKVNRILNKARDKAGKSAQKSLSEDNNFKAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGP 692

                        810       820       830       840       850
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 133327    818 ESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD 876
Cdd:cd02733  693 ESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
PRK08566 PRK08566
DNA-directed RNA polymerase subunit A'; Validated
 18-895 0e+00

DNA-directed RNA polymerase subunit A'; Validated


Pssm-ID: 236292 [Multi-domain]  Cd Length: 882  Bit Score: 992.05  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      18 IKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFH 96
Cdd:PRK08566    9 IGSIKFGLLSPEEIRKMSVTK--IITADTyDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIH 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      97 VGFLVKTMKVLRCVCFFCSKLLVDSNnpKIKDIL-----AKSKGQPKKRLT-HVYDLCKGKNICeggeemdnkfgveqPe 170
Cdd:PRK08566   87 VGFAKLIYKLLRATCRECGRLKLTEE--EIEEYLeklerLKEWGSLADDLIkEVKKEAAKRMVC--------------P- 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     171 gdedltkekgHggCGRYQPRIRRSGLELYAEwkhVNEDSQEKkilLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIV 250
Cdd:PRK08566  150 ----------H--CGEKQYKIKFEKPTTFYE---ERKEGLVK---LTPSDIRERLEKIPDEDLELLGINPEVARPEWMVL 211

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     251 TVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIaEDV-KLLQFHVATMVDNELPGLPRAM 329
Cdd:PRK08566  212 TVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLII-EDLwELLQYHVTTYFDNEIPGIPPAR 290

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     330 QKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRG 409
Cdd:PRK08566  291 HRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNG 370

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     410 NSQYPGAKYIIRDNGDRIDLRFHPKpSDL--HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLS 487
Cdd:PRK08566  371 PEKHPGANYVIRPDGRRIKLTDKNK-EELaeKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLA 449

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     488 VTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFL 567
Cdd:PRK08566  450 VCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAA 529

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     568 STWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKhiSPGDTKVVVENGELIMGILCKKSLGT 647
Cdd:PRK08566  530 GIDELPEPEPAIENGKPYWTGKQIFSLFLPKDLNLEFKAKICSGCDECKKED--CEHDAYVVIKNGKLLEGVIDKKAIGA 607

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     648 SAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEP 727
Cdd:PRK08566  608 EQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEP 687

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     728 TPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTL 807
Cdd:PRK08566  688 LPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTL 767

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     808 PHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVV 887
Cdd:PRK08566  768 PHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIV 847


                  ....*...
gi 133327     888 QLRYGEDG 895
Cdd:PRK08566  848 QFKYGEDG 855
RNA_pol_rpoA1 TIGR02390
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
 18-897 0e+00

DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.


Pssm-ID: 274106 [Multi-domain]  Cd Length: 868  Bit Score: 940.68  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327       18 IKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFH 96
Cdd:TIGR02390    4 IGSIKFGLLSPEEIRKMSVVE--VVTADTyDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVVH 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327       97 VGFLVKTMKVLRCVCFFCSKLLV-----DSNNPKIKDILAKSkGQPKKRL-THVYDLCKGKNICEGGEEMDNKFGVEQPe 170
Cdd:TIGR02390   82 VGFAKEIYKILRATCRKCGRITLteeeiEQYLEKINKLKEEG-GDLASTLiEKIVKEAAKRMKCPHCGEEQKKIKFEKP- 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      171 gdedltkekghggcgryqprirrsglelyaewKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIV 250
Cdd:TIGR02390  160 --------------------------------TYFYEEGKEGDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWMVL 207

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      251 TVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQ 330
Cdd:TIGR02390  208 TVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPARH 287

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      331 KSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGN 410
Cdd:TIGR02390  288 RSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGP 367

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      411 SQYPGAKYIIRDNGDRIDLRFHPKPSDL-HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVT 489
Cdd:TIGR02390  368 DSWPGANYVIRPDGRRIKIRDENKEELAeRLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVC 447

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      490 TPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMnLLMFLST 569
Cdd:TIGR02390  448 PPYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQ-TILGVAG 526

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      570 WDGKVPQPAILKPRPLWTGKQIFSLIIPGHINC-IRTHSTHPDDEDSgpyKHISPGDTKVVVENGELIMGILCKKSLGTS 648
Cdd:TIGR02390  527 YFGDPPEPAIEKPKEYWTGKQIFSAFLPEDLNFeGRAKICSGSDACK---KEECPHDAYVVIKNGKLLKGVIDKKAIGAE 603

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      649 AGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPT 728
Cdd:TIGR02390  604 KGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPL 683

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      729 PGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLP 808
Cdd:TIGR02390  684 PGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLP 763

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      809 HFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQ 888
Cdd:TIGR02390  764 HFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQ 843


                   ....*....
gi 133327      889 LRYGEDGLA 897
Cdd:TIGR02390  844 FKYGEDGVD 852
RNAP_II_Rpb1_C cd02584
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
 1058-1476 0e+00

Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.


Pssm-ID: 132720 [Multi-domain]  Cd Length: 410  Bit Score: 821.84  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1058 FRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTP 1137
Cdd:cd02584    1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1138 SLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVA--RISPWLLRVE 1215
Cdd:cd02584   81 SLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEqdRLSPWLLRIE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1216 LDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKMQEeeevvdkMDDDVFLRCIESNMLTD 1295
Cdd:cd02584  161 LDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEED-------SEDDVFLKKIESNMLSD 233

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1296 MTLQGIEQISKVYMhlpQTDNKKKIIItEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVR 1375
Cdd:cd02584  234 MTLKGIEGIRKVFI---REENKKKVDI-ETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAAR 309

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1376 KALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVS 1455
Cdd:cd02584  310 KALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVS 389

                        410       420
                 ....*....|....*....|.
gi 133327   1456 ENIMLGQLAPAGTGCFDLLLD 1476
Cdd:cd02584  390 ENIMLGQLAPIGTGCFDLLLD 410
RNA_pol_Rpb1_5 pfam04998
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 830-1427 3.40e-176

RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.


Pssm-ID: 398596 [Multi-domain]  Cd Length: 516  Bit Score: 545.03  E-value: 3.40e-176
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      830 GLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLAGESVEFQNLATL 909
Cdd:pfam04998    1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      910 KPSNKAFEKKFRFDYTNERALrrtlqedlvkdvlsnahiqnelEREFERMREDREVLRVIFptgdskvvlpcnllrmiwn 989
Cdd:pfam04998   81 EFSDLKLEDKFKNDLLDDLLL----------------------LSEFSLSYKKEILVRDSK------------------- 119

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      990 aqkifhinprlpsdlhpikvvegvkelskklvivNGDDPLSRQAQENATLLFNIHLRSTLCSRRMAEEFRLSGEAFDWLL 1069
Cdd:pfam04998  120 ----------------------------------LGRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKAFVCLL 165

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1070 GEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSAR 1149
Cdd:pfam04998  166 CYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYLFDEVGR 245

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1150 DAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVAR--------ISPWLLRVELDRKHM 1221
Cdd:pfam04998  246 ELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEeeidpetgLLILVIRLLKILNKS 325

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1222 TDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKmqeEEEVVDKMDDDVFLRCIESNMLTDMTLQGI 1301
Cdd:pfam04998  326 IKKVVKSEVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGL---RRVDELFMEEDPKLAILVASLLGNITLRGI 402

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1302 EQISKVYMhlPQTDNKKKIiitedgefkalQEWILETDGVSLMRVLSEKD-VDPVRTTSNDIVEIFTVLGIEAVRKALER 1380
Cdd:pfam04998  403 PGIKRILV--NEDDKGKVE-----------PDWVLETEGVNLLRVLLVPGfVDAGRILSNDIHEILEILGIEAARNALLN 469

                          570       580       590       600
                   ....*....|....*....|....*....|....*....|....*..
gi 133327     1381 ELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPL 1427
Cdd:pfam04998  470 EIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
RPOLA_N smart00663
RNA polymerase I subunit A N-terminus;
246-546 4.31e-172

RNA polymerase I subunit A N-terminus;


Pssm-ID: 214767 [Multi-domain]  Cd Length: 295  Bit Score: 524.78  E-value: 4.31e-172
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327       246 EWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNElpGL 325
Cdd:smart00663    1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GL 78

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327       326 PRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQEL 405
Cdd:smart00663   79 PRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKL 158

                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327       406 VRRGNsqyPGAKYIIRdnGDRIDLRFHPK-PSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRL 484
Cdd:smart00663  159 VRNGP---NGAKYIIR--GKKTNLKLAKKsKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRL 233

                           250       260       270       280       290       300
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 133327       485 NLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVR 546
Cdd:smart00663  234 NPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
 15-354 3.45e-142

RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.


Pssm-ID: 398595  Cd Length: 320  Bit Score: 444.04  E-value: 3.45e-142
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327       15 LRTIKRVQFGVLSPDELKRMSVTEggIKYPETTE--GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAK 92
Cdd:pfam04997    1 LKKIKEIQFGIASPEEIRKWSVGE--VTKPETYNygSLKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAK 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327       93 PVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQ--PKKRLTHVYDLCKGKNICEGGEEMDnkfgveqpe 170
Cdd:pfam04997   79 PVFHIGFFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGLenLKMGAKAILELCKKKDLCEHCGGKN--------- 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      171 gdedltkekghGGCGRYQPRIRRSGLELYAEWKHVNEDsqEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIV 250
Cdd:pfam04997  150 -----------GVCGSQQPVSRKEGLKLKAAIKKSKEE--EEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMIL 216

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      251 TVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQ 330
Cdd:pfam04997  217 TVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGLPPALQ 296

                          330       340
                   ....*....|....*....|....
gi 133327      331 KSGRPLKSLKQRLKGKEGRVRGNL 354
Cdd:pfam04997  297 KSKRPLKSISQRLKGKEGRFRGNL 320
RNA_pol_Rpb1_6 pfam04992
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 896-1079 3.06e-96

RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.


Pssm-ID: 461511  Cd Length: 188  Bit Score: 308.27  E-value: 3.06e-96
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      896 LAGESVEFQNLATLKPSNKAFEKKFRFDYTNERA--LRRTLQEDLVKDVLSNAHIQNELEREFERMREDREVLR-VIFPT 972
Cdd:pfam04992    1 LDGAFIEKQKIDTLKLSDAAFEKRYRLDVMDEKSgfLPGYLEEGVIKEIAGDPEVQQLLDEEYEQLLEDRELLReIIFPT 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      973 GDSKVV-LPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLLFNIHLRSTLCS 1051
Cdd:pfam04992   81 GDSKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVVVRGDDPLSKEAQENATLLFKILLRSRLAS 160

                          170       180
                   ....*....|....*....|....*...
gi 133327     1052 RRMAEEFRLSGEAFDWLLGEIESKFNQA 1079
Cdd:pfam04992  161 KRVLEEYRLNKEAFDWVLGEIESRFLQA 188
PRK04309 PRK04309
DNA-directed RNA polymerase subunit A''; Validated
 1052-1479 2.14e-88

DNA-directed RNA polymerase subunit A''; Validated


Pssm-ID: 235277 [Multi-domain]  Cd Length: 383  Bit Score: 294.06  E-value: 2.14e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1052 RRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINIS 1131
Cdd:PRK04309   27 REKLEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDAR 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1132 KKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqstvvaeDqewvnvYYEMpdfdvarispwL 1211
Cdd:PRK04309  107 KEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISV-------------D------LANM-----------T 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1212 LRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNcifnddnAEKLVLRIRImnsDENKMQEEEEVVDKmdddvflrciesn 1291
Cdd:PRK04309  157 IIIELDEEMLEDRGLTVDDVKEAIEKKKGGEVE-------IEGNTLIISP---KEPSYRELRKLAEK------------- 213

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1292 mLTDMTLQGIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGI 1371
Cdd:PRK04309  214 -IRNIKIKGIKGIKRV-------------IIRKEGD-----EYVIYTEGSNLKEVLKVEGVDATRTTTNNIHEIEEVLGI 274

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1372 EAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPM 1451
Cdd:PRK04309  275 EAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDEL 354

                         410       420
                  ....*....|....*....|....*...
gi 133327    1452 KGVSENIMLGQLAPAGTGCFDLLLDAEK 1479
Cdd:PRK04309  355 KGVTENIIVGQPIPLGTGDVELTMDPPL 382
RNA_pol_rpoA2 TIGR02389
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
 1054-1476 5.76e-85

DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 274105 [Multi-domain]  Cd Length: 367  Bit Score: 283.48  E-value: 5.76e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1054 MAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKK 1133
Cdd:TIGR02389   14 VKKREISDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKT 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1134 PKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqstvvaedqewvnvyyempdfDVARISpwlLR 1213
Cdd:TIGR02389   94 PSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISI---------------------------DLADMT---VI 143

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1214 VELDRKHMTDRKLTMEQIAEKINAgfgddlncifnddnaeklVLRIRIMNSDenkmQEEEEVVDKMDDDVF--LRCIEsN 1291
Cdd:TIGR02389  144 IELDEEQLKERGITVDDVEKAIKK------------------AKLGKVIEID----MDNNTITIKPGNPSLkeLRKLK-E 200

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1292 MLTDMTLQGIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGI 1371
Cdd:TIGR02389  201 KIKNLHIKGIKGIKRV-------------VIRKEGD-----EYVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAEVLGI 262

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1372 EAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPM 1451
Cdd:TIGR02389  263 EAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDEL 342

                          410       420
                   ....*....|....*....|....*
gi 133327     1452 KGVSENIMLGQLAPAGTGCFDLLLD 1476
Cdd:TIGR02389  343 KGVIENIIVGQPIPLGTGDVDLVMD 367
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
 20-948 2.36e-64

DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439856 [Multi-domain]  Cd Length: 1165  Bit Score: 241.22  E-value: 2.36e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     20 RVQFGVLSPDELkrMSVTEGGIKYPETT--EGGRPKLGGLMDPR--------------------QGVIertgrCQTCAGN 77
Cdd:COG0086    9 AIKIGLASPEKI--RSWSYGEVKKPETInyRTFKPERDGLFCERifgpckdyecycgkykrmvyKGVV-----CEKCGVE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     78 MTECP---GHFGHIELAKPVFHVGF-----------LVKTMKVLRCVCFFCSKLLVDSNNPKIK--DILAKSKGQPKkrl 141
Cdd:COG0086   82 VTLSKvrrERMGHIELAMPVFHIWGlkslpsrigllLDMSLRDLERVLYFESYVVIDPGDTPLEkgQLLTEDEYREI--- 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    142 thvydlckgknICEGGEEMDNKFG---VEQPEGDEDLTKEKGhggcgryqprirrsglELYAEWKHVNedSQEKKIllsp 218
Cdd:COG0086  159 -----------LEEYGDEFVAKMGaeaIKDLLGRIDLEKESE----------------ELREELKETT--SEQKRK---- 205

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    219 ervhEIFKRISDEECFVLgmepRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGA 298
Cdd:COG0086  206 ----KLIKRLKVVEAFRE----SGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKA 277

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    299 AAHVIAEDVKLLQFHVATMVDNELPGlpRAMQKSG-RPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQ 377
Cdd:COG0086  278 PDIIVRNEKRMLQEAVDALFDNGRRG--RAVTGANkRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQ 355

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    378 VGVPRSIAanmtfAEIVTPFNIDRLQElvrRGNSQ-YPGAKYIIRDNGDRI------DLRFHPkpsdlhlqtgykverhm 450
Cdd:COG0086  356 CGLPKKMA-----LELFKPFIYRKLEE---RGLATtIKSAKKMVEREEPEVwdileeVIKEHP----------------- 410

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    451 cdgdiVIFNRQPTLHKMSMM--------GHRVRILPWstfrlnlsVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVP 522
Cdd:COG0086  411 -----VLLNRAPTLHRLGIQafepvlieGKAIQLHPL--------VCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLST 477

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    523 RMIVTPQSNRPVMGIVQDT------LTAVRKFTKRD--VFLERGEVMNLLMflstwDGKVPQPAILKPRPLWTGKQ---- 590
Cdd:COG0086  478 NNILSPANGKPIIVPSQDMvlglyyLTREREGAKGEgmIFADPEEVLRAYE-----NGAVDLHARIKVRITEDGEQvgki 552

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    591 --------IFSLIIP---GHINcirthsthpddedsgpykhispgdtKVvvengelimgiLCKKSLGTsagsLVHISYLE 659
Cdd:COG0086  553 vettvgryLVNEILPqevPFYN-------------------------QV-----------INKKHIEV----IIRQMYRR 592

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    660 MGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTyqdiQNTIKKAKQDVIEvIEKAHNNELePTPGNTlrqtfEN 739
Cdd:COG0086  593 CGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKEK----QEIFEEANKEVKE-IEKQYAEGL-ITEPER-----YN 661

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    740 QVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVG-QQNVEGKRIPFGFKHrtlphfikddygpe 818
Cdd:COG0086  662 KVIDGWTKASLETESFLMAAFSSQNTTYMMADSGARGSADQLRQLAGMRGlMAKPSGNIIETPIGS-------------- 727

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    819 srgfvenSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIK-SMESVMVKYDATVRNSINqVVQLRYGedgla 897
Cdd:COG0086  728 -------NFREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDvAQDVIVTEEDCGTDRGIT-VTAIKEG----- 794

                        970       980       990      1000      1010
                 ....*....|....*....|....*....|....*....|....*....|.
gi 133327    898 GESVEfqnlaTLKpsnkafekkfrfdytnERALRRTLQEDlVKDVLSNAHI 948
Cdd:COG0086  795 GEVIE-----PLK----------------ERILGRVAAED-VVDPGTGEVL 823
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 1857-1961 1.96e-14

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 79.19  E-value: 1.96e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1857 SPKYSPTSPKYSPTSPKYSP------------TSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYS 1924
Cdd:pfam05109  475 SPTPAGTTSGASPVTPSPSPrdngteskapdmTSPTSAVTTPTPNATSPTPAVTTPTPNATSPTLGKTSPTSAVTTPTPN 554

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 133327     1925 PTSPTYSPTSPKGSTYSP----TSPGYSPTSPTYSLTSPAI 1961
Cdd:pfam05109  555 ATSPTPAVTTPTPNATIPtlgkTSPTSAVTTPTPNATSPTV 595
rpoC2 PRK02597
DNA-directed RNA polymerase subunit beta'; Provisional
 764-1117 3.95e-12

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 235052 [Multi-domain]  Cd Length: 1331  Bit Score: 71.95  E-value: 3.95e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     764 NNFKS---------MVVSGAKGskiNISQVIAVVGQQ----NVEGKRIpfgfkhrTLPhfIKDDygpesrgFVEnsylaG 830
Cdd:PRK02597  111 KNFRQndplnsvymMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--IKTN-------FRE-----G 166

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     831 LTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVK-YDATVRNSInqVVQlryGEDGLAGESVEFQNlatl 909
Cdd:PRK02597  167 LTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVReEDCGTTRGI--VVE---AMDDGDRVLIPLGD---- 237

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     910 kpsnkafekkfrfdytneRALRRTLQEDLVKDvlsnahiqnelerefermreDREVLrvifptgdskvvlpcnllrmiwn 989
Cdd:PRK02597  238 ------------------RLLGRVLAEDVVDP--------------------EGEVI----------------------- 256

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     990 AQKIFHINPRLPsdlhpiKVVE--GVKElskklVIVNgdDPLSRQAQenatllfnihlRStLCSRrmaeefrlsgeAFDW 1067
Cdd:PRK02597  257 AERNTAIDPDLA------KKIEkaGVEE-----VMVR--SPLTCEAA-----------RS-VCRK-----------CYGW 300

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|...
gi 133327    1068 LLgeieskfnqAIAHP---GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNV 1117
Cdd:PRK02597  301 SL---------AHNHLvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 344
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 1491-1610 3.16e-10

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 59.46  E-value: 3.16e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      1491 PGLGAAGPTGMFFGSAPSPMGgiSPAMTP-WNQ--GATPAYGAWSPSVGSgmTP----GAAGFSPSAASDASGFSPGYSP 1563
Cdd:smart01104   15 PAWGSRTPGTAAGGAPTARGG--SGSRTPaWGGagSRTPAWGGAGPTGSR--TPawggASAWGNKSSEGSASSWAAGPGG 90

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 133327      1564 AWsptpgspgspgpsspyipspgGAMSPSYSPTSPAYEPRSPGGYTP 1610
Cdd:smart01104   91 AY---------------------GAPTPGYGGTPSAYGPATPGGGAM 116
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 1855-1952 2.58e-07

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 55.85  E-value: 2.58e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1855 PASPKySPTSPKySPTSPKySPTSPTySPTTPKySPTSPTYSPTspvytPTSPKySPTSPTySPTSPKySPTSPTySPTS 1934
Cdd:PTZ00449  582 PKDPK-HPKDPE-EPKKPK-RPRSAQ-RPTRPK-SPKLPELLDI-----PKSPK-RPESPK-SPKRPP-PPQRPS-SPER 647

                          90
                  ....*....|....*...
gi 133327    1935 PKGsTYSPTSPGySPTSP 1952
Cdd:PTZ00449  648 PEG-PKIIKSPK-PPKSP 663
Chi1 COG3469
Chitinase [Carbohydrate transport and metabolism];
1853-1967 2.30e-06

Chitinase [Carbohydrate transport and metabolism];


Pssm-ID: 442692 [Multi-domain]  Cd Length: 534  Bit Score: 52.45  E-value: 2.30e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1853 YTPASPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSP---TSPKYSPTSPT 1929
Cdd:COG3469   89 ATSTSATLVATSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVSgteTATGGTTTTST 168

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 133327   1930 YSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSD 1967
Cdd:COG3469  169 TTTTTSASTTPSATTTATATTASGATTPSATTTATTTG 206
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 1854-1960 1.52e-05

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 45.98  E-value: 1.52e-05
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      1854 TPASPKYSPTSPKYSPTSPKYSPTSPTysPTTPKYSPTSPTYSpTSPVYTPTS---PKYSPTSPTYSPTSPKY--SPTSP 1928
Cdd:smart01104    4 TPAWGASGSKTPAWGSRTPGTAAGGAP--TARGGSGSRTPAWG-GAGSRTPAWggaGPTGSRTPAWGGASAWGnkSSEGS 80

                            90       100       110
                    ....*....|....*....|....*....|..
gi 133327      1929 TYSPTSPKGSTYSPTSPGYSPTSPTYSLTSPA 1960
Cdd:smart01104   81 ASSWAAGPGGAYGAPTPGYGGTPSAYGPATPG 112
rad23 TIGR00601
UV excision repair protein Rad23; All proteins in this family for which functions are known ...
 1870-1942 1.46e-04

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273167 [Multi-domain]  Cd Length: 378  Bit Score: 46.43  E-value: 1.46e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 133327     1870 TSPKYSPTSPTYSPTTPKYSPTSptySPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSP 1942
Cdd:TIGR00601   75 SKPKTGTGKVAPPAATPTSAPTP---TPSPPASPASGMSAAPASAVEEKSPSEESATATAPESPSTSVPSSGS 144
 
Name Accession Description Interval E-value
RNAP_II_RPB1_N cd02733
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
 19-876 0e+00

Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.


Pssm-ID: 259848 [Multi-domain]  Cd Length: 751  Bit Score: 1611.06  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     19 KRVQFGVLSPDELKRMSVTEggIKYPETTE-GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHV 97
Cdd:cd02733    1 KRVQFGILSPDEIRAMSVAE--IEHPETYEnGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     98 GFLVKTMKVLRCVCffcskllvdsnnpkikdilakskgqpkkrlthvydlckgkniceggeemdnkfgveqpegdedltk 177
Cdd:cd02733   79 GFLTKILKILRCVC------------------------------------------------------------------ 92

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    178 ekghggcgryqprirrsglelyaewkhvnedsqekKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPP 257
Cdd:cd02733   93 -----------------------------------KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPP 137

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    258 LSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLK 337
Cdd:cd02733  138 PAVRPSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLK 217

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    338 SLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAK 417
Cdd:cd02733  218 SIRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAK 297

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    418 YIIRDNGDRIDLRFHPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFD 497
Cdd:cd02733  298 YIIRDDGERIDLRYLKKASDLHLQYGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFD 377

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    498 GDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQP 577
Cdd:cd02733  378 GDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMWLPDWDGKIPQP 457

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    578 AILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPddedsGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISY 657
Cdd:cd02733  458 AILKPKPLWTGKQIFSLIIPKINNLIRSSSHHD-----GDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIW 532

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    658 LEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTF 737
Cdd:cd02733  533 LEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIGDTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESF 612

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    738 ENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGP 817
Cdd:cd02733  613 ENKVNRILNKARDKAGKSAQKSLSEDNNFKAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGP 692

                        810       820       830       840       850
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 133327    818 ESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD 876
Cdd:cd02733  693 ESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
RNAP_archeal_A' cd02582
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
 15-895 0e+00

A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins.


Pssm-ID: 259846 [Multi-domain]  Cd Length: 861  Bit Score: 1006.77  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     15 LRTIKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKP 93
Cdd:cd02582    1 PKRIKGIKFGLLSPEEIRKMSVVE--IITPDTyDEDGYPIEGGLMDPRLGVIEPGLRCKTCGNTAGECPGHFGHIELARP 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     94 VFHVGFLVKTMKVLRCVCFFCSKLLV-DSNNPKIKDILAKSKG---QPKKRL-THVYDLCKGKNICeggeemdnkfgveq 168
Cdd:cd02582   79 VIHVGFAKHIYDLLRATCRSCGRILLpEEEIEKYLERIRRLKEkwpELVKRViEKVKKKAKKRKVC-------------- 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    169 PegdedltkekgHggCGRYQPRIRrsgLELYAEWKHVNEDSQEKkilLSPERVHEIFKRISDEECFVLGMEPRYARPEWM 248
Cdd:cd02582  145 P-----------H--CGAPQYKIK---LEKPTTFYEEKEEGEVK---LTPSEIRERLEKIPDEDLELLGIDPKTARPEWM 205

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    249 IVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRA 328
Cdd:cd02582  206 VLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVTTYFDNEIPGIPPA 285

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    329 MQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRR 408
Cdd:cd02582  286 RHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVTEWNIEKMRKLVLN 365

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    409 GNSQYPGAKYIIRDNGDRIDLRFHPKpSDL--HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNL 486
Cdd:cd02582  366 GPDKWPGANYVIRPDGRRIRLRYVNR-EELaeRLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNL 444

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    487 SVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMF 566
Cdd:cd02582  445 AVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLTRKTTLFTKEEALQLLSA 524

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    567 LStWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKHisPGDTKVVVENGELIMGILCKKSLG 646
Cdd:cd02582  525 AG-YDGLLPEPAILEPKPLWTGKQLFSLFLPKDLNFEGKAKVCSGCSECKDEDC--PNDGYVVIKNGKLLEGVIDKKAIG 601

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    647 T-SAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNEL 725
Cdd:cd02582  602 AeQPGSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDEDIPEEARKEIEEIIKEAEKKVYELIEQYKNGEL 681

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    726 EPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHR 805
Cdd:cd02582  682 EPLPGRTLEETLEMKIMQVLGKARDEAGKVASKYLDPFNNAVIMARTGARGSMLNLTQMAACLGQQSVRGERINRGYRNR 761

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    806 TLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQ 885
Cdd:cd02582  762 TLPHFKPGDLGPEARGFVRSSFRDGLSPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDSRGN 841

                        890
                 ....*....|
gi 133327    886 VVQLRYGEDG 895
Cdd:cd02582  842 IIQFKYGEDG 851
PRK08566 PRK08566
DNA-directed RNA polymerase subunit A'; Validated
 18-895 0e+00

DNA-directed RNA polymerase subunit A'; Validated


Pssm-ID: 236292 [Multi-domain]  Cd Length: 882  Bit Score: 992.05  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      18 IKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFH 96
Cdd:PRK08566    9 IGSIKFGLLSPEEIRKMSVTK--IITADTyDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIH 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      97 VGFLVKTMKVLRCVCFFCSKLLVDSNnpKIKDIL-----AKSKGQPKKRLT-HVYDLCKGKNICeggeemdnkfgveqPe 170
Cdd:PRK08566   87 VGFAKLIYKLLRATCRECGRLKLTEE--EIEEYLeklerLKEWGSLADDLIkEVKKEAAKRMVC--------------P- 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     171 gdedltkekgHggCGRYQPRIRRSGLELYAEwkhVNEDSQEKkilLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIV 250
Cdd:PRK08566  150 ----------H--CGEKQYKIKFEKPTTFYE---ERKEGLVK---LTPSDIRERLEKIPDEDLELLGINPEVARPEWMVL 211

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     251 TVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIaEDV-KLLQFHVATMVDNELPGLPRAM 329
Cdd:PRK08566  212 TVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLII-EDLwELLQYHVTTYFDNEIPGIPPAR 290

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     330 QKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRG 409
Cdd:PRK08566  291 HRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNG 370

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     410 NSQYPGAKYIIRDNGDRIDLRFHPKpSDL--HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLS 487
Cdd:PRK08566  371 PEKHPGANYVIRPDGRRIKLTDKNK-EELaeKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLA 449

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     488 VTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFL 567
Cdd:PRK08566  450 VCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAA 529

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     568 STWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKhiSPGDTKVVVENGELIMGILCKKSLGT 647
Cdd:PRK08566  530 GIDELPEPEPAIENGKPYWTGKQIFSLFLPKDLNLEFKAKICSGCDECKKED--CEHDAYVVIKNGKLLEGVIDKKAIGA 607

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     648 SAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEP 727
Cdd:PRK08566  608 EQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEP 687

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     728 TPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTL 807
Cdd:PRK08566  688 LPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTL 767

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     808 PHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVV 887
Cdd:PRK08566  768 PHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIV 847


                  ....*...
gi 133327     888 QLRYGEDG 895
Cdd:PRK08566  848 QFKYGEDG 855
RNA_pol_rpoA1 TIGR02390
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ...
 18-897 0e+00

DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.


Pssm-ID: 274106 [Multi-domain]  Cd Length: 868  Bit Score: 940.68  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327       18 IKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFH 96
Cdd:TIGR02390    4 IGSIKFGLLSPEEIRKMSVVE--VVTADTyDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVVH 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327       97 VGFLVKTMKVLRCVCFFCSKLLV-----DSNNPKIKDILAKSkGQPKKRL-THVYDLCKGKNICEGGEEMDNKFGVEQPe 170
Cdd:TIGR02390   82 VGFAKEIYKILRATCRKCGRITLteeeiEQYLEKINKLKEEG-GDLASTLiEKIVKEAAKRMKCPHCGEEQKKIKFEKP- 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      171 gdedltkekghggcgryqprirrsglelyaewKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIV 250
Cdd:TIGR02390  160 --------------------------------TYFYEEGKEGDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWMVL 207

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      251 TVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQ 330
Cdd:TIGR02390  208 TVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPARH 287

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      331 KSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGN 410
Cdd:TIGR02390  288 RSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGP 367

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      411 SQYPGAKYIIRDNGDRIDLRFHPKPSDL-HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVT 489
Cdd:TIGR02390  368 DSWPGANYVIRPDGRRIKIRDENKEELAeRLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVC 447

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      490 TPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMnLLMFLST 569
Cdd:TIGR02390  448 PPYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQ-TILGVAG 526

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      570 WDGKVPQPAILKPRPLWTGKQIFSLIIPGHINC-IRTHSTHPDDEDSgpyKHISPGDTKVVVENGELIMGILCKKSLGTS 648
Cdd:TIGR02390  527 YFGDPPEPAIEKPKEYWTGKQIFSAFLPEDLNFeGRAKICSGSDACK---KEECPHDAYVVIKNGKLLKGVIDKKAIGAE 603

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      649 AGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPT 728
Cdd:TIGR02390  604 KGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPL 683

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      729 PGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLP 808
Cdd:TIGR02390  684 PGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLP 763

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      809 HFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQ 888
Cdd:TIGR02390  764 HFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQ 843


                   ....*....
gi 133327      889 LRYGEDGLA 897
Cdd:TIGR02390  844 FKYGEDGVD 852
PRK14977 PRK14977
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
 14-1481 0e+00

bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional


Pssm-ID: 184940 [Multi-domain]  Cd Length: 1321  Bit Score: 914.41  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      14 PLRTIKRVQFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAK 92
Cdd:PRK14977    5 AVKAIDGIIFGLISPADARKIGFAE--ITAPEAyDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      93 PVFHVGFLVKTMKVLRCVCFFCSKLLV---DSNNPK-IKDILAKSKGQPKKRLThvydlckgkniceggEEMDNKFGvEQ 168
Cdd:PRK14977   83 PVIHIAFIDNIKDLLNSTCHKCAKLKLpqeDLNVFKlIEEAHAAARDIPEKRID---------------DEIIEEVR-DQ 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     169 PEGDEDLTKEKGHggCGRYQPRirrsgLELYAEWKHVNEDSQEKKILLsPERVHEIFKRISDEECFVLGMEPRYARPEWM 248
Cdd:PRK14977  147 VKVYAKKAKECPH--CGAPQHE-----LEFEEPTIFIEKTEIEEHRLL-PIEIRDIFEKIIDDDLELIGFDPKKARPEWA 218

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     249 IVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRA 328
Cdd:PRK14977  219 VLQAFLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGIPQA 298

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     329 MQK-SGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVR 407
Cdd:PRK14977  299 HHKgSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVI 378

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     408 RGNSQYPGAKYIIRDNGDRIDLRFHPKPSDL-------HLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWS 480
Cdd:PRK14977  379 NGPDEFPGANAIRKGDGTKIRLDFLEDKGKDalreaaeQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGA 458

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     481 TFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEV 560
Cdd:PRK14977  459 TFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEA 538

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     561 MNLLMfLSTWDGKVPQPAI-LKPRPLWTGKQIFSLIIPGHINCIRThSTHPDDEDSGPYKHISPGDTKVVVENGELIMGI 639
Cdd:PRK14977  539 SNIAM-LAGITDPLPEPAIkTKDGPAWTGKQLFSLFLPKDFNFEGI-AKWSAGKAGEAKDPSCLGDGYVLIKEGELISGV 616

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     640 LCKKSLGTSAG---SLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEV 716
Cdd:PRK14977  617 IDDNIIGALVEepeSLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDEVSDL 696

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     717 IEK--------AHNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVV 788
Cdd:PRK14977  697 IDQrkitrkitIYKGKEELLRGMKEEEALEADIVNELDKARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGAL 776

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     789 GQQNVE--------GKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYI 860
Cdd:PRK14977  777 GQQKRKtrigfvltGGRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYF 856

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     861 QRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLagesvefqnlatlkpsnkAFEKKFRFDYTN-ERALRRTLQEDLV 939
Cdd:PRK14977  857 QRRLANALEDIRLEYDETVRDPHGHIIQFKFGEDGI------------------DPQKLDHGEAFNlERIIEKQKIEDRG 918

                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     940 KDVlSNAHIQnELEREFERMREDRevlrvifptgdskvvLPCNLLRMIWNAQkifhinprlPSDlhpikvvEGVKELSKK 1019
Cdd:PRK14977  919 KGA-SKDEIE-ELAKEYTKTFNAN---------------LPKLLADAIHGAE---------LKE-------DELEAICAE 965

                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1020 LvivngddplsrqaqenatllfnihlrstlcsrrmaeefrlsgeafdwLLGeieskFNQAIAHPGEMVGALAAQSLGEPA 1099
Cdd:PRK14977  966 G-----------------------------------------------KEG-----FEKAKVEPGQAIGIISAQSIAEPG 993

                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1100 TQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYdP 1179
Cdd:PRK14977  994 TQMTLRTFHAAGIKAMDVTHGLERFIELVDARAKPSTPTMDIYLDDECKEDIEKAIEIARNLKELKVRALIADSAIDN-A 1072

                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1180 NPQSTVVAEDQEWVNVYYEMPDFdvarispwllrVELDRKHMTDRKLTMEQIAEKINAgfgddlncifnddnaeKLVlri 1259
Cdd:PRK14977 1073 NEIKLIKPDKRALENGCIPMERF-----------AEIEAALAKGKKFEMELEDDLIIL----------------DLV--- 1122

                        1290      1300      1310      1320      1330      1340      1350      1360
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1260 rimnsdenkmqeeeEVVDKMDDDVFLRCIeSNMLTDMTLQGIEQISKVYMHLPQTDNKKkiiitedgefkalqEWILETD 1339
Cdd:PRK14977 1123 --------------EAADRDKPLATLIAI-RNKILDKPVKGVPDIERAWVELVEKDGRD--------------EWIIQTS 1173

                        1370      1380      1390      1400      1410      1420      1430      1440
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1340 GVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAI----- 1414
Cdd:PRK14977 1174 GSNLAAVLEMKCIDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGTIEAIglqaa 1253

                        1450      1460      1470      1480      1490      1500
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 133327    1415 -TRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAEKCK 1481
Cdd:PRK14977 1254 gVRHGFAGEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDLLMDFSGKA 1321
RNAP_III_RPC1_N cd02583
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
 26-880 0e+00

Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 (C160) subunit forms part of the active site region of RNAP III. RNAP III is one of the three distinct classes of nuclear RNAP in eukaryotes that is responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA genes, and some others. RNAP III is the largest nuclear RNA polymerase with 17 subunits. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site, making up the head and core of the one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between Rpc1 and Rpb1 suggests a similar functional and structural role.


Pssm-ID: 259847 [Multi-domain]  Cd Length: 816  Bit Score: 897.29  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     26 LSPDELKRMSVTEggIKYPE--TTEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKT 103
Cdd:cd02583    1 LSPEDIIRLSEVE--VTNRNlyDIETRKPLPYGVLDPRLGTSDKDGICETCGLNLADCVGHFGYIKLELPVFHIGYFKAI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    104 MKVLRCVCFFCSKLLVDSNnpKIKDILAKSKGQPKKRLTH------VYDLCKGKNICeggeemdnkfgveqPEgdedltk 177
Cdd:cd02583   79 INILQCICKTCSRVLLPEE--EKRKFLKRLRRPNLDNLQKkalkkkILEKCKKVRKC--------------PH------- 135

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    178 ekghggCGRYqprirrsglelyaewKHVNEDsqekkilLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPP 257
Cdd:cd02583  136 ------CGLL---------------KKAQED-------LNPLKVLNLFKNIPPEDVELLLMNPLAGRPENLILTRIPVPP 187

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    258 LSVRPAVVMQG-SARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSgRPL 336
Cdd:cd02583  188 LCIRPSVVMDEkSGTNEDDLTVKLSEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQLQCALYINSELPGLPLSMQPK-KPI 266

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    337 KSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGA 416
Cdd:cd02583  267 RGFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPERVTRYNIEKLRKLVLNGPDVHPGA 346

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    417 KYII-RDNGDRIDLRF-HPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNA 494
Cdd:cd02583  347 NFVIkRDGGKKKFLKYgNRRKIARELKIGDIVERHLEDGDIVLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNA 426

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    495 DFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLStwDGK- 573
Cdd:cd02583  427 DFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYLLTSKDVFFDRAQFCQLCSYML--DGEi 504

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    574 ---VPQPAILKPRPLWTGKQIFSLII-PGHINCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMGILCKKSLGT-S 648
Cdd:cd02583  505 kidLPPPAILKPVELWTGKQIFSLLLrPNKKSPVLVNLEAKEKSYTKKSPDMCPNDGYVVIRNSELLCGRLDKSTLGSgS 584

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    649 AGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPT 728
Cdd:cd02583  585 KNSLFYVLLRDYGPEAAAAAMNRLAKLSSRWLSNRGFSIGIDDVTPSKELLKKKEELVDNGYAKCDEYIKQYKKGKLELQ 664

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    729 PGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLP 808
Cdd:cd02583  665 PGCTAEQTLEAKISGELSKIREDAGKACLKELHKSNSPLIMALCGSKGSNINISQMIACVGQQIISGKRIPNGFEDRTLP 744

                        810       820       830       840       850       860       870
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 133327    809 HFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVR 880
Cdd:cd02583  745 HFPRNSKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSVQYDGTVR 816
RNAP_II_Rpb1_C cd02584
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
 1058-1476 0e+00

Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.


Pssm-ID: 132720 [Multi-domain]  Cd Length: 410  Bit Score: 821.84  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1058 FRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTP 1137
Cdd:cd02584    1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1138 SLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVA--RISPWLLRVE 1215
Cdd:cd02584   81 SLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEqdRLSPWLLRIE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1216 LDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKMQEeeevvdkMDDDVFLRCIESNMLTD 1295
Cdd:cd02584  161 LDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLVIRIRIINDDEEKEED-------SEDDVFLKKIESNMLSD 233

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1296 MTLQGIEQISKVYMhlpQTDNKKKIIItEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVR 1375
Cdd:cd02584  234 MTLKGIEGIRKVFI---REENKKKVDI-ETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAAR 309

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1376 KALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVS 1455
Cdd:cd02584  310 KALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVS 389

                        410       420
                 ....*....|....*....|.
gi 133327   1456 ENIMLGQLAPAGTGCFDLLLD 1476
Cdd:cd02584  390 ENIMLGQLAPIGTGCFDLLLD 410
RNAP_I_RPA1_N cd01435
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ...
 22-876 0e+00

Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the largest subunit of the eukaryotic RNA polymerase I (RNAP I). RNAP I is a multi-subunit protein complex responsible for the synthesis of rRNA precursors. RNAP I consists of at least 14 different subunits, the largest being homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. The yeast member of this family is known as Rpb190. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site. It makes up the head and core of one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between RPA1 and Rpb1 suggests a similar functional and structural role.


Pssm-ID: 259844 [Multi-domain]  Cd Length: 779  Bit Score: 631.53  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     22 QFGVLSPDELKRMSVTEggIKYPET-TEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFL 100
Cdd:cd01435    1 SFSFYSAEEIRKLSVKE--ITNPVTfDSLGHPVPGGLYDPALGPLDKDDICSTCGLNYLNCPGHFGHIELPLPVYNPLFF 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    101 VKTMKVLRCVCFFCSKLLVdsnnPKIKDILAKSKGQPkkrlthvydLCKGKNiceggeemdnkfgveqpegdedltkekg 180
Cdd:cd01435   79 DLLYKLLRGSCFYCHRFRI----SKWEVKLFVAKLKL---------LDKGLL---------------------------- 117

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    181 hggcgryqprirrsglelyaewkhvnedsQEKKILLSPervheifkrisdeecfvlgmepryarPEWMIVTVLPVPPLSV 260
Cdd:cd01435  118 -----------------------------VEAAELDFG--------------------------YDMFFLDVLLVPPNRF 142

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    261 RPAVVMQGSArnqddLTHK----LADIVKINNQLR------RNEQNGAAAHVIAEDVKL---------LQFHVATMVDNE 321
Cdd:cd01435  143 RPPSFLGDKV-----FENPqnvlLSKILKDNQQIRdllasmRQAESQSKLDLISGKTNSeklinawlqLQSAVNELFDST 217

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    322 LPGLPRAMQKSGrplksLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDR 401
Cdd:cd01435  218 KAPKSGKKSPPG-----IKQLLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKLTFPEPVTPFNVEE 292

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    402 LQELVRRGNSQYPGAKYIIRDNGDRIDLRFH--------------PKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKM 467
Cdd:cd01435  293 LRQAVINGPDVYPGANAIEDEDGRLILLSALseerrkalakllllLSSAKLLLNGPKKVYRHLLDGDVVLLNRQPTLHKP 372

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    468 SMMGHRVRILPWS-TFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVR 546
Cdd:cd01435  373 SIMAHKVRVLPGEkTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQDHVVSGV 452

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    547 KFTKRDVFLERGEVMNLLMF-LSTWDG-------KVPQPAILKPRPLWTGKQIFSLIIpghINCIRTHStHPDDEDS--- 615
Cdd:cd01435  453 LLTSRDTFFTREEYQQLVYAaLRPLFTsdkdgriKLLPPAILKPKPLWTGKQVISTIL---KNLIPGNA-PLLNLSGkkk 528

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    616 ------GPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGI 689
Cdd:cd01435  529 tkkkvgGGKWGGGSEESQVIIRNGELLTGVLDKSQFGASAYGLVHAVYELYGGETAGKLLSALGRLFTAYLQMRGFTCGI 608

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    690 GDSIADSKTYQDIQNTIKKAKQDVIEVIEKAhnneleptpgntlrqtFENQVNRILNDARDKTGSSAQKSLSEYNNFKSM 769
Cdd:cd01435  609 EDLLLTPKADEKRRKILRKAKKLGLEAAAEF----------------LGLKLNKVTSSIIKACLPKGLLKPFPENNLQLM 672

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    770 VVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLID 849
Cdd:cd01435  673 VQSGAKGSMVNASQISCLLGQQELEGRRVPLMVSGKTLPSFPPYDTSPRAGGFITDRFLTGIRPQEYFFHCMAGREGLID 752

                        890       900
                 ....*....|....*....|....*..
gi 133327    850 TAVKTAETGYIQRRLIKSMESVMVKYD 876
Cdd:cd01435  753 TAVKTSRSGYLQRCLIKHLEGLKVNYD 779
RNAP_largest_subunit_N cd00399
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
 26-876 2.85e-180

Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.


Pssm-ID: 259843 [Multi-domain]  Cd Length: 528  Bit Score: 556.66  E-value: 2.85e-180
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     26 LSPDELKRMSVTEggIKYPETTE--GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLvkt 103
Cdd:cd00399    1 MSPEEIRKWSVAK--VIKPETIDnrTLKAERGGKYDPRLGSIDRCEKCGTCGTGLNDCPGHFGHIELAKPVFHVGFI--- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    104 mkvlrcvcffcskllvdsnnpkikdilakskgqpkkrlTHVYDLCKgkniceggeemdnkfgveqpegdedltkekghgg 183
Cdd:cd00399   76 --------------------------------------KKVPSFLG---------------------------------- 83

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    184 cgryqprirrsglelyaewkhvnedsqekkillspervheifkrisdeecfvlgmepryarPEWMIVTVLPVPPLSVRPA 263
Cdd:cd00399   84 -------------------------------------------------------------PEWMILTCLPVPPPCLRPS 102

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    264 VVmqgsarnqddlthkladivkinnqlrrneqngaaahvIAEDVKLLQFHVATMVDNELPGLPRAMqKSGRPLKSLKQRL 343
Cdd:cd00399  103 VI-------------------------------------IEERWRLLQEHVDTYLDNGIAGQPQTQ-KSGRPLRSLAQRL 144

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    344 KGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMtfaeivtpfnidrlqelvrrgnsqypgakyiirdn 423
Cdd:cd00399  145 KGKEGRFRGNLMGKRVDFSGRSVISPDPNLRLDQVGVPKSIALTL----------------------------------- 189

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    424 gdridlrfhpkpsdlhlqtgykverhmcDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNL 503
Cdd:cd00399  190 ----------------------------DGDPVLFNRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNL 241

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    504 HLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKrdvflergevmnllmflstwdgkvpqpailkpr 583
Cdd:cd00399  242 HVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQDTLLGAYLLTL--------------------------------- 288

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    584 plwtGKQIFSLIIPGhincirthsthpddedsgpykhispgdtkvvvengelimgilckkslgtsagSLVHISYLEMGHD 663
Cdd:cd00399  289 ----GKQIVSAALPG----------------------------------------------------GLLHTVTRELGPE 312

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    664 ITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNR 743
Cdd:cd00399  313 KAAKLLSNLQRVGFVFLTTSGFSVGIGDVIDDGVIPEEKTELIEEAKKKVDEVEEAFQAGLLTAQEGMTLEESLEDNILD 392

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    744 ILNDARDKTGSSAQKSL---SEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESR 820
Cdd:cd00399  393 FLNEARDKAGSAASVNLdlvSKFNSIYVMAMSGAKGSFINIRQMSACVGQQSVEGKRIPRGFSDRTLPHFSKDDYSPEAK 472

                        810       820       830       840       850
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 133327    821 GFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYD 876
Cdd:cd00399  473 GFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQRRLVKALEDLVVHYD 528
RNA_pol_Rpb1_5 pfam04998
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 830-1427 3.40e-176

RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.


Pssm-ID: 398596 [Multi-domain]  Cd Length: 516  Bit Score: 545.03  E-value: 3.40e-176
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      830 GLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLAGESVEFQNLATL 909
Cdd:pfam04998    1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      910 KPSNKAFEKKFRFDYTNERALrrtlqedlvkdvlsnahiqnelEREFERMREDREVLRVIFptgdskvvlpcnllrmiwn 989
Cdd:pfam04998   81 EFSDLKLEDKFKNDLLDDLLL----------------------LSEFSLSYKKEILVRDSK------------------- 119

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      990 aqkifhinprlpsdlhpikvvegvkelskklvivNGDDPLSRQAQENATLLFNIHLRSTLCSRRMAEEFRLSGEAFDWLL 1069
Cdd:pfam04998  120 ----------------------------------LGRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKAFVCLL 165

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1070 GEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSAR 1149
Cdd:pfam04998  166 CYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYLFDEVGR 245

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1150 DAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVAR--------ISPWLLRVELDRKHM 1221
Cdd:pfam04998  246 ELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEeeidpetgLLILVIRLLKILNKS 325

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1222 TDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKmqeEEEVVDKMDDDVFLRCIESNMLTDMTLQGI 1301
Cdd:pfam04998  326 IKKVVKSEVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGL---RRVDELFMEEDPKLAILVASLLGNITLRGI 402

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1302 EQISKVYMhlPQTDNKKKIiitedgefkalQEWILETDGVSLMRVLSEKD-VDPVRTTSNDIVEIFTVLGIEAVRKALER 1380
Cdd:pfam04998  403 PGIKRILV--NEDDKGKVE-----------PDWVLETEGVNLLRVLLVPGfVDAGRILSNDIHEILEILGIEAARNALLN 469

                          570       580       590       600
                   ....*....|....*....|....*....|....*....|....*..
gi 133327     1381 ELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPL 1427
Cdd:pfam04998  470 EIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
RPOLA_N smart00663
RNA polymerase I subunit A N-terminus;
246-546 4.31e-172

RNA polymerase I subunit A N-terminus;


Pssm-ID: 214767 [Multi-domain]  Cd Length: 295  Bit Score: 524.78  E-value: 4.31e-172
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327       246 EWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNElpGL 325
Cdd:smart00663    1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GL 78

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327       326 PRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQEL 405
Cdd:smart00663   79 PRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKL 158

                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327       406 VRRGNsqyPGAKYIIRdnGDRIDLRFHPK-PSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRL 484
Cdd:smart00663  159 VRNGP---NGAKYIIR--GKKTNLKLAKKsKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRL 233

                           250       260       270       280       290       300
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 133327       485 NLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVR 546
Cdd:smart00663  234 NPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
RNA_pol_Rpb1_1 pfam04997
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ...
 15-354 3.45e-142

RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.


Pssm-ID: 398595  Cd Length: 320  Bit Score: 444.04  E-value: 3.45e-142
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327       15 LRTIKRVQFGVLSPDELKRMSVTEggIKYPETTE--GGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAK 92
Cdd:pfam04997    1 LKKIKEIQFGIASPEEIRKWSVGE--VTKPETYNygSLKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAK 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327       93 PVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQ--PKKRLTHVYDLCKGKNICEGGEEMDnkfgveqpe 170
Cdd:pfam04997   79 PVFHIGFFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGLenLKMGAKAILELCKKKDLCEHCGGKN--------- 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      171 gdedltkekghGGCGRYQPRIRRSGLELYAEWKHVNEDsqEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIV 250
Cdd:pfam04997  150 -----------GVCGSQQPVSRKEGLKLKAAIKKSKEE--EEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMIL 216

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      251 TVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQ 330
Cdd:pfam04997  217 TVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGLPPALQ 296

                          330       340
                   ....*....|....*....|....
gi 133327      331 KSGRPLKSLKQRLKGKEGRVRGNL 354
Cdd:pfam04997  297 KSKRPLKSISQRLKGKEGRFRGNL 320
RNA_pol_Rpb1_2 pfam00623
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
 356-521 1.03e-97

RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion.


Pssm-ID: 395498  Cd Length: 166  Bit Score: 311.54  E-value: 1.03e-97
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      356 GKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPKP 435
Cdd:pfam00623    1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLRQLVENGPNVYPGANYIIRINGARRDLRYQKRR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      436 SDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEI 515
Cdd:pfam00623   81 LDKELEIGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160


                   ....*.
gi 133327      516 QELAMV 521
Cdd:pfam00623  161 EELMLV 166
RNA_pol_Rpb1_6 pfam04992
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 896-1079 3.06e-96

RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.


Pssm-ID: 461511  Cd Length: 188  Bit Score: 308.27  E-value: 3.06e-96
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      896 LAGESVEFQNLATLKPSNKAFEKKFRFDYTNERA--LRRTLQEDLVKDVLSNAHIQNELEREFERMREDREVLR-VIFPT 972
Cdd:pfam04992    1 LDGAFIEKQKIDTLKLSDAAFEKRYRLDVMDEKSgfLPGYLEEGVIKEIAGDPEVQQLLDEEYEQLLEDRELLReIIFPT 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      973 GDSKVV-LPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLLFNIHLRSTLCS 1051
Cdd:pfam04992   81 GDSKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVVVRGDDPLSKEAQENATLLFKILLRSRLAS 160

                          170       180
                   ....*....|....*....|....*...
gi 133327     1052 RRMAEEFRLSGEAFDWLLGEIESKFNQA 1079
Cdd:pfam04992  161 KRVLEEYRLNKEAFDWVLGEIESRFLQA 188
RNAP_IV_RPD1_N cd10506
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ...
 57-880 3.96e-91

Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 are the largest subunits of plant DNA-dependent RNA polymerase IV and V that, together with second largest subunits (NRPD2 and NRPE2), form the active site region of the DNA entry and RNA exit channel. Higher plants have five multi-subunit nuclear RNA polymerases; RNAP I, RNAP II and RNAP III, which are essential for viability, plus the two isoforms of the non-essential polymerase RNAP IV and V, which specialize in small RNA-mediated gene silencing pathways. RNAP IV and/or V might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. The subunit compositions of RNAP IV and V reveal that they evolved from RNAP II.


Pssm-ID: 259849 [Multi-domain]  Cd Length: 744  Bit Score: 314.34  E-value: 3.96e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     57 LMDPRQGVIERTGRCQTC-AGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCffcskllvdsnnPKIKDILAKSKG 135
Cdd:cd10506   20 VTNPRLGLPNESGQCTTCgAKDNKKCEGHFGVIKLPVTIYHPYFISEVAQILNKIC------------PGCKSIKQKKKK 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    136 QPKKRLTHVY-DLCKGKniceggeemdnkfgvEQPEGdEDLTKekghggcgryqprirrsglelyaewkhvnedsqekki 214
Cdd:cd10506   88 PPRETLPPDYwDFIPKD---------------GQQEE-SCVTK------------------------------------- 114

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    215 lLSPERVHEIFKRISDEECFVLGMEpRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNE 294
Cdd:cd10506  115 -NLPILSLAQVKKILKEIDPKLIAK-GLPRQEGLFLKCLPVPPNCHRVTEFTHGFSTGSRLIFDERTRAYKKLVDFIGTA 192

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    295 QNGAAAHviaedvkllqfhvatmvdnelpglpramqKSGrpLKSLKQrlkgkegrvrgNLMGKRVDFSARTVITPDPNLS 374
Cdd:cd10506  193 NESAASK-----------------------------KSG--LKWMKD-----------LLLGKRSGHSFRSVVVGDPYLE 230

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    375 IDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGnsqyPGAKYII--RDNGDRIDLRFHPKpsdlhLQTGYKVERHMCD 452
Cdd:cd10506  231 LNEIGIPCEIAERLTVSERVSSWNRERLQEYCDLT----LLLKGVIgvRRNGRLVGVRSHNT-----LQIGDVIHRPLVD 301

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    453 GDIVIFNRQPTLHKMSMMGHRVRILPW-STFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSN 531
Cdd:cd10506  302 GDVVLVNRPPSIHQHSLIALSVKVLPTnSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAELEELVALPKQLISSQSG 381

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    532 RPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTwdgKVPQPAILK--PR--PLWTGKQIFSLIIPGHINCirths 607
Cdd:cd10506  382 QNLLSLTQDSLLAAHLMTERGVFLDKAQMQQLQMLCPS---QLPPPAIIKspPSngPLWTGKQLFQMLLPTDLDY----- 453

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    608 thpddedSGPykhispgDTKVVVENGELIMGiLCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTI 687
Cdd:cd10506  454 -------SFP-------SNLVFISDGELISS-SGGSSWLRDSEGNLFSILVKHGPGKALDFLDSAQGLLCEWLSMRGFSV 518

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    688 GIGD------SIADSKTYQDIQNTIKKAKQ----DVIEV----IEKAHNNELEPTPGNTLRQTFENQVN-RILNDARDK- 751
Cdd:cd10506  519 SLSDlylssdSYSRQKMIEEISLGLREAEIacniKQLLVdsrkDFLSGSGEENDVSSDVERVIYERQKSaALSQASVSAf 598

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    752 ------TGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKrIPFGFKH---------RTLPHFIKDDY- 815
Cdd:cd10506  599 kqvfrdIQNLVYKYASKDNSLLAMIKAGSKGSLLKLVQQSGCLGLQLSLVK-LSYRIPRqlscaawnsQKSPRVIEKDGs 677

                        810       820       830       840       850       860       870
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    816 ----GPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDtavKTAET-GYIQRRLIKSMESVMVKYDATVR 880
Cdd:cd10506  678 ecteSYIPYGVVESSFLDGLNPLECFVHSITSRDSSFS---SNADLpGTLFRKLMFFMRDIYVAYDGTVR 744
RNAP_A'' cd06528
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ...
 1054-1477 1.99e-90

A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.


Pssm-ID: 132725 [Multi-domain]  Cd Length: 363  Bit Score: 299.17  E-value: 1.99e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1054 MAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKK 1133
Cdd:cd06528   10 VLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIVDARKE 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1134 PKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyyDpnpqstvvaedqewvnvYYEMPdfdvarispwlLR 1213
Cdd:cd06528   90 PSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISI--D-----------------LFNMR-----------IT 139

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1214 VELDRKHMTDRKLTMEQIAEKINAGFGDDlncIFNDDNAEKLVLRIrimnsDENKMQEEEEVVDKmdddvflrciesnmL 1293
Cdd:cd06528  140 IELDEEMLEDRGITVDDVLKAIEKLKKGK---VGEEGDVTLIVLKA-----EEPSIKELRKLAEK--------------I 197

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1294 TDMTLQGIEQISKVymhlpqtdnkkkIIITEDGefkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEA 1373
Cdd:cd06528  198 LNTKIKGIKGIKRV------------IVRKEED------EYVIYTEGSNLKAVLKVEGVDPTRTTTNNIHEIEEVLGIEA 259

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1374 VRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKG 1453
Cdd:cd06528  260 ARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLARAAFEVTVKHLLDAAVRGEVDELRG 339

                        410       420
                 ....*....|....*....|....
gi 133327   1454 VSENIMLGQLAPAGTGCFDLLLDA 1477
Cdd:cd06528  340 VIENIIVGQPIPLGTGDVELTMDP 363
PRK04309 PRK04309
DNA-directed RNA polymerase subunit A''; Validated
 1052-1479 2.14e-88

DNA-directed RNA polymerase subunit A''; Validated


Pssm-ID: 235277 [Multi-domain]  Cd Length: 383  Bit Score: 294.06  E-value: 2.14e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1052 RRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINIS 1131
Cdd:PRK04309   27 REKLEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDAR 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1132 KKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqstvvaeDqewvnvYYEMpdfdvarispwL 1211
Cdd:PRK04309  107 KEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISV-------------D------LANM-----------T 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1212 LRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNcifnddnAEKLVLRIRImnsDENKMQEEEEVVDKmdddvflrciesn 1291
Cdd:PRK04309  157 IIIELDEEMLEDRGLTVDDVKEAIEKKKGGEVE-------IEGNTLIISP---KEPSYRELRKLAEK------------- 213

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1292 mLTDMTLQGIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGI 1371
Cdd:PRK04309  214 -IRNIKIKGIKGIKRV-------------IIRKEGD-----EYVIYTEGSNLKEVLKVEGVDATRTTTNNIHEIEEVLGI 274

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1372 EAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPM 1451
Cdd:PRK04309  275 EAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDEL 354

                         410       420
                  ....*....|....*....|....*...
gi 133327    1452 KGVSENIMLGQLAPAGTGCFDLLLDAEK 1479
Cdd:PRK04309  355 KGVTENIIVGQPIPLGTGDVELTMDPPL 382
RNA_pol_rpoA2 TIGR02389
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
 1054-1476 5.76e-85

DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 274105 [Multi-domain]  Cd Length: 367  Bit Score: 283.48  E-value: 5.76e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1054 MAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKK 1133
Cdd:TIGR02389   14 VKKREISDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKT 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1134 PKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyydpnpqstvvaedqewvnvyyempdfDVARISpwlLR 1213
Cdd:TIGR02389   94 PSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISI---------------------------DLADMT---VI 143

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1214 VELDRKHMTDRKLTMEQIAEKINAgfgddlncifnddnaeklVLRIRIMNSDenkmQEEEEVVDKMDDDVF--LRCIEsN 1291
Cdd:TIGR02389  144 IELDEEQLKERGITVDDVEKAIKK------------------AKLGKVIEID----MDNNTITIKPGNPSLkeLRKLK-E 200

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1292 MLTDMTLQGIEQISKVymhlpqtdnkkkiIITEDGEfkalqEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGI 1371
Cdd:TIGR02389  201 KIKNLHIKGIKGIKRV-------------VIRKEGD-----EYVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAEVLGI 262

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1372 EAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPM 1451
Cdd:TIGR02389  263 EAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKHLLDAAIRGEVDEL 342

                          410       420
                   ....*....|....*....|....*
gi 133327     1452 KGVSENIMLGQLAPAGTGCFDLLLD 1476
Cdd:TIGR02389  343 KGVIENIIVGQPIPLGTGDVDLVMD 367
rpoC_TIGR TIGR02386
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
 20-1135 2.98e-76

DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 274103 [Multi-domain]  Cd Length: 1140  Bit Score: 278.09  E-value: 2.98e-76
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327       20 RVQFGVLSPDELKRMSvtEGGIKYPETT--EGGRPKLGGLMDPR--------------------QGVIertgrCQTCAGN 77
Cdd:TIGR02386    1 AIKISIASPDTIRNWS--YGEVKKPETInyRTLKPEKDGLFCEKifgptkdwecycgkykkiryKGVV-----CERCGVE 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327       78 MTECP---GHFGHIELAKPVFHVGF-----------LVKTMKVLRCVCFFCSKLLVDSNNPKI--KDILAkskgqpkkrL 141
Cdd:TIGR02386   74 VTESKvrrERMGHIELAAPVAHIWYfkglpsrigllLDITAKELESVLYFENYVVLDPGDTKLdkKEVLD---------E 144

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      142 THVYDLCK----GKNICEGGEemdnkfGVEQPEGDEDLTKEkghggcgryqprIRRSGLELyaewKHVNEDSQEKKILls 217
Cdd:TIGR02386  145 TEYREVLKrygdGFRAGMGAE------AIKELLEKIDLDKE------------IEELKIQL----RESKSDQKRKKLL-- 200

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      218 pervheifKRISDEECFVLGMepryARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNG 297
Cdd:TIGR02386  201 --------KRLEIVEAFKDSG----NRPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELG 268

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      298 AAAHVIAEDVKLLQFHVATMVDNELPGLPrAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQ 377
Cdd:TIGR02386  269 APEIIVRNEKRMLQEAVDALFDNGRRGKP-VVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQ 347

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      378 VGVPRSIAAnmtfaEIVTPFNIDRLQE------------LVRRGNSQ-YPGAKYIIRDngdridlrfHPkpsdlhlqtgy 444
Cdd:TIGR02386  348 CGLPKKMAL-----ELFKPFIIKRLIDrelaaniksakkMIEQEDPEvWDVLEDVIKE---------HP----------- 402

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      445 kverhmcdgdiVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRM 524
Cdd:TIGR02386  403 -----------VLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNN 471

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      525 IVTPQSNRPVMGIVQDT------LTAVRKFTKRD--VFLERGEVmnllmFLSTWDGKVPQPAILKPRP----LWT--GKQ 590
Cdd:TIGR02386  472 ILNPKDGKPIVTPSQDMvlglyyLTTEKPGAKGEgkIFSNVDEA-----IRAYDNGKVHLHALIGVRTsgeiLETtvGRV 546

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      591 IFSLIIPghincirthsthpddeDSGPYKHISPgdtkvvvengelimgILCKKSLgtsaGSLVHISYLEMGHDITRLFYS 670
Cdd:TIGR02386  547 IFNEILP----------------EGFPYINDNE---------------PLSKKEI----SSLIDLLYEVHGIEETAEMLD 591

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      671 NIQTVINNWLLIEGHTIGIGDSIadskTYQDIQNTIKKAKQDVIEVIEKAHNNELepTPGNTLRQTFEnqvnrILNDARD 750
Cdd:TIGR02386  592 KIKALGFKYATKSGTTISASDIV----VPDEKYEILKEADKEVAKIQKFYNKGLI--TDEERYRKVVS-----IWSETKD 660

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      751 KTGSSAQKSLS----EYNNFKSMVVSGAKGSKINISQVIAVVG-QQNVEGKRIPFGFKHrtlphfikddygpesrgfven 825
Cdd:TIGR02386  661 KVTDAMMKLLKkdtyKFNPIFMMADSGARGNISQFRQLAGMRGlMAKPSGDIIELPIKS--------------------- 719

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      826 SYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKY-DATVRNSInQVVQLRYGEDglagESVEfq 904
Cdd:TIGR02386  720 SFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREeDCGTEEGI-EVEAIVEGKD----EIIE-- 792

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      905 nlaTLKpsnkafekkfrfdytnERALRRTLQEDLVKDVLSNAHIQ-NELerefermrEDREVLRVIFPTGDSKV----VL 979
Cdd:TIGR02386  793 ---SLK----------------DRIVGRYSAEDVYDPDTGKLIAEaNTL--------ITEEIAEKIENSGIEKVkvrsVL 845

                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      980 PCNLLRMIwnAQKIFHINprlpsdlhpikvvegvkelskklvivngddpLSRQAqenatlLFNIhlrstlcsrrmaeefr 1059
Cdd:TIGR02386  846 TCESEHGV--CQKCYGRD-------------------------------LATGK------LVEI---------------- 870

                         1130      1140      1150      1160      1170      1180      1190
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 133327     1060 lsgeafdwllgeieskfnqaiahpGEMVGALAAQSLGEPATQMTLNTFHYAGVSA--KNVTLGVPRLKELINiSKKPK 1135
Cdd:TIGR02386  871 ------------------------GEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGasGDITQGLPRVKELFE-ARTPK 923
RNA_pol_Rpb1_7 pfam04990
RNA polymerase Rpb1, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ...
 1164-1299 2.00e-75

RNA polymerase Rpb1, domain 7; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (pfam04561).


Pssm-ID: 461510 [Multi-domain]  Cd Length: 136  Bit Score: 246.29  E-value: 2.00e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1164 TTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVA---RISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFG 1240
Cdd:pfam04990    1 TTLRSVTAATEIYYDPDPRNTVIEEDREFVESYFEIPDEDVEdldRQSPWLLRIELDRKKMLDKGLTMEDVAEKIKEEFG 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 133327     1241 DDLNCIFNDDNAEKLVLRIRIMNSDENKmqeEEEVVDKMDDDVFLRCIESNMLTDMTLQ 1299
Cdd:pfam04990   81 NDLFVIFSDDNAEKLVIRIRIINDEKEK---DEEQEDKAEDDVFLKRLEANMLDSLTLR 136
RNAP_III_Rpc1_C cd02736
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ...
 1075-1471 3.64e-72

Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.


Pssm-ID: 132723 [Multi-domain]  Cd Length: 300  Bit Score: 244.05  E-value: 3.64e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1075 KFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLgqSARDAERA 1154
Cdd:cd02736    1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITAKLE--NDRDEKSA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1155 KDILCRLEHTTLRKVTANTAIYYDPNpqstvvaedqewvNVYyempdfdvarispwlLRVELDRKHMTDRKLTMEQIAEK 1234
Cdd:cd02736   79 RIVKGRIEKTYLGEVASYIEEVYSPD-------------DCY---------------ILIKLDKKIIEKLQLSKSNLYFL 130

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1235 INagfgddlncifnddnaeklvlririmnsdenkmqeeeevvdkmdddvFLRciesNMLTDMTLQGIEQISKVYMHLPQT 1314
Cdd:cd02736  131 LQ-----------------------------------------------SLK----RKLPDVVVSGIPEVKRAVINKDKK 159

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1315 DNKKKIIItEDGEFKAlqewILETDGVslmrvlsekdvDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVN 1394
Cdd:cd02736  160 KGKYKLLV-EGYGLRA----VMNTPGV-----------IGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSID 223

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 133327   1395 YRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGCF 1471
Cdd:cd02736  224 PRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300
PRK14897 PRK14897
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
 1053-1474 4.10e-69

unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional


Pssm-ID: 237853 [Multi-domain]  Cd Length: 509  Bit Score: 242.79  E-value: 4.10e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1053 RMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISK 1132
Cdd:PRK14897  151 KAMKKKELSDDEYEEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVDARK 230

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1133 KPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVtANTAIyydpnpqstvvaedqewvnvyyempdfDVARISpwlL 1212
Cdd:PRK14897  231 KPSTPTMTIYLKKDYREDEEKVREVAKKIENTTLIDV-ADIIT---------------------------DIAEMS---V 279

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1213 RVELDRKHMTDRKLTMEQIAEKInagfgddlncifnddnaEKLVLRIRIMNSDENKMQEEEEVVDKmdddvfLRCIESNm 1292
Cdd:PRK14897  280 VVELDEEKMKERLIEYDDILAAI-----------------SKLTFKTVEIDDGIIRLKPQQPSFKK------LYLLAEK- 335

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1293 LTDMTLQGIEQISKVymhlpqtdnkkkIIITEDGEfkalQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIE 1372
Cdd:PRK14897  336 VKSLTIKGIKGIKRA------------IARKENDE----RRWVIYTQGSNLKDVLEIDEVDPTRTYTNDIIEIATVLGIE 399

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1373 AVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMK 1452
Cdd:PRK14897  400 AARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLARAAFEITGKHLLRAGILGEVDKLA 479

                         410       420
                  ....*....|....*....|..
gi 133327    1453 GVSENIMLGQLAPAGTGCFDLL 1474
Cdd:PRK14897  480 GVAENIIVGQPITLGTGAVSLV 501
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
 20-948 2.36e-64

DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439856 [Multi-domain]  Cd Length: 1165  Bit Score: 241.22  E-value: 2.36e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     20 RVQFGVLSPDELkrMSVTEGGIKYPETT--EGGRPKLGGLMDPR--------------------QGVIertgrCQTCAGN 77
Cdd:COG0086    9 AIKIGLASPEKI--RSWSYGEVKKPETInyRTFKPERDGLFCERifgpckdyecycgkykrmvyKGVV-----CEKCGVE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     78 MTECP---GHFGHIELAKPVFHVGF-----------LVKTMKVLRCVCFFCSKLLVDSNNPKIK--DILAKSKGQPKkrl 141
Cdd:COG0086   82 VTLSKvrrERMGHIELAMPVFHIWGlkslpsrigllLDMSLRDLERVLYFESYVVIDPGDTPLEkgQLLTEDEYREI--- 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    142 thvydlckgknICEGGEEMDNKFG---VEQPEGDEDLTKEKGhggcgryqprirrsglELYAEWKHVNedSQEKKIllsp 218
Cdd:COG0086  159 -----------LEEYGDEFVAKMGaeaIKDLLGRIDLEKESE----------------ELREELKETT--SEQKRK---- 205

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    219 ervhEIFKRISDEECFVLgmepRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGA 298
Cdd:COG0086  206 ----KLIKRLKVVEAFRE----SGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKA 277

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    299 AAHVIAEDVKLLQFHVATMVDNELPGlpRAMQKSG-RPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQ 377
Cdd:COG0086  278 PDIIVRNEKRMLQEAVDALFDNGRRG--RAVTGANkRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQ 355

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    378 VGVPRSIAanmtfAEIVTPFNIDRLQElvrRGNSQ-YPGAKYIIRDNGDRI------DLRFHPkpsdlhlqtgykverhm 450
Cdd:COG0086  356 CGLPKKMA-----LELFKPFIYRKLEE---RGLATtIKSAKKMVEREEPEVwdileeVIKEHP----------------- 410

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    451 cdgdiVIFNRQPTLHKMSMM--------GHRVRILPWstfrlnlsVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVP 522
Cdd:COG0086  411 -----VLLNRAPTLHRLGIQafepvlieGKAIQLHPL--------VCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLST 477

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    523 RMIVTPQSNRPVMGIVQDT------LTAVRKFTKRD--VFLERGEVMNLLMflstwDGKVPQPAILKPRPLWTGKQ---- 590
Cdd:COG0086  478 NNILSPANGKPIIVPSQDMvlglyyLTREREGAKGEgmIFADPEEVLRAYE-----NGAVDLHARIKVRITEDGEQvgki 552

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    591 --------IFSLIIP---GHINcirthsthpddedsgpykhispgdtKVvvengelimgiLCKKSLGTsagsLVHISYLE 659
Cdd:COG0086  553 vettvgryLVNEILPqevPFYN-------------------------QV-----------INKKHIEV----IIRQMYRR 592

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    660 MGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTyqdiQNTIKKAKQDVIEvIEKAHNNELePTPGNTlrqtfEN 739
Cdd:COG0086  593 CGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKEK----QEIFEEANKEVKE-IEKQYAEGL-ITEPER-----YN 661

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    740 QVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVG-QQNVEGKRIPFGFKHrtlphfikddygpe 818
Cdd:COG0086  662 KVIDGWTKASLETESFLMAAFSSQNTTYMMADSGARGSADQLRQLAGMRGlMAKPSGNIIETPIGS-------------- 727

                        890       900       910       920       930       940       950       960
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    819 srgfvenSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIK-SMESVMVKYDATVRNSINqVVQLRYGedgla 897
Cdd:COG0086  728 -------NFREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDvAQDVIVTEEDCGTDRGIT-VTAIKEG----- 794

                        970       980       990      1000      1010
                 ....*....|....*....|....*....|....*....|....*....|.
gi 133327    898 GESVEfqnlaTLKpsnkafekkfrfdytnERALRRTLQEDlVKDVLSNAHI 948
Cdd:COG0086  795 GEVIE-----PLK----------------ERILGRVAAED-VVDPGTGEVL 823
RNA_pol_Rpb1_3 pfam04983
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 525-691 1.62e-61

RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking.


Pssm-ID: 461507  Cd Length: 158  Bit Score: 207.48  E-value: 1.62e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      525 IVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLStwdgKVPQPAILKP-RPLWTGKQIFSLIIPGHINCI 603
Cdd:pfam04983    2 ILSPQNGKPIIGPSQDMVLGAYLLTREDTFFDREEVMQLLMYGI----VLPHPAILKPiKPLWTGKQTFSRLLPNEINPK 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      604 RTHSTHPDDEdsgpykhiSPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIE 683
Cdd:pfam04983   78 GKPKTNEEDL--------CENDSYVLINNGELISGVIDKKTVGKSLGSLIHIIYKEYGPEETAKFLDRLQKLGFRYLTKS 149


                   ....*...
gi 133327      684 GHTIGIGD 691
Cdd:pfam04983  150 GFSIGIDD 157
RNAP_beta'_N cd01609
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ...
 244-874 2.72e-61

Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; Beta' is the largest subunit of bacterial DNA-dependent RNA polymerase (RNAP). This family also includes the eukaryotic plastid-encoded RNAP beta' subunit. Bacterial RNAP is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. Structure studies suggest that RNA polymerase complexes from different organisms share a crab-claw-shaped structure with two "pincers" defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. Beta' contains part of the active site and binds two zinc ions that have a structural role in the formation of the active polymerase.


Pssm-ID: 259845 [Multi-domain]  Cd Length: 659  Bit Score: 223.93  E-value: 2.72e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    244 RPEWMIVTVLPVPPLSVRPAVVMQG-----SARNqdDLTHKladIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMV 318
Cdd:cd01609  138 RPEWMILTVLPVIPPDLRPMVQLDGgrfatSDLN--DLYRR---VINRNNRLKKLLELGAPEIIVRNEKRMLQEAVDALI 212

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    319 DNELPGLPrAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAanmtfAEIVTPFN 398
Cdd:cd01609  213 DNGRRGKP-VTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMA-----LELFKPFV 286

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    399 IdrlQELVRRGNSQYP-GAKYIIRDNGDRIdlrfhpkpsdlhlqtgYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRIL 477
Cdd:cd01609  287 I---RELIERGLAPNIkSAKKMIERKDPEV----------------WDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLI 347

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    478 PWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDT------LTAVRKFTKr 551
Cdd:cd01609  348 EGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPASGKPIVTPSQDMvlglyyLTKERKGDK- 426

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    552 dvflerGEVMnllmfLSTWDGKVpqpailkprplwtgkqIFSLIIPghincirthsthpddedsgpykhispgdtkvvvE 631
Cdd:cd01609  427 ------GEGI-----IETTVGRV----------------IFNEILP---------------------------------E 446

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    632 NGELIMGILCKKSLgtsaGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGD-SIADSKtyqdiQNTIKKAK 710
Cdd:cd01609  447 GLPFINKTLKKKVL----KKLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDiVVPPEK-----KEIIKEAE 517

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    711 QDVIEvIEKAHNNeleptpGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEY--NNFKSMVVSGAKGSKINISQVIAVV 788
Cdd:cd01609  518 EKVKE-IEKQYEK------GLLTEEERYNKVIEIWTEVTEKVADAMMKNLDKDpfNPIYMMADSGARGSKSQIRQLAGMR 590

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    789 G-QQNVEGKRIPfgfkhrtLPhfIKDdygpesrgfvenSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKS 867
Cdd:cd01609  591 GlMAKPSGKIIE-------LP--IKS------------NFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDV 649


                 ....*..
gi 133327    868 MESVMVK 874
Cdd:cd01609  650 AQDVIVT 656
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
22-1116 7.50e-60

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 229.42  E-value: 7.50e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      22 QFGVLSPDELkrMSVTEGGIKYPETT--EGGRPKLGGLM-------------------DPR-QGViertGRCQTCAGNMT 79
Cdd:PRK09603 1400 QLTLASPEKI--HSWSYGEVKKPETInyRTLKPERDGLFcmkifgptkdyeclcgkykKPRfKDI----GTCEKCGVAIT 1473

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      80 ECP---GHFGHIELAKPVFHVGFL------------VKtMKVLRCVCFFCSKLLV---------DSNNPKIK-DILAKSK 134
Cdd:PRK09603 1474 HSKvrrFRMGHIELATPVAHIWYVnslpsrigtllgVK-MKDLERVLYYEAYIVKepgeaaydnEGTKLVMKyDILNEEQ 1552

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     135 GQP-KKRLTHvydlcKGKNICEGGEEMdnKFGVEQPEGDEDLTKekghggcgryqprirrsgleLYAEWKHVNEDSQEKK 213
Cdd:PRK09603 1553 YQNiSRRYED-----RGFVAQMGGEAI--KDLLEEIDLITLLQS--------------------LKEEVKDTNSDAKKKK 1605

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     214 ILlspervheifKRISDEECFVLGMEpryaRPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRN 293
Cdd:PRK09603 1606 LI----------KRLKVVESFLNSGN----RPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRL 1671

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     294 EQNGAAAHVIAEDVKLLQFHVATMVDNelpGLPRAMQKSG--RPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDP 371
Cdd:PRK09603 1672 MELGAPEIIVRNEKRMLQEAVDVLFDN---GRSTNAVKGAnkRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGP 1748

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     372 NLSIDQVGVPRSIAanmtfAEIVTPFNIDRLQElvrRGN-SQYPGAKYIIRDNGDRIdlrfhpkpsdlhlqtgYKVERHM 450
Cdd:PRK09603 1749 NLKMDECGLPKNMA-----LELFKPHLLSKLEE---RGYaTTLKQAKRMIEQKSNEV----------------WECLQEI 1804

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     451 CDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQS 530
Cdd:PRK09603 1805 TEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPAS 1884

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     531 NRPVMGIVQDTLTAVRKFT--KRDVFLER---GEVMNLLMFLST--WDGKVPQPAILKPRPLWT--GKQIFSLIIPGHIn 601
Cdd:PRK09603 1885 GKAVAIPSQDMVLGLYYLSleKSGVKGEHklfSSVNEIITAIDTkeLDIHAKIRVLDQGNIIATsaGRMIIKSILPDFI- 1963

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     602 cirthsthPDDEDSGPYKhispgdtkvvvengelimgilcKKSLGTsagsLVHISYLEMGHDITRLFYSNIQTVINNWll 681
Cdd:PRK09603 1964 --------PTDLWNRPMK----------------------KKDIGV----LVDYVHKVGGIGITATFLDNLKTLGFRY-- 2007

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     682 ieGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEViekahnnELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLS 761
Cdd:PRK09603 2008 --ATKAGISISMEDIITPKDKQKMVEKAKVEVKKI-------QQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAIA 2078

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     762 E----YNNFKSMVVSGAKGSKINISQVIAVVGqqnVEGKriPFGFKHRTlphfikddygPESRGFVEnsylaGLTPTEFF 837
Cdd:PRK09603 2079 KdkegFNSIYMMADSGARGSAAQIRQLSAMRG---LMTK--PDGSIIET----------PIISNFKE-----GLNVLEYF 2138

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     838 FHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYdatvrnsinqvvqlrygEDGLAGESVEFQNLATLKPSNKAFE 917
Cdd:PRK09603 2139 NSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVVS-----------------DDCGTHEGIEITDIAVGSELIEPLE 2201

                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     918 kkfrfdytnERALRRTLQEDLVKDvlsnahIQNElerefermredrevlrvifptgdskVVLPCNLLRMIWNAQKIfhin 997
Cdd:PRK09603 2202 ---------ERIFGRVLLEDVIDP------ITNE-------------------------ILLYADTLIDEEGAKKV---- 2237

                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     998 prlpsdlhpikvvegvKELSKKLVIVNgdDPLSRQAQENatllfnihlrstLCSRrmaeefrlsgeAFDWLLGEieskfn 1077
Cdd:PRK09603 2238 ----------------VEAGIKSITIR--TPVTCKAPKG------------VCAK-----------CYGLNLGE------ 2270

                        1130      1140      1150
                  ....*....|....*....|....*....|....*....
gi 133327    1078 QAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKN 1116
Cdd:PRK09603 2271 GKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRS 2309
PRK14898 PRK14898
DNA-directed RNA polymerase subunit A''; Provisional
 1100-1478 2.65e-57

DNA-directed RNA polymerase subunit A''; Provisional


Pssm-ID: 237854 [Multi-domain]  Cd Length: 858  Bit Score: 215.53  E-value: 2.65e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1100 TQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIyyDP 1179
Cdd:PRK14898  541 THNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPSTPIMTVHLKGEYATDREKAEEVAKKIESLTLGDVATSIAI--DL 618

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1180 NPQStvvaedqewvnvyyempdfdvarispwlLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNcifnddnAEKLVLRI 1259
Cdd:PRK14898  619 WTQS----------------------------IKVELDEETLADRGLTIESVEEAIEKKLGVKID-------RKGTVLYL 663

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1260 RImnsdenkmqEEEEVVDkmdddvFLRCIESnmLTDMTLQGIEQISKVYMHLPQTDNKkkiiitedgefkalQEWILETD 1339
Cdd:PRK14898  664 KP---------KTPSYKA------LRKRIPK--IKNIVLKGIPGIERVLVKKEEHEND--------------EEYVLYTQ 712

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1340 GVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGV 1419
Cdd:PRK14898  713 GSNLREVFKIEGVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIGRHGV 792

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 133327    1420 NRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAE 1478
Cdd:PRK14898  793 AGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDLRIDRE 851
RNAP_I_Rpa1_C cd02735
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ...
 1075-1474 3.01e-55

Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.


Pssm-ID: 132722 [Multi-domain]  Cd Length: 309  Bit Score: 195.49  E-value: 3.01e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1075 KFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKE-LINISKKPKTPSLTV-FLLGQSARDAE 1152
Cdd:cd02735    1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREiLMTASKNIKTPSMTLpLKNGKSAERAE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1153 RAK---------DILCRLEHTTLRKVTANTAIyydpnPQStvvaedQEWVNVYYEMPdfdvarispwllrveLDRKhmtd 1223
Cdd:cd02735   81 TLKkrlsrvtlsDVVEKVEVTEILKTIERVFK-----KLL------GKWCEVTIKLP---------------LSSP---- 130

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1224 rKLTMEQIAEKInagfgddlncifnddnAEKLVLRirimnsdenkmqeeeEVvdkmdddvflrciesnmltdmtlQGIEQ 1303
Cdd:cd02735  131 -KLLLLSIVEKL----------------ARKAVIR---------------EI-----------------------PGITR 155

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1304 ISKVYmhlpqTDNKKKiiitedgefkalQEWILETDGVSL--MRVLSEKdVDPVRTTSNDIVEIFTVLGIEAVRKALERE 1381
Cdd:cd02735  156 CFVVE-----EDKGGK------------TKYLVITEGVNLaaLWKFSDI-LDVNRIYTNDIHAMLNTYGIEAARRAIVKE 217

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1382 LYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVnRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLG 1461
Cdd:cd02735  218 ISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGM-ESSTSPLQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVG 296

                        410
                 ....*....|...
gi 133327   1462 QLAPAGTGCFDLL 1474
Cdd:cd02735  297 KPVNGGTGLFDLL 309
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
16-1469 3.11e-54

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 211.02  E-value: 3.11e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      16 RTIKRVQFGVLSPDELKRMS------VTEGGIKYPETTEGGR--PKLGGLMDPRQGVIER------TGR-CQTCAGNMTE 80
Cdd:PRK14844 1446 QSFNEVSISIASPESIKRMSygeiedVSTANYRTFKVEKGGLfcPKIFGPVNDDECLCGKykkrrhRGRiCEKCGVEVTS 1525

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      81 CP---GHFGHIELAKPVFHVGFLvKTMKvlrcvcffcSKL--LVDSNNPKIKDILAKSKGQPKKRLTHVYDlcKGKNICE 155
Cdd:PRK14844 1526 SKvrrERMGHIELASPVAHIWFL-KSLP---------SRIgaLLDMSLRDIENILYSDNYIVIDPLVSPFE--KGEIISE 1593

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     156 GG-EEMDNKFGVEQ---PEGDED----LTKEKGHggcgryqpRIRRsglELYAEWKHVNEDSQEKKILlspervheifKR 227
Cdd:PRK14844 1594 KAyNEAKDSYGIDSfvaMQGVEAirelLTRLDLH--------EIRK---DLRLELESVASEIRRKKII----------KR 1652

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     228 ISDEECFVLGMEpryaRPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDV 307
Cdd:PRK14844 1653 LRIVENFIKSGN----RPEWMILTTIPILPPDLRPLVSLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEK 1728

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     308 KLLQFHVATMVDNELPGlpRAMQKSGRP--LKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIA 385
Cdd:PRK14844 1729 RMLQEAVDSLFDNSRRN--ALVNKAGAVgyKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMA 1806

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     386 anmtfAEIVTPFNIDRLQELVRRGNSQYpgAKYIIRDNgdridlrfHPKPSDLHLQTgykVERHMcdgdiVIFNRQPTLH 465
Cdd:PRK14844 1807 -----LELFKPFVYSKLKMYGMAPTIKF--ASKLIRAE--------KPEVWDMLEEV---IKEHP-----VLLNRAPTLH 1863

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     466 KMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAV 545
Cdd:PRK14844 1864 RLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSKDIVLGI 1943

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     546 RKFT----KRD---VFLERGEVMNllmflSTWDGKVpqpailkprplwtgkqifsliipgHINC-IRTHSTHPDDEDSGP 617
Cdd:PRK14844 1944 YYLTlqepKEDdlpSFGAFCEVEH-----SLSDGTL------------------------HIHSsIKYRMEYINSSGETH 1994

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     618 YKHISPGDTKVVV-------EN--GELIMGILCKKSLgtsaGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIG 688
Cdd:PRK14844 1995 YKTICTTPGRLILwqifpkhENlgFDLINQVLTVKEI----TSIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFS 2070

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     689 IGDSIADSKTYQDIQNT---IKKAK---QDVIEVIEKAHNNELEptpgntlrqTFENQVNRILNDARDKTgsSAQKSLSE 762
Cdd:PRK14844 2071 RCDMVIPETKATHVDHArgeIKKFSmqyQDGLITRSERYNKVID---------EWSKCTDMIANDMLKAI--SIYDGNSK 2139

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     763 YNNFKSMVVSGAKGSKiniSQVIAVVGQQNVEGKriPFGFKHRTlphfikddygPESRGFVEnsylaGLTPTEFFFHAMG 842
Cdd:PRK14844 2140 YNSVYMMVNSGARGST---SQMKQLAGMRGLMTK--PSGEIIET----------PIISNFRE-----GLNVFEYFNSTHG 2199

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     843 GREGLIDTAVKTAETGYIQRRLIK-SMESVMVKYDATVRNSINQVVQLRYGEDGLAGESVefqnlatlkpsnkafekkfr 921
Cdd:PRK14844 2200 ARKGLADTALKTANSGYLTRRLVDvSQNCIVTKHDCKTKNGLVVRATVEGSTIVASLESV-------------------- 2259

                         970       980       990      1000      1010      1020      1030      1040
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     922 fdytnerALRRTLQEDLVKDVlsnahIQNELEREFERMREDRevlrvifptgdskvvlpcnllrmiwnaqkifhinprlp 1001
Cdd:PRK14844 2260 -------VLGRTAANDIYNPV-----TKELLVKAGELIDEDK-------------------------------------- 2289

                        1050      1060      1070      1080      1090      1100      1110      1120
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1002 sdlhpikvvegVKELS-KKLVIVNGDDPLSRQAQENAtllfnihlrSTLCSRRmaeefrlsgeafDWLLGEIESKfnqai 1080
Cdd:PRK14844 2290 -----------VKQINiAGLDVVKIRSPLTCEISPGV---------CSLCYGR------------DLATGKIVSI----- 2332

                        1130      1140      1150      1160      1170      1180      1190      1200
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1081 ahpGEMVGALAAQSLGEPATQMTLNTFHYAGVsaknVTLGVPRLKELINISKKPKTPSLTVFLLGQSARDA-ERAKDILC 1159
Cdd:PRK14844 2333 ---GEAVGVIAAQSVGEPGTQLTMRTFHIGGV----MTRGVESSNIIASINAKIKLNNSNIIIDKNGNKIViSRSCEVVL 2405

                        1210      1220      1230      1240      1250      1260      1270      1280
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1160 -------RLEHTtlrkVTANTAIYYDPNPQSTVVAEDQEW-------------VNVYYEMPD------------------ 1201
Cdd:PRK14844 2406 idslgseKLKHS----VPYGAKLYVDEGGSVKIGDKVAEWdpytlpiitektgTVSYQDLKDgisitevmdestgisskv 2481

                        1290      1300      1310      1320      1330      1340      1350      1360
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1202 -------FDVARISPWLLRVELDRKHMTdrkltmeqIAEKINAGFGDDLNCIFNDDNAEK-----LVLRI---------- 1259
Cdd:PRK14844 2482 vkdwklySGGANLRPRIVLLDDNGKVMT--------LASGVEACYFIPIGAVLNVQDGQKvhagdVITRTpresvktrdi 2553

                        1370      1380      1390      1400      1410      1420      1430      1440
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1260 -----RIMNSDENKMQEEEEVVDKMDDDVFLRCIESNMLTDMTLQGI-EQISKVYMHLpqtdNKKKIIITEDGEFkaLQE 1333
Cdd:PRK14844 2554 tgglpRVIELFEARRPKEHAIVSEIDGYVAFSEKDRRGKRSILIKPVdEQISPVEYLV----SRSKHVIVNEGDF--VRK 2627

                        1450      1460      1470      1480      1490      1500      1510      1520
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1334 WILETDGvslmrvlsekdvDPvrttsnDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLC----------- 1402
Cdd:PRK14844 2628 GDLLMDG------------DP------DLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILkqmlqkveitd 2689

                        1530      1540      1550      1560      1570      1580      1590      1600
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1403 --DTMTCRGHlmAITRHGVNRQDTG------------PLMK---------------CSFEETVDVLMEAAAHGESDPMKG 1453
Cdd:PRK14844 2690 pgDTMYLVGE--SIDKLEVDRENDAmsnsgkrpahylPILQgitrasletssfisaASFQETTKVLTEAAFCGKSDPLSG 2767

                        1610
                  ....*....|....*.
gi 133327    1454 VSENIMLGQLAPAGTG 1469
Cdd:PRK14844 2768 LKENVIVGRLIPAGTG 2783
PRK14906 PRK14906
DNA-directed RNA polymerase subunit beta';
244-1135 9.82e-54

DNA-directed RNA polymerase subunit beta';


Pssm-ID: 184899 [Multi-domain]  Cd Length: 1460  Bit Score: 208.19  E-value: 9.82e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     244 RPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELP 323
Cdd:PRK14906  311 DPADMILDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRR 390

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     324 GLPrAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAanmtfAEIVTPFNIDRLQ 403
Cdd:PRK14906  391 GRP-VTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMA-----LELFKPFVMKRLV 464

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     404 ELVRRGNSQypGAKYIIrdngdridlrfhpkpsDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFR 483
Cdd:PRK14906  465 ELEYAANIK--AAKRAV----------------DRGASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIK 526

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     484 LNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFT-KRDVFLERGEVmn 562
Cdd:PRK14906  527 LHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTtERDGFEGEGRT-- 604

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     563 llmFLSTWDGkvpqpailkprplwtgkqifsliipghincIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMgilCK 642
Cdd:PRK14906  605 ---FADFDDA------------------------------LNAYDARADLDLQAKIVVRLSRDMTVRGSYGDLEE---TK 648

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     643 --KSLGTSAGSLV----------HISYLEMGHDITRLfysnIQTVINNWLLIEGHTI---------------GIGDSIAD 695
Cdd:PRK14906  649 agERIETTVGRIIfnqvlpedypYLNYKMVKKDIGRL----VNDCCNRYSTAEVEPIldgikktgfhyatraGLTVSVYD 724

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     696 SKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPtpgntlrQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAK 775
Cdd:PRK14906  725 ATIPDDKPEILAEADEKVAAIDEDYEDGFLSE-------RERHKQVVDIWTEATEEVGEAMLAGFDEDNPIYMMADSGAR 797

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     776 GSKINISQVIAVVG-QQNVEGKRIpfgfkhrTLPhfikddygpesrgfVENSYLAGLTPTEFFFHAMGGREGLIDTAVKT 854
Cdd:PRK14906  798 GNIKQIRQLAGMRGlMADMKGEII-------DLP--------------IKANFREGLSVLEYFISTHGARKGLVDTALRT 856

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     855 AETGYIQRRLiksmesVMVKYDATVRNsinqvvqlrygEDGLAGESVEfqnlatlkpsnkafekkfrFDYTNERAlrrTL 934
Cdd:PRK14906  857 ADSGYLTRRL------VDVAQDVIVRE-----------EDCGTDEGVT-------------------YPLVKPKG---DV 897

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     935 QEDLVKDVLSNAHIQNELErefermredrevlrVIFPTGDskvvlpcnllrmiwnaqkifhinprlpsdlhpikvvegvk 1014
Cdd:PRK14906  898 DTNLIGRCLLEDVCDPNGE--------------VLLSAGD---------------------------------------- 923

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1015 elskklvIVNGDDPLSRQAQENATllfNIHLRSTLCSRrmaEEFRLSGEAFDWLLgeieskfnqAIAHP---GEMVGALA 1091
Cdd:PRK14906  924 -------YIESMDDLKRLVEAGVT---KVQIRTLMTCH---AEYGVCQKCYGWDL---------ATRRPvniGTAVGIIA 981

                         890       900       910       920
                  ....*....|....*....|....*....|....*....|....
gi 133327    1092 AQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINIsKKPK 1135
Cdd:PRK14906  982 AQSIGEPGTQLTMRTFHSGGVAGDDITQGLPRVAELFEA-RKPK 1024
PRK00566 PRK00566
DNA-directed RNA polymerase subunit beta'; Provisional
 244-1137 1.33e-53

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 234794 [Multi-domain]  Cd Length: 1156  Bit Score: 206.84  E-value: 1.33e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     244 RPEWMIVTVLPVPPLSVRPAVVMQG-----SARNqdDLTHKLadivkI--NNQLRR------------NEQngaaahvia 304
Cdd:PRK00566  223 KPEWMILDVLPVIPPDLRPLVQLDGgrfatSDLN--DLYRRV-----InrNNRLKRllelgapeiivrNEK--------- 286

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     305 edvKLLQFHVATMVDNELPGlpRAMQ-KSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRS 383
Cdd:PRK00566  287 ---RMLQEAVDALFDNGRRG--RPVTgPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKK 361

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     384 IAanmtfAEIVTPFNIDRLQE------------LVRRGNSQ-YPGAKYIIRDngdridlrfHPkpsdlhlqtgykverhm 450
Cdd:PRK00566  362 MA-----LELFKPFIMKKLVErglattiksakkMVEREDPEvWDVLEEVIKE---------HP----------------- 410

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     451 cdgdiVIFNRQPTLHKMSMM--------GHRVRILPwstfrLnlsVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVP 522
Cdd:PRK00566  411 -----VLLNRAPTLHRLGIQafepvlieGKAIQLHP-----L---VCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSS 477

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     523 RMIVTPQSNRPVmgIV--QD------TLTAVRKFTKrdvflerGEVMnllMFLSTWD-------GKVPQPAILKPRP--- 584
Cdd:PRK00566  478 NNILSPANGKPI--IVpsQDmvlglyYLTREREGAK-------GEGM---VFSSPEEalrayenGEVDLHARIKVRItsk 545

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     585 --LWT--GKQIFSLIIPGHIncirthsthpddedsgPYkhispgdtkvvvENGELIMGilcKKSLgtsaGSLVHISYLEM 660
Cdd:PRK00566  546 klVETtvGRVIFNEILPEGL----------------PF------------INVNKPLK---KKEI----SKIINEVYRRY 590

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     661 GHDITRLFYSNIQTVINNWLLIEGHTIGIGD-SIADSKtyQDIqntIKKAKQDVIEvIEKAHNNELeptpgntlrQTFE- 738
Cdd:PRK00566  591 GLKETVIFLDKIKDLGFKYATRSGISIGIDDiVIPPEK--KEI---IEEAEKEVAE-IEKQYRRGL---------ITDGe 655

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     739 --NQVNRILNDARDKTGSSAQKSLSEYNN-FKS---MVVSGAKGSKINISQVIAVVG-QQNVEGKRIPfgfkhrtLPhfI 811
Cdd:PRK00566  656 ryNKVIDIWSKATDEVAKAMMKNLSKDQEsFNPiymMADSGARGSASQIRQLAGMRGlMAKPSGEIIE-------TP--I 726

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     812 KddygpesrgfveNSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLiksmesVMVKYDATVRN----SINQVV 887
Cdd:PRK00566  727 K------------SNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRL------VDVAQDVIVREddcgTDRGIE 788

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     888 QLRYGEDGLAGESVEfqnlatlkpsnkafekkfrfdytnERALRRTLQEDLVKDVLSNahiqnelerefermredrevlr 967
Cdd:PRK00566  789 VTAIIEGGEVIEPLE------------------------ERILGRVLAEDVVDPETGE---------------------- 822

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     968 VIFPTGDskvvlpcnLLRMIWnAQKIfhinprlpsdlhpikVVEGVKElskklvivngddplsrqaqenatllfnIHLRS 1047
Cdd:PRK00566  823 VIVPAGT--------LIDEEI-ADKI---------------EEAGIEE---------------------------VKIRS 851

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1048 TL-CsrrmaeefrlsgeafdwllgeiESKF---------NQAIAHP---GEMVGALAAQSLGEPATQMTLNTFHYAGVsa 1114
Cdd:PRK00566  852 VLtC----------------------ETRHgvcakcygrDLATGKLvniGEAVGVIAAQSIGEPGTQLTMRTFHTGGV-- 907

                         970       980
                  ....*....|....*....|...
gi 133327    1115 kNVTLGVPRLKELINiSKKPKTP 1137
Cdd:PRK00566  908 -DITGGLPRVAELFE-ARKPKGP 928
RNA_pol_Rpb1_4 pfam05000
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 717-823 2.50e-45

RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors.


Pssm-ID: 398598  Cd Length: 108  Bit Score: 159.45  E-value: 2.50e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      717 IEKA-HNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEG 795
Cdd:pfam05000    1 ITDAeRYGKLEDIWGMTLEESFEALINNILNKARDPAGNIASKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEG 80

                           90       100
                   ....*....|....*....|....*...
gi 133327      796 KRIPFGFKHRTLPHFIKDDYGPESRGFV 823
Cdd:pfam05000   81 KRIPFGFSGRTLPHFKKDDEGPESRGFV 108
rpoC1 PRK02625
DNA-directed RNA polymerase subunit gamma; Provisional
 243-540 4.40e-42

DNA-directed RNA polymerase subunit gamma; Provisional


Pssm-ID: 235055 [Multi-domain]  Cd Length: 627  Bit Score: 165.69  E-value: 4.40e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     243 ARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNEL 322
Cdd:PRK02625  240 SRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGR 319

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     323 PGlPRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAanmtfAEIVTPFNIDRl 402
Cdd:PRK02625  320 RG-RTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMA-----IELFQPFVIHR- 392

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     403 qeLVRRGN-SQYPGAKYIIRDNGDRIdlrfhpkpsdlhlqtgYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWST 481
Cdd:PRK02625  393 --LIRQGIvNNIKAAKKLIQRADPEV----------------WQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRA 454

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 133327     482 FRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQD 540
Cdd:PRK02625  455 IQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQD 513
rpoC1 CHL00018
RNA polymerase beta' subunit
 86-514 7.16e-40

RNA polymerase beta' subunit


Pssm-ID: 214336 [Multi-domain]  Cd Length: 663  Bit Score: 159.30  E-value: 7.16e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      86 GHIELAKPVFHVGF-----------LVKTMKVLRCVCFFCSKLLVDSNNpkiKDILAKSKGqpkkrlTHVYDLCKGKNIc 154
Cdd:CHL00018  105 GYIKLACPVTHVWYlkrlpsyianlLDKPLKELEGLVYCDFSFARPIAK---KPTFLRLRG------LFEYEIQSWKYS- 174

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     155 eggeemDNKFgVEQPEGDEDLTKEKGHGGcgryqPRIRR--SGLEL-------YAEWKHVNEDSQ------EKKILLspe 219
Cdd:CHL00018  175 ------IPLF-FSTQGFDTFRNREISTGA-----GAIREqlADLDLriiidnsLVEWKELGEEGStgneweDRKIGR--- 239

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     220 RVHEIFKRISDEECFVLgmepRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRR--NEQNG 297
Cdd:CHL00018  240 RKDFLVRRIKLAKHFIR----TNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDllTTSRS 315

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     298 AAAHVIAEDVKLLQFHVATMVDNELPGLPraMQKS-GRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSID 376
Cdd:CHL00018  316 TPGELVMCQKKLLQEAVDALLDNGIRGQP--MRDGhNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLH 393

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     377 QVGVPRSIAanmtfAEIVTPFNIdrlQELVRRGNSQYPG-AKYIIRDNGDRIDlrfhpkpsdlhlqtgyKVERHMCDGDI 455
Cdd:CHL00018  394 QCGLPREIA-----IELFQPFVI---RGLIRQHLASNIRaAKSKIREKEPIVW----------------EILQEVMQGHP 449

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 133327     456 VIFNRQPTLHKMSMM--------GHRVRILPwstfrlnlSVTTPYNADFDGDEMNLHLPQSLETRAE 514
Cdd:CHL00018  450 VLLNRAPTLHRLGIQafqpilveGRAICLHP--------LVCKGFNADFDGDQMAVHVPLSLEAQAE 508
RNAP_largest_subunit_C cd00630
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ...
 1361-1470 1.61e-38

Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.


Pssm-ID: 132719 [Multi-domain]  Cd Length: 158  Bit Score: 141.79  E-value: 1.61e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1361 DIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLM 1440
Cdd:cd00630   49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEKTTKHLL 128

                         90       100       110
                 ....*....|....*....|....*....|
gi 133327   1441 EAAAHGESDPMKGVSENIMLGQLAPAGTGC 1470
Cdd:cd00630  129 DAAAAGEKDELEGVSENIILGRPAPLGTGS 158
RNAP_largest_subunit_C cd00630
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ...
 1084-1131 4.41e-21

Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.


Pssm-ID: 132719 [Multi-domain]  Cd Length: 158  Bit Score: 91.71  E-value: 4.41e-21
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 133327   1084 GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINIS 1131
Cdd:cd00630    1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA 48
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 1857-1961 1.96e-14

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 79.19  E-value: 1.96e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1857 SPKYSPTSPKYSPTSPKYSP------------TSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYS 1924
Cdd:pfam05109  475 SPTPAGTTSGASPVTPSPSPrdngteskapdmTSPTSAVTTPTPNATSPTPAVTTPTPNATSPTLGKTSPTSAVTTPTPN 554

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 133327     1925 PTSPTYSPTSPKGSTYSP----TSPGYSPTSPTYSLTSPAI 1961
Cdd:pfam05109  555 ATSPTPAVTTPTPNATIPtlgkTSPTSAVTTPTPNATSPTV 595
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 1854-1959 1.98e-14

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 79.19  E-value: 1.98e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1854 TP--ASPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYS 1931
Cdd:pfam05109  517 TPnaTSPTPAVTTPTPNATSPTLGKTSPTSAVTTPTPNATSPTPAVTTPTPNATIPTLGKTSPTSAVTTPTPNATSPTVG 596

                           90       100
                   ....*....|....*....|....*...
gi 133327     1932 PTSPKGSTYSPTSPGyspTSPTYSLTSP 1959
Cdd:pfam05109  597 ETSPQANTTNHTLGG---TSSTPVVTSP 621
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 1854-1959 7.49e-14

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 77.26  E-value: 7.49e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1854 TPA--SPKYSPTSPKYSP------------TSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPT 1919
Cdd:pfam05109  477 TPAgtTSGASPVTPSPSPrdngteskapdmTSPTSAVTTPTPNATSPTPAVTTPTPNATSPTLGKTSPTSAVTTPTPNAT 556

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 133327     1920 SPKYSPTSPTYSPTSPKGSTYSPTSPGYSP----TSPTYSLTSP 1959
Cdd:pfam05109  557 SPTPAVTTPTPNATIPTLGKTSPTSAVTTPtpnaTSPTVGETSP 600
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 1855-1963 2.01e-12

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 72.64  E-value: 2.01e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1855 PASPkySPTSPKYSPTSPKYSPTSPTYSPTTPKYSP------------TSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPK 1922
Cdd:pfam05109  461 PAST--GPTVSTADVTSPTPAGTTSGASPVTPSPSPrdngteskapdmTSPTSAVTTPTPNATSPTPAVTTPTPNATSPT 538

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 133327     1923 YSPTSPTYSPTSPKGSTYSPTS-----------PGYSPTSPTYSLTSP---AISP 1963
Cdd:pfam05109  539 LGKTSPTSAVTTPTPNATSPTPavttptpnatiPTLGKTSPTSAVTTPtpnATSP 593
rpoC2 PRK02597
DNA-directed RNA polymerase subunit beta'; Provisional
 764-1117 3.95e-12

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 235052 [Multi-domain]  Cd Length: 1331  Bit Score: 71.95  E-value: 3.95e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     764 NNFKS---------MVVSGAKGskiNISQVIAVVGQQ----NVEGKRIpfgfkhrTLPhfIKDDygpesrgFVEnsylaG 830
Cdd:PRK02597  111 KNFRQndplnsvymMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--IKTN-------FRE-----G 166

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     831 LTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVK-YDATVRNSInqVVQlryGEDGLAGESVEFQNlatl 909
Cdd:PRK02597  167 LTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVReEDCGTTRGI--VVE---AMDDGDRVLIPLGD---- 237

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     910 kpsnkafekkfrfdytneRALRRTLQEDLVKDvlsnahiqnelerefermreDREVLrvifptgdskvvlpcnllrmiwn 989
Cdd:PRK02597  238 ------------------RLLGRVLAEDVVDP--------------------EGEVI----------------------- 256

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     990 AQKIFHINPRLPsdlhpiKVVE--GVKElskklVIVNgdDPLSRQAQenatllfnihlRStLCSRrmaeefrlsgeAFDW 1067
Cdd:PRK02597  257 AERNTAIDPDLA------KKIEkaGVEE-----VMVR--SPLTCEAA-----------RS-VCRK-----------CYGW 300

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|...
gi 133327    1068 LLgeieskfnqAIAHP---GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNV 1117
Cdd:PRK02597  301 SL---------AHNHLvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 344
rpoC2_cyan TIGR02388
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ...
 764-1234 7.03e-12

DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 274104 [Multi-domain]  Cd Length: 1227  Bit Score: 71.03  E-value: 7.03e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      764 NNFKSMVVSGAKGskiNISQVIAVVGQQ----NVEGKRIpfgfkhrTLPhfikddygpesrgfVENSYLAGLTPTEFFFH 839
Cdd:TIGR02388  119 NSVYMMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--------------IKTNFREGLTVTEYVIS 174

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      840 AMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVK-YDATVRNSInqvvQLRYGEDGlaGESVEFQNlatlkpsnkafek 918
Cdd:TIGR02388  175 SYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVReEDCGTERSI----VVRAMTEG--DKKISLGD------------- 235

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      919 kfrfdytneRALRRTLQEDLVkdvlsnaHIQNElerefermredrevlrVIFPTGDSkvvlpcnllrmiwnaqkifhINP 998
Cdd:TIGR02388  236 ---------RLLGRLVAEDVL-------HPEGE----------------VIVPKNTA--------------------IDP 263

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      999 RLPSDLHPIKVVEgvkelskklviVNGDDPLSRQAQenatllfnihlRStLCSRrmaeefrlsgeAFDWllgeieskfnq 1078
Cdd:TIGR02388  264 DLAKTIETAGISE-----------VVVRSPLTCEAA-----------RS-VCRK-----------CYGW----------- 298

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1079 AIAHP-----GEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGV-PRLKELINISKKPKT-PSLTVFllGQSARDA 1151
Cdd:TIGR02388  299 SLAHAhlvdlGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARQVrSKIDGTVEFGKKLRTrGYRTRH--GEDAKQV 376

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1152 ERAKDILCRlehttLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDF--------------DVA-RISPWLLRVEL 1216
Cdd:TIGR02388  377 EVAGLLIIK-----PTGSITNKAQEIEVTQGSLLFVEDGQTVDAGQLLAEIalgavrkstekatkDVAsDLAGEVKFDKV 451

                          490
                   ....*....|....*...
gi 133327     1217 DRKHMTDRKLTMEQIAEK 1234
Cdd:TIGR02388  452 VPEEKTDRQGNTTRIAQR 469
RNAP_beta'_C cd02655
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ...
 1084-1127 5.94e-11

Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.


Pssm-ID: 132721 [Multi-domain]  Cd Length: 204  Bit Score: 63.70  E-value: 5.94e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 133327   1084 GEMVGALAAQSLGEPATQMTLNTFHYAGVsAKNVTLGVPRLKEL 1127
Cdd:cd02655    6 GEAVGIIAAQSIGEPGTQLTMRTFHTGGV-ATDITQGLPRVEEL 48
RNAP_IV_NRPD1_C cd02737
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ...
 1084-1475 6.13e-11

Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.


Pssm-ID: 132724 [Multi-domain]  Cd Length: 381  Bit Score: 66.68  E-value: 6.13e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1084 GEMVGALAAQSLGEPATQMTLNTFHYAGVSAknvtlgVPRLKELI--NISKKPKTPSLTVFL---LGQSARDAE---RAK 1155
Cdd:cd02737    1 GEPVGSLAATAISEPAYKALLDPPQSLESSP------LELLKEVLecRSKSKSKENDRRVILslhLCKCDHGFEyerAAL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1156 DILCRLEHTTLRKVTANTAIYYDPNPQstvvaedqewvnvyyEMPDFDVARISPWLLRVELDRKHMTDRKLTmeqiaeKI 1235
Cdd:cd02737   75 EVKNHLERVTLEDLATTSMIKYSPQAT---------------EAIVGEIGDQLNTKKKGKKKAIFSTSLKIT------KF 133

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1236 NAGfgddlNCIFNDDNAEKLVLR---IRIMNSDENKmQEEEEVVDKMDDDVFlrciesNMLTDMTLQGIEQISKVYMhLP 1312
Cdd:cd02737  134 SPW-----VCHFHLDKECQKLSDgpcLTFSVSKEVS-KSSEELLDVLRDRII------PFLLETVIKGDERIKSVNI-LW 200

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1313 QTDNKKKIIITEDGEFKAlqEWILETdGVSLMRVLSEKD---------------VDPVRTTSNDIVEIFTVLGIEAVRKA 1377
Cdd:cd02737  201 EDSPSTSWVKSVGKSSRG--ELVLEV-TVEESCKKTRGNawnvvmdacipvmdlIDWERSMPYSIQQIKSVLGIDAAFEQ 277

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1378 LERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDT-----GPLMKCSFEETVDVLMEAAAHGESDPMK 1452
Cdd:cd02737  278 FVQRLESAVSMTGKSVLREHLLLVADSMTYSGEFVGLNAKGYKAQRRslkisAPFTEACFSSPIKCFLKAAKKGASDSLS 357

                        410       420
                 ....*....|....*....|....
gi 133327   1453 GVSENIMLGQLAPAGTGC-FDLLL 1475
Cdd:cd02737  358 GVLDACAWGKEAPVGTGSkFEILW 381
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 1491-1610 3.16e-10

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 59.46  E-value: 3.16e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      1491 PGLGAAGPTGMFFGSAPSPMGgiSPAMTP-WNQ--GATPAYGAWSPSVGSgmTP----GAAGFSPSAASDASGFSPGYSP 1563
Cdd:smart01104   15 PAWGSRTPGTAAGGAPTARGG--SGSRTPaWGGagSRTPAWGGAGPTGSR--TPawggASAWGNKSSEGSASSWAAGPGG 90

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*..
gi 133327      1564 AWsptpgspgspgpsspyipspgGAMSPSYSPTSPAYEPRSPGGYTP 1610
Cdd:smart01104   91 AY---------------------GAPTPGYGGTPSAYGPATPGGGAM 116
PARM pfam17061
PARM; Human PARM-1 is a mucin-like, androgen-regulated transmembrane protein that is present ...
 1854-1970 1.41e-08

PARM; Human PARM-1 is a mucin-like, androgen-regulated transmembrane protein that is present in most tissues, with high levels in the heart, kidney and placenta. It has been shown to be induced and expressed in prostate after castration and may have a role in cell proliferation and immortalization in prostate cancer.


Pssm-ID: 465341 [Multi-domain]  Cd Length: 296  Bit Score: 58.33  E-value: 1.41e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1854 TPASPKY--SPTSPKYSPTSPKySPTSPTYSPTTPKYSPTSPT----------YSPTSPV-------YTPTSPKYSPTS- 1913
Cdd:pfam17061   22 TPPTATWtsSPQNTAAVTASPT-SGTHNNSVLPVTASAPTSPLpknvsvepreEESTSPAsnwegtsTDPSPPGLSPTSs 100

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 133327     1914 -----PT---YSPTSPKYS-PT----SPTYSP--TSPKGSTYSPTSPgysPTSPTySLTSPAISPDDSDEEN 1970
Cdd:pfam17061  101 gvhltPTpeeHSSGTPETSvPAtgsqSPAESPtlTSPQAPASSPSSP---STSPP-EVSSASVTTNHSSTET 168
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 1855-1952 2.58e-07

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 55.85  E-value: 2.58e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1855 PASPKySPTSPKySPTSPKySPTSPTySPTTPKySPTSPTYSPTspvytPTSPKySPTSPTySPTSPKySPTSPTySPTS 1934
Cdd:PTZ00449  582 PKDPK-HPKDPE-EPKKPK-RPRSAQ-RPTRPK-SPKLPELLDI-----PKSPK-RPESPK-SPKRPP-PPQRPS-SPER 647

                          90
                  ....*....|....*...
gi 133327    1935 PKGsTYSPTSPGySPTSP 1952
Cdd:PTZ00449  648 PEG-PKIIKSPK-PPKSP 663
rpoC2 PRK02597
DNA-directed RNA polymerase subunit beta'; Provisional
 1431-1469 3.60e-07

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 235052 [Multi-domain]  Cd Length: 1331  Bit Score: 55.77  E-value: 3.60e-07
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 133327    1431 SFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTG 1469
Cdd:PRK02597 1184 SFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1222
rpoC2 CHL00117
RNA polymerase beta'' subunit; Reviewed
 1084-1112 8.89e-07

RNA polymerase beta'' subunit; Reviewed


Pssm-ID: 214368 [Multi-domain]  Cd Length: 1364  Bit Score: 54.56  E-value: 8.89e-07
                          10        20
                  ....*....|....*....|....*....
gi 133327    1084 GEMVGALAAQSLGEPATQMTLNTFHYAGV 1112
Cdd:CHL00117  315 GEAVGIIAGQSIGEPGTQLTLRTFHTGGV 343
PHA03291 PHA03291
envelope glycoprotein I; Provisional
 1853-1961 9.25e-07

envelope glycoprotein I; Provisional


Pssm-ID: 223033 [Multi-domain]  Cd Length: 401  Bit Score: 53.42  E-value: 9.25e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1853 YTPASPKYSPTSPKYSPTSpKYSPTSPTYSPTTPKYSPTSPTysPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSP 1932
Cdd:PHA03291  183 DGSCDPALPLSAPRLGPAD-VFVPATPRPTPRTTASPETTPT--PSTTTSPPSTTIPAPSTTIAAPQAGTTPEAEGTPAP 259

                          90       100
                  ....*....|....*....|....*....
gi 133327    1933 TSPKGSTYSPTSPGYSPTSPTYSLTSPAI 1961
Cdd:PHA03291  260 PTPGGGEAPPANATPAPEASRYELTVTQI 288
rpoC2 CHL00117
RNA polymerase beta'' subunit; Reviewed
 761-865 1.80e-06

RNA polymerase beta'' subunit; Reviewed


Pssm-ID: 214368 [Multi-domain]  Cd Length: 1364  Bit Score: 53.40  E-value: 1.80e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     761 SEY------NNFKS---------MVVSGAKGskiNISQVIAVVG--------QqnveGKRIpfgfkhrTLPhfIKddygp 817
Cdd:CHL00117  108 SEYlkqemnPNFRMtdplnpvymMSFSGARG---NASQVHQLVGmrglmsdpQ----GQII-------DLP--IQ----- 166

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 133327     818 esRGFVEnsylaGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLI 865
Cdd:CHL00117  167 --SNFRE-----GLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLV 207
Chi1 COG3469
Chitinase [Carbohydrate transport and metabolism];
1853-1967 2.30e-06

Chitinase [Carbohydrate transport and metabolism];


Pssm-ID: 442692 [Multi-domain]  Cd Length: 534  Bit Score: 52.45  E-value: 2.30e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1853 YTPASPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSP---TSPKYSPTSPT 1929
Cdd:COG3469   89 ATSTSATLVATSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTTVSgteTATGGTTTTST 168

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 133327   1930 YSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSD 1967
Cdd:COG3469  169 TTTTTSASTTPSATTTATATTASGATTPSATTTATTTG 206
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 1871-1963 8.15e-06

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 51.07  E-value: 8.15e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1871 SPKYSPTSPTYSpTTPKYSPTSPTYSP------------------------TSPVYTPTSPKYSPTSPTYSP-------- 1918
Cdd:pfam05109  424 APESTTTSPTLN-TTGFAAPNTTTGLPssthvptnltapastgptvstadvTSPTPAGTTSGASPVTPSPSPrdngtesk 502

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 133327     1919 ----TSPKYSPTSPTYSPTSPKGSTYSP----TSPGYSPTSPTYSLTSP---AISP 1963
Cdd:pfam05109  503 apdmTSPTSAVTTPTPNATSPTPAVTTPtpnaTSPTLGKTSPTSAVTTPtpnATSP 558
PHA03291 PHA03291
envelope glycoprotein I; Provisional
 1858-1962 1.02e-05

envelope glycoprotein I; Provisional


Pssm-ID: 223033 [Multi-domain]  Cd Length: 401  Bit Score: 49.95  E-value: 1.02e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1858 PKYSPTSPKYSPTSPKYSPTSpTYSPTTPKYSPTSPTYSPTSPvyTPTSPKySPTSPTYSPTSPKYSPTSPTYSPTSPkg 1937
Cdd:PHA03291  181 SADGSCDPALPLSAPRLGPAD-VFVPATPRPTPRTTASPETTP--TPSTTT-SPPSTTIPAPSTTIAAPQAGTTPEAE-- 254

                          90       100
                  ....*....|....*....|....*
gi 133327    1938 STYSPTSPGYSPTSPTYSLTSPAIS 1962
Cdd:PHA03291  255 GTPAPPTPGGGEAPPANATPAPEAS 279
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
 1875-1969 1.15e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 50.19  E-value: 1.15e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1875 SPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPT--YSPTSPKGSTYSPTSPGYSPTSP 1952
Cdd:PRK14950  370 KPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPHTpeSAPKLTRAAIPVDEKPKYTPPAP 449

                          90
                  ....*....|....*..
gi 133327    1953 TYSLTSPAISPDDSDEE 1969
Cdd:PRK14950  450 PKEEEKALIADGDVLEQ 466
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 1854-1960 1.52e-05

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 45.98  E-value: 1.52e-05
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      1854 TPASPKYSPTSPKYSPTSPKYSPTSPTysPTTPKYSPTSPTYSpTSPVYTPTS---PKYSPTSPTYSPTSPKY--SPTSP 1928
Cdd:smart01104    4 TPAWGASGSKTPAWGSRTPGTAAGGAP--TARGGSGSRTPAWG-GAGSRTPAWggaGPTGSRTPAWGGASAWGnkSSEGS 80

                            90       100       110
                    ....*....|....*....|....*....|..
gi 133327      1929 TYSPTSPKGSTYSPTSPGYSPTSPTYSLTSPA 1960
Cdd:smart01104   81 ASSWAAGPGGAYGAPTPGYGGTPSAYGPATPG 112
rpoC2 CHL00117
RNA polymerase beta'' subunit; Reviewed
 1431-1470 1.88e-05

RNA polymerase beta'' subunit; Reviewed


Pssm-ID: 214368 [Multi-domain]  Cd Length: 1364  Bit Score: 49.94  E-value: 1.88e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 133327    1431 SFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGC 1470
Cdd:CHL00117 1278 SFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGF 1317
PTZ00436 PTZ00436
60S ribosomal protein L19-like protein; Provisional
 1854-1960 3.22e-05

60S ribosomal protein L19-like protein; Provisional


Pssm-ID: 185616 [Multi-domain]  Cd Length: 357  Bit Score: 48.41  E-value: 3.22e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1854 TPASPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPT 1933
Cdd:PTZ00436  232 AAAPPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAA 311

                          90       100       110
                  ....*....|....*....|....*....|.
gi 133327    1934 SPKGSTYSP----TSPGYSPTSPTYSLTSPA 1960
Cdd:PTZ00436  312 APAKAAAPPakaaAPPAKAATPPAKAAAPPA 342
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 1854-1953 5.26e-05

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 48.53  E-value: 5.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1854 TPASPKYSPTSPKYSPTSPKYSPTSPTYS--PTTPKYSPtsptySPTSPvYTPTSPKySPTSPTySPTSPKySPTSPTYS 1931
Cdd:PTZ00449  548 KPGETKEGEVGKKPGPAKEHKPSKIPTLSkkPEFPKDPK-----HPKDP-EEPKKPK-RPRSAQ-RPTRPK-SPKLPELL 618

                          90       100
                  ....*....|....*....|....
gi 133327    1932 --PTSPKGSTySPTSPgYSPTSPT 1953
Cdd:PTZ00449  619 diPKSPKRPE-SPKSP-KRPPPPQ 640
DUF1373 pfam07117
Protein of unknown function (DUF1373); This family consists of several hypothetical proteins ...
 1855-1968 5.62e-05

Protein of unknown function (DUF1373); This family consists of several hypothetical proteins which seem to be specific to Oryzias latipes (Japanese ricefish). Members of this family are typically around 200 residues in length. The function of this family is unknown.


Pssm-ID: 462093 [Multi-domain]  Cd Length: 212  Bit Score: 46.32  E-value: 5.62e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1855 PASPKYSPTSPKYSPTSPKY----SPTSP-TYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPT 1929
Cdd:pfam07117   33 PLPPGQEPEPPRPEEEEGQGggggTFPFPgSPEPEPGGGGSGPMPMSASAPEPEPAKAKPQRPAPAQGHGHGGGGDSDSS 112

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 133327     1930 YSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSDE 1968
Cdd:pfam07117  113 GSGSGHQGSGGAGAGAGAPGHQHEQEQESSSSDDDDEDE 151
Endomucin pfam07010
Endomucin; This family consists of several mammalian endomucin proteins. Endomucin is an early ...
 1868-1959 7.81e-05

Endomucin; This family consists of several mammalian endomucin proteins. Endomucin is an early endothelial-specific antigen that is also expressed on putative hematopoietic progenitor cells.


Pssm-ID: 429246 [Multi-domain]  Cd Length: 260  Bit Score: 46.40  E-value: 7.81e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1868 SPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTS--PKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSPTSP 1945
Cdd:pfam07010   29 ANITLSTTPSTTAETASTPKTTNLNTPTGGTSPVGTTSSelSKTSLVSTTISLTTTKKGVGTTTTDVSKNESSTTKPTVT 108

                           90
                   ....*....|....
gi 133327     1946 GYSPTSPTYSLTSP 1959
Cdd:pfam07010  109 STPLSNAVSTLQSS 122
Chi1 COG3469
Chitinase [Carbohydrate transport and metabolism];
1854-1957 8.08e-05

Chitinase [Carbohydrate transport and metabolism];


Pssm-ID: 442692 [Multi-domain]  Cd Length: 534  Bit Score: 47.44  E-value: 8.08e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327   1854 TPASPKYSPTSPKYSPTSPKYSPTSPTYSP---TTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTY 1930
Cdd:COG3469  114 TTSTGAGSVTSTTSSTAGSTTTSGASATSSagsTTTTTTVSGTETATGGTTTTSTTTTTTSASTTPSATTTATATTASGA 193

                         90       100
                 ....*....|....*....|....*..
gi 133327   1931 SPTSPKGSTysPTSPGYSPTSPTYSLT 1957
Cdd:COG3469  194 TTPSATTTA--TTTGPPTPGLPKHVLV 218
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
 1854-1938 8.71e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 47.50  E-value: 8.71e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1854 TPASPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPkySPTSPTYSPTSPKYSPTSPTYSPT 1933
Cdd:PRK14950  370 KPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPH--TPESAPKLTRAAIPVDEKPKYTPP 447


                  ....*
gi 133327    1934 SPKGS 1938
Cdd:PRK14950  448 APPKE 452
rad23 TIGR00601
UV excision repair protein Rad23; All proteins in this family for which functions are known ...
 1870-1942 1.46e-04

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273167 [Multi-domain]  Cd Length: 378  Bit Score: 46.43  E-value: 1.46e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 133327     1870 TSPKYSPTSPTYSPTTPKYSPTSptySPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSP 1942
Cdd:TIGR00601   75 SKPKTGTGKVAPPAATPTSAPTP---TPSPPASPASGMSAAPASAVEEKSPSEESATATAPESPSTSVPSSGS 144
PRK14898 PRK14898
DNA-directed RNA polymerase subunit A''; Provisional
 1060-1104 1.87e-04

DNA-directed RNA polymerase subunit A''; Provisional


Pssm-ID: 237854 [Multi-domain]  Cd Length: 858  Bit Score: 46.42  E-value: 1.87e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 133327    1060 LSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTL 1104
Cdd:PRK14898   33 VTEEMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSL 77
PTZ00436 PTZ00436
60S ribosomal protein L19-like protein; Provisional
 1856-1959 2.56e-04

60S ribosomal protein L19-like protein; Provisional


Pssm-ID: 185616 [Multi-domain]  Cd Length: 357  Bit Score: 45.71  E-value: 2.56e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1856 ASPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSP 1935
Cdd:PTZ00436  248 AAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAAAPAKAAAPPAKAAAPP 327

                          90       100
                  ....*....|....*....|....
gi 133327    1936 KGSTyspTSPGYSPTSPTYSLTSP 1959
Cdd:PTZ00436  328 AKAA---TPPAKAAAPPAKAAAAP 348
PHA03291 PHA03291
envelope glycoprotein I; Provisional
 1865-1952 2.58e-04

envelope glycoprotein I; Provisional


Pssm-ID: 223033 [Multi-domain]  Cd Length: 401  Bit Score: 45.72  E-value: 2.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1865 PKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSpVYTPTSPKYSPTSPTySP--TSPKYSPTSPTYSPTSPKGSTYSP 1942
Cdd:PHA03291  167 PAEGTLAAPPLGEGSADGSCDPALPLSAPRLGPAD-VFVPATPRPTPRTTA-SPetTPTPSTTTSPPSTTIPAPSTTIAA 244

                          90
                  ....*....|
gi 133327    1943 TSPGYSPTSP 1952
Cdd:PHA03291  245 PQAGTTPEAE 254
PLN02217 PLN02217
probable pectinesterase/pectinesterase inhibitor
 1869-1966 3.33e-04

probable pectinesterase/pectinesterase inhibitor


Pssm-ID: 215130 [Multi-domain]  Cd Length: 670  Bit Score: 45.85  E-value: 3.33e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1869 PTSPKYSPTSPTYSPTTPKYS--PTSPTYSPTSPVyTPTSPKYSPtsPTYSPTSPKYSPT---SPTYSPtsPKGSTYSPT 1943
Cdd:PLN02217  556 PYIPGLFAGNPGSTNSTPTGSaaSSNTTFSSDSPS-TVVAPSTSP--PAGHLGSPPATPSkivSPSTSP--PASHLGSPS 630

                          90       100
                  ....*....|....*....|...
gi 133327    1944 SPGYSPTSPTYSLTSPAISPDDS 1966
Cdd:PLN02217  631 TTPSSPESSIKVASTETASPESS 653
PTZ00436 PTZ00436
60S ribosomal protein L19-like protein; Provisional
 1856-1960 3.81e-04

60S ribosomal protein L19-like protein; Provisional


Pssm-ID: 185616 [Multi-domain]  Cd Length: 357  Bit Score: 44.94  E-value: 3.81e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1856 ASPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSP 1935
Cdd:PTZ00436  220 AAPAKAAAAPAKAAAPPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAP 299

                          90       100
                  ....*....|....*....|....*....
gi 133327    1936 KGSTYSP----TSPGYSPTSPTYSLTSPA 1960
Cdd:PTZ00436  300 AKAAAAPakaaAAPAKAAAPPAKAAAPPA 328
PTZ00436 PTZ00436
60S ribosomal protein L19-like protein; Provisional
 1856-1937 3.81e-04

60S ribosomal protein L19-like protein; Provisional


Pssm-ID: 185616 [Multi-domain]  Cd Length: 357  Bit Score: 44.94  E-value: 3.81e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1856 ASPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSP 1935
Cdd:PTZ00436  269 APPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAATPPAKAAAPPAKAAAAP 348


                  ..
gi 133327    1936 KG 1937
Cdd:PTZ00436  349 VG 350
PTZ00436 PTZ00436
60S ribosomal protein L19-like protein; Provisional
 1855-1960 4.09e-04

60S ribosomal protein L19-like protein; Provisional


Pssm-ID: 185616 [Multi-domain]  Cd Length: 357  Bit Score: 44.94  E-value: 4.09e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1855 PASPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTS 1934
Cdd:PTZ00436  226 AAAPAKAAAPPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAA 305

                          90       100       110
                  ....*....|....*....|....*....|
gi 133327    1935 PKGSTYSP----TSPGYSPTSPTYSLTSPA 1960
Cdd:PTZ00436  306 PAKAAAAPakaaAPPAKAAAPPAKAATPPA 335
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 1515-1621 5.32e-04

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 41.74  E-value: 5.32e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      1515 PAMTP-WNQGA--TPAYGAWSPSVGSGMTPGAAGFSPSAASdASGFSPGYSPAWSPTpgspgspgpsspyipSPGGAMSP 1591
Cdd:smart01104    1 GGRTPaWGASGskTPAWGSRTPGTAAGGAPTARGGSGSRTP-AWGGAGSRTPAWGGA---------------GPTGSRTP 64

                            90       100       110
                    ....*....|....*....|....*....|
gi 133327      1592 SYSPTSPAYEPRSPGGYTPQSPSYSPTSPS 1621
Cdd:smart01104   65 AWGGASAWGNKSSEGSASSWAAGPGGAYGA 94
GATA-N pfam05349
GATA-type transcription activator, N-terminal; GATA transcription factors mediate cell ...
 1861-1969 5.40e-04

GATA-type transcription activator, N-terminal; GATA transcription factors mediate cell differentiation in a diverse range of tissues. Mutation are often associated with certain congenital human disorders. The six classical vertebrate GATA proteins, GATA-1 to GATA-6, are highly homologous and have two tandem zinc fingers. The classical GATA transcription factors function transcription activators. In lower metazoans GATA proteins carry a single canonical zinc finger. This family represents the N-terminal domain of the family of GATA transcription activators.


Pssm-ID: 461628 [Multi-domain]  Cd Length: 174  Bit Score: 42.81  E-value: 5.40e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1861 SPTSPKYSPTSPKY---SPTSPTYSPTT--PKYSPTSPtYSPTSPVYTPTSPKYS-PTSPTYSPTSPKYSPTSPTYSPts 1934
Cdd:pfam05349   10 NHGQAAYDHDSGGFlhsAASSPVYVPTTrvPSMLPTLP-YLQGCGSSQQSHPVSShSGWAQAGAESSSYNPGSPHPSP-- 86

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 133327     1935 pkGSTYSPTSPGYSPTSPTYSLTSPAISPDDSDEE 1969
Cdd:pfam05349   87 --RFSYSHSPPGSNGTSRDAAYQSPLLISAGGREQ 119
PHA03269 PHA03269
envelope glycoprotein C; Provisional
 1858-1959 5.85e-04

envelope glycoprotein C; Provisional


Pssm-ID: 165527 [Multi-domain]  Cd Length: 566  Bit Score: 44.72  E-value: 5.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1858 PKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPT---SPKYSP-TSPTYSPT 1933
Cdd:PHA03269   42 PAPAPHQAASRAPDPAVAPTSAASRKPDLAQAPTPAASEKFDPAPAPHQAASRAPDPAVAPQlaaAPKPDAaEAFTSAAQ 121

                          90       100
                  ....*....|....*....|....*..
gi 133327    1934 SPKGSTYSPTSP-GYSPTSPTYSLTSP 1959
Cdd:PHA03269  122 AHEAPADAGTSAaSKKPDPAAHTQHSP 148
KAR9 pfam08580
Yeast cortical protein KAR9; The KAR9 protein in Saccharomyces cerevisiae is a cytoskeletal ...
 1854-1970 9.07e-04

Yeast cortical protein KAR9; The KAR9 protein in Saccharomyces cerevisiae is a cytoskeletal protein required for karyogamy, correct positioning of the mitotic spindle and for orientation of cytoplasmic microtubules. KAR9 localizes at the shmoo tip in mating cells and at the tip of the growing bud in anaphase.


Pssm-ID: 430088 [Multi-domain]  Cd Length: 684  Bit Score: 44.44  E-value: 9.07e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1854 TPASPKYSPTSPKYSPTSP---------------KYSPTSPTY-SPTTPKYSPTSPTYSPTSPVYTPTSPKYSPT----- 1912
Cdd:pfam08580  518 TPALRPPSRPQPPPPGNRPrwnastntndldvghNFKPLTLTTpSPTPSRSSRSSSTLPPVSPLSRDKSRSPAPTcrsvs 597

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 133327     1913 SPTYSPTSPK----YSPTSPTY--SPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSDEEN 1970
Cdd:pfam08580  598 RASRRRASRKptriGSPNSRTSllDEPPYPKLTLSKGLPRTPRNRQSYAGTSPSRSVSVSSGLG 661
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
 1855-1960 1.11e-03

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 43.76  E-value: 1.11e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1855 PASP--KYSPTSPkysPTSPKYSPTSPTYSPTTpkySPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPK------YSPT 1926
Cdd:PLN03209  437 PLSPyaRYEDLKP---PTSPSPTAPTGVSPSVS---STSSVPAVPDTAPATAATDAAAPPPANMRPLSPYavyddlKPPT 510

                          90       100       110
                  ....*....|....*....|....*....|....
gi 133327    1927 SPTysPTSPKGSTYSPTSPGYSPTSPTYSLTSPA 1960
Cdd:PLN03209  511 SPS--PAAPVGKVAPSSTNEVVKVGNSAPPTALA 542
rad23 TIGR00601
UV excision repair protein Rad23; All proteins in this family for which functions are known ...
 1862-1943 1.12e-03

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273167 [Multi-domain]  Cd Length: 378  Bit Score: 43.73  E-value: 1.12e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1862 PTSPKYSPTSPKYSPTS-PTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTY 1940
Cdd:TIGR00601   77 PKTGTGKVAPPAATPTSaPTPTPSPPASPASGMSAAPASAVEEKSPSEESATATAPESPSTSVPSSGSDAASTLVVGSER 156


                   ...
gi 133327     1941 SPT 1943
Cdd:TIGR00601  157 ETT 159
Pneumo_att_G pfam05539
Pneumovirinae attachment membrane glycoprotein G;
1863-1970 1.27e-03

Pneumovirinae attachment membrane glycoprotein G;


Pssm-ID: 114270 [Multi-domain]  Cd Length: 408  Bit Score: 43.50  E-value: 1.27e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1863 TSPKYSPtsPKYSPTSPTYSPT-TPKYSPTSPTYSPTSpvyTPTSPKYSP---TSPTYSPTSPKYSPTSPtySPTSPKGS 1938
Cdd:pfam05539  225 TTSSNPE--PQTEPPPSQRGPSgSPQHPPSTTSQDQST---TGDGQEHTQrrkTPPATSNRRSPHSTATP--PPTTKRQE 297

                           90       100       110
                   ....*....|....*....|....*....|..
gi 133327     1939 TYSPTspgYSPTSPTYSLTSPAISPDDSDEEN 1970
Cdd:pfam05539  298 TGRPT---PRPTATTQSGSSPPHSSPPGVQAN 326
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 1854-1945 1.45e-03

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 40.58  E-value: 1.45e-03
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327      1854 TPASPKYSPTSPKYS-PTSPKYSP-TSPTYSPT---TP------KYSPTSPTYSPTSPVY-----TPTSPKYSPTSPTYS 1917
Cdd:smart01104   14 TPAWGSRTPGTAAGGaPTARGGSGsRTPAWGGAgsrTPawggagPTGSRTPAWGGASAWGnksseGSASSWAAGPGGAYG 93

                            90       100
                    ....*....|....*....|....*...
gi 133327      1918 PTSPKYSPTSPTYSPTSPKGSTYSPTSP 1945
Cdd:smart01104   94 APTPGYGGTPSAYGPATPGGGAMAGSAS 121
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 1855-1959 2.23e-03

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 43.14  E-value: 2.23e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1855 PASPKY--SPTSPKySPTSPKySPTSP-----TYSPTTPKySPTSPTySPTSP-----VYTPTSPKYSPTSPT------- 1915
Cdd:PTZ00449  621 PKSPKRpeSPKSPK-RPPPPQ-RPSSPerpegPKIIKSPK-PPKSPK-PPFDPkfkekFYDDYLDAAAKSKETkttvvld 696

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 133327    1916 ------------YSPTSPKYSPTS-PTYSPTSPKGSTYSPTSPGYSPTSPTYSLTSP 1959
Cdd:PTZ00449  697 esfesilketlpETPGTPFTTPRPlPPKLPRDEEFPFEPIGDPDAEQPDDIEFFTPP 753
CytochromB561_N pfam09786
Cytochrome B561, N terminal; Members of this family are found in the N terminal region of ...
 1855-1941 2.75e-03

Cytochrome B561, N terminal; Members of this family are found in the N terminal region of cytochrome B561, as well as in various other putative uncharacterized proteins.


Pssm-ID: 462899  Cd Length: 579  Bit Score: 42.51  E-value: 2.75e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1855 PASPKYSPTSPKYSPTSPKYSP--TSPTYSPTTPKYSPTSP-TYSPTSPVYTPTSPkySPTSPTYSpTSPKYSP--TSPT 1929
Cdd:pfam09786  145 PLHQSVSPSSSESRKGGDKSPAgsGKKLRSFSTSSKSPASPsVYLRGSPVPLNSSP--LPSDRNYE-NSVQSSPeiDSAV 221

                           90
                   ....*....|..
gi 133327     1930 YSPTSPKGSTYS 1941
Cdd:pfam09786  222 STPWSRKRATIG 233
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 1852-1922 2.92e-03

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 42.75  E-value: 2.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1852 EYTPASPKYSPTSPKYSPTSPKYSPTSP-TYSPTTPKYSP--------------TSPTYSPTSPVYTPTSP-KYSPTSPT 1915
Cdd:PTZ00449  729 EEFPFEPIGDPDAEQPDDIEFFTPPEEErTFFHETPADTPlpdilaeefkeediHAETGEPDEAMKRPDSPsEHEDKPPG 808


                  ....*..
gi 133327    1916 YSPTSPK 1922
Cdd:PTZ00449  809 DHPSLPK 815
CTF_NFI pfam00859
CTF/NF-I family transcription modulation region;
1855-1965 3.03e-03

CTF/NF-I family transcription modulation region;


Pssm-ID: 459967 [Multi-domain]  Cd Length: 288  Bit Score: 41.82  E-value: 3.03e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1855 PASPKYSPTSPKYSPTSPKYSPTSPTYSPTTPK-----------YSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPtSPKY 1923
Cdd:pfam00859  153 PSSALHFPSSSILQQPSSYFPHPAIRYPPHLPQdplkdlvslacYDPSSQQPSQPNGSGQGKVPGHFISTQMLAP-PPHP 231

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 133327     1924 SPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSL--TSPA-----ISPDD 1965
Cdd:pfam00859  232 PVARPVPLPMDTKPITTSTEGGASSPTSPTYSApgTPPAnrfvgLGPRD 280
2A1904 TIGR00927
K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying ...
 1852-1967 3.37e-03

K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying compounds]


Pssm-ID: 273344 [Multi-domain]  Cd Length: 1096  Bit Score: 42.68  E-value: 3.37e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1852 EYTPASPKyspTSPKYSPTSPK--YSPTSPTY------SPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKY 1923
Cdd:TIGR00927  109 ENTPSPPR---RTAKITPTTPKnnYSPTAAGTervkedTPATPSRALNHYISTSGRQRVKSYTPKPRGEVKSSSPTQTRE 185

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 133327     1924 SPTSPTYSPTSPKGSTYSPTSPGYSPTSPTyslTSPAISPDDSD 1967
Cdd:TIGR00927  186 KVRKYTPSPLGRMVNSYAPSTFMTMPRSHG---ITPRTTVKDSE 226
Pneumo_att_G pfam05539
Pneumovirinae attachment membrane glycoprotein G;
1855-1951 3.51e-03

Pneumovirinae attachment membrane glycoprotein G;


Pssm-ID: 114270 [Multi-domain]  Cd Length: 408  Bit Score: 41.96  E-value: 3.51e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1855 PASPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYS-PTSPVYTPTSPKYSPTSPTYSPTspkYSPTSPTYSPT 1933
Cdd:pfam05539  237 PPSQRGPSGSPQHPPSTTSQDQSTTGDGQEHTQRRKTPPATSnRRSPHSTATPPPTTKRQETGRPT---PRPTATTQSGS 313

                           90
                   ....*....|....*...
gi 133327     1934 SPKGStySPTSPGYSPTS 1951
Cdd:pfam05539  314 SPPHS--SPPGVQANPTT 329
PHA02682 PHA02682
ORF080 virion core protein; Provisional
 1854-1968 4.67e-03

ORF080 virion core protein; Provisional


Pssm-ID: 177464 [Multi-domain]  Cd Length: 280  Bit Score: 41.00  E-value: 4.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1854 TPASPKYSPTSPKYSPTSPkySPTSPTYSPTTPKYSPTSPtySPTSPVYTPTSPKySPTSPTYSPtspkysptSPTYSPT 1933
Cdd:PHA02682   99 APAAPAPAVTCPAPAPACP--PATAPTCPPPAVCPAPARP--APACPPSTRQCPP-APPLPTPKP--------APAAKPI 165

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 133327    1934 SPKGSTYSPTSPGYS-PTSPTYSLTSPAISPDDSDE 1968
Cdd:PHA02682  166 FLHNQLPPPDYPAAScPTIETAPAASPVLEPRIPDK 201
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
 1855-1968 4.97e-03

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 41.84  E-value: 4.97e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1855 PASPKYSPtSPKYSPTSP----------KYSPTSP--TYSPTTPkysPTSPTYSPTSPVYTPTSpkySPTSPTYSPTSPK 1922
Cdd:PLN03209  407 PAEPDVVP-SPGSASNVPevepaqveakKTRPLSPyaRYEDLKP---PTSPSPTAPTGVSPSVS---STSSVPAVPDTAP 479

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 133327    1923 YSPTSPTYSPTSPKGSTYSP---TSPGYSPTSPTYSLTSPAISPDDSDE 1968
Cdd:PLN03209  480 ATAATDAAAPPPANMRPLSPyavYDDLKPPTSPSPAAPVGKVAPSSTNE 528
Hamartin pfam04388
Hamartin protein; This family includes the hamartin protein which is thought to function as a ...
 1876-1955 5.45e-03

Hamartin protein; This family includes the hamartin protein which is thought to function as a tumour suppressor. The hamartin protein interacts with the tuberin protein pfam03542. Tuberous sclerosis complex (TSC) is an autosomal dominant disorder and is characterized by the presence of hamartomas in many organs, such as brain, skin, heart, lung, and kidney. It is caused by mutation either TSC1 or TSC2 tumour suppressor gene. TSC1 encodes a protein, hamartin, containing two coiled-coil regions, which have been shown to mediate binding to tuberin. The TSC2 gene codes for tuberin pfam03542. These two proteins function within the same pathway(s) regulating cell cycle, cell growth, adhesion, and vesicular trafficking.


Pssm-ID: 461287 [Multi-domain]  Cd Length: 730  Bit Score: 41.58  E-value: 5.45e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1876 PTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTsPTYSPTSPKGSTYSPTSPGYSPTSPTYS 1955
Cdd:pfam04388  276 PTASPYTDQQSSYGSSTSTPSSTPRLQLSSSSGTSPPYLSPPSIRLKTDSF-PLWSPSSVCGMTTPPTSPGMVPTTPSEL 354
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1862-1966 7.50e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 41.46  E-value: 7.50e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1862 PTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVyTPTSPKySPTSPTYSPTSPKySPTSPTYSPTSPKGSTYS 1941
Cdd:PHA03247 2554 PLPPAAPPAAPDRSVPPPRPAPRPSEPAVTSRARRPDAPP-QSARPR-APVDDRGDPRGPA-PPSPLPPDTHAPDPPPPS 2630

                          90       100
                  ....*....|....*....|....*
gi 133327    1942 PTSPGYSPTSPTYSLTSPAISPDDS 1966
Cdd:PHA03247 2631 PSPAANEPDPHPPPTVPPPERPRDD 2655
DUF4045 pfam13254
Domain of unknown function (DUF4045); This presumed domain is functionally uncharacterized. ...
 1855-1966 7.59e-03

Domain of unknown function (DUF4045); This presumed domain is functionally uncharacterized. This domain family is found in bacteria and eukaryotes, and is typically between 384 and 430 amino acids in length.


Pssm-ID: 433066 [Multi-domain]  Cd Length: 415  Bit Score: 40.92  E-value: 7.59e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327     1855 PASPKYSPT-------SPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSP-TSPVYTPTSPKYSPTSPTYSPTS---PKY 1923
Cdd:pfam13254  197 PNSFKEVTPvglmrspAPGGHSKSPSVSGISADSSPTKEEPSEEADTLSTdKEQSPAPTSASEPPPKTKELPKDseePAA 276

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 133327     1924 SPTSPTYSPTSPKGSTYSptSPGYSPTSPTYSLTSPAISPDDS 1966
Cdd:pfam13254  277 PSKSAEASTEKKEPDTES--SPETSSEKSAPSLLSPVSKASID 317
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 1854-1952 9.06e-03

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 41.21  E-value: 9.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 133327    1854 TPASPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKyspTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTyspt 1933
Cdd:PTZ00449  728 DEEFPFEPIGDPDAEQPDDIEFFTPPEEERTFFH---ETPADTPLPDILAEEFKEEDIHAETGEPDEAMKRPDSPS---- 800

                          90
                  ....*....|....*....
gi 133327    1934 spkgsTYSPTSPGYSPTSP 1952
Cdd:PTZ00449  801 -----EHEDKPPGDHPSLP 814
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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