|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
12-336 |
1.73e-90 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 292.25 E-value: 1.73e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1336472829 12 NLTLAVKSQTITDGLRYSLATGNWGeqkkamSARAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLV 91
Cdd:PRK08565 372 DLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRI 445
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1336472829 92 CPAETPEGQACGLVKNLSLMTCISVGTASEPILYFLEEWGMEPLEDYVPSNSPDCTRVFVNGVWVGTHREPAQLVDTMRR 171
Cdd:PRK08565 446 CPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRE 525
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1336472829 172 LRRRGDIAPEVSI--IRDIREREFKIFTDAGRVYRPLFIVDDdpesetkGELVLQKEHIHKLMNSEydeydddpsashYT 249
Cdd:PRK08565 526 LRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKLTREHVEKLKKGE------------LT 586
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1336472829 250 WSSLVNDGVVEYVDAEEEETIMIAMTPEDleasksslsetqqkslqmeeqdldpakrikptyVSSTHtfTHCEIHPSMIL 329
Cdd:PRK08565 587 FDDLVKMGVIEYLDAEEEENAYVALDPED---------------------------------LTPEH--THLEIWPPAIL 631
|
....*..
gi 1336472829 330 GVAASII 336
Cdd:PRK08565 632 GITASII 638
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
1-115 |
1.54e-47 |
|
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: 171.60 E-value: 1.54e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1336472829 1 MQRCVENDKEFNLTLAVKSQTITDGLRYSLATGNWGEQKKAMSaRAGVSQVLNRYTYSSTLSHLRRTNT-PIGRDGKIAK 79
Cdd:cd00653 267 LQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFE 345
|
90 100 110
....*....|....*....|....*....|....*.
gi 1336472829 80 PRQLHNTHWGLVCPAETPEGQACGLVKNLSLMTCIS 115
Cdd:cd00653 346 VRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
149-210 |
4.86e-35 |
|
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: 122.09 E-value: 4.86e-35
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1336472829 149 VFVNGVWVGTHREPAQLVDTMRRLRRRGDIAPEVSIIRDIREREFKIFTDAGRVYRPLFIVD 210
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
44-116 |
6.16e-17 |
|
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: 81.69 E-value: 6.16e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1336472829 44 ARAGVSQVLNRYTYSSTLSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMTCIS 115
Cdd:COG0085 367 GSSQLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN 442
|
.
gi 1336472829 116 V 116
Cdd:COG0085 443 E 443
|
|
|
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
12-336 |
1.73e-90 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 292.25 E-value: 1.73e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1336472829 12 NLTLAVKSQTITDGLRYSLATGNWGeqkkamSARAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLV 91
Cdd:PRK08565 372 DLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRI 445
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1336472829 92 CPAETPEGQACGLVKNLSLMTCISVGTASEPILYFLEEWGMEPLEDYVPSNSPDCTRVFVNGVWVGTHREPAQLVDTMRR 171
Cdd:PRK08565 446 CPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRE 525
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1336472829 172 LRRRGDIAPEVSI--IRDIREREFKIFTDAGRVYRPLFIVDDdpesetkGELVLQKEHIHKLMNSEydeydddpsashYT 249
Cdd:PRK08565 526 LRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKLTREHVEKLKKGE------------LT 586
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1336472829 250 WSSLVNDGVVEYVDAEEEETIMIAMTPEDleasksslsetqqkslqmeeqdldpakrikptyVSSTHtfTHCEIHPSMIL 329
Cdd:PRK08565 587 FDDLVKMGVIEYLDAEEEENAYVALDPED---------------------------------LTPEH--THLEIWPPAIL 631
|
....*..
gi 1336472829 330 GVAASII 336
Cdd:PRK08565 632 GITASII 638
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
1-115 |
1.54e-47 |
|
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: 171.60 E-value: 1.54e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1336472829 1 MQRCVENDKEFNLTLAVKSQTITDGLRYSLATGNWGEQKKAMSaRAGVSQVLNRYTYSSTLSHLRRTNT-PIGRDGKIAK 79
Cdd:cd00653 267 LQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGSKRFLMQ-RSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFE 345
|
90 100 110
....*....|....*....|....*....|....*.
gi 1336472829 80 PRQLHNTHWGLVCPAETPEGQACGLVKNLSLMTCIS 115
Cdd:cd00653 346 VRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
147-336 |
8.45e-36 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 136.63 E-value: 8.45e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1336472829 147 TRVFVNGVWVGTHREPAQLVDTMRRLRRRGDIAPEVSIIRDIREREFKIFTDAGRVYRPLFIVDDdpesetkGELVLQKE 226
Cdd:PRK07225 5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLTEE 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1336472829 227 HIHKLMNSEydeydddpsashYTWSSLVNDGVVEYVDAEEEETIMIAMTPEDLeasksslsetqqkslqmeeqdldpakr 306
Cdd:PRK07225 78 HIEKLKNGE------------LTFDDLVKQGVIEYLDAEEEENAYIAVYEEDL--------------------------- 118
|
170 180 190
....*....|....*....|....*....|
gi 1336472829 307 ikptyvssTHTFTHCEIHPSMILGVAASII 336
Cdd:PRK07225 119 --------TEEHTHLEIDPSLILGIGAGMI 140
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
9-135 |
4.65e-35 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 133.15 E-value: 4.65e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1336472829 9 KEFNLTLAVKSQTITDGLRYSLATGNWgeqkkaMSARAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKIAKPRQLHNTHW 88
Cdd:PRK09606 372 RELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQW 445
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 1336472829 89 GLVCPAETPEGQACGLVKNLSLMTCISVGTASEPILYFLEEWGMEPL 135
Cdd:PRK09606 446 GRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVEPE 492
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
149-210 |
4.86e-35 |
|
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: 122.09 E-value: 4.86e-35
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1336472829 149 VFVNGVWVGTHREPAQLVDTMRRLRRRGDIAPEVSIIRDIREREFKIFTDAGRVYRPLFIVD 210
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
50-112 |
6.92e-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: 111.46 E-value: 6.92e-31
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1336472829 50 QVLNRYTYSSTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMT 112
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYA 66
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
250-325 |
5.21e-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: 89.91 E-value: 5.21e-23
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1336472829 250 WSSLVNDGVVEYVDAEEEETIMIAMTPEDLEASKSSLSETqqkslqmeeqdldpakrikptyvSSTHTFTHCEIHP 325
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREEREG-----------------------PYAHTYTHCEIHP 53
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
44-116 |
6.16e-17 |
|
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: 81.69 E-value: 6.16e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1336472829 44 ARAGVSQVLNRYTYSSTLSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMTCIS 115
Cdd:COG0085 367 GSSQLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN 442
|
.
gi 1336472829 116 V 116
Cdd:COG0085 443 E 443
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
48-112 |
4.92e-07 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 51.46 E-value: 4.92e-07
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1336472829 48 VSQVLNRYTYSSTLSHLRRTNTpIGRDGKIA-----KPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMT 112
Cdd:PRK09603 525 LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLINTLSTFT 593
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
48-110 |
1.84e-06 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 50.01 E-value: 1.84e-06
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1336472829 48 VSQVLNRYTYSSTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSL 110
Cdd:PRK14844 532 LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAI 598
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
48-116 |
7.16e-06 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 47.78 E-value: 7.16e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1336472829 48 VSQVLNRYTYSSTLSHLRRTNT--PIGRDG-KIAKP-RQLHNTHWGLVCPAETPEGQACGLVKnlSLMTCISV 116
Cdd:CHL00207 366 LSQYMDQTNPLSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIG--SLATNARI 436
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
81-109 |
1.11e-04 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 43.94 E-value: 1.11e-04
10 20
....*....|....*....|....*....
gi 1336472829 81 RQLHNTHWGLVCPAETPEGQACGLVKNLS 109
Cdd:PRK00405 469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
49-117 |
6.00e-04 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 41.81 E-value: 6.00e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1336472829 49 SQVLNRYTYSSTLSHLRRTNT--PIGRDGKIA--KPRQLHNTHWGLVCPAETPEGQACGLVKnlSLMTCISVG 117
Cdd:CHL00001 375 SQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIG--SLAIHARIG 445
|
|
|