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Conserved domains on  [gi|1181244651|gb|ARI48293|]
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DNA-directed RNA polymerase II subunit two, partial [Suillus fuscotomentosus]

Protein Classification

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;
1-254 4.30e-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: 271.44  E-value: 4.30e-84
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651    1 WGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTP-CTKVFVNGVWMGVHRDPANLVK 79
Cdd:PRK08565   442 WGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYIsWSRVYLNGRLIGYHPDGEELAE 521

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651   80 TIKKLRRKDDISPEVSV--VRDIRERELRLYTDAGRVCRPLFIVENQQLALQKKHIKWLNQGyrdddgeEFKWEQLVKNG 157
Cdd:PRK08565   522 KIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKG-------ELTFDDLVKMG 594

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651  158 IIELLDAEEEETVMICMTPEDLensrlqsagidphqndgdydpaarlkagISAHTwtHCEIHPSMILGVCASIIPFPDHN 237
Cdd:PRK08565   595 VIEYLDAEEEENAYVALDPEDL----------------------------TPEHT--HLEIWPPAILGITASIIPYPEHN 644

                          250
                   ....*....|....*..
gi 1181244651  238 QSPRNTYQSAMGKQAMG 254
Cdd:PRK08565   645 QSPRNTYQAAMAKQSLG 661
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-254 4.30e-84

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 271.44  E-value: 4.30e-84
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651    1 WGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTP-CTKVFVNGVWMGVHRDPANLVK 79
Cdd:PRK08565   442 WGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYIsWSRVYLNGRLIGYHPDGEELAE 521

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651   80 TIKKLRRKDDISPEVSV--VRDIRERELRLYTDAGRVCRPLFIVENQQLALQKKHIKWLNQGyrdddgeEFKWEQLVKNG 157
Cdd:PRK08565   522 KIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKG-------ELTFDDLVKMG 594

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651  158 IIELLDAEEEETVMICMTPEDLensrlqsagidphqndgdydpaarlkagISAHTwtHCEIHPSMILGVCASIIPFPDHN 237
Cdd:PRK08565   595 VIEYLDAEEEENAYVALDPEDL----------------------------TPEHT--HLEIWPPAILGITASIIPYPEHN 644

                          250
                   ....*....|....*..
gi 1181244651  238 QSPRNTYQSAMGKQAMG 254
Cdd:PRK08565   645 QSPRNTYQAAMAKQSLG 661
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 61-122 5.33e-37

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: 124.79  E-value: 5.33e-37
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1181244651  61 VFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVE 122
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-254 3.09e-33

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: 127.30  E-value: 3.09e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651   1 WGMVCPAETPEGQACGLVKNLALMACISvgsysapviefleewglesleenahsstpctkvfvngvwmgvhrdpanlvkt 80
Cdd:cd00653   354 WGRICPIETPEGENCGLVKNLALMARIS---------------------------------------------------- 381

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651  81 ikklrrkddispevsvvrdirerelrlytdaGRVCRPLFIVENQqlalqkkhikwlnqgyrdddgeefkweqlvkngiie 160
Cdd:cd00653   382 -------------------------------GRIERPYRIVEKE------------------------------------ 394

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651 161 lldaeeeetvmicmtpedlensrlqsagidphqndgdydpaarlkagisahtWTHCEIHPSMILGVCASIIPFPDHNQSP 240
Cdd:cd00653   395 ----------------------------------------------------VTHIEISPSQILSVAASLIPFPEHNQSP 422

                         250
                  ....*....|....
gi 1181244651 241 RNTYQSAMGKQAMG 254
Cdd:cd00653   423 RNLYQSNMQKQAVG 436
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-254 2.38e-22

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: 95.56  E-value: 2.38e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651    1 WGMVCPAETPEGQACGLVKNLALMACISvgsysapviEFleewglesleenahsstpctkvfvngvwmgvhrdpanlvkt 80
Cdd:COG0085    415 YGRMCPIETPEGPNIGLIGSLALYARVN---------EY----------------------------------------- 444

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651   81 ikklrrkddispevsvvrdirerelrlytdaGRVCRPLFIVENqqlalqkkhikwlnqGYRDDDgeefkweqlvkngiIE 160
Cdd:COG0085    445 -------------------------------GFIETPYRKVEN---------------GKVTDE--------------IE 464

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651  161 LLDAEEEETVMICMTPEDL-ENSRLQSAGID-PHQNDGDYDPAARLkagisahtwTHCEIHPSMILGVCASIIPFPDHNQ 238
Cdd:COG0085    465 YLTADEEENYYIAQANAPLdEDGNFLEERVLvRYRGEEVLVPPEEV---------DYMDVSPKQIVSVATSLIPFLEHDD 535

                          250
                   ....*....|....*.
gi 1181244651  239 SPRNTYQSAMGKQAMG 254
Cdd:COG0085    536 ANRALMGANMQRQAVP 551
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-254 4.30e-84

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 271.44  E-value: 4.30e-84
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651    1 WGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTP-CTKVFVNGVWMGVHRDPANLVK 79
Cdd:PRK08565   442 WGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYIsWSRVYLNGRLIGYHPDGEELAE 521

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651   80 TIKKLRRKDDISPEVSV--VRDIRERELRLYTDAGRVCRPLFIVENQQLALQKKHIKWLNQGyrdddgeEFKWEQLVKNG 157
Cdd:PRK08565   522 KIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKG-------ELTFDDLVKMG 594

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651  158 IIELLDAEEEETVMICMTPEDLensrlqsagidphqndgdydpaarlkagISAHTwtHCEIHPSMILGVCASIIPFPDHN 237
Cdd:PRK08565   595 VIEYLDAEEEENAYVALDPEDL----------------------------TPEHT--HLEIWPPAILGITASIIPYPEHN 644

                          250
                   ....*....|....*..
gi 1181244651  238 QSPRNTYQSAMGKQAMG 254
Cdd:PRK08565   645 QSPRNTYQAAMAKQSLG 661
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 59-254 8.13e-56

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 188.25  E-value: 8.13e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651  59 TKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLALQKKHIKWLNQ 138
Cdd:PRK07225    5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKN 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651 139 GyrdddgeEFKWEQLVKNGIIELLDAEEEETVMICMTPEDLEnsrlqsagiDPHqndgdydpaarlkagisahtwTHCEI 218
Cdd:PRK07225   85 G-------ELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLT---------EEH---------------------THLEI 127

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1181244651 219 HPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 254
Cdd:PRK07225  128 DPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLG 163
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 61-122 5.33e-37

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: 124.79  E-value: 5.33e-37
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1181244651  61 VFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVE 122
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-254 3.09e-33

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: 127.30  E-value: 3.09e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651   1 WGMVCPAETPEGQACGLVKNLALMACISvgsysapviefleewglesleenahsstpctkvfvngvwmgvhrdpanlvkt 80
Cdd:cd00653   354 WGRICPIETPEGENCGLVKNLALMARIS---------------------------------------------------- 381

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651  81 ikklrrkddispevsvvrdirerelrlytdaGRVCRPLFIVENQqlalqkkhikwlnqgyrdddgeefkweqlvkngiie 160
Cdd:cd00653   382 -------------------------------GRIERPYRIVEKE------------------------------------ 394

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651 161 lldaeeeetvmicmtpedlensrlqsagidphqndgdydpaarlkagisahtWTHCEIHPSMILGVCASIIPFPDHNQSP 240
Cdd:cd00653   395 ----------------------------------------------------VTHIEISPSQILSVAASLIPFPEHNQSP 422

                         250
                  ....*....|....
gi 1181244651 241 RNTYQSAMGKQAMG 254
Cdd:cd00653   423 RNLYQSNMQKQAVG 436
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 150-220 8.83e-25

RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain.


Pssm-ID: 428013 [Multi-domain]  Cd Length: 53  Bit Score: 92.99  E-value: 8.83e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1181244651 150 WEQLVKNGIIELLDAEEEETVMICMTPEDLENSRLQSagidphqndgdydpaarlKAGISAHTWTHCEIHP 220
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREE------------------REGPYAHTYTHCEIHP 53
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-254 2.38e-22

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: 95.56  E-value: 2.38e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651    1 WGMVCPAETPEGQACGLVKNLALMACISvgsysapviEFleewglesleenahsstpctkvfvngvwmgvhrdpanlvkt 80
Cdd:COG0085    415 YGRMCPIETPEGPNIGLIGSLALYARVN---------EY----------------------------------------- 444

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651   81 ikklrrkddispevsvvrdirerelrlytdaGRVCRPLFIVENqqlalqkkhikwlnqGYRDDDgeefkweqlvkngiIE 160
Cdd:COG0085    445 -------------------------------GFIETPYRKVEN---------------GKVTDE--------------IE 464

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1181244651  161 LLDAEEEETVMICMTPEDL-ENSRLQSAGID-PHQNDGDYDPAARLkagisahtwTHCEIHPSMILGVCASIIPFPDHNQ 238
Cdd:COG0085    465 YLTADEEENYYIAQANAPLdEDGNFLEERVLvRYRGEEVLVPPEEV---------DYMDVSPKQIVSVATSLIPFLEHDD 535

                          250
                   ....*....|....*.
gi 1181244651  239 SPRNTYQSAMGKQAMG 254
Cdd:COG0085    536 ANRALMGANMQRQAVP 551
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 227-254 5.36e-13

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: 67.55  E-value: 5.36e-13
                          10        20
                  ....*....|....*....|....*...
gi 1181244651 227 CASIIPFPDHNQSPRNTYQSAMGKQAMG 254
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMGKQAMG 28
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-46 6.39e-13

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 67.67  E-value: 6.39e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1181244651   1 WGMVCPAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLE 46
Cdd:PRK09606  445 WGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVE 490
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-25 2.27e-12

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: 60.62  E-value: 2.27e-12
                          10        20
                  ....*....|....*....|....*
gi 1181244651   1 WGMVCPAETPEGQACGLVKNLALMA 25
Cdd:pfam04565  42 WGRICPVETPEGPNCGLVKHLALYA 66
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
217-253 2.69e-03

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 39.14  E-value: 2.69e-03
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1181244651  217 EIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAM 253
Cdd:PRK09603   668 DLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAV 704
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-28 4.73e-03

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 38.06  E-value: 4.73e-03
                           10        20
                   ....*....|....*....|....*...
gi 1181244651    1 WGMVCPAETPEGQACGLVKNLALMACIS 28
Cdd:PRK14844   576 YGRICPIETPEGQNIGLINSLAIYARIN 603
 
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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