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Conserved domains on  [gi|955689357|gb|ALP92357|]
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RNA polymerase II, partial [Balboana sp. PO395]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNAP_largest_subunit_N super family cl19114
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ...
 1-185 1.50e-110

Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a 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 transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.


The actual alignment was detected with superfamily member cd02733:

Pssm-ID: 473139 [Multi-domain]  Cd Length: 751  Bit Score: 331.81  E-value: 1.50e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955689357   1 KMTKRDVFIEKEQMMNILMFLPSWDGKMPQPCILKPKPLWTGKQIFSLIIPGNVNMIRTHSTHpdeedDGPYKWISPGDT 80
Cdd:cd02733  427 KLTKRDTFLEKDQVMNLLMWLPDWDGKIPQPAILKPKPLWTGKQIFSLIIPKINNLIRSSSHH-----DGDKKWISPGDT 501

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955689357  81 KVMVEHGELVMGILCKKTLGTSAGSLLHICMLELGHEVCGRFYGNIQTVINNWLLLEGHSIGIGDTIADPQTYLEIQKAI 160
Cdd:cd02733  502 KVIIENGELLSGILCKKTVGASSGGLIHVIWLEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIGDTIADKETMKKIQETI 581

                        170       180
                 ....*....|....*....|....*
gi 955689357 161 KKAKEDVIEVIQKAHNMELEPTPGN 185
Cdd:cd02733  582 KKAKRDVIKLIEKAQNGELEPQPGK 606
 
Name Accession Description Interval E-value
RNAP_II_RPB1_N cd02733
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
 1-185 1.50e-110

Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.


Pssm-ID: 259848 [Multi-domain]  Cd Length: 751  Bit Score: 331.81  E-value: 1.50e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955689357   1 KMTKRDVFIEKEQMMNILMFLPSWDGKMPQPCILKPKPLWTGKQIFSLIIPGNVNMIRTHSTHpdeedDGPYKWISPGDT 80
Cdd:cd02733  427 KLTKRDTFLEKDQVMNLLMWLPDWDGKIPQPAILKPKPLWTGKQIFSLIIPKINNLIRSSSHH-----DGDKKWISPGDT 501

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955689357  81 KVMVEHGELVMGILCKKTLGTSAGSLLHICMLELGHEVCGRFYGNIQTVINNWLLLEGHSIGIGDTIADPQTYLEIQKAI 160
Cdd:cd02733  502 KVIIENGELLSGILCKKTVGASSGGLIHVIWLEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIGDTIADKETMKKIQETI 581

                        170       180
                 ....*....|....*....|....*
gi 955689357 161 KKAKEDVIEVIQKAHNMELEPTPGN 185
Cdd:cd02733  582 KKAKRDVIKLIEKAQNGELEPQPGK 606
RNA_pol_Rpb1_3 pfam04983
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-146 7.99e-48

RNA polymerase Rpb1, 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). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking.


Pssm-ID: 461507  Cd Length: 158  Bit Score: 153.17  E-value: 7.99e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955689357    1 KMTKRDVFIEKEQMMNILMFLPswdgKMPQPCILKP-KPLWTGKQIFSLIIPGNVNMIRTHSTHPDeeddgpykWISPGD 79
Cdd:pfam04983  24 LLTREDTFFDREEVMQLLMYGI----VLPHPAILKPiKPLWTGKQTFSRLLPNEINPKGKPKTNEE--------DLCEND 91

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 955689357   80 TKVMVEHGELVMGILCKKTLGTSAGSLLHICMLELGHEVCGRFYGNIQTVINNWLLLEGHSIGIGDT 146
Cdd:pfam04983  92 SYVLINNGELISGVIDKKTVGKSLGSLIHIIYKEYGPEETAKFLDRLQKLGFRYLTKSGFSIGIDDI 158
PRK08566 PRK08566
DNA-directed RNA polymerase subunit A'; Validated
 3-184 8.11e-32

DNA-directed RNA polymerase subunit A'; Validated


Pssm-ID: 236292 [Multi-domain]  Cd Length: 882  Bit Score: 120.35  E-value: 8.11e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955689357   3 TKRDVFIEKEQMMNILMFLPSWDGKMPQPCILKPKPLWTGKQIFSLIIPGNVNMIRTHSTHPDEEDDGPYKwiSPGDTKV 82
Cdd:PRK08566 511 TRKSTLFTKEEALDLLRAAGIDELPEPEPAIENGKPYWTGKQIFSLFLPKDLNLEFKAKICSGCDECKKED--CEHDAYV 588

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955689357  83 MVEHGELVMGILCKKTLGTSAGSLLHICMLELGHEVCGRFYGNIQTVINNWLLLEGHSIGIGDTIADPQTYLEIQKAIKK 162
Cdd:PRK08566 589 VIKNGKLLEGVIDKKAIGAEQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEE 668

                        170       180
                 ....*....|....*....|..
gi 955689357 163 AKEDVIEVIQKAHNMELEPTPG 184
Cdd:PRK08566 669 AEKRVEELIEAYENGELEPLPG 690
 
Name Accession Description Interval E-value
RNAP_II_RPB1_N cd02733
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ...
 1-185 1.50e-110

Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.


Pssm-ID: 259848 [Multi-domain]  Cd Length: 751  Bit Score: 331.81  E-value: 1.50e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955689357   1 KMTKRDVFIEKEQMMNILMFLPSWDGKMPQPCILKPKPLWTGKQIFSLIIPGNVNMIRTHSTHpdeedDGPYKWISPGDT 80
Cdd:cd02733  427 KLTKRDTFLEKDQVMNLLMWLPDWDGKIPQPAILKPKPLWTGKQIFSLIIPKINNLIRSSSHH-----DGDKKWISPGDT 501

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955689357  81 KVMVEHGELVMGILCKKTLGTSAGSLLHICMLELGHEVCGRFYGNIQTVINNWLLLEGHSIGIGDTIADPQTYLEIQKAI 160
Cdd:cd02733  502 KVIIENGELLSGILCKKTVGASSGGLIHVIWLEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIGDTIADKETMKKIQETI 581

                        170       180
                 ....*....|....*....|....*
gi 955689357 161 KKAKEDVIEVIQKAHNMELEPTPGN 185
Cdd:cd02733  582 KKAKRDVIKLIEKAQNGELEPQPGK 606
RNA_pol_Rpb1_3 pfam04983
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 1-146 7.99e-48

RNA polymerase Rpb1, 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). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking.


Pssm-ID: 461507  Cd Length: 158  Bit Score: 153.17  E-value: 7.99e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955689357    1 KMTKRDVFIEKEQMMNILMFLPswdgKMPQPCILKP-KPLWTGKQIFSLIIPGNVNMIRTHSTHPDeeddgpykWISPGD 79
Cdd:pfam04983  24 LLTREDTFFDREEVMQLLMYGI----VLPHPAILKPiKPLWTGKQTFSRLLPNEINPKGKPKTNEE--------DLCEND 91

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 955689357   80 TKVMVEHGELVMGILCKKTLGTSAGSLLHICMLELGHEVCGRFYGNIQTVINNWLLLEGHSIGIGDT 146
Cdd:pfam04983  92 SYVLINNGELISGVIDKKTVGKSLGSLIHIIYKEYGPEETAKFLDRLQKLGFRYLTKSGFSIGIDDI 158
RNAP_archeal_A' cd02582
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ...
 2-184 8.00e-35

A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins.


Pssm-ID: 259846 [Multi-domain]  Cd Length: 861  Bit Score: 129.29  E-value: 8.00e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955689357   2 MTKRDVFIEKEQMMNILMFLpSWDGKMPQPCILKPKPLWTGKQIFSLIIPGNVNMI-RTHSTHPDEEDDGPYKwisPGDT 80
Cdd:cd02582  506 LTRKTTLFTKEEALQLLSAA-GYDGLLPEPAILEPKPLWTGKQLFSLFLPKDLNFEgKAKVCSGCSECKDEDC---PNDG 581

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955689357  81 KVMVEHGELVMGILCKKTLGT-SAGSLLHICMLELGHEVCGRFYGNIQTVINNWLLLEGHSIGIGDTIADPQTYLEIQKA 159
Cdd:cd02582  582 YVVIKNGKLLEGVIDKKAIGAeQPGSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDEDIPEEARKEIEEI 661

                        170       180
                 ....*....|....*....|....*
gi 955689357 160 IKKAKEDVIEVIQKAHNMELEPTPG 184
Cdd:cd02582  662 IKEAEKKVYELIEQYKNGELEPLPG 686
RNAP_I_RPA1_N cd01435
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ...
 1-174 2.80e-33

Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the largest subunit of the eukaryotic RNA polymerase I (RNAP I). RNAP I is a multi-subunit protein complex responsible for the synthesis of rRNA precursors. RNAP I consists of at least 14 different subunits, the largest being homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. The yeast member of this family is known as Rpb190. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site. It makes up the head and core of one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between RPA1 and Rpb1 suggests a similar functional and structural role.


Pssm-ID: 259844 [Multi-domain]  Cd Length: 779  Bit Score: 124.60  E-value: 2.80e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955689357   1 KMTKRDVFIEKEQMMNILM----FLPSWDG----KMPQPCILKPKPLWTGKQIFSLI----IPGNVNMIRTHSTHPDEED 68
Cdd:cd01435  453 LLTSRDTFFTREEYQQLVYaalrPLFTSDKdgriKLLPPAILKPKPLWTGKQVISTIlknlIPGNAPLLNLSGKKKTKKK 532

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955689357  69 DGPYKW-ISPGDTKVMVEHGELVMGILCKKTLGTSAGSLLHiCMLEL-GHEVCGRFYGNIQTVINNWLLLEGHSIGIGDT 146
Cdd:cd01435  533 VGGGKWgGGSEESQVIIRNGELLTGVLDKSQFGASAYGLVH-AVYELyGGETAGKLLSALGRLFTAYLQMRGFTCGIEDL 611

                        170       180
                 ....*....|....*....|....*...
gi 955689357 147 IADPQTYLEIQKAIKKAKEDVIEVIQKA 174
Cdd:cd01435  612 LLTPKADEKRRKILRKAKKLGLEAAAEF 639
PRK08566 PRK08566
DNA-directed RNA polymerase subunit A'; Validated
 3-184 8.11e-32

DNA-directed RNA polymerase subunit A'; Validated


Pssm-ID: 236292 [Multi-domain]  Cd Length: 882  Bit Score: 120.35  E-value: 8.11e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955689357   3 TKRDVFIEKEQMMNILMFLPSWDGKMPQPCILKPKPLWTGKQIFSLIIPGNVNMIRTHSTHPDEEDDGPYKwiSPGDTKV 82
Cdd:PRK08566 511 TRKSTLFTKEEALDLLRAAGIDELPEPEPAIENGKPYWTGKQIFSLFLPKDLNLEFKAKICSGCDECKKED--CEHDAYV 588

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955689357  83 MVEHGELVMGILCKKTLGTSAGSLLHICMLELGHEVCGRFYGNIQTVINNWLLLEGHSIGIGDTIADPQTYLEIQKAIKK 162
Cdd:PRK08566 589 VIKNGKLLEGVIDKKAIGAEQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEE 668

                        170       180
                 ....*....|....*....|..
gi 955689357 163 AKEDVIEVIQKAHNMELEPTPG 184
Cdd:PRK08566 669 AEKRVEELIEAYENGELEPLPG 690
RNAP_III_RPC1_N cd02583
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ...
 2-184 4.86e-25

Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 (C160) subunit forms part of the active site region of RNAP III. RNAP III is one of the three distinct classes of nuclear RNAP in eukaryotes that is responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA genes, and some others. RNAP III is the largest nuclear RNA polymerase with 17 subunits. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site, making up the head and core of the one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between Rpc1 and Rpb1 suggests a similar functional and structural role.


Pssm-ID: 259847 [Multi-domain]  Cd Length: 816  Bit Score: 101.09  E-value: 4.86e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955689357   2 MTKRDVFIEKEQMMNIL--MFLPSWDGKMPQPCILKPKPLWTGKQIFSLII------PGNVNMI-RTHSTHPDEEDDgpy 72
Cdd:cd02583  480 LTSKDVFFDRAQFCQLCsyMLDGEIKIDLPPPAILKPVELWTGKQIFSLLLrpnkksPVLVNLEaKEKSYTKKSPDM--- 556

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955689357  73 kwiSPGDTKVMVEHGELVMGILCKKTLGT-SAGSLLHICMLELGHEVCGRFYGNIQTVINNWLLLEGHSIGIGDTIADPQ 151
Cdd:cd02583  557 ---CPNDGYVVIRNSELLCGRLDKSTLGSgSKNSLFYVLLRDYGPEAAAAAMNRLAKLSSRWLSNRGFSIGIDDVTPSKE 633

                        170       180       190
                 ....*....|....*....|....*....|...
gi 955689357 152 TYLEIQKAIKKAKEDVIEVIQKAHNMELEPTPG 184
Cdd:cd02583  634 LLKKKEELVDNGYAKCDEYIKQYKKGKLELQPG 666
PRK14977 PRK14977
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
 2-173 9.62e-18

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


Pssm-ID: 184940 [Multi-domain]  Cd Length: 1321  Bit Score: 80.07  E-value: 9.62e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955689357    2 MTKRDVFIEKEQMMNILMfLPSWDGKMPQPCI-LKPKPLWTGKQIFSLIIPGNVNMIRT--HSTHPDEEDDGPYkwiSPG 78
Cdd:PRK14977  526 ITKDDALFDKNEASNIAM-LAGITDPLPEPAIkTKDGPAWTGKQLFSLFLPKDFNFEGIakWSAGKAGEAKDPS---CLG 601

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955689357   79 DTKVMVEHGELVMGILCKKTLGTSAG---SLLHICMLELGHEVCGRFYGNIQTVINNWLLLEGHSIGIGDTIADPQTYLE 155
Cdd:PRK14977  602 DGYVLIKEGELISGVIDDNIIGALVEepeSLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQE 681

                         170
                  ....*....|....*...
gi 955689357  156 IQKAIKKAKEDVIEVIQK 173
Cdd:PRK14977  682 IEDDIQGMKDEVSDLIDQ 699
RNAP_IV_RPD1_N cd10506
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ...
 2-145 3.36e-11

Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 are the largest subunits of plant DNA-dependent RNA polymerase IV and V that, together with second largest subunits (NRPD2 and NRPE2), form the active site region of the DNA entry and RNA exit channel. Higher plants have five multi-subunit nuclear RNA polymerases; RNAP I, RNAP II and RNAP III, which are essential for viability, plus the two isoforms of the non-essential polymerase RNAP IV and V, which specialize in small RNA-mediated gene silencing pathways. RNAP IV and/or V might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. The subunit compositions of RNAP IV and V reveal that they evolved from RNAP II.


Pssm-ID: 259849 [Multi-domain]  Cd Length: 744  Bit Score: 60.88  E-value: 3.36e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955689357   2 MTKRDVFIEKEQMMNILMFLPSwdgKMPQPCILK----PKPLWTGKQIFSLIIPGNVNmirthSTHPDEEddgpykwisp 77
Cdd:cd10506  398 MTERGVFLDKAQMQQLQMLCPS---QLPPPAIIKsppsNGPLWTGKQLFQMLLPTDLD-----YSFPSNL---------- 459

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 955689357  78 gdtkVMVEHGELVMGILCKKTLGTSAGSLLHICMLELGHEVCGRFYGnIQTVINNWLLLEGHSIGIGD 145
Cdd:cd10506  460 ----VFISDGELISSSGGSSWLRDSEGNLFSILVKHGPGKALDFLDS-AQGLLCEWLSMRGFSVSLSD 522
 
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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