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Conserved domains on  [gi|325560020|gb|ADZ31153|]
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RNA polymerase II second largest subunit, partial [Cladonia corsicana]

Protein Classification

DNA-directed RNA polymerase III subunit RPC2( domain architecture ID 10518874)

DNA-directed RNA polymerase III subunit RPC2 is the second largest core component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs

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;
16-258 3.35e-71

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: 237.55  E-value: 3.35e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325560020   16 KAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPII 95
Cdd:PRK08565  399 RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVE 478

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325560020   96 DfmIQRNMEV--LEEYEPLSSPNATKIFVNGVWVGVHRDPAHLVSTVQNLRRKGMISHEVSL--IRDIRDREFKIFTDAG 171
Cdd:PRK08565  479 E--ILYELGVvpVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSG 556

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325560020  172 RVCRPLFVIENnpaspnrGNLVLTKQMLEQLeqdkqdlaaraaggdsddmDKAKLGWYRLINNGVVEYVDAEEEETIMIV 251
Cdd:PRK08565  557 RVRRPLIVVEN-------GKPKLTREHVEKL-------------------KKGELTFDDLVKMGVIEYLDAEEEENAYVA 610


                  ....*..
gi 325560020  252 MTPEDLL 258
Cdd:PRK08565  611 LDPEDLT 617
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 228-294 9.86e-17

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: 72.57  E-value: 9.86e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 325560020  228 WYRLINNGVVEYVDAEEEETIMIVMTPEDLLISQQLQQGfvlpednsndlnkrvkatpNPTAHTWTH 294
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREERE-------------------GPYAHTYTH 48
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 16-258 3.35e-71

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 237.55  E-value: 3.35e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325560020   16 KAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPII 95
Cdd:PRK08565  399 RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVE 478

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325560020   96 DfmIQRNMEV--LEEYEPLSSPNATKIFVNGVWVGVHRDPAHLVSTVQNLRRKGMISHEVSL--IRDIRDREFKIFTDAG 171
Cdd:PRK08565  479 E--ILYELGVvpVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSG 556

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325560020  172 RVCRPLFVIENnpaspnrGNLVLTKQMLEQLeqdkqdlaaraaggdsddmDKAKLGWYRLINNGVVEYVDAEEEETIMIV 251
Cdd:PRK08565  557 RVRRPLIVVEN-------GKPKLTREHVEKL-------------------KKGELTFDDLVKMGVIEYLDAEEEENAYVA 610


                  ....*..
gi 325560020  252 MTPEDLL 258
Cdd:PRK08565  611 LDPEDLT 617
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 6-86 1.85e-35

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: 135.00  E-value: 1.85e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325560020   6 WGDQKKAaQSKAGVSQVLNRYTFASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCY 84
Cdd:cd00653  301 WGSKRFL-MQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMAR 379


                 ..
gi 325560020  85 IT 86
Cdd:cd00653  380 IS 381
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 120-181 1.46e-34

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: 119.78  E-value: 1.46e-34
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 325560020  120 IFVNGVWVGVHRDPAHLVSTVQNLRRKGMISHEVSLIRDIRDREFKIFTDAGRVCRPLFVIE 181
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 18-87 4.10e-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: 81.31  E-value: 4.10e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 325560020   18 GVSQVLNRYTFASTLSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITV 87
Cdd:COG0085   370 QLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNE 443
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 228-294 9.86e-17

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: 72.57  E-value: 9.86e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 325560020  228 WYRLINNGVVEYVDAEEEETIMIVMTPEDLLISQQLQQGfvlpednsndlnkrvkatpNPTAHTWTH 294
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREERE-------------------GPYAHTYTH 48
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 16-258 3.35e-71

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 237.55  E-value: 3.35e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325560020   16 KAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPII 95
Cdd:PRK08565  399 RTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVE 478

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325560020   96 DfmIQRNMEV--LEEYEPLSSPNATKIFVNGVWVGVHRDPAHLVSTVQNLRRKGMISHEVSL--IRDIRDREFKIFTDAG 171
Cdd:PRK08565  479 E--ILYELGVvpVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSG 556

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325560020  172 RVCRPLFVIENnpaspnrGNLVLTKQMLEQLeqdkqdlaaraaggdsddmDKAKLGWYRLINNGVVEYVDAEEEETIMIV 251
Cdd:PRK08565  557 RVRRPLIVVEN-------GKPKLTREHVEKL-------------------KKGELTFDDLVKMGVIEYLDAEEEENAYVA 610


                  ....*..
gi 325560020  252 MTPEDLL 258
Cdd:PRK08565  611 LDPEDLT 617
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 6-86 1.85e-35

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: 135.00  E-value: 1.85e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325560020   6 WGDQKKAaQSKAGVSQVLNRYTFASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCY 84
Cdd:cd00653  301 WGSKRFL-MQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMAR 379


                 ..
gi 325560020  85 IT 86
Cdd:cd00653  380 IS 381
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 120-181 1.46e-34

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: 119.78  E-value: 1.46e-34
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 325560020  120 IFVNGVWVGVHRDPAHLVSTVQNLRRKGMISHEVSLIRDIRDREFKIFTDAGRVCRPLFVIE 181
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 21-84 8.47e-33

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: 115.32  E-value: 8.47e-33
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 325560020   21 QVLNRYTFASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCY 84
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 16-110 7.87e-29

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 114.66  E-value: 7.87e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325560020  16 KAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITVGTPSEPII 95
Cdd:PRK09606 402 RTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVK 481

                         90
                 ....*....|....*
gi 325560020  96 DFMiqRNMEVLEEYE 110
Cdd:PRK09606 482 EIL--KELGVEPERG 494
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 118-257 1.21e-27

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 111.98  E-value: 1.21e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325560020 118 TKIFVNGVWVGVHRDPAHLVSTVQNLRRKGMISHEVSLIRDIRDREFKIFTDAGRVCRPLFVIENnpaspnrGNLVLTKQ 197
Cdd:PRK07225   5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLTEE 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 325560020 198 MLEQLEqdkqdlaaraaggdsddmdKAKLGWYRLINNGVVEYVDAEEEETIMIVMTPEDL 257
Cdd:PRK07225  78 HIEKLK-------------------NGELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDL 118
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 18-87 4.10e-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: 81.31  E-value: 4.10e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 325560020   18 GVSQVLNRYTFASTLSHLRRTNT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLALMCYITV 87
Cdd:COG0085   370 QLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNE 443
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 228-294 9.86e-17

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: 72.57  E-value: 9.86e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 325560020  228 WYRLINNGVVEYVDAEEEETIMIVMTPEDLLISQQLQQGfvlpednsndlnkrvkatpNPTAHTWTH 294
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREERE-------------------GPYAHTYTH 48
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
19-106 7.44e-08

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 53.86  E-value: 7.44e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 325560020   19 VSQVLNRYTFASTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCYIT----VGTP 90
Cdd:PRK14844  532 LSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINkygfIESP 611

                          90
                  ....*....|....*.
gi 325560020   91 SEPIIDFMIQRNMEVL 106
Cdd:PRK14844  612 YRKVVNRVVTDQIEYL 627
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
19-80 1.87e-06

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 49.15  E-value: 1.87e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 325560020   19 VSQVLNRYTFASTLSHLRRTNTpIGRDGKIA-----KPRQLHNTHWGLVCPAETPEGQACGLVKNLA 80
Cdd:PRK09603  525 LSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEGQNIGLINTLS 590
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 19-80 8.76e-06

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 47.01  E-value: 8.76e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 325560020   19 VSQVLNRYTFASTLSHLRRTNT--PIGRDG-KIAKP-RQLHNTHWGLVCPAETPEGQACGLVKNLA 80
Cdd:CHL00207  366 LSQYMDQTNPLSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIGSLA 431
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 52-80 5.50e-05

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 44.71  E-value: 5.50e-05
                          10        20
                  ....*....|....*....|....*....
gi 325560020   52 RQLHNTHWGLVCPAETPEGQACGLVKNLA 80
Cdd:PRK00405  469 RDVHPTHYGRICPIETPEGPNIGLINSLA 497
rpoB CHL00001
RNA polymerase beta subunit
 20-80 1.86e-04

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 42.97  E-value: 1.86e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 325560020   20 SQVLNRYTFASTLSHLRRTNT--PIGRDGKIA--KPRQLHNTHWGLVCPAETPEGQACGLVKNLA 80
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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