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Conserved domains on  [gi|295873300|gb|ADG48732|]
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CG1554, partial [Drosophila melanogaster]

Protein Classification

RNA_pol_Rpb1_6 and RNAP_largest_subunit_C domain-containing protein( domain architecture ID 13706573)

RNA_pol_Rpb1_6 and RNAP_largest_subunit_C domain-containing protein

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 ...
 117-264 3.40e-106

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: 313.76  E-value: 3.40e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295873300 117 FRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAP 196
Cdd:cd02584    1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 295873300 197 SLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIYYDPDPQRTVISEDQEFVNVYYEMPDFDPT 264
Cdd:cd02584   81 SLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVE 148
RNA_pol_Rpb1_6 pfam04992
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 4-138 7.55e-76

RNA polymerase Rpb1, 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, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.


:

Pssm-ID: 461511  Cd Length: 188  Bit Score: 228.54  E-value: 7.55e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295873300    4 SSEAIQELEAEWDRLVSDRDSLRQ-IFPNGESKVV-LPCNLQRMIWNVQKIFHINKRLPTDLSPIRVIKGVKTLLERCVI 81
Cdd:pfam04992  52 DPEVQQLLDEEYEQLLEDRELLREiIFPTGDSKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVV 131

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 295873300   82 VTGNDRISKQANENATLLFQCLIRSTLCTKYVSEEFRLSTEAFEWLVGEIETRFQQA 138
Cdd:pfam04992 132 VRGDDPLSKEAQENATLLFKILLRSRLASKRVLEEYRLNKEAFDWVLGEIESRFLQA 188
 
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 ...
 117-264 3.40e-106

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: 313.76  E-value: 3.40e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295873300 117 FRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAP 196
Cdd:cd02584    1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 295873300 197 SLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIYYDPDPQRTVISEDQEFVNVYYEMPDFDPT 264
Cdd:cd02584   81 SLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVE 148
RNA_pol_Rpb1_6 pfam04992
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 4-138 7.55e-76

RNA polymerase Rpb1, 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, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.


Pssm-ID: 461511  Cd Length: 188  Bit Score: 228.54  E-value: 7.55e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295873300    4 SSEAIQELEAEWDRLVSDRDSLRQ-IFPNGESKVV-LPCNLQRMIWNVQKIFHINKRLPTDLSPIRVIKGVKTLLERCVI 81
Cdd:pfam04992  52 DPEVQQLLDEEYEQLLEDRELLREiIFPTGDSKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVV 131

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 295873300   82 VTGNDRISKQANENATLLFQCLIRSTLCTKYVSEEFRLSTEAFEWLVGEIETRFQQA 138
Cdd:pfam04992 132 VRGDDPLSKEAQENATLLFKILLRSRLASKRVLEEYRLNKEAFDWVLGEIESRFLQA 188
RNA_pol_Rpb1_5 pfam04998
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 80-267 4.68e-75

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: 237.25  E-value: 4.68e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295873300   80 VIVTGNDRISKQANENATLLFQCLIRSTLCTKYVSEEFRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPAT 159
Cdd:pfam04998 117 DSKLGRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKAFVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGT 196

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295873300  160 QMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIYYDPD 239
Cdd:pfam04998 197 QMTLNTFHFAGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYLFDEVGRELEKAKKVYGAIEKVTLGSVVESGEILYDPD 276

                         170       180
                  ....*....|....*....|....*...
gi 295873300  240 PQRTVISEDQEFVNVYYEMPDFDPTRNS 267
Cdd:pfam04998 277 PFNTPIISDVKGVVKFFDIIDEVTNEEE 304
PRK04309 PRK04309
DNA-directed RNA polymerase subunit A''; Validated
 115-250 2.84e-36

DNA-directed RNA polymerase subunit A''; Validated


Pssm-ID: 235277 [Multi-domain]  Cd Length: 383  Bit Score: 132.66  E-value: 2.84e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295873300 115 EEFRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPK 194
Cdd:PRK04309  31 EERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKEPS 110

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 295873300 195 APSLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIyyDPDPQRTVISEDQE 250
Cdd:PRK04309 111 TPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISV--DLANMTIIIELDEE 164
RNA_pol_rpoA2 TIGR02389
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
 119-250 3.71e-34

DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 274105 [Multi-domain]  Cd Length: 367  Bit Score: 126.71  E-value: 3.71e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295873300  119 LSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSL 198
Cdd:TIGR02389  20 SDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKTPSTPSM 99

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 295873300  199 TVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIYYdpdPQRTVISE-DQE 250
Cdd:TIGR02389 100 TIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISIDL---ADMTVIIElDEE 149
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
 141-173 3.48e-04

DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439856 [Multi-domain]  Cd Length: 1165  Bit Score: 41.68  E-value: 3.48e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 295873300  141 NPGEMVGALAAQSLGEPATQMTLNTFHFAGVSS 173
Cdd:COG0086   876 NIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAAS 908
 
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 ...
 117-264 3.40e-106

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: 313.76  E-value: 3.40e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295873300 117 FRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAP 196
Cdd:cd02584    1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 295873300 197 SLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIYYDPDPQRTVISEDQEFVNVYYEMPDFDPT 264
Cdd:cd02584   81 SLTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVE 148
RNA_pol_Rpb1_6 pfam04992
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 4-138 7.55e-76

RNA polymerase Rpb1, 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, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.


Pssm-ID: 461511  Cd Length: 188  Bit Score: 228.54  E-value: 7.55e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295873300    4 SSEAIQELEAEWDRLVSDRDSLRQ-IFPNGESKVV-LPCNLQRMIWNVQKIFHINKRLPTDLSPIRVIKGVKTLLERCVI 81
Cdd:pfam04992  52 DPEVQQLLDEEYEQLLEDRELLREiIFPTGDSKVPqLPVNIQRIIQNAQKIFHIDDRKPSDLHPIYVIEGVRELLDRLVV 131

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 295873300   82 VTGNDRISKQANENATLLFQCLIRSTLCTKYVSEEFRLSTEAFEWLVGEIETRFQQA 138
Cdd:pfam04992 132 VRGDDPLSKEAQENATLLFKILLRSRLASKRVLEEYRLNKEAFDWVLGEIESRFLQA 188
RNA_pol_Rpb1_5 pfam04998
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ...
 80-267 4.68e-75

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: 237.25  E-value: 4.68e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295873300   80 VIVTGNDRISKQANENATLLFQCLIRSTLCTKYVSEEFRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPAT 159
Cdd:pfam04998 117 DSKLGRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKAFVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGT 196

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295873300  160 QMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIYYDPD 239
Cdd:pfam04998 197 QMTLNTFHFAGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYLFDEVGRELEKAKKVYGAIEKVTLGSVVESGEILYDPD 276

                         170       180
                  ....*....|....*....|....*...
gi 295873300  240 PQRTVISEDQEFVNVYYEMPDFDPTRNS 267
Cdd:pfam04998 277 PFNTPIISDVKGVVKFFDIIDEVTNEEE 304
RNAP_A'' cd06528
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ...
 113-250 3.35e-39

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: 139.69  E-value: 3.35e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295873300 113 VSEEFRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKK 192
Cdd:cd06528   10 VLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIVDARKE 89

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 295873300 193 PKAPSLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIyyDPDPQRTVISEDQE 250
Cdd:cd06528   90 PSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISI--DLFNMRITIELDEE 145
RNAP_III_Rpc1_C cd02736
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ...
 134-239 9.23e-37

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: 131.96  E-value: 9.23e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295873300 134 RFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGGaaRDAEKA 213
Cdd:cd02736    1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITAKLEND--RDEKSA 78

                         90       100
                 ....*....|....*....|....*.
gi 295873300 214 KNVLCRLEHTTLRKVTANTAIYYDPD 239
Cdd:cd02736   79 RIVKGRIEKTYLGEVASYIEEVYSPD 104
PRK04309 PRK04309
DNA-directed RNA polymerase subunit A''; Validated
 115-250 2.84e-36

DNA-directed RNA polymerase subunit A''; Validated


Pssm-ID: 235277 [Multi-domain]  Cd Length: 383  Bit Score: 132.66  E-value: 2.84e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295873300 115 EEFRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPK 194
Cdd:PRK04309  31 EERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKEPS 110

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 295873300 195 APSLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIyyDPDPQRTVISEDQE 250
Cdd:PRK04309 111 TPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISV--DLANMTIIIELDEE 164
RNA_pol_rpoA2 TIGR02389
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ...
 119-250 3.71e-34

DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 274105 [Multi-domain]  Cd Length: 367  Bit Score: 126.71  E-value: 3.71e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295873300  119 LSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSL 198
Cdd:TIGR02389  20 SDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKTPSTPSM 99

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 295873300  199 TVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIYYdpdPQRTVISE-DQE 250
Cdd:TIGR02389 100 TIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISIDL---ADMTVIIElDEE 149
RNAP_I_Rpa1_C cd02735
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ...
 134-220 5.93e-33

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: 121.92  E-value: 5.93e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295873300 134 RFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEII-NISKKPKAPSLTV-FLTGGAARDAE 211
Cdd:cd02735    1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILmTASKNIKTPSMTLpLKNGKSAERAE 80


                 ....*....
gi 295873300 212 KAKNVLCRL 220
Cdd:cd02735   81 TLKKRLSRV 89
PRK14897 PRK14897
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
 113-243 6.03e-33

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


Pssm-ID: 237853 [Multi-domain]  Cd Length: 509  Bit Score: 125.69  E-value: 6.03e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295873300 113 VSEEFRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKK 192
Cdd:PRK14897 152 AMKKKELSDDEYEEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVDARKK 231

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 295873300 193 PKAPSLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVT------ANTAIYYDPDPQRT 243
Cdd:PRK14897 232 PSTPTMTIYLKKDYREDEEKVREVAKKIENTTLIDVAdiitdiAEMSVVVELDEEKM 288
PRK14977 PRK14977
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
 7-236 2.67e-25

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


Pssm-ID: 184940 [Multi-domain]  Cd Length: 1321  Bit Score: 104.72  E-value: 2.67e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295873300    7 AIQELEAEWDRLVsdRDSLRQI--FPNGESKVvlpcnlqrmiwNVQKIFHINKRLPTDLSPIRVIKGVKTLLERCVIVTG 84
Cdd:PRK14977  863 ALEDIRLEYDETV--RDPHGHIiqFKFGEDGI-----------DPQKLDHGEAFNLERIIEKQKIEDRGKGASKDEIEEL 929

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 295873300   85 NDRISKQANENATLLFQCLIRSTlctkyvseefRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTLN 164
Cdd:PRK14977  930 AKEYTKTFNANLPKLLADAIHGA----------ELKEDELEAICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLR 999

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 295873300  165 TFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAIYY 236
Cdd:PRK14977 1000 TFHAAGIKAMDVTHGLERFIELVDARAKPSTPTMDIYLDDECKEDIEKAIEIARNLKELKVRALIADSAIDN 1071
RNAP_largest_subunit_C cd00630
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ...
 143-190 9.03e-25

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.


Pssm-ID: 132719 [Multi-domain]  Cd Length: 158  Bit Score: 96.72  E-value: 9.03e-25
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 295873300 143 GEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINIS 190
Cdd:cd00630    1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA 48
RNA_pol_Rpb1_7 pfam04990
RNA polymerase Rpb1, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ...
 223-263 1.17e-21

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: 87.59  E-value: 1.17e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 295873300  223 TTLRKVTANTAIYYDPDPQRTVISEDQEFVNVYYEMPDFDP 263
Cdd:pfam04990   1 TTLRSVTAATEIYYDPDPRNTVIEEDREFVESYFEIPDEDV 41
PRK14898 PRK14898
DNA-directed RNA polymerase subunit A''; Provisional
 159-234 1.85e-17

DNA-directed RNA polymerase subunit A''; Provisional


Pssm-ID: 237854 [Multi-domain]  Cd Length: 858  Bit Score: 81.86  E-value: 1.85e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 295873300 159 TQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGGAARDAEKAKNVLCRLEHTTLRKVTANTAI 234
Cdd:PRK14898 541 THNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPSTPIMTVHLKGEYATDREKAEEVAKKIESLTLGDVATSIAI 616
rpoC_TIGR TIGR02386
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ...
 140-195 1.65e-12

DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 274103 [Multi-domain]  Cd Length: 1140  Bit Score: 67.00  E-value: 1.65e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 295873300   140 ANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSS--KNVTLGVPRLKEIINiSKKPKA 195
Cdd:TIGR02386  868 VEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGasGDITQGLPRVKELFE-ARTPKD 924
RNAP_beta'_C cd02655
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ...
 141-186 1.43e-11

Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.


Pssm-ID: 132721 [Multi-domain]  Cd Length: 204  Bit Score: 62.16  E-value: 1.43e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 295873300 141 NPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSkNVTLGVPRLKEI 186
Cdd:cd02655    4 ELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT-DITQGLPRVEEL 48
PRK00566 PRK00566
DNA-directed RNA polymerase subunit beta'; Provisional
 141-196 5.48e-11

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 234794 [Multi-domain]  Cd Length: 1156  Bit Score: 62.39  E-value: 5.48e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 295873300  141 NPGEMVGALAAQSLGEPATQMTLNTFHFAGVsskNVTLGVPRLKEIINiSKKPKAP 196
Cdd:PRK00566  877 NIGEAVGVIAAQSIGEPGTQLTMRTFHTGGV---DITGGLPRVAELFE-ARKPKGP 928
PRK14906 PRK14906
DNA-directed RNA polymerase subunit beta';
141-194 2.91e-10

DNA-directed RNA polymerase subunit beta';


Pssm-ID: 184899 [Multi-domain]  Cd Length: 1460  Bit Score: 60.66  E-value: 2.91e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 295873300  141 NPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINIsKKPK 194
Cdd:PRK14906  972 NIGTAVGIIAAQSIGEPGTQLTMRTFHSGGVAGDDITQGLPRVAELFEA-RKPK 1024
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
140-175 2.37e-09

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 57.63  E-value: 2.37e-09
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 295873300  140 ANPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKN 175
Cdd:PRK09603 2274 SYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRS 2309
rpoC2 PRK02597
DNA-directed RNA polymerase subunit beta'; Provisional
 143-176 2.26e-08

DNA-directed RNA polymerase subunit beta'; Provisional


Pssm-ID: 235052 [Multi-domain]  Cd Length: 1331  Bit Score: 54.62  E-value: 2.26e-08
                          10        20        30
                  ....*....|....*....|....*....|....
gi 295873300  143 GEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNV 176
Cdd:PRK02597  311 GEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 344
rpoC2 CHL00117
RNA polymerase beta'' subunit; Reviewed
 143-171 5.90e-08

RNA polymerase beta'' subunit; Reviewed


Pssm-ID: 214368 [Multi-domain]  Cd Length: 1364  Bit Score: 53.40  E-value: 5.90e-08
                          10        20
                  ....*....|....*....|....*....
gi 295873300  143 GEMVGALAAQSLGEPATQMTLNTFHFAGV 171
Cdd:CHL00117  315 GEAVGIIAGQSIGEPGTQLTLRTFHTGGV 343
rpoC2_cyan TIGR02388
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ...
 143-176 2.01e-07

DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 274104 [Multi-domain]  Cd Length: 1227  Bit Score: 51.77  E-value: 2.01e-07
                           10        20        30
                   ....*....|....*....|....*....|....
gi 295873300   143 GEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNV 176
Cdd:TIGR02388  309 GEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 342
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
143-176 5.03e-07

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 50.78  E-value: 5.03e-07
                          10        20        30
                  ....*....|....*....|....*....|....
gi 295873300  143 GEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNV 176
Cdd:PRK14844 2333 GEAVGVIAAQSVGEPGTQLTMRTFHIGGVMTRGV 2366
PRK14898 PRK14898
DNA-directed RNA polymerase subunit A''; Provisional
 113-163 9.33e-07

DNA-directed RNA polymerase subunit A''; Provisional


Pssm-ID: 237854 [Multi-domain]  Cd Length: 858  Bit Score: 49.89  E-value: 9.33e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 295873300 113 VSEEFRLSTEAFEWLVGEIETRFQQAQANPGEMVGALAAQSLGEPATQMTL 163
Cdd:PRK14898  27 LSKRDGVTEEMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSL 77
RpoC COG0086
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ...
 141-173 3.48e-04

DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439856 [Multi-domain]  Cd Length: 1165  Bit Score: 41.68  E-value: 3.48e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 295873300  141 NPGEMVGALAAQSLGEPATQMTLNTFHFAGVSS 173
Cdd:COG0086   876 NIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAAS 908
 
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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