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Conserved domains on  [gi|2277734242|gb|UUA86280|]
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RNA polymerase II second largest subunit, partial [Tuber excelsum-reticulatum]

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

 Zoom to residue level

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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;
1-347 3.80e-91

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: 294.56  E-value: 3.80e-91
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242    1 FRTLWRKLTKDVYKYLEKCVETSKDFNLTLAVKSNTITNGLKYSLATGNWGeqkkaaSSKAGVSQVLNRYTFASTLSHLR 80
Cdd:PRK08565   346 FRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLR 419

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242   81 RTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSYITIGTPGYPLVDFLSSNDMELLEEYEPQRSPN 160
Cdd:PRK08565   420 RVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYIS 499

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242  161 ATKVFVNGVWVGTHRDPLMLAKVVQDVRRQGVVSHEVSV--IRDIRDREFKIFTDAGRVCRPLFVIDNdprserrGQLVL 238
Cdd:PRK08565   500 WSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKL 572

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242  239 QKEHIEKLEddhqldiEDRFGWEGLLFAGAVEYLDAEEEEGVMIVMTPEDLdlsrqvqlgyeieqetdqakrvkapinst 318
Cdd:PRK08565   573 TREHVEKLK-------KGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDL----------------------------- 616

                          330       340
                   ....*....|....*....|....*....
gi 2277734242  319 THTWTHCEIHPSMILGICASIIPFPDHNQ 347
Cdd:PRK08565   617 TPEHTHLEIWPPAILGITASIIPYPEHNQ 645
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-347 3.80e-91

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 294.56  E-value: 3.80e-91
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242    1 FRTLWRKLTKDVYKYLEKCVETSKDFNLTLAVKSNTITNGLKYSLATGNWGeqkkaaSSKAGVSQVLNRYTFASTLSHLR 80
Cdd:PRK08565   346 FRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLR 419

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242   81 RTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSYITIGTPGYPLVDFLSSNDMELLEEYEPQRSPN 160
Cdd:PRK08565   420 RVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYIS 499

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242  161 ATKVFVNGVWVGTHRDPLMLAKVVQDVRRQGVVSHEVSV--IRDIRDREFKIFTDAGRVCRPLFVIDNdprserrGQLVL 238
Cdd:PRK08565   500 WSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKL 572

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242  239 QKEHIEKLEddhqldiEDRFGWEGLLFAGAVEYLDAEEEEGVMIVMTPEDLdlsrqvqlgyeieqetdqakrvkapinst 318
Cdd:PRK08565   573 TREHVEKLK-------KGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDL----------------------------- 616

                          330       340
                   ....*....|....*....|....*....
gi 2277734242  319 THTWTHCEIHPSMILGICASIIPFPDHNQ 347
Cdd:PRK08565   617 TPEHTHLEIWPPAILGITASIIPYPEHNQ 645
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-347 1.22e-53

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: 188.93  E-value: 1.22e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242   1 FRTLWRKLTKDVYKYLEKCVETSKDFNLTLAVKSNTITNGLKYSLATGNWGeQKKAASSKAGVSQVLNRYTFASTLSHLR 80
Cdd:cd00653   252 FRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWG-SKRFLMQRSGLSQVLDRLNPLSELSHKR 330

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242  81 RTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSYITigtpgyplvdflssndmelleeyepqrsp 159
Cdd:cd00653   331 RISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS----------------------------- 381

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242 160 natkvfvngvwvgthrdplmlakvvqdvrrqgvvshevsvirdirdrefkiftdaGRVCRPLFVIDNDprserrgqlvlq 239
Cdd:cd00653   382 -------------------------------------------------------GRIERPYRIVEKE------------ 394

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242 240 kehiekleddhqldiedrfgwegllfagaveyldaeeeegvmivmtpedldlsrqvqlgyeieqetdqakrvkapinstt 319
Cdd:cd00653       --------------------------------------------------------------------------------

                         330       340
                  ....*....|....*....|....*...
gi 2277734242 320 htWTHCEIHPSMILGICASIIPFPDHNQ 347
Cdd:cd00653   395 --VTHIEISPSQILSVAASLIPFPEHNQ 420
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 65-128 3.70e-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: 112.23  E-value: 3.70e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2277734242  65 QVLNRYTFASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSY 128
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-347 2.92e-21

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: 95.18  E-value: 2.92e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242    1 FRTLWRKLTKDV-YKylekcVETSKDFNLTLA--VKSNTITNGLKYSLATGnwgeqkkaasskaGVSQVLNRYTFASTLS 77
Cdd:COG0085    324 FRVGLSRMERVVrER-----MTTQDVEAITPQslINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELT 385

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242   78 HLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMSYITigtpgyplvdflssndmel 149
Cdd:COG0085    386 HKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN------------------- 442

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242  150 leEYepqrspnatkvfvngvwvgthrdplmlakvvqdvrrqgvvshevsvirdirdrefkiftdaGRVCRPLFVIDNdpr 229
Cdd:COG0085    443 --EY-------------------------------------------------------------GFIETPYRKVEN--- 456

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242  230 serrGqlvlqkehieKLEDDhqldiedrfgwegllfagaVEYLDAEEEEGVMIVMTPEDLD-----LSRQVQLGYEIEQE 304
Cdd:COG0085    457 ----G----------KVTDE-------------------IEYLTADEEENYYIAQANAPLDedgnfLEERVLVRYRGEEV 503

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|...
gi 2277734242  305 TDQAKRVkapinstthtwTHCEIHPSMILGICASIIPFPDHNQ 347
Cdd:COG0085    504 LVPPEEV-----------DYMDVSPKQIVSVATSLIPFLEHDD 535
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-347 3.80e-91

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 294.56  E-value: 3.80e-91
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242    1 FRTLWRKLTKDVYKYLEKCVETSKDFNLTLAVKSNTITNGLKYSLATGNWGeqkkaaSSKAGVSQVLNRYTFASTLSHLR 80
Cdd:PRK08565   346 FRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLR 419

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242   81 RTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSYITIGTPGYPLVDFLSSNDMELLEEYEPQRSPN 160
Cdd:PRK08565   420 RVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYIS 499

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242  161 ATKVFVNGVWVGTHRDPLMLAKVVQDVRRQGVVSHEVSV--IRDIRDREFKIFTDAGRVCRPLFVIDNdprserrGQLVL 238
Cdd:PRK08565   500 WSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPKL 572

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242  239 QKEHIEKLEddhqldiEDRFGWEGLLFAGAVEYLDAEEEEGVMIVMTPEDLdlsrqvqlgyeieqetdqakrvkapinst 318
Cdd:PRK08565   573 TREHVEKLK-------KGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDL----------------------------- 616

                          330       340
                   ....*....|....*....|....*....
gi 2277734242  319 THTWTHCEIHPSMILGICASIIPFPDHNQ 347
Cdd:PRK08565   617 TPEHTHLEIWPPAILGITASIIPYPEHNQ 645
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-347 1.22e-53

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: 188.93  E-value: 1.22e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242   1 FRTLWRKLTKDVYKYLEKCVETSKDFNLTLAVKSNTITNGLKYSLATGNWGeQKKAASSKAGVSQVLNRYTFASTLSHLR 80
Cdd:cd00653   252 FRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWG-SKRFLMQRSGLSQVLDRLNPLSELSHKR 330

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242  81 RTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSYITigtpgyplvdflssndmelleeyepqrsp 159
Cdd:cd00653   331 RISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS----------------------------- 381

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242 160 natkvfvngvwvgthrdplmlakvvqdvrrqgvvshevsvirdirdrefkiftdaGRVCRPLFVIDNDprserrgqlvlq 239
Cdd:cd00653   382 -------------------------------------------------------GRIERPYRIVEKE------------ 394

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242 240 kehiekleddhqldiedrfgwegllfagaveyldaeeeegvmivmtpedldlsrqvqlgyeieqetdqakrvkapinstt 319
Cdd:cd00653       --------------------------------------------------------------------------------

                         330       340
                  ....*....|....*....|....*...
gi 2277734242 320 htWTHCEIHPSMILGICASIIPFPDHNQ 347
Cdd:cd00653   395 --VTHIEISPSQILSVAASLIPFPEHNQ 420
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 162-347 1.06e-40

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 150.50  E-value: 1.06e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242 162 TKVFVNGVWVGTHRDPLMLAKVVQDVRRQGVVSHEVSVIRDIRDREFKIFTDAGRVCRPLFVIDNdprserrGQLVLQKE 241
Cdd:PRK07225    5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLTEE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242 242 HIEKLEDDhqlDIEdrfgWEGLLFAGAVEYLDAEEEEGVMIVMTPEDLdlsrqvqlgyeieqetdqakrvkapinstTHT 321
Cdd:PRK07225   78 HIEKLKNG---ELT----FDDLVKQGVIEYLDAEEEENAYIAVYEEDL-----------------------------TEE 121

                         170       180
                  ....*....|....*....|....*.
gi 2277734242 322 WTHCEIHPSMILGICASIIPFPDHNQ 347
Cdd:PRK07225  122 HTHLEIDPSLILGIGAGMIPYPEHNA 147
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-152 3.09e-34

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 131.23  E-value: 3.09e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242   1 FRTLWRKLTKDVyKY-LEKCVETSKDFNLTLAVKSNTITNGLKYSLATGNWgeqkkaASSKAGVSQVLNRYTFASTLSHL 79
Cdd:PRK09606  349 FRVAFNRLARDV-KYqLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATLSHL 421

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2277734242  80 RRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSYITIGTPGYPLVDFLSSNDMELLEE 152
Cdd:PRK09606  422 RRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVEPERG 494
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 65-128 3.70e-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: 112.23  E-value: 3.70e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2277734242  65 QVLNRYTFASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSY 128
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 164-225 3.91e-30

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: 109.38  E-value: 3.91e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2277734242 164 VFVNGVWVGTHRDPLMLAKVVQDVRRQGVVSHEVSVIRDIRDREFKIFTDAGRVCRPLFVID 225
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-347 2.92e-21

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: 95.18  E-value: 2.92e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242    1 FRTLWRKLTKDV-YKylekcVETSKDFNLTLA--VKSNTITNGLKYSLATGnwgeqkkaasskaGVSQVLNRYTFASTLS 77
Cdd:COG0085    324 FRVGLSRMERVVrER-----MTTQDVEAITPQslINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELT 385

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242   78 HLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMSYITigtpgyplvdflssndmel 149
Cdd:COG0085    386 HKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN------------------- 442

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242  150 leEYepqrspnatkvfvngvwvgthrdplmlakvvqdvrrqgvvshevsvirdirdrefkiftdaGRVCRPLFVIDNdpr 229
Cdd:COG0085    443 --EY-------------------------------------------------------------GFIETPYRKVEN--- 456

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242  230 serrGqlvlqkehieKLEDDhqldiedrfgwegllfagaVEYLDAEEEEGVMIVMTPEDLD-----LSRQVQLGYEIEQE 304
Cdd:COG0085    457 ----G----------KVTDE-------------------IEYLTADEEENYYIAQANAPLDedgnfLEERVLVRYRGEEV 503

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|...
gi 2277734242  305 TDQAKRVkapinstthtwTHCEIHPSMILGICASIIPFPDHNQ 347
Cdd:COG0085    504 LVPPEEV-----------DYMDVSPKQIVSVATSLIPFLEHDD 535
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 260-329 5.78e-20

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: 82.20  E-value: 5.78e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242 260 WEGLLFAGAVEYLDAEEEEGVMIVMTPEDLDLSRQVQLGYeieqetdqakrvkapinSTTHTWTHCEIHP 329
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREEREG-----------------PYAHTYTHCEIHP 53
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
63-150 1.83e-07

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 53.09  E-value: 1.83e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242   63 VSQVLNRYTFASTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSYIT----IGTP 134
Cdd:PRK14844   532 LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINkygfIESP 611

                           90
                   ....*....|....*.
gi 2277734242  135 GYPLVDFLSSNDMELL 150
Cdd:PRK14844   612 YRKVVNRVVTDQIEYL 627
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-39 5.96e-07

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: 50.84  E-value: 5.96e-07
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 2277734242   1 FRTLWRKLTKDVYKYLEKCVETSKDFNLTLAVKSNTITN 39
Cdd:pfam04563 358 FRVLFKKLVRDVRERLQKVLGSPDDLMLQLLVNAKPITS 396
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
63-129 7.88e-07

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 51.08  E-value: 7.88e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2277734242   63 VSQVLNRYTFASTLSHLRRTNTpIGRDGKIA-----KPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSYI 129
Cdd:PRK09603   525 LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRV 595
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 63-146 1.68e-05

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 46.62  E-value: 1.68e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2277734242   63 VSQVLNRYTFASTLSHLRRTNT--PIGRDG-KIAKP-RQLHNTHWGLVCPAETPEGQACGLVKnlSLMSYITIGTPGYPL 138
Cdd:CHL00207   366 LSQYMDQTNPLSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIG--SLATNARINKFGFIE 443


                   ....*...
gi 2277734242  139 VDFLSSND 146
Cdd:CHL00207   444 TPFYKVIN 451
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 96-124 1.13e-04

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 43.94  E-value: 1.13e-04
                           10        20
                   ....*....|....*....|....*....
gi 2277734242   96 RQLHNTHWGLVCPAETPEGQACGLVKNLS 124
Cdd:PRK00405   469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
rpoB CHL00001
RNA polymerase beta subunit
 64-136 3.96e-04

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 42.20  E-value: 3.96e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2277734242   64 SQVLNRYTFASTLSHLRRTNT--PIGRDGKIA--KPRQLHNTHWGLVCPAETPEGQACGLVKnlSLMSYITIGTPGY 136
Cdd:CHL00001   375 SQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIG--SLAIHARIGHWGS 449
 
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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