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Conserved domains on  [gi|1899287339|gb|QNO58436|]
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RNA polymerase II second largest subunit, partial [Xeromphalina campanelloides]

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;
2-223 7.25e-59

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: 199.80  E-value: 7.25e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899287339    2 ETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTP-CTKVFVNGVWMGVHRDPANLVKTIKKLRR 80
Cdd:PRK08565   449 ETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYIsWSRVYLNGRLIGYHPDGEELAEKIRELRR 528

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899287339   81 KDDISPEVSV--VRDIREKELRLYTDAGRVCRPLFIVENQQLALQKKHVRWLNQGynadgeEYKWEQLVKSGIVELLDAE 158
Cdd:PRK08565   529 SGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKG------ELTFDDLVKMGVIEYLDAE 602

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1899287339  159 EEETVMISMTPEDLensrlqasgIDPHendgefdpaarlkaginshtwTHCEIHPSMILGICASI 223
Cdd:PRK08565   603 EEENAYVALDPEDL---------TPEH---------------------THLEIWPPAILGITASI 637
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 2-223 7.25e-59

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 199.80  E-value: 7.25e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899287339    2 ETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTP-CTKVFVNGVWMGVHRDPANLVKTIKKLRR 80
Cdd:PRK08565   449 ETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYIsWSRVYLNGRLIGYHPDGEELAEKIRELRR 528

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899287339   81 KDDISPEVSV--VRDIREKELRLYTDAGRVCRPLFIVENQQLALQKKHVRWLNQGynadgeEYKWEQLVKSGIVELLDAE 158
Cdd:PRK08565   529 SGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKG------ELTFDDLVKMGVIEYLDAE 602

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1899287339  159 EEETVMISMTPEDLensrlqasgIDPHendgefdpaarlkaginshtwTHCEIHPSMILGICASI 223
Cdd:PRK08565   603 EEENAYVALDPEDL---------TPEH---------------------THLEIWPPAILGITASI 637
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 55-116 6.36e-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: 6.36e-37
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1899287339  55 VFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVE 116
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-31 4.97e-08

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: 52.57  E-value: 4.97e-08
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1899287339   1 AETPEGQACGLVKNLALMACISvGSYSAPVI 31
Cdd:cd00653   360 IETPEGENCGLVKNLALMARIS-GRIERPYR 389
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 2-23 4.27e-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: 43.94  E-value: 4.27e-05
                           10        20
                   ....*....|....*....|..
gi 1899287339    2 ETPEGQACGLVKNLALMACISV 23
Cdd:COG0085    422 ETPEGPNIGLIGSLALYARVNE 443
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 2-223 7.25e-59

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 199.80  E-value: 7.25e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899287339    2 ETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLESLEENAHSSTP-CTKVFVNGVWMGVHRDPANLVKTIKKLRR 80
Cdd:PRK08565   449 ETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYIsWSRVYLNGRLIGYHPDGEELAEKIRELRR 528

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899287339   81 KDDISPEVSV--VRDIREKELRLYTDAGRVCRPLFIVENQQLALQKKHVRWLNQGynadgeEYKWEQLVKSGIVELLDAE 158
Cdd:PRK08565   529 SGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKG------ELTFDDLVKMGVIEYLDAE 602

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1899287339  159 EEETVMISMTPEDLensrlqasgIDPHendgefdpaarlkaginshtwTHCEIHPSMILGICASI 223
Cdd:PRK08565   603 EEENAYVALDPEDL---------TPEH---------------------THLEIWPPAILGITASI 637
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 53-223 3.16e-37

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 136.63  E-value: 3.16e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899287339  53 TKVFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVENQQLALQKKHVRWLNQ 132
Cdd:PRK07225    5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKN 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1899287339 133 GynadgeEYKWEQLVKSGIVELLDAEEEETVMISMTPEDLEnsrlqasgiDPHendgefdpaarlkaginshtwTHCEIH 212
Cdd:PRK07225   85 G------ELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLT---------EEH---------------------THLEID 128

                         170
                  ....*....|.
gi 1899287339 213 PSMILGICASI 223
Cdd:PRK07225  129 PSLILGIGAGM 139
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 55-116 6.36e-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: 6.36e-37
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1899287339  55 VFVNGVWMGVHRDPANLVKTIKKLRRKDDISPEVSVVRDIREKELRLYTDAGRVCRPLFIVE 116
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 143-213 3.01e-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: 87.98  E-value: 3.01e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1899287339 143 WEQLVKSGIVELLDAEEEETVMISMTPEDLENSRLQAsgidphendgefdpaarlKAGINSHTWTHCEIHP 213
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREE------------------REGPYAHTYTHCEIHP 53
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 2-40 1.73e-08

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 53.80  E-value: 1.73e-08
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1899287339   2 ETPEGQACGLVKNLALMACISVGSYSAPVIEFLEEWGLE 40
Cdd:PRK09606  452 ETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGVE 490
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-31 4.97e-08

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: 52.57  E-value: 4.97e-08
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1899287339   1 AETPEGQACGLVKNLALMACISvGSYSAPVI 31
Cdd:cd00653   360 IETPEGENCGLVKNLALMARIS-GRIERPYR 389
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-19 1.86e-06

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: 44.05  E-value: 1.86e-06
                          10
                  ....*....|....*....
gi 1899287339   1 AETPEGQACGLVKNLALMA 19
Cdd:pfam04565  48 VETPEGPNCGLVKHLALYA 66
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 2-23 4.27e-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: 43.94  E-value: 4.27e-05
                           10        20
                   ....*....|....*....|..
gi 1899287339    2 ETPEGQACGLVKNLALMACISV 23
Cdd:COG0085    422 ETPEGPNIGLIGSLALYARVNE 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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