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Conserved domains on  [gi|374923047|gb|AFA26645|]
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RNA polymerase II second largest subunit, partial [Botrytis sinoviticola]

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

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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;
2-355 2.52e-90

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: 292.63  E-value: 2.52e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047    2 FRRLTTDVYRYLQRCVENNREFNLTLGVKSTTITNGLKYSLATGNWGDQKkaasstAGVSQVLNRYTFASTLSHLRRTNT 81
Cdd:PRK08565  350 FKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGR------TGVSQLLDRTNYLSTLSHLRRVVS 423

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047   82 PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYVTVGTPSDPIVEfmIQRNMEV--LEEYEPLRAPNAT 159
Cdd:PRK08565  424 PLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEE--ILYELGVvpVEEAREEEYISWS 501

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047  160 KVFVNGVWVGIHRDPAHLVKCVQDLRRSHLISHEVSL--IREIRDREFKIFTDAGRVCRPLLVIDNdpdsankGNLVLNK 237
Cdd:PRK08565  502 RVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKLTR 574

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047  238 DHIrrleddqllpanmdkdEKVRNGYYGFQGLINDGVVEYLDAEEEETVMITMTPEDldisrqlqagyqIRPDesgdlnk 317
Cdd:PRK08565  575 EHV----------------EKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPED------------LTPE------- 619

                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 374923047  318 rvkapinptaHvwTHCEIHPSMILGICASIIPFPDHNQ 355
Cdd:PRK08565  620 ----------H--THLEIWPPAILGITASIIPYPEHNQ 645
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 2-355 2.52e-90

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 292.63  E-value: 2.52e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047    2 FRRLTTDVYRYLQRCVENNREFNLTLGVKSTTITNGLKYSLATGNWGDQKkaasstAGVSQVLNRYTFASTLSHLRRTNT 81
Cdd:PRK08565  350 FKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGR------TGVSQLLDRTNYLSTLSHLRRVVS 423

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047   82 PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYVTVGTPSDPIVEfmIQRNMEV--LEEYEPLRAPNAT 159
Cdd:PRK08565  424 PLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEE--ILYELGVvpVEEAREEEYISWS 501

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047  160 KVFVNGVWVGIHRDPAHLVKCVQDLRRSHLISHEVSL--IREIRDREFKIFTDAGRVCRPLLVIDNdpdsankGNLVLNK 237
Cdd:PRK08565  502 RVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKLTR 574

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047  238 DHIrrleddqllpanmdkdEKVRNGYYGFQGLINDGVVEYLDAEEEETVMITMTPEDldisrqlqagyqIRPDesgdlnk 317
Cdd:PRK08565  575 EHV----------------EKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPED------------LTPE------- 619

                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 374923047  318 rvkapinptaHvwTHCEIHPSMILGICASIIPFPDHNQ 355
Cdd:PRK08565  620 ----------H--THLEIWPPAILGITASIIPYPEHNQ 645
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-355 7.86e-51

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: 181.23  E-value: 7.86e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047   1 LFRRLTTDVYRYLQRCVENNREFNLTLGVKSTTITNGLKYSLATGNWGDQKKAaSSTAGVSQVLNRYTFASTLSHLRRTN 80
Cdd:cd00653  255 GLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFL-MQRSGLSQVLDRLNPLSELSHKRRIS 333

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047  81 T-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYVTvgtpsdpivefmiqrnmevleeyeplrapnat 159
Cdd:cd00653  334 SlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-------------------------------- 381

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047 160 kvfvngvwvgihrdpahlvkcvqdlrrshlishevslireirdrefkiftdaGRVCRPLLVIDNDpdsankgnlvlnkdh 239
Cdd:cd00653  382 ----------------------------------------------------GRIERPYRIVEKE--------------- 394

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047 240 irrleddqllpanmdkdekvrngyygfqglindgvveyldaeeeetvmitmtpedldisrqlqagyqirpdesgdlnkrv 319
Cdd:cd00653      --------------------------------------------------------------------------------

                        330       340       350
                 ....*....|....*....|....*....|....*.
gi 374923047 320 kapinptahvWTHCEIHPSMILGICASIIPFPDHNQ 355
Cdd:cd00653  395 ----------VTHIEISPSQILSVAASLIPFPEHNQ 420
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 62-125 7.30e-32

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: 114.16  E-value: 7.30e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 374923047   62 QVLNRYTFASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCY 125
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 57-355 9.81e-21

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: 93.64  E-value: 9.81e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047   57 TAGVSQVLNRYTFASTLSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYVTv 128
Cdd:COG0085   368 SSQLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN- 442

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047  129 gtpsdpivefmiqrnmevleEYeplrapnatkvfvngvwvgihrdpahlvkcvqdlrrshlishevslireirdrefkif 208
Cdd:COG0085   443 --------------------EY---------------------------------------------------------- 444

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047  209 tdaGRVCRPLLVIDNdpdsankgnlvlnkdhirrleddqllpanmdkdekvrngyygfqGLINDGvVEYLDAEEEETVMI 288
Cdd:COG0085   445 ---GFIETPYRKVEN--------------------------------------------GKVTDE-IEYLTADEEENYYI 476

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 374923047  289 TMTPEDLDisrqlqagyqirpDESGDLNKRVKA------PINPTAHVwTHCEIHPSMILGICASIIPFPDHNQ 355
Cdd:COG0085   477 AQANAPLD-------------EDGNFLEERVLVryrgeeVLVPPEEV-DYMDVSPKQIVSVATSLIPFLEHDD 535
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 2-355 2.52e-90

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 292.63  E-value: 2.52e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047    2 FRRLTTDVYRYLQRCVENNREFNLTLGVKSTTITNGLKYSLATGNWGDQKkaasstAGVSQVLNRYTFASTLSHLRRTNT 81
Cdd:PRK08565  350 FKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWVGGR------TGVSQLLDRTNYLSTLSHLRRVVS 423

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047   82 PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYVTVGTPSDPIVEfmIQRNMEV--LEEYEPLRAPNAT 159
Cdd:PRK08565  424 PLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEE--ILYELGVvpVEEAREEEYISWS 501

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047  160 KVFVNGVWVGIHRDPAHLVKCVQDLRRSHLISHEVSL--IREIRDREFKIFTDAGRVCRPLLVIDNdpdsankGNLVLNK 237
Cdd:PRK08565  502 RVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKLTR 574

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047  238 DHIrrleddqllpanmdkdEKVRNGYYGFQGLINDGVVEYLDAEEEETVMITMTPEDldisrqlqagyqIRPDesgdlnk 317
Cdd:PRK08565  575 EHV----------------EKLKKGELTFDDLVKMGVIEYLDAEEEENAYVALDPED------------LTPE------- 619

                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 374923047  318 rvkapinptaHvwTHCEIHPSMILGICASIIPFPDHNQ 355
Cdd:PRK08565  620 ----------H--THLEIWPPAILGITASIIPYPEHNQ 645
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-355 7.86e-51

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: 181.23  E-value: 7.86e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047   1 LFRRLTTDVYRYLQRCVENNREFNLTLGVKSTTITNGLKYSLATGNWGDQKKAaSSTAGVSQVLNRYTFASTLSHLRRTN 80
Cdd:cd00653  255 GLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFL-MQRSGLSQVLDRLNPLSELSHKRRIS 333

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047  81 T-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYVTvgtpsdpivefmiqrnmevleeyeplrapnat 159
Cdd:cd00653  334 SlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-------------------------------- 381

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047 160 kvfvngvwvgihrdpahlvkcvqdlrrshlishevslireirdrefkiftdaGRVCRPLLVIDNDpdsankgnlvlnkdh 239
Cdd:cd00653  382 ----------------------------------------------------GRIERPYRIVEKE--------------- 394

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047 240 irrleddqllpanmdkdekvrngyygfqglindgvveyldaeeeetvmitmtpedldisrqlqagyqirpdesgdlnkrv 319
Cdd:cd00653      --------------------------------------------------------------------------------

                        330       340       350
                 ....*....|....*....|....*....|....*.
gi 374923047 320 kapinptahvWTHCEIHPSMILGICASIIPFPDHNQ 355
Cdd:cd00653  395 ----------VTHIEISPSQILSVAASLIPFPEHNQ 420
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 159-355 1.28e-38

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 145.10  E-value: 1.28e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047 159 TKVFVNGVWVGIHRDPAHLVKCVQDLRRSHLISHEVSLIREIRDREFKIFTDAGRVCRPLLVIDNdpdsankGNLVLNKD 238
Cdd:PRK07225   5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLTEE 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047 239 HIrrleddqllpanmdkdEKVRNGYYGFQGLINDGVVEYLDAEEEETVMITMTPEDLdisrqlqagyqiRPDesgdlnkr 318
Cdd:PRK07225  78 HI----------------EKLKNGELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDL------------TEE-------- 121

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 374923047 319 vkapinptaHvwTHCEIHPSMILGICASIIPFPDHNQ 355
Cdd:PRK07225 122 ---------H--THLEIDPSLILGIGAGMIPYPEHNA 147
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-151 4.25e-36

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 136.62  E-value: 4.25e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047   1 LFR----RLTTDVYRYLQRCVENNREFNLTLGVKSTTITNGLKYSLATGNWgdqkkaASSTAGVSQVLNRYTFASTLSHL 76
Cdd:PRK09606 348 LFRvafnRLARDVKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATLSHL 421

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 374923047  77 RRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYVTVGTPSDPIVEFMiqRNMEVLEEYE 151
Cdd:PRK09606 422 RRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEIL--KELGVEPERG 494
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 62-125 7.30e-32

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: 114.16  E-value: 7.30e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 374923047   62 QVLNRYTFASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCY 125
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 161-222 7.67e-29

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: 105.91  E-value: 7.67e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 374923047  161 VFVNGVWVGIHRDPAHLVKCVQDLRRSHLISHEVSLIREIRDREFKIFTDAGRVCRPLLVID 222
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 266-337 2.93e-23

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: 91.06  E-value: 2.93e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 374923047  266 FQGLINDGVVEYLDAEEEETVMITMTPEDLDISRQLQAGYqirpdesgdlnkrvkapinPTAHVWTHCEIHP 337
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREEREG-------------------PYAHTYTHCEIHP 53
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 57-355 9.81e-21

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: 93.64  E-value: 9.81e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047   57 TAGVSQVLNRYTFASTLSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYVTv 128
Cdd:COG0085   368 SSQLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN- 442

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047  129 gtpsdpivefmiqrnmevleEYeplrapnatkvfvngvwvgihrdpahlvkcvqdlrrshlishevslireirdrefkif 208
Cdd:COG0085   443 --------------------EY---------------------------------------------------------- 444

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047  209 tdaGRVCRPLLVIDNdpdsankgnlvlnkdhirrleddqllpanmdkdekvrngyygfqGLINDGvVEYLDAEEEETVMI 288
Cdd:COG0085   445 ---GFIETPYRKVEN--------------------------------------------GKVTDE-IEYLTADEEENYYI 476

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 374923047  289 TMTPEDLDisrqlqagyqirpDESGDLNKRVKA------PINPTAHVwTHCEIHPSMILGICASIIPFPDHNQ 355
Cdd:COG0085   477 AQANAPLD-------------EDGNFLEERVLVryrgeeVLVPPEEV-DYMDVSPKQIVSVATSLIPFLEHDD 535
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
56-147 2.57e-07

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 52.70  E-value: 2.57e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047   56 STAGVSQVLNRYTFASTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMC----YVT 127
Cdd:PRK14844  528 NSSQLSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYArinkYGF 607

                          90       100
                  ....*....|....*....|
gi 374923047  128 VGTPSDPIVEFMIQRNMEVL 147
Cdd:PRK14844  608 IESPYRKVVNRVVTDQIEYL 627
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
60-165 1.76e-06

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 49.92  E-value: 1.76e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374923047   60 VSQVLNRYTFASTLSHLRRTNTpIGRDGKIA-----KPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYVT----VGT 130
Cdd:PRK09603  525 LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNdlgfIEA 603

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 374923047  131 PSDPIVEFMIQRNMEVL---EEYEPLRAPNATKVFVNG 165
Cdd:PRK09603  604 PYKKVVDGKVVGETIYLtaiQEDSHIIAPASTPIDEEG 641
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 60-121 1.69e-05

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 46.62  E-value: 1.69e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 374923047   60 VSQVLNRYTFASTLSHLRRTNT--PIGRDG-KIAKP-RQLHNTHWGLVCPAETPEGQACGLVKNLA 121
Cdd:CHL00207  366 LSQYMDQTNPLSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-36 4.26e-05

RNA polymerase beta subunit; 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 forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.


Pssm-ID: 367994 [Multi-domain]  Cd Length: 396  Bit Score: 45.06  E-value: 4.26e-05
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 374923047    1 LFRRLTTDVYRYLQRCVENNREFNLTLGVKSTTITN 36
Cdd:pfam04563 361 LFKKLVRDVRERLQKVLGSPDDLMLQLLVNAKPITS 396
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 93-121 9.20e-05

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 44.32  E-value: 9.20e-05
                          10        20
                  ....*....|....*....|....*....
gi 374923047   93 RQLHNTHWGLVCPAETPEGQACGLVKNLA 121
Cdd:PRK00405  469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
rpoB CHL00001
RNA polymerase beta subunit
 61-129 3.21e-04

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 42.58  E-value: 3.21e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 374923047   61 SQVLNRYTFASTLSHLRRTNT--PIGRDGKIA--KPRQLHNTHWGLVCPAETPEGQACGLVKNLALmcYVTVG 129
Cdd:CHL00001  375 SQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIGSLAI--HARIG 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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