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Conserved domains on  [gi|89274928|gb|ABD65905|]
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RNA polymerase II second largest subunit, partial [Trechispora alnicola]

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;
1-360 6.81e-97

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: 310.74  E-value: 6.81e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928     1 RDHFGKKRLDLAGPLLSSLFRLLFKKLTRDVSRHLQKCVETNKEFHLNAAVKHNTITNGLKYSLATGNWGdqkkflSAKA 80
Cdd:PRK08565  327 KDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRT 400

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928    81 GVSQVLNRYTFASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMACISVGSLSAPIIEF 160
Cdd:PRK08565  401 GVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEI 480

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928   161 LEEWGLERMED---HNHSDATKVFVNGVWMGVHRDPAGLVKTIKKLRRKDDISAEVSV--VRDIRERELRIYTDAGRVCR 235
Cdd:PRK08565  481 LYELGVVPVEEareEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRR 560

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928   236 PLFIVEDQQLLITKDHIKWLtqvfkdgdepdDSGSMppyKWERLIKEGVVELLDAEEEETVMICMTPEDLTnsrlqkmgh 315
Cdd:PRK08565  561 PLIVVENGKPKLTREHVEKL-----------KKGEL---TFDDLVKMGVIEYLDAEEEENAYVALDPEDLT--------- 617

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*
gi 89274928   316 dihandgefdpaarlkatlTAHtwTHCEIHPSMILGICASIIPFP 360
Cdd:PRK08565  618 -------------------PEH--THLEIWPPAILGITASIIPYP 641
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-360 6.81e-97

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 310.74  E-value: 6.81e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928     1 RDHFGKKRLDLAGPLLSSLFRLLFKKLTRDVSRHLQKCVETNKEFHLNAAVKHNTITNGLKYSLATGNWGdqkkflSAKA 80
Cdd:PRK08565  327 KDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRT 400

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928    81 GVSQVLNRYTFASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMACISVGSLSAPIIEF 160
Cdd:PRK08565  401 GVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEI 480

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928   161 LEEWGLERMED---HNHSDATKVFVNGVWMGVHRDPAGLVKTIKKLRRKDDISAEVSV--VRDIRERELRIYTDAGRVCR 235
Cdd:PRK08565  481 LYELGVVPVEEareEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRR 560

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928   236 PLFIVEDQQLLITKDHIKWLtqvfkdgdepdDSGSMppyKWERLIKEGVVELLDAEEEETVMICMTPEDLTnsrlqkmgh 315
Cdd:PRK08565  561 PLIVVENGKPKLTREHVEKL-----------KKGEL---TFDDLVKMGVIEYLDAEEEENAYVALDPEDLT--------- 617

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*
gi 89274928   316 dihandgefdpaarlkatlTAHtwTHCEIHPSMILGICASIIPFP 360
Cdd:PRK08565  618 -------------------PEH--THLEIWPPAILGITASIIPYP 641
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-158 3.65e-56

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: 196.64  E-value: 3.65e-56
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928   1 RDHFGKKRLDLAGPLLSSLFRLLFKKLTRDVSRHLQKCVETNKEFHLNAAVKHNTITNGLKYSLATGNWGDqKKFLSAKA 80
Cdd:cd00653 233 IDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGS-KRFLMQRS 311

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 89274928  81 GVSQVLNRYTFASTLSHLRRCNT-PLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMACISvGSLSAPII 158
Cdd:cd00653 312 GLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-GRIERPYR 389
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 180-241 1.35e-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: 1.35e-35
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 89274928   180 VFVNGVWMGVHRDPAGLVKTIKKLRRKDDISAEVSVVRDIRERELRIYTDAGRVCRPLFIVE 241
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 2-360 1.08e-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: 90.55  E-value: 1.08e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928    2 DHFGKKRLDLAGPLLSSLFRLLFKKLTRDVSRHLQKcvETNKEFHLNAAVKHNTITNGLKYSLATGnwgdqkkflsakaG 81
Cdd:COG0085  306 DHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTT--QDVEAITPQSLINIRPVVAAIKEFFGSS-------------Q 370

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928   82 VSQVLNRYTFASTLSHLRRCNT----PLGREgkiaKP----RQLHNTHWGMVCPAETPEGQACGLVKNLALMACISvgsl 153
Cdd:COG0085  371 LSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---- 442

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928  154 sapiiEFleewglermedhnhsdatkvfvngvwmgvhrdpaglvktikklrrkddisaevsvvrdirerelriytdaGRV 233
Cdd:COG0085  443 -----EY----------------------------------------------------------------------GFI 447

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928  234 CRPLFIVEDQQLliTKDhikwltqvfkdgdepddsgsmppykwerlikegvVELLDAEEEETVMICMTPEDLTnsrlqkm 313
Cdd:COG0085  448 ETPYRKVENGKV--TDE----------------------------------IEYLTADEEENYYIAQANAPLD------- 484

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|...
gi 89274928  314 ghdihaNDGEFD----PAARLKATLTAHT--WTHCEIHPSMILGICASIIPFP 360
Cdd:COG0085  485 ------EDGNFLeervLVRYRGEEVLVPPeeVDYMDVSPKQIVSVATSLIPFL 531
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-360 6.81e-97

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 310.74  E-value: 6.81e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928     1 RDHFGKKRLDLAGPLLSSLFRLLFKKLTRDVSRHLQKCVETNKEFHLNAAVKHNTITNGLKYSLATGNWGdqkkflSAKA 80
Cdd:PRK08565  327 KDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRT 400

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928    81 GVSQVLNRYTFASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMACISVGSLSAPIIEF 160
Cdd:PRK08565  401 GVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEI 480

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928   161 LEEWGLERMED---HNHSDATKVFVNGVWMGVHRDPAGLVKTIKKLRRKDDISAEVSV--VRDIRERELRIYTDAGRVCR 235
Cdd:PRK08565  481 LYELGVVPVEEareEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRR 560

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928   236 PLFIVEDQQLLITKDHIKWLtqvfkdgdepdDSGSMppyKWERLIKEGVVELLDAEEEETVMICMTPEDLTnsrlqkmgh 315
Cdd:PRK08565  561 PLIVVENGKPKLTREHVEKL-----------KKGEL---TFDDLVKMGVIEYLDAEEEENAYVALDPEDLT--------- 617

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*
gi 89274928   316 dihandgefdpaarlkatlTAHtwTHCEIHPSMILGICASIIPFP 360
Cdd:PRK08565  618 -------------------PEH--THLEIWPPAILGITASIIPYP 641
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-158 3.65e-56

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: 196.64  E-value: 3.65e-56
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928   1 RDHFGKKRLDLAGPLLSSLFRLLFKKLTRDVSRHLQKCVETNKEFHLNAAVKHNTITNGLKYSLATGNWGDqKKFLSAKA 80
Cdd:cd00653 233 IDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWGS-KRFLMQRS 311

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 89274928  81 GVSQVLNRYTFASTLSHLRRCNT-PLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMACISvGSLSAPII 158
Cdd:cd00653 312 GLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-GRIERPYR 389
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-169 7.98e-44

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 157.80  E-value: 7.98e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928    1 RDHFGKKRLDLAGPLLSSLFRLLFKKLTRDVSRHLQKCVETNKEFHLNAAVKHNTITNGLKYSLATGNWgdqkkfLSAKA 80
Cdd:PRK09606 330 KDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRT 403

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928   81 GVSQVLNRYTFASTLSHLRRCNTPLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMACISVGSLSAPIIEF 160
Cdd:PRK09606 404 GVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEI 483


                 ....*....
gi 89274928  161 LEEWGLERM 169
Cdd:PRK09606 484 LKELGVEPE 492
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 178-361 2.18e-40

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 150.11  E-value: 2.18e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928  178 TKVFVNGVWMGVHRDPAGLVKTIKKLRRKDDISAEVSVVRDIRERELRIYTDAGRVCRPLFIVEDQQLLITKDHIKWLtq 257
Cdd:PRK07225   5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKL-- 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928  258 vfKDGDEpddsgsmppyKWERLIKEGVVELLDAEEEETVMICMTPEDLTnsrlqkmghdihandgefdpaarlkatlTAH 337
Cdd:PRK07225  83 --KNGEL----------TFDDLVKQGVIEYLDAEEEENAYIAVYEEDLT----------------------------EEH 122

                        170       180
                 ....*....|....*....|....
gi 89274928  338 twTHCEIHPSMILGICASIIPFPD 361
Cdd:PRK07225 123 --THLEIDPSLILGIGAGMIPYPE 144
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 180-241 1.35e-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: 1.35e-35
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 89274928   180 VFVNGVWMGVHRDPAGLVKTIKKLRRKDDISAEVSVVRDIRERELRIYTDAGRVCRPLFIVE 241
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 84-146 6.34e-32

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: 114.55  E-value: 6.34e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 89274928    84 QVLNRYTFASTLSHLRRCNTP---LGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMA 146
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPrggLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYA 66
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 276-346 7.01e-24

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: 92.60  E-value: 7.01e-24
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 89274928   276 WERLIKEGVVELLDAEEEETVMICMTPEDLTNS-RLQKMGHdihandgefdpaarlkatlTAHTWTHCEIHP 346
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESsREEREGP-------------------YAHTYTHCEIHP 53
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 2-360 1.08e-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: 90.55  E-value: 1.08e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928    2 DHFGKKRLDLAGPLLSSLFRLLFKKLTRDVSRHLQKcvETNKEFHLNAAVKHNTITNGLKYSLATGnwgdqkkflsakaG 81
Cdd:COG0085  306 DHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTT--QDVEAITPQSLINIRPVVAAIKEFFGSS-------------Q 370

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928   82 VSQVLNRYTFASTLSHLRRCNT----PLGREgkiaKP----RQLHNTHWGMVCPAETPEGQACGLVKNLALMACISvgsl 153
Cdd:COG0085  371 LSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---- 442

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928  154 sapiiEFleewglermedhnhsdatkvfvngvwmgvhrdpaglvktikklrrkddisaevsvvrdirerelriytdaGRV 233
Cdd:COG0085  443 -----EY----------------------------------------------------------------------GFI 447

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928  234 CRPLFIVEDQQLliTKDhikwltqvfkdgdepddsgsmppykwerlikegvVELLDAEEEETVMICMTPEDLTnsrlqkm 313
Cdd:COG0085  448 ETPYRKVENGKV--TDE----------------------------------IEYLTADEEENYYIAQANAPLD------- 484

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|...
gi 89274928  314 ghdihaNDGEFD----PAARLKATLTAHT--WTHCEIHPSMILGICASIIPFP 360
Cdd:COG0085  485 ------EDGNFLeervLVRYRGEEVLVPPeeVDYMDVSPKQIVSVATSLIPFL 531
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-58 2.50e-10

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: 61.24  E-value: 2.50e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 89274928     1 RDHFGKKRLDLAGPLLSSLFRLLFKKLTRDVSRHLQKCVETNKEFHLNAAVKHNTITN 58
Cdd:pfam04563 339 RDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLMLQLLVNAKPITS 396
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
82-156 8.20e-08

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 54.24  E-value: 8.20e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928    82 VSQVLNRYTFASTLSHLRRCNT----PLGREGKIAKPRQLHNTHWGMVCPAETPEGQACGLVKNLALMACIS-VGSLSAP 156
Cdd:PRK14844  532 LSQFMDQTNPLSEITHKRRLSAlgpgGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINkYGFIESP 611
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
82-156 3.24e-07

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 52.62  E-value: 3.24e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928    82 VSQVLNRYTFASTLSHLRRCNTpLGrEGKIAK------PRQLHNTHWGMVCPAETPEGQACGLVKNLALMACIS-VGSLS 154
Cdd:PRK09603  525 LSQFMDQTNPLSEVTHKRRLSA-LG-EGGLVKdrvgfeARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNdLGFIE 602


                  ..
gi 89274928   155 AP 156
Cdd:PRK09603  603 AP 604
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 2-143 1.32e-06

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 50.47  E-value: 1.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928     2 DHFGKKRLDLAGPLLSSLFRLLFKKLTRDVSRHLQKCVETNKEfhlnaavKHNTITNGLKYSLAtgnwgdqKKFLSAKAg 81
Cdd:CHL00207  301 DHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICDIDSLS-------KFNLINPKPLIALI-------REFFGSSQ- 365

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 89274928    82 VSQVLNRYTFASTLSHLRRCNTpLGREG----KIAKP-RQLHNTHWGMVCPAETPEGQACGLVKNLA 143
Cdd:CHL00207  366 LSQYMDQTNPLSELTHKRRISI-LGPGGldkdRISFAvRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
rpoB CHL00001
RNA polymerase beta subunit
 83-169 2.42e-06

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 49.52  E-value: 2.42e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89274928    83 SQVLNRYTFASTLSHLRRCNT--PLGREGKIA--KPRQLHNTHWGMVCPAETPEGQACGLVKNLALMACI-SVGSLSAPI 157
Cdd:CHL00001  375 SQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIgHWGSLESPF 454

                          90
                  ....*....|..
gi 89274928   158 IEFLEEWGLERM 169
Cdd:CHL00001  455 YEISERSKEERM 466
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 115-148 4.94e-05

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 45.48  E-value: 4.94e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 89274928   115 RQLHNTHWGMVCPAETPEGQACGLVKNLALMACI 148
Cdd:PRK00405  469 RDVHPTHYGRICPIETPEGPNIGLINSLATYARV 502
 
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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