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Conserved domains on  [gi|116563666|gb|ABJ99849|]
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RpoB, partial [Bacillus amyloliquefaciens]

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;
1-179 3.10e-122

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: 370.20  E-value: 3.10e-122
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666    1 VLELPNLIEIQTSSYQWFL-------DEGLREMFQDISPIEDFTGNLSLEFIDYSLGDPKYPVEESKERDVTYSAPLRVK 73
Cdd:PRK00405   21 VLELPNLLEIQLDSFDWFLqldvppeDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPKYDVEECKERGLTYSAPLRVK 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666   74 VRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDK--NGKKGFTATVIPNRGAWLEYE 151
Cdd:PRK00405  101 LRLINKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDHDKDKtsSGKLLYSARIIPYRGSWLEFE 180

                         170       180
                  ....*....|....*....|....*...
gi 116563666  152 TDAKDVVYVRIDRTRKLPVTVLLRALGF 179
Cdd:PRK00405  181 FDPKDILYVRIDRRRKLPVTVLLRALGY 208
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-179 3.10e-122

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 370.20  E-value: 3.10e-122
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666    1 VLELPNLIEIQTSSYQWFL-------DEGLREMFQDISPIEDFTGNLSLEFIDYSLGDPKYPVEESKERDVTYSAPLRVK 73
Cdd:PRK00405   21 VLELPNLLEIQLDSFDWFLqldvppeDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPKYDVEECKERGLTYSAPLRVK 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666   74 VRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDK--NGKKGFTATVIPNRGAWLEYE 151
Cdd:PRK00405  101 LRLINKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDHDKDKtsSGKLLYSARIIPYRGSWLEFE 180

                         170       180
                  ....*....|....*....|....*...
gi 116563666  152 TDAKDVVYVRIDRTRKLPVTVLLRALGF 179
Cdd:PRK00405  181 FDPKDILYVRIDRRRKLPVTVLLRALGY 208
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-182 3.45e-120

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: 362.50  E-value: 3.45e-120
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666    1 VLELPNLIEIQTSSYQWFLDEGLREMFQDISPIEDFTGNLSLEFIDYSLGDPKYPVEESKERDVTYSAPLRVKVRLINKE 80
Cdd:COG0085    10 PLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKERDLTYAAPLYVKVRLVNKE 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666   81 TGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNGKKGFTATVIPNRGAWLEYETDAKDVVYV 160
Cdd:COG0085    90 TGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPSRGAWLEFETDKDGTIYV 169

                         170       180
                  ....*....|....*....|..
gi 116563666  161 RIDRTRKLPVTVLLRALGFGSD 182
Cdd:COG0085   170 RIDRKRKIPVTVLLRALGLETD 191
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-182 1.89e-106

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: 327.78  E-value: 1.89e-106
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666     1 VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLGDPKYPVEESKERDVTYSAPL 70
Cdd:TIGR02013   14 VLEVPNLLEIQLDSYDWFLqqdtppekrkEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVEECKERGLTYSAPL 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666    71 RVKVRLINKE---TGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVD--KNGKKGFTATVIPNRG 145
Cdd:TIGR02013   94 KVKLRLINKEedgTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKDttKSGKVLFSARIIPYRG 173

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 116563666   146 AWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSD 182
Cdd:TIGR02013  174 SWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTID 210
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 6-182 6.52e-35

RNA polymerase beta subunit; 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). This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.


Pssm-ID: 367994 [Multi-domain]  Cd Length: 396  Bit Score: 125.96  E-value: 6.52e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666    6 NLIEIQTSSYQWFLDEGLREMFQDISPIE---------DFTGNLSLEFIDYSLGDPKYPV----------EESKERDVTY 66
Cdd:pfam04563   1 GLVRQQLDSFNEFVDNDLQKIIDENALIEsefeiqhpgENGDKLSLKFGQIRLGKPMFDEtdgstreiypQECRLRNLTY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666   67 SAPLRVKVRLINKETGEVKDQDVFMGDFPIMTDT------------------------GTFIINGAERVIVSQLVRS--- 119
Cdd:pfam04563  81 SAPLYVDLELSVYNGEDIKPIEVFIGRLPIMLRSnacilsgateselvklgecpldpgGYFIINGSEKVIVAQEHRSrnh 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 116563666  120 PSVYFsgKVDKnGKKGFTA--------TVIPNRGAWLE-YETDAKDVVYVRIDRTRK-LPVTVLLRALGFGSD 182
Cdd:pfam04563 161 PIVFK--KADP-KKRGSVAsvrssaeiSVRPDSTSWVNvLEYLSNGTIYFKFPYIKKeIPIVIILRALGFTSD 230
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-179 3.10e-122

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 370.20  E-value: 3.10e-122
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666    1 VLELPNLIEIQTSSYQWFL-------DEGLREMFQDISPIEDFTGNLSLEFIDYSLGDPKYPVEESKERDVTYSAPLRVK 73
Cdd:PRK00405   21 VLELPNLLEIQLDSFDWFLqldvppeDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPKYDVEECKERGLTYSAPLRVK 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666   74 VRLINKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDK--NGKKGFTATVIPNRGAWLEYE 151
Cdd:PRK00405  101 LRLINKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDHDKDKtsSGKLLYSARIIPYRGSWLEFE 180

                         170       180
                  ....*....|....*....|....*...
gi 116563666  152 TDAKDVVYVRIDRTRKLPVTVLLRALGF 179
Cdd:PRK00405  181 FDPKDILYVRIDRRRKLPVTVLLRALGY 208
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-182 3.45e-120

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: 362.50  E-value: 3.45e-120
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666    1 VLELPNLIEIQTSSYQWFLDEGLREMFQDISPIEDFTGNLSLEFIDYSLGDPKYPVEESKERDVTYSAPLRVKVRLINKE 80
Cdd:COG0085    10 PLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKERDLTYAAPLYVKVRLVNKE 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666   81 TGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNGKKGFTATVIPNRGAWLEYETDAKDVVYV 160
Cdd:COG0085    90 TGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPSRGAWLEFETDKDGTIYV 169

                         170       180
                  ....*....|....*....|..
gi 116563666  161 RIDRTRKLPVTVLLRALGFGSD 182
Cdd:COG0085   170 RIDRKRKIPVTVLLRALGLETD 191
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-182 1.89e-106

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: 327.78  E-value: 1.89e-106
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666     1 VLELPNLIEIQTSSYQWFL----------DEGLREMFQDISPIEDFTGNLSLEFIDYSLGDPKYPVEESKERDVTYSAPL 70
Cdd:TIGR02013   14 VLEVPNLLEIQLDSYDWFLqqdtppekrkEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVEECKERGLTYSAPL 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666    71 RVKVRLINKE---TGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVD--KNGKKGFTATVIPNRG 145
Cdd:TIGR02013   94 KVKLRLINKEedgTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKDttKSGKVLFSARIIPYRG 173

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 116563666   146 AWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSD 182
Cdd:TIGR02013  174 SWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTID 210
rpoB CHL00001
RNA polymerase beta subunit
 4-179 7.31e-57

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 192.04  E-value: 7.31e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666    4 LPNLIEIQTSSYQWFLDEGLREMFQDISPIEDFTGNLSLEFI--DYSLGDPKYpveesKERD-----VTYSAPLRVKVRL 76
Cdd:CHL00001   12 IPGFNQIQFEGFCRFIDQGLTEELSKFPKIEDTDQEIEFQLFveTYQLVEPLI-----KERDavyesLTYSSELYVPAGL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666   77 INKETGEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNGKKGFTATVIPNRGAWLEYETDAKD 156
Cdd:CHL00001   87 IWKKSRDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYRSELDHNGISVYTGTIISDWGGRLELEIDRKA 166

                         170       180
                  ....*....|....*....|...
gi 116563666  157 VVYVRIDRTRKLPVTVLLRALGF 179
Cdd:CHL00001  167 RIWARVSRKQKISILVLLSAMGL 189
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
2-179 4.87e-54

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 184.36  E-value: 4.87e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666    2 LELPNLIEIQTSSYQWFL------DEGLREMFQDISPIEDFTGNLSLEFIDYSLGDPKYPVEESKERDVTYSAPLRVKVR 75
Cdd:PRK09603   22 LEVPNLLLLQRDSYDSFLyskdgkESGIEKVFKSIFPIQDEHNRITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVR 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666   76 LI----NKETGE------VKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGK--VDKNGKKGFTATVIPN 143
Cdd:PRK09603  102 LIlwekDTKSGEkngikdIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEesSTSLNKLIYTGQIIPD 181

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 116563666  144 RGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGF 179
Cdd:PRK09603  182 RGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDY 217
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 4-178 6.07e-54

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 183.75  E-value: 6.07e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666    4 LPNLIEIQTSSYQWFLDEGLREMFQDISPIEDFTGNLSLEFI--DYSLGDPKYPVEESKERDVTYSAPLRVKVRLINKET 81
Cdd:CHL00207    7 LPDFLEIQRTSFCWFLNEGLNEELNIFSKIFDYTGNLELLLFgkNYKLKYPKYNLLSAKSYDSNYSIQIYLPLKFINLKT 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666   82 GEVKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFSGKVDKNGKKGFTATVIPNRGAWLEYETDAKDVVYVR 161
Cdd:CHL00207   87 NKIKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIKKNSNKIYSATLIPNRGSWIKFELDKNKEIWIR 166

                         170
                  ....*....|....*..
gi 116563666  162 IDRTRKLPVTVLLRALG 178
Cdd:CHL00207  167 IDKNRKKPLIIFLKALG 183
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
4-182 2.70e-42

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 150.54  E-value: 2.70e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666    4 LPNLIEIQTSSYQWFL-----DEGLREMFQDISPIEDFTGNLSLEFIDYSLGDPKYPVEESKERDVTYSAPLRVKVRLIN 78
Cdd:PRK14844   29 LLDLVKVQKESYDSFTpknkgNERLEVIFHTIFPINDPLHRATIEFISCRVDDPKYDESECIKRGITFSAQVIASIRLVI 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666   79 -------------KETGE----------VKDQDVFMGDFPIMTDTGTFIINGAERVIVSQLVRSPSVYFS---GKVDKNG 132
Cdd:PRK14844  109 mqdgisldeyksiKESGDhsklatviksIEEQEVHFCELPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDsdkGKTYNSG 188

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 116563666  133 KKGFTATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSD 182
Cdd:PRK14844  189 KLIYSARVIPYRGSWLDIEFDVKDHLYFRIDRKRKLPISVLLKALGLSNN 238
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 6-182 6.52e-35

RNA polymerase beta subunit; 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). This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.


Pssm-ID: 367994 [Multi-domain]  Cd Length: 396  Bit Score: 125.96  E-value: 6.52e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666    6 NLIEIQTSSYQWFLDEGLREMFQDISPIE---------DFTGNLSLEFIDYSLGDPKYPV----------EESKERDVTY 66
Cdd:pfam04563   1 GLVRQQLDSFNEFVDNDLQKIIDENALIEsefeiqhpgENGDKLSLKFGQIRLGKPMFDEtdgstreiypQECRLRNLTY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666   67 SAPLRVKVRLINKETGEVKDQDVFMGDFPIMTDT------------------------GTFIINGAERVIVSQLVRS--- 119
Cdd:pfam04563  81 SAPLYVDLELSVYNGEDIKPIEVFIGRLPIMLRSnacilsgateselvklgecpldpgGYFIINGSEKVIVAQEHRSrnh 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 116563666  120 PSVYFsgKVDKnGKKGFTA--------TVIPNRGAWLE-YETDAKDVVYVRIDRTRK-LPVTVLLRALGFGSD 182
Cdd:pfam04563 161 PIVFK--KADP-KKRGSVAsvrssaeiSVRPDSTSWVNvLEYLSNGTIYFKFPYIKKeIPIVIILRALGFTSD 230
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 6-182 2.76e-25

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 101.57  E-value: 2.76e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666    6 NLIEIQTSSYQWFLDEGLREMFQDISPIEDFTGNLSLEFIDYSLGDPK-----------YPVEeSKERDVTYSAPLRVKV 74
Cdd:PRK08565   13 GLVRQHLDSYNDFIERGLQEIVDEFGEIKTEIPGLKIVLGKIRVGEPEikeadgserpiTPME-ARLRNLTYAAPLYLTM 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666   75 RLINkETGEVKDQDVFMGDFPIMTDT------------------------GTFIINGAERVIVSQLVRSPSVYFSGKVDK 130
Cdd:PRK08565   92 IPVE-NGIEYEPEEVKIGDLPIMVKSkicplsglspdelieigedpkdpgGYFIINGSERVIVSQEDLAPNRVLVDKGEA 170

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 116563666  131 NGKKGFTATVIPNRGAW-----LEYETDAkdVVYVRIDRTR-KLPVTVLLRALGFGSD 182
Cdd:PRK08565  171 GSSITHTAKVISSRAGYraqvtVERRKDG--TIYVSFPAVPgKIPFVILMRALGLETD 226
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 7-182 1.61e-18

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 81.92  E-value: 1.61e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666   7 LIEIQTSSYQWFLDEGLREMFQDISPIE-DFTGNLSLEFIDYSLGDPK-----------YPVEeSKERDVTYSAPLRVKV 74
Cdd:PRK09606  18 LVRHHIDSYNDFVDNGLQKIIDEQGPIEtEIEDGVYVELGKIRVGKPVvkeadgsereiYPME-ARLRNLTYSAPLYLEM 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116563666  75 RLInKETGEVKDQDVFMGDFPIM-----------TDT-------------GTFIINGAERVIVSQLVRSPSVYFSGKVDK 130
Cdd:PRK09606  97 SPV-EGGEEEEPEEVYIGELPVMvgskicnlyglSEEelievgedpldpgGYFIVNGSERVLMTLEDLAPNKILVEKDER 175

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 116563666 131 NGKKGFTATVIPNRG---AWLEYETDAKDVVYVRIDR-TRKLPVTVLLRALGFGSD 182
Cdd:PRK09606 176 YGDRIEVAKVFSQRRgyrALVTVERNRDGLLEVSFPSvPGSIPFVILMRALGLETD 231
RNA_pol_Rpb2_2 pfam04561
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
 118-182 1.20e-11

RNA polymerase Rpb2, domain 2; 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). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).


Pssm-ID: 398318 [Multi-domain]  Cd Length: 185  Bit Score: 60.44  E-value: 1.20e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 116563666  118 RSPSVYFSGKVDKNGKKGF-TATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPVTVLLRALGFGSD 182
Cdd:pfam04561   1 RSNGIYVEKELDKNGIIATyTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSD 66
 
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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