NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1314927214|gb|AUG31819|]
View 

DNA-directed RNA polymerase II second largest subunit, partial [Stenella araguata]

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

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Ricin_B_lectin super family cl47023
Ricin-type beta-trefoil lectin domain;
7-313 1.66e-84

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: 275.30  E-value: 1.66e-84
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214    7 KAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCFVSVGTPGTPLI 86
Cdd:PRK08565   399 RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVE 478

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214   87 EYMRYRGMELLEEWDAVLNPNATKVFLNGTWVGVHNNGGQLTDALRNLKRKNTIGFEVTI--IRDVREREIKVFTDAGRV 164
Cdd:PRK08565   479 EILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRV 558

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214  165 CRPLFVVDNdpssenrGNLVLNREHIQRLENDRLileqmeaqgfseeekqertfGWHGLVSNGVVEYLDAEEEETAMIIM 244
Cdd:PRK08565   559 RRPLIVVEN-------GKPKLTREHVEKLKKGEL--------------------TFDDLVKMGVIEYLDAEEEENAYVAL 611

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214  245 APDEL-EEHrqiragnpwieakddphrrikakpnpmvrtwTHCEIHPAMILGICASIIPFPDHNQSPRNT 313
Cdd:PRK08565   612 DPEDLtPEH-------------------------------THLEIWPPAILGITASIIPYPEHNQSPRNT 650
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 7-313 1.66e-84

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 275.30  E-value: 1.66e-84
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214    7 KAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCFVSVGTPGTPLI 86
Cdd:PRK08565   399 RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVE 478

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214   87 EYMRYRGMELLEEWDAVLNPNATKVFLNGTWVGVHNNGGQLTDALRNLKRKNTIGFEVTI--IRDVREREIKVFTDAGRV 164
Cdd:PRK08565   479 EILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRV 558

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214  165 CRPLFVVDNdpssenrGNLVLNREHIQRLENDRLileqmeaqgfseeekqertfGWHGLVSNGVVEYLDAEEEETAMIIM 244
Cdd:PRK08565   559 RRPLIVVEN-------GKPKLTREHVEKLKKGEL--------------------TFDDLVKMGVIEYLDAEEEENAYVAL 611

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214  245 APDEL-EEHrqiragnpwieakddphrrikakpnpmvrtwTHCEIHPAMILGICASIIPFPDHNQSPRNT 313
Cdd:PRK08565   612 DPEDLtPEH-------------------------------THLEIWPPAILGITASIIPYPEHNQSPRNT 650
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-313 6.82e-39

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: 145.79  E-value: 6.82e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214   1 KKAASAKAGVSQVLNRYTYASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCFVSvg 79
Cdd:cd00653   304 KRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-- 381

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214  80 tpgtplieymryrgmelleewdavlnpnatkvflngtwvgvhnnggqltdalrnlkrkntigfevtiirdvrereikvft 159
Cdd:cd00653       --------------------------------------------------------------------------------

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214 160 daGRVCRPLFVVDNDpssenrgnlvlnrehiqrlendrlileqmeaqgfseeekqertfgwhglvsngvveyldaeeeet 239
Cdd:cd00653   382 --GRIERPYRIVEKE----------------------------------------------------------------- 394

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1314927214 240 amiimapdeleehrqiragnpwieakddphrrikakpnpmvrtWTHCEIHPAMILGICASIIPFPDHNQSPRNT 313
Cdd:cd00653   395 -------------------------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNL 425
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 12-75 4.50e-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: 113.78  E-value: 4.50e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1314927214  12 QVLNRYTYASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCF 75
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 2-313 5.43e-25

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: 105.19  E-value: 5.43e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214    2 KAASAKAGVSQVLNRYTYASTLSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLALM 73
Cdd:COG0085    363 KEFFGSSQLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALY 438

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214   74 CFVSvgtpgtpliEYmryrgmelleewdavlnpnatkvflngtwvgvhnnggqltdalrnlkrkntigfevtiirdvrer 153
Cdd:COG0085    439 ARVN---------EY----------------------------------------------------------------- 444

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214  154 eikvftdaGRVCRPLFVVDNdpssenrgnlvlnrehiqrlendrlileqmeaqgfseeekqertfgwhGLVSNGvVEYLD 233
Cdd:COG0085    445 --------GFIETPYRKVEN------------------------------------------------GKVTDE-IEYLT 467

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214  234 AEEEETAMIIMAPDELEEHRQIRAGNPWIEAKDDPhrriKAKPNPMVrtwTHCEIHPAMILGICASIIPFPDHNQSPRNT 313
Cdd:COG0085    468 ADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEE----VLVPPEEV---DYMDVSPKQIVSVATSLIPFLEHDDANRAL 540
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 7-313 1.66e-84

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 275.30  E-value: 1.66e-84
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214    7 KAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCFVSVGTPGTPLI 86
Cdd:PRK08565   399 RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVE 478

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214   87 EYMRYRGMELLEEWDAVLNPNATKVFLNGTWVGVHNNGGQLTDALRNLKRKNTIGFEVTI--IRDVREREIKVFTDAGRV 164
Cdd:PRK08565   479 EILYELGVVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRV 558

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214  165 CRPLFVVDNdpssenrGNLVLNREHIQRLENDRLileqmeaqgfseeekqertfGWHGLVSNGVVEYLDAEEEETAMIIM 244
Cdd:PRK08565   559 RRPLIVVEN-------GKPKLTREHVEKLKKGEL--------------------TFDDLVKMGVIEYLDAEEEENAYVAL 611

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214  245 APDEL-EEHrqiragnpwieakddphrrikakpnpmvrtwTHCEIHPAMILGICASIIPFPDHNQSPRNT 313
Cdd:PRK08565   612 DPEDLtPEH-------------------------------THLEIWPPAILGITASIIPYPEHNQSPRNT 650
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 109-313 5.05e-42

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 153.19  E-value: 5.05e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214 109 TKVFLNGTWVGVHNNGGQLTDALRNLKRKNTIGFEVTIIRDVREREIKVFTDAGRVCRPLFVVDNdpssenrGNLVLNRE 188
Cdd:PRK07225    5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLTEE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214 189 HIQRLENDRLIleqmeaqgfseeekqertfgWHGLVSNGVVEYLDAEEEETAMIIMAPDEL-EEHrqiragnpwieakdd 267
Cdd:PRK07225   78 HIEKLKNGELT--------------------FDDLVKQGVIEYLDAEEEENAYIAVYEEDLtEEH--------------- 122

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1314927214 268 phrrikakpnpmvrtwTHCEIHPAMILGICASIIPFPDHNQSPRNT 313
Cdd:PRK07225  123 ----------------THLEIDPSLILGIGAGMIPYPEHNASPRIT 152
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-313 6.82e-39

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: 145.79  E-value: 6.82e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214   1 KKAASAKAGVSQVLNRYTYASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCFVSvg 79
Cdd:cd00653   304 KRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS-- 381

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214  80 tpgtplieymryrgmelleewdavlnpnatkvflngtwvgvhnnggqltdalrnlkrkntigfevtiirdvrereikvft 159
Cdd:cd00653       --------------------------------------------------------------------------------

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214 160 daGRVCRPLFVVDNDpssenrgnlvlnrehiqrlendrlileqmeaqgfseeekqertfgwhglvsngvveyldaeeeet 239
Cdd:cd00653   382 --GRIERPYRIVEKE----------------------------------------------------------------- 394

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1314927214 240 amiimapdeleehrqiragnpwieakddphrrikakpnpmvrtWTHCEIHPAMILGICASIIPFPDHNQSPRNT 313
Cdd:cd00653   395 -------------------------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNL 425
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 12-75 4.50e-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: 113.78  E-value: 4.50e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1314927214  12 QVLNRYTYASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCF 75
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 111-172 2.33e-28

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: 103.99  E-value: 2.33e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1314927214 111 VFLNGTWVGVHNNGGQLTDALRNLKRKNTIGFEVTIIRDVREREIKVFTDAGRVCRPLFVVD 172
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 7-99 1.68e-26

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 108.88  E-value: 1.68e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214   7 KAGVSQVLNRYTYASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCFVSVGTPGTPLI 86
Cdd:PRK09606  402 RTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVK 481

                          90
                  ....*....|...
gi 1314927214  87 EYMRYRGMELLEE 99
Cdd:PRK09606  482 EILKELGVEPERG 494
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 2-313 5.43e-25

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: 105.19  E-value: 5.43e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214    2 KAASAKAGVSQVLNRYTYASTLSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLALM 73
Cdd:COG0085    363 KEFFGSSQLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALY 438

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214   74 CFVSvgtpgtpliEYmryrgmelleewdavlnpnatkvflngtwvgvhnnggqltdalrnlkrkntigfevtiirdvrer 153
Cdd:COG0085    439 ARVN---------EY----------------------------------------------------------------- 444

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214  154 eikvftdaGRVCRPLFVVDNdpssenrgnlvlnrehiqrlendrlileqmeaqgfseeekqertfgwhGLVSNGvVEYLD 233
Cdd:COG0085    445 --------GFIETPYRKVEN------------------------------------------------GKVTDE-IEYLT 467

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314927214  234 AEEEETAMIIMAPDELEEHRQIRAGNPWIEAKDDPhrriKAKPNPMVrtwTHCEIHPAMILGICASIIPFPDHNQSPRNT 313
Cdd:COG0085    468 ADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEE----VLVPPEEV---DYMDVSPKQIVSVATSLIPFLEHDDANRAL 540
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 220-290 2.10e-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: 82.59  E-value: 2.10e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1314927214 220 WHGLVSNGVVEYLDAEEEETAMIIMAPDELEEHrqiragnpwieakddpHRRIKAKPNpmVRTWTHCEIHP 290
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEES----------------SREEREGPY--AHTYTHCEIHP 53
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
10-72 3.56e-07

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 51.93  E-value: 3.56e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1314927214   10 VSQVLNRYTYASTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLAL 72
Cdd:PRK14844   532 LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAI 598
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
10-71 1.78e-06

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 49.54  E-value: 1.78e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1314927214   10 VSQVLNRYTYASTLSHLRRTNTpIGRDGKIA-----KPRQLHNTHWGLVCPAETPEGQACGLVKNLA 71
Cdd:PRK09603   525 LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLINTLS 590
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 10-71 1.04e-05

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 47.01  E-value: 1.04e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1314927214   10 VSQVLNRYTYASTLSHLRRTNT--PIGRDG-KIAKP-RQLHNTHWGLVCPAETPEGQACGLVKNLA 71
Cdd:CHL00207   366 LSQYMDQTNPLSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 43-71 6.92e-05

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 44.32  E-value: 6.92e-05
                           10        20
                   ....*....|....*....|....*....
gi 1314927214   43 RQLHNTHWGLVCPAETPEGQACGLVKNLA 71
Cdd:PRK00405   469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 297-313 1.82e-04

RNA polymerase Rpb2, domain 6; 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 represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 42.52  E-value: 1.82e-04
                          10
                  ....*....|....*..
gi 1314927214 297 CASIIPFPDHNQSPRNT 313
Cdd:pfam00562   1 VASLIPFVDHNQSPRNT 17
rpoB CHL00001
RNA polymerase beta subunit
 11-71 2.19e-04

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 42.97  E-value: 2.19e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1314927214   11 SQVLNRYTYASTLSHLRRTNT--PIGRDGKIA--KPRQLHNTHWGLVCPAETPEGQACGLVKNLA 71
Cdd:CHL00001   375 SQFLDQTNPLTEIVHGRKLSSlgPGGLTGRTAsfRVRDIHPSHYGRICPIDTSEGINAGLIGSLA 439
MobB_Trc-like cd21780
Mob-binding domain found in Drosophila melanogaster tricorner and similar proteins; Drosophila ...
 182-216 7.34e-03

Mob-binding domain found in Drosophila melanogaster tricorner and similar proteins; Drosophila melanogaster tricorner, also called serine/threonine-protein kinase 38-like, or NDR protein kinase, is a serine/threonine-protein kinase that plays an important role in controlling cell structure and proliferation of a variety of polarized outgrowths including epidermal hairs, bristles, arista laterals, and dendrites. It affects cellular morphogenesis by regulating the expression of target genes that encode cytoskeleton-interacting proteins and not via the direct modification of the cytoskeleton. It maintains the integrity of epidermal hairs and is an essential component of the signaling pathway regulating dendritic branching of sensory neurons. Tricorner belongs to the NDR/LATS family of kinases that bind to highly conserved Mob (Mps One binder) coactivators, forming regulatory complexes that control a diverse set of in vivo effector proteins, and are essential and evolutionarily conserved components of "Hippo" signaling pathways. Mob association creates a novel binding pocket that participates in the formation of the active state of NDR/LATS kinases. These kinases contain a regulatory domain located N-terminal to the serine/threonine kinase domain (called the N-terminal regulatory (NTR) domain) and an insert within the catalytic domain that contains an auto-inhibitory sequence. This model corresponds to the NTR or Mob-binding domain of Tricorner-like serine/threonine protein kinases.


Pssm-ID: 439274  Cd Length: 65  Bit Score: 34.64  E-value: 7.34e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1314927214 182 NLVlnREHIQRLENDRLILEQMEAQGFSEEEKQER 216
Cdd:cd21780    14 NLI--AQHKERENRLKKLEESMEEEGLTEEQKQEK 46
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH