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Conserved domains on  [gi|1134676763|gb|APX42497|]
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DNA-dependemt RNA polymerase beta subunit, partial [Pasteurellaceae bacterium]

Protein Classification

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;
1-178 6.23e-145

Ricin-type beta-trefoil lectin domain;


The actual alignment was detected with superfamily member PRK00405:

Pssm-ID: 481363 [Multi-domain]  Cd Length: 1112  Bit Score: 429.52  E-value: 6.23e-145
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763    1 FGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYG 80
Cdd:PRK00405   427 FGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYG 506

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763   81 FLETPYRKVIDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARgERGESGLYKPEDIHYMDVSTQQVVSVA 160
Cdd:PRK00405   507 FIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTAR-YKGEFVLVPPEEVDYMDVSPKQVVSVA 585

                          170
                   ....*....|....*...
gi 1134676763  161 AALIPFLEHDDANRALMG 178
Cdd:PRK00405   586 ASLIPFLEHDDANRALMG 603
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-178 6.23e-145

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 429.52  E-value: 6.23e-145
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763    1 FGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYG 80
Cdd:PRK00405   427 FGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYG 506

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763   81 FLETPYRKVIDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARgERGESGLYKPEDIHYMDVSTQQVVSVA 160
Cdd:PRK00405   507 FIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTAR-YKGEFVLVPPEEVDYMDVSPKQVVSVA 585

                          170
                   ....*....|....*...
gi 1134676763  161 AALIPFLEHDDANRALMG 178
Cdd:PRK00405   586 ASLIPFLEHDDANRALMG 603
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-178 1.05e-123

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: 371.75  E-value: 1.05e-123
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763    1 FGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYG 80
Cdd:COG0085    366 FGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYG 445

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763   81 FLETPYRKVIDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARgERGESGLYKPEDIHYMDVSTQQVVSVA 160
Cdd:COG0085    446 FIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVR-YRGEEVLVPPEEVDYMDVSPKQIVSVA 524

                          170
                   ....*....|....*...
gi 1134676763  161 AALIPFLEHDDANRALMG 178
Cdd:COG0085    525 TSLIPFLEHDDANRALMG 542
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-178 9.99e-119

DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 273928 [Multi-domain]  Cd Length: 1065  Bit Score: 360.13  E-value: 9.99e-119
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763    1 FGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYG 80
Cdd:TIGR02013  382 FGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYG 461

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763   81 FLETPYRKVIDGQV--TEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARgERGESGLYKPEDIHYMDVSTQQVVS 158
Cdd:TIGR02013  462 FIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVAR-YRGEITLVSPDQVDYMDVSPKQVVS 540

                          170       180
                   ....*....|....*....|
gi 1134676763  159 VAAALIPFLEHDDANRALMG 178
Cdd:TIGR02013  541 VAASLIPFLEHDDANRALMG 560
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 4-178 1.04e-56

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: 190.86  E-value: 1.04e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763   4 SQLSQFMDQNNPLSEVTHKRRISAlgpGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNdyGFLE 83
Cdd:cd00653   311 SGLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIE 385

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763  84 TPYRKVIdgqvteeieylsaideanyiiaqansnldennrftdafvtargergesglykpEDIHYMDVSTQQVVSVAAAL 163
Cdd:cd00653   386 RPYRIVE-----------------------------------------------------KEVTHIEISPSQILSVAASL 412

                         170
                  ....*....|....*
gi 1134676763 164 IPFLEHDDANRALMG 178
Cdd:cd00653   413 IPFPEHNQSPRNLYQ 427
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 8-75 4.00e-39

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: 127.64  E-value: 4.00e-39
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1134676763   8 QFMDQNNPLSEVTHKRRISAlGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFAR 75
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-178 6.23e-145

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 429.52  E-value: 6.23e-145
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763    1 FGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYG 80
Cdd:PRK00405   427 FGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYG 506

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763   81 FLETPYRKVIDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARgERGESGLYKPEDIHYMDVSTQQVVSVA 160
Cdd:PRK00405   507 FIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTAR-YKGEFVLVPPEEVDYMDVSPKQVVSVA 585

                          170
                   ....*....|....*...
gi 1134676763  161 AALIPFLEHDDANRALMG 178
Cdd:PRK00405   586 ASLIPFLEHDDANRALMG 603
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-178 1.05e-123

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: 371.75  E-value: 1.05e-123
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763    1 FGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYG 80
Cdd:COG0085    366 FGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYG 445

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763   81 FLETPYRKVIDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARgERGESGLYKPEDIHYMDVSTQQVVSVA 160
Cdd:COG0085    446 FIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVR-YRGEEVLVPPEEVDYMDVSPKQIVSVA 524

                          170
                   ....*....|....*...
gi 1134676763  161 AALIPFLEHDDANRALMG 178
Cdd:COG0085    525 TSLIPFLEHDDANRALMG 542
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-178 9.99e-119

DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 273928 [Multi-domain]  Cd Length: 1065  Bit Score: 360.13  E-value: 9.99e-119
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763    1 FGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYG 80
Cdd:TIGR02013  382 FGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYG 461

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763   81 FLETPYRKVIDGQV--TEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARgERGESGLYKPEDIHYMDVSTQQVVS 158
Cdd:TIGR02013  462 FIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVAR-YRGEITLVSPDQVDYMDVSPKQVVS 540

                          170       180
                   ....*....|....*....|
gi 1134676763  159 VAAALIPFLEHDDANRALMG 178
Cdd:TIGR02013  541 VAASLIPFLEHDDANRALMG 560
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-178 9.92e-86

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 274.96  E-value: 9.92e-86
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763    1 FGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYG 80
Cdd:PRK14844   527 FNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINKYG 606

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763   81 FLETPYRKVIDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARgERGESGLYKPEDIHYMDVSTQQVVSVA 160
Cdd:PRK14844   607 FIESPYRKVVNRVVTDQIEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYCR-YAGSFVMVSSDQVSYIDVSPKQVISVA 685

                          170
                   ....*....|....*...
gi 1134676763  161 AALIPFLEHDDANRALMG 178
Cdd:PRK14844   686 ASLIPFLENDDANRALMG 703
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-178 2.38e-81

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 262.17  E-value: 2.38e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763    1 FGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYG 80
Cdd:PRK09603   520 FMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLG 599

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763   81 FLETPYRKVIDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARGErGESGLYKPEDIHYMDVSTQQVVSVA 160
Cdd:PRK09603   600 FIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVE-GEIVLNEKSKVTLMDLSSSMLVGVA 678

                          170
                   ....*....|....*...
gi 1134676763  161 AALIPFLEHDDANRALMG 178
Cdd:PRK09603   679 ASLIPFLEHDDANRALMG 696
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-178 2.63e-75

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 243.84  E-value: 2.63e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763    1 FGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYG 80
Cdd:CHL00207   361 FGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKFG 440

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763   81 FLETPYRKVIDGQV--TEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARgERGESGLYKPEDIHYMDVSTQQVVS 158
Cdd:CHL00207   441 FIETPFYKVINGKVkkFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVR-YKQEFKTVNPSKVDFIAISPIQVFS 519

                          170       180
                   ....*....|....*....|
gi 1134676763  159 VAAALIPFLEHDDANRALMG 178
Cdd:CHL00207   520 IAESLIPFLEHNDANRALMG 539
rpoB CHL00001
RNA polymerase beta subunit
 1-178 3.26e-73

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 237.88  E-value: 3.26e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763    1 FGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYG 80
Cdd:CHL00001   369 FGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWG 448

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763   81 FLETPYRKVIDGQVTEEIEYLSAIDEANYIIAQANSnLDENNRFTDAFVTARGERGESGLYKPEDIHYMDVSTQQVVSVA 160
Cdd:CHL00001   449 SLESPFYEISERSKEERMVYLSPSEDEYYMIAAGNS-LALNQGIQEEQVVPARYRQEFLTIAWEQIHLRSIFPFQYFSIG 527

                          170
                   ....*....|....*...
gi 1134676763  161 AALIPFLEHDDANRALMG 178
Cdd:CHL00001   528 ASLIPFLEHNDANRALMG 545
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 4-178 1.04e-56

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: 190.86  E-value: 1.04e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763   4 SQLSQFMDQNNPLSEVTHKRRISAlgpGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNdyGFLE 83
Cdd:cd00653   311 SGLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIE 385

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676763  84 TPYRKVIdgqvteeieylsaideanyiiaqansnldennrftdafvtargergesglykpEDIHYMDVSTQQVVSVAAAL 163
Cdd:cd00653   386 RPYRIVE-----------------------------------------------------KEVTHIEISPSQILSVAASL 412

                         170
                  ....*....|....*
gi 1134676763 164 IPFLEHDDANRALMG 178
Cdd:cd00653   413 IPFPEHNQSPRNLYQ 427
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 8-75 4.00e-39

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: 127.64  E-value: 4.00e-39
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1134676763   8 QFMDQNNPLSEVTHKRRISAlGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFAR 75
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_45 pfam10385
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ...
 86-152 5.18e-34

RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region.


Pssm-ID: 463067 [Multi-domain]  Cd Length: 66  Bit Score: 114.77  E-value: 5.18e-34
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1134676763  86 YRKVIDGQVTEEIEYLSAIDEANYIIAQANSNLDENNRFTDAFVTARgERGESGLYKPEDIHYMDVS 152
Cdd:pfam10385   1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSAR-YRGEFPLVPPEEVDYMDVS 66
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 7-74 2.38e-19

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 84.62  E-value: 2.38e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1134676763    7 SQFMDQNNPLSEVTHKRRIsaLGPggLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFA 74
Cdd:PRK08565   403 SQLLDRTNYLSTLSHLRRV--VSP--LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMA 466
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 2-70 2.28e-17

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 78.45  E-value: 2.28e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1134676763   2 GSSQLSQFMDQNNPLSEVTHKRRISAlgPggLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSL 70
Cdd:PRK09606  401 GRTGVSQLLDRTDYMATLSHLRRVVS--P--LSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNF 465
 
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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