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Conserved domains on  [gi|1789848679|gb|QHB74097|]
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RNA polymerase II second largest subunit, partial [Debaryomyces sp.]

Protein Classification

DNA-directed RNA polymerase subunit B family protein( domain architecture ID 1000145)

DNA-directed RNA polymerase subunit B family protein similar to fungal DNA-directed RNA polymerase II subunit RPB2

CATH:  3.90.1110.10|3.90.1070.20
EC:  2.7.7.6
Gene Ontology:  GO:0003899|GO:0000428|GO:0008270|GO:0003677|GO:0006351
PubMed:  11839495
SCOP:  4003708

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;
2-345 1.56e-95

Ricin-type beta-trefoil lectin domain;


The actual alignment was detected with superfamily member PRK08565:

Pssm-ID: 481363 [Multi-domain]  Cd Length: 1103  Bit Score: 306.50  E-value: 1.56e-95
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679    2 LTKDIYNYMQRCVENDKEFNLTLAVKSQTITDGLRYSLATGNWGeqkkamSSRAGVSQVLNRYTYSSTLSHLRRTNTPIG 81
Cdd:PRK08565   353 LVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLS 426

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679   82 RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTPSEPILYFLEEWGMEPLEDYVPSNSPDSTRVFVN 161
Cdd:PRK08565   427 RGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLN 506

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679  162 GVWVGTHREPAHLVDTMRNLRRRGDISPEVSI--IRDIREKEFKIFTDAGRVYRPLFIVDDdpdsegrGQLKLKKEHVHK 239
Cdd:PRK08565   507 GRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKLTREHVEK 579

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679  240 LINAEyddfgdepeslsYSWSSLVSEGIVEYVDAEEEETIMIAMTPEDLetsrstlsaseqknmqleeqevdpakrikpt 319
Cdd:PRK08565   580 LKKGE------------LTFDDLVKMGVIEYLDAEEEENAYVALDPEDL------------------------------- 616

                          330       340
                   ....*....|....*....|....*.
gi 1789848679  320 fSSSHtfTHCEIHPSMILGVAASIIP 345
Cdd:PRK08565   617 -TPEH--THLEIWPPAILGITASIIP 639
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 2-345 1.56e-95

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 306.50  E-value: 1.56e-95
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679    2 LTKDIYNYMQRCVENDKEFNLTLAVKSQTITDGLRYSLATGNWGeqkkamSSRAGVSQVLNRYTYSSTLSHLRRTNTPIG 81
Cdd:PRK08565   353 LVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLS 426

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679   82 RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTPSEPILYFLEEWGMEPLEDYVPSNSPDSTRVFVN 161
Cdd:PRK08565   427 RGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLN 506

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679  162 GVWVGTHREPAHLVDTMRNLRRRGDISPEVSI--IRDIREKEFKIFTDAGRVYRPLFIVDDdpdsegrGQLKLKKEHVHK 239
Cdd:PRK08565   507 GRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKLTREHVEK 579

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679  240 LINAEyddfgdepeslsYSWSSLVSEGIVEYVDAEEEETIMIAMTPEDLetsrstlsaseqknmqleeqevdpakrikpt 319
Cdd:PRK08565   580 LKKGE------------LTFDDLVKMGVIEYLDAEEEENAYVALDPEDL------------------------------- 616

                          330       340
                   ....*....|....*....|....*.
gi 1789848679  320 fSSSHtfTHCEIHPSMILGVAASIIP 345
Cdd:PRK08565   617 -TPEH--THLEIWPPAILGITASIIP 639
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-124 1.23e-49

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: 177.76  E-value: 1.23e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679   1 KLTKDIYNYMQRCVENDKEFNLTLAVKSQTITDGLRYSLATGNWGeQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNT-P 79
Cdd:cd00653   258 RLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWG-SKRFLMQRSGLSQVLDRLNPLSELSHKRRISSlG 336

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1789848679  80 IGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCIS 124
Cdd:cd00653   337 LFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 158-219 1.04e-35

RNA polymerase Rpb2, domain 4; 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 4, is also known as the external 2 domain.


Pssm-ID: 428012 [Multi-domain]  Cd Length: 62  Bit Score: 124.02  E-value: 1.04e-35
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1789848679 158 VFVNGVWVGTHREPAHLVDTMRNLRRRGDISPEVSIIRDIREKEFKIFTDAGRVYRPLFIVD 219
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 54-345 5.22e-19

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: 88.24  E-value: 5.22e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679   54 RAGVSQVLNRYTYSSTLSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISv 125
Cdd:COG0085    368 SSQLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN- 442

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679  126 gtpsepilyfleewgmepledyvpsnspdstrvfvngvwvgthrepahlvdtmrnlrrrgdispevsiirdirekEFkif 205
Cdd:COG0085    443 ---------------------------------------------------------------------------EY--- 444

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679  206 tdaGRVYRPLFIVDDdpdseGRgqlklkkehvhklinaeyddfgdepeslsyswsslVSEGIvEYVDAEEEETIMIAMTP 285
Cdd:COG0085    445 ---GFIETPYRKVEN-----GK-----------------------------------VTDEI-EYLTADEEENYYIAQAN 480

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679  286 EDLEtsrstlsaseqKNMQLEEQEVDPAKRIKPTFSSSHTFTHCEIHPSMILGVAASIIP 345
Cdd:COG0085    481 APLD-----------EDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIP 529
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 2-345 1.56e-95

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 306.50  E-value: 1.56e-95
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679    2 LTKDIYNYMQRCVENDKEFNLTLAVKSQTITDGLRYSLATGNWGeqkkamSSRAGVSQVLNRYTYSSTLSHLRRTNTPIG 81
Cdd:PRK08565   353 LVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLS 426

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679   82 RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTPSEPILYFLEEWGMEPLEDYVPSNSPDSTRVFVN 161
Cdd:PRK08565   427 RGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLN 506

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679  162 GVWVGTHREPAHLVDTMRNLRRRGDISPEVSI--IRDIREKEFKIFTDAGRVYRPLFIVDDdpdsegrGQLKLKKEHVHK 239
Cdd:PRK08565   507 GRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKLTREHVEK 579

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679  240 LINAEyddfgdepeslsYSWSSLVSEGIVEYVDAEEEETIMIAMTPEDLetsrstlsaseqknmqleeqevdpakrikpt 319
Cdd:PRK08565   580 LKKGE------------LTFDDLVKMGVIEYLDAEEEENAYVALDPEDL------------------------------- 616

                          330       340
                   ....*....|....*....|....*.
gi 1789848679  320 fSSSHtfTHCEIHPSMILGVAASIIP 345
Cdd:PRK08565   617 -TPEH--THLEIWPPAILGITASIIP 639
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-124 1.23e-49

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: 177.76  E-value: 1.23e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679   1 KLTKDIYNYMQRCVENDKEFNLTLAVKSQTITDGLRYSLATGNWGeQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNT-P 79
Cdd:cd00653   258 RLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWG-SKRFLMQRSGLSQVLDRLNPLSELSHKRRISSlG 336

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1789848679  80 IGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCIS 124
Cdd:cd00653   337 LFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-144 1.45e-37

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 140.47  E-value: 1.45e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679   1 KLTKDIYNYMQRCVENDKEFNLTLAVKSQTITDGLRYSLATGNWgeqkkaMSSRAGVSQVLNRYTYSSTLSHLRRTNTPI 80
Cdd:PRK09606  355 RLARDVKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATLSHLRRVVSPL 428

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1789848679  81 GRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTPSEPILYFLEEWGMEPL 144
Cdd:PRK09606  429 SRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVEPE 492
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 156-345 5.70e-36

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 137.40  E-value: 5.70e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679 156 TRVFVNGVWVGTHREPAHLVDTMRNLRRRGDISPEVSIIRDIREKEFKIFTDAGRVYRPLFIVDDdpdsegrGQLKLKKE 235
Cdd:PRK07225    5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLTEE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679 236 HVHKLINAEyddfgdepeslsYSWSSLVSEGIVEYVDAEEEETIMIAMTPEDLetsrstlsaseqknmqleeqevdpakr 315
Cdd:PRK07225   78 HIEKLKNGE------------LTFDDLVKQGVIEYLDAEEEENAYIAVYEEDL--------------------------- 118

                         170       180       190
                  ....*....|....*....|....*....|
gi 1789848679 316 ikptfSSSHtfTHCEIHPSMILGVAASIIP 345
Cdd:PRK07225  119 -----TEEH--THLEIDPSLILGIGAGMIP 141
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 158-219 1.04e-35

RNA polymerase Rpb2, domain 4; 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 4, is also known as the external 2 domain.


Pssm-ID: 428012 [Multi-domain]  Cd Length: 62  Bit Score: 124.02  E-value: 1.04e-35
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1789848679 158 VFVNGVWVGTHREPAHLVDTMRNLRRRGDISPEVSIIRDIREKEFKIFTDAGRVYRPLFIVD 219
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 59-121 4.98e-31

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: 111.85  E-value: 4.98e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1789848679  59 QVLNRYTYSSTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMS 121
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYA 66
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 259-333 6.17e-23

RNA polymerase Rpb2, domain 5; 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 5, is also known as the external 2 domain.


Pssm-ID: 428013 [Multi-domain]  Cd Length: 53  Bit Score: 89.91  E-value: 6.17e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1789848679 259 WSSLVSEGIVEYVDAEEEETIMIAMTPEDLETSrstlsaseqknmqleeqevdpaKRIKPTFSSSHTFTHCEIHP 333
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEES----------------------SREEREGPYAHTYTHCEIHP 53
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 54-345 5.22e-19

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: 88.24  E-value: 5.22e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679   54 RAGVSQVLNRYTYSSTLSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISv 125
Cdd:COG0085    368 SSQLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN- 442

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679  126 gtpsepilyfleewgmepledyvpsnspdstrvfvngvwvgthrepahlvdtmrnlrrrgdispevsiirdirekEFkif 205
Cdd:COG0085    443 ---------------------------------------------------------------------------EY--- 444

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679  206 tdaGRVYRPLFIVDDdpdseGRgqlklkkehvhklinaeyddfgdepeslsyswsslVSEGIvEYVDAEEEETIMIAMTP 285
Cdd:COG0085    445 ---GFIETPYRKVEN-----GK-----------------------------------VTDEI-EYLTADEEENYYIAQAN 480

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679  286 EDLEtsrstlsaseqKNMQLEEQEVDPAKRIKPTFSSSHTFTHCEIHPSMILGVAASIIP 345
Cdd:COG0085    481 APLD-----------EDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIP 529
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
57-121 1.22e-06

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 50.31  E-value: 1.22e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789848679   57 VSQVLNRYTYSSTLSHLRRTNTpIGRDGKIA-----KPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMS 121
Cdd:PRK09603   525 LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLINTLSTFT 593
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
57-124 1.90e-06

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 50.01  E-value: 1.90e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1789848679   57 VSQVLNRYTYSSTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCIS 124
Cdd:PRK14844   532 LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARIN 603
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 57-125 3.75e-05

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 45.47  E-value: 3.75e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1789848679   57 VSQVLNRYTYSSTLSHLRRTNT--PIGRDG-KIAKP-RQLHNTHWGLVCPAETPEGQACGLVKnlSLMSCISV 125
Cdd:CHL00207   366 LSQYMDQTNPLSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIG--SLATNARI 436
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 90-118 1.27e-04

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 43.94  E-value: 1.27e-04
                           10        20
                   ....*....|....*....|....*....
gi 1789848679   90 RQLHNTHWGLVCPAETPEGQACGLVKNLS 118
Cdd:PRK00405   469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
rpoB CHL00001
RNA polymerase beta subunit
 58-118 1.42e-03

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 40.66  E-value: 1.42e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1789848679   58 SQVLNRYTYSSTLSHLRRTNT--PIGRDGKIA--KPRQLHNTHWGLVCPAETPEGQACGLVKNLS 118
Cdd:CHL00001   375 SQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIGSLA 439
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-32 2.66e-03

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: 39.29  E-value: 2.66e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1789848679   1 KLTKDIYNYMQRCVENDKEFNLTLAVKSQTIT 32
Cdd:pfam04563 364 KLVRDVRERLQKVLGSPDDLMLQLLVNAKPIT 395
 
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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