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Conserved domains on  [gi|110629958|gb|ABG80495|]
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RNA polymerase II second largest subunit, partial [Calonarius albertii]

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;
1-229 1.29e-66

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: 222.14  E-value: 1.29e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110629958    1 KNLALMACISVGSIAAPVIEFLEEWGLESLEEHSHSM*PS-TKIFVNGVWIGVHRDPANLVKTLKKLRRKDDISPEISV- 78
Cdd:PRK08565  460 KNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISwSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVa 539

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110629958   79 -VRDIREKELRVYTDAGRVCRPLFIVENQHLVLQKKHVRWLNNGvndegeEFKWDRLIKGGIVELLDAEEEETVMISMTP 157
Cdd:PRK08565  540 yIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKG------ELTFDDLVKMGVIEYLDAEEEENAYVALDP 613

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 110629958  158 EDLensrlqrtgadlqandsdfdpaarlkagTHAHtwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAM 229
Cdd:PRK08565  614 EDL----------------------------TPEH--THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAM 655
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-229 1.29e-66

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 222.14  E-value: 1.29e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110629958    1 KNLALMACISVGSIAAPVIEFLEEWGLESLEEHSHSM*PS-TKIFVNGVWIGVHRDPANLVKTLKKLRRKDDISPEISV- 78
Cdd:PRK08565  460 KNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISwSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVa 539

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110629958   79 -VRDIREKELRVYTDAGRVCRPLFIVENQHLVLQKKHVRWLNNGvndegeEFKWDRLIKGGIVELLDAEEEETVMISMTP 157
Cdd:PRK08565  540 yIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKG------ELTFDDLVKMGVIEYLDAEEEENAYVALDP 613

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 110629958  158 EDLensrlqrtgadlqandsdfdpaarlkagTHAHtwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAM 229
Cdd:PRK08565  614 EDL----------------------------TPEH--THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAM 655
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 43-104 5.89e-36

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: 121.32  E-value: 5.89e-36
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 110629958   43 IFVNGVWIGVHRDPANLVKTLKKLRRKDDISPEISVVRDIREKELRVYTDAGRVCRPLFIVE 104
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 195-230 7.85e-23

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: 96.48  E-value: 7.85e-23
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 110629958 195 THCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMG 230
Cdd:cd00653  396 THIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQ 431
 
Name Accession Description Interval E-value
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 1-229 1.29e-66

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 222.14  E-value: 1.29e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110629958    1 KNLALMACISVGSIAAPVIEFLEEWGLESLEEHSHSM*PS-TKIFVNGVWIGVHRDPANLVKTLKKLRRKDDISPEISV- 78
Cdd:PRK08565  460 KNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISwSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVa 539

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110629958   79 -VRDIREKELRVYTDAGRVCRPLFIVENQHLVLQKKHVRWLNNGvndegeEFKWDRLIKGGIVELLDAEEEETVMISMTP 157
Cdd:PRK08565  540 yIETGEINEVYVNCDSGRVRRPLIVVENGKPKLTREHVEKLKKG------ELTFDDLVKMGVIEYLDAEEEENAYVALDP 613

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 110629958  158 EDLensrlqrtgadlqandsdfdpaarlkagTHAHtwTHCEIHPSMILGICASIIPFPDHNQSPRNTYQSAM 229
Cdd:PRK08565  614 EDL----------------------------TPEH--THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAM 655
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 41-230 7.46e-51

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 173.99  E-value: 7.46e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110629958  41 TKIFVNGVWIGVHRDPANLVKTLKKLRRKDDISPEISVVRDIREKELRVYTDAGRVCRPLFIVENQHLVLQKKHVRWLNN 120
Cdd:PRK07225   5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEPLLTEEHIEKLKN 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110629958 121 GvndegeEFKWDRLIKGGIVELLDAEEEETVMISMTPEDLensrlqrtgadlqandsdfdpaarlkagTHAHTwtHCEIH 200
Cdd:PRK07225  85 G------ELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDL----------------------------TEEHT--HLEID 128

                        170       180       190
                 ....*....|....*....|....*....|
gi 110629958 201 PSMILGICASIIPFPDHNQSPRNTYQSAMG 230
Cdd:PRK07225 129 PSLILGIGAGMIPYPEHNASPRITMGAGMI 158
RNA_pol_Rpb2_4 pfam04566
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ...
 43-104 5.89e-36

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: 121.32  E-value: 5.89e-36
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 110629958   43 IFVNGVWIGVHRDPANLVKTLKKLRRKDDISPEISVVRDIREKELRVYTDAGRVCRPLFIVE 104
Cdd:pfam04566   1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 195-230 7.85e-23

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: 96.48  E-value: 7.85e-23
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 110629958 195 THCEIHPSMILGICASIIPFPDHNQSPRNTYQSAMG 230
Cdd:cd00653  396 THIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQ 431
RNA_pol_Rpb2_5 pfam04567
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 131-201 2.34e-22

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: 86.06  E-value: 2.34e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 110629958  131 WDRLIKGGIVELLDAEEEETVMISMTPEDLENSRLQRtgadlqandsdfdpaarlKAGTHAHTWTHCEIHP 201
Cdd:pfam04567   1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREE------------------REGPYAHTYTHCEIHP 53
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 208-230 4.92e-09

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: 55.61  E-value: 4.92e-09
                          10        20
                  ....*....|....*....|...
gi 110629958  208 CASIIPFPDHNQSPRNTYQSAMG 230
Cdd:pfam00562   1 VASLIPFVDHNQSPRNTYQCAMG 23
 
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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