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Conserved domains on  [gi|375813900|gb|AFA85120|]
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RNA polymerase beta subunit, partial [Aeromonas taiwanensis]

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;
1-142 2.32e-109

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: 334.38  E-value: 2.32e-109
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813900    1 PLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYSRTNEYGFLETPYRKVIDGVI 80
Cdd:PRK00405  441 PLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKV 520

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 375813900   81 TDEVDYLSAIEEGKYVIAQANAATTEDGRLKDELIPCRHKGESTFMNADQIQYMDVSPQQIV 142
Cdd:PRK00405  521 TDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVV 582
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-142 2.32e-109

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 334.38  E-value: 2.32e-109
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813900    1 PLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYSRTNEYGFLETPYRKVIDGVI 80
Cdd:PRK00405  441 PLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKV 520

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 375813900   81 TDEVDYLSAIEEGKYVIAQANAATTEDGRLKDELIPCRHKGESTFMNADQIQYMDVSPQQIV 142
Cdd:PRK00405  521 TDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVV 582
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-142 5.15e-91

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: 283.54  E-value: 5.15e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813900    1 PLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYSRTNEYGFLETPYRKVIDGVI 80
Cdd:COG0085   380 PLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKV 459

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 375813900   81 TDEVDYLSAIEEGKYVIAQANAATTEDGRLKDELIPCRHKGESTFMNADQIQYMDVSPQQIV 142
Cdd:COG0085   460 TDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIV 521
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-142 1.32e-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: 1.32e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813900     1 PLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYSRTNEYGFLETPYRKVIDG-- 78
Cdd:TIGR02013  396 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGkv 475

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 375813900    79 VITDEVDYLSAIEEGKYVIAQANAATTEDGRLKDELIPCRHKGESTFMNADQIQYMDVSPQQIV 142
Cdd:TIGR02013  476 VVTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVV 539
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-88 2.69e-38

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: 137.31  E-value: 2.69e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813900   1 PLSEVTHKRRISAlgpGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYSRTNeyGFLETPYRKVIdgvi 80
Cdd:cd00653  322 PLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVE---- 392


                 ....*...
gi 375813900  81 tDEVDYLS 88
Cdd:cd00653  393 -KEVTHIE 399
RNA_pol_Rpb2_45 pfam10385
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ...
 72-137 4.38e-37

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: 120.93  E-value: 4.38e-37
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 375813900   72 YRKVIDGVITDEVDYLSAIEEGKYVIAQANAATTEDGRLKDELIPCRHKGESTFMNADQIQYMDVS 137
Cdd:pfam10385   1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-142 2.32e-109

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 334.38  E-value: 2.32e-109
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813900    1 PLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYSRTNEYGFLETPYRKVIDGVI 80
Cdd:PRK00405  441 PLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKV 520

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 375813900   81 TDEVDYLSAIEEGKYVIAQANAATTEDGRLKDELIPCRHKGESTFMNADQIQYMDVSPQQIV 142
Cdd:PRK00405  521 TDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVV 582
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-142 5.15e-91

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: 283.54  E-value: 5.15e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813900    1 PLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYSRTNEYGFLETPYRKVIDGVI 80
Cdd:COG0085   380 PLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKV 459

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 375813900   81 TDEVDYLSAIEEGKYVIAQANAATTEDGRLKDELIPCRHKGESTFMNADQIQYMDVSPQQIV 142
Cdd:COG0085   460 TDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIV 521
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-142 1.32e-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: 1.32e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813900     1 PLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYSRTNEYGFLETPYRKVIDG-- 78
Cdd:TIGR02013  396 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGkv 475

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 375813900    79 VITDEVDYLSAIEEGKYVIAQANAATTEDGRLKDELIPCRHKGESTFMNADQIQYMDVSPQQIV 142
Cdd:TIGR02013  476 VVTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVV 539
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-142 1.19e-69

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 227.20  E-value: 1.19e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813900    1 PLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYSRTNEYGFLETPYRKVIDGVI 80
Cdd:PRK14844  541 PLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFIESPYRKVVNRVV 620

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 375813900   81 TDEVDYLSAIEEGKYVIAQANAATTEDGRLKDELIPCRHKGESTFMNADQIQYMDVSPQQIV 142
Cdd:PRK14844  621 TDQIEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVI 682
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-142 2.06e-62

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 206.31  E-value: 2.06e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813900    1 PLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYSRTNEYGFLETPYRKVIDGVI 80
Cdd:PRK09603  534 PLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKV 613

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 375813900   81 TDEVDYLSAIEEGKYVIAQANAATTEDGRLKDELIPCRHKGESTFMNADQIQYMDVSPQQIV 142
Cdd:PRK09603  614 VGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLV 675
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-142 2.05e-51

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 174.89  E-value: 2.05e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813900    1 PLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYSRTNEYGFLETPYRKVIDGVI 80
Cdd:CHL00207  375 PLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKFGFIETPFYKVINGKV 454

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 375813900   81 --TDEVDYLSAIEEGKYVIAQANAATTEDGRLKDELIPCRHKGESTFMNADQIQYMDVSPQQIV 142
Cdd:CHL00207  455 kkFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQVF 518
rpoB CHL00001
RNA polymerase beta subunit
 1-140 1.09e-49

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 169.70  E-value: 1.09e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813900    1 PLSEVTHKRRISALGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYSRTNEYGFLETPYRKVIDGVI 80
Cdd:CHL00001  383 PLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYEISERSK 462

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813900   81 TDEVDYLSAIEEGKYVIAQANAATTEDGRLKDELIPCRHKGESTFMNADQIQYMDVSPQQ 140
Cdd:CHL00001  463 EERMVYLSPSEDEYYMIAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQIHLRSIFPFQ 522
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-88 2.69e-38

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: 137.31  E-value: 2.69e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 375813900   1 PLSEVTHKRRISAlgpGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYSRTNeyGFLETPYRKVIdgvi 80
Cdd:cd00653  322 PLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVE---- 392


                 ....*...
gi 375813900  81 tDEVDYLS 88
Cdd:cd00653  393 -KEVTHIE 399
RNA_pol_Rpb2_45 pfam10385
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ...
 72-137 4.38e-37

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: 120.93  E-value: 4.38e-37
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 375813900   72 YRKVIDGVITDEVDYLSAIEEGKYVIAQANAATTEDGRLKDELIPCRHKGESTFMNADQIQYMDVS 137
Cdd:pfam10385   1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-61 2.26e-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: 116.86  E-value: 2.26e-35
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 375813900    1 PLSEVTHKRRISAlGPGGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYSR 61
Cdd:pfam04565   8 YLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 2-57 5.82e-17

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 76.15  E-value: 5.82e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 375813900    2 LSEVTHKRRIsaLGPggLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLS 57
Cdd:PRK08565  412 LSTLSHLRRV--VSP--LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLA 463
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 2-60 2.65e-16

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 74.22  E-value: 2.65e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 375813900   2 LSEVTHKRRISAlgpgGLTRERAGFEVRDVHPTHYGRLCPIETPEGPNIGLINSLSVYS 60
Cdd:PRK09606 415 MATLSHLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMV 469
 
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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