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Conserved domains on  [gi|38232393|gb|AAR15032|]
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RNA polymerase II largest subunit, partial [Trachyiulus nordquisti]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNAP_largest_subunit_C super family cl29012
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ...
 1-139 1.21e-88

Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.


The actual alignment was detected with superfamily member cd02584:

Pssm-ID: 355888 [Multi-domain]  Cd Length: 410  Bit Score: 263.30  E-value: 1.21e-88
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38232393   1 AGVSAKNVTLGVPRLKEIINISKKPKTPSLTVFLTGAAARDAEKAKDVLCRLEHTTLRKVTANTAIYYDPDPQNTVIAED 80
Cdd:cd02584  53 AGVSAKNVTLGVPRLKEIINVAKNIKTPSLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEED 132

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 38232393  81 QEFVNVYYEMPDFDPT--RISPWLLRIELDRKRMTDKKLTMEQISEKINAGFGDDLNCIFN 139
Cdd:cd02584 133 KEFVESYFEFPDEDVEqdRLSPWLLRIELDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFS 193
 
Name Accession Description Interval E-value
RNAP_II_Rpb1_C cd02584
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
 1-139 1.21e-88

Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.


Pssm-ID: 132720 [Multi-domain]  Cd Length: 410  Bit Score: 263.30  E-value: 1.21e-88
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38232393   1 AGVSAKNVTLGVPRLKEIINISKKPKTPSLTVFLTGAAARDAEKAKDVLCRLEHTTLRKVTANTAIYYDPDPQNTVIAED 80
Cdd:cd02584  53 AGVSAKNVTLGVPRLKEIINVAKNIKTPSLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEED 132

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 38232393  81 QEFVNVYYEMPDFDPT--RISPWLLRIELDRKRMTDKKLTMEQISEKINAGFGDDLNCIFN 139
Cdd:cd02584 133 KEFVESYFEFPDEDVEqdRLSPWLLRIELDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFS 193
RNA_pol_Rpb1_7 pfam04990
RNA polymerase Rpb1, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ...
 55-139 1.90e-53

RNA polymerase Rpb1, domain 7; 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, domain 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (pfam04561).


Pssm-ID: 461510 [Multi-domain]  Cd Length: 136  Bit Score: 164.63  E-value: 1.90e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38232393    55 TTLRKVTANTAIYYDPDPQNTVIAEDQEFVNVYYEMPDFD---PTRISPWLLRIELDRKRMTDKKLTMEQISEKINAGFG 131
Cdd:pfam04990   1 TTLRSVTAATEIYYDPDPRNTVIEEDREFVESYFEIPDEDvedLDRQSPWLLRIELDRKKMLDKGLTMEDVAEKIKEEFG 80


                  ....*...
gi 38232393   132 DDLNCIFN 139
Cdd:pfam04990  81 NDLFVIFS 88
PRK04309 PRK04309
DNA-directed RNA polymerase subunit A''; Validated
 1-133 5.27e-18

DNA-directed RNA polymerase subunit A''; Validated


Pssm-ID: 235277 [Multi-domain]  Cd Length: 383  Bit Score: 78.35  E-value: 5.27e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38232393    1 AGVSAKNVTLGVPRLKEIINISKKPKTPSLTVFLTGAAARDAEKAKDVLCRLEHTTLRKVTANTAIyydpDPQNTVIaed 80
Cdd:PRK04309  85 AGVAEINVTLGLPRLIEIVDARKEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISV----DLANMTI--- 157

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 38232393   81 qefvnvyyempdfdptrispwllRIELDRKRMTDKKLTMEQISEKINAGFGDD 133
Cdd:PRK04309 158 -----------------------IIELDEEMLEDRGLTVDDVKEAIEKKKGGE 187
 
Name Accession Description Interval E-value
RNAP_II_Rpb1_C cd02584
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ...
 1-139 1.21e-88

Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.


Pssm-ID: 132720 [Multi-domain]  Cd Length: 410  Bit Score: 263.30  E-value: 1.21e-88
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38232393   1 AGVSAKNVTLGVPRLKEIINISKKPKTPSLTVFLTGAAARDAEKAKDVLCRLEHTTLRKVTANTAIYYDPDPQNTVIAED 80
Cdd:cd02584  53 AGVSAKNVTLGVPRLKEIINVAKNIKTPSLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEED 132

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 38232393  81 QEFVNVYYEMPDFDPT--RISPWLLRIELDRKRMTDKKLTMEQISEKINAGFGDDLNCIFN 139
Cdd:cd02584 133 KEFVESYFEFPDEDVEqdRLSPWLLRIELDRKKMTDKKLSMEQIAKKIKEEFKDDLNVIFS 193
RNA_pol_Rpb1_7 pfam04990
RNA polymerase Rpb1, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ...
 55-139 1.90e-53

RNA polymerase Rpb1, domain 7; 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, domain 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (pfam04561).


Pssm-ID: 461510 [Multi-domain]  Cd Length: 136  Bit Score: 164.63  E-value: 1.90e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38232393    55 TTLRKVTANTAIYYDPDPQNTVIAEDQEFVNVYYEMPDFD---PTRISPWLLRIELDRKRMTDKKLTMEQISEKINAGFG 131
Cdd:pfam04990   1 TTLRSVTAATEIYYDPDPRNTVIEEDREFVESYFEIPDEDvedLDRQSPWLLRIELDRKKMLDKGLTMEDVAEKIKEEFG 80


                  ....*...
gi 38232393   132 DDLNCIFN 139
Cdd:pfam04990  81 NDLFVIFS 88
RNA_pol_Rpb1_5 pfam04998
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-127 3.31e-34

RNA polymerase Rpb1, 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). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.


Pssm-ID: 398596 [Multi-domain]  Cd Length: 516  Bit Score: 124.00  E-value: 3.31e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38232393     1 AGVSAKNVTLGVPRLKEIINISKKPKTPSLTVFLTGAAARDAEKAKDVLCRLEHTTLRKVTANTAIYYDPDPQNTVIAED 80
Cdd:pfam04998 206 AGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYLFDEVGRELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISD 285

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 38232393    81 QEFVNVYYEMPDF--------DPTRISPWLLRIELDRKRMTDKKLTMEQISEKIN 127
Cdd:pfam04998 286 VKGVVKFFDIIDEvtneeeidPETGLLILVIRLLKILNKSIKKVVKSEVIPRSIR 340
RNAP_A'' cd06528
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ...
 1-133 1.74e-21

A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.


Pssm-ID: 132725 [Multi-domain]  Cd Length: 363  Bit Score: 88.08  E-value: 1.74e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38232393   1 AGVSAKNVTLGVPRLKEIINISKKPKTPSLTVFLTGAAARDAEKAKDVLCRLEHTTLRKVTANTAIyydpDPQNTVIaed 80
Cdd:cd06528  66 AGVAEINVTLGLPRLIEIVDARKEPSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISI----DLFNMRI--- 138

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 38232393  81 qefvnvyyempdfdptrispwllRIELDRKRMTDKKLTMEQISEKINAGFGDD 133
Cdd:cd06528 139 -----------------------TIELDEEMLEDRGITVDDVLKAIEKLKKGK 168
PRK04309 PRK04309
DNA-directed RNA polymerase subunit A''; Validated
 1-133 5.27e-18

DNA-directed RNA polymerase subunit A''; Validated


Pssm-ID: 235277 [Multi-domain]  Cd Length: 383  Bit Score: 78.35  E-value: 5.27e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38232393    1 AGVSAKNVTLGVPRLKEIINISKKPKTPSLTVFLTGAAARDAEKAKDVLCRLEHTTLRKVTANTAIyydpDPQNTVIaed 80
Cdd:PRK04309  85 AGVAEINVTLGLPRLIEIVDARKEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISV----DLANMTI--- 157

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 38232393   81 qefvnvyyempdfdptrispwllRIELDRKRMTDKKLTMEQISEKINAGFGDD 133
Cdd:PRK04309 158 -----------------------IIELDEEMLEDRGLTVDDVKEAIEKKKGGE 187
PRK14898 PRK14898
DNA-directed RNA polymerase subunit A''; Provisional
 1-126 3.82e-16

DNA-directed RNA polymerase subunit A''; Provisional


Pssm-ID: 237854 [Multi-domain]  Cd Length: 858  Bit Score: 73.77  E-value: 3.82e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38232393    1 AGVSAKNVTLGVPRLKEIINISKKPKTPSLTVFLTGAAARDAEKAKDVLCRLEHTTLRKVTANTAIyydpdpqntviaed 80
Cdd:PRK14898 551 AGVAEINVTLGLPRMIEIVDARKEPSTPIMTVHLKGEYATDREKAEEVAKKIESLTLGDVATSIAI-------------- 616

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 38232393   81 qefvnvyyempDFDPTRIspwllRIELDRKRMTDKKLTMEQISEKI 126
Cdd:PRK14898 617 -----------DLWTQSI-----KVELDEETLADRGLTIESVEEAI 646
RNAP_III_Rpc1_C cd02736
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ...
 1-127 1.46e-14

Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.


Pssm-ID: 132723 [Multi-domain]  Cd Length: 300  Bit Score: 68.40  E-value: 1.46e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38232393   1 AGVSAKNVTLGVPRLKEIINISKKPKTPSLTVFLTgaAARDAEKAKDVLCRLEHTTLRKVTANTAIYYDPDpqntviaed 80
Cdd:cd02736  36 AGVASMNITLGVPRIKEIINASKNISTPIITAKLE--NDRDEKSARIVKGRIEKTYLGEVASYIEEVYSPD--------- 104

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
gi 38232393  81 qefvNVYyempdfdptrispwlLRIELDRKRMTDKKLTMEQISEKIN 127
Cdd:cd02736 105 ----DCY---------------ILIKLDKKIIEKLQLSKSNLYFLLQ 132
PRK14897 PRK14897
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
 1-126 4.82e-13

unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional


Pssm-ID: 237853 [Multi-domain]  Cd Length: 509  Bit Score: 64.83  E-value: 4.82e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38232393    1 AGVSAKNVTLGVPRLKEIINISKKPKTPSLTVFLTGAAARDAEKAKDVLCRLEHTTLRKVtantaiyydpdpqntviaed 80
Cdd:PRK14897 208 AGVAEMNVTLGLPRLIEIVDARKKPSTPTMTIYLKKDYREDEEKVREVAKKIENTTLIDV-------------------- 267

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 38232393   81 QEFVNVYYEMPdfdptrispwlLRIELDRKRMTDKKLTMEQISEKI 126
Cdd:PRK14897 268 ADIITDIAEMS-----------VVVELDEEKMKERLIEYDDILAAI 302
RNAP_I_Rpa1_C cd02735
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ...
 1-52 2.12e-10

Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.


Pssm-ID: 132722 [Multi-domain]  Cd Length: 309  Bit Score: 56.82  E-value: 2.12e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 38232393   1 AGVSAKNVTLGVPRLKEII-NISKKPKTPSLTV-FLTGAAARDAEKAKDVLCRL 52
Cdd:cd02735  36 AGRGEMNVTLGIPRLREILmTASKNIKTPSMTLpLKNGKSAERAETLKKRLSRV 89
PRK14977 PRK14977
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
 1-68 2.23e-10

bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional


Pssm-ID: 184940 [Multi-domain]  Cd Length: 1321  Bit Score: 57.34  E-value: 2.23e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 38232393     1 AGVSAKNVTLGVPRLKEIINISKKPKTPSLTVFLTGAAARDAEKAKDVLCRLEHTTLRKVTANTAIYY 68
Cdd:PRK14977 1004 AGIKAMDVTHGLERFIELVDARAKPSTPTMDIYLDDECKEDIEKAIEIARNLKELKVRALIADSAIDN 1071
 
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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