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Conserved domains on  [gi|663314451|gb|AIF27636|]
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RNA polymerase II subunit B2, partial [Trichoderma atrogelatinosum]

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;
1-287 1.77e-74

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: 246.41  E-value: 1.77e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451    1 RYTFASTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSPSEPLIEFMINRGME 80
Cdd:PRK08565  408 RTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVV 487

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451   81 VVEEYEPLRYPHATKIFVNGVWVGVHQDPKHLVNQVLDTRRKSYLQYEVSlVREIRDQEFK---IFSDAGRVMRPVFTVq 157
Cdd:PRK08565  488 PVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVN-VAYIETGEINevyVNCDSGRVRRPLIVV- 565

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451  158 qeddpetgiNKGHLVLTKELVNRLAKEqaeppedpsmKIGWEGLIRAGAVEYLDAEEEETSMICMTPEDLelyrlqkagi 237
Cdd:PRK08565  566 ---------ENGKPKLTREHVEKLKKG----------ELTFDDLVKMGVIEYLDAEEEENAYVALDPEDL---------- 616

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 663314451  238 sTEEdmgddpnkrlktktnptthmYTHCEIHPSMILGICASIIPFPDHNQ 287
Cdd:PRK08565  617 -TPE--------------------HTHLEIWPPAILGITASIIPYPEHNQ 645
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-287 1.77e-74

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 246.41  E-value: 1.77e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451    1 RYTFASTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSPSEPLIEFMINRGME 80
Cdd:PRK08565  408 RTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVV 487

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451   81 VVEEYEPLRYPHATKIFVNGVWVGVHQDPKHLVNQVLDTRRKSYLQYEVSlVREIRDQEFK---IFSDAGRVMRPVFTVq 157
Cdd:PRK08565  488 PVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVN-VAYIETGEINevyVNCDSGRVRRPLIVV- 565

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451  158 qeddpetgiNKGHLVLTKELVNRLAKEqaeppedpsmKIGWEGLIRAGAVEYLDAEEEETSMICMTPEDLelyrlqkagi 237
Cdd:PRK08565  566 ---------ENGKPKLTREHVEKLKKG----------ELTFDDLVKMGVIEYLDAEEEENAYVALDPEDL---------- 616

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 663314451  238 sTEEdmgddpnkrlktktnptthmYTHCEIHPSMILGICASIIPFPDHNQ 287
Cdd:PRK08565  617 -TPE--------------------HTHLEIWPPAILGITASIIPYPEHNQ 645
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-60 1.34e-29

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: 106.84  E-value: 1.34e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 663314451    1 RYTFASTLSHLRRTNTPIG---RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCY 60
Cdd:pfam04565   5 RTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-287 3.95e-29

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: 116.51  E-value: 3.95e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451   1 RYTFASTLSHLRRTNT-PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSvgspsepliefminrgm 79
Cdd:cd00653  319 RLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS----------------- 381

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451  80 evveeyeplryphatkifvngvwvgvhqdpkhlvnqvldtrrksylqyevslvreirdqefkifsdaGRVMRPVFTVQQE 159
Cdd:cd00653  382 -------------------------------------------------------------------GRIERPYRIVEKE 394

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451 160 ddpetginkghlvltkelvnrlakeqaeppedpsmkigwegliragaveyldaeeeetsmicmtpedlelyrlqkagist 239
Cdd:cd00653      --------------------------------------------------------------------------------

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 663314451 240 eedmgddpnkrlktktnptthmYTHCEIHPSMILGICASIIPFPDHNQ 287
Cdd:cd00653  395 ----------------------VTHIEISPSQILSVAASLIPFPEHNQ 420
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 6-287 2.55e-18

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: 84.78  E-value: 2.55e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451    6 STLSHLRRTNT----PIGRDgklaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSvgspsepliefminr 77
Cdd:COG0085   382 SELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN--------------- 442

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451   78 gmevveEYeplryphatkifvngvwvgvhqdpkhlvnqvldtrrksylqyevslvreirdqefkifsdaGRVMRPVFTVq 157
Cdd:COG0085   443 ------EY-------------------------------------------------------------GFIETPYRKV- 454

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451  158 qeddpETGinkghlVLTKElvnrlakeqaeppedpsmkigwegliragaVEYLDAEEEETSMICMTPEDLElyrlQKAGI 237
Cdd:COG0085   455 -----ENG------KVTDE------------------------------IEYLTADEEENYYIAQANAPLD----EDGNF 489

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 663314451  238 STEEDMGDDPNKRLKTKTNPTTHMythcEIHPSMILGICASIIPFPDHNQ 287
Cdd:COG0085   490 LEERVLVRYRGEEVLVPPEEVDYM----DVSPKQIVSVATSLIPFLEHDD 535
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-287 1.77e-74

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 246.41  E-value: 1.77e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451    1 RYTFASTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSPSEPLIEFMINRGME 80
Cdd:PRK08565  408 RTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVV 487

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451   81 VVEEYEPLRYPHATKIFVNGVWVGVHQDPKHLVNQVLDTRRKSYLQYEVSlVREIRDQEFK---IFSDAGRVMRPVFTVq 157
Cdd:PRK08565  488 PVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVN-VAYIETGEINevyVNCDSGRVRRPLIVV- 565

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451  158 qeddpetgiNKGHLVLTKELVNRLAKEqaeppedpsmKIGWEGLIRAGAVEYLDAEEEETSMICMTPEDLelyrlqkagi 237
Cdd:PRK08565  566 ---------ENGKPKLTREHVEKLKKG----------ELTFDDLVKMGVIEYLDAEEEENAYVALDPEDL---------- 616

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 663314451  238 sTEEdmgddpnkrlktktnptthmYTHCEIHPSMILGICASIIPFPDHNQ 287
Cdd:PRK08565  617 -TPE--------------------HTHLEIWPPAILGITASIIPYPEHNQ 645
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 94-287 4.76e-35

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 132.78  E-value: 4.76e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451  94 TKIFVNGVWVGVHQDPKHLVNQVLDTRRKSYLQYEVSLVREIRDQEFKIFSDAGRVMRPVFTVQqeddpetginKGHLVL 173
Cdd:PRK07225   5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVE----------NGEPLL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451 174 TKELVNRLAKEqaeppedpsmKIGWEGLIRAGAVEYLDAEEEETSMICMTPEDLelyrlqkagisTEEdmgddpnkrlkt 253
Cdd:PRK07225  75 TEEHIEKLKNG----------ELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDL-----------TEE------------ 121

                        170       180       190
                 ....*....|....*....|....*....|....
gi 663314451 254 ktnptthmYTHCEIHPSMILGICASIIPFPDHNQ 287
Cdd:PRK07225 122 --------HTHLEIDPSLILGIGAGMIPYPEHNA 147
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-60 1.34e-29

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: 106.84  E-value: 1.34e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 663314451    1 RYTFASTLSHLRRTNTPIG---RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCY 60
Cdd:pfam04565   5 RTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-287 3.95e-29

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: 116.51  E-value: 3.95e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451   1 RYTFASTLSHLRRTNT-PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSvgspsepliefminrgm 79
Cdd:cd00653  319 RLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS----------------- 381

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451  80 evveeyeplryphatkifvngvwvgvhqdpkhlvnqvldtrrksylqyevslvreirdqefkifsdaGRVMRPVFTVQQE 159
Cdd:cd00653  382 -------------------------------------------------------------------GRIERPYRIVEKE 394

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451 160 ddpetginkghlvltkelvnrlakeqaeppedpsmkigwegliragaveyldaeeeetsmicmtpedlelyrlqkagist 239
Cdd:cd00653      --------------------------------------------------------------------------------

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 663314451 240 eedmgddpnkrlktktnptthmYTHCEIHPSMILGICASIIPFPDHNQ 287
Cdd:cd00653  395 ----------------------VTHIEISPSQILSVAASLIPFPEHNQ 420
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 96-157 5.76e-26

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: 97.05  E-value: 5.76e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 663314451   96 IFVNGVWVGVHQDPKHLVNQVLDTRRKSYLQYEVSLVREIRDQEFKIFSDAGRVMRPVFTVQ 157
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 198-269 2.49e-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: 2.49e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 663314451  198 WEGLIRAGAVEYLDAEEEETSMICMTPEDLE-LYRLQKAGisteedmgddpnkrlktktnPTTHMYTHCEIHP 269
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEeSSREEREG--------------------PYAHTYTHCEIHP 53
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-86 2.34e-22

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 96.17  E-value: 2.34e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451   1 RYTFASTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSVGSPSEPLIEFMinRGME 80
Cdd:PRK09606 411 RTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEIL--KELG 488


                 ....*.
gi 663314451  81 VVEEYE 86
Cdd:PRK09606 489 VEPERG 494
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 6-287 2.55e-18

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: 84.78  E-value: 2.55e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451    6 STLSHLRRTNT----PIGRDgklaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVSvgspsepliefminr 77
Cdd:COG0085   382 SELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN--------------- 442

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451   78 gmevveEYeplryphatkifvngvwvgvhqdpkhlvnqvldtrrksylqyevslvreirdqefkifsdaGRVMRPVFTVq 157
Cdd:COG0085   443 ------EY-------------------------------------------------------------GFIETPYRKV- 454

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451  158 qeddpETGinkghlVLTKElvnrlakeqaeppedpsmkigwegliragaVEYLDAEEEETSMICMTPEDLElyrlQKAGI 237
Cdd:COG0085   455 -----ENG------KVTDE------------------------------IEYLTADEEENYYIAQANAPLD----EDGNF 489

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 663314451  238 STEEDMGDDPNKRLKTKTNPTTHMythcEIHPSMILGICASIIPFPDHNQ 287
Cdd:COG0085   490 LEERVLVRYRGEEVLVPPEEVDYM----DVSPKQIVSVATSLIPFLEHDD 535
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
6-56 3.86e-06

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 48.38  E-value: 3.86e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 663314451    6 STLSHLRRTNTpIGrDGKLAK------PRQLHNTHWGLVCPAETPEGQACGLVKNLS 56
Cdd:PRK09603  536 SEVTHKRRLSA-LG-EGGLVKdrvgfeARDVHPTHYGRICPIETPEGQNIGLINTLS 590
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
6-80 5.48e-06

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 47.69  E-value: 5.48e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663314451    6 STLSHLRRTNT--PIG--RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMCYVS----VGSPSEPLIEFMINR 77
Cdd:PRK14844  543 SEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINkygfIESPYRKVVNRVVTD 622


                  ...
gi 663314451   78 GME 80
Cdd:PRK14844  623 QIE 625
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 6-56 6.05e-05

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 44.31  E-value: 6.05e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 663314451    6 STLSHLRRTNT--PIGRDgKLAKP---RQLHNTHWGLVCPAETPEGQACGLVKNLS 56
Cdd:CHL00207  377 SELTHKRRISIlgPGGLD-KDRISfavRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 28-56 8.61e-05

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 43.94  E-value: 8.61e-05
                          10        20
                  ....*....|....*....|....*....
gi 663314451   28 RQLHNTHWGLVCPAETPEGQACGLVKNLS 56
Cdd:PRK00405  469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
rpoB CHL00001
RNA polymerase beta subunit
 28-65 4.67e-03

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 38.34  E-value: 4.67e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 663314451   28 RQLHNTHWGLVCPAETPEGQACGLVKnlSLMCYVSVGS 65
Cdd:CHL00001  411 RDIHPSHYGRICPIDTSEGINAGLIG--SLAIHARIGH 446
 
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.
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