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Conserved domains on  [gi|170799393|gb|ACB38488|]
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RNA polymerase II subunit, partial [Yamadazyma scolyti]

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;
1-352 5.46e-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: 305.34  E-value: 5.46e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393    1 LFRILF*KLTRDIYNYMQRCVENDKVFNLTLAVKSQTITDGLRYSLATGNWGeqkkamSSRAGVSQVLNRYTYSSTLSHL 80
Cdd:PRK08565  345 LFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHL 418

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393   81 RRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGSSSEPILVFLEEWGLEPLEDYSPATSP 160
Cdd:PRK08565  419 RRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYI 498

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393  161 DTTRVFVNGVWVGTHRDPASLVDTIRSLRRKGDISPEVSI--IRDIREKEFKIFTDAGRVYRPLFIVDDnpssetkGELL 238
Cdd:PRK08565  499 SWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPK 571

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393  239 LNKTHIKKLMDSEYDdynyddeqetygWSSLVRDGIIEYVDAEEEETIMIAMTPEDLeaskssLSETqqktiqmeeqerd 318
Cdd:PRK08565  572 LTREHVEKLKKGELT------------FDDLVKMGVIEYLDAEEEENAYVALDPEDL------TPEH------------- 620

                         330       340       350
                  ....*....|....*....|....*....|....
gi 170799393  319 pakrikptysgnlhtfTHCEIHPSMILGVAASII 352
Cdd:PRK08565  621 ----------------THLEIWPPAILGITASII 638
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-352 5.46e-95

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 305.34  E-value: 5.46e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393    1 LFRILF*KLTRDIYNYMQRCVENDKVFNLTLAVKSQTITDGLRYSLATGNWGeqkkamSSRAGVSQVLNRYTYSSTLSHL 80
Cdd:PRK08565  345 LFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHL 418

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393   81 RRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGSSSEPILVFLEEWGLEPLEDYSPATSP 160
Cdd:PRK08565  419 RRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYI 498

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393  161 DTTRVFVNGVWVGTHRDPASLVDTIRSLRRKGDISPEVSI--IRDIREKEFKIFTDAGRVYRPLFIVDDnpssetkGELL 238
Cdd:PRK08565  499 SWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPK 571

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393  239 LNKTHIKKLMDSEYDdynyddeqetygWSSLVRDGIIEYVDAEEEETIMIAMTPEDLeaskssLSETqqktiqmeeqerd 318
Cdd:PRK08565  572 LTREHVEKLKKGELT------------FDDLVKMGVIEYLDAEEEENAYVALDPEDL------TPEH------------- 620

                         330       340       350
                  ....*....|....*....|....*....|....
gi 170799393  319 pakrikptysgnlhtfTHCEIHPSMILGVAASII 352
Cdd:PRK08565  621 ----------------THLEIWPPAILGITASII 638
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-131 2.87e-52

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: 185.46  E-value: 2.87e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393   1 LFRILF*KLTRDIYNYMQRCVENDKVFNLTLAVKSQTITDGLRYSLATGNWGeQKKAMSSRAGVSQVLNRYTYSSTLSHL 80
Cdd:cd00653  251 LFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWG-SKRFLMQRSGLSQVLDRLNPLSELSHK 329

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 170799393  81 RRTNT-PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCIS 131
Cdd:cd00653  330 RRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 165-226 1.21e-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: 1.21e-35
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 170799393  165 VFVNGVWVGTHRDPASLVDTIRSLRRKGDISPEVSIIRDIREKEFKIFTDAGRVYRPLFIVD 226
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-352 1.71e-17

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: 84.01  E-value: 1.71e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393    1 LFRILF*KLTRDIYNYMqrcvENDKVFNLTLA--VKSQTITDGLRYSLATGnwgeqkkamssraGVSQVLNRYTYSSTLS 78
Cdd:COG0085   323 QFRVGLSRMERVVRERM----TTQDVEAITPQslINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELT 385

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393   79 HLRRTNT----PIGRDgklaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISvgsssepilvfleewglep 150
Cdd:COG0085   386 HKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN------------------- 442

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393  151 ledyspatspdttrvfvngvwvgthrdpaslvdtirslrrkgdispevsiirdirekEFkiftdaGRVYRPLFIVDDNps 230
Cdd:COG0085   443 ---------------------------------------------------------EY------GFIETPYRKVENG-- 457

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393  231 setkgelllnkthikklmdseyddynyddeqetygwssLVRDGiIEYVDAEEEETIMIAMTPEDLEASKSSLSETQQKTI 310
Cdd:COG0085   458 --------------------------------------KVTDE-IEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRY 498

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|..
gi 170799393  311 QMEEQERDPAKrikptysgnlhtFTHCEIHPSMILGVAASII 352
Cdd:COG0085   499 RGEEVLVPPEE------------VDYMDVSPKQIVSVATSLI 528
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-352 5.46e-95

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 305.34  E-value: 5.46e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393    1 LFRILF*KLTRDIYNYMQRCVENDKVFNLTLAVKSQTITDGLRYSLATGNWGeqkkamSSRAGVSQVLNRYTYSSTLSHL 80
Cdd:PRK08565  345 LFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHL 418

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393   81 RRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGSSSEPILVFLEEWGLEPLEDYSPATSP 160
Cdd:PRK08565  419 RRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYI 498

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393  161 DTTRVFVNGVWVGTHRDPASLVDTIRSLRRKGDISPEVSI--IRDIREKEFKIFTDAGRVYRPLFIVDDnpssetkGELL 238
Cdd:PRK08565  499 SWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVEN-------GKPK 571

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393  239 LNKTHIKKLMDSEYDdynyddeqetygWSSLVRDGIIEYVDAEEEETIMIAMTPEDLeaskssLSETqqktiqmeeqerd 318
Cdd:PRK08565  572 LTREHVEKLKKGELT------------FDDLVKMGVIEYLDAEEEENAYVALDPEDL------TPEH------------- 620

                         330       340       350
                  ....*....|....*....|....*....|....
gi 170799393  319 pakrikptysgnlhtfTHCEIHPSMILGVAASII 352
Cdd:PRK08565  621 ----------------THLEIWPPAILGITASII 638
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-131 2.87e-52

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: 185.46  E-value: 2.87e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393   1 LFRILF*KLTRDIYNYMQRCVENDKVFNLTLAVKSQTITDGLRYSLATGNWGeQKKAMSSRAGVSQVLNRYTYSSTLSHL 80
Cdd:cd00653  251 LFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNWG-SKRFLMQRSGLSQVLDRLNPLSELSHK 329

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 170799393  81 RRTNT-PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCIS 131
Cdd:cd00653  330 RRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS 381
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-151 1.32e-40

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 148.94  E-value: 1.32e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393   1 LFRILF*KLTRDIYNYMQRCVENDKVFNLTLAVKSQTITDGLRYSLATGNWgeqkkaMSSRAGVSQVLNRYTYSSTLSHL 80
Cdd:PRK09606 348 LFRVAFNRLARDVKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATLSHL 421

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 170799393  81 RRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGSSSEPILVFLEEWGLEPL 151
Cdd:PRK09606 422 RRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVEPE 492
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 163-352 2.97e-36

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 138.17  E-value: 2.97e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393 163 TRVFVNGVWVGTHRDPASLVDTIRSLRRKGDISPEVSIIRDIREKEFKIFTDAGRVYRPLFIVDDnpssetkGELLLNKT 242
Cdd:PRK07225   5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLTEE 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393 243 HIKKLMDSEYDdynyddeqetygWSSLVRDGIIEYVDAEEEETIMIAMTPEDLEasksslsetqqktiqmEEQerdpakr 322
Cdd:PRK07225  78 HIEKLKNGELT------------FDDLVKQGVIEYLDAEEEENAYIAVYEEDLT----------------EEH------- 122

                        170       180       190
                 ....*....|....*....|....*....|
gi 170799393 323 ikptysgnlhtfTHCEIHPSMILGVAASII 352
Cdd:PRK07225 123 ------------THLEIDPSLILGIGAGMI 140
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 165-226 1.21e-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: 1.21e-35
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 170799393  165 VFVNGVWVGTHRDPASLVDTIRSLRRKGDISPEVSIIRDIREKEFKIFTDAGRVYRPLFIVD 226
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 66-128 6.94e-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: 111.46  E-value: 6.94e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 170799393   66 QVLNRYTYSSTLSHLRRTNTPIG---RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMS 128
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYA 66
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 266-341 2.41e-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: 91.06  E-value: 2.41e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 170799393  266 WSSLVRDGIIEYVDAEEEETIMIAMTPEDLEASksslsetqqktiqmEEQERDPAKRikptysgnlHTFTHCEIHP 341
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEES--------------SREEREGPYA---------HTYTHCEIHP 53
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-352 1.71e-17

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: 84.01  E-value: 1.71e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393    1 LFRILF*KLTRDIYNYMqrcvENDKVFNLTLA--VKSQTITDGLRYSLATGnwgeqkkamssraGVSQVLNRYTYSSTLS 78
Cdd:COG0085   323 QFRVGLSRMERVVRERM----TTQDVEAITPQslINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELT 385

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393   79 HLRRTNT----PIGRDgklaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISvgsssepilvfleewglep 150
Cdd:COG0085   386 HKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN------------------- 442

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393  151 ledyspatspdttrvfvngvwvgthrdpaslvdtirslrrkgdispevsiirdirekEFkiftdaGRVYRPLFIVDDNps 230
Cdd:COG0085   443 ---------------------------------------------------------EY------GFIETPYRKVENG-- 457

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393  231 setkgelllnkthikklmdseyddynyddeqetygwssLVRDGiIEYVDAEEEETIMIAMTPEDLEASKSSLSETQQKTI 310
Cdd:COG0085   458 --------------------------------------KVTDE-IEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRY 498

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|..
gi 170799393  311 QMEEQERDPAKrikptysgnlhtFTHCEIHPSMILGVAASII 352
Cdd:COG0085   499 RGEEVLVPPEE------------VDYMDVSPKQIVSVATSLI 528
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
64-128 1.29e-06

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 50.31  E-value: 1.29e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 170799393   64 VSQVLNRYTYSSTLSHLRRTNTpIGrDGKLAK------PRQLHNTHWGLVCPAETPEGQACGLVKNLSLMS 128
Cdd:PRK09603  525 LSQFMDQTNPLSEVTHKRRLSA-LG-EGGLVKdrvgfeARDVHPTHYGRICPIETPEGQNIGLINTLSTFT 593
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
64-131 1.99e-06

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 50.01  E-value: 1.99e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 170799393   64 VSQVLNRYTYSSTLSHLRRTNT--PIG--RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCIS 131
Cdd:PRK14844  532 LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARIN 603
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-132 5.60e-06

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 48.16  E-value: 5.60e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170799393    1 LFRILF*KLTRDIYNYMQRCV-ENDKVFNLtlaVKSQTITDGLRYSLAtgnwgeqkkamSSRagVSQVLNRYTYSSTLSH 79
Cdd:CHL00207  318 QFRIGLKRLERILRNRMTICDiDSLSKFNL---INPKPLIALIREFFG-----------SSQ--LSQYMDQTNPLSELTH 381

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 170799393   80 LRRTNT--PIGRDgKLAKP---RQLHNTHWGLVCPAETPEGQACGLVKnlSLMSCISV 132
Cdd:CHL00207  382 KRRISIlgPGGLD-KDRISfavRDIHPSHYGRICPIETPEGPNCGLIG--SLATNARI 436
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-39 8.12e-06

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: 47.37  E-value: 8.12e-06
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 170799393    1 LFRILF*KLTRDIYNYMQRCVENDKVFNLTLAVKSQTIT 39
Cdd:pfam04563 357 LFRVLFKKLVRDVRERLQKVLGSPDDLMLQLLVNAKPIT 395
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 97-125 1.32e-04

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 43.94  E-value: 1.32e-04
                          10        20
                  ....*....|....*....|....*....
gi 170799393   97 RQLHNTHWGLVCPAETPEGQACGLVKNLS 125
Cdd:PRK00405  469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
rpoB CHL00001
RNA polymerase beta subunit
 65-125 2.83e-03

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 39.50  E-value: 2.83e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 170799393   65 SQVLNRYTYSSTLSHLRRTNT--PIGRDGKLA--KPRQLHNTHWGLVCPAETPEGQACGLVKNLS 125
Cdd:CHL00001  375 SQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIGSLA 439
 
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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