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Conserved domains on  [gi|79602097|ref|NP_973525|]
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DNA/RNA polymerases superfamily protein [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RNA_pol pfam00940
DNA-dependent RNA polymerase; This is a family of single chain RNA polymerases.
602-879 1.42e-157

DNA-dependent RNA polymerase; This is a family of single chain RNA polymerases.


:

Pssm-ID: 460006  Cd Length: 411  Bit Score: 467.75  E-value: 1.42e-157
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097   602 RPLGKSGLHWLKIHLANLYagGVEKLSHDARLAFVENHLDDIMDSAENPIHGKRWWLKAEDPFQCLAACVILTQALKSPS 681
Cdd:pfam00940   1 KPLGERGLRWLKIHLANLY--GFDKASLDERVAFVEDNLEDILDSAENPLDGRRWWLKAEDPWQCLAACFELANALRSPD 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097   682 PYSVISHLPIHQDGSCNGLQHYAALGRDSFEAAAVNLVAGEKPADVYSEISRRVHEIMKKDSSKDPEsnptaaLAKILIT 761
Cdd:pfam00940  79 PEEYVSHLPVHQDGSCNGLQHYAALGGDEEGAKQVNLVPSDRPQDVYSGVAELVEEKIEKDAAKGNE------IAKLLKG 152
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097   762 QVDRKLVKQTVMTSVYGVTYVGAREQIKRRLEEKGVITDERMLFAAACYSAKVTLAALGEIFEAARAIMSWLGDCAKIIA 841
Cdd:pfam00940 153 KITRKVVKQTVMTNVYGVTFIGAREQIEKQLKEIGDFPGEEDLYKASSYLAKKIFDSIGELFTGAHEIQDWLGECAKRIA 232
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 79602097   842 S------DNHPVRWITPLGLPVVQPYCRSERHLIRTSLQVLALQ 879
Cdd:pfam00940 233 KsvppeqSMSPVIWTTPLGLPVVQPYRKSKKKQVKTNLQSVSIS 276
PHA00452 super family cl42978
T3/T7-like RNA polymerase
162-873 4.05e-145

T3/T7-like RNA polymerase


The actual alignment was detected with superfamily member PHA00452:

Pssm-ID: 222797 [Multi-domain]  Cd Length: 807  Bit Score: 449.47  E-value: 4.05e-145
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  162 LRRRQVKEETEAWERMVDEYRDLEKEMCEKNLAPNLPYVKHMFLGWFQPLKDVIEREQKLQKNKSKKvrAAYAPHIELLP 241
Cdd:PHA00452   5 LAAEQLQLEEEAYGEGEERFRKALERQLEAGEADDNPVARRLLATLLPPVAEAIDAWKEEYKKRGRA--AKARGLLRLVD 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  242 ADKMAVIVMHKMMGLVMSGhEDGCIQVVqaAVSIGIAIEQEVRIHNFlkrtRKNNAGDSQEELKEkqLLRKRVNSLIRRK 321
Cdd:PHA00452  83 PEVLAVITLKVTLDMLLSK-ETPTAQAV--ATAIGRAIEDEIRFGRI----EDLNPKYFKKVVEY--LKRSRTGSVYHIA 153
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  322 RIID-ALKVVKSEGTKPWGRATQAKLGSRLLELLIEAayvqppltqsgDSIPEFrpafrhrfKTVTKYPGSKLVRRYGVI 400
Cdd:PHA00452 154 FMMVvEADMVLLGEWDPWPKEDYIHVGKWLLEALIES-----------TGLVEL--------VRHTGGNGGKDHEYLELS 214
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  401 ECDSLLLAGLDKSAKHMLIPYVPMLVPPKRWKGYDKGGYL---FLPSYIMRTHGSKkqqdALKDISHKTAHRVFEALDTL 477
Cdd:PHA00452 215 EEAVELLQDIAAAAAGISPMYQPMVVPPKPWTSIVGGGYHtegRRPLAPLVRKTKK----ALRRYRQKQMPEVYKAVNAL 290
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  478 GNTKWRVNRNILDVVERLWADGgNIAGLVNREDVPIPEKPSSED--PEELQSWKWSARKANKINRERHSLRCDVELKLSV 555
Cdd:PHA00452 291 QNTAWRINKDVLAVVNEVVNWG-PVGDVLGIPRRPLPPKPEFLDenEEAFKAWKRAAAAWYTKEKERVSKRRRLEFMLRV 369
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  556 ARKMKDEEGFYYPHNLDFRGRAYPMhPHLNHLSSDLCRGTLEFAEGRPLGKSGLHWLKIHLANLYagGVEKLSHDARLAF 635
Cdd:PHA00452 370 ANKFADYKAIYFPYNMDWRGRVYAV-SMLNPQGSDLQKALLRFAEGKPLGKRGLYWLKVHGANCY--GVDKVTFDERAAW 446
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  636 VENHLDDIMDSAENPIHGkRWWLKAEDPFQCLAACVILTQALKSPSPYsvISHLPIHQDGSCNGLQHYAALGRDSFEAAA 715
Cdd:PHA00452 447 VDENHDNILAAAEDPLNN-TWWAEADSPLCFLAACFEYAAAVHSGTSY--VSGLPVAMDGTCSGLQHFSAMLRDEVGGRA 523
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  716 VNLVAGEKPADVYSEISRRVHEIMKKDsSKDPESNPTAALAKILITQVDRKLVKQTVMTSVYGVTYVGAREQIKRRLEEK 795
Cdd:PHA00452 524 VNLLPSDKPQDIYGIVAEVVNEKLERD-AINGTDNTRALARLWLAYGITRSLTKRPVMTLPYGSTRFSCRDYILEDLLQP 602
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  796 GVI-TDERML-FAAACYSAKVTLAALGEIFEAARAIMSWLGDCAKIIASD-NHPVRWITPLGLPVVQPYCRSERHLIRTS 872
Cdd:PHA00452 603 GIDeGDGAMFtNQAASYMAKLIWDAISETVPAAVEAMNWLQQAAKLLAAKgAEALHWTTPTGFPVWQEYRKPEEKRVRLR 682

                 .
gi 79602097  873 L 873
Cdd:PHA00452 683 L 683
 
Name Accession Description Interval E-value
RNA_pol pfam00940
DNA-dependent RNA polymerase; This is a family of single chain RNA polymerases.
602-879 1.42e-157

DNA-dependent RNA polymerase; This is a family of single chain RNA polymerases.


Pssm-ID: 460006  Cd Length: 411  Bit Score: 467.75  E-value: 1.42e-157
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097   602 RPLGKSGLHWLKIHLANLYagGVEKLSHDARLAFVENHLDDIMDSAENPIHGKRWWLKAEDPFQCLAACVILTQALKSPS 681
Cdd:pfam00940   1 KPLGERGLRWLKIHLANLY--GFDKASLDERVAFVEDNLEDILDSAENPLDGRRWWLKAEDPWQCLAACFELANALRSPD 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097   682 PYSVISHLPIHQDGSCNGLQHYAALGRDSFEAAAVNLVAGEKPADVYSEISRRVHEIMKKDSSKDPEsnptaaLAKILIT 761
Cdd:pfam00940  79 PEEYVSHLPVHQDGSCNGLQHYAALGGDEEGAKQVNLVPSDRPQDVYSGVAELVEEKIEKDAAKGNE------IAKLLKG 152
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097   762 QVDRKLVKQTVMTSVYGVTYVGAREQIKRRLEEKGVITDERMLFAAACYSAKVTLAALGEIFEAARAIMSWLGDCAKIIA 841
Cdd:pfam00940 153 KITRKVVKQTVMTNVYGVTFIGAREQIEKQLKEIGDFPGEEDLYKASSYLAKKIFDSIGELFTGAHEIQDWLGECAKRIA 232
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 79602097   842 S------DNHPVRWITPLGLPVVQPYCRSERHLIRTSLQVLALQ 879
Cdd:pfam00940 233 KsvppeqSMSPVIWTTPLGLPVVQPYRKSKKKQVKTNLQSVSIS 276
PHA00452 PHA00452
T3/T7-like RNA polymerase
162-873 4.05e-145

T3/T7-like RNA polymerase


Pssm-ID: 222797 [Multi-domain]  Cd Length: 807  Bit Score: 449.47  E-value: 4.05e-145
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  162 LRRRQVKEETEAWERMVDEYRDLEKEMCEKNLAPNLPYVKHMFLGWFQPLKDVIEREQKLQKNKSKKvrAAYAPHIELLP 241
Cdd:PHA00452   5 LAAEQLQLEEEAYGEGEERFRKALERQLEAGEADDNPVARRLLATLLPPVAEAIDAWKEEYKKRGRA--AKARGLLRLVD 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  242 ADKMAVIVMHKMMGLVMSGhEDGCIQVVqaAVSIGIAIEQEVRIHNFlkrtRKNNAGDSQEELKEkqLLRKRVNSLIRRK 321
Cdd:PHA00452  83 PEVLAVITLKVTLDMLLSK-ETPTAQAV--ATAIGRAIEDEIRFGRI----EDLNPKYFKKVVEY--LKRSRTGSVYHIA 153
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  322 RIID-ALKVVKSEGTKPWGRATQAKLGSRLLELLIEAayvqppltqsgDSIPEFrpafrhrfKTVTKYPGSKLVRRYGVI 400
Cdd:PHA00452 154 FMMVvEADMVLLGEWDPWPKEDYIHVGKWLLEALIES-----------TGLVEL--------VRHTGGNGGKDHEYLELS 214
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  401 ECDSLLLAGLDKSAKHMLIPYVPMLVPPKRWKGYDKGGYL---FLPSYIMRTHGSKkqqdALKDISHKTAHRVFEALDTL 477
Cdd:PHA00452 215 EEAVELLQDIAAAAAGISPMYQPMVVPPKPWTSIVGGGYHtegRRPLAPLVRKTKK----ALRRYRQKQMPEVYKAVNAL 290
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  478 GNTKWRVNRNILDVVERLWADGgNIAGLVNREDVPIPEKPSSED--PEELQSWKWSARKANKINRERHSLRCDVELKLSV 555
Cdd:PHA00452 291 QNTAWRINKDVLAVVNEVVNWG-PVGDVLGIPRRPLPPKPEFLDenEEAFKAWKRAAAAWYTKEKERVSKRRRLEFMLRV 369
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  556 ARKMKDEEGFYYPHNLDFRGRAYPMhPHLNHLSSDLCRGTLEFAEGRPLGKSGLHWLKIHLANLYagGVEKLSHDARLAF 635
Cdd:PHA00452 370 ANKFADYKAIYFPYNMDWRGRVYAV-SMLNPQGSDLQKALLRFAEGKPLGKRGLYWLKVHGANCY--GVDKVTFDERAAW 446
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  636 VENHLDDIMDSAENPIHGkRWWLKAEDPFQCLAACVILTQALKSPSPYsvISHLPIHQDGSCNGLQHYAALGRDSFEAAA 715
Cdd:PHA00452 447 VDENHDNILAAAEDPLNN-TWWAEADSPLCFLAACFEYAAAVHSGTSY--VSGLPVAMDGTCSGLQHFSAMLRDEVGGRA 523
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  716 VNLVAGEKPADVYSEISRRVHEIMKKDsSKDPESNPTAALAKILITQVDRKLVKQTVMTSVYGVTYVGAREQIKRRLEEK 795
Cdd:PHA00452 524 VNLLPSDKPQDIYGIVAEVVNEKLERD-AINGTDNTRALARLWLAYGITRSLTKRPVMTLPYGSTRFSCRDYILEDLLQP 602
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  796 GVI-TDERML-FAAACYSAKVTLAALGEIFEAARAIMSWLGDCAKIIASD-NHPVRWITPLGLPVVQPYCRSERHLIRTS 872
Cdd:PHA00452 603 GIDeGDGAMFtNQAASYMAKLIWDAISETVPAAVEAMNWLQQAAKLLAAKgAEALHWTTPTGFPVWQEYRKPEEKRVRLR 682

                 .
gi 79602097  873 L 873
Cdd:PHA00452 683 L 683
RPO41 COG5108
Mitochondrial DNA-directed RNA polymerase [Transcription];
165-874 4.17e-114

Mitochondrial DNA-directed RNA polymerase [Transcription];


Pssm-ID: 444054 [Multi-domain]  Cd Length: 826  Bit Score: 368.47  E-value: 4.17e-114
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097 165 RQVKEETEAWERMVDE-YRDLEKEMCEKNLAPNlPYVKHMFLGWFQPLKDVIEREQKLQKNKSKKVRAAYAPHIELLPAD 243
Cdd:COG5108  13 RQIALEEEMAEAGRSRfVERIEKARKRGEESGT-QYGRRIISDAVELLAEAIEATIDESSSGGAGNWHTAYAYLRELDAE 91
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097 244 KMAVIVMHKMMGLVMSGHedgciQVVQAAVSIGIAIEQEVRIHNFLKRTRknnagDSQEELKEKqlLRKRVNSLIRRKRI 323
Cdd:COG5108  92 VLAYLALRQCLDAVTQRH-----TLQAVAIRIASMVEDEVRGEAIREAFK-----DFYPRGKKK--IESRTSRAVRYKDD 159
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097 324 IDALKVVKSEGTKPWGRATQAKLGSRLLELLIEAAYVqppltqsgdsipefrpafrhrFKTVTKYPGSKLVRRYGVIECD 403
Cdd:COG5108 160 FERRVKNAVAKEEDWPVSDKIHVGFKLIELVVESTGL---------------------VEIARDTEGINDTPVFVRPTET 218
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097 404 SL-LLAGLDKSAKHMLIPYVPMLVPPKRWKGYDKGGYLflpSYIMRT-----HGSKKQQDALKDISHKtahRVFEALDTL 477
Cdd:COG5108 219 TLeWIAEANLRMAMLSPAYLPMVVPPRNWTTPFRGGYL---SGEVRRlplvkTRNRKYLEELKNGDMP---EVYAAVNAL 292
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097 478 GNTKWRVNRNILDVVERLWADGGNiAGLVNREDVPIPEKPSSE---DPEEL--QSWKWSARKANKINRERHSLRCDVELK 552
Cdd:COG5108 293 QQTPWTINRYVLAVMKWLWERDLD-LGLPQREPITPPIKPENRediTTNQVarKRWKKAARKIYIANAKLCSKRVQFRRD 371
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097 553 LSVARKMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDLCRGTLEFAEGRPLGKSGLHWLKIHLANLYagGVEKLSHDAR 632
Cdd:COG5108 372 LNEAERFSDYREFYFPYQLDFRGRVYAVPAFLNPQGQDHAKGLLMFADGKPIGDGGAKWLAIHGANVW--GYDKASLEER 449
                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097 633 LAFVENHLDDIMDSAENpiHGKRWWLKAEDPFQCLAACVILTQALKspSPYSVISHLPIHQDGSCNGLQHYAALGRDSFE 712
Cdd:COG5108 450 VKWVEDNYEAILAAAAD--YVAEFWSKADKPWQFLAFCREWYGYDQ--HGEGYVSGLPIAMDGSCSGLQHYSAMLRDEVG 525
                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097 713 AAAVNLVAGEKPADVYSEISR----RVHEIMKKDSSKDPE-SNPTAALA-KILITQVDRKLVKQTVMTSVYGVTYVGARE 786
Cdd:COG5108 526 GAAVNLVPSDKPQDIYAFVAEvdinLAQRIGCPDELTTNEiLNGIMDMAhNWLAFGITRKVTKRNVMTLPYGSTEYGFRD 605
                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097 787 QIKRRL-EEKGVITDERMLFAAACYSAKVTLA-----ALGEIFEAARAIMSWLGDCAKIIASDNHPVRWITPLGLPVVQP 860
Cdd:COG5108 606 QVREDMiTRKKEEEGEPFPFGGDGFSAAMWLAkliwdAIGEVVVAARRGMDWLQDLAGIAAKEGLPVIWTTPLGFPVMQD 685
                       730
                ....*....|....
gi 79602097 861 YCRSERHLIRTSLQ 874
Cdd:COG5108 686 YRSSKARRINTTTR 699
RPOL_N pfam14700
DNA-directed RNA polymerase N-terminal; This is the N-terminal domain of DNA-directed RNA ...
165-479 1.96e-91

DNA-directed RNA polymerase N-terminal; This is the N-terminal domain of DNA-directed RNA polymerase. This domain has a role in interaction with regions of upstream promoter DNA and the nascent RNA chain, leading to the processivity of the enzyme. In order to make mRNA transcripts the RNA polymerase undergoes a transition from the initiation phase (which only makes short fragments of RNA) to an elongation phase. This domain undergoes a structural change in the transition from initiation to elongation phase. The structural change results in abolition of the promoter binding site, creation of a channel accommodating the heteroduplex in the active site and formation of an exit tunnel which the RNA transcript passes through after peeling off the heteroduplex.


Pssm-ID: 464270  Cd Length: 286  Bit Score: 290.67  E-value: 1.96e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097   165 RQVKEETEAWERMVDEYRDLEKEMCEKNLAPNLP-YVKHMFLGWFQPLKDVIEREQKLQKNKSKKV-------RAAYAPH 236
Cdd:pfam14700   1 RQLRLERDSVEAAVERWREEFEELQKRGLNTNLPkSLNALLWQWYEALLPAIKEEIELLKAAEAKPkktkdkeRCEYGPY 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097   237 IELLPADKMAVIVMHKMMGLVMSGHEDGCIQVVQAAVSIGIAIEQEVRIHNFLKRTRKNnagdsqeelkekqllrkrvns 316
Cdd:pfam14700  81 LRLLPPEKLAAITILELLSLLSTGGVDKGMKVSRLAISIGKAVEDEYRAQQLLKKEKKK--------------------- 139
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097   317 lirrkriidalkvvKSEGTKPWGRATQAKLGSRLLELLIEAAYVQPPLTQSGDSIPEFR--PAFRHRFKtvtkypgSKLV 394
Cdd:pfam14700 140 --------------IKKKKIPWPQEVRAKVGAVLLSLLIETAKVPVTAEDPETGEKVIQpqPAFYHSYQ-------YKRG 198
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097   395 RRYGVIECDSLLLAGL-DKSAKHMLIP-YVPMLVPPKRWKGYDKGGYLFLPSYIMRTHGSKKQQDALKD-ISHKTAHRVF 471
Cdd:pfam14700 199 KKVGVIKPHPELVKLLlREPARDTLTPrHLPMLVPPKPWTSYNKGGYLLSPSKLMRTKDGDEQRAYLKAaSERGDLDQVF 278

                  ....*...
gi 79602097   472 EALDTLGN 479
Cdd:pfam14700 279 DGLDVLGN 286
 
Name Accession Description Interval E-value
RNA_pol pfam00940
DNA-dependent RNA polymerase; This is a family of single chain RNA polymerases.
602-879 1.42e-157

DNA-dependent RNA polymerase; This is a family of single chain RNA polymerases.


Pssm-ID: 460006  Cd Length: 411  Bit Score: 467.75  E-value: 1.42e-157
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097   602 RPLGKSGLHWLKIHLANLYagGVEKLSHDARLAFVENHLDDIMDSAENPIHGKRWWLKAEDPFQCLAACVILTQALKSPS 681
Cdd:pfam00940   1 KPLGERGLRWLKIHLANLY--GFDKASLDERVAFVEDNLEDILDSAENPLDGRRWWLKAEDPWQCLAACFELANALRSPD 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097   682 PYSVISHLPIHQDGSCNGLQHYAALGRDSFEAAAVNLVAGEKPADVYSEISRRVHEIMKKDSSKDPEsnptaaLAKILIT 761
Cdd:pfam00940  79 PEEYVSHLPVHQDGSCNGLQHYAALGGDEEGAKQVNLVPSDRPQDVYSGVAELVEEKIEKDAAKGNE------IAKLLKG 152
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097   762 QVDRKLVKQTVMTSVYGVTYVGAREQIKRRLEEKGVITDERMLFAAACYSAKVTLAALGEIFEAARAIMSWLGDCAKIIA 841
Cdd:pfam00940 153 KITRKVVKQTVMTNVYGVTFIGAREQIEKQLKEIGDFPGEEDLYKASSYLAKKIFDSIGELFTGAHEIQDWLGECAKRIA 232
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 79602097   842 S------DNHPVRWITPLGLPVVQPYCRSERHLIRTSLQVLALQ 879
Cdd:pfam00940 233 KsvppeqSMSPVIWTTPLGLPVVQPYRKSKKKQVKTNLQSVSIS 276
PHA00452 PHA00452
T3/T7-like RNA polymerase
162-873 4.05e-145

T3/T7-like RNA polymerase


Pssm-ID: 222797 [Multi-domain]  Cd Length: 807  Bit Score: 449.47  E-value: 4.05e-145
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  162 LRRRQVKEETEAWERMVDEYRDLEKEMCEKNLAPNLPYVKHMFLGWFQPLKDVIEREQKLQKNKSKKvrAAYAPHIELLP 241
Cdd:PHA00452   5 LAAEQLQLEEEAYGEGEERFRKALERQLEAGEADDNPVARRLLATLLPPVAEAIDAWKEEYKKRGRA--AKARGLLRLVD 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  242 ADKMAVIVMHKMMGLVMSGhEDGCIQVVqaAVSIGIAIEQEVRIHNFlkrtRKNNAGDSQEELKEkqLLRKRVNSLIRRK 321
Cdd:PHA00452  83 PEVLAVITLKVTLDMLLSK-ETPTAQAV--ATAIGRAIEDEIRFGRI----EDLNPKYFKKVVEY--LKRSRTGSVYHIA 153
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  322 RIID-ALKVVKSEGTKPWGRATQAKLGSRLLELLIEAayvqppltqsgDSIPEFrpafrhrfKTVTKYPGSKLVRRYGVI 400
Cdd:PHA00452 154 FMMVvEADMVLLGEWDPWPKEDYIHVGKWLLEALIES-----------TGLVEL--------VRHTGGNGGKDHEYLELS 214
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  401 ECDSLLLAGLDKSAKHMLIPYVPMLVPPKRWKGYDKGGYL---FLPSYIMRTHGSKkqqdALKDISHKTAHRVFEALDTL 477
Cdd:PHA00452 215 EEAVELLQDIAAAAAGISPMYQPMVVPPKPWTSIVGGGYHtegRRPLAPLVRKTKK----ALRRYRQKQMPEVYKAVNAL 290
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  478 GNTKWRVNRNILDVVERLWADGgNIAGLVNREDVPIPEKPSSED--PEELQSWKWSARKANKINRERHSLRCDVELKLSV 555
Cdd:PHA00452 291 QNTAWRINKDVLAVVNEVVNWG-PVGDVLGIPRRPLPPKPEFLDenEEAFKAWKRAAAAWYTKEKERVSKRRRLEFMLRV 369
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  556 ARKMKDEEGFYYPHNLDFRGRAYPMhPHLNHLSSDLCRGTLEFAEGRPLGKSGLHWLKIHLANLYagGVEKLSHDARLAF 635
Cdd:PHA00452 370 ANKFADYKAIYFPYNMDWRGRVYAV-SMLNPQGSDLQKALLRFAEGKPLGKRGLYWLKVHGANCY--GVDKVTFDERAAW 446
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  636 VENHLDDIMDSAENPIHGkRWWLKAEDPFQCLAACVILTQALKSPSPYsvISHLPIHQDGSCNGLQHYAALGRDSFEAAA 715
Cdd:PHA00452 447 VDENHDNILAAAEDPLNN-TWWAEADSPLCFLAACFEYAAAVHSGTSY--VSGLPVAMDGTCSGLQHFSAMLRDEVGGRA 523
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  716 VNLVAGEKPADVYSEISRRVHEIMKKDsSKDPESNPTAALAKILITQVDRKLVKQTVMTSVYGVTYVGAREQIKRRLEEK 795
Cdd:PHA00452 524 VNLLPSDKPQDIYGIVAEVVNEKLERD-AINGTDNTRALARLWLAYGITRSLTKRPVMTLPYGSTRFSCRDYILEDLLQP 602
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097  796 GVI-TDERML-FAAACYSAKVTLAALGEIFEAARAIMSWLGDCAKIIASD-NHPVRWITPLGLPVVQPYCRSERHLIRTS 872
Cdd:PHA00452 603 GIDeGDGAMFtNQAASYMAKLIWDAISETVPAAVEAMNWLQQAAKLLAAKgAEALHWTTPTGFPVWQEYRKPEEKRVRLR 682

                 .
gi 79602097  873 L 873
Cdd:PHA00452 683 L 683
RPO41 COG5108
Mitochondrial DNA-directed RNA polymerase [Transcription];
165-874 4.17e-114

Mitochondrial DNA-directed RNA polymerase [Transcription];


Pssm-ID: 444054 [Multi-domain]  Cd Length: 826  Bit Score: 368.47  E-value: 4.17e-114
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097 165 RQVKEETEAWERMVDE-YRDLEKEMCEKNLAPNlPYVKHMFLGWFQPLKDVIEREQKLQKNKSKKVRAAYAPHIELLPAD 243
Cdd:COG5108  13 RQIALEEEMAEAGRSRfVERIEKARKRGEESGT-QYGRRIISDAVELLAEAIEATIDESSSGGAGNWHTAYAYLRELDAE 91
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097 244 KMAVIVMHKMMGLVMSGHedgciQVVQAAVSIGIAIEQEVRIHNFLKRTRknnagDSQEELKEKqlLRKRVNSLIRRKRI 323
Cdd:COG5108  92 VLAYLALRQCLDAVTQRH-----TLQAVAIRIASMVEDEVRGEAIREAFK-----DFYPRGKKK--IESRTSRAVRYKDD 159
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097 324 IDALKVVKSEGTKPWGRATQAKLGSRLLELLIEAAYVqppltqsgdsipefrpafrhrFKTVTKYPGSKLVRRYGVIECD 403
Cdd:COG5108 160 FERRVKNAVAKEEDWPVSDKIHVGFKLIELVVESTGL---------------------VEIARDTEGINDTPVFVRPTET 218
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097 404 SL-LLAGLDKSAKHMLIPYVPMLVPPKRWKGYDKGGYLflpSYIMRT-----HGSKKQQDALKDISHKtahRVFEALDTL 477
Cdd:COG5108 219 TLeWIAEANLRMAMLSPAYLPMVVPPRNWTTPFRGGYL---SGEVRRlplvkTRNRKYLEELKNGDMP---EVYAAVNAL 292
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097 478 GNTKWRVNRNILDVVERLWADGGNiAGLVNREDVPIPEKPSSE---DPEEL--QSWKWSARKANKINRERHSLRCDVELK 552
Cdd:COG5108 293 QQTPWTINRYVLAVMKWLWERDLD-LGLPQREPITPPIKPENRediTTNQVarKRWKKAARKIYIANAKLCSKRVQFRRD 371
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097 553 LSVARKMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDLCRGTLEFAEGRPLGKSGLHWLKIHLANLYagGVEKLSHDAR 632
Cdd:COG5108 372 LNEAERFSDYREFYFPYQLDFRGRVYAVPAFLNPQGQDHAKGLLMFADGKPIGDGGAKWLAIHGANVW--GYDKASLEER 449
                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097 633 LAFVENHLDDIMDSAENpiHGKRWWLKAEDPFQCLAACVILTQALKspSPYSVISHLPIHQDGSCNGLQHYAALGRDSFE 712
Cdd:COG5108 450 VKWVEDNYEAILAAAAD--YVAEFWSKADKPWQFLAFCREWYGYDQ--HGEGYVSGLPIAMDGSCSGLQHYSAMLRDEVG 525
                       570       580       590       600       610       620       630       640
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097 713 AAAVNLVAGEKPADVYSEISR----RVHEIMKKDSSKDPE-SNPTAALA-KILITQVDRKLVKQTVMTSVYGVTYVGARE 786
Cdd:COG5108 526 GAAVNLVPSDKPQDIYAFVAEvdinLAQRIGCPDELTTNEiLNGIMDMAhNWLAFGITRKVTKRNVMTLPYGSTEYGFRD 605
                       650       660       670       680       690       700       710       720
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097 787 QIKRRL-EEKGVITDERMLFAAACYSAKVTLA-----ALGEIFEAARAIMSWLGDCAKIIASDNHPVRWITPLGLPVVQP 860
Cdd:COG5108 606 QVREDMiTRKKEEEGEPFPFGGDGFSAAMWLAkliwdAIGEVVVAARRGMDWLQDLAGIAAKEGLPVIWTTPLGFPVMQD 685
                       730
                ....*....|....
gi 79602097 861 YCRSERHLIRTSLQ 874
Cdd:COG5108 686 YRSSKARRINTTTR 699
RPOL_N pfam14700
DNA-directed RNA polymerase N-terminal; This is the N-terminal domain of DNA-directed RNA ...
165-479 1.96e-91

DNA-directed RNA polymerase N-terminal; This is the N-terminal domain of DNA-directed RNA polymerase. This domain has a role in interaction with regions of upstream promoter DNA and the nascent RNA chain, leading to the processivity of the enzyme. In order to make mRNA transcripts the RNA polymerase undergoes a transition from the initiation phase (which only makes short fragments of RNA) to an elongation phase. This domain undergoes a structural change in the transition from initiation to elongation phase. The structural change results in abolition of the promoter binding site, creation of a channel accommodating the heteroduplex in the active site and formation of an exit tunnel which the RNA transcript passes through after peeling off the heteroduplex.


Pssm-ID: 464270  Cd Length: 286  Bit Score: 290.67  E-value: 1.96e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097   165 RQVKEETEAWERMVDEYRDLEKEMCEKNLAPNLP-YVKHMFLGWFQPLKDVIEREQKLQKNKSKKV-------RAAYAPH 236
Cdd:pfam14700   1 RQLRLERDSVEAAVERWREEFEELQKRGLNTNLPkSLNALLWQWYEALLPAIKEEIELLKAAEAKPkktkdkeRCEYGPY 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097   237 IELLPADKMAVIVMHKMMGLVMSGHEDGCIQVVQAAVSIGIAIEQEVRIHNFLKRTRKNnagdsqeelkekqllrkrvns 316
Cdd:pfam14700  81 LRLLPPEKLAAITILELLSLLSTGGVDKGMKVSRLAISIGKAVEDEYRAQQLLKKEKKK--------------------- 139
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097   317 lirrkriidalkvvKSEGTKPWGRATQAKLGSRLLELLIEAAYVQPPLTQSGDSIPEFR--PAFRHRFKtvtkypgSKLV 394
Cdd:pfam14700 140 --------------IKKKKIPWPQEVRAKVGAVLLSLLIETAKVPVTAEDPETGEKVIQpqPAFYHSYQ-------YKRG 198
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79602097   395 RRYGVIECDSLLLAGL-DKSAKHMLIP-YVPMLVPPKRWKGYDKGGYLFLPSYIMRTHGSKKQQDALKD-ISHKTAHRVF 471
Cdd:pfam14700 199 KKVGVIKPHPELVKLLlREPARDTLTPrHLPMLVPPKPWTSYNKGGYLLSPSKLMRTKDGDEQRAYLKAaSERGDLDQVF 278

                  ....*...
gi 79602097   472 EALDTLGN 479
Cdd:pfam14700 279 DGLDVLGN 286
 
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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