Citrus Sinensis ID: 015409

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------
Protein Sequence
MPLVKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLRKHLIYGGALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRVI
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHcccHHHHHHHHcccHHHHHHHHHccHHHHHHHHHHHcccccccHHHHHHHcccccHHHHHHHHHHHHccccccccccccccEEEcHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHccccccccccccccccccHHccccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHcccEEEEccccccEEEccHHHHHHHccccccccccccEEEEEEccEEEEccccHHHHHHHHHHHHHHccccccEEEEEcHHHHHHHHHccccHHHHHHHHHHccccccccccccccccHHHHHHHHHHHcccEEEcccEEEcccccccc
Secondary Structure Prediction (SSPRO)
ccccEEEHHcHHHHHHHccHHHHHHHHccHHHHHHHHHHccHHHHHHHHHHHHccccccHHHHHHHHcHHHHHHHHHHHHHHHcccEEEEccccccEEEEcHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHccccccccccccccHHHHHHHHccHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHccEEEEEcccccccEcccEEEEEEEccccccccccccEEEEEEcEEEEEEcccHHHHHHHHHHHHHHHHcccEEEEEEcHHHHHHHHHccccHHHHHHHHHHcccHHHHcccccccccHHHHHHHHHHHHccEEEcccEEHccccHHcc
Coil and Loop (DISEMBL)
MPLVKIIAKNFMDMVASLTARdldrlyenpfICEAILRSLPPLAKKYVMQMFYIdgaipakmmeewvlpdgftkhRVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLRKHLiyggalprepmpsgitarlptledLEAYAIGQWECFLLQLISstqaerptnfssSMMKVFQRGllsrrdkeaprltesGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLqqgrkenwfiptklatnlsmsltdssarkegFIVVETNFRMYAYSTSKLHCEILRLFSKVeyqlpnlivgAITKESLYNAFENGITAEQIISFLQqnahprvadrmpsvpenvCDQIRLWESDlnrvemtpahyydefpsrvi
Flexible Loop (DISEMBL)
MPLVKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVqlrlfseekkkettyrlnstfqsnLRKHLIYggalprepmpSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLatnlsmsltdssarkEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWEsdlnrvemtpahyydefpsrvi
Low Complexity Region (SEG)
MPLVKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLRKHLIYGGALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRVI
Disordered region (IsUnstruct)
***VKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLRKHLIYGGALPRE*MPSGITARLPTLEDLEAYAIGQWECFLLQLIS**********************************ESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVAD***SVPENVCDQIRLWESDLNRVEMTPAHYY********
Disordered Region (DISOPRED)
*********NFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLRKHLIYGGALP**************LEDLEAYAIGQWECFLLQLI****************KV******************SGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLAT*****************VVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNA*********SVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRV*
Disordered Region (DISEMBL)
MPLVKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLRKHLIYGGALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRVI
Disordered Region (DISPRO)
*PLVKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLRKHLIYGGALPREPMPSGI*ARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPS***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPLVKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLRKHLIYGGALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRVI
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	407	2.2.26 [Sep-21-2011]
P60027	462	General transcription fac	yes	no	0.980	0.863	0.349	7e-66
Q92759	462	General transcription fac	yes	no	0.980	0.863	0.349	7e-66
O70422	463	General transcription fac	yes	no	0.970	0.853	0.350	2e-65
P87303	447	RNA polymerase II transcr	yes	no	0.911	0.829	0.332	8e-57
Q6BZX4	467	RNA polymerase II transcr	yes	no	0.941	0.820	0.315	2e-56
Q54C29	483	General transcription fac	yes	no	0.941	0.792	0.317	3e-55
Q6BGW8	515	RNA polymerase II transcr	yes	no	0.901	0.712	0.300	4e-53
Q6CLR2	496	RNA polymerase II transcr	yes	no	0.921	0.756	0.299	1e-51
Q02939	513	RNA polymerase II transcr	yes	no	0.923	0.732	0.290	6e-48
Q75B51	514	RNA polymerase II transcr	yes	no	0.906	0.717	0.292	6e-48

>sp|P60027|TF2H4_PANTR General transcription factor IIH subunit 4 OS=Pan troglodytes GN=GTF2H4 PE=3 SV=1

 Score =  251 bits (641), Expect = 7e-66,   Method: Compositional matrix adjust.
 Identities = 143/409 (34%), Positives = 230/409 (56%), Gaps = 10/409 (2%)

Query: 4   VKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMM 63
           V +  +N  + +  L+   LDRLY +P  C A+ R LP LAK +VM+M +++  +P   +
Sbjct: 12  VHLQCRNLQEFLGGLSPGVLDRLYGHPATCLAVFRELPSLAKNWVMRMLFLEQPLPQAAV 71

Query: 64  EEWVLPDGFTKHRVAIDRLVQLRLFSEE--KKKETTYRLNSTFQSNLRKHLIYGG-ALPR 120
             WV  +       +   L  LR++  +          LN  F+ NLR  L+ GG A   
Sbjct: 72  ALWVKKEFSKAQEESTGLLSGLRIWHTQLLPGGLQGLILNPIFRQNLRIALLGGGKAWSD 131

Query: 121 EPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLL-SR 179
           +    G       +  L+ YA  +WE  L  ++ S  A    + +  +    Q GL+ S 
Sbjct: 132 DTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQLLS---QAGLMKST 188

Query: 180 RDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEA 239
              E P +T +GFQFLL+DT AQLWY + +Y+  +Q RG++  +++SFL +LSF   G+ 
Sbjct: 189 EPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQLSFSTLGKD 248

Query: 240 YNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSA--RKEGFI 297
           Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +     + GFI
Sbjct: 249 YSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGFI 307

Query: 298 VVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISF 357
           VVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII F
Sbjct: 308 VVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHF 367

Query: 358 LQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRV 406
           L+  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+V
Sbjct: 368 LRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQV 416

Component of the core-TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II.
Pan troglodytes (taxid: 9598)

>sp|Q92759|TF2H4_HUMAN General transcription factor IIH subunit 4 OS=Homo sapiens GN=GTF2H4 PE=2 SV=1

 Score =  251 bits (641), Expect = 7e-66,   Method: Compositional matrix adjust.
 Identities = 143/409 (34%), Positives = 230/409 (56%), Gaps = 10/409 (2%)

Query: 4   VKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMM 63
           V +  +N  + +  L+   LDRLY +P  C A+ R LP LAK +VM+M +++  +P   +
Sbjct: 12  VHLQCRNLQEFLGGLSPGVLDRLYGHPATCLAVFRELPSLAKNWVMRMLFLEQPLPQAAV 71

Query: 64  EEWVLPDGFTKHRVAIDRLVQLRLFSEE--KKKETTYRLNSTFQSNLRKHLIYGG-ALPR 120
             WV  +       +   L  LR++  +          LN  F+ NLR  L+ GG A   
Sbjct: 72  ALWVKKEFSKAQEESTGLLSGLRIWHTQLLPGGLQGLILNPIFRQNLRIALLGGGKAWSD 131

Query: 121 EPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLL-SR 179
           +    G       +  L+ YA  +WE  L  ++ S  A    + +  +    Q GL+ S 
Sbjct: 132 DTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQLLS---QAGLMKST 188

Query: 180 RDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEA 239
              E P +T +GFQFLL+DT AQLWY + +Y+  +Q RG++  +++SFL +LSF   G+ 
Sbjct: 189 EPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQLSFSTLGKD 248

Query: 240 YNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSA--RKEGFI 297
           Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +     + GFI
Sbjct: 249 YSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGFI 307

Query: 298 VVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISF 357
           VVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII F
Sbjct: 308 VVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHF 367

Query: 358 LQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRV 406
           L+  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+V
Sbjct: 368 LRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQV 416

Component of the core-TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II.

Homo sapiens (taxid: 9606)

>sp|O70422|TF2H4_MOUSE General transcription factor IIH subunit 4 OS=Mus musculus GN=Gtf2h4 PE=2 SV=1

 Score =  249 bits (637), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 142/405 (35%), Positives = 228/405 (56%), Gaps = 10/405 (2%)

Query: 8   AKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWV 67
            +N  + +  L+   LDRLY +P  C A+ R LP LAK +VM+M +++  +P   +  WV
Sbjct: 17  CRNLQEFLGGLSPGVLDRLYGHPATCLAVFRELPSLAKNWVMRMLFLEQPLPQAAVALWV 76

Query: 68  LPDGFTKHRVAIDRLVQLRLFSEE--KKKETTYRLNSTFQSNLRKHLIYGG-ALPREPMP 124
             +       +   L  LR++  +          LN  F+ NLR  L+ GG A   +   
Sbjct: 77  KKEFSKAQEESTGLLSGLRIWHTQLLPGGLQGLILNPVFRQNLRIALLGGGKAWSDDTSQ 136

Query: 125 SGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLL-SRRDKE 183
            G       +  L+ YA  +WE  L  ++ S  A    + +  +    Q GL+ S    E
Sbjct: 137 LGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQLLS---QAGLMKSTEPGE 193

Query: 184 APRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLN 243
            P +T +GFQFLL+DT AQLWY + +Y+  +Q RG++  +++SFL +LSF   G+ Y++ 
Sbjct: 194 PPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQLSFSTLGKDYSVE 253

Query: 244 TLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSA--RKEGFIVVET 301
            +S+   + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +     + GFIVVET
Sbjct: 254 GMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGFIVVET 312

Query: 302 NFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQN 361
           N+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII FL+  
Sbjct: 313 NYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLRTR 372

Query: 362 AHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRV 406
           AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+V
Sbjct: 373 AHPVMLKQNPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQV 417

Component of the core-TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II.

Mus musculus (taxid: 10090)

>sp|P87303|TFB2_SCHPO RNA polymerase II transcription factor B subunit 2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=tfb2 PE=1 SV=2

 Score =  221 bits (563), Expect = 8e-57,   Method: Compositional matrix adjust.
 Identities = 128/385 (33%), Positives = 212/385 (55%), Gaps = 14/385 (3%)

Query: 25  RLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQ 84
           RLY+ P  C A+ R LP LA++YVM M +    +     + W+          + ++LV+
Sbjct: 21  RLYQKPAACLAVFRLLPILARQYVMSMLFNPMPVALSDFDLWIKLSSKVYQSESFNKLVR 80

Query: 85  LRLFSEEKKKETTYRLNSTFQSNLRKHLIYGGALPREPMP-SGITARLPTLEDLEAYAIG 143
           + +F  + +  T   LNS F+      L  GG      +P +     L T++ L+AYA  
Sbjct: 81  MHIFQFDGQYIT---LNSEFRKQFITALTGGGNHNSFGVPCTDEDKHLVTVDFLDAYAKE 137

Query: 144 QWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQL 203
            WE  L  ++ + +A+ P      ++ + +RG L    K   R+T +GFQFLL D NAQ+
Sbjct: 138 TWETILHFMVGTPEAKFP---GEGVLSLLKRGGLMSGPKNQLRITRAGFQFLLQDINAQI 194

Query: 204 WYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVK 263
           W ++ +Y+  S++  ++   ++ FL  L     G AY+++ L++ Q+ M++D  + GLV 
Sbjct: 195 WTLLLDYLKLSEDTHMDPVQVLHFLFMLGSLDLGRAYSVDFLTDTQQIMLEDLREYGLV- 253

Query: 264 LQQGRKENWFIPTKLATNLSMSLTDSSARK------EGFIVVETNFRMYAYSTSKLHCEI 317
            Q+      F PT+LAT L+        ++      +GFI+VETN+R+YAY++S L   I
Sbjct: 254 YQRKITSKRFYPTRLATGLTTDYRSLHGKQSENDDDKGFIIVETNYRLYAYTSSPLQIAI 313

Query: 318 LRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENV 377
           + LF+ +  +  NL+VG IT++S+  A  NGI AEQII++L  +AHP++   +P +P  +
Sbjct: 314 IGLFANLRARFSNLVVGVITRDSIRRALMNGIAAEQIITYLTTHAHPQMRSNVPLLPPTL 373

Query: 378 CDQIRLWESDLNRVEMTPAHYYDEF 402
            DQI LWE + NR+  TP   + +F
Sbjct: 374 VDQIYLWELEKNRLRATPGILFRDF 398

Component of the core-TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q6BZX4|TFB2_YARLI RNA polymerase II transcription factor B subunit 2 OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=TFB2 PE=3 SV=1

 Score =  220 bits (560), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 129/409 (31%), Positives = 217/409 (53%), Gaps = 26/409 (6%)

Query: 13  DMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGF 72
           D +  L    L RLY++P  C A+ R LP LA+  +M M +    I    ++  V P   
Sbjct: 11  DYLEGLPEAVLTRLYQSPATCLAVFRLLPALARTLIMGMIFNPDPIAVADVDALVKP--- 67

Query: 73  TKHRVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLRKHLIYGGALPREPMPSGITARLP 132
           +  R+ ++   +LRL     + +    +N TF+ NLR  L+ G       +P     +  
Sbjct: 68  SSQRLKLETQKKLRLLHIFTETQAHIIINPTFKKNLRAALVGGDQNISFGVPCDTEDKHK 127

Query: 133 T-LEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESG 191
             +  L+A+A+ QWE  L  ++ ++    P   S  ++ + +   L   ++   R+T +G
Sbjct: 128 VDVAFLDAHAVSQWEMILHFMVGTSIGRTP---SDGVLNLLKHSGLMEPERGGLRITNAG 184

Query: 192 FQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKS 251
           FQFLL D NAQ+W ++ +Y++ S+   ++  D+++F+  L     G+ Y+L+ LSE QK 
Sbjct: 185 FQFLLQDVNAQIWTLLLQYLNMSEYLQMDPVDVLNFIFMLGSLELGQDYSLSALSETQKH 244

Query: 252 MIKDFADLGLVKLQQGRKENWFIPTKLATNLSM------------------SLTDSSARK 293
           M++D  D G+V  Q+      F PT+LAT L+                   +++ S A  
Sbjct: 245 MLEDLRDYGIV-YQRKASSRRFYPTRLATTLTSETAALRTASQSMEAATQDTISSSVAAD 303

Query: 294 EGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQ 353
            GFI++ETNFR+YAY+ S L   +L LF  ++ +  N++ G I ++S+  A  NGITAEQ
Sbjct: 304 SGFIILETNFRLYAYTESPLQIAVLNLFVNLKTRFANMVTGQINRDSVRFALSNGITAEQ 363

Query: 354 IISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEF 402
           II++L  +AHPR+      +P  V DQI+LW+ +++R+  T  + + EF
Sbjct: 364 IITYLSVHAHPRMKGMEHVLPPTVVDQIKLWQLEMDRIRATDGYLFSEF 412

Component of the core-TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA.

Yarrowia lipolytica (strain CLIB 122 / E 150) (taxid: 284591)

>sp|Q54C29|TF2H4_DICDI General transcription factor IIH subunit 4 OS=Dictyostelium discoideum GN=gtf2h4 PE=3 SV=1

 Score =  216 bits (550), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 138/435 (31%), Positives = 238/435 (54%), Gaps = 52/435 (11%)

Query: 15  VASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTK 74
           +ASL ++DL+ LY++P+ C+AILRSLPP +K+Y+++M  +D   P  + ++W       +
Sbjct: 10  LASLDSKDLEELYKDPWTCQAILRSLPPRSKQYILKMLLVD-TYPLSLAKDWSTQASIQQ 68

Query: 75  HRVAIDRLVQLRLFSEEK-----------------------------KKETTYRLNSTFQ 105
           H+ ++ +L  L++   +K                             + E T RLN  FQ
Sbjct: 69  HKESLKKLFDLKIIFLDKINKPIQPQQQQSSQQSSSQQQQQQQQQQQQTEQTIRLNPLFQ 128

Query: 106 SNLRKHLIYGGALPREPMPS-GITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNF 164
            N+++ L+    +      S     + P+++DL++Y+  QWE  L  L  S    +P+  
Sbjct: 129 DNIKRSLVQVNQVIFSNNSSIKDNHKPPSIDDLDSYSKSQWEKVLYFL--SDDTVQPSKL 186

Query: 165 SSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQER----GIN 220
            S ++       L++++ +   +T  GF+FLL D   Q+W ++  Y+ + +++      +
Sbjct: 187 ISELL---LSSNLTKQEGDGLSITSEGFKFLLKDVYTQIWTLLIVYLDDLEKKKGKGSGS 243

Query: 221 QADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLAT 280
           + DL+SFL  LSF   G  Y ++ LSE QK  +      GL+ ++       F PT+L  
Sbjct: 244 RNDLLSFLFRLSFLNLGRGYLVSELSEQQKEYLFALKQFGLIYMRTD-SSILFYPTRLII 302

Query: 281 NLS----MSLTDS-------SARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLP 329
           +L+    +SL  S       + +++G+IV+ETN+R+YAY++S L   +L LF K+ Y+LP
Sbjct: 303 SLTTGKTLSLIQSISSERTQTQKEQGYIVLETNYRLYAYTSSSLQISLLSLFVKMLYRLP 362

Query: 330 NLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLN 389
           NL VG IT+ES+  A  +GITA+QII F++ N+HP  A+    +P+ V +QI LWE++ N
Sbjct: 363 NLAVGIITRESIRTALIHGITADQIIDFVRHNSHPNAANSGQPIPDVVAEQILLWEAERN 422

Query: 390 RVEMTPAHYYDEFPS 404
           R+  T +  Y+ FP+
Sbjct: 423 RITYTKSVLYNSFPT 437

Component of the core-TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II.

Dictyostelium discoideum (taxid: 44689)

>sp|Q6BGW8|TFB2_DEBHA RNA polymerase II transcription factor B subunit 2 OS=Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) GN=TFB2 PE=3 SV=2

 Score =  209 bits (531), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 138/459 (30%), Positives = 225/459 (49%), Gaps = 92/459 (20%)

Query: 25  RLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQ 84
           RLYE P  C +I R LPP+AK Y+M M + +  +  K +++W  P   T  +   D L +
Sbjct: 25  RLYEAPATCLSIYRLLPPIAKFYIMTMLFYETPVALKDLDKWCKP---TSRKFQFDSLKR 81

Query: 85  LRLFS--EEKKKETTYRLNSTFQSNLRKHLIYG------GALPREPMPSGITARLPTLED 136
           LR     EE    +  RL+ TF+ N R  L         G L   P    ++ +      
Sbjct: 82  LRALHLIEEDSSGSHIRLHPTFRQNFRDCLTGSQARNAFGNLSTTPDEQSVSIKF----- 136

Query: 137 LEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRL--TESGFQF 194
           L+++A+ +WE  L  ++ +  +  P+N   S++K    GL+   +K   RL  T SGFQF
Sbjct: 137 LDSFALQKWESILHFMVGTELSVTPSNSVLSLLK--SGGLMEGTNKGGNRLNITNSGFQF 194

Query: 195 LLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIK 254
           LL D NAQ+W ++ +Y++ +Q+  ++  D+++F+  L     G+ Y +++LSE Q SM+ 
Sbjct: 195 LLQDINAQIWTLLLQYLNLTQDLNMDPVDVLNFIFILGSLELGKGYTVSSLSETQISMLA 254

Query: 255 DFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARK--------------------- 293
           D  D GL+  Q+      F PT+LAT L+   +DS+A K                     
Sbjct: 255 DLRDYGLI-YQRSENSERFYPTRLATTLT---SDSAALKSPSMAMEQALESTTETEEQQN 310

Query: 294 ------EGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFEN 347
                 +G I++ETNF++YAY+ S L   IL LF  ++ +  N++ G IT+ES+ NA  N
Sbjct: 311 LASNSNQGTIILETNFKIYAYTNSPLEIAILNLFVHLKTRFSNMVCGQITRESIRNALYN 370

Query: 348 GITAEQIISFLQQNAHPRVA---------------------------------------- 367
           GITA+QII FL+ +AH ++                                         
Sbjct: 371 GITADQIIKFLETHAHSQMKILAKERLDKKIEFDTSNNINTAGGAPQSQMMTNENGTTVA 430

Query: 368 -DRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSR 405
             ++  +P  V DQI+LW+ +L+R++    + + +F S+
Sbjct: 431 QHKLEVLPPTVVDQIKLWQLELDRIQTFEGYLFKDFASQ 469

Component of the core-TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA.

Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) (taxid: 284592)

>sp|Q6CLR2|TFB2_KLULA RNA polymerase II transcription factor B subunit 2 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) GN=TFB2 PE=3 SV=1

 Score =  204 bits (518), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 129/431 (29%), Positives = 216/431 (50%), Gaps = 56/431 (12%)

Query: 25  RLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQ 84
           RLYE+P  C AI R L P+AK ++M M + D  +  + +++WV PD   + + +I  +  
Sbjct: 24  RLYESPATCLAIYRLLSPMAKFFIMSMLFQDHDVSLRDLDKWVKPDAKYQLQYSIKSMKS 83

Query: 85  LRLFSE-EKKKETTYRLNSTFQSNLRKHLIYGGALPREPMPSGITARLP-TLEDLEAYAI 142
           L L  E E K+    RLN  F+ +  K+++ GG +             P +   L+ Y+ 
Sbjct: 84  LNLIIEGESKQPLLIRLNPIFKKSF-KNVLTGGEINNSFGDVADDDTNPVSTATLDQYSA 142

Query: 143 GQWECFLLQLISSTQAERPTNFSSSMMKVFQR-GLLSRRDKEAPRLTESGFQFLLMDTNA 201
            +WE  L  ++ +     P      ++ + Q  GL+   +    ++T  GFQFLL D NA
Sbjct: 143 EKWETILHYMVGTPNTNTP---GGKVLDLLQHSGLMEEAEYGELKITNQGFQFLLQDVNA 199

Query: 202 QLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGL 261
           Q+W ++ +Y+  ++   ++  D+++F+  L     G+AY  + LS  Q++M++D  D GL
Sbjct: 200 QMWTLLLQYLKMAESLQMDPVDVLNFIFMLGALQLGKAYKCDQLSNTQRTMLQDMRDYGL 259

Query: 262 VKLQQGRKENWFIPTKLAT-----------------------NLSMSLTDSSARKE---- 294
           +   Q      F PT+LAT                       N + ++   S + E    
Sbjct: 260 IYQNQSDYAK-FYPTRLATLLTSDTKAFRSASVALDSVLNKANETTAVEGDSGQDETTER 318

Query: 295 ---GFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITA 351
              G +++ETNF++Y+YS S L   IL LF  ++ +  N++ G +T+ES+ NA  NGITA
Sbjct: 319 TQDGALIIETNFKLYSYSNSPLQIAILSLFVHLKSRFANMVTGQLTRESVRNALLNGITA 378

Query: 352 EQIISFLQQNAHPR------------------VADRMPSVPENVCDQIRLWESDLNRVEM 393
           EQII++L+ +AHPR                  V + +  +P  V DQIRLW+ +L+R+  
Sbjct: 379 EQIIAYLETHAHPRMRRLAEENLSKKLELDPTVKETLQVLPPTVVDQIRLWQLELDRIIS 438

Query: 394 TPAHYYDEFPS 404
              + Y +F S
Sbjct: 439 YDGYLYTDFES 449

Component of the core-TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA.

Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid: 284590)

>sp|Q02939|TFB2_YEAST RNA polymerase II transcription factor B subunit 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TFB2 PE=1 SV=1

 Score =  191 bits (486), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 130/447 (29%), Positives = 221/447 (49%), Gaps = 71/447 (15%)

Query: 24  DRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLV 83
           +RLY +P  C AI R LPPLAK ++M M + +  +P   +++WV  +G  + + AI  + 
Sbjct: 23  NRLYTSPATCLAIYRILPPLAKFFIMAMVFNENEVPLLDLDKWVNSNGKLQFQNAIKSMK 82

Query: 84  QLRLFSEEKKKET-TYRLNSTFQSNLRKHLIYGGALPREPMPSGITARLPTLEDLEAYAI 142
            L L    K   T    LN TF+ +LR  L  GG + +      +   + +L+ L+ Y+ 
Sbjct: 83  SLHLLIPNKSSGTLMINLNPTFKISLRNALT-GGEV-QNSFGVVVEENVVSLDLLDEYSA 140

Query: 143 GQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLSRRDKEAP-RLTESGFQFLLMDTNA 201
            +WE  L  ++ +  A+ P+    +++K     L+   +     ++T  GFQFLL + N+
Sbjct: 141 NKWETILHFMVGTPLAKIPSEKVLNLLK--HSKLMEEVNSTGEFKITNEGFQFLLQEINS 198

Query: 202 QLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGL 261
           QLW ++ +Y+   +   ++  D++ F+  L     G+AY ++ LSE Q+ M++D  D GL
Sbjct: 199 QLWTLLLQYLKMIETSKMDLVDVLHFIFMLGALEVGKAYKIDALSETQRIMLQDMRDYGL 258

Query: 262 VKLQQGRKENWFIPTKLATNLS---------MSLTDSSARK------------------- 293
           V  Q+   ++ F PTKLA  L+          +  DS  R+                   
Sbjct: 259 V-FQKHSNDSIFYPTKLALMLTSDTKTIRSASNAMDSVLRQNREEPSVNEDGANGKSTTD 317

Query: 294 ------------------EGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGA 335
                             +G ++VETNF++Y+YS S L   +L LF  ++ +  N+++G 
Sbjct: 318 ITTSDDLNKAGLKNQDIPDGSLIVETNFKIYSYSNSPLQIAVLSLFVHLKARFVNMVLGQ 377

Query: 336 ITKESLYNAFENGITAEQIISFLQQNAHPRV------------------ADRMPSVPENV 377
           IT+ES+  A  NGITA+QII++L+ +AHP++                   + +  +P  V
Sbjct: 378 ITRESIRRALTNGITADQIIAYLETHAHPQMRRLAEEKLEKKLELDPNCKEPLQVLPPTV 437

Query: 378 CDQIRLWESDLNRVEMTPAHYYDEFPS 404
            DQIRLW+ +L+RV       Y +F +
Sbjct: 438 VDQIRLWQLELDRVITYEGSLYSDFET 464

Acts as component of the general transcription and DNA repair factor IIH (TFIIH) core, which is essential for both basal and activated transcription, and is involved in nucleotide excision repair (NER) of damaged DNA. TFIIH has CTD kinase and DNA-dependent ATPase activity, and is essential for polymerase II transcription in vitro.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q75B51|TFB2_ASHGO RNA polymerase II transcription factor B subunit 2 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=TFB2 PE=3 SV=1

 Score =  191 bits (486), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 129/441 (29%), Positives = 222/441 (50%), Gaps = 72/441 (16%)

Query: 25  RLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQ 84
           RLY++P  C AI R L P+AK ++M M + D  +  + ++ WV PD   +   AI  +  
Sbjct: 33  RLYQSPATCLAIYRLLSPMAKFFIMSMIFQDEEVSLRDLDRWVKPDAKFQLHDAIKSMKL 92

Query: 85  LRLFSEEKKKE-TTYRLNSTFQSNLRKHLI-------YGGALPREPMPSGITARLPTLED 136
           L L +E +  +    +LNS F+ + +  L        +G  +  E  P        T+  
Sbjct: 93  LHLITEGRSGQPLMVQLNSIFKESFKNALTGGEVKNSFGNVVEEENDPV-------TMAM 145

Query: 137 LEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLL 196
           L++YA  +WE  L  ++ +   + P     S+++  +   +    KE  ++T  GFQFLL
Sbjct: 146 LDSYAADKWETILHFMVGTPLTKSPGKNVLSLLRHSKLMEVDESSKEL-KITNEGFQFLL 204

Query: 197 MDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDF 256
            D NAQ+W ++ +Y++ ++   ++  D+++ +  +     G+AY++  LSE QK+M++D 
Sbjct: 205 QDANAQIWTLLLQYLTMAETFQMDPVDVLNLIFMIGALELGKAYSVVGLSETQKTMLQDL 264

Query: 257 ADLGLVKLQQGRKENWFIPTKLATNLS---MSLTDSSA--------RKEGF--------- 296
            D GLV  Q+    + F PT+LAT L+   +S+  +S         R EG          
Sbjct: 265 RDYGLV-FQKQSNLSKFYPTRLATMLTSDVVSIRSASGAVNSVLRQRAEGVDGKVLNGTA 323

Query: 297 -----------------IVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKE 339
                            ++VETNF++Y+YS S L   IL LF  ++ +  N++ G IT+E
Sbjct: 324 LGDDDLQAGGEGALDGALIVETNFKLYSYSNSPLQIAILSLFIHLKTRFQNMVTGQITRE 383

Query: 340 SLYNAFENGITAEQIISFLQQNAHP---RVA---------------DRMPSVPENVCDQI 381
           S+  A  NGITA+QII++++ +AHP   R+A               D +  +P  V DQI
Sbjct: 384 SIRRALHNGITADQIIAYMETHAHPQMRRLAGDNLEKKLELDPNCRDTLQVLPPTVVDQI 443

Query: 382 RLWESDLNRVEMTPAHYYDEF 402
           +LW+ +L+R+     + + +F
Sbjct: 444 KLWQLELDRIISYDGYLFRDF 464

Component of the core-TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA.

Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (taxid: 284811)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	407
147854406	451	hypothetical protein VITISV_005315 [Viti	0.995	0.898	0.820	0.0
255556021	451	tfiih, polypeptide, putative [Ricinus co	0.995	0.898	0.798	0.0
449433857	451	PREDICTED: general transcription factor	1.0	0.902	0.799	0.0
357461579	452	General transcription factor IIH subunit	0.995	0.896	0.767	0.0
224077128	449	predicted protein [Populus trichocarpa]	0.990	0.897	0.769	0.0
358346685	451	General transcription factor IIH subunit	0.995	0.898	0.764	0.0
356521347	451	PREDICTED: general transcription factor	0.995	0.898	0.764	0.0
356548733	451	PREDICTED: general transcription factor	0.995	0.898	0.769	0.0
42566894	452	transcription initiation factor TFIIH su	0.995	0.896	0.756	0.0
334186626	482	transcription initiation factor TFIIH su	1.0	0.844	0.753	0.0

>gi|147854406|emb|CAN81292.1| hypothetical protein VITISV_005315 [Vitis vinifera]

 Score =  712 bits (1839), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/407 (82%), Positives = 375/407 (92%), Gaps = 2/407 (0%)

Query: 1   MPLVKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPA 60
           MP VKIIAKNFMDMVASL A  LD LY N FICEAILRSLPPLAKKY++QM YID  + A
Sbjct: 1   MPQVKIIAKNFMDMVASLPAMKLDALYHNTFICEAILRSLPPLAKKYILQMLYIDVPVTA 60

Query: 61  KMMEEWVLPDGFTKHRVAIDRLVQLRLFSE--EKKKETTYRLNSTFQSNLRKHLIYGGAL 118
           K MEEWVL DGF+KHRVAIDRL+QLR+F+E  ++KKET+YRLN TFQ+NL+KHLIYGG L
Sbjct: 61  KAMEEWVLADGFSKHRVAIDRLIQLRVFTETSDRKKETSYRLNPTFQTNLQKHLIYGGVL 120

Query: 119 PREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLS 178
           PREPMPS IT RLP+L+DLEAYA+GQWECFLLQLISSTQ E+ TNFSSS+MKVFQRGLL+
Sbjct: 121 PREPMPSNITVRLPSLDDLEAYALGQWECFLLQLISSTQTEKLTNFSSSLMKVFQRGLLT 180

Query: 179 RRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGE 238
           +R+KEAPRLTESGFQFLLMDTNAQLWYI+REYISNS+ERG++ ADLISFLLELSFHV GE
Sbjct: 181 QREKEAPRLTESGFQFLLMDTNAQLWYIMREYISNSEERGVDPADLISFLLELSFHVTGE 240

Query: 239 AYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIV 298
           AYN+NTL+E Q++ IKD  DLGLVKLQQGRKE+WFIPTKLATNLSMSL+D+S+RK+GF+V
Sbjct: 241 AYNINTLTEFQRNTIKDLVDLGLVKLQQGRKESWFIPTKLATNLSMSLSDTSSRKQGFVV 300

Query: 299 VETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFL 358
           VETNFR+YAYS+SKLHCEILRLFS+VEYQLPNLIVGAITKESLYNAFENGITAEQIISFL
Sbjct: 301 VETNFRLYAYSSSKLHCEILRLFSRVEYQLPNLIVGAITKESLYNAFENGITAEQIISFL 360

Query: 359 QQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSR 405
           QQNAHPRVA+R P+VPENV DQIRLWE+DLNRVE  P+H YDEFPSR
Sbjct: 361 QQNAHPRVAERTPAVPENVTDQIRLWETDLNRVETMPSHLYDEFPSR 407

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255556021|ref|XP_002519045.1| tfiih, polypeptide, putative [Ricinus communis] gi|223541708|gb|EEF43256.1| tfiih, polypeptide, putative [Ricinus communis]

 Score =  696 bits (1797), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 325/407 (79%), Positives = 371/407 (91%), Gaps = 2/407 (0%)

Query: 1   MPLVKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPA 60
           MP V+IIAKNFMDMVASL A  LD+LY NPFIC+AILRSLPPLAKKYV+Q+ YIDG +  
Sbjct: 1   MPQVRIIAKNFMDMVASLPAMKLDKLYTNPFICQAILRSLPPLAKKYVVQILYIDGPVAD 60

Query: 61  KMMEEWVLPDGFTKHRVAIDRLVQLRLFSE--EKKKETTYRLNSTFQSNLRKHLIYGGAL 118
           K +EEW+LPDG +KHRVAIDRL QLR+F+E  ++KKE +Y+LN TFQ+NL+KHLI GG L
Sbjct: 61  KTLEEWLLPDGSSKHRVAIDRLTQLRIFTEIVDRKKEISYKLNPTFQTNLQKHLIDGGVL 120

Query: 119 PREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLS 178
           P EP+ S I  RLPTLE+L+ YA+GQWECFLL LI+S  AER TNFSSSMMK+FQRGLL+
Sbjct: 121 PGEPLASNIAVRLPTLEELDTYALGQWECFLLHLINSGHAERSTNFSSSMMKIFQRGLLT 180

Query: 179 RRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGE 238
           +RDKEAPRLTESGFQFLLMDTNAQLWYI+REYISNS+ERG++ ADLISFLLELSFH+ GE
Sbjct: 181 QRDKEAPRLTESGFQFLLMDTNAQLWYIIREYISNSEERGLDSADLISFLLELSFHITGE 240

Query: 239 AYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIV 298
           AYN+  L+E Q++MIKD ADLGLVKLQQGRKE+WFIPTKLATNLSMSLTDSS+RK+GF+V
Sbjct: 241 AYNMIMLTEFQRNMIKDLADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSSRKQGFVV 300

Query: 299 VETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFL 358
           VETNFRMYAYSTSKLHCEI+RLFS+VEYQLPNL+VGA+TKESLY+AFENGITAEQIISFL
Sbjct: 301 VETNFRMYAYSTSKLHCEIMRLFSRVEYQLPNLVVGAMTKESLYSAFENGITAEQIISFL 360

Query: 359 QQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSR 405
           QQNAHPRVA+R+PSVPENV DQIRLWESD+NRVEMTPAH YDEFPSR
Sbjct: 361 QQNAHPRVAERIPSVPENVTDQIRLWESDMNRVEMTPAHLYDEFPSR 407

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449433857|ref|XP_004134713.1| PREDICTED: general transcription factor IIH subunit 4-like [Cucumis sativus]

 Score =  695 bits (1794), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 327/409 (79%), Positives = 376/409 (91%), Gaps = 2/409 (0%)

Query: 1   MPLVKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPA 60
           MP VKIIAKNFMDMVASL A  LD+LYEN FICEAILRSLPPLAKK+V+QM YIDG + A
Sbjct: 1   MPQVKIIAKNFMDMVASLPAMKLDQLYENAFICEAILRSLPPLAKKFVLQMLYIDGPVSA 60

Query: 61  KMMEEWVLPDGFTKHRVAIDRLVQLRLFSE--EKKKETTYRLNSTFQSNLRKHLIYGGAL 118
           K MEEWVLPDG +K++VA+DRL+QLR+F E  ++K+ETTYRLN TFQ+NL+K LI+G  L
Sbjct: 61  KSMEEWVLPDGVSKYKVAVDRLIQLRVFIETADRKRETTYRLNPTFQANLQKLLIHGEVL 120

Query: 119 PREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLS 178
            REPMPS IT RLP+LEDLEAYA+ QWECFLLQLI+S QAE+P+N SSS+MKVFQ+GLLS
Sbjct: 121 AREPMPSNITVRLPSLEDLEAYALDQWECFLLQLINSGQAEKPSNISSSVMKVFQKGLLS 180

Query: 179 RRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGE 238
           +RDKEAPRLTESGFQFLLM+TNAQLWYI+REYISN++ERG++ ADLISFLLELSFHV GE
Sbjct: 181 QRDKEAPRLTESGFQFLLMETNAQLWYIIREYISNAEERGVDPADLISFLLELSFHVTGE 240

Query: 239 AYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIV 298
           AY+++TLS+ Q+  IKD ADLGLVKLQQGRKE+WFIPTKLATNLSMSL DSS+RK GF+V
Sbjct: 241 AYDIDTLSDEQRYAIKDLADLGLVKLQQGRKESWFIPTKLATNLSMSLADSSSRKLGFVV 300

Query: 299 VETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFL 358
           VETNFRMYAYSTSKLHCEILRLFS++EYQLPNLIVGAITKESLYNAF+NGITAEQI++FL
Sbjct: 301 VETNFRMYAYSTSKLHCEILRLFSRIEYQLPNLIVGAITKESLYNAFKNGITAEQIVTFL 360

Query: 359 QQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRVI 407
           QQNAHPRVA+R+PSVPENV DQIRLWESDLNRV++TPAH+YDEFPSR +
Sbjct: 361 QQNAHPRVAERIPSVPENVTDQIRLWESDLNRVDITPAHFYDEFPSREV 409

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357461579|ref|XP_003601071.1| General transcription factor IIH subunit [Medicago truncatula] gi|355490119|gb|AES71322.1| General transcription factor IIH subunit [Medicago truncatula]

 Score =  673 bits (1736), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 313/408 (76%), Positives = 368/408 (90%), Gaps = 3/408 (0%)

Query: 1   MPLVKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPA 60
           MP V+IIAKNFMDMVAS+ A  LD+LY+N FICEAILRSLPPLAKKYV+Q+ +IDG +PA
Sbjct: 1   MPEVRIIAKNFMDMVASMPAIKLDKLYQNGFICEAILRSLPPLAKKYVLQLLHIDGPVPA 60

Query: 61  KMMEEWVLPDGFTKHRVAIDRLVQLRLFSE---EKKKETTYRLNSTFQSNLRKHLIYGGA 117
           K++ EWVLPDG +KH+VAIDRLVQLR+F E    +K E TY++NST+Q +L+  L++GG 
Sbjct: 61  KLLAEWVLPDGLSKHKVAIDRLVQLRVFVEAFDNRKNEKTYQVNSTYQKSLQNLLVHGGT 120

Query: 118 LPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLL 177
           LPRE MPS IT RLPTLEDLE YA+ QWECFLLQLIS +  ++  N SSS+MKVFQR LL
Sbjct: 121 LPRESMPSNITVRLPTLEDLETYALEQWECFLLQLISPSHVDKTLNISSSLMKVFQRRLL 180

Query: 178 SRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAG 237
           S+RD+EAP+LTESGFQFLLMDTNAQLWYI+REYI+NS+ERG++  DLISF+LELSFHV G
Sbjct: 181 SQRDREAPKLTESGFQFLLMDTNAQLWYIIREYITNSEERGVDAGDLISFMLELSFHVIG 240

Query: 238 EAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFI 297
           EAYN+NTL+E Q+++IKD ADLGLVKLQQGRKE+WFIPTKLATNLS+S+T+SS+RKEGF+
Sbjct: 241 EAYNINTLTEFQRNIIKDLADLGLVKLQQGRKESWFIPTKLATNLSVSMTESSSRKEGFV 300

Query: 298 VVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISF 357
           VVETNFR+YAYSTSKLHCEILRLFS+VEYQLPNLIVGAITKESLYNAF+NGITA+QI+SF
Sbjct: 301 VVETNFRVYAYSTSKLHCEILRLFSRVEYQLPNLIVGAITKESLYNAFDNGITADQIVSF 360

Query: 358 LQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSR 405
           L+QNAHPRVA R+P+VPENV DQIRLWESDLNRVEMT A+YYDEFPSR
Sbjct: 361 LRQNAHPRVAQRVPAVPENVTDQIRLWESDLNRVEMTEAYYYDEFPSR 408

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224077128|ref|XP_002305144.1| predicted protein [Populus trichocarpa] gi|222848108|gb|EEE85655.1| predicted protein [Populus trichocarpa]

 Score =  673 bits (1736), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 313/407 (76%), Positives = 368/407 (90%), Gaps = 4/407 (0%)

Query: 1   MPLVKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPA 60
           MP V+IIAKNFMDMVASL A  LD LY+N FICEAILRSLPPLAKKYV+Q+ + DG +  
Sbjct: 1   MPQVRIIAKNFMDMVASLPAMKLDTLYQNAFICEAILRSLPPLAKKYVVQILFFDGPVSG 60

Query: 61  KMMEEWVLPDGFTKHRVAIDRLVQLRLFSE--EKKKETTYRLNSTFQSNLRKHLIYGGAL 118
           K++E+WVL DG TKHRVAIDRL+QLR+F E  +KK+E++Y+LN TFQ+NLRKHL  GG L
Sbjct: 61  KLLEQWVLADGVTKHRVAIDRLIQLRIFIEVSDKKRESSYKLNQTFQANLRKHLTNGGVL 120

Query: 119 PREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLS 178
           PRE M + +  +LP+LE+L+ YA+ QWECFLL LISS QAE+PT+ SSSMMK+FQRGLLS
Sbjct: 121 PRETMAAVV--KLPSLEELDTYALEQWECFLLLLISSGQAEKPTSLSSSMMKIFQRGLLS 178

Query: 179 RRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGE 238
           +RD++APRLTE GFQFLLMDTNAQLWYI+REYI+NS+ERG   ADLISFLLELSFHV GE
Sbjct: 179 QRDRDAPRLTEGGFQFLLMDTNAQLWYIIREYITNSEERGTEPADLISFLLELSFHVTGE 238

Query: 239 AYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIV 298
           AYN+NTL+EIQ++ IKD A+LGLVKLQQGRKE+WFIPTKLATNLS+SLTDSS+RK+G++V
Sbjct: 239 AYNMNTLTEIQRNTIKDLAELGLVKLQQGRKESWFIPTKLATNLSVSLTDSSSRKQGYVV 298

Query: 299 VETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFL 358
           VETNFR+YAYS+SKLHCEILRLFSK+EYQLPNLIVGAITKESLY AFENGIT++QIISFL
Sbjct: 299 VETNFRLYAYSSSKLHCEILRLFSKIEYQLPNLIVGAITKESLYTAFENGITSDQIISFL 358

Query: 359 QQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSR 405
           QQNAHPRVA+R+PSVPENV DQIRLWE+DLNRVE+TP+H+YDEFPSR
Sbjct: 359 QQNAHPRVAERLPSVPENVTDQIRLWEADLNRVEITPSHFYDEFPSR 405

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358346685|ref|XP_003637396.1| General transcription factor IIH subunit [Medicago truncatula] gi|355503331|gb|AES84534.1| General transcription factor IIH subunit [Medicago truncatula]

 Score =  668 bits (1723), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 311/407 (76%), Positives = 365/407 (89%), Gaps = 2/407 (0%)

Query: 1   MPLVKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPA 60
           MP V+IIAKNFMDMVAS+    LD+LYEN FICEAILRSLPPLAKKYV+Q+F+IDG +PA
Sbjct: 1   MPEVRIIAKNFMDMVASMPTIKLDKLYENGFICEAILRSLPPLAKKYVLQLFHIDGPVPA 60

Query: 61  KMMEEWVLPDGFTKHRVAIDRLVQLRLFSE--EKKKETTYRLNSTFQSNLRKHLIYGGAL 118
           K++ EWVLPDG +KH+VAIDRLVQL +F E  + K   TY++N T+Q +L+K L++GG L
Sbjct: 61  KLLAEWVLPDGLSKHKVAIDRLVQLGVFVEALDSKNGKTYKVNPTYQRSLQKLLVHGGTL 120

Query: 119 PREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLS 178
           PRE MPS IT RLPTLEDLE YA+ QWECFLLQLIS +  ++  N SSS+MKVFQR LLS
Sbjct: 121 PRESMPSNITVRLPTLEDLETYALEQWECFLLQLISPSHVDKTLNISSSLMKVFQRRLLS 180

Query: 179 RRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGE 238
           +RD+EAP+LTESGFQFLLMDTNAQLWYI+REYI+NS+ERG++  DLISF+LELSFHV GE
Sbjct: 181 QRDREAPKLTESGFQFLLMDTNAQLWYIIREYITNSEERGVDAGDLISFMLELSFHVIGE 240

Query: 239 AYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIV 298
           AYN+NTL+E Q+++IKD ADLGLVKLQQGRKE+WFIPTKLATNLS+S+T+SS+RKEGF+V
Sbjct: 241 AYNINTLTEFQRNIIKDLADLGLVKLQQGRKESWFIPTKLATNLSVSMTESSSRKEGFVV 300

Query: 299 VETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFL 358
           VETNFR+YAYSTSKLHCEILRLFS+VEYQLPNLIVGAITKESLYNAF+NGITA+QI+SF 
Sbjct: 301 VETNFRVYAYSTSKLHCEILRLFSRVEYQLPNLIVGAITKESLYNAFDNGITADQIVSFF 360

Query: 359 QQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSR 405
           +QNAHPRVA R+P+VPENV DQIRLWESDLNRVEMT A+YYDEFPSR
Sbjct: 361 RQNAHPRVAQRIPAVPENVTDQIRLWESDLNRVEMTEAYYYDEFPSR 407

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356521347|ref|XP_003529318.1| PREDICTED: general transcription factor IIH subunit 4-like [Glycine max]

 Score =  664 bits (1713), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 311/407 (76%), Positives = 365/407 (89%), Gaps = 2/407 (0%)

Query: 1   MPLVKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPA 60
           MP V+IIAKNFMDMVAS+ A  LD+LYEN FICEAILRS+PPLAKKYV+QM +ID  + A
Sbjct: 1   MPEVRIIAKNFMDMVASMPAMKLDKLYENGFICEAILRSVPPLAKKYVIQMLHIDVPVAA 60

Query: 61  KMMEEWVLPDGFTKHRVAIDRLVQLRLFSE--EKKKETTYRLNSTFQSNLRKHLIYGGAL 118
           K++EEWVLP G +KHRVAIDRLVQLR+F E  ++K E TY++N TFQ +L+K L+ GG L
Sbjct: 61  KLLEEWVLPAGVSKHRVAIDRLVQLRVFLEAVDRKNEKTYKVNPTFQRSLQKLLVQGGTL 120

Query: 119 PREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLS 178
           PRE MPS IT RLPTLE+LEAYA+ QWECFLLQLIS +Q E+P N SSS+MKVFQR +LS
Sbjct: 121 PRESMPSNITVRLPTLENLEAYALEQWECFLLQLISPSQVEKPLNISSSLMKVFQRRILS 180

Query: 179 RRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGE 238
            RDKEAP+LTESGFQFLLMDTNAQLWYI+REYISNS++RG++ ADLISF+LELSFHV GE
Sbjct: 181 HRDKEAPKLTESGFQFLLMDTNAQLWYIIREYISNSEDRGVDAADLISFMLELSFHVIGE 240

Query: 239 AYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIV 298
           AY+++TL+  Q+++I D ADLGLVK+QQGRK +WFIPTKLATNLSMSL DSS+RK+GF+V
Sbjct: 241 AYSVDTLTSFQRTIINDLADLGLVKIQQGRKGSWFIPTKLATNLSMSLADSSSRKQGFVV 300

Query: 299 VETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFL 358
           VETNFR+YAYSTSKLHCEILRLFS+VEYQLPNLIVGAITKESLY+A+ENGITAEQI++FL
Sbjct: 301 VETNFRVYAYSTSKLHCEILRLFSRVEYQLPNLIVGAITKESLYSAYENGITAEQIVTFL 360

Query: 359 QQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSR 405
           QQNAHPRVA+R+PSVPENV +QIRLWE+DLNRVEMT  +YYDEFPSR
Sbjct: 361 QQNAHPRVAERVPSVPENVTEQIRLWEADLNRVEMTDTYYYDEFPSR 407

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356548733|ref|XP_003542754.1| PREDICTED: general transcription factor IIH subunit 4-like [Glycine max]

 Score =  662 bits (1708), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 313/407 (76%), Positives = 365/407 (89%), Gaps = 2/407 (0%)

Query: 1   MPLVKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPA 60
           MP V+IIAKNFMDMVAS+ A  LD+LYEN FICEAILRSL PLAKKYV+QM +ID ++ A
Sbjct: 1   MPEVRIIAKNFMDMVASMPAMKLDKLYENGFICEAILRSLLPLAKKYVIQMLHIDVSVAA 60

Query: 61  KMMEEWVLPDGFTKHRVAIDRLVQLRLFSE--EKKKETTYRLNSTFQSNLRKHLIYGGAL 118
           K++EEWVLP G +KHRVAIDRLVQLR+F E  ++K E TY++N TFQ +L+K L+ GG L
Sbjct: 61  KLLEEWVLPGGVSKHRVAIDRLVQLRVFLEAVDRKNEKTYKVNPTFQRSLQKLLVQGGTL 120

Query: 119 PREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLS 178
           PRE MPS IT RLPTLE+LEAYA+ QWECFLLQLIS +Q E+P N SSS+MKVFQR +LS
Sbjct: 121 PRESMPSNITVRLPTLENLEAYALEQWECFLLQLISPSQVEKPLNISSSLMKVFQRRILS 180

Query: 179 RRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGE 238
            RDKEAP+LTESGFQFLLMDTNAQLWYI+REYISNS++RG++ ADLISF+LELSFH  GE
Sbjct: 181 YRDKEAPKLTESGFQFLLMDTNAQLWYIIREYISNSEDRGVDAADLISFMLELSFHDIGE 240

Query: 239 AYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIV 298
           AY+++TL+  Q+++I D ADLGLVK+QQGRK +WFIPTKLATNLSMSL DSS+RK+GF+V
Sbjct: 241 AYSVDTLTSFQRTIINDLADLGLVKIQQGRKGSWFIPTKLATNLSMSLADSSSRKQGFVV 300

Query: 299 VETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFL 358
           VETNFR+YAYSTSKLHCEILRLFS+VEYQLPNLIVGAITKESLY+AFENGITAEQII+FL
Sbjct: 301 VETNFRVYAYSTSKLHCEILRLFSRVEYQLPNLIVGAITKESLYSAFENGITAEQIITFL 360

Query: 359 QQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSR 405
           QQNAHPRVA+R+PSVPENV +QIRLWE+DLNRVEMT A+YYDEFPSR
Sbjct: 361 QQNAHPRVAERIPSVPENVTEQIRLWEADLNRVEMTDAYYYDEFPSR 407

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42566894|ref|NP_193435.2| transcription initiation factor TFIIH subunit H4 [Arabidopsis thaliana] gi|51969678|dbj|BAD43531.1| unnamed protein product [Arabidopsis thaliana] gi|115646777|gb|ABJ17114.1| At4g17020 [Arabidopsis thaliana] gi|332658439|gb|AEE83839.1| transcription initiation factor TFIIH subunit H4 [Arabidopsis thaliana]

 Score =  660 bits (1702), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 308/407 (75%), Positives = 360/407 (88%), Gaps = 2/407 (0%)

Query: 1   MPLVKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPA 60
           MP VKIIAKNFMDMVASL A  LD+LY N FICEAILRSLPPLAKKYV+QM YID  +PA
Sbjct: 1   MPQVKIIAKNFMDMVASLPAIKLDKLYNNVFICEAILRSLPPLAKKYVLQMLYIDVPVPA 60

Query: 61  KMMEEWVLPDGFTKHRVAIDRLVQLRLFSE--EKKKETTYRLNSTFQSNLRKHLIYGGAL 118
            MMEEWVL DG +KHRVAIDRL+QLR+FSE  ++K+ T+Y LN TFQ+NL+KH+I GG L
Sbjct: 61  TMMEEWVLADGTSKHRVAIDRLIQLRIFSEISDRKRGTSYSLNPTFQNNLQKHIISGGVL 120

Query: 119 PREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLS 178
           PREPM S    +LP+L++LE YA+ QWECFLLQLI+S Q E+ T  SSSMMK+FQRGLLS
Sbjct: 121 PREPMNSDNAIKLPSLQELETYALKQWECFLLQLINSGQGEKLTGISSSMMKIFQRGLLS 180

Query: 179 RRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGE 238
           +RDK+ PRLTESGFQFLLMDTNAQLWYI+REYI N++ER ++ ADLISFLLELSFHV G+
Sbjct: 181 QRDKDGPRLTESGFQFLLMDTNAQLWYIIREYILNAEERDVDPADLISFLLELSFHVTGQ 240

Query: 239 AYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIV 298
           AYNLNTL+E+Q + +KD ADLGLVKLQQGRK++WFIPTKLATNLS+SL DSSARKEGF+V
Sbjct: 241 AYNLNTLTEVQNNTLKDLADLGLVKLQQGRKDSWFIPTKLATNLSVSLADSSARKEGFVV 300

Query: 299 VETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFL 358
           +ETNFRMYAYSTSKL CEILRLF+++EYQLPNLI  AITKESLYNAF+NGIT++QII+FL
Sbjct: 301 METNFRMYAYSTSKLQCEILRLFARIEYQLPNLIACAITKESLYNAFDNGITSDQIITFL 360

Query: 359 QQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSR 405
           QQN+HPR ADR+PS+PENV DQIRLWE+DL R+EMT AH+YDEFPS+
Sbjct: 361 QQNSHPRCADRVPSIPENVTDQIRLWETDLQRIEMTQAHFYDEFPSK 407

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334186626|ref|NP_001190745.1| transcription initiation factor TFIIH subunit H4 [Arabidopsis thaliana] gi|332658440|gb|AEE83840.1| transcription initiation factor TFIIH subunit H4 [Arabidopsis thaliana]

 Score =  659 bits (1701), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 308/409 (75%), Positives = 361/409 (88%), Gaps = 2/409 (0%)

Query: 1   MPLVKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPA 60
           MP VKIIAKNFMDMVASL A  LD+LY N FICEAILRSLPPLAKKYV+QM YID  +PA
Sbjct: 1   MPQVKIIAKNFMDMVASLPAIKLDKLYNNVFICEAILRSLPPLAKKYVLQMLYIDVPVPA 60

Query: 61  KMMEEWVLPDGFTKHRVAIDRLVQLRLFSE--EKKKETTYRLNSTFQSNLRKHLIYGGAL 118
            MMEEWVL DG +KHRVAIDRL+QLR+FSE  ++K+ T+Y LN TFQ+NL+KH+I GG L
Sbjct: 61  TMMEEWVLADGTSKHRVAIDRLIQLRIFSEISDRKRGTSYSLNPTFQNNLQKHIISGGVL 120

Query: 119 PREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLS 178
           PREPM S    +LP+L++LE YA+ QWECFLLQLI+S Q E+ T  SSSMMK+FQRGLLS
Sbjct: 121 PREPMNSDNAIKLPSLQELETYALKQWECFLLQLINSGQGEKLTGISSSMMKIFQRGLLS 180

Query: 179 RRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGE 238
           +RDK+ PRLTESGFQFLLMDTNAQLWYI+REYI N++ER ++ ADLISFLLELSFHV G+
Sbjct: 181 QRDKDGPRLTESGFQFLLMDTNAQLWYIIREYILNAEERDVDPADLISFLLELSFHVTGQ 240

Query: 239 AYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIV 298
           AYNLNTL+E+Q + +KD ADLGLVKLQQGRK++WFIPTKLATNLS+SL DSSARKEGF+V
Sbjct: 241 AYNLNTLTEVQNNTLKDLADLGLVKLQQGRKDSWFIPTKLATNLSVSLADSSARKEGFVV 300

Query: 299 VETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFL 358
           +ETNFRMYAYSTSKL CEILRLF+++EYQLPNLI  AITKESLYNAF+NGIT++QII+FL
Sbjct: 301 METNFRMYAYSTSKLQCEILRLFARIEYQLPNLIACAITKESLYNAFDNGITSDQIITFL 360

Query: 359 QQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRVI 407
           QQN+HPR ADR+PS+PENV DQIRLWE+DL R+EMT AH+YDEFPS+ +
Sbjct: 361 QQNSHPRCADRVPSIPENVTDQIRLWETDLQRIEMTQAHFYDEFPSKDV 409

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	407
ZFIN|ZDB-GENE-030131-6779	466	gtf2h4 "general transcription	0.975	0.851	0.364	1.7e-66
UNIPROTKB|Q767M2	463	TFIIH "Uncharacterized protein	0.977	0.859	0.356	4.2e-63
UNIPROTKB|A6H7G8	463	GTF2H4 "Uncharacterized protei	0.977	0.859	0.356	5.4e-63
UNIPROTKB|F1PGI3	463	GTF2H4 "Uncharacterized protei	0.977	0.859	0.353	8.8e-63
UNIPROTKB|Q92759	462	GTF2H4 "General transcription	0.977	0.861	0.353	8.8e-63
UNIPROTKB|P60027	462	GTF2H4 "General transcription	0.977	0.861	0.353	8.8e-63
RGD|1303309	463	Gtf2h4 "general transcription	0.965	0.848	0.355	1.1e-62
MGI|MGI:1338799	463	Gtf2h4 "general transcription	0.965	0.848	0.355	1.4e-62
DICTYBASE|DDB_G0293228	483	gtf2h4 "TFIIH subunit" [Dictyo	0.759	0.639	0.338	1.6e-59
FB|FBgn0261109	499	mrn "marionette" [Drosophila m	0.958	0.781	0.319	3.7e-55

ZFIN|ZDB-GENE-030131-6779 gtf2h4 "general transcription factor IIH, polypeptide 4" [Danio rerio (taxid:7955)]

 Score = 676 (243.0 bits), Expect = 1.7e-66, P = 1.7e-66
 Identities = 153/420 (36%), Positives = 234/420 (55%)

Query:     4 VKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMM 63
             V++  KN  + +  LT   LDRLY +P  C A+ R LPPLAK YVM+M ++D  +P   +
Sbjct:     5 VQLQCKNLHEYLKELTPEILDRLYNHPATCLAVYRELPPLAKNYVMRMLFLDHPLPQAAV 64

Query:    64 EEWVLPDGFTKHRVAIDRLVQLRLFSEEKKKETT--YRLNSTFQSNLRKHLIYGGALP-- 119
               WV       H   +  L  LRL+  +  +     + LN  F+ NLR  L+ GG  P  
Sbjct:    65 ALWVKKGSQKDHDQCVSVLTGLRLWHSQHLQGGLQGFVLNPVFKDNLRIALL-GGGKPWA 123

Query:   120 REPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLSR 179
              E    G       +E L+ YA+ +WE  L  ++ S  A    + +  ++   Q GL+  
Sbjct:   124 DEGANLGPDRHARDVESLDRYAMERWEVILHFMVGSPSAAVSQDLAQLLI---QAGLMKS 180

Query:   180 RDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEA 239
                EAP +T +GFQFLL+DT +QLWY   +Y+  +Q RG++  +++SFL +LSF   G  
Sbjct:   181 ETGEAPCITSAGFQFLLLDTASQLWYFTLQYLKTAQSRGMDLVEILSFLFQLSFSTLGRD 240

Query:   240 YNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKE----- 294
             Y++  +SE   + ++   + GLV  Q+ RK   + PT+LA  L+  +T + A        
Sbjct:   241 YSVEGMSESLLTFLQHLREFGLV-FQRKRKSRRYYPTRLAITLAAGVTANPASGSASSAL 299

Query:   295 ---------GFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAF 345
                      GFIVVETN+R+YAY+ S+L   ++ LFS++ Y+ PNL+V  +T+ES+  A 
Sbjct:   300 GAIPGTGDTGFIVVETNYRIYAYTNSELQIALVALFSEMLYRFPNLVVAQVTRESVQQAI 359

Query:   346 ENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSR 405
              NGITA+QII FL+  AHP +  + P +P  + DQIRLWE + +R++ T    Y++F S+
Sbjct:   360 SNGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELEKDRLQFTEGVLYNQFLSQ 419

GO:0005634 "nucleus" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=IEA

GO:0000439 "core TFIIH complex" evidence=IEA

UNIPROTKB|Q767M2 TFIIH "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 644 (231.8 bits), Expect = 4.2e-63, P = 4.2e-63
 Identities = 146/410 (35%), Positives = 236/410 (57%)

Query:     4 VKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMM 63
             V +  +N  + +  L+   LDRLY +P  C A+ R LP LAK +VM+M +++  +P   +
Sbjct:    13 VHLQCRNLQEFLGGLSPVVLDRLYGHPATCLAVFRELPSLAKNWVMRMLFLEQPLPQAAV 72

Query:    64 EEWVLPDGFTKHRVAIDRLVQ-LRLFSEEKKKETTYRL--NSTFQSNLRKHLIYGG-ALP 119
               WV  + F+K +     L+  LR++  +        L  N  F+ NLR  L+ GG A  
Sbjct:    73 ALWVKKE-FSKAQEESTGLLSGLRIWHTQLLPGGLQGLILNPIFRQNLRIALLGGGKAWS 131

Query:   120 REPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLL-S 178
              +    G       +  L+ YA  +WE  L  ++ S  A    + +  +    Q GL+ S
Sbjct:   132 DDTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQLLS---QAGLMKS 188

Query:   179 RRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGE 238
                 E P +T +GFQFLL+DT AQLWY + +Y+  +Q RG++  +++SFL +LSF   G+
Sbjct:   189 AEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQLSFSTLGK 248

Query:   239 AYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS--SARKEGF 296
              Y++  +S+   + ++   +LGLV  Q+ RK   + PT+LA NLS  ++ +  +  + GF
Sbjct:   249 DYSVEGMSDSLLNFLQHLRELGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGF 307

Query:   297 IVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIIS 356
             IVVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII 
Sbjct:   308 IVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIH 367

Query:   357 FLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRV 406
             FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+V
Sbjct:   368 FLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQV 417

GO:0008353 "RNA polymerase II carboxy-terminal domain kinase activity" evidence=IEA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IEA

GO:0005675 "holo TFIIH complex" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0000439 "core TFIIH complex" evidence=IEA

UNIPROTKB|A6H7G8 GTF2H4 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 643 (231.4 bits), Expect = 5.4e-63, P = 5.4e-63
 Identities = 146/410 (35%), Positives = 236/410 (57%)

Query:     4 VKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMM 63
             V +  +N  + +  L+   LDRLY +P  C A+ R LP LAK +VM+M +++  +P   +
Sbjct:    13 VHLQCRNLQEFLGGLSPGILDRLYGHPATCLAVFRELPSLAKNWVMRMLFLEQPLPQAAV 72

Query:    64 EEWVLPDGFTKHRVAIDRLVQ-LRLFSEEKKKETTYRL--NSTFQSNLRKHLIYGG-ALP 119
               WV  + F+K +     L+  LR++  +        L  N  F+ NLR  L+ GG A  
Sbjct:    73 ALWVKKE-FSKAQEESTGLLSGLRIWHTQLLPGGLQGLILNPIFRQNLRIALLGGGKAWS 131

Query:   120 REPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLL-S 178
              +    G       +  L+ YA  +WE  L  ++ S  A    + +  +    Q GL+ S
Sbjct:   132 DDTSQLGPDKHARDVLSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQLLS---QAGLMKS 188

Query:   179 RRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGE 238
                 E P +T +GFQFLL+DT AQLWY + +Y+  +Q RG++  +++SFL +LSF   G+
Sbjct:   189 AEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQLSFSTLGK 248

Query:   239 AYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS--SARKEGF 296
              Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +  +A + GF
Sbjct:   249 DYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGGTAHQPGF 307

Query:   297 IVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIIS 356
             IVVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII 
Sbjct:   308 IVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIH 367

Query:   357 FLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRV 406
             FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+V
Sbjct:   368 FLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQV 417

GO:0008353 "RNA polymerase II carboxy-terminal domain kinase activity" evidence=IEA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IEA

GO:0005675 "holo TFIIH complex" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0000439 "core TFIIH complex" evidence=IEA

UNIPROTKB|F1PGI3 GTF2H4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 641 (230.7 bits), Expect = 8.8e-63, P = 8.8e-63
 Identities = 145/410 (35%), Positives = 236/410 (57%)

Query:     4 VKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMM 63
             V +  +N  + +  L+   LDRLY +P  C A+ R LP LAK +VM+M +++  +P   +
Sbjct:    13 VHLQCRNLQEFLGGLSPGVLDRLYGHPATCLAVFRELPFLAKNWVMRMLFLEQPLPQAAV 72

Query:    64 EEWVLPDGFTKHRVAIDRLVQ-LRLFSEEKKKETTYRL--NSTFQSNLRKHLIYGG-ALP 119
               WV  + F+K +     L+  LR++  +        L  N  F+ NLR  L+ GG A  
Sbjct:    73 ALWVKKE-FSKAQEESTGLLSGLRIWHTQLLPGGLQGLILNPIFRQNLRIALLGGGKAWS 131

Query:   120 REPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLL-S 178
              +    G       +  L+ YA  +WE  L  ++ S  A    + +  +    Q GL+ S
Sbjct:   132 DDTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQLLS---QAGLMKS 188

Query:   179 RRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGE 238
                 E P +T +GFQFLL+DT AQLWY + +Y+  +Q RG++  +++SFL +LSF   G+
Sbjct:   189 TEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQLSFSTLGK 248

Query:   239 AYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS--SARKEGF 296
              Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +  +A + GF
Sbjct:   249 DYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGGTAHQPGF 307

Query:   297 IVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIIS 356
             I+VETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII 
Sbjct:   308 IIVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIH 367

Query:   357 FLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRV 406
             FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+V
Sbjct:   368 FLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQV 417

GO:0006289 "nucleotide-excision repair" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0000439 "core TFIIH complex" evidence=IEA

UNIPROTKB|Q92759 GTF2H4 "General transcription factor IIH subunit 4" [Homo sapiens (taxid:9606)]

 Score = 641 (230.7 bits), Expect = 8.8e-63, P = 8.8e-63
 Identities = 145/410 (35%), Positives = 235/410 (57%)

Query:     4 VKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMM 63
             V +  +N  + +  L+   LDRLY +P  C A+ R LP LAK +VM+M +++  +P   +
Sbjct:    12 VHLQCRNLQEFLGGLSPGVLDRLYGHPATCLAVFRELPSLAKNWVMRMLFLEQPLPQAAV 71

Query:    64 EEWVLPDGFTKHRVAIDRLVQ-LRLFSEEKKKETTYRL--NSTFQSNLRKHLIYGG-ALP 119
               WV  + F+K +     L+  LR++  +        L  N  F+ NLR  L+ GG A  
Sbjct:    72 ALWVKKE-FSKAQEESTGLLSGLRIWHTQLLPGGLQGLILNPIFRQNLRIALLGGGKAWS 130

Query:   120 REPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLL-S 178
              +    G       +  L+ YA  +WE  L  ++ S  A    + +  +    Q GL+ S
Sbjct:   131 DDTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQLLS---QAGLMKS 187

Query:   179 RRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGE 238
                 E P +T +GFQFLL+DT AQLWY + +Y+  +Q RG++  +++SFL +LSF   G+
Sbjct:   188 TEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQLSFSTLGK 247

Query:   239 AYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS--SARKEGF 296
              Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +  +  + GF
Sbjct:   248 DYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGF 306

Query:   297 IVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIIS 356
             IVVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII 
Sbjct:   307 IVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIH 366

Query:   357 FLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRV 406
             FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+V
Sbjct:   367 FLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQV 416

GO:0000439 "core TFIIH complex" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IDA;TAS

GO:0004672 "protein kinase activity" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005675 "holo TFIIH complex" evidence=IDA

GO:0008353 "RNA polymerase II carboxy-terminal domain kinase activity" evidence=IDA

GO:0008094 "DNA-dependent ATPase activity" evidence=IDA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=TAS

GO:0000718 "nucleotide-excision repair, DNA damage removal" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=TAS

GO:0006289 "nucleotide-excision repair" evidence=TAS

GO:0006360 "transcription from RNA polymerase I promoter" evidence=TAS

GO:0006361 "transcription initiation from RNA polymerase I promoter" evidence=TAS

GO:0006362 "transcription elongation from RNA polymerase I promoter" evidence=TAS

GO:0006363 "termination of RNA polymerase I transcription" evidence=TAS

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=TAS

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=TAS

GO:0006370 "7-methylguanosine mRNA capping" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0050434 "positive regulation of viral transcription" evidence=TAS

GO:0006468 "protein phosphorylation" evidence=IDA

UNIPROTKB|P60027 GTF2H4 "General transcription factor IIH subunit 4" [Pan troglodytes (taxid:9598)]

 Score = 641 (230.7 bits), Expect = 8.8e-63, P = 8.8e-63
 Identities = 145/410 (35%), Positives = 235/410 (57%)

Query:     4 VKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMM 63
             V +  +N  + +  L+   LDRLY +P  C A+ R LP LAK +VM+M +++  +P   +
Sbjct:    12 VHLQCRNLQEFLGGLSPGVLDRLYGHPATCLAVFRELPSLAKNWVMRMLFLEQPLPQAAV 71

Query:    64 EEWVLPDGFTKHRVAIDRLVQ-LRLFSEEKKKETTYRL--NSTFQSNLRKHLIYGG-ALP 119
               WV  + F+K +     L+  LR++  +        L  N  F+ NLR  L+ GG A  
Sbjct:    72 ALWVKKE-FSKAQEESTGLLSGLRIWHTQLLPGGLQGLILNPIFRQNLRIALLGGGKAWS 130

Query:   120 REPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLL-S 178
              +    G       +  L+ YA  +WE  L  ++ S  A    + +  +    Q GL+ S
Sbjct:   131 DDTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQLLS---QAGLMKS 187

Query:   179 RRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGE 238
                 E P +T +GFQFLL+DT AQLWY + +Y+  +Q RG++  +++SFL +LSF   G+
Sbjct:   188 TEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQLSFSTLGK 247

Query:   239 AYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS--SARKEGF 296
              Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +  +  + GF
Sbjct:   248 DYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGF 306

Query:   297 IVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIIS 356
             IVVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII 
Sbjct:   307 IVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIH 366

Query:   357 FLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRV 406
             FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+V
Sbjct:   367 FLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQV 416

GO:0005675 "holo TFIIH complex" evidence=ISS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISS

GO:0004672 "protein kinase activity" evidence=ISS

GO:0008094 "DNA-dependent ATPase activity" evidence=ISS

GO:0008353 "RNA polymerase II carboxy-terminal domain kinase activity" evidence=ISS

RGD|1303309 Gtf2h4 "general transcription factor II H, polypeptide 4" [Rattus norvegicus (taxid:10116)]

 Score = 640 (230.4 bits), Expect = 1.1e-62, P = 1.1e-62
 Identities = 144/405 (35%), Positives = 233/405 (57%)

Query:     9 KNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVL 68
             +N  + +  L+   LDRLY +P  C A+ R LP LAK +VM+M +++  +P   +  WV 
Sbjct:    18 RNLQEFLGGLSPGVLDRLYGHPATCLAVFRELPSLAKNWVMRMLFLEQPLPQAAVALWVK 77

Query:    69 PDGFTKHRVAIDRLVQ-LRLFSEEKKKETTYRL--NSTFQSNLRKHLIYGG-ALPREPMP 124
              + F+K +     L+  LR++  +        L  N  F+ NLR  L+ GG A   +   
Sbjct:    78 KE-FSKAQEESTGLLSGLRIWHTQLLPGGLQGLILNPVFRQNLRIALLGGGKAWSDDTSQ 136

Query:   125 SGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLL-SRRDKE 183
              G       +  L+ YA  +WE  L  ++ S  A    + +  +    Q GL+ S    E
Sbjct:   137 LGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQLLS---QAGLMKSTEPGE 193

Query:   184 APRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLN 243
              P +T +GFQFLL+DT AQLWY + +Y+  +Q RG++  +++SFL +LSF   G+ Y++ 
Sbjct:   194 PPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQLSFSTLGKDYSVE 253

Query:   244 TLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS--SARKEGFIVVET 301
              +S+   + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +  +  + GFIVVET
Sbjct:   254 GMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGFIVVET 312

Query:   302 NFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQN 361
             N+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII FL+  
Sbjct:   313 NYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLRTR 372

Query:   362 AHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRV 406
             AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+V
Sbjct:   373 AHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQV 417

GO:0000439 "core TFIIH complex" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0005675 "holo TFIIH complex" evidence=IEA;ISO

GO:0006289 "nucleotide-excision repair" evidence=IEA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IEA;ISO

GO:0006468 "protein phosphorylation" evidence=ISO

GO:0008353 "RNA polymerase II carboxy-terminal domain kinase activity" evidence=IEA;ISO

GO:0004672 "protein kinase activity" evidence=ISO

GO:0008094 "DNA-dependent ATPase activity" evidence=ISO

MGI|MGI:1338799 Gtf2h4 "general transcription factor II H, polypeptide 4" [Mus musculus (taxid:10090)]

 Score = 639 (230.0 bits), Expect = 1.4e-62, P = 1.4e-62
 Identities = 144/405 (35%), Positives = 233/405 (57%)

Query:     9 KNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVL 68
             +N  + +  L+   LDRLY +P  C A+ R LP LAK +VM+M +++  +P   +  WV 
Sbjct:    18 RNLQEFLGGLSPGVLDRLYGHPATCLAVFRELPSLAKNWVMRMLFLEQPLPQAAVALWVK 77

Query:    69 PDGFTKHRVAIDRLVQ-LRLFSEEKKKETTYRL--NSTFQSNLRKHLIYGG-ALPREPMP 124
              + F+K +     L+  LR++  +        L  N  F+ NLR  L+ GG A   +   
Sbjct:    78 KE-FSKAQEESTGLLSGLRIWHTQLLPGGLQGLILNPVFRQNLRIALLGGGKAWSDDTSQ 136

Query:   125 SGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLL-SRRDKE 183
              G       +  L+ YA  +WE  L  ++ S  A    + +  +    Q GL+ S    E
Sbjct:   137 LGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQLLS---QAGLMKSTEPGE 193

Query:   184 APRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLN 243
              P +T +GFQFLL+DT AQLWY + +Y+  +Q RG++  +++SFL +LSF   G+ Y++ 
Sbjct:   194 PPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQLSFSTLGKDYSVE 253

Query:   244 TLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS--SARKEGFIVVET 301
              +S+   + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +  +  + GFIVVET
Sbjct:   254 GMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGFIVVET 312

Query:   302 NFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQN 361
             N+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII FL+  
Sbjct:   313 NYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLRTR 372

Query:   362 AHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRV 406
             AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+V
Sbjct:   373 AHPVMLKQNPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQV 417

GO:0000439 "core TFIIH complex" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005675 "holo TFIIH complex" evidence=ISO

GO:0006281 "DNA repair" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISO

GO:0006468 "protein phosphorylation" evidence=ISO

GO:0006974 "response to DNA damage stimulus" evidence=IEA

DICTYBASE|DDB_G0293228 gtf2h4 "TFIIH subunit" [Dictyostelium discoideum (taxid:44689)]

 Score = 469 (170.2 bits), Expect = 1.6e-59, Sum P(2) = 1.6e-59
 Identities = 112/331 (33%), Positives = 190/331 (57%)

Query:    90 EEKKKETTYRLNSTFQSNLRKHLIYGGALPREPMPS-GITARLPTLEDLEAYAIGQWECF 148
             ++++ E T RLN  FQ N+++ L+    +      S     + P+++DL++Y+  QWE  
Sbjct:   113 QQQQTEQTIRLNPLFQDNIKRSLVQVNQVIFSNNSSIKDNHKPPSIDDLDSYSKSQWEKV 172

Query:   149 LLQLISSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVR 208
             L  L   T   +P+   S ++       L++++ +   +T  GF+FLL D   Q+W ++ 
Sbjct:   173 LYFLSDDTV--QPSKLISELLLSSN---LTKQEGDGLSITSEGFKFLLKDVYTQIWTLLI 227

Query:   209 EYISNSQER---GI-NQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKL 264
              Y+ + +++   G  ++ DL+SFL  LSF   G  Y ++ LSE QK  +      GL+ +
Sbjct:   228 VYLDDLEKKKGKGSGSRNDLLSFLFRLSFLNLGRGYLVSELSEQQKEYLFALKQFGLIYM 287

Query:   265 QQGRKENWFIPTKLATNLS----MSLTDS-------SARKEGFIVVETNFRMYAYSTSKL 313
             +       F PT+L  +L+    +SL  S       + +++G+IV+ETN+R+YAY++S L
Sbjct:   288 RTD-SSILFYPTRLIISLTTGKTLSLIQSISSERTQTQKEQGYIVLETNYRLYAYTSSSL 346

Query:   314 HCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSV 373
                +L LF K+ Y+LPNL VG IT+ES+  A  +GITA+QII F++ N+HP  A+    +
Sbjct:   347 QISLLSLFVKMLYRLPNLAVGIITRESIRTALIHGITADQIIDFVRHNSHPNAANSGQPI 406

Query:   374 PENVCDQIRLWESDLNRVEMTPAHYYDEFPS 404
             P+ V +QI LWE++ NR+  T +  Y+ FP+
Sbjct:   407 PDVVAEQILLWEAERNRITYTKSVLYNSFPT 437

GO:0006289 "nucleotide-excision repair" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0000439 "core TFIIH complex" evidence=IEA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISS

GO:0005675 "holo TFIIH complex" evidence=ISS

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

FB|FBgn0261109 mrn "marionette" [Drosophila melanogaster (taxid:7227)]

 Score = 569 (205.4 bits), Expect = 3.7e-55, P = 3.7e-55
 Identities = 135/422 (31%), Positives = 234/422 (55%)

Query:     9 KNFMDMVASL-TARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWV 67
             K+F + + +  T   L++LY  P IC A+ R LP +A+++++++ ++D  +P  ++  W 
Sbjct:    35 KDFQEYLRTRQTPESLEKLYNYPPICLAVFRELPEIARQFIIRILFVDQPVPQAVVTSWG 94

Query:    68 LPDGFTKHRVAIDRLVQLRLFSEEKKKE--TTYRLNSTFQSNLRKHLIYGGALPREPMPS 125
                   +   A   L  L ++         + + L+ TF+ ++R+ L+ GG  P  PM +
Sbjct:    95 AQRCAKEQAEATSCLTALNVWRVTAIPGGLSAWELSPTFKKSVRQVLL-GGGKPW-PMTN 152

Query:   126 GIT--ARLPTLEDLEAYAIGQWECFLLQLISS-----TQAERPTNFSSSMMKVFQRGLLS 178
              +   ++   +  L+ YA+ +W C L  ++ +     T AE     S   +++     L 
Sbjct:   153 TLDKDSKPRDIAFLDTYAMSRWRCVLHYMVGTGNRNGTDAEA---ISPDAVRILLHANLM 209

Query:   179 RRD-KEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAG 237
             +RD ++   +T  GFQFLL+DT AQ+W+ + +Y+   +ERGI+  + +S L +LSF   G
Sbjct:   210 KRDERDGITITRQGFQFLLLDTRAQVWHFMLQYLDTCEERGISLPECLSMLFQLSFSTLG 269

Query:   238 EAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNL---------SMSLTD 288
               Y+   ++    + ++   + GLV  Q+ RKE  F PT+LA N+         S+++ +
Sbjct:   270 RDYSSEGMNSQMLTFLQHLREFGLV-FQRKRKEGRFYPTRLALNVTSKEAAATASVAMDE 328

Query:   289 SSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENG 348
              + +  G+IVVETN+R+YAY+ S L   +L LF+++ Y+ PNL+VG +T++S+  A   G
Sbjct:   329 EATQDCGYIVVETNYRVYAYTDSPLQVAVLGLFTELLYRFPNLVVGVLTRDSVRQALRGG 388

Query:   349 ITAEQIISFLQQNAHPR---VADRMPS---VPENVCDQIRLWESDLNRVEMTPAHYYDEF 402
             ITAEQI+S+L+Q AHP    V   + S   +P  V DQI+LWE + NR   T    Y++F
Sbjct:   389 ITAEQIVSYLEQYAHPNMRMVESAIHSKSCLPPTVVDQIKLWELERNRFTYTEGVLYNQF 448

Query:   403 PS 404
              S
Sbjct:   449 LS 450

GO:0005675 "holo TFIIH complex" evidence=ISS;IDA

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=ISS

GO:0000439 "core TFIIH complex" evidence=ISS;IPI

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0001671 "ATPase activator activity" evidence=IDA

GO:0001111 "promoter clearance from RNA polymerase II promoter" evidence=ISS

GO:0006289 "nucleotide-excision repair" evidence=IDA;IMP

GO:0010224 "response to UV-B" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

GO:0001113 "transcriptional open complex formation at RNA polymerase II promoter" evidence=ISS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P60027	TF2H4_PANTR	No assigned EC number	0.3496	0.9803	0.8636	yes	no
O70422	TF2H4_MOUSE	No assigned EC number	0.3506	0.9705	0.8531	yes	no
P87303	TFB2_SCHPO	No assigned EC number	0.3324	0.9115	0.8299	yes	no
Q92759	TF2H4_HUMAN	No assigned EC number	0.3496	0.9803	0.8636	yes	no
Q6BZX4	TFB2_YARLI	No assigned EC number	0.3154	0.9410	0.8201	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_fgenesh4_pg.C_LG_IV0538	hypothetical protein (449 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	fgenesh4_pg.C_LG_I000900	hypothetical protein (803 aa)				•	•	•	•		0.885
	eugene3.00020503	hypothetical protein (758 aa)				•	•	•	•		0.836
	gw1.V.5266.1	hypothetical protein (289 aa)					•	•	•		0.795
	estExt_fgenesh4_pm.C_1650003	hypothetical protein (413 aa)				•	•	•	•		0.744
	estExt_Genewise1_v1.C_1330021	hypothetical protein (334 aa)						•	•		0.573
	estExt_Genewise1_v1.C_LG_IX3069	SubName- Full=Putative uncharacterized protein; (117 aa)				•		•			0.494
	grail3.0014029901	hypothetical protein (52 aa)						•			0.479
	gw1.70.559.1	hypothetical protein (329 aa)						•	•		0.472
	gw1.IX.2304.1	hypothetical protein (321 aa)						•			0.442
	fgenesh4_pg.C_scaffold_82000017	hypothetical protein (603 aa)						•	•		0.432

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	407
pfam03849	365	pfam03849, Tfb2, Transcription factor Tfb2	1e-168
TIGR00625	448	TIGR00625, tfb2, Transcription factor tfb2	1e-89
COG5144	447	COG5144, TFB2, RNA polymerase II transcription ini	4e-78
pfam13625	128	pfam13625, Helicase_C_3, Helicase conserved C-term	2e-04

>gnl|CDD|217760 pfam03849, Tfb2, Transcription factor Tfb2

 Score =  474 bits (1223), Expect = e-168
 Identities = 149/368 (40%), Positives = 228/368 (61%), Gaps = 19/368 (5%)

Query: 13  DMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGF 72
           D + SL    LDRLY++P  C AI R LPPLAK+++M+M ++D  +PA  +++WV P+  
Sbjct: 1   DYLESLPPTVLDRLYQSPATCLAIFRLLPPLAKQFIMRMLFVDQPVPAADLDKWVKPESK 60

Query: 73  TKHRVAIDRLVQLRLF--SEEKKKETTYRLNSTFQSNLRKHLIYGGALPREPMPSGIT-A 129
            +H  AI RL  L +   +    K+ + RLN TF+ NLR+ L  GG      +PS     
Sbjct: 61  KQHEEAIKRLKSLHIITETPSGGKKQSIRLNPTFKKNLRRALTGGGVNNSFGVPSDEPDK 120

Query: 130 RLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTE 189
           +L  +  L++YA  +WE  L  ++ S++A+  T  S S++ + + G L  R     R+T 
Sbjct: 121 KLVDVAFLDSYAREKWETILHYMVGSSEAK--TQPSKSVLNLLKHGGLMERSDGGLRITN 178

Query: 190 SGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQ 249
            GFQFLL D NAQ+W ++ +Y+  ++ERG++  D++SFL  L F   G+AY+ + LSE Q
Sbjct: 179 EGFQFLLQDVNAQIWTLLLQYLKLAEERGMDPVDVLSFLFMLGFLELGKAYSTDGLSETQ 238

Query: 250 KSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSS-------------ARKEGF 296
           ++M++D  D GLV  ++ +   ++ PT+LAT L+   +                A  +GF
Sbjct: 239 RNMLQDLRDYGLVYQRKRKSRRFY-PTRLATTLTSDSSALRTASSAMEAATSSEAASKGF 297

Query: 297 IVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIIS 356
           I+VETNFR+YAY++S L   IL LF +++Y+ PNL+VG IT+ES+ NA ENGITA+QIIS
Sbjct: 298 IIVETNFRLYAYTSSPLQIAILALFVELKYRFPNLVVGQITRESIRNALENGITADQIIS 357

Query: 357 FLQQNAHP 364
           +L+ +AHP
Sbjct: 358 YLETHAHP 365

Length = 365

>gnl|CDD|233058 TIGR00625, tfb2, Transcription factor tfb2

 Score =  277 bits (711), Expect = 1e-89
 Identities = 142/407 (34%), Positives = 228/407 (56%), Gaps = 13/407 (3%)

Query: 10  NFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLP 69
           +  + +  L    LDRLY +P  C A+ R LP LAK +VM+M + +  +P   ++ WV  
Sbjct: 1   SLQEFLEGLPPGVLDRLYGHPATCLAVFRELPSLAKNWVMRMLFNEQPVPLADVDLWVKK 60

Query: 70  DGFTKHRVAIDRLVQLRLFSEEKKKETTY-RLNSTFQSNLRKHLIYGGALPREPMP-SGI 127
           +       +   L  L ++  +         LN  F+ NLR  L  GG      +   G 
Sbjct: 61  EFKKAQEESTGLLSGLHIWHTQLLPGLQGIILNPIFRQNLRIALTGGGKANSFGVSQLGP 120

Query: 128 TARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLSR-RDKEAPR 186
                 ++ L+ YA  +WE  L  ++ +  A+ P+     ++K  Q GL+      E P 
Sbjct: 121 DKHAVDVDSLDKYAEERWETILHFMVGTPSAKVPSEDVLQLLK--QAGLMKSTEPGEPPC 178

Query: 187 LTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLS 246
           +T +GFQFLL D NAQLW ++ +Y+  ++ RG++  +++ FL  L F   G+AY+++ LS
Sbjct: 179 ITSAGFQFLLQDINAQLWTLLLQYLKTAESRGMDLVEVLHFLFMLGFLTLGKAYSVDGLS 238

Query: 247 EIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSM-SLTDSSARKE-----GFIVVE 300
           + Q  M++D  + GLV  Q+ RK   F PT+LA NL+  + T S A        GFI+VE
Sbjct: 239 DTQLIMLQDLREYGLV-FQRKRKSRRFYPTRLAINLTSDTKTVSGAGGTVDDDLGFIIVE 297

Query: 301 TNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQ 360
           TN+R+YAY+ S L   ++ LFS++  + PN++VG IT+ES+  A  NGITA+QII +L+ 
Sbjct: 298 TNYRLYAYTESPLQIALIALFSELLARFPNMVVGQITRESIRRALANGITAQQIIHYLRT 357

Query: 361 NAHPRV-ADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRV 406
           +AHP++  ++ P +P  + DQIRLWE + +R+  T    Y++F ++V
Sbjct: 358 HAHPQMRKEQTPVLPPTIVDQIRLWELERDRLRFTEGVLYNDFLTQV 404

All proteins in this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 448

>gnl|CDD|227473 COG5144, TFB2, RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription / DNA replication, recombination, and repair]

 Score =  247 bits (633), Expect = 4e-78
 Identities = 124/384 (32%), Positives = 204/384 (53%), Gaps = 15/384 (3%)

Query: 25  RLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQ 84
           RLY  P  C A LR LP LA K+VM M +   ++     +EW+        R+ +     
Sbjct: 24  RLYGAPAFCLAFLRVLPELATKFVMDMLFNSHSVSLLDEDEWIKETLKILLRIQVIGKKG 83

Query: 85  LRLFSEEKKKETTYRLNSTFQSNLRKHLIYGGALPREPMPSGITARLPTLEDLEAYAIGQ 144
             ++ +E       RLN  F+ +L   L  G           I  +L +++ L++Y+  +
Sbjct: 84  NHIYLDEGL---MIRLNPEFKISLMDALTGGTM--ENSFGVCIGEKLVSVDMLDSYSSRK 138

Query: 145 WECFLLQLISSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLW 204
           WE  L  ++ + +A+ P   +  ++++ + G L  RD+   ++T  GFQFLL   N QLW
Sbjct: 139 WETILHFMVGTPEAKIP---AEGVLELLKFGGLMGRDRNEFKITNRGFQFLLQTINEQLW 195

Query: 205 YIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKL 264
            ++  Y+   +   +++  ++ FL  L     G AY ++ LS+ Q+ M+ D    GLV+ 
Sbjct: 196 TLLLLYLKYFEGSVMDEVAVLHFLFMLGALAVGTAYKIDALSDTQQIMLMDRRLYGLVE- 254

Query: 265 QQGRKENWFIPTKLATNLSM-SLTDSSARKE-----GFIVVETNFRMYAYSTSKLHCEIL 318
           Q G     F PT LA  L+   L ++S +       GFI+VETN ++YAY+ S L   ++
Sbjct: 255 QLGILRKIFYPTGLAIGLTFDQLFEASEQNRREDDKGFIIVETNNKIYAYTNSPLQIAVI 314

Query: 319 RLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVC 378
            LF  +  + PNL+ G IT+ES+  A +NGITA+QII +L+ +AHP++  ++  +P  + 
Sbjct: 315 HLFCNLTARFPNLVKGIITRESIRRALDNGITAKQIIHYLETHAHPQMRKKLELLPPTIV 374

Query: 379 DQIRLWESDLNRVEMTPAHYYDEF 402
           DQI LWE + NR+ M P + Y +F
Sbjct: 375 DQIVLWELERNRIFMVPGYLYSDF 398

Length = 447

>gnl|CDD|205803 pfam13625, Helicase_C_3, Helicase conserved C-terminal domain

 Score = 40.6 bits (96), Expect = 2e-04
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 9/65 (13%)

Query: 336 ITKESLYNAFENGITAEQIISFLQQNA-HPRVADRMPSVPENVCDQIRLWESDLNRVEMT 394
           +T  SL  A + G+TAE+II FL++++  P        VP+++   IR       R+ + 
Sbjct: 41  LTPLSLRRALDAGLTAEEIIEFLERHSRTP--------VPQSLLYLIRDVARRHGRLRLG 92

Query: 395 PAHYY 399
            A  Y
Sbjct: 93  KAGLY 97

This domain family is found in a wide variety of helicases and helicase-related proteins. Length = 128

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	407
TIGR00625	448	tfb2 Transcription factor tfb2. This family is bas	100.0
KOG3471	465	consensus RNA polymerase II transcription initiati	100.0
PF03849	366	Tfb2: Transcription factor Tfb2; InterPro: IPR0045	100.0
COG5144	447	TFB2 RNA polymerase II transcription initiation/nu	100.0
PF13625	129	Helicase_C_3: Helicase conserved C-terminal domain	99.56
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	97.17
PF08671	30	SinI: Anti-repressor SinI; InterPro: IPR010981 The	91.25

>TIGR00625 tfb2 Transcription factor tfb2

Probab=100.00  E-value=1.6e-132  Score=1017.76  Aligned_cols=392  Identities=34%  Similarity=0.616  Sum_probs=363.7

Q ss_pred             hHHHHHhhCCHHHHHHHhcCchhHHHHHhcCChhHHHHHHHHhcCCCCCChHHHHhhcCCcchhHHHHHHHHHhccceee
Q 015409           10 NFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFS   89 (407)
Q Consensus        10 ~~~~yL~~Lp~~~~~~LY~~p~tclaifR~Lp~lak~~vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~L~I~~   89 (407)
                      +++|||++||+.++++||++||||+||||+||||||+|||||||+++|+|.++++.|+++++++++++|+++|++||||+
T Consensus         1 ~~~~yL~~Lp~~~~~~LY~~PatclAIfR~Lp~lAK~~vmrlL~~~~pv~~~~l~~Wv~~~~~~~~~~al~~L~~L~I~~   80 (448)
T TIGR00625         1 SLQEFLEGLPPGVLDRLYGHPATCLAVFRELPSLAKNWVMRMLFNEQPVPLADVDLWVKKEFKKAQEESTGLLSGLHIWH   80 (448)
T ss_pred             ChHHHHHhCCHHHHHHHhCCcHHHHHHHHcCcHHHHHHHHHHHcCCCCCCHHHHHHHhCccchHHHHHHHHHHHhCEeEE
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ec-CCCceeEEeCHHHHHHHHHHHHcCCCCCCCCCCCCCCC-CCCChHHHHHHHhhhHHHHHHHHhCCCCCCCCCCCchH
Q 015409           90 EE-KKKETTYRLNSTFQSNLRKHLIYGGALPREPMPSGITA-RLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSS  167 (407)
Q Consensus        90 ~~-~~~~~~~~Ln~~F~~~lr~aL~ggg~~~~~~~~~~~~~-~~~~~~~Ld~ya~~~WE~IL~~mV~~~~~~~~~~~s~~  167 (407)
                      +. .+|.+.|.||++||+|||.||+|||.+++++++...++ +.+++++||+||++|||+|||||||++..   ..++++
T Consensus        81 ~~~~~~~~~~~Ln~~F~~~lr~aL~g~~~~~s~~v~~~~~d~~~~~~~~Ld~yA~~~WE~IL~fmVgs~~~---~~~s~~  157 (448)
T TIGR00625        81 TQLLPGLQGIILNPIFRQNLRIALTGGGKANSFGVSQLGPDKHAVDVDSLDKYAEERWETILHFMVGTPSA---KVPSED  157 (448)
T ss_pred             ecCCCCceeEEECHHHHHHHHHHhcCCCCCCCCCCcccCCCCCCCCHHHHHHHHHHHHHHHHHHHcCCCCc---CCCchH
Confidence            73 34557899999999999999999999999988876555 48999999999999999999999997653   347889


Q ss_pred             HHHHHHhcCcccc-C-CCCCccchhhhhhhccChhhHHHHHHHHHHHHHHHcCCChHHHHHHHHhhcccccCccccCCCC
Q 015409          168 MMKVFQRGLLSRR-D-KEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTL  245 (407)
Q Consensus       168 ~~~lL~~~ll~~~-~-~~~~~IT~~GFqFLL~d~~~Q~W~lll~yl~~~e~~~~~~~~~l~fLf~Ls~~~~G~~Y~~~~l  245 (407)
                      ++++|++|+|+++ + ++.+.||++||||||+|+|+|+|+||++||+++|++|+|.+|+|+|||+||++++|++|++++|
T Consensus       158 v~~lL~~~~Lm~~~~~~~~~~IT~~GFqFLLqd~n~QvW~lll~YL~~~e~~g~d~vevLsFLf~Ls~l~lG~~Y~~~~L  237 (448)
T TIGR00625       158 VLQLLKQAGLMKSTEPGEPPCITSAGFQFLLQDINAQLWTLLLQYLKTAESRGMDLVEVLHFLFMLGFLTLGKAYSVDGL  237 (448)
T ss_pred             HHHHHHhCCCCcccCCCCCccCchhhHHHHcCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHhccccCCccCCCCC
Confidence            9999988666655 3 3347999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHhhcCceeeecCCCccccccchhhhhhccccccc----c--ccccceEEEeeCceEEEecCCHhHHHHHH
Q 015409          246 SEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS----S--ARKEGFIVVETNFRMYAYSTSKLHCEILR  319 (407)
Q Consensus       246 t~~q~~~L~~L~d~GLvy~~~~~~~~~f~pT~La~~L~~~~~~~----~--~~~~g~IIVETNFrvYAYT~S~lqiaiL~  319 (407)
                      |++|++||+||+|+||||++ +.++++||||+||++||+++...    +  +.++|+|||||||||||||+||||++||+
T Consensus       238 t~tq~~~L~dL~dlGLVy~~-~~~~~~fYPTrLAt~Lts~~~~l~~~~~~~~~~~g~iivEtNfrvYaYt~s~l~~~il~  316 (448)
T TIGR00625       238 SDTQLIMLQDLREYGLVFQR-KRKSRRFYPTRLAINLTSDTKTVSGAGGTVDDDLGFIIVETNYRLYAYTESPLQIALIA  316 (448)
T ss_pred             CHHHHHHHHHHHHcCeEEEe-cCCCCcccchHHHHHHhcCccccccccccccCCCceEEEEecceEEEecCCHHHHHHHH
Confidence            99999999999999999855 45677899999999999874421    1  25679999999999999999999999999


Q ss_pred             HHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCccccc-cCCCCCChhHHHHHHHHHHhcCceeeeCeee
Q 015409          320 LFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVA-DRMPSVPENVCDQIRLWESDLNRVEMTPAHY  398 (407)
Q Consensus       320 lF~~l~~r~Pnlvvg~iTReSvr~Al~~GITA~QII~fL~~hAHp~m~-~~~p~lP~tV~dQIrLWe~Er~R~~~~~g~L  398 (407)
                      +||++.|||||||||+||||||++|+++||||||||+||++||||+|+ ++.|+|||||+|||||||.||||+++++|||
T Consensus       317 lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GITa~qIi~fl~~~ahp~~~~~~~~~lP~tv~dQi~lWe~e~~R~~~~~~~l  396 (448)
T TIGR00625       317 LFSELLARFPNMVVGQITRESIRRALANGITAQQIIHYLRTHAHPQMRKEQTPVLPPTIVDQIRLWELERDRLRFTEGVL  396 (448)
T ss_pred             HHHHHHhcCCceEEEEecHHHHHHHHHcCCCHHHHHHHHHhcCChhhhccCCCCCChHHHHHHHHHHHHhcceEeeccee
Confidence            999999999999999999999999999999999999999999999998 5889999999999999999999999999999


Q ss_pred             ecCCCCC
Q 015409          399 YDEFPSR  405 (407)
Q Consensus       399 y~~F~s~  405 (407)
                      |+||+|.
T Consensus       397 ~~~f~s~  403 (448)
T TIGR00625       397 YNDFLTQ  403 (448)
T ss_pred             eeecCCH
Confidence            9999985

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG3471 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription; Replication, recombination and repair]

Probab=100.00  E-value=3e-131  Score=982.47  Aligned_cols=399  Identities=38%  Similarity=0.644  Sum_probs=365.3

Q ss_pred             chhhhhhhHHHHHhhCCH--HHHHHHhcCchhHHHHHhcCChhHHHHHHHHhcCCCCCChHHHHhhcCCcchhHHHHHHH
Q 015409            3 LVKIIAKNFMDMVASLTA--RDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAID   80 (407)
Q Consensus         3 ~~~~~~~~~~~yL~~Lp~--~~~~~LY~~p~tclaifR~Lp~lak~~vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~   80 (407)
                      +.--.++++.+||+.||.  .+++|||++|++|+||||+|||+||+|||+|||.++|||.++++.|++.++++++++|++
T Consensus         7 ~~~~~~~~~c~~leeLp~~~~~l~RLY~~Pa~ClAIfR~LPpLAkqfVm~MLf~~~pVP~a~~~~Wv~~~~tk~q~eaik   86 (465)
T KOG3471|consen    7 QGWPYAKNICDYLEELPRIPHSLDRLYGKPAICLAIFRELPPLAKQFVMQMLFKDQPVPLADVDLWVKVEETKEQEEAIK   86 (465)
T ss_pred             ccCcccchHHHHHHHhhccchHHHHHhCCchHHHHHHHhCcHHHHHHHHHHHhcCCCccHHHHHHHhhhhhHHHHHHHHH
Confidence            333478899999999999  589999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhccceeeecC-CCceeEEeCHHHHHHHHHHHHcCCCCCCCCCCCCC-CCCCCChHHHHHHHhhhHHHHHHHHhCCCCC
Q 015409           81 RLVQLRLFSEEK-KKETTYRLNSTFQSNLRKHLIYGGALPREPMPSGI-TARLPTLEDLEAYAIGQWECFLLQLISSTQA  158 (407)
Q Consensus        81 ~L~~L~I~~~~~-~~~~~~~Ln~~F~~~lr~aL~ggg~~~~~~~~~~~-~~~~~~~~~Ld~ya~~~WE~IL~~mV~~~~~  158 (407)
                      .|.+||||.+.. .| +.+.|||+||+|+|.||+|||..++++.+.-. ..+.+++++||+||.+|||||||||||++.+
T Consensus        87 ~L~~L~I~~~~~~~g-~~i~Lnp~fr~s~~~al~gg~~~~s~~s~~l~~~~~~r~v~~ld~ya~~rwe~ILh~mvgt~~a  165 (465)
T KOG3471|consen   87 LLKRLRIFHKQGTPG-QAINLNPTFRRSLRDALTGGGKQNSFGSLVLGEDKHNRDVDFLDKYASERWECILHFMVGTPEA  165 (465)
T ss_pred             HHhheeeEeecCCCC-ceEEeCHHHHHHHHHHHhcCCCcccCCCcccCCCcCcccchhhHHHHHHHHHHHHHHHhCCccc
Confidence            999999999732 23 67999999999999999999999887543322 2258999999999999999999999998743


Q ss_pred             CCCCCCchHHHHHHHhcCccccCCCCCccchhhhhhhccChhhHHHHHHHHHHHHHHHcCCChHHHHHHHHhhcccccCc
Q 015409          159 ERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGE  238 (407)
Q Consensus       159 ~~~~~~s~~~~~lL~~~ll~~~~~~~~~IT~~GFqFLL~d~~~Q~W~lll~yl~~~e~~~~~~~~~l~fLf~Ls~~~~G~  238 (407)
                         ..+|.++.++|..|++++++.....||++||||||+|+++|+|+++++||++.|++|||.+|+|+|||+||++++|+
T Consensus       166 ---~~~se~v~~ll~~a~lm~~~~~~~~IT~~GFQFLL~~~~aQlW~~~LqyLk~~~~~~~dlvevL~~LfqL~~~~~G~  242 (465)
T KOG3471|consen  166 ---KAVSEGVLNLLKHAGLMSRDENQIEITNAGFQFLLLDINAQLWTLVLQYLKLFESSGMDLVEVLEFLFQLSALALGR  242 (465)
T ss_pred             ---cccChhHHHHHHhcCccCCCCCCceEeecchhhhhcCcHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcc
Confidence               46889999999766666665667899999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCHHHHHHHHHHhhcCceeeecCCCccccccchhhhhhccccccc--------cccccceEEEeeCceEEEecC
Q 015409          239 AYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS--------SARKEGFIVVETNFRMYAYST  310 (407)
Q Consensus       239 ~Y~~~~lt~~q~~~L~~L~d~GLvy~~~~~~~~~f~pT~La~~L~~~~~~~--------~~~~~g~IIVETNFrvYAYT~  310 (407)
                      +|+++++|++|+.||+||||+|||| |++.|+.+||||+||++++++....        .+.+.|||||||||||||||+
T Consensus       243 ~Ysvd~~~~~~~~~lq~Lre~Glvf-Qrk~k~~rfyptrla~~~ss~~~~~~~~~~~~~~edd~G~iIVETN~riYAYT~  321 (465)
T KOG3471|consen  243 AYSVDALTETQRILLQHLRELGLVF-QRKIKILRFYPTRLAIGLSSDQLGAASLVHQNRNEDDVGFIIVETNYRIYAYTN  321 (465)
T ss_pred             cceeehhhHHHHHHHHHHHHhhHHH-HhhhhhheecchhhhhccchhhhhhhhhhhcccccccCceEEEEeccEEEEecC
Confidence            9999999999999999999999996 7778999999999999998863321        123459999999999999999


Q ss_pred             CHhHHHHHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCccccccCC--CCCChhHHHHHHHHHHhc
Q 015409          311 SKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRM--PSVPENVCDQIRLWESDL  388 (407)
Q Consensus       311 S~lqiaiL~lF~~l~~r~Pnlvvg~iTReSvr~Al~~GITA~QII~fL~~hAHp~m~~~~--p~lP~tV~dQIrLWe~Er  388 (407)
                      ||||+||++|||++.|||||||||+|||||||+|+++||||+|||+||++||||||+...  |++||||+|||||||.||
T Consensus       322 S~lQiAvi~LF~~l~~rf~nlvvG~iTreSVr~Al~~GITa~QII~fLet~ahpqm~~~~~~~~LPpTv~dQIrLWEler  401 (465)
T KOG3471|consen  322 SPLQIAVIALFTELTYRFPNLVVGVITRESVRRALDNGITAEQIIHFLETHAHPQMRMLSPVPCLPPTVVDQIRLWELER  401 (465)
T ss_pred             CHHHHHHHHHHHHHHhhccccceeeeeHHHHHHHHhcCCcHHHHHHHHHhccCchhhhcCCCCCCCchHHhHHHHHHHhh
Confidence            999999999999999999999999999999999999999999999999999999998755  899999999999999999


Q ss_pred             CceeeeCeeeecCCCCCC
Q 015409          389 NRVEMTPAHYYDEFPSRV  406 (407)
Q Consensus       389 ~R~~~~~g~Ly~~F~s~~  406 (407)
                      ||+.++|||||++|+|.+
T Consensus       402 nR~~~~~g~LYs~Fls~~  419 (465)
T KOG3471|consen  402 NRLRMTEGYLYSDFLSLS  419 (465)
T ss_pred             cceecccchhHHhhhhhh
Confidence            999999999999999853

>PF03849 Tfb2: Transcription factor Tfb2; InterPro: IPR004598 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair

Probab=100.00  E-value=1.7e-116  Score=890.17  Aligned_cols=350  Identities=43%  Similarity=0.747  Sum_probs=324.8

Q ss_pred             HHHhhCCHHHHHHHhcCchhHHHHHhcCChhHHHHHHHHhcCCCCCChHHHHhhcCCcchhHHHHHHHHHhccceeeec-
Q 015409           13 DMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEE-   91 (407)
Q Consensus        13 ~yL~~Lp~~~~~~LY~~p~tclaifR~Lp~lak~~vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~L~I~~~~-   91 (407)
                      |||++||++++++||++||||+||||+||++||||||||||+++|||++++++||++++++++++|+++|.+||||++. 
T Consensus         1 eYL~~Lp~~~l~~LY~~P~tclAIfR~LP~LAK~~VmrLL~~~~pv~~~~l~~Wv~~~~~~~~~~al~~L~~L~Ii~~~~   80 (366)
T PF03849_consen    1 EYLESLPPATLDRLYQSPATCLAIFRSLPPLAKQYVMRLLFVEQPVPQADLESWVKPESKKEHDEALKRLRSLHIIQESE   80 (366)
T ss_pred             ChhHHCCHHHHHHHHcCcHHHHHHHHhccHHHHHHHHHHHhcCCCcCHHHHHHHhCccchHHHHHHHHHHhhCeeEeecc
Confidence            6999999999999999999999999999999999999999999999999999999999999999999999999999873 


Q ss_pred             -CCCceeEEeCHHHHHHHHHHHHcCCCCCCCCCCCCCC-CCCCChHHHHHHHhhhHHHHHHHHhCCCCCCCCCCCchHHH
Q 015409           92 -KKKETTYRLNSTFQSNLRKHLIYGGALPREPMPSGIT-ARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMM  169 (407)
Q Consensus        92 -~~~~~~~~Ln~~F~~~lr~aL~ggg~~~~~~~~~~~~-~~~~~~~~Ld~ya~~~WE~IL~~mV~~~~~~~~~~~s~~~~  169 (407)
                       +++.+.|.|||+||+|||.||+|||..+++++++... .+.+++++||+||++|||+|||||||++...... +|++++
T Consensus        81 ~~~~~~~~~Ln~~F~~~Lr~aL~ggg~~~~~~~~~~~~~~~~~~~~~Ld~yA~~rWE~IL~~mVgs~~~~~~~-~s~~v~  159 (366)
T PF03849_consen   81 SPGGKQQYQLNPIFRKNLRNALTGGGKPWSFGVPSEEPDKKAPDVEFLDEYARERWESILHYMVGSSSSSNSS-PSQDVK  159 (366)
T ss_pred             CCCCceeEEeCHHHHHHHHHHHhCCCCCcccCcccccccCCCCCHHHHHHHHHHHHHHHHHHHhcCcccccCC-CCHHHH
Confidence             3344789999999999999999999999998887765 4689999999999999999999999998764333 789999


Q ss_pred             HHHHhcCcccc--CCCCCccchhhhhhhccChhhHHHHHHHHHHHHHHHcCCChHHHHHHHHhhcccccCccccCCCCCH
Q 015409          170 KVFQRGLLSRR--DKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSE  247 (407)
Q Consensus       170 ~lL~~~ll~~~--~~~~~~IT~~GFqFLL~d~~~Q~W~lll~yl~~~e~~~~~~~~~l~fLf~Ls~~~~G~~Y~~~~lt~  247 (407)
                      ++|+.++|++.  .+++..||++||||||+|+|+|+|+||++||+.+|++|+|.+|+|+|||+||++++|++|++++||+
T Consensus       160 ~lL~~sgLm~~~~~~~~~~IT~~GFqFLL~d~~~QlW~lll~yL~~~e~~~~~~~~~l~flf~L~~~~~g~~Y~~~~ls~  239 (366)
T PF03849_consen  160 QLLKRSGLMKRSESGGSLKITSKGFQFLLQDTNAQLWTLLLQYLKMAEARGMDLVEVLSFLFQLSFLELGKAYSTEGLSE  239 (366)
T ss_pred             HHHHHcCCCcCcCCCCCCcEehhheeeecCChHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhcccccCCcCcCCCCCH
Confidence            99977555554  4567899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhcCceeeecCCCccccccchhhhhhccccccc-----------cccccceEEEeeCceEEEecCCHhHHH
Q 015409          248 IQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS-----------SARKEGFIVVETNFRMYAYSTSKLHCE  316 (407)
Q Consensus       248 ~q~~~L~~L~d~GLvy~~~~~~~~~f~pT~La~~L~~~~~~~-----------~~~~~g~IIVETNFrvYAYT~S~lqia  316 (407)
                      +|++||+||+|+||||.++ +++++|||||||++|+++++..           ...++|||||||||||||||+||||+|
T Consensus       240 ~q~~~L~~l~~~GLvy~~~-~~~~~fypT~La~~l~~~~~~~~~~~~~~~~~~~~~~~g~iivETNfrvYAYT~s~l~ia  318 (366)
T PF03849_consen  240 TQKNMLQDLRELGLVYQRK-RKSRRFYPTRLATNLTSGSSALRSASSALDSSSSSNKEGFIIVETNFRVYAYTNSPLQIA  318 (366)
T ss_pred             HHHHHHHHHHHCCeEEEec-CCCCeEechHHHHHHhcCCCcccccccccccccccccCceEEEEecceEEEecCCHHHHH
Confidence            9999999999999998554 5788899999999999976521           235789999999999999999999999


Q ss_pred             HHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCcc
Q 015409          317 ILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHP  364 (407)
Q Consensus       317 iL~lF~~l~~r~Pnlvvg~iTReSvr~Al~~GITA~QII~fL~~hAHp  364 (407)
                      ||++||++.|||||||||+|||||||+|+++||||||||+||++||||
T Consensus       319 iL~lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GIta~qIi~fL~~~aHp  366 (366)
T PF03849_consen  319 ILSLFCELKYRFPNLVVGQITRESVRRALKNGITADQIISFLRSHAHP  366 (366)
T ss_pred             HHHHHHHHHhcCCCeEEEEEcHHHHHHHHHcCCCHHHHHHHHHhcCCC
Confidence            999999999999999999999999999999999999999999999998

The core-TFIIH basal transcription factor complex has six subunits, this is the p52 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus

>COG5144 TFB2 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription / DNA replication, recombination, and repair]

Probab=100.00  E-value=1.1e-114  Score=841.86  Aligned_cols=390  Identities=31%  Similarity=0.541  Sum_probs=362.1

Q ss_pred             hhhhHHHHHhhCCHHHHHHHhcCchhHHHHHhcCChhHHHHHHHHhcCCCCCChHHHHhhcCCcchhHHHHHHHHHhccc
Q 015409            7 IAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLR   86 (407)
Q Consensus         7 ~~~~~~~yL~~Lp~~~~~~LY~~p~tclaifR~Lp~lak~~vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~L~   86 (407)
                      .+.++.+|||.||.....|||+.|++|+|+||.||++|++|||.|||.+.+||..+.+.|++.+.+-...+++..+.++|
T Consensus         6 ~k~si~~ylE~lP~~~~~rLY~~Pa~cla~~rvlp~la~~fvm~mlfn~~~v~lld~d~wik~~~Ki~~~~~v~~~k~~h   85 (447)
T COG5144           6 YKISIIEYLEMLPRHSKTRLYGAPAFCLAFLRVLPELATKFVMDMLFNSHSVSLLDEDEWIKETLKILLRIQVIGKKGNH   85 (447)
T ss_pred             ccccHHHHHHHhhhhhhhhhhcCcHHHHHHHHhccHHHHHHHHHHHcCCCCcchhhHHHHHhhhhHHHHHHHHhhhccce
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeeecCCCceeEEeCHHHHHHHHHHHHcCCCCCCCCCCCCCCCCCCChHHHHHHHhhhHHHHHHHHhCCCCCCCCCCCch
Q 015409           87 LFSEEKKKETTYRLNSTFQSNLRKHLIYGGALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSS  166 (407)
Q Consensus        87 I~~~~~~~~~~~~Ln~~F~~~lr~aL~ggg~~~~~~~~~~~~~~~~~~~~Ld~ya~~~WE~IL~~mV~~~~~~~~~~~s~  166 (407)
                      |...+  | ..+++||.||.+|+.|||||+..+++++  -+..+.+++++||+||.++||+|||||||...+.   -++.
T Consensus        86 i~~~~--g-~~i~ln~~fk~sl~~altgg~~~nsfgv--~i~E~lvsvd~ld~ys~~kwEtILhfmVgtpeak---ip~e  157 (447)
T COG5144          86 IYLDE--G-LMIRLNPEFKISLMDALTGGTMENSFGV--CIGEKLVSVDMLDSYSSRKWETILHFMVGTPEAK---IPAE  157 (447)
T ss_pred             EEecC--C-ceEEeChHHHHHHHHHhhccccccccce--eeccceeeeehhhhhhhhhHHHHHHHHhCCcccc---Ccch
Confidence            99863  3 6899999999999999999999887776  2233578999999999999999999999987652   3577


Q ss_pred             HHHHHHHhcCccccCCCCCccchhhhhhhccChhhHHHHHHHHHHHHHHHcCCChHHHHHHHHhhcccccCccccCCCCC
Q 015409          167 SMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLS  246 (407)
Q Consensus       167 ~~~~lL~~~ll~~~~~~~~~IT~~GFqFLL~d~~~Q~W~lll~yl~~~e~~~~~~~~~l~fLf~Ls~~~~G~~Y~~~~lt  246 (407)
                      .|+++|+.|+++.++....+||++|||||||+.|+|+|+++++||++.|...||++++|+||||||.+++|++|+++.||
T Consensus       158 gVl~lLk~ggLm~~~~ne~kITn~GFqFLLq~in~QlWtLlL~yLK~~e~s~md~v~VLhflFmLgal~vG~aY~id~ls  237 (447)
T COG5144         158 GVLELLKFGGLMGRDRNEFKITNRGFQFLLQTINEQLWTLLLLYLKYFEGSVMDEVAVLHFLFMLGALAVGTAYKIDALS  237 (447)
T ss_pred             hHHHHHHhcccccCCcccceeehhHHHHHHHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHhcchhhcceeeecccc
Confidence            89999988777777667889999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhcCceeeecCCCccccccchhhhhhccccc----cc--cccccceEEEeeCceEEEecCCHhHHHHHHH
Q 015409          247 EIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLT----DS--SARKEGFIVVETNFRMYAYSTSKLHCEILRL  320 (407)
Q Consensus       247 ~~q~~~L~~L~d~GLvy~~~~~~~~~f~pT~La~~L~~~~~----~~--~~~~~g~IIVETNFrvYAYT~S~lqiaiL~l  320 (407)
                      ++|+-||+|+|++|||+ +++-.++.||||+||+.+++.-.    ..  .+.+.|||||||||||||||+||||+|+++|
T Consensus       238 dtqqiml~D~R~yglv~-q~~i~~~~fYpt~LA~glt~d~~~~~s~qnr~edd~gfiIVETN~kiYaYtnSplqiavi~L  316 (447)
T COG5144         238 DTQQIMLMDRRLYGLVE-QLGILRKIFYPTGLAIGLTFDQLFEASEQNRREDDKGFIIVETNNKIYAYTNSPLQIAVIHL  316 (447)
T ss_pred             hHHHHHHHHHHHhhHHH-HhccchhhccccccchhhhhHHHHHhhhhccccccCceEEEEecceEEEecCChHHHHHHHH
Confidence            99999999999999996 66666788999999999988521    11  2256799999999999999999999999999


Q ss_pred             HHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCccccccCCCCCChhHHHHHHHHHHhcCceeeeCeeeec
Q 015409          321 FSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYD  400 (407)
Q Consensus       321 F~~l~~r~Pnlvvg~iTReSvr~Al~~GITA~QII~fL~~hAHp~m~~~~p~lP~tV~dQIrLWe~Er~R~~~~~g~Ly~  400 (407)
                      ||++..||||||+|+|||||||+|+.+||||+|||.||++||||||+++.+.+||||+|||+|||.|+||+...||+||+
T Consensus       317 F~nl~arf~Nlv~GiITreSirrAl~nGIta~QII~yLethahpqmr~~l~llPPtivdQI~lWele~nRi~~~pG~Lys  396 (447)
T COG5144         317 FCNLTARFPNLVKGIITRESIRRALDNGITAKQIIHYLETHAHPQMRKKLELLPPTIVDQIVLWELERNRIFMVPGYLYS  396 (447)
T ss_pred             hhhhhcccchhhhhhccHHHHHHHHhcCccHHHHHHHHHhccChhhhhcCCCCChhhhhheeeeeeccCcEEeecchHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 015409          401 EFPSR  405 (407)
Q Consensus       401 ~F~s~  405 (407)
                      ||.+.
T Consensus       397 dFlt~  401 (447)
T COG5144         397 DFLTL  401 (447)
T ss_pred             hhhch
Confidence            99874

>PF13625 Helicase_C_3: Helicase conserved C-terminal domain

Probab=99.56  E-value=2.8e-14  Score=124.95  Aligned_cols=94  Identities=27%  Similarity=0.444  Sum_probs=85.1

Q ss_pred             EEEeeCceEEEecCCH-hH-HHHHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCccccccCCCCCC
Q 015409          297 IVVETNFRMYAYSTSK-LH-CEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVP  374 (407)
Q Consensus       297 IIVETNFrvYAYT~S~-lq-iaiL~lF~~l~~r~Pnlvvg~iTReSvr~Al~~GITA~QII~fL~~hAHp~m~~~~p~lP  374 (407)
                      +||++||.|.+++.+| .. ...|..||++ .+..+|.+++||+.|+.+|++.|+|+++|++||+.|+.       ..||
T Consensus         2 liVqpd~~I~v~~~~~~~~~~~~L~~fae~-~s~~~~~~yrlT~~Sl~~A~~~G~~~e~i~~~L~~~S~-------~~lP   73 (129)
T PF13625_consen    2 LIVQPDFEILVEPGHPSPADAWFLARFAEL-KSPDTMHVYRLTPASLWRAASAGLTAEEIIEFLERYSK-------NPLP   73 (129)
T ss_pred             EEECCCCEEEEeCCCCCHHHHHHHHHHhcc-cccCceEEEEECHHHHHHHHHcCCCHHHHHHHHHHHcC-------CCCC
Confidence            7999999999977666 34 4599999999 56799999999999999999999999999999999995       5789


Q ss_pred             hhHHHHHHHHHHhcCceeeeCeee
Q 015409          375 ENVCDQIRLWESDLNRVEMTPAHY  398 (407)
Q Consensus       375 ~tV~dQIrLWe~Er~R~~~~~g~L  398 (407)
                      +||..+|+-|+...+|+++.++..
T Consensus        74 ~~v~~~i~~w~~~~g~v~l~~~~~   97 (129)
T PF13625_consen   74 QNVEQSIEDWARRYGRVRLYKGAY   97 (129)
T ss_pred             HHHHHHHHHHHHhcCCEEEecCeE
Confidence            999999999999999999998433

>TIGR00603 rad25 DNA repair helicase rad25

Probab=97.17  E-value=0.0019  Score=71.73  Aligned_cols=88  Identities=23%  Similarity=0.385  Sum_probs=75.7

Q ss_pred             cceEEEeeCceEEEecCCHhHH-HHHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCccccccCCCC
Q 015409          294 EGFIVVETNFRMYAYSTSKLHC-EILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPS  372 (407)
Q Consensus       294 ~g~IIVETNFrvYAYT~S~lqi-aiL~lF~~l~~r~Pnlvvg~iTReSvr~Al~~GITA~QII~fL~~hAHp~m~~~~p~  372 (407)
                      +|.|++||--.+|      =|. .-|..|+|+.+|--+|..++||-=|+-.|...|+++++||++|...+.       ..
T Consensus        22 d~~i~lE~~~p~~------~~a~~fl~~~aEp~~rp~~iHeY~lT~~sl~~A~s~g~~~~~ii~~L~~~sk-------~~   88 (732)
T TIGR00603        22 DGHIFLESFSPLY------KQAQDFLVAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLETEDIIEVLGRLSK-------TP   88 (732)
T ss_pred             CCeEEEEeCCccH------HHHHHHHHHhcccccChhheEEEeccHHHHHHHHHcCCCHHHHHHHHHHHhC-------CC
Confidence            5667777643322      122 289999999999999999999999999999999999999999999985       57


Q ss_pred             CChhHHHHHHHHHHhcCceeee
Q 015409          373 VPENVCDQIRLWESDLNRVEMT  394 (407)
Q Consensus       373 lP~tV~dQIrLWe~Er~R~~~~  394 (407)
                      ||++|.+.|+.+-.-.+++++.
T Consensus        89 ~p~~i~~~i~~~~~~ygk~klv  110 (732)
T TIGR00603        89 IPKGIIEFIRLCTQSYGKVKLV  110 (732)
T ss_pred             CCHHHHHHHHHHHHhcCcEEEE
Confidence            9999999999999999999883

All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []

Probab=91.25  E-value=0.19  Score=33.80  Aligned_cols=22  Identities=36%  Similarity=0.525  Sum_probs=17.7

Q ss_pred             HHHHHHHcCCCHHHHHHHHhhc
Q 015409          340 SLYNAFENGITAEQIISFLQQN  361 (407)
Q Consensus       340 Svr~Al~~GITA~QII~fL~~h  361 (407)
                      =|+.|...|||.+||-.||+.+
T Consensus         8 Li~eA~~~Gls~eeir~FL~~~   29 (30)
T PF08671_consen    8 LIKEAKESGLSKEEIREFLEFN   29 (30)
T ss_dssp             HHHHHHHTT--HHHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHhC
Confidence            3789999999999999999864

SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.

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Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	407
3dom_A	108	RNA polymerase II transcription factor B subunit;	1e-17
3dgp_A	80	RNA polymerase II transcription factor B subunit;	7e-10

>3dom_A RNA polymerase II transcription factor B subunit; protein-protein complex, heterodimer, beta-alpha-beta split, strand addition; 2.60A {Saccharomyces cerevisiae} Length = 108

 Score = 76.9 bits (189), Expect = 1e-17
 Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 351 AEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSR 405
           AE+ +   +    P   + +  +P  V DQIRLW+ +L+RV       Y +F + 
Sbjct: 7   AEEKLEK-KLELDPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETS 60

>3dgp_A RNA polymerase II transcription factor B subunit; protein-protein complex, beta-alpha-beta spilt, heterodimer, damage, DNA excision; 1.80A {Saccharomyces cerevisiae} Length = 80

 Score = 54.4 bits (131), Expect = 7e-10
 Identities = 12/30 (40%), Positives = 17/30 (56%)

Query: 376 NVCDQIRLWESDLNRVEMTPAHYYDEFPSR 405
            V DQIRLW+ +L+RV       Y +F + 
Sbjct: 3   TVVDQIRLWQLELDRVITYEGSLYSDFETS 32

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	407
3dom_A	108	RNA polymerase II transcription factor B subunit;	99.55
3dgp_A	80	RNA polymerase II transcription factor B subunit;	99.31

>3dom_A RNA polymerase II transcription factor B subunit; protein-protein complex, heterodimer, beta-alpha-beta split, strand addition; 2.60A {Saccharomyces cerevisiae}

Probab=99.55  E-value=3.3e-16  Score=132.07  Aligned_cols=44  Identities=32%  Similarity=0.659  Sum_probs=28.8

Q ss_pred             ccccccCCCCCChhHHHHHHHHHHhcCceeeeCeeeecCCCCCC
Q 015409          363 HPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRV  406 (407)
Q Consensus       363 Hp~m~~~~p~lP~tV~dQIrLWe~Er~R~~~~~g~Ly~~F~s~~  406 (407)
                      .|+++...|+|||||+|||||||.|||||++++||||++|+|++
T Consensus        18 ~~~~~~~~p~lPpTVvDQIrLWE~ErnRl~~~~G~LY~dF~s~~   61 (108)
T 3dom_A           18 DPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQ   61 (108)
T ss_dssp             --------------CCCHHHHHHHHHTTCEEEEEEEEECCSCHH
T ss_pred             CcccccCCCCCCCcHHHHHHHHHHhhCceeccceEEEecCCCHH
Confidence            35556678999999999999999999999999999999999853

>3dgp_A RNA polymerase II transcription factor B subunit; protein-protein complex, beta-alpha-beta spilt, heterodimer, damage, DNA excision; 1.80A {Saccharomyces cerevisiae}

Probab=99.31  E-value=1.8e-13  Score=109.96  Aligned_cols=32  Identities=38%  Similarity=0.690  Sum_probs=18.8

Q ss_pred             hhHHHHHHHHHHhcCceeeeCeeeecCCCCCC
Q 015409          375 ENVCDQIRLWESDLNRVEMTPAHYYDEFPSRV  406 (407)
Q Consensus       375 ~tV~dQIrLWe~Er~R~~~~~g~Ly~~F~s~~  406 (407)
                      |||+|||||||.|||||++++||||++|+|++
T Consensus         2 pTV~DQIrLWe~ErnRl~~~~g~Ly~~F~s~~   33 (80)
T 3dgp_A            2 PTVVDQIRLWQLELDRVITYEGSLYSDFETSQ   33 (80)
T ss_dssp             ------------CGGGCEEEEEEEEECCSCHH
T ss_pred             CchHHHHHHHHHhhCceeccceEEEecCCCHH
Confidence            79999999999999999999999999999863

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Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

No hit with probability above 80.00