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Conserved domains on  [gi|1833300123|gb|QJC44991|]
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RNA polymerase II second largest subunit, partial [Alpova cinnamomeus]

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;
1-207 4.46e-55

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: 188.63  E-value: 4.46e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833300123    1 PAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTP-CTKVFVNGVWMGVHRDPANLVKTIKKL 79
Cdd:PRK08565   447 PFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYIsWSRVYLNGRLIGYHPDGEELAEKIREL 526

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833300123   80 RRKDDISPEVSV--VRDIRERELRLYTDAGRVCRPLFIVENQQLALQKKHIKWINQGyrdddgeEFKWEQLVKSGIIELL 157
Cdd:PRK08565   527 RRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKG-------ELTFDDLVKMGVIEYL 599

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 1833300123  158 DAEEEETVMISMTPEDlensrlqsagVNPQENDSDFDPAARLkaGINAHT 207
Cdd:PRK08565   600 DAEEEENAYVALDPED----------LTPEHTHLEIWPPAIL--GITASI 637
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-207 4.46e-55

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 188.63  E-value: 4.46e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833300123    1 PAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTP-CTKVFVNGVWMGVHRDPANLVKTIKKL 79
Cdd:PRK08565   447 PFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYIsWSRVYLNGRLIGYHPDGEELAEKIREL 526

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833300123   80 RRKDDISPEVSV--VRDIRERELRLYTDAGRVCRPLFIVENQQLALQKKHIKWINQGyrdddgeEFKWEQLVKSGIIELL 157
Cdd:PRK08565   527 RRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKG-------ELTFDDLVKMGVIEYL 599

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 1833300123  158 DAEEEETVMISMTPEDlensrlqsagVNPQENDSDFDPAARLkaGINAHT 207
Cdd:PRK08565   600 DAEEEENAYVALDPED----------LTPEHTHLEIWPPAIL--GITASI 637
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 56-117 4.11e-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: 123.63  E-value: 4.11e-37
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1833300123  56 VFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVE 117
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-32 3.10e-09

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: 56.04  E-value: 3.10e-09
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1833300123   1 PAETPEGQACGLVKNLALMACISvGSYSAPVI 32
Cdd:cd00653   359 PIETPEGENCGLVKNLALMARIS-GRIERPYR 389
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-24 1.04e-05

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: 45.49  E-value: 1.04e-05
                           10        20
                   ....*....|....*....|....
gi 1833300123    1 PAETPEGQACGLVKNLALMACISV 24
Cdd:COG0085    420 PIETPEGPNIGLIGSLALYARVNE 443
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-207 4.46e-55

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 188.63  E-value: 4.46e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833300123    1 PAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTP-CTKVFVNGVWMGVHRDPANLVKTIKKL 79
Cdd:PRK08565   447 PFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYIsWSRVYLNGRLIGYHPDGEELAEKIREL 526

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833300123   80 RRKDDISPEVSV--VRDIRERELRLYTDAGRVCRPLFIVENQQLALQKKHIKWINQGyrdddgeEFKWEQLVKSGIIELL 157
Cdd:PRK08565   527 RRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKG-------ELTFDDLVKMGVIEYL 599

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 1833300123  158 DAEEEETVMISMTPEDlensrlqsagVNPQENDSDFDPAARLkaGINAHT 207
Cdd:PRK08565   600 DAEEEENAYVALDPED----------LTPEHTHLEIWPPAIL--GITASI 637
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 56-117 4.11e-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: 123.63  E-value: 4.11e-37
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1833300123  56 VFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVE 117
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 54-174 1.86e-33

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 125.84  E-value: 1.86e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833300123  54 TKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIRERELRLYTDAGRVCRPLFIVENQQLALQKKHIKWINQ 133
Cdd:PRK07225    5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKN 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1833300123 134 GyrdddgeEFKWEQLVKSGIIELLDAEEEETVMISMTPEDL 174
Cdd:PRK07225   85 G-------ELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDL 118
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 145-212 8.40e-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: 79.12  E-value: 8.40e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1833300123 145 WEQLVKSGIIELLDAEEEETVMISMTPEDLENSRLQSagvnpqendsdfdpaarlKAGINAHTWTHCE 212
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREE------------------REGPYAHTYTHCE 50
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 1-41 1.91e-09

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 56.50  E-value: 1.91e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1833300123   1 PAETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLE 41
Cdd:PRK09606  450 PSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVE 490
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-32 3.10e-09

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: 56.04  E-value: 3.10e-09
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1833300123   1 PAETPEGQACGLVKNLALMACISvGSYSAPVI 32
Cdd:cd00653   359 PIETPEGENCGLVKNLALMARIS-GRIERPYR 389
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-20 1.04e-07

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: 47.52  E-value: 1.04e-07
                          10        20
                  ....*....|....*....|
gi 1833300123   1 PAETPEGQACGLVKNLALMA 20
Cdd:pfam04565  47 PVETPEGPNCGLVKHLALYA 66
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-24 1.04e-05

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: 45.49  E-value: 1.04e-05
                           10        20
                   ....*....|....*....|....
gi 1833300123    1 PAETPEGQACGLVKNLALMACISV 24
Cdd:COG0085    420 PIETPEGPNIGLIGSLALYARVNE 443
 
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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