NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|425884813|gb|AFY07751|]
View 

RNA polymerase beta-subunit, partial [Bartonella sp. A140]

Protein Classification

DNA-directed RNA polymerase subunit beta( domain architecture ID 1000195)

DNA-directed RNA polymerase subunit beta catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

CATH:  3.90.1110.10
EC:  2.7.7.6
Gene Ontology:  GO:0000428|GO:0003899|GO:0006351
PubMed:  6266829
SCOP:  4003708

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Ricin_B_lectin super family cl47023
Ricin-type beta-trefoil lectin domain;
1-262 0e+00

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: 620.19  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813    1 IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTH 80
Cdd:PRK00405  396 VRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTH 475

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813   81 YGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRRIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFV 160
Cdd:PRK00405  476 YGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELV 555

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813  161 VCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240
Cdd:PRK00405  556 TARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGA 635

                         250       260
                  ....*....|....*....|..
gi 425884813  241 AVSAKRGGIVDQVDATRIVIRA 262
Cdd:PRK00405  636 VVVAKRDGVVEYVDASRIVVRV 657
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-262 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 620.19  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813    1 IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTH 80
Cdd:PRK00405  396 VRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTH 475

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813   81 YGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRRIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFV 160
Cdd:PRK00405  476 YGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELV 555

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813  161 VCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240
Cdd:PRK00405  556 TARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGA 635

                         250       260
                  ....*....|....*....|..
gi 425884813  241 AVSAKRGGIVDQVDATRIVIRA 262
Cdd:PRK00405  636 VVVAKRDGVVEYVDASRIVVRV 657
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-263 0e+00

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: 526.92  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813     1 IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTH 80
Cdd:TIGR02013  351 VRERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTH 430

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813    81 YGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRRIIDGKV--TTEVIYLSAMEESKHYVAQANSSLDSEGRFTEE 158
Cdd:TIGR02013  431 YGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVED 510

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813   159 FVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDS 238
Cdd:TIGR02013  511 LVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDS 590

                          250       260
                   ....*....|....*....|....*
gi 425884813   239 GAAVSAKRGGIVDQVDATRIVIRAT 263
Cdd:TIGR02013  591 GAVIVAKRGGVVEYVDAKRIVIRYD 615
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-225 3.85e-157

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: 462.27  E-value: 3.85e-157
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813    1 IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTH 80
Cdd:COG0085   335 VRERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSH 414

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813   81 YGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRRIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFV 160
Cdd:COG0085   415 YGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERV 494

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 425884813  161 VCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPF 225
Cdd:COG0085   495 LVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL 559
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-237 1.55e-79

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: 256.34  E-value: 1.55e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813   1 IKERMSSVEI--DTVMPQDLINAKPAAAAVREFFGSSQ------------LSQFMDQTNPLSEITHKRRLSAlgpGGLTR 66
Cdd:cd00653  263 VKEKLQKQLSkkKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFR 339

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813  67 ERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNkyGFIESPYrRIIDGKVTteviylsameeskhyvaqan 146
Cdd:cd00653  340 ERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPY-RIVEKEVT-------------------- 396

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813 147 ssldsegrfteefvvcrhagevlmaprdhvdLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVP--------- 217
Cdd:cd00653  397 -------------------------------HIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGtpalnqqyr 445

                        250       260
                 ....*....|....*....|....*..
gi 425884813 218 -------LVRAEAPFVGTGMESIVARD 237
Cdd:cd00653  446 mdtklylLLYPQKPLVGTGIEEYIAFG 472
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 39-106 5.13e-41

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: 135.35  E-value: 5.13e-41
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 425884813   39 QFMDQTNPLSEITHKRRLSAlGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFAR 106
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-262 0e+00

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 620.19  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813    1 IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTH 80
Cdd:PRK00405  396 VRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTH 475

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813   81 YGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRRIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFV 160
Cdd:PRK00405  476 YGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELV 555

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813  161 VCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240
Cdd:PRK00405  556 TARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGA 635

                         250       260
                  ....*....|....*....|..
gi 425884813  241 AVSAKRGGIVDQVDATRIVIRA 262
Cdd:PRK00405  636 VVVAKRDGVVEYVDASRIVVRV 657
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-263 0e+00

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: 526.92  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813     1 IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTH 80
Cdd:TIGR02013  351 VRERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTH 430

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813    81 YGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRRIIDGKV--TTEVIYLSAMEESKHYVAQANSSLDSEGRFTEE 158
Cdd:TIGR02013  431 YGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVED 510

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813   159 FVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDS 238
Cdd:TIGR02013  511 LVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDS 590

                          250       260
                   ....*....|....*....|....*
gi 425884813   239 GAAVSAKRGGIVDQVDATRIVIRAT 263
Cdd:TIGR02013  591 GAVIVAKRGGVVEYVDAKRIVIRYD 615
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-225 3.85e-157

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: 462.27  E-value: 3.85e-157
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813    1 IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTH 80
Cdd:COG0085   335 VRERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSH 414

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813   81 YGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRRIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFV 160
Cdd:COG0085   415 YGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERV 494

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 425884813  161 VCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPF 225
Cdd:COG0085   495 LVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL 559
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-262 1.27e-127

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 399.00  E-value: 1.27e-127
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813    1 IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTH 80
Cdd:PRK14844  496 VVDSMSTSSLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTH 575

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813   81 YGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRRIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFV 160
Cdd:PRK14844  576 YGRICPIETPEGQNIGLINSLAIYARINKYGFIESPYRKVVNRVVTDQIEYLSAIDEGLYYIADTSAKLDENNCFVDDML 655

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813  161 VCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGA 240
Cdd:PRK14844  656 YCRYAGSFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGA 735

                         250       260
                  ....*....|....*....|..
gi 425884813  241 AVSAKRGGIVDQVDATRIVIRA 262
Cdd:PRK14844  736 VVLAKRDGIVDSSDSNSIVIRA 757
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-260 1.10e-124

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 390.82  E-value: 1.10e-124
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813    1 IKERMSSVEI--DTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHP 78
Cdd:PRK09603  487 IKDKLTTMSGafDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHP 566

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813   79 THYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRRIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEE 158
Cdd:PRK09603  567 THYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGD 646

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813  159 FVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDS 238
Cdd:PRK09603  647 LIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDS 726

                         250       260
                  ....*....|....*....|..
gi 425884813  239 GAAVSAKRGGIVDQVDATRIVI 260
Cdd:PRK09603  727 WGAIKANRAGVVEKIDSKNIYI 748
rpoB CHL00001
RNA polymerase beta subunit
 15-261 4.96e-118

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 362.30  E-value: 4.96e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813   15 PQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPN 94
Cdd:CHL00001  352 PQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGIN 431

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813   95 IGLINSLATFARVNKYGFIESPYRRIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRD 174
Cdd:CHL00001  432 AGLIGSLAIHARIGHWGSLESPFYEISERSKEERMVYLSPSEDEYYMIAAGNSLALNQGIQEEQVVPARYRQEFLTIAWE 511

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813  175 HVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDSGAAVSAKRGGIVDQVD 254
Cdd:CHL00001  512 QIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTD 591


                  ....*..
gi 425884813  255 ATRIVIR 261
Cdd:CHL00001  592 TDKIILS 598
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-261 1.25e-111

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 345.54  E-value: 1.25e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813    1 IKERMSSVEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTH 80
Cdd:CHL00207  330 LRNRMTICDIDSLSKFNLINPKPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSH 409

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813   81 YGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRRIIDGKV--TTEVIYLSAMEESKHYVAQANSSLDSEGRFTEE 158
Cdd:CHL00207  410 YGRICPIETPEGPNCGLIGSLATNARINKFGFIETPFYKVINGKVkkFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKN 489

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813  159 FVVCRHAGEVLMAPRDHVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMESIVARDS 238
Cdd:CHL00207  490 IIPVRYKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDS 569

                         250       260
                  ....*....|....*....|...
gi 425884813  239 GAAVSAKRGGIVDQVDATRIVIR 261
Cdd:CHL00207  570 GMTIISLTEGIVVSVSAYKIIIQ 592
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-237 1.55e-79

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: 256.34  E-value: 1.55e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813   1 IKERMSSVEI--DTVMPQDLINAKPAAAAVREFFGSSQ------------LSQFMDQTNPLSEITHKRRLSAlgpGGLTR 66
Cdd:cd00653  263 VKEKLQKQLSkkKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFR 339

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813  67 ERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNkyGFIESPYrRIIDGKVTteviylsameeskhyvaqan 146
Cdd:cd00653  340 ERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPY-RIVEKEVT-------------------- 396

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813 147 ssldsegrfteefvvcrhagevlmaprdhvdLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVP--------- 217
Cdd:cd00653  397 -------------------------------HIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGtpalnqqyr 445

                        250       260
                 ....*....|....*....|....*..
gi 425884813 218 -------LVRAEAPFVGTGMESIVARD 237
Cdd:cd00653  446 mdtklylLLYPQKPLVGTGIEEYIAFG 472
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 39-106 5.13e-41

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: 135.35  E-value: 5.13e-41
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 425884813   39 QFMDQTNPLSEITHKRRLSAlGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFAR 106
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_45 pfam10385
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ...
 117-182 7.88e-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: 117.08  E-value: 7.88e-34
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 425884813  117 YRRIIDGKVTTEVIYLSAMEESKHYVAQANSSLDSEGRFTEEFVVCRHAGEVLMAPRDHVDLMDVS 182
Cdd:pfam10385   1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 38-107 1.42e-21

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 93.87  E-value: 1.42e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425884813   38 SQFMDQTNPLSEITHKRRLsaLGPggLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARV 107
Cdd:PRK08565  403 SQLLDRTNYLSTLSHLRRV--VSP--LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQI 468
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 33-109 1.28e-19

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 87.70  E-value: 1.28e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 425884813  33 GSSQLSQFMDQTNPLSEITHKRRLSAlgPggLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNK 109
Cdd:PRK09606 401 GRTGVSQLLDRTDYMATLSHLRRVVS--P--LSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEIST 473
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH