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Conserved domains on  [gi|257717204|emb|CBD32931|]
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unnamed protein product [Arabidopsis thaliana]

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.
602-993 0e+00

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


:

Pssm-ID: 460006  Cd Length: 411  Bit Score: 686.93  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  602 RPLGKSGLHWLKIHLANLYagGVEKLSHDARLAFVENHLDDIMDSAENPIHGKRWWLKAEDPFQCLAACVILTQALKSPS 681
Cdd:pfam00940   1 KPLGERGLRWLKIHLANLY--GFDKASLDERVAFVEDNLEDILDSAENPLDGRRWWLKAEDPWQCLAACFELANALRSPD 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  682 PYSVISHLPIHQDGSCNGLQHYAALGRDSFEAAAVNLVAGEKPADVYSEISRRVHEIMKKDSSKDPEsnptaaLAKILIT 761
Cdd:pfam00940  79 PEEYVSHLPVHQDGSCNGLQHYAALGGDEEGAKQVNLVPSDRPQDVYSGVAELVEEKIEKDAAKGNE------IAKLLKG 152
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  762 QVDRKLVKQTVMTSVYGVTYVGAREQIKRRLEEKGVITDERMLFAAACYSAKVTLAALGEIFEAARAIMSWLGDCAKIIA 841
Cdd:pfam00940 153 KITRKVVKQTVMTNVYGVTFIGAREQIEKQLKEIGDFPGEEDLYKASSYLAKKIFDSIGELFTGAHEIQDWLGECAKRIA 232
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  842 S------DNHPVRWITPLGLPVVQPYCRSERHLIRTSLQVLALQR--EGNTVDVRKQRTAFPPNFVHSLDGTHMMMTAVA 913
Cdd:pfam00940 233 KsvppeqSMSPVIWTTPLGLPVVQPYRKSKKKQVKTNLQSVSISDpnDTDPVDKRKQLQAFPPNFIHSLDATHMMLTALA 312
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  914 CREAGLNFAGVHDSYWTHACDVDTMNRILREKFVELYNTPILEDLLQSFQESYPN-------------------LVFPPV 974
Cdd:pfam00940 313 CDEAGLTFAAVHDSFWTHACDVDEMNKILREQFVKLHSEDILERLREEFKERYKGslqlakipkdspltpvwlpLTFPEV 392
                         410
                  ....*....|....*....
gi 257717204  975 PKRGDFDLKEVLKSQYFFN 993
Cdd:pfam00940 393 PKKGDFDLNRVLDSKYFFS 411
PHA00452 super family cl42978
T3/T7-like RNA polymerase
162-992 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: 575.82  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 162 LRRRQVKEETEAWERMVDEYRDLEKEMCEKNLAPNLPYVKHMFLGWFQPLKDVIEREQKLQKNKSKKvrAAYAPHIELLP 241
Cdd:PHA00452   5 LAAEQLQLEEEAYGEGEERFRKALERQLEAGEADDNPVARRLLATLLPPVAEAIDAWKEEYKKRGRA--AKARGLLRLVD 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 242 ADKMAVIVMHKMMGLVMSGhEDGCIQVVqaAVSIGIAIEQEVRIHNFlkrtRKNNAGDSQEELKEkqLLRKRVNSLIRRK 321
Cdd:PHA00452  83 PEVLAVITLKVTLDMLLSK-ETPTAQAV--ATAIGRAIEDEIRFGRI----EDLNPKYFKKVVEY--LKRSRTGSVYHIA 153
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 322 RIID-ALKVVKSEGTKPWGRATQAKLGSRLLELLIEAayvqppltqsgDSIPEFrpafrhrfKTVTKYPGSKLVRRYGVI 400
Cdd:PHA00452 154 FMMVvEADMVLLGEWDPWPKEDYIHVGKWLLEALIES-----------TGLVEL--------VRHTGGNGGKDHEYLELS 214
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 401 ECDSLLLAGLDKSAKHMLIPYVPMLVPPKRWKGYDKGGYL---FLPSYIMRTHGSKkqqdALKDISHKTAHRVFEALDTL 477
Cdd:PHA00452 215 EEAVELLQDIAAAAAGISPMYQPMVVPPKPWTSIVGGGYHtegRRPLAPLVRKTKK----ALRRYRQKQMPEVYKAVNAL 290
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 478 GNTKWRVNRNILDVVERLWADGgNIAGLVNREDVPIPEKPSSED--PEELQSWKWSARKANKINRERHSLRCDVELKLSV 555
Cdd:PHA00452 291 QNTAWRINKDVLAVVNEVVNWG-PVGDVLGIPRRPLPPKPEFLDenEEAFKAWKRAAAAWYTKEKERVSKRRRLEFMLRV 369
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 556 ARKMKDEEGFYYPHNLDFRGRAYPMhPHLNHLSSDLCRGTLEFAEGRPLGKSGLHWLKIHLANLYagGVEKLSHDARLAF 635
Cdd:PHA00452 370 ANKFADYKAIYFPYNMDWRGRVYAV-SMLNPQGSDLQKALLRFAEGKPLGKRGLYWLKVHGANCY--GVDKVTFDERAAW 446
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 636 VENHLDDIMDSAENPIHGkRWWLKAEDPFQCLAACVILTQALKSPSPYsvISHLPIHQDGSCNGLQHYAALGRDSFEAAA 715
Cdd:PHA00452 447 VDENHDNILAAAEDPLNN-TWWAEADSPLCFLAACFEYAAAVHSGTSY--VSGLPVAMDGTCSGLQHFSAMLRDEVGGRA 523
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 716 VNLVAGEKPADVYSEISRRVHEIMKKDsSKDPESNPTAALAKILITQVDRKLVKQTVMTSVYGVTYVGAREQIKRRLEEK 795
Cdd:PHA00452 524 VNLLPSDKPQDIYGIVAEVVNEKLERD-AINGTDNTRALARLWLAYGITRSLTKRPVMTLPYGSTRFSCRDYILEDLLQP 602
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 796 GVI-TDERML-FAAACYSAKVTLAALGEIFEAARAIMSWLGDCAKIIASD-NHPVRWITPLGLPVVQPYCRSERHLIRTS 872
Cdd:PHA00452 603 GIDeGDGAMFtNQAASYMAKLIWDAISETVPAAVEAMNWLQQAAKLLAAKgAEALHWTTPTGFPVWQEYRKPEEKRVRLR 682
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 873 L--QV-LALQREGNTVDVRKQRTAFPPNFVHSLDGTHMMMTAVACREAGL-NFAGVHDSYWTHACDVDTMNRILREKFVE 948
Cdd:PHA00452 683 LmgVArVQLYVNTDTIDARKHASGIAPNFVHSLDASHLRLTVVACAEKGIeSFAVIHDSFGTHAADADNLHRAIRETFVE 762
                        810       820       830       840
                 ....*....|....*....|....*....|....*....|....*..
gi 257717204 949 LYNTPileDLLQSFQESYPN---LVFPPVPKRGDFDLKEVLKSQYFF 992
Cdd:PHA00452 763 MYEEN---DVLADFADQFGDqlqLKMPELPEKGSLDLEEVLDSDFFF 806
 
Name Accession Description Interval E-value
RNA_pol pfam00940
DNA-dependent RNA polymerase; This is a family of single chain RNA polymerases.
602-993 0e+00

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


Pssm-ID: 460006  Cd Length: 411  Bit Score: 686.93  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  602 RPLGKSGLHWLKIHLANLYagGVEKLSHDARLAFVENHLDDIMDSAENPIHGKRWWLKAEDPFQCLAACVILTQALKSPS 681
Cdd:pfam00940   1 KPLGERGLRWLKIHLANLY--GFDKASLDERVAFVEDNLEDILDSAENPLDGRRWWLKAEDPWQCLAACFELANALRSPD 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  682 PYSVISHLPIHQDGSCNGLQHYAALGRDSFEAAAVNLVAGEKPADVYSEISRRVHEIMKKDSSKDPEsnptaaLAKILIT 761
Cdd:pfam00940  79 PEEYVSHLPVHQDGSCNGLQHYAALGGDEEGAKQVNLVPSDRPQDVYSGVAELVEEKIEKDAAKGNE------IAKLLKG 152
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  762 QVDRKLVKQTVMTSVYGVTYVGAREQIKRRLEEKGVITDERMLFAAACYSAKVTLAALGEIFEAARAIMSWLGDCAKIIA 841
Cdd:pfam00940 153 KITRKVVKQTVMTNVYGVTFIGAREQIEKQLKEIGDFPGEEDLYKASSYLAKKIFDSIGELFTGAHEIQDWLGECAKRIA 232
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  842 S------DNHPVRWITPLGLPVVQPYCRSERHLIRTSLQVLALQR--EGNTVDVRKQRTAFPPNFVHSLDGTHMMMTAVA 913
Cdd:pfam00940 233 KsvppeqSMSPVIWTTPLGLPVVQPYRKSKKKQVKTNLQSVSISDpnDTDPVDKRKQLQAFPPNFIHSLDATHMMLTALA 312
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  914 CREAGLNFAGVHDSYWTHACDVDTMNRILREKFVELYNTPILEDLLQSFQESYPN-------------------LVFPPV 974
Cdd:pfam00940 313 CDEAGLTFAAVHDSFWTHACDVDEMNKILREQFVKLHSEDILERLREEFKERYKGslqlakipkdspltpvwlpLTFPEV 392
                         410
                  ....*....|....*....
gi 257717204  975 PKRGDFDLKEVLKSQYFFN 993
Cdd:pfam00940 393 PKKGDFDLNRVLDSKYFFS 411
PHA00452 PHA00452
T3/T7-like RNA polymerase
162-992 0e+00

T3/T7-like RNA polymerase


Pssm-ID: 222797 [Multi-domain]  Cd Length: 807  Bit Score: 575.82  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 162 LRRRQVKEETEAWERMVDEYRDLEKEMCEKNLAPNLPYVKHMFLGWFQPLKDVIEREQKLQKNKSKKvrAAYAPHIELLP 241
Cdd:PHA00452   5 LAAEQLQLEEEAYGEGEERFRKALERQLEAGEADDNPVARRLLATLLPPVAEAIDAWKEEYKKRGRA--AKARGLLRLVD 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 242 ADKMAVIVMHKMMGLVMSGhEDGCIQVVqaAVSIGIAIEQEVRIHNFlkrtRKNNAGDSQEELKEkqLLRKRVNSLIRRK 321
Cdd:PHA00452  83 PEVLAVITLKVTLDMLLSK-ETPTAQAV--ATAIGRAIEDEIRFGRI----EDLNPKYFKKVVEY--LKRSRTGSVYHIA 153
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 322 RIID-ALKVVKSEGTKPWGRATQAKLGSRLLELLIEAayvqppltqsgDSIPEFrpafrhrfKTVTKYPGSKLVRRYGVI 400
Cdd:PHA00452 154 FMMVvEADMVLLGEWDPWPKEDYIHVGKWLLEALIES-----------TGLVEL--------VRHTGGNGGKDHEYLELS 214
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 401 ECDSLLLAGLDKSAKHMLIPYVPMLVPPKRWKGYDKGGYL---FLPSYIMRTHGSKkqqdALKDISHKTAHRVFEALDTL 477
Cdd:PHA00452 215 EEAVELLQDIAAAAAGISPMYQPMVVPPKPWTSIVGGGYHtegRRPLAPLVRKTKK----ALRRYRQKQMPEVYKAVNAL 290
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 478 GNTKWRVNRNILDVVERLWADGgNIAGLVNREDVPIPEKPSSED--PEELQSWKWSARKANKINRERHSLRCDVELKLSV 555
Cdd:PHA00452 291 QNTAWRINKDVLAVVNEVVNWG-PVGDVLGIPRRPLPPKPEFLDenEEAFKAWKRAAAAWYTKEKERVSKRRRLEFMLRV 369
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 556 ARKMKDEEGFYYPHNLDFRGRAYPMhPHLNHLSSDLCRGTLEFAEGRPLGKSGLHWLKIHLANLYagGVEKLSHDARLAF 635
Cdd:PHA00452 370 ANKFADYKAIYFPYNMDWRGRVYAV-SMLNPQGSDLQKALLRFAEGKPLGKRGLYWLKVHGANCY--GVDKVTFDERAAW 446
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 636 VENHLDDIMDSAENPIHGkRWWLKAEDPFQCLAACVILTQALKSPSPYsvISHLPIHQDGSCNGLQHYAALGRDSFEAAA 715
Cdd:PHA00452 447 VDENHDNILAAAEDPLNN-TWWAEADSPLCFLAACFEYAAAVHSGTSY--VSGLPVAMDGTCSGLQHFSAMLRDEVGGRA 523
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 716 VNLVAGEKPADVYSEISRRVHEIMKKDsSKDPESNPTAALAKILITQVDRKLVKQTVMTSVYGVTYVGAREQIKRRLEEK 795
Cdd:PHA00452 524 VNLLPSDKPQDIYGIVAEVVNEKLERD-AINGTDNTRALARLWLAYGITRSLTKRPVMTLPYGSTRFSCRDYILEDLLQP 602
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 796 GVI-TDERML-FAAACYSAKVTLAALGEIFEAARAIMSWLGDCAKIIASD-NHPVRWITPLGLPVVQPYCRSERHLIRTS 872
Cdd:PHA00452 603 GIDeGDGAMFtNQAASYMAKLIWDAISETVPAAVEAMNWLQQAAKLLAAKgAEALHWTTPTGFPVWQEYRKPEEKRVRLR 682
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 873 L--QV-LALQREGNTVDVRKQRTAFPPNFVHSLDGTHMMMTAVACREAGL-NFAGVHDSYWTHACDVDTMNRILREKFVE 948
Cdd:PHA00452 683 LmgVArVQLYVNTDTIDARKHASGIAPNFVHSLDASHLRLTVVACAEKGIeSFAVIHDSFGTHAADADNLHRAIRETFVE 762
                        810       820       830       840
                 ....*....|....*....|....*....|....*....|....*..
gi 257717204 949 LYNTPileDLLQSFQESYPN---LVFPPVPKRGDFDLKEVLKSQYFF 992
Cdd:PHA00452 763 MYEEN---DVLADFADQFGDqlqLKMPELPEKGSLDLEEVLDSDFFF 806
RPO41 COG5108
Mitochondrial DNA-directed RNA polymerase [Transcription];
165-992 2.58e-153

Mitochondrial DNA-directed RNA polymerase [Transcription];


Pssm-ID: 444054 [Multi-domain]  Cd Length: 826  Bit Score: 474.40  E-value: 2.58e-153
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 165 RQVKEETEAWERMVDE-YRDLEKEMCEKNLAPNlPYVKHMFLGWFQPLKDVIEREQKLQKNKSKKVRAAYAPHIELLPAD 243
Cdd:COG5108   13 RQIALEEEMAEAGRSRfVERIEKARKRGEESGT-QYGRRIISDAVELLAEAIEATIDESSSGGAGNWHTAYAYLRELDAE 91
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 244 KMAVIVMHKMMGLVMSGHedgciQVVQAAVSIGIAIEQEVRIHNFLKRTRknnagDSQEELKEKqlLRKRVNSLIRRKRI 323
Cdd:COG5108   92 VLAYLALRQCLDAVTQRH-----TLQAVAIRIASMVEDEVRGEAIREAFK-----DFYPRGKKK--IESRTSRAVRYKDD 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 324 IDALKVVKSEGTKPWGRATQAKLGSRLLELLIEAAYVqppltqsgdsipefrpafrhrFKTVTKYPGSKLVRRYGVIECD 403
Cdd:COG5108  160 FERRVKNAVAKEEDWPVSDKIHVGFKLIELVVESTGL---------------------VEIARDTEGINDTPVFVRPTET 218
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 404 SL-LLAGLDKSAKHMLIPYVPMLVPPKRWKGYDKGGYLflpSYIMRT-----HGSKKQQDALKDISHKtahRVFEALDTL 477
Cdd:COG5108  219 TLeWIAEANLRMAMLSPAYLPMVVPPRNWTTPFRGGYL---SGEVRRlplvkTRNRKYLEELKNGDMP---EVYAAVNAL 292
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 478 GNTKWRVNRNILDVVERLWADGGNiAGLVNREDVPIPEKPSSE---DPEEL--QSWKWSARKANKINRERHSLRCDVELK 552
Cdd:COG5108  293 QQTPWTINRYVLAVMKWLWERDLD-LGLPQREPITPPIKPENRediTTNQVarKRWKKAARKIYIANAKLCSKRVQFRRD 371
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 553 LSVARKMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDLCRGTLEFAEGRPLGKSGLHWLKIHLANLYagGVEKLSHDAR 632
Cdd:COG5108  372 LNEAERFSDYREFYFPYQLDFRGRVYAVPAFLNPQGQDHAKGLLMFADGKPIGDGGAKWLAIHGANVW--GYDKASLEER 449
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 633 LAFVENHLDDIMDSAENpiHGKRWWLKAEDPFQCLAACVILTQALKSPspYSVISHLPIHQDGSCNGLQHYAALGRDSFE 712
Cdd:COG5108  450 VKWVEDNYEAILAAAAD--YVAEFWSKADKPWQFLAFCREWYGYDQHG--EGYVSGLPIAMDGSCSGLQHYSAMLRDEVG 525
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 713 AAAVNLVAGEKPADVYSEISR----RVHEIMKKDSSKDPE-SNPTAALA-KILITQVDRKLVKQTVMTSVYGVTYVGARE 786
Cdd:COG5108  526 GAAVNLVPSDKPQDIYAFVAEvdinLAQRIGCPDELTTNEiLNGIMDMAhNWLAFGITRKVTKRNVMTLPYGSTEYGFRD 605
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 787 QIKRRL-EEKGVITDERMLFAAACYSAKVTLA-----ALGEIFEAARAIMSWLGDCAKIIASDNHPVRWITPLGLPVVQP 860
Cdd:COG5108  606 QVREDMiTRKKEEEGEPFPFGGDGFSAAMWLAkliwdAIGEVVVAARRGMDWLQDLAGIAAKEGLPVIWTTPLGFPVMQD 685
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 861 YCRSERHLIRTSLQ----VLALQREGNTVDVRKQRTAFPPNFVHSLDGTHMMMTAVACREAGL-NFAGVHDSYWTHACDV 935
Cdd:COG5108  686 YRSSKARRINTTTRkvrvRLTLREEQDTIDKRKQKQGIAPNFVHSMDATHLMMTVNRSNEYGAsSFALVHDSFGTDAGSA 765
                        810       820       830       840       850       860
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 257717204 936 DTMNRILREKFVELYNTpilEDLLQSFQESY------PNLVFPPVPKRGDFDLKEVLKSQYFF 992
Cdd:COG5108  766 ELMLDCLRKAFIELYEE---SDVLEDFKSEIadmlsdDAYALPEVPKKGSLDVSAVLESDFFF 825
RPOL_N pfam14700
DNA-directed RNA polymerase N-terminal; This is the N-terminal domain of DNA-directed RNA ...
165-479 2.50e-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: 292.21  E-value: 2.50e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  165 RQVKEETEAWERMVDEYRDLEKEMCEKNLAPNLP-YVKHMFLGWFQPLKDVIEREQKLQKNKSKKV-------RAAYAPH 236
Cdd:pfam14700   1 RQLRLERDSVEAAVERWREEFEELQKRGLNTNLPkSLNALLWQWYEALLPAIKEEIELLKAAEAKPkktkdkeRCEYGPY 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  237 IELLPADKMAVIVMHKMMGLVMSGHEDGCIQVVQAAVSIGIAIEQEVRIHNFLKRTRKNnagdsqeelkekqllrkrvns 316
Cdd:pfam14700  81 LRLLPPEKLAAITILELLSLLSTGGVDKGMKVSRLAISIGKAVEDEYRAQQLLKKEKKK--------------------- 139
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  317 lirrkriidalkvvKSEGTKPWGRATQAKLGSRLLELLIEAAYVQPPLTQSGDSIPEFR--PAFRHRFKtvtkypgSKLV 394
Cdd:pfam14700 140 --------------IKKKKIPWPQEVRAKVGAVLLSLLIETAKVPVTAEDPETGEKVIQpqPAFYHSYQ-------YKRG 198
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  395 RRYGVIECDSLLLAGL-DKSAKHMLIP-YVPMLVPPKRWKGYDKGGYLFLPSYIMRTHGSKKQQDALKD-ISHKTAHRVF 471
Cdd:pfam14700 199 KKVGVIKPHPELVKLLlREPARDTLTPrHLPMLVPPKPWTSYNKGGYLLSPSKLMRTKDGDEQRAYLKAaSERGDLDQVF 278

                  ....*...
gi 257717204  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.
602-993 0e+00

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


Pssm-ID: 460006  Cd Length: 411  Bit Score: 686.93  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  602 RPLGKSGLHWLKIHLANLYagGVEKLSHDARLAFVENHLDDIMDSAENPIHGKRWWLKAEDPFQCLAACVILTQALKSPS 681
Cdd:pfam00940   1 KPLGERGLRWLKIHLANLY--GFDKASLDERVAFVEDNLEDILDSAENPLDGRRWWLKAEDPWQCLAACFELANALRSPD 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  682 PYSVISHLPIHQDGSCNGLQHYAALGRDSFEAAAVNLVAGEKPADVYSEISRRVHEIMKKDSSKDPEsnptaaLAKILIT 761
Cdd:pfam00940  79 PEEYVSHLPVHQDGSCNGLQHYAALGGDEEGAKQVNLVPSDRPQDVYSGVAELVEEKIEKDAAKGNE------IAKLLKG 152
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  762 QVDRKLVKQTVMTSVYGVTYVGAREQIKRRLEEKGVITDERMLFAAACYSAKVTLAALGEIFEAARAIMSWLGDCAKIIA 841
Cdd:pfam00940 153 KITRKVVKQTVMTNVYGVTFIGAREQIEKQLKEIGDFPGEEDLYKASSYLAKKIFDSIGELFTGAHEIQDWLGECAKRIA 232
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  842 S------DNHPVRWITPLGLPVVQPYCRSERHLIRTSLQVLALQR--EGNTVDVRKQRTAFPPNFVHSLDGTHMMMTAVA 913
Cdd:pfam00940 233 KsvppeqSMSPVIWTTPLGLPVVQPYRKSKKKQVKTNLQSVSISDpnDTDPVDKRKQLQAFPPNFIHSLDATHMMLTALA 312
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  914 CREAGLNFAGVHDSYWTHACDVDTMNRILREKFVELYNTPILEDLLQSFQESYPN-------------------LVFPPV 974
Cdd:pfam00940 313 CDEAGLTFAAVHDSFWTHACDVDEMNKILREQFVKLHSEDILERLREEFKERYKGslqlakipkdspltpvwlpLTFPEV 392
                         410
                  ....*....|....*....
gi 257717204  975 PKRGDFDLKEVLKSQYFFN 993
Cdd:pfam00940 393 PKKGDFDLNRVLDSKYFFS 411
PHA00452 PHA00452
T3/T7-like RNA polymerase
162-992 0e+00

T3/T7-like RNA polymerase


Pssm-ID: 222797 [Multi-domain]  Cd Length: 807  Bit Score: 575.82  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 162 LRRRQVKEETEAWERMVDEYRDLEKEMCEKNLAPNLPYVKHMFLGWFQPLKDVIEREQKLQKNKSKKvrAAYAPHIELLP 241
Cdd:PHA00452   5 LAAEQLQLEEEAYGEGEERFRKALERQLEAGEADDNPVARRLLATLLPPVAEAIDAWKEEYKKRGRA--AKARGLLRLVD 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 242 ADKMAVIVMHKMMGLVMSGhEDGCIQVVqaAVSIGIAIEQEVRIHNFlkrtRKNNAGDSQEELKEkqLLRKRVNSLIRRK 321
Cdd:PHA00452  83 PEVLAVITLKVTLDMLLSK-ETPTAQAV--ATAIGRAIEDEIRFGRI----EDLNPKYFKKVVEY--LKRSRTGSVYHIA 153
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 322 RIID-ALKVVKSEGTKPWGRATQAKLGSRLLELLIEAayvqppltqsgDSIPEFrpafrhrfKTVTKYPGSKLVRRYGVI 400
Cdd:PHA00452 154 FMMVvEADMVLLGEWDPWPKEDYIHVGKWLLEALIES-----------TGLVEL--------VRHTGGNGGKDHEYLELS 214
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 401 ECDSLLLAGLDKSAKHMLIPYVPMLVPPKRWKGYDKGGYL---FLPSYIMRTHGSKkqqdALKDISHKTAHRVFEALDTL 477
Cdd:PHA00452 215 EEAVELLQDIAAAAAGISPMYQPMVVPPKPWTSIVGGGYHtegRRPLAPLVRKTKK----ALRRYRQKQMPEVYKAVNAL 290
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 478 GNTKWRVNRNILDVVERLWADGgNIAGLVNREDVPIPEKPSSED--PEELQSWKWSARKANKINRERHSLRCDVELKLSV 555
Cdd:PHA00452 291 QNTAWRINKDVLAVVNEVVNWG-PVGDVLGIPRRPLPPKPEFLDenEEAFKAWKRAAAAWYTKEKERVSKRRRLEFMLRV 369
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 556 ARKMKDEEGFYYPHNLDFRGRAYPMhPHLNHLSSDLCRGTLEFAEGRPLGKSGLHWLKIHLANLYagGVEKLSHDARLAF 635
Cdd:PHA00452 370 ANKFADYKAIYFPYNMDWRGRVYAV-SMLNPQGSDLQKALLRFAEGKPLGKRGLYWLKVHGANCY--GVDKVTFDERAAW 446
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 636 VENHLDDIMDSAENPIHGkRWWLKAEDPFQCLAACVILTQALKSPSPYsvISHLPIHQDGSCNGLQHYAALGRDSFEAAA 715
Cdd:PHA00452 447 VDENHDNILAAAEDPLNN-TWWAEADSPLCFLAACFEYAAAVHSGTSY--VSGLPVAMDGTCSGLQHFSAMLRDEVGGRA 523
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 716 VNLVAGEKPADVYSEISRRVHEIMKKDsSKDPESNPTAALAKILITQVDRKLVKQTVMTSVYGVTYVGAREQIKRRLEEK 795
Cdd:PHA00452 524 VNLLPSDKPQDIYGIVAEVVNEKLERD-AINGTDNTRALARLWLAYGITRSLTKRPVMTLPYGSTRFSCRDYILEDLLQP 602
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 796 GVI-TDERML-FAAACYSAKVTLAALGEIFEAARAIMSWLGDCAKIIASD-NHPVRWITPLGLPVVQPYCRSERHLIRTS 872
Cdd:PHA00452 603 GIDeGDGAMFtNQAASYMAKLIWDAISETVPAAVEAMNWLQQAAKLLAAKgAEALHWTTPTGFPVWQEYRKPEEKRVRLR 682
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 873 L--QV-LALQREGNTVDVRKQRTAFPPNFVHSLDGTHMMMTAVACREAGL-NFAGVHDSYWTHACDVDTMNRILREKFVE 948
Cdd:PHA00452 683 LmgVArVQLYVNTDTIDARKHASGIAPNFVHSLDASHLRLTVVACAEKGIeSFAVIHDSFGTHAADADNLHRAIRETFVE 762
                        810       820       830       840
                 ....*....|....*....|....*....|....*....|....*..
gi 257717204 949 LYNTPileDLLQSFQESYPN---LVFPPVPKRGDFDLKEVLKSQYFF 992
Cdd:PHA00452 763 MYEEN---DVLADFADQFGDqlqLKMPELPEKGSLDLEEVLDSDFFF 806
RPO41 COG5108
Mitochondrial DNA-directed RNA polymerase [Transcription];
165-992 2.58e-153

Mitochondrial DNA-directed RNA polymerase [Transcription];


Pssm-ID: 444054 [Multi-domain]  Cd Length: 826  Bit Score: 474.40  E-value: 2.58e-153
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 165 RQVKEETEAWERMVDE-YRDLEKEMCEKNLAPNlPYVKHMFLGWFQPLKDVIEREQKLQKNKSKKVRAAYAPHIELLPAD 243
Cdd:COG5108   13 RQIALEEEMAEAGRSRfVERIEKARKRGEESGT-QYGRRIISDAVELLAEAIEATIDESSSGGAGNWHTAYAYLRELDAE 91
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 244 KMAVIVMHKMMGLVMSGHedgciQVVQAAVSIGIAIEQEVRIHNFLKRTRknnagDSQEELKEKqlLRKRVNSLIRRKRI 323
Cdd:COG5108   92 VLAYLALRQCLDAVTQRH-----TLQAVAIRIASMVEDEVRGEAIREAFK-----DFYPRGKKK--IESRTSRAVRYKDD 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 324 IDALKVVKSEGTKPWGRATQAKLGSRLLELLIEAAYVqppltqsgdsipefrpafrhrFKTVTKYPGSKLVRRYGVIECD 403
Cdd:COG5108  160 FERRVKNAVAKEEDWPVSDKIHVGFKLIELVVESTGL---------------------VEIARDTEGINDTPVFVRPTET 218
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 404 SL-LLAGLDKSAKHMLIPYVPMLVPPKRWKGYDKGGYLflpSYIMRT-----HGSKKQQDALKDISHKtahRVFEALDTL 477
Cdd:COG5108  219 TLeWIAEANLRMAMLSPAYLPMVVPPRNWTTPFRGGYL---SGEVRRlplvkTRNRKYLEELKNGDMP---EVYAAVNAL 292
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 478 GNTKWRVNRNILDVVERLWADGGNiAGLVNREDVPIPEKPSSE---DPEEL--QSWKWSARKANKINRERHSLRCDVELK 552
Cdd:COG5108  293 QQTPWTINRYVLAVMKWLWERDLD-LGLPQREPITPPIKPENRediTTNQVarKRWKKAARKIYIANAKLCSKRVQFRRD 371
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 553 LSVARKMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDLCRGTLEFAEGRPLGKSGLHWLKIHLANLYagGVEKLSHDAR 632
Cdd:COG5108  372 LNEAERFSDYREFYFPYQLDFRGRVYAVPAFLNPQGQDHAKGLLMFADGKPIGDGGAKWLAIHGANVW--GYDKASLEER 449
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 633 LAFVENHLDDIMDSAENpiHGKRWWLKAEDPFQCLAACVILTQALKSPspYSVISHLPIHQDGSCNGLQHYAALGRDSFE 712
Cdd:COG5108  450 VKWVEDNYEAILAAAAD--YVAEFWSKADKPWQFLAFCREWYGYDQHG--EGYVSGLPIAMDGSCSGLQHYSAMLRDEVG 525
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 713 AAAVNLVAGEKPADVYSEISR----RVHEIMKKDSSKDPE-SNPTAALA-KILITQVDRKLVKQTVMTSVYGVTYVGARE 786
Cdd:COG5108  526 GAAVNLVPSDKPQDIYAFVAEvdinLAQRIGCPDELTTNEiLNGIMDMAhNWLAFGITRKVTKRNVMTLPYGSTEYGFRD 605
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 787 QIKRRL-EEKGVITDERMLFAAACYSAKVTLA-----ALGEIFEAARAIMSWLGDCAKIIASDNHPVRWITPLGLPVVQP 860
Cdd:COG5108  606 QVREDMiTRKKEEEGEPFPFGGDGFSAAMWLAkliwdAIGEVVVAARRGMDWLQDLAGIAAKEGLPVIWTTPLGFPVMQD 685
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204 861 YCRSERHLIRTSLQ----VLALQREGNTVDVRKQRTAFPPNFVHSLDGTHMMMTAVACREAGL-NFAGVHDSYWTHACDV 935
Cdd:COG5108  686 YRSSKARRINTTTRkvrvRLTLREEQDTIDKRKQKQGIAPNFVHSMDATHLMMTVNRSNEYGAsSFALVHDSFGTDAGSA 765
                        810       820       830       840       850       860
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 257717204 936 DTMNRILREKFVELYNTpilEDLLQSFQESY------PNLVFPPVPKRGDFDLKEVLKSQYFF 992
Cdd:COG5108  766 ELMLDCLRKAFIELYEE---SDVLEDFKSEIadmlsdDAYALPEVPKKGSLDVSAVLESDFFF 825
RPOL_N pfam14700
DNA-directed RNA polymerase N-terminal; This is the N-terminal domain of DNA-directed RNA ...
165-479 2.50e-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: 292.21  E-value: 2.50e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  165 RQVKEETEAWERMVDEYRDLEKEMCEKNLAPNLP-YVKHMFLGWFQPLKDVIEREQKLQKNKSKKV-------RAAYAPH 236
Cdd:pfam14700   1 RQLRLERDSVEAAVERWREEFEELQKRGLNTNLPkSLNALLWQWYEALLPAIKEEIELLKAAEAKPkktkdkeRCEYGPY 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  237 IELLPADKMAVIVMHKMMGLVMSGHEDGCIQVVQAAVSIGIAIEQEVRIHNFLKRTRKNnagdsqeelkekqllrkrvns 316
Cdd:pfam14700  81 LRLLPPEKLAAITILELLSLLSTGGVDKGMKVSRLAISIGKAVEDEYRAQQLLKKEKKK--------------------- 139
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  317 lirrkriidalkvvKSEGTKPWGRATQAKLGSRLLELLIEAAYVQPPLTQSGDSIPEFR--PAFRHRFKtvtkypgSKLV 394
Cdd:pfam14700 140 --------------IKKKKIPWPQEVRAKVGAVLLSLLIETAKVPVTAEDPETGEKVIQpqPAFYHSYQ-------YKRG 198
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257717204  395 RRYGVIECDSLLLAGL-DKSAKHMLIP-YVPMLVPPKRWKGYDKGGYLFLPSYIMRTHGSKKQQDALKD-ISHKTAHRVF 471
Cdd:pfam14700 199 KKVGVIKPHPELVKLLlREPARDTLTPrHLPMLVPPKPWTSYNKGGYLLSPSKLMRTKDGDEQRAYLKAaSERGDLDQVF 278

                  ....*...
gi 257717204  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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