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Conserved domains on  [gi|1314927194|gb|AUG31809|]
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DNA-directed RNA polymerase II second largest subunit, partial [Zasmidium xenoparkii]

Protein Classification

DNA-directed RNA polymerase subunit B family protein( domain architecture ID 1000145)

DNA-directed RNA polymerase subunit B family protein similar to fungal DNA-directed RNA polymerase II subunit RPB2

CATH:  3.90.1110.10|3.90.1070.20
EC:  2.7.7.6
Gene Ontology:  GO:0003899|GO:0000428|GO:0008270|GO:0003677|GO:0006351
PubMed:  11839495
SCOP:  4003708

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
Ricin_B_lectin super family cl47023
Ricin-type beta-trefoil lectin domain;
1-352 1.78e-94

Ricin-type beta-trefoil lectin domain;


The actual alignment was detected with superfamily member PRK08565:

Pssm-ID: 481363 [Multi-domain]  Cd Length: 1103  Bit Score: 303.80  E-value: 1.78e-94
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194    1 KQYLHRCVETGREFNITLAVKTNIITAGLRYCLATGNWGdqkkaaSAKAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKI 80
Cdd:PRK08565   358 KYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPH 431

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194   81 AKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTVGTPATPLIDFMRSRGLDLLEEYDPVMDPKATKIFLNGTWVG 160
Cdd:PRK08565   432 FEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIG 511

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194  161 VHKNAGQLTDMLRGLRRKGVLSFEVTI--IRDVREREIRIFTDAGRVCRPLFVVdnnptsqDNGSLVLKQEHITKLhqdq 238
Cdd:PRK08565   512 YHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVV-------ENGKPKLTREHVEKL---- 580

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194  239 dilsqlegvseqdREASIfGWKGLVDAGVVEYLDAEEEETAMIIMTPEDL-EEHrnmrqgfnlgdgnpdphmrikprpnq 317
Cdd:PRK08565   581 -------------KKGEL-TFDDLVKMGVIEYLDAEEEENAYVALDPEDLtPEH-------------------------- 620

                          330       340       350
                   ....*....|....*....|....*....|....*
gi 1314927194  318 fvrtwTHCEIHPAMILGICASIIPFPDHNQSPRNT 352
Cdd:PRK08565   621 -----THLEIWPPAILGITASIIPYPEHNQSPRNT 650
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-352 1.78e-94

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 303.80  E-value: 1.78e-94
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194    1 KQYLHRCVETGREFNITLAVKTNIITAGLRYCLATGNWGdqkkaaSAKAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKI 80
Cdd:PRK08565   358 KYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPH 431

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194   81 AKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTVGTPATPLIDFMRSRGLDLLEEYDPVMDPKATKIFLNGTWVG 160
Cdd:PRK08565   432 FEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIG 511

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194  161 VHKNAGQLTDMLRGLRRKGVLSFEVTI--IRDVREREIRIFTDAGRVCRPLFVVdnnptsqDNGSLVLKQEHITKLhqdq 238
Cdd:PRK08565   512 YHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVV-------ENGKPKLTREHVEKL---- 580

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194  239 dilsqlegvseqdREASIfGWKGLVDAGVVEYLDAEEEETAMIIMTPEDL-EEHrnmrqgfnlgdgnpdphmrikprpnq 317
Cdd:PRK08565   581 -------------KKGEL-TFDDLVKMGVIEYLDAEEEENAYVALDPEDLtPEH-------------------------- 620

                          330       340       350
                   ....*....|....*....|....*....|....*
gi 1314927194  318 fvrtwTHCEIHPAMILGICASIIPFPDHNQSPRNT 352
Cdd:PRK08565   621 -----THLEIWPPAILGITASIIPYPEHNQSPRNT 650
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-352 7.88e-53

RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.


Pssm-ID: 238353 [Multi-domain]  Cd Length: 866  Bit Score: 187.01  E-value: 7.88e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194   1 KQYLHRCVETGREFNITLAVKTNIITAGLRYCLATGNWGDQKKAASaKAGVSQVLNRYTYASTLSHLRRTNT-PIGRDGK 79
Cdd:cd00653   264 KEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKRRISSlGLFRERK 342

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194  80 IAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTvgtpatplidfmrsrgldlleeydpvmdpkatkiflngtwv 159
Cdd:cd00653   343 GFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS----------------------------------------- 381

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194 160 gvhknagqltdmlrglrrkgvlsfevtiirdvrereiriftdaGRVCRPLFVVDNNptsqdngslvlkqehitklhqdqd 239
Cdd:cd00653   382 -------------------------------------------GRIERPYRIVEKE------------------------ 394

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194 240 ilsqlegvseqdreasifgwkglvdagvveyldaeeeetamiimtpedleehrnmrqgfnlgdgnpdphmrikprpnqfv 319
Cdd:cd00653       --------------------------------------------------------------------------------

                         330       340       350
                  ....*....|....*....|....*....|...
gi 1314927194 320 rtWTHCEIHPAMILGICASIIPFPDHNQSPRNT 352
Cdd:cd00653   395 --VTHIEISPSQILSVAASLIPFPEHNQSPRNL 425
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 53-116 1.54e-31

RNA polymerase Rpb2, 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). Domain 3, s also known as the fork domain and is proximal to catalytic site.


Pssm-ID: 428011 [Multi-domain]  Cd Length: 67  Bit Score: 113.39  E-value: 1.54e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1314927194  53 QVLNRYTYASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCY 116
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 15-352 8.76e-25

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 105.58  E-value: 8.76e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194   15 NITLA--VKTNIITAGLRYCLATGnwgdqkkaasakaGVSQVLNRYTYASTLSHLRRTNT----PIGRDgkiaKP----R 84
Cdd:COG0085    346 AITPQslINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevR 408

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194   85 QLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTvgtpatplidfmrsrgldlleEYdpvmdpkatkiflngtwvgvhkn 164
Cdd:COG0085    409 DVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------------------EY----------------------- 444

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194  165 agqltdmlrglrrkgvlsfevtiirdvrereiriftdaGRVCRPLFVVDNnptsqdngslvlkqehitklhqdqdilsql 244
Cdd:COG0085    445 --------------------------------------GFIETPYRKVEN------------------------------ 456

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194  245 eG-VSEQdreasifgwkglvdagvVEYLDAEEEETAMIIMTPEDLEEHRN-------MRQGFNLGDGNPDPHmrikprpn 316
Cdd:COG0085    457 -GkVTDE-----------------IEYLTADEEENYYIAQANAPLDEDGNfleervlVRYRGEEVLVPPEEV-------- 510

                          330       340       350
                   ....*....|....*....|....*....|....*.
gi 1314927194  317 qfvrtwTHCEIHPAMILGICASIIPFPDHNQSPRNT 352
Cdd:COG0085    511 ------DYMDVSPKQIVSVATSLIPFLEHDDANRAL 540
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-352 1.78e-94

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 303.80  E-value: 1.78e-94
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194    1 KQYLHRCVETGREFNITLAVKTNIITAGLRYCLATGNWGdqkkaaSAKAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKI 80
Cdd:PRK08565   358 KYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPH 431

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194   81 AKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTVGTPATPLIDFMRSRGLDLLEEYDPVMDPKATKIFLNGTWVG 160
Cdd:PRK08565   432 FEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIG 511

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194  161 VHKNAGQLTDMLRGLRRKGVLSFEVTI--IRDVREREIRIFTDAGRVCRPLFVVdnnptsqDNGSLVLKQEHITKLhqdq 238
Cdd:PRK08565   512 YHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVV-------ENGKPKLTREHVEKL---- 580

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194  239 dilsqlegvseqdREASIfGWKGLVDAGVVEYLDAEEEETAMIIMTPEDL-EEHrnmrqgfnlgdgnpdphmrikprpnq 317
Cdd:PRK08565   581 -------------KKGEL-TFDDLVKMGVIEYLDAEEEENAYVALDPEDLtPEH-------------------------- 620

                          330       340       350
                   ....*....|....*....|....*....|....*
gi 1314927194  318 fvrtwTHCEIHPAMILGICASIIPFPDHNQSPRNT 352
Cdd:PRK08565   621 -----THLEIWPPAILGITASIIPYPEHNQSPRNT 650
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-352 7.88e-53

RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.


Pssm-ID: 238353 [Multi-domain]  Cd Length: 866  Bit Score: 187.01  E-value: 7.88e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194   1 KQYLHRCVETGREFNITLAVKTNIITAGLRYCLATGNWGDQKKAASaKAGVSQVLNRYTYASTLSHLRRTNT-PIGRDGK 79
Cdd:cd00653   264 KEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKRRISSlGLFRERK 342

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194  80 IAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTvgtpatplidfmrsrgldlleeydpvmdpkatkiflngtwv 159
Cdd:cd00653   343 GFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS----------------------------------------- 381

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194 160 gvhknagqltdmlrglrrkgvlsfevtiirdvrereiriftdaGRVCRPLFVVDNNptsqdngslvlkqehitklhqdqd 239
Cdd:cd00653   382 -------------------------------------------GRIERPYRIVEKE------------------------ 394

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194 240 ilsqlegvseqdreasifgwkglvdagvveyldaeeeetamiimtpedleehrnmrqgfnlgdgnpdphmrikprpnqfv 319
Cdd:cd00653       --------------------------------------------------------------------------------

                         330       340       350
                  ....*....|....*....|....*....|...
gi 1314927194 320 rtWTHCEIHPAMILGICASIIPFPDHNQSPRNT 352
Cdd:cd00653   395 --VTHIEISPSQILSVAASLIPFPEHNQSPRNL 425
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 148-352 8.32e-46

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 164.75  E-value: 8.32e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194 148 KATKIFLNGTWVGVHKNAGQLTDMLRGLRRKGVLSFEVTIIRDVREREIRIFTDAGRVCRPLFVVdnnptsqDNGSLVLK 227
Cdd:PRK07225    3 RKAKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVV-------ENGEPLLT 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194 228 QEHITKLHQDQdilsqlegvseqdreasiFGWKGLVDAGVVEYLDAEEEETAMIIMTPEDL-EEHrnmrqgfnlgdgnpd 306
Cdd:PRK07225   76 EEHIEKLKNGE------------------LTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLtEEH--------------- 122

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1314927194 307 phmrikprpnqfvrtwTHCEIHPAMILGICASIIPFPDHNQSPRNT 352
Cdd:PRK07225  123 ----------------THLEIDPSLILGIGAGMIPYPEHNASPRIT 152
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 11-140 1.78e-35

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 134.69  E-value: 1.78e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194  11 GREFNITLAVKTNIITAGLRYCLATGNWgdqkkaASAKAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTH 90
Cdd:PRK09606  371 NRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQ 444

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1314927194  91 WGLVCPAETPEGQACGLVKNLSLMCYVTVGTPATPLIDFMRSRGLDLLEE 140
Cdd:PRK09606  445 WGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVEPERG 494
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 53-116 1.54e-31

RNA polymerase Rpb2, 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). Domain 3, s also known as the fork domain and is proximal to catalytic site.


Pssm-ID: 428011 [Multi-domain]  Cd Length: 67  Bit Score: 113.39  E-value: 1.54e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1314927194  53 QVLNRYTYASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCY 116
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 152-213 1.71e-30

RNA polymerase Rpb2, 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). Domain 4, is also known as the external 2 domain.


Pssm-ID: 428012 [Multi-domain]  Cd Length: 62  Bit Score: 110.53  E-value: 1.71e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1314927194 152 IFLNGTWVGVHKNAGQLTDMLRGLRRKGVLSFEVTIIRDVREREIRIFTDAGRVCRPLFVVD 213
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 15-352 8.76e-25

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 105.58  E-value: 8.76e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194   15 NITLA--VKTNIITAGLRYCLATGnwgdqkkaasakaGVSQVLNRYTYASTLSHLRRTNT----PIGRDgkiaKP----R 84
Cdd:COG0085    346 AITPQslINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevR 408

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194   85 QLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVTvgtpatplidfmrsrgldlleEYdpvmdpkatkiflngtwvgvhkn 164
Cdd:COG0085    409 DVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------------------EY----------------------- 444

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194  165 agqltdmlrglrrkgvlsfevtiirdvrereiriftdaGRVCRPLFVVDNnptsqdngslvlkqehitklhqdqdilsql 244
Cdd:COG0085    445 --------------------------------------GFIETPYRKVEN------------------------------ 456

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927194  245 eG-VSEQdreasifgwkglvdagvVEYLDAEEEETAMIIMTPEDLEEHRN-------MRQGFNLGDGNPDPHmrikprpn 316
Cdd:COG0085    457 -GkVTDE-----------------IEYLTADEEENYYIAQANAPLDEDGNfleervlVRYRGEEVLVPPEEV-------- 510

                          330       340       350
                   ....*....|....*....|....*....|....*.
gi 1314927194  317 qfvrtwTHCEIHPAMILGICASIIPFPDHNQSPRNT 352
Cdd:COG0085    511 ------DYMDVSPKQIVSVATSLIPFLEHDDANRAL 540
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 259-329 1.16e-22

RNA polymerase Rpb2, 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). Domain 5, is also known as the external 2 domain.


Pssm-ID: 428013 [Multi-domain]  Cd Length: 53  Bit Score: 89.52  E-value: 1.16e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1314927194 259 WKGLVDAGVVEYLDAEEEETAMIIMTPEDLEEH-RNMRQGFNlgdgnpdphmrikprpnqfVRTWTHCEIHP 329
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESsREEREGPY-------------------AHTYTHCEIHP 53
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
51-112 7.32e-07

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 51.08  E-value: 7.32e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1314927194   51 VSQVLNRYTYASTLSHLRRTNTpIGRDGKIA-----KPRQLHNTHWGLVCPAETPEGQACGLVKNLS 112
Cdd:PRK09603   525 LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLINTLS 590
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
51-113 1.27e-06

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 50.39  E-value: 1.27e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1314927194   51 VSQVLNRYTYASTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSL 113
Cdd:PRK14844   532 LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAI 598
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 51-112 3.52e-05

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 45.85  E-value: 3.52e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1314927194   51 VSQVLNRYTYASTLSHLRRTNT--PIGRDG-KIAKP-RQLHNTHWGLVCPAETPEGQACGLVKNLS 112
Cdd:CHL00207   366 LSQYMDQTNPLSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 84-112 1.13e-04

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 44.32  E-value: 1.13e-04
                           10        20
                   ....*....|....*....|....*....
gi 1314927194   84 RQLHNTHWGLVCPAETPEGQACGLVKNLS 112
Cdd:PRK00405   469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 336-352 2.51e-04

RNA polymerase Rpb2, 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 represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 42.52  E-value: 2.51e-04
                          10
                  ....*....|....*..
gi 1314927194 336 CASIIPFPDHNQSPRNT 352
Cdd:pfam00562   1 VASLIPFVDHNQSPRNT 17
rpoB CHL00001
RNA polymerase beta subunit
 52-120 7.36e-04

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 41.43  E-value: 7.36e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1314927194   52 SQVLNRYTYASTLSHLRRTNT--PIGRDGKIA--KPRQLHNTHWGLVCPAETPEGQACGLVKnlSLMCYVTVG 120
Cdd:CHL00001   375 SQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIG--SLAIHARIG 445
 
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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