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Conserved domains on  [gi|1281019559|ref|XP_022993982|]
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DNA-directed RNA polymerase 2, chloroplastic/mitochondrial-like [Cucurbita maxima]

Protein Classification

RPOL_N and RNA_pol domain-containing protein( domain architecture ID 13418561)

RPOL_N and RNA_pol domain-containing protein

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.
 636-1027 0e+00

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


:

Pssm-ID: 460006  Cd Length: 411  Bit Score: 689.24  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  636 RPLRKSGLRWLKIHLANLFagGVDKLSHDGRITFIDDHVEDIFDSADRPLEGRRWWLNAEDPFQFLAGCMNLTEALRSSS 715
Cdd:pfam00940    1 KPLGERGLRWLKIHLANLY--GFDKASLDERVAFVEDNLEDILDSAENPLDGRRWWLKAEDPWQCLAACFELANALRSPD 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  716 PETVISHIPIHQDGSCNGLQHYAALGRDKLGAAAVNLTVTEKPADVYSGIAARVLEIVRKDAQRDPETfpdalrAKTLID 795
Cdd:pfam00940   79 PEEYVSHLPVHQDGSCNGLQHYAALGGDEEGAKQVNLVPSDRPQDVYSGVAELVEEKIEKDAAKGNEI------AKLLKG 152

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  796 QVDRKLVKQTVMTSVYGVTYIGARDQIKRRLKERAAISDDTELFGCACYAAKTTLTALGEMFEAARGIMSWLGDCAKIIA 875
Cdd:pfam00940  153 KITRKVVKQTVMTNVYGVTFIGAREQIEKQLKEIGDFPGEEDLYKASSYLAKKIFDSIGELFTGAHEIQDWLGECAKRIA 232

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  876 SE------NQPVRWTTPLGLPVVQPYRKLGRHLVKTSLQVLTLQQ--ETDKVLVKRQRTAFPPNFVHSLDGSHMMMTAVA 947
Cdd:pfam00940  233 KSvppeqsMSPVIWTTPLGLPVVQPYRKSKKKQVKTNLQSVSISDpnDTDPVDKRKQLQAFPPNFIHSLDATHMMLTALA 312

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  948 CKKAGLNFAGVHDSYWTHACDVDEMNRILREKFVELYETPILENLLEGFQQSFP-------------------VLDFPPL 1008
Cdd:pfam00940  313 CDEAGLTFAAVHDSFWTHACDVDEMNKILREQFVKLHSEDILERLREEFKERYKgslqlakipkdspltpvwlPLTFPEV 392

                          410
                   ....*....|....*....
gi 1281019559 1009 PERGELDLKEVLESPYFFN 1027
Cdd:pfam00940  393 PKKGDFDLNRVLDSKYFFS 411
PHA00452 super family cl42978
T3/T7-like RNA polymerase
 190-1026 0e+00

T3/T7-like RNA polymerase


The actual alignment was detected with superfamily member PHA00452:

Pssm-ID: 222797 [Multi-domain]  Cd Length: 807  Bit Score: 562.72  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  190 LKRRQVAIETEAWKQAVKEYKELLMDMCEQKLAPNLPYMKSLFLGWFEPLRDAISKEQELIRIGKNRTAYAPYFDQLSAD 269
Cdd:PHA00452     5 LAAEQLQLEEEAYGEGEERFRKALERQLEAGEADDNPVARRLLATLLPPVAEAIDAWKEEYKKRGRAAKARGLLRLVDPE 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  270 MMSVVTMHKLMGLLMMGHEHGNARVVQAacvIGDAIEQEVRIHRFlekmkkkkhdkDNENNDKPDSQLKEQERLRKKVTN 349
Cdd:PHA00452    85 VLAVITLKVTLDMLLSKETPTAQAVATA---IGRAIEDEIRFGRI-----------EDLNPKYFKKVVEYLKRSRTGSVY 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  350 LIKMQKLPAVRHIVKGADDskPWGPDAKAKVGSRLIELLTQtayiqppadqlADGPPDIrpaFRHSFRIVMKeanknssr 429
Cdd:PHA00452   151 HIAFMMVVEADMVLLGEWD--PWPKEDYIHVGKWLLEALIE-----------STGLVEL---VRHTGGNGGK-------- 206

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  430 RYGVIECDPLVVKGLERTARHM--VIP-YMPMLVPPVNWTGYDKGGhiFL-----PSFIMRTRGanqqREAVKRTPKQQL 501
Cdd:PHA00452   207 DHEYLELSEEAVELLQDIAAAAagISPmYQPMVVPPKPWTSIVGGG--YHtegrrPLAPLVRKT----KKALRRYRQKQM 280

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  502 TPVFEALDTLGNTKWRINKKILSIVDRIWTSGGcLADLVDRDDVPLPEKPDSEDETL--LRKWKWKVKSVKKENVERHSQ 579
Cdd:PHA00452   281 PEVYKAVNALQNTAWRINKDVLAVVNEVVNWGP-VGDVLGIPRRPLPPKPEFLDENEeaFKAWKRAAAAWYTKEKERVSK 359

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  580 RCDIELKLAVARKMKDEEGFYFPHNIDFRGRAYPMhPYLNHLGSDLCRGILEFAEGRPLRKSGLRWLKIHLANLFagGVD 659
Cdd:PHA00452   360 RRRLEFMLRVANKFADYKAIYFPYNMDWRGRVYAV-SMLNPQGSDLQKALLRFAEGKPLGKRGLYWLKVHGANCY--GVD 436

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  660 KLSHDGRITFIDDHVEDIFDSADRPLEGRrWWLNAEDPFQFLAGCMNLTEALRSssPETVISHIPIHQDGSCNGLQHYAA 739
Cdd:PHA00452   437 KVTFDERAAWVDENHDNILAAAEDPLNNT-WWAEADSPLCFLAACFEYAAAVHS--GTSYVSGLPVAMDGTCSGLQHFSA 513

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  740 LGRDKLGAAAVNLTVTEKPADVYSGIAARVLEIVRKDAqRDPETFPDALRAKTLIDQVDRKLVKQTVMTSVYGVTYIGAR 819
Cdd:PHA00452   514 MLRDEVGGRAVNLLPSDKPQDIYGIVAEVVNEKLERDA-INGTDNTRALARLWLAYGITRSLTKRPVMTLPYGSTRFSCR 592

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  820 DQIKRRLKERAAISDDTELFG--CACYAAKTTLTALGEMFEAARGIMSWLGDCAKIIASE-NQPVRWTTPLGLPVVQPYR 896
Cdd:PHA00452   593 DYILEDLLQPGIDEGDGAMFTnqAASYMAKLIWDAISETVPAAVEAMNWLQQAAKLLAAKgAEALHWTTPTGFPVWQEYR 672

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  897 KLGRHLVKTSL--QV-LTLQQETDKVLVKRQRTAFPPNFVHSLDGSHMMMTAVACKKAGL-NFAGVHDSYWTHACDVDEM 972
Cdd:PHA00452   673 KPEEKRVRLRLmgVArVQLYVNTDTIDARKHASGIAPNFVHSLDASHLRLTVVACAEKGIeSFAVIHDSFGTHAADADNL 752

                          810       820       830       840       850
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1281019559  973 NRILREKFVELYETP-ILENLLEGFQQSFPVLDfPPLPERGELDLKEVLESPYFF 1026
Cdd:PHA00452   753 HRAIRETFVEMYEENdVLADFADQFGDQLQLKM-PELPEKGSLDLEEVLDSDFFF 806
 
Name Accession Description Interval E-value
RNA_pol pfam00940
DNA-dependent RNA polymerase; This is a family of single chain RNA polymerases.
 636-1027 0e+00

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


Pssm-ID: 460006  Cd Length: 411  Bit Score: 689.24  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  636 RPLRKSGLRWLKIHLANLFagGVDKLSHDGRITFIDDHVEDIFDSADRPLEGRRWWLNAEDPFQFLAGCMNLTEALRSSS 715
Cdd:pfam00940    1 KPLGERGLRWLKIHLANLY--GFDKASLDERVAFVEDNLEDILDSAENPLDGRRWWLKAEDPWQCLAACFELANALRSPD 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  716 PETVISHIPIHQDGSCNGLQHYAALGRDKLGAAAVNLTVTEKPADVYSGIAARVLEIVRKDAQRDPETfpdalrAKTLID 795
Cdd:pfam00940   79 PEEYVSHLPVHQDGSCNGLQHYAALGGDEEGAKQVNLVPSDRPQDVYSGVAELVEEKIEKDAAKGNEI------AKLLKG 152

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  796 QVDRKLVKQTVMTSVYGVTYIGARDQIKRRLKERAAISDDTELFGCACYAAKTTLTALGEMFEAARGIMSWLGDCAKIIA 875
Cdd:pfam00940  153 KITRKVVKQTVMTNVYGVTFIGAREQIEKQLKEIGDFPGEEDLYKASSYLAKKIFDSIGELFTGAHEIQDWLGECAKRIA 232

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  876 SE------NQPVRWTTPLGLPVVQPYRKLGRHLVKTSLQVLTLQQ--ETDKVLVKRQRTAFPPNFVHSLDGSHMMMTAVA 947
Cdd:pfam00940  233 KSvppeqsMSPVIWTTPLGLPVVQPYRKSKKKQVKTNLQSVSISDpnDTDPVDKRKQLQAFPPNFIHSLDATHMMLTALA 312

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  948 CKKAGLNFAGVHDSYWTHACDVDEMNRILREKFVELYETPILENLLEGFQQSFP-------------------VLDFPPL 1008
Cdd:pfam00940  313 CDEAGLTFAAVHDSFWTHACDVDEMNKILREQFVKLHSEDILERLREEFKERYKgslqlakipkdspltpvwlPLTFPEV 392

                          410
                   ....*....|....*....
gi 1281019559 1009 PERGELDLKEVLESPYFFN 1027
Cdd:pfam00940  393 PKKGDFDLNRVLDSKYFFS 411
PHA00452 PHA00452
T3/T7-like RNA polymerase
 190-1026 0e+00

T3/T7-like RNA polymerase


Pssm-ID: 222797 [Multi-domain]  Cd Length: 807  Bit Score: 562.72  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  190 LKRRQVAIETEAWKQAVKEYKELLMDMCEQKLAPNLPYMKSLFLGWFEPLRDAISKEQELIRIGKNRTAYAPYFDQLSAD 269
Cdd:PHA00452     5 LAAEQLQLEEEAYGEGEERFRKALERQLEAGEADDNPVARRLLATLLPPVAEAIDAWKEEYKKRGRAAKARGLLRLVDPE 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  270 MMSVVTMHKLMGLLMMGHEHGNARVVQAacvIGDAIEQEVRIHRFlekmkkkkhdkDNENNDKPDSQLKEQERLRKKVTN 349
Cdd:PHA00452    85 VLAVITLKVTLDMLLSKETPTAQAVATA---IGRAIEDEIRFGRI-----------EDLNPKYFKKVVEYLKRSRTGSVY 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  350 LIKMQKLPAVRHIVKGADDskPWGPDAKAKVGSRLIELLTQtayiqppadqlADGPPDIrpaFRHSFRIVMKeanknssr 429
Cdd:PHA00452   151 HIAFMMVVEADMVLLGEWD--PWPKEDYIHVGKWLLEALIE-----------STGLVEL---VRHTGGNGGK-------- 206

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  430 RYGVIECDPLVVKGLERTARHM--VIP-YMPMLVPPVNWTGYDKGGhiFL-----PSFIMRTRGanqqREAVKRTPKQQL 501
Cdd:PHA00452   207 DHEYLELSEEAVELLQDIAAAAagISPmYQPMVVPPKPWTSIVGGG--YHtegrrPLAPLVRKT----KKALRRYRQKQM 280

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  502 TPVFEALDTLGNTKWRINKKILSIVDRIWTSGGcLADLVDRDDVPLPEKPDSEDETL--LRKWKWKVKSVKKENVERHSQ 579
Cdd:PHA00452   281 PEVYKAVNALQNTAWRINKDVLAVVNEVVNWGP-VGDVLGIPRRPLPPKPEFLDENEeaFKAWKRAAAAWYTKEKERVSK 359

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  580 RCDIELKLAVARKMKDEEGFYFPHNIDFRGRAYPMhPYLNHLGSDLCRGILEFAEGRPLRKSGLRWLKIHLANLFagGVD 659
Cdd:PHA00452   360 RRRLEFMLRVANKFADYKAIYFPYNMDWRGRVYAV-SMLNPQGSDLQKALLRFAEGKPLGKRGLYWLKVHGANCY--GVD 436

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  660 KLSHDGRITFIDDHVEDIFDSADRPLEGRrWWLNAEDPFQFLAGCMNLTEALRSssPETVISHIPIHQDGSCNGLQHYAA 739
Cdd:PHA00452   437 KVTFDERAAWVDENHDNILAAAEDPLNNT-WWAEADSPLCFLAACFEYAAAVHS--GTSYVSGLPVAMDGTCSGLQHFSA 513

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  740 LGRDKLGAAAVNLTVTEKPADVYSGIAARVLEIVRKDAqRDPETFPDALRAKTLIDQVDRKLVKQTVMTSVYGVTYIGAR 819
Cdd:PHA00452   514 MLRDEVGGRAVNLLPSDKPQDIYGIVAEVVNEKLERDA-INGTDNTRALARLWLAYGITRSLTKRPVMTLPYGSTRFSCR 592

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  820 DQIKRRLKERAAISDDTELFG--CACYAAKTTLTALGEMFEAARGIMSWLGDCAKIIASE-NQPVRWTTPLGLPVVQPYR 896
Cdd:PHA00452   593 DYILEDLLQPGIDEGDGAMFTnqAASYMAKLIWDAISETVPAAVEAMNWLQQAAKLLAAKgAEALHWTTPTGFPVWQEYR 672

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  897 KLGRHLVKTSL--QV-LTLQQETDKVLVKRQRTAFPPNFVHSLDGSHMMMTAVACKKAGL-NFAGVHDSYWTHACDVDEM 972
Cdd:PHA00452   673 KPEEKRVRLRLmgVArVQLYVNTDTIDARKHASGIAPNFVHSLDASHLRLTVVACAEKGIeSFAVIHDSFGTHAADADNL 752

                          810       820       830       840       850
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1281019559  973 NRILREKFVELYETP-ILENLLEGFQQSFPVLDfPPLPERGELDLKEVLESPYFF 1026
Cdd:PHA00452   753 HRAIRETFVEMYEENdVLADFADQFGDQLQLKM-PELPEKGSLDLEEVLDSDFFF 806
RPO41 COG5108
Mitochondrial DNA-directed RNA polymerase [Transcription];
193-1026 2.28e-149

Mitochondrial DNA-directed RNA polymerase [Transcription];


Pssm-ID: 444054 [Multi-domain]  Cd Length: 826  Bit Score: 465.16  E-value: 2.28e-149
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  193 RQVAIETEAWKQAVKEYKELLMDMCEQKLAPNLPYMKSLFLGWFEPLRDAISKEQELIRIGK--NRTAYAPYFDQLSADM 270
Cdd:COG5108     13 RQIALEEEMAEAGRSRFVERIEKARKRGEESGTQYGRRIISDAVELLAEAIEATIDESSSGGagNWHTAYAYLRELDAEV 92

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  271 MSVVTMHKLMGLLmmghehGNARVVQAACV-IGDAIEQEVRIHRFLEKMkkkkhdkdnenndkPDSQLKEQERLRKKVTN 349
Cdd:COG5108     93 LAYLALRQCLDAV------TQRHTLQAVAIrIASMVEDEVRGEAIREAF--------------KDFYPRGKKKIESRTSR 152

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  350 LIKMQKLPAVRHIVKGADDSKpWGPDAKAKVGSRLIELLTQTAYIQPPADQlADGPPDIrpafrhSFRIVMKEANKNSSR 429
Cdd:COG5108    153 AVRYKDDFERRVKNAVAKEED-WPVSDKIHVGFKLIELVVESTGLVEIARD-TEGINDT------PVFVRPTETTLEWIA 224

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  430 RYgviecdplvvkglERTARHMVIPYMPMLVPPVNWTGYDKGGhiFLPSFIMRTRGA-NQQREAVKRTPKQQLTPVFEAL 508
Cdd:COG5108    225 EA-------------NLRMAMLSPAYLPMVVPPRNWTTPFRGG--YLSGEVRRLPLVkTRNRKYLEELKNGDMPEVYAAV 289

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  509 DTLGNTKWRINKKILSIVDRIWTSGGCLAdLVDRDDVPLPEKP----DSEDETLLRKWKWKVKSVKKE-NVERHSQRCDI 583
Cdd:COG5108    290 NALQQTPWTINRYVLAVMKWLWERDLDLG-LPQREPITPPIKPenreDITTNQVARKRWKKAARKIYIaNAKLCSKRVQF 368

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  584 ELKLAVARKMKDEEGFYFPHNIDFRGRAYPMHPYLNHLGSDLCRGILEFAEGRPLRKSGLRWLKIHLANLFagGVDKLSH 663
Cdd:COG5108    369 RRDLNEAERFSDYREFYFPYQLDFRGRVYAVPAFLNPQGQDHAKGLLMFADGKPIGDGGAKWLAIHGANVW--GYDKASL 446

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  664 DGRITFIDDHVEDIFDSADRplEGRRWWLNAEDPFQFLAGCMNLTEALRSSspETVISHIPIHQDGSCNGLQHYAALGRD 743
Cdd:COG5108    447 EERVKWVEDNYEAILAAAAD--YVAEFWSKADKPWQFLAFCREWYGYDQHG--EGYVSGLPIAMDGSCSGLQHYSAMLRD 522

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  744 KLGAAAVNLTVTEKPADVYSGIAARVLEIVRKDAQRDPETFPDALRA------KTLIDQVDRKLVKQTVMTSVYGVTYIG 817
Cdd:COG5108    523 EVGGAAVNLVPSDKPQDIYAFVAEVDINLAQRIGCPDELTTNEILNGimdmahNWLAFGITRKVTKRNVMTLPYGSTEYG 602

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  818 ARDQIKRRLKERAAISDDTEL------FGCACYAAKTTLTALGEMFEAARGIMSWLGDCAKIIASENQPVRWTTPLGLPV 891
Cdd:COG5108    603 FRDQVREDMITRKKEEEGEPFpfggdgFSAAMWLAKLIWDAIGEVVVAARRGMDWLQDLAGIAAKEGLPVIWTTPLGFPV 682

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  892 VQPYRKLGRHLVKTSLQ----VLTLQQETDKVLVKRQRTAFPPNFVHSLDGSHMMMTAVACKKAGL-NFAGVHDSYWTHA 966
Cdd:COG5108    683 MQDYRSSKARRINTTTRkvrvRLTLREEQDTIDKRKQKQGIAPNFVHSMDATHLMMTVNRSNEYGAsSFALVHDSFGTDA 762

                          810       820       830       840       850       860
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1281019559  967 CDVDEMNRILREKFVELYETpilENLLEGF------QQSFPVLDFPPLPERGELDLKEVLESPYFF 1026
Cdd:COG5108    763 GSAELMLDCLRKAFIELYEE---SDVLEDFkseiadMLSDDAYALPEVPKKGSLDVSAVLESDFFF 825
RPOL_N pfam14700
DNA-directed RNA polymerase N-terminal; This is the N-terminal domain of DNA-directed RNA ...
 193-513 5.17e-97

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: 308.00  E-value: 5.17e-97
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  193 RQVAIETEAWKQAVKEYKELLMDMCEQKLAPNLP-YMKSLFLGWFEPLRDAISKEQELIRIGKN---------RTAYAPY 262
Cdd:pfam14700    1 RQLRLERDSVEAAVERWREEFEELQKRGLNTNLPkSLNALLWQWYEALLPAIKEEIELLKAAEAkpkktkdkeRCEYGPY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  263 FDQLSADMMSVVTMHKLMGLLMMGHEHGNARVVQAACVIGDAIEQEVRIhrflekmkkkkhdkdnenndkpdsqlkeqER 342
Cdd:pfam14700   81 LRLLPPEKLAAITILELLSLLSTGGVDKGMKVSRLAISIGKAVEDEYRA-----------------------------QQ 131

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  343 LRKKVTNLIKMQKLPavrhivkgaddskpWGPDAKAKVGSRLIELLTQTAYIQPPADQLADGPPDIR--PAFRHSFRIVm 420
Cdd:pfam14700  132 LLKKEKKKIKKKKIP--------------WPQEVRAKVGAVLLSLLIETAKVPVTAEDPETGEKVIQpqPAFYHSYQYK- 196

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  421 keanknSSRRYGVIECDPLVVKGLERT-ARHMVIP-YMPMLVPPVNWTGYDKGGHIFLPSFIMRTRGANQQREAVKRTPK 498
Cdd:pfam14700  197 ------RGKKVGVIKPHPELVKLLLREpARDTLTPrHLPMLVPPKPWTSYNKGGYLLSPSKLMRTKDGDEQRAYLKAASE 270

                          330
                   ....*....|....*.
gi 1281019559  499 Q-QLTPVFEALDTLGN 513
Cdd:pfam14700  271 RgDLDQVFDGLDVLGN 286
 
Name Accession Description Interval E-value
RNA_pol pfam00940
DNA-dependent RNA polymerase; This is a family of single chain RNA polymerases.
 636-1027 0e+00

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


Pssm-ID: 460006  Cd Length: 411  Bit Score: 689.24  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  636 RPLRKSGLRWLKIHLANLFagGVDKLSHDGRITFIDDHVEDIFDSADRPLEGRRWWLNAEDPFQFLAGCMNLTEALRSSS 715
Cdd:pfam00940    1 KPLGERGLRWLKIHLANLY--GFDKASLDERVAFVEDNLEDILDSAENPLDGRRWWLKAEDPWQCLAACFELANALRSPD 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  716 PETVISHIPIHQDGSCNGLQHYAALGRDKLGAAAVNLTVTEKPADVYSGIAARVLEIVRKDAQRDPETfpdalrAKTLID 795
Cdd:pfam00940   79 PEEYVSHLPVHQDGSCNGLQHYAALGGDEEGAKQVNLVPSDRPQDVYSGVAELVEEKIEKDAAKGNEI------AKLLKG 152

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  796 QVDRKLVKQTVMTSVYGVTYIGARDQIKRRLKERAAISDDTELFGCACYAAKTTLTALGEMFEAARGIMSWLGDCAKIIA 875
Cdd:pfam00940  153 KITRKVVKQTVMTNVYGVTFIGAREQIEKQLKEIGDFPGEEDLYKASSYLAKKIFDSIGELFTGAHEIQDWLGECAKRIA 232

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  876 SE------NQPVRWTTPLGLPVVQPYRKLGRHLVKTSLQVLTLQQ--ETDKVLVKRQRTAFPPNFVHSLDGSHMMMTAVA 947
Cdd:pfam00940  233 KSvppeqsMSPVIWTTPLGLPVVQPYRKSKKKQVKTNLQSVSISDpnDTDPVDKRKQLQAFPPNFIHSLDATHMMLTALA 312

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  948 CKKAGLNFAGVHDSYWTHACDVDEMNRILREKFVELYETPILENLLEGFQQSFP-------------------VLDFPPL 1008
Cdd:pfam00940  313 CDEAGLTFAAVHDSFWTHACDVDEMNKILREQFVKLHSEDILERLREEFKERYKgslqlakipkdspltpvwlPLTFPEV 392

                          410
                   ....*....|....*....
gi 1281019559 1009 PERGELDLKEVLESPYFFN 1027
Cdd:pfam00940  393 PKKGDFDLNRVLDSKYFFS 411
PHA00452 PHA00452
T3/T7-like RNA polymerase
 190-1026 0e+00

T3/T7-like RNA polymerase


Pssm-ID: 222797 [Multi-domain]  Cd Length: 807  Bit Score: 562.72  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  190 LKRRQVAIETEAWKQAVKEYKELLMDMCEQKLAPNLPYMKSLFLGWFEPLRDAISKEQELIRIGKNRTAYAPYFDQLSAD 269
Cdd:PHA00452     5 LAAEQLQLEEEAYGEGEERFRKALERQLEAGEADDNPVARRLLATLLPPVAEAIDAWKEEYKKRGRAAKARGLLRLVDPE 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  270 MMSVVTMHKLMGLLMMGHEHGNARVVQAacvIGDAIEQEVRIHRFlekmkkkkhdkDNENNDKPDSQLKEQERLRKKVTN 349
Cdd:PHA00452    85 VLAVITLKVTLDMLLSKETPTAQAVATA---IGRAIEDEIRFGRI-----------EDLNPKYFKKVVEYLKRSRTGSVY 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  350 LIKMQKLPAVRHIVKGADDskPWGPDAKAKVGSRLIELLTQtayiqppadqlADGPPDIrpaFRHSFRIVMKeanknssr 429
Cdd:PHA00452   151 HIAFMMVVEADMVLLGEWD--PWPKEDYIHVGKWLLEALIE-----------STGLVEL---VRHTGGNGGK-------- 206

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  430 RYGVIECDPLVVKGLERTARHM--VIP-YMPMLVPPVNWTGYDKGGhiFL-----PSFIMRTRGanqqREAVKRTPKQQL 501
Cdd:PHA00452   207 DHEYLELSEEAVELLQDIAAAAagISPmYQPMVVPPKPWTSIVGGG--YHtegrrPLAPLVRKT----KKALRRYRQKQM 280

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  502 TPVFEALDTLGNTKWRINKKILSIVDRIWTSGGcLADLVDRDDVPLPEKPDSEDETL--LRKWKWKVKSVKKENVERHSQ 579
Cdd:PHA00452   281 PEVYKAVNALQNTAWRINKDVLAVVNEVVNWGP-VGDVLGIPRRPLPPKPEFLDENEeaFKAWKRAAAAWYTKEKERVSK 359

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  580 RCDIELKLAVARKMKDEEGFYFPHNIDFRGRAYPMhPYLNHLGSDLCRGILEFAEGRPLRKSGLRWLKIHLANLFagGVD 659
Cdd:PHA00452   360 RRRLEFMLRVANKFADYKAIYFPYNMDWRGRVYAV-SMLNPQGSDLQKALLRFAEGKPLGKRGLYWLKVHGANCY--GVD 436

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  660 KLSHDGRITFIDDHVEDIFDSADRPLEGRrWWLNAEDPFQFLAGCMNLTEALRSssPETVISHIPIHQDGSCNGLQHYAA 739
Cdd:PHA00452   437 KVTFDERAAWVDENHDNILAAAEDPLNNT-WWAEADSPLCFLAACFEYAAAVHS--GTSYVSGLPVAMDGTCSGLQHFSA 513

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  740 LGRDKLGAAAVNLTVTEKPADVYSGIAARVLEIVRKDAqRDPETFPDALRAKTLIDQVDRKLVKQTVMTSVYGVTYIGAR 819
Cdd:PHA00452   514 MLRDEVGGRAVNLLPSDKPQDIYGIVAEVVNEKLERDA-INGTDNTRALARLWLAYGITRSLTKRPVMTLPYGSTRFSCR 592

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  820 DQIKRRLKERAAISDDTELFG--CACYAAKTTLTALGEMFEAARGIMSWLGDCAKIIASE-NQPVRWTTPLGLPVVQPYR 896
Cdd:PHA00452   593 DYILEDLLQPGIDEGDGAMFTnqAASYMAKLIWDAISETVPAAVEAMNWLQQAAKLLAAKgAEALHWTTPTGFPVWQEYR 672

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  897 KLGRHLVKTSL--QV-LTLQQETDKVLVKRQRTAFPPNFVHSLDGSHMMMTAVACKKAGL-NFAGVHDSYWTHACDVDEM 972
Cdd:PHA00452   673 KPEEKRVRLRLmgVArVQLYVNTDTIDARKHASGIAPNFVHSLDASHLRLTVVACAEKGIeSFAVIHDSFGTHAADADNL 752

                          810       820       830       840       850
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1281019559  973 NRILREKFVELYETP-ILENLLEGFQQSFPVLDfPPLPERGELDLKEVLESPYFF 1026
Cdd:PHA00452   753 HRAIRETFVEMYEENdVLADFADQFGDQLQLKM-PELPEKGSLDLEEVLDSDFFF 806
RPO41 COG5108
Mitochondrial DNA-directed RNA polymerase [Transcription];
193-1026 2.28e-149

Mitochondrial DNA-directed RNA polymerase [Transcription];


Pssm-ID: 444054 [Multi-domain]  Cd Length: 826  Bit Score: 465.16  E-value: 2.28e-149
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  193 RQVAIETEAWKQAVKEYKELLMDMCEQKLAPNLPYMKSLFLGWFEPLRDAISKEQELIRIGK--NRTAYAPYFDQLSADM 270
Cdd:COG5108     13 RQIALEEEMAEAGRSRFVERIEKARKRGEESGTQYGRRIISDAVELLAEAIEATIDESSSGGagNWHTAYAYLRELDAEV 92

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  271 MSVVTMHKLMGLLmmghehGNARVVQAACV-IGDAIEQEVRIHRFLEKMkkkkhdkdnenndkPDSQLKEQERLRKKVTN 349
Cdd:COG5108     93 LAYLALRQCLDAV------TQRHTLQAVAIrIASMVEDEVRGEAIREAF--------------KDFYPRGKKKIESRTSR 152

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  350 LIKMQKLPAVRHIVKGADDSKpWGPDAKAKVGSRLIELLTQTAYIQPPADQlADGPPDIrpafrhSFRIVMKEANKNSSR 429
Cdd:COG5108    153 AVRYKDDFERRVKNAVAKEED-WPVSDKIHVGFKLIELVVESTGLVEIARD-TEGINDT------PVFVRPTETTLEWIA 224

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  430 RYgviecdplvvkglERTARHMVIPYMPMLVPPVNWTGYDKGGhiFLPSFIMRTRGA-NQQREAVKRTPKQQLTPVFEAL 508
Cdd:COG5108    225 EA-------------NLRMAMLSPAYLPMVVPPRNWTTPFRGG--YLSGEVRRLPLVkTRNRKYLEELKNGDMPEVYAAV 289

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  509 DTLGNTKWRINKKILSIVDRIWTSGGCLAdLVDRDDVPLPEKP----DSEDETLLRKWKWKVKSVKKE-NVERHSQRCDI 583
Cdd:COG5108    290 NALQQTPWTINRYVLAVMKWLWERDLDLG-LPQREPITPPIKPenreDITTNQVARKRWKKAARKIYIaNAKLCSKRVQF 368

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  584 ELKLAVARKMKDEEGFYFPHNIDFRGRAYPMHPYLNHLGSDLCRGILEFAEGRPLRKSGLRWLKIHLANLFagGVDKLSH 663
Cdd:COG5108    369 RRDLNEAERFSDYREFYFPYQLDFRGRVYAVPAFLNPQGQDHAKGLLMFADGKPIGDGGAKWLAIHGANVW--GYDKASL 446

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  664 DGRITFIDDHVEDIFDSADRplEGRRWWLNAEDPFQFLAGCMNLTEALRSSspETVISHIPIHQDGSCNGLQHYAALGRD 743
Cdd:COG5108    447 EERVKWVEDNYEAILAAAAD--YVAEFWSKADKPWQFLAFCREWYGYDQHG--EGYVSGLPIAMDGSCSGLQHYSAMLRD 522

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  744 KLGAAAVNLTVTEKPADVYSGIAARVLEIVRKDAQRDPETFPDALRA------KTLIDQVDRKLVKQTVMTSVYGVTYIG 817
Cdd:COG5108    523 EVGGAAVNLVPSDKPQDIYAFVAEVDINLAQRIGCPDELTTNEILNGimdmahNWLAFGITRKVTKRNVMTLPYGSTEYG 602

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  818 ARDQIKRRLKERAAISDDTEL------FGCACYAAKTTLTALGEMFEAARGIMSWLGDCAKIIASENQPVRWTTPLGLPV 891
Cdd:COG5108    603 FRDQVREDMITRKKEEEGEPFpfggdgFSAAMWLAKLIWDAIGEVVVAARRGMDWLQDLAGIAAKEGLPVIWTTPLGFPV 682

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  892 VQPYRKLGRHLVKTSLQ----VLTLQQETDKVLVKRQRTAFPPNFVHSLDGSHMMMTAVACKKAGL-NFAGVHDSYWTHA 966
Cdd:COG5108    683 MQDYRSSKARRINTTTRkvrvRLTLREEQDTIDKRKQKQGIAPNFVHSMDATHLMMTVNRSNEYGAsSFALVHDSFGTDA 762

                          810       820       830       840       850       860
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1281019559  967 CDVDEMNRILREKFVELYETpilENLLEGF------QQSFPVLDFPPLPERGELDLKEVLESPYFF 1026
Cdd:COG5108    763 GSAELMLDCLRKAFIELYEE---SDVLEDFkseiadMLSDDAYALPEVPKKGSLDVSAVLESDFFF 825
RPOL_N pfam14700
DNA-directed RNA polymerase N-terminal; This is the N-terminal domain of DNA-directed RNA ...
 193-513 5.17e-97

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: 308.00  E-value: 5.17e-97
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  193 RQVAIETEAWKQAVKEYKELLMDMCEQKLAPNLP-YMKSLFLGWFEPLRDAISKEQELIRIGKN---------RTAYAPY 262
Cdd:pfam14700    1 RQLRLERDSVEAAVERWREEFEELQKRGLNTNLPkSLNALLWQWYEALLPAIKEEIELLKAAEAkpkktkdkeRCEYGPY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  263 FDQLSADMMSVVTMHKLMGLLMMGHEHGNARVVQAACVIGDAIEQEVRIhrflekmkkkkhdkdnenndkpdsqlkeqER 342
Cdd:pfam14700   81 LRLLPPEKLAAITILELLSLLSTGGVDKGMKVSRLAISIGKAVEDEYRA-----------------------------QQ 131

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  343 LRKKVTNLIKMQKLPavrhivkgaddskpWGPDAKAKVGSRLIELLTQTAYIQPPADQLADGPPDIR--PAFRHSFRIVm 420
Cdd:pfam14700  132 LLKKEKKKIKKKKIP--------------WPQEVRAKVGAVLLSLLIETAKVPVTAEDPETGEKVIQpqPAFYHSYQYK- 196

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1281019559  421 keanknSSRRYGVIECDPLVVKGLERT-ARHMVIP-YMPMLVPPVNWTGYDKGGHIFLPSFIMRTRGANQQREAVKRTPK 498
Cdd:pfam14700  197 ------RGKKVGVIKPHPELVKLLLREpARDTLTPrHLPMLVPPKPWTSYNKGGYLLSPSKLMRTKDGDEQRAYLKAASE 270

                          330
                   ....*....|....*.
gi 1281019559  499 Q-QLTPVFEALDTLGN 513
Cdd:pfam14700  271 RgDLDQVFDGLDVLGN 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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