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Conserved domains on  [gi|1134676941|gb|APX42586|]
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DNA-dependemt RNA polymerase beta subunit, partial [Rodentibacter caecimuris]

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;
1-151 1.71e-110

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: 337.84  E-value: 1.71e-110
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676941    1 NNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPYRKVVDG 80
Cdd:PRK00405   439 TNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDG 518

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1134676941   81 QVTEEIEYLSAIDEANYFIAEANSNLDENNRFTDAFVTARgERGESGLYKPEDIHYMDVSTQQVVSVAAAL 151
Cdd:PRK00405   519 KVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTAR-YKGEFVLVPPEEVDYMDVSPKQVVSVAASL 588
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-151 1.71e-110

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 337.84  E-value: 1.71e-110
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676941    1 NNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPYRKVVDG 80
Cdd:PRK00405   439 TNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDG 518

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1134676941   81 QVTEEIEYLSAIDEANYFIAEANSNLDENNRFTDAFVTARgERGESGLYKPEDIHYMDVSTQQVVSVAAAL 151
Cdd:PRK00405   519 KVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTAR-YKGEFVLVPPEEVDYMDVSPKQVVSVAASL 588
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-151 2.41e-93

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: 290.47  E-value: 2.41e-93
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676941    1 NNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPYRKVVDG 80
Cdd:COG0085    378 TNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENG 457

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1134676941   81 QVTEEIEYLSAIDEANYFIAEANSNLDENNRFTDAFVTARgERGESGLYKPEDIHYMDVSTQQVVSVAAAL 151
Cdd:COG0085    458 KVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVR-YRGEEVLVPPEEVDYMDVSPKQIVSVATSL 527
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-151 2.07e-89

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: 280.78  E-value: 2.07e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676941    1 NNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPYRKVVDG 80
Cdd:TIGR02013  394 TNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDG 473

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1134676941   81 QV--TEEIEYLSAIDEANYFIAEANSNLDENNRFTDAFVTARgERGESGLYKPEDIHYMDVSTQQVVSVAAAL 151
Cdd:TIGR02013  474 KVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVAR-YRGEITLVSPDQVDYMDVSPKQVVSVAASL 545
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 2-87 2.96e-39

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: 140.40  E-value: 2.96e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676941   2 NPLSEVTHKRRISAlgpGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNdyGFLETPYRKvVDGQ 81
Cdd:cd00653   321 NPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRI-VEKE 394


                  ....*..
gi 1134676941  82 VT-EEIE 87
Cdd:cd00653   395 VThIEIS 401
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 2-63 1.46e-35

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: 117.63  E-value: 1.46e-35
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1134676941   2 NPLSEVTHKRRISAlGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFAR 63
Cdd:pfam04565   7 NYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-151 1.71e-110

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 337.84  E-value: 1.71e-110
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676941    1 NNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPYRKVVDG 80
Cdd:PRK00405   439 TNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDG 518

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1134676941   81 QVTEEIEYLSAIDEANYFIAEANSNLDENNRFTDAFVTARgERGESGLYKPEDIHYMDVSTQQVVSVAAAL 151
Cdd:PRK00405   519 KVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTAR-YKGEFVLVPPEEVDYMDVSPKQVVSVAASL 588
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-151 2.41e-93

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: 290.47  E-value: 2.41e-93
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676941    1 NNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPYRKVVDG 80
Cdd:COG0085    378 TNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENG 457

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1134676941   81 QVTEEIEYLSAIDEANYFIAEANSNLDENNRFTDAFVTARgERGESGLYKPEDIHYMDVSTQQVVSVAAAL 151
Cdd:COG0085    458 KVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVR-YRGEEVLVPPEEVDYMDVSPKQIVSVATSL 527
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-151 2.07e-89

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: 280.78  E-value: 2.07e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676941    1 NNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPYRKVVDG 80
Cdd:TIGR02013  394 TNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDG 473

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1134676941   81 QV--TEEIEYLSAIDEANYFIAEANSNLDENNRFTDAFVTARgERGESGLYKPEDIHYMDVSTQQVVSVAAAL 151
Cdd:TIGR02013  474 KVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVAR-YRGEITLVSPDQVDYMDVSPKQVVSVAASL 545
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
2-151 1.15e-67

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 221.80  E-value: 1.15e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676941    2 NPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPYRKVVDGQ 81
Cdd:PRK14844   540 NPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFIESPYRKVVNRV 619

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676941   82 VTEEIEYLSAIDEANYFIAEANSNLDENNRFTDAFVTARgERGESGLYKPEDIHYMDVSTQQVVSVAAAL 151
Cdd:PRK14844   620 VTDQIEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYCR-YAGSFVMVSSDQVSYIDVSPKQVISVAASL 688
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
2-151 2.52e-60

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 200.92  E-value: 2.52e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676941    2 NPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPYRKVVDGQ 81
Cdd:PRK09603   533 NPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGK 612

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676941   82 VTEEIEYLSAIDEANYFIAEANSNLDENNRFTDAFVTARGErGESGLYKPEDIHYMDVSTQQVVSVAAAL 151
Cdd:PRK09603   613 VVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVE-GEIVLNEKSKVTLMDLSSSMLVGVAASL 681
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 2-151 2.62e-52

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 177.59  E-value: 2.62e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676941    2 NPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPYRKVVDGQ 81
Cdd:CHL00207   374 NPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKFGFIETPFYKVINGK 453

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1134676941   82 V--TEEIEYLSAIDEANYFIAEANSNLDENNRFTDAFVTARgERGESGLYKPEDIHYMDVSTQQVVSVAAAL 151
Cdd:CHL00207   454 VkkFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVR-YKQEFKTVNPSKVDFIAISPIQVFSIAESL 524
rpoB CHL00001
RNA polymerase beta subunit
 2-151 1.49e-48

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 167.00  E-value: 1.49e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676941    2 NPLSEVTHKRRISALGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNDYGFLETPYRKVVDGQ 81
Cdd:CHL00001   382 NPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYEISERS 461

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676941   82 VTEEIEYLSAIDEANYFIAEANSnLDENNRFTDAFVTARGERGESGLYKPEDIHYMDVSTQQVVSVAAAL 151
Cdd:CHL00001   462 KEERMVYLSPSEDEYYMIAAGNS-LALNQGIQEEQVVPARYRQEFLTIAWEQIHLRSIFPFQYFSIGASL 530
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 2-87 2.96e-39

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: 140.40  E-value: 2.96e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1134676941   2 NPLSEVTHKRRISAlgpGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFARTNdyGFLETPYRKvVDGQ 81
Cdd:cd00653   321 NPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRI-VEKE 394


                  ....*..
gi 1134676941  82 VT-EEIE 87
Cdd:cd00653   395 VThIEIS 401
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 2-63 1.46e-35

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: 117.63  E-value: 1.46e-35
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1134676941   2 NPLSEVTHKRRISAlGPGGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFAR 63
Cdd:pfam04565   7 NYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_45 pfam10385
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ...
 74-140 2.06e-31

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: 107.07  E-value: 2.06e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1134676941  74 YRKVVDGQVTEEIEYLSAIDEANYFIAEANSNLDENNRFTDAFVTARgERGESGLYKPEDIHYMDVS 140
Cdd:pfam10385   1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSAR-YRGEFPLVPPEEVDYMDVS 66
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 2-62 4.87e-17

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 76.92  E-value: 4.87e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1134676941    2 NPLSEVTHKRRIsaLGPggLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSLSAFA 62
Cdd:PRK08565   410 NYLSTLSHLRRV--VSP--LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMA 466
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 4-58 2.49e-14

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 68.82  E-value: 2.49e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1134676941   4 LSEVTHKRRISAlgpgGLTRERAGFEVRDVHNTHYGRLCPIETPEGPNIGLINSL 58
Cdd:PRK09606  415 MATLSHLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNF 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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