Citrus Sinensis ID: 015440

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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
MPQVKIIAKNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLQKHLINGGALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHcccHHHHHHHHcccHHHHHHHHcccHHHHHHHHHHHcccccccHHHHHHHcccccccHHHHHHHHHHcccEEEEcccccccEEEcHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHcHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHccEEEEEcccccccEEccHHHHHHHccccccccccccEEEEEEccEEEEccccHHHHHHHHHHHHHHHcccccEEEEEcHHHHHHHHHccccHHHHHHHHHHccccccccccccccccHHHHHHHHHHHcccEEEcccEEccccccHHHHHHHHHHHHHccEEEEEcccccEEEEEccccHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccEEEHHcHHHHHHHccHHHHHHHHccHHHHHHHHHHccHHHHHHHHHHHHccccccHHHHHHHHcHHHHHHHHHHHHHHHccEEEEEccccccEEEEcHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHcccccccccHHcccccEEccccccHcHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHccEEEEEcccccccEcccEEEEEEcccccccccccccEEEEEEcEEEEEEcccHHHHHHHHHHHHHHHHcccEEEEEEcHHHHHHHHHccccHHHHHHHHHHcccHHHccccccccccHHHHHHHHHHHHccEEEcccEEEcccccHHHHHHHHHHHHHcccEEEEccccEEEEEccccHHHHHHHHHHccc
Coil and Loop (DISEMBL)
MPQVKIIAKNFMDMVASLTARDlnklyenpfICEAILRSLPPLAKKYVFQMLYidgaipaktmeewvlpdgftkhKVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLQKHLinggalprepmpsgitarlptledLEAYAIGQWECFLLQLISSaqaerptnfssSMMKVFQRGLLIQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLqqgrkeswfiptklatnlsmsltdssarkegFVVVETNFRMYAYSTSKLHCEILRLFSKIEyqlpnlivgAITKESLYNAFENGITAEQIISFLQqnahprvadripsvpenvCDQIRLWESDlnrvemtpahyyeefpsrdvFEAACDYArdrsgllwedskKMRLVVNAEIHMHMREFLRGQNK
Flexible Loop (DISEMBL)
MPQVKIIAKNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQlrlfseekkkettyrlnSTFQSNLQKHLINGGALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLatnlsmsltdssarkEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAhyyeefpsrdVFEAACDYARDrsgllwedskKMRLVVNAEIHMHMREFLRGQNK
Low Complexity Region (SEG)
MPQVKIIAKNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLQKHLINGGALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK
Disordered region (IsUnstruct)
****KIIAKNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFSE******TYRLNSTF***LQKHLIN************ITARLPTLEDLEAYAIGQWECFLLQLISSA**********SMMKVFQRGLLIQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTD*SARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMR********
Disordered Region (DISOPRED)
*********NFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLQKHLINGGA*******************LEAYAIGQWECFL*********************VFQRGLLIQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATN****************VVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQN**********SVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ**
Disordered Region (DISEMBL)
MPQVKIIAKNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLQKHLINGGALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK
Disordered Region (DISPRO)
*PQVKIIAKNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLQKHLINGGALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTD***RKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPQVKIIAKNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLQKHLINGGALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK
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	406	2.2.26 [Sep-21-2011]
P60027	462	General transcription fac	yes	no	0.990	0.870	0.288	2e-47
Q92759	462	General transcription fac	yes	no	0.990	0.870	0.288	2e-47
Q54C29	483	General transcription fac	yes	no	0.918	0.772	0.288	9e-47
O70422	463	General transcription fac	yes	no	0.975	0.855	0.290	9e-47
P87303	447	RNA polymerase II transcr	yes	no	0.913	0.829	0.284	1e-45
Q6CLR2	496	RNA polymerase II transcr	yes	no	0.948	0.776	0.270	4e-44
Q6BZX4	467	RNA polymerase II transcr	yes	no	0.955	0.830	0.271	5e-44
Q6BGW8	515	RNA polymerase II transcr	yes	no	0.871	0.687	0.264	5e-42
Q75B51	514	RNA polymerase II transcr	yes	no	0.908	0.717	0.278	4e-41
Q02939	513	RNA polymerase II transcr	yes	no	0.926	0.732	0.275	5e-39

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

 Score =  190 bits (482), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 130/450 (28%), Positives = 219/450 (48%), Gaps = 48/450 (10%)

Query: 3   QVKIIAKNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKT 62
           +V +  +N  + +  L+   L++LY +P  C A+ R LP LAK +V +ML+++  +P   
Sbjct: 11  RVHLQCRNLQEFLGGLSPGVLDRLYGHPATCLAVFRELPSLAKNWVMRMLFLEQPLPQAA 70

Query: 63  MEEWVLPDGFTKHKVAIDRLVQLRLFSEE--KKKETTYRLNSTFQSNLQKHLINGG-ALP 119
           +  WV  +     + +   L  LR++  +          LN  F+ NL+  L+ GG A  
Sbjct: 71  VALWVKKEFSKAQEESTGLLSGLRIWHTQLLPGGLQGLILNPIFRQNLRIALLGGGKAWS 130

Query: 120 REPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQA--------------------- 158
            +    G       +  L+ YA  +WE  L  ++ S  A                     
Sbjct: 131 DDTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQLLSQAGLMKSTEP 190

Query: 159 ----------------ERPTNFSSSMMKVFQ----RGLLIQSILRSLKFLCQGIL-EAYN 197
                           + P      M++  Q    RG+ +  IL  L  L    L + Y+
Sbjct: 191 GEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQLSFSTLGKDYS 250

Query: 198 LNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSA--RKEGFVVV 255
           +  +S+   + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +     + GF+VV
Sbjct: 251 VEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGFIVV 309

Query: 256 ETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQ 315
           ETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII FL+
Sbjct: 310 ETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLR 369

Query: 316 QNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRS 375
             AHP +  + P +P  + DQIRLWE + +R+  T    Y +F S+  FE    +AR+  
Sbjct: 370 TRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARELG 429

Query: 376 GLLWEDSKKMRLVVNAEIHMHMREFLRGQN 405
            L++E+S K  +VV    H  ++ F + Q 
Sbjct: 430 VLVFENSAKRLMVVTPAGHSDVKRFWKRQK 459

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 =  190 bits (482), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 130/450 (28%), Positives = 219/450 (48%), Gaps = 48/450 (10%)

Query: 3   QVKIIAKNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKT 62
           +V +  +N  + +  L+   L++LY +P  C A+ R LP LAK +V +ML+++  +P   
Sbjct: 11  RVHLQCRNLQEFLGGLSPGVLDRLYGHPATCLAVFRELPSLAKNWVMRMLFLEQPLPQAA 70

Query: 63  MEEWVLPDGFTKHKVAIDRLVQLRLFSEE--KKKETTYRLNSTFQSNLQKHLINGG-ALP 119
           +  WV  +     + +   L  LR++  +          LN  F+ NL+  L+ GG A  
Sbjct: 71  VALWVKKEFSKAQEESTGLLSGLRIWHTQLLPGGLQGLILNPIFRQNLRIALLGGGKAWS 130

Query: 120 REPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQA--------------------- 158
            +    G       +  L+ YA  +WE  L  ++ S  A                     
Sbjct: 131 DDTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQLLSQAGLMKSTEP 190

Query: 159 ----------------ERPTNFSSSMMKVFQ----RGLLIQSILRSLKFLCQGIL-EAYN 197
                           + P      M++  Q    RG+ +  IL  L  L    L + Y+
Sbjct: 191 GEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQLSFSTLGKDYS 250

Query: 198 LNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSA--RKEGFVVV 255
           +  +S+   + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +     + GF+VV
Sbjct: 251 VEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGFIVV 309

Query: 256 ETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQ 315
           ETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII FL+
Sbjct: 310 ETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLR 369

Query: 316 QNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRS 375
             AHP +  + P +P  + DQIRLWE + +R+  T    Y +F S+  FE    +AR+  
Sbjct: 370 TRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARELG 429

Query: 376 GLLWEDSKKMRLVVNAEIHMHMREFLRGQN 405
            L++E+S K  +VV    H  ++ F + Q 
Sbjct: 430 VLVFENSAKRLMVVTPAGHSDVKRFWKRQK 459

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

 Score =  187 bits (476), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 140/485 (28%), Positives = 232/485 (47%), Gaps = 112/485 (23%)

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

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

Query: 106 SNLQKHLI--------NGGALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQ 157
            N+++ L+        N  ++     P       P+++DL++Y+  QWE  L  L  S  
Sbjct: 129 DNIKRSLVQVNQVIFSNNSSIKDNHKP-------PSIDDLDSYSKSQWEKVLYFL--SDD 179

Query: 158 AERPTNF------SSSMMKVFQRGLLIQSILRSLKFLCQGIL------------------ 193
             +P+        SS++ K    GL I S     KFL + +                   
Sbjct: 180 TVQPSKLISELLLSSNLTKQEGDGLSITS--EGFKFLLKDVYTQIWTLLIVYLDDLEKKK 237

Query: 194 -----------------------EAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKES--W 228
                                    Y ++ LSE Q+  +      GL+ +   R +S   
Sbjct: 238 GKGSGSRNDLLSFLFRLSFLNLGRGYLVSELSEQQKEYLFALKQFGLIYM---RTDSSIL 294

Query: 229 FIPTKLATNLS----MSLTDS-------SARKEGFVVVETNFRMYAYSTSKLHCEILRLF 277
           F PT+L  +L+    +SL  S       + +++G++V+ETN+R+YAY++S L   +L LF
Sbjct: 295 FYPTRLIISLTTGKTLSLIQSISSERTQTQKEQGYIVLETNYRLYAYTSSSLQISLLSLF 354

Query: 278 SKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQI 337
            K+ Y+LPNL VG IT+ES+  A  +GITA+QII F++ N+HP  A+    +P+ V +QI
Sbjct: 355 VKMLYRLPNLAVGIITRESIRTALIHGITADQIIDFVRHNSHPNAANSGQPIPDVVAEQI 414

Query: 338 RLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHM 397
            LWE++ NR+  T +  Y  FP+ D + A   +A+++   +W       LVV  E +  +
Sbjct: 415 LLWEAERNRITYTKSVLYNSFPTNDCYIATLKFAKEQDYYIWSHDPLKTLVVKEEGNDPI 474

Query: 398 REFLR 402
           R F++
Sbjct: 475 RNFIK 479

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

 Score =  187 bits (476), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 129/444 (29%), Positives = 216/444 (48%), Gaps = 48/444 (10%)

Query: 9   KNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVL 68
           +N  + +  L+   L++LY +P  C A+ R LP LAK +V +ML+++  +P   +  WV 
Sbjct: 18  RNLQEFLGGLSPGVLDRLYGHPATCLAVFRELPSLAKNWVMRMLFLEQPLPQAAVALWVK 77

Query: 69  PDGFTKHKVAIDRLVQLRLFSEE--KKKETTYRLNSTFQSNLQKHLINGG-ALPREPMPS 125
            +     + +   L  LR++  +          LN  F+ NL+  L+ GG A   +    
Sbjct: 78  KEFSKAQEESTGLLSGLRIWHTQLLPGGLQGLILNPVFRQNLRIALLGGGKAWSDDTSQL 137

Query: 126 GITARLPTLEDLEAYAIGQWECFLLQLISSAQA--------------------------- 158
           G       +  L+ YA  +WE  L  ++ S  A                           
Sbjct: 138 GPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQLLSQAGLMKSTEPGEPPCI 197

Query: 159 ----------ERPTNFSSSMMKVFQ----RGLLIQSILRSLKFLCQGIL-EAYNLNTLSE 203
                     + P      M++  Q    RG+ +  IL  L  L    L + Y++  +S+
Sbjct: 198 TSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQLSFSTLGKDYSVEGMSD 257

Query: 204 IQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSA--RKEGFVVVETNFRM 261
              + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +     + GF+VVETN+R+
Sbjct: 258 SLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGFIVVETNYRL 316

Query: 262 YAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPR 321
           YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII FL+  AHP 
Sbjct: 317 YAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLRTRAHPV 376

Query: 322 VADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWED 381
           +  + P +P  + DQIRLWE + +R+  T    Y +F S+  FE    +AR+   L++E+
Sbjct: 377 MLKQNPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARELGVLVFEN 436

Query: 382 SKKMRLVVNAEIHMHMREFLRGQN 405
           S K  +VV    H  ++ F + Q 
Sbjct: 437 SAKRLMVVTPAGHSDVKRFWKRQK 460

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 =  184 bits (467), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 122/429 (28%), Positives = 208/429 (48%), Gaps = 58/429 (13%)

Query: 25  KLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQ 84
           +LY+ P  C A+ R LP LA++YV  ML+    +     + W+          + ++LV+
Sbjct: 21  RLYQKPAACLAVFRLLPILARQYVMSMLFNPMPVALSDFDLWIKLSSKVYQSESFNKLVR 80

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

Query: 144 QWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQS------ILRS-LKFLCQGI---- 192
            WE  L  ++ + +A+ P      ++ + +RG L+        I R+  +FL Q I    
Sbjct: 138 TWETILHFMVGTPEAKFP---GEGVLSLLKRGGLMSGPKNQLRITRAGFQFLLQDINAQI 194

Query: 193 ---------------------------------LEAYNLNTLSEIQRSMIKDFADLGLVK 219
                                              AY+++ L++ Q+ M++D  + GLV 
Sbjct: 195 WTLLLDYLKLSEDTHMDPVQVLHFLFMLGSLDLGRAYSVDFLTDTQQIMLEDLREYGLV- 253

Query: 220 LQQGRKESWFIPTKLATNLSMSLTDSSARK------EGFVVVETNFRMYAYSTSKLHCEI 273
            Q+      F PT+LAT L+        ++      +GF++VETN+R+YAY++S L   I
Sbjct: 254 YQRKITSKRFYPTRLATGLTTDYRSLHGKQSENDDDKGFIIVETNYRLYAYTSSPLQIAI 313

Query: 274 LRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENV 333
           + LF+ +  +  NL+VG IT++S+  A  NGI AEQII++L  +AHP++   +P +P  +
Sbjct: 314 IGLFANLRARFSNLVVGVITRDSIRRALMNGIAAEQIITYLTTHAHPQMRSNVPLLPPTL 373

Query: 334 CDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEI 393
            DQI LWE + NR+  TP   + +F +   F+ A +YA++   L+W+ S K    +    
Sbjct: 374 VDQIYLWELEKNRLRATPGILFRDFLTDSGFDQAVEYAKELGVLVWDSSLKRMFFITTTG 433

Query: 394 HMHMREFLR 402
              M  +L+
Sbjct: 434 AQPMIAYLK 442

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|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 =  179 bits (454), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 131/485 (27%), Positives = 218/485 (44%), Gaps = 100/485 (20%)

Query: 13  DMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGF 72
           D +  L  +  ++LYE+P  C AI R L P+AK ++  ML+ D  +  + +++WV PD  
Sbjct: 12  DYLEGLPEQVQSRLYESPATCLAIYRLLSPMAKFFIMSMLFQDHDVSLRDLDKWVKPDAK 71

Query: 73  TKHKVAIDRLVQLRLFSE-EKKKETTYRLNSTFQSNLQKHLINGGALPREPMPSGITARL 131
            + + +I  +  L L  E E K+    RLN  F+ +  K+++ GG +             
Sbjct: 72  YQLQYSIKSMKSLNLIIEGESKQPLLIRLNPIFKKSF-KNVLTGGEINNSFGDVADDDTN 130

Query: 132 P-TLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQR-GLLIQSILRSLKFLC 189
           P +   L+ Y+  +WE  L  ++ +     P      ++ + Q  GL+ ++    LK   
Sbjct: 131 PVSTATLDQYSAEKWETILHYMVGTPNTNTP---GGKVLDLLQHSGLMEEAEYGELKITN 187

Query: 190 QG--------------------------------------------ILEAYNLNTLSEIQ 205
           QG                                            + +AY  + LS  Q
Sbjct: 188 QGFQFLLQDVNAQMWTLLLQYLKMAESLQMDPVDVLNFIFMLGALQLGKAYKCDQLSNTQ 247

Query: 206 RSMIKDFADLGLVKLQQGRKESWFIPTKLAT-----------------------NLSMSL 242
           R+M++D  D GL+  Q     + F PT+LAT                       N + ++
Sbjct: 248 RTMLQDMRDYGLI-YQNQSDYAKFYPTRLATLLTSDTKAFRSASVALDSVLNKANETTAV 306

Query: 243 TDSSARKE-------GFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKE 295
              S + E       G +++ETNF++Y+YS S L   IL LF  ++ +  N++ G +T+E
Sbjct: 307 EGDSGQDETTERTQDGALIIETNFKLYSYSNSPLQIAILSLFVHLKSRFANMVTGQLTRE 366

Query: 296 SLYNAFENGITAEQIISFLQQNAHPR------------------VADRIPSVPENVCDQI 337
           S+ NA  NGITAEQII++L+ +AHPR                  V + +  +P  V DQI
Sbjct: 367 SVRNALLNGITAEQIIAYLETHAHPRMRRLAEENLSKKLELDPTVKETLQVLPPTVVDQI 426

Query: 338 RLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHM 397
           RLW+ +L+R+     + Y +F S   ++   DYA+D   LLW++ KK    V+ E +  +
Sbjct: 427 RLWQLELDRIISYDGYLYTDFESYQEYQTVADYAKDIGVLLWQNEKKKMFFVSTEGNSQV 486

Query: 398 REFLR 402
            +F R
Sbjct: 487 LDFHR 491

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|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 =  178 bits (452), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 124/456 (27%), Positives = 216/456 (47%), Gaps = 68/456 (14%)

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

Query: 73  TKHKVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLQKHLINGGALPREPMPSGITARLP 132
           +  ++ ++   +LRL     + +    +N TF+ NL+  L+ G       +P     +  
Sbjct: 68  SSQRLKLETQKKLRLLHIFTETQAHIIINPTFKKNLRAALVGGDQNISFGVPCDTEDKHK 127

Query: 133 T-LEDLEAYAIGQWECFLLQLISSAQAERPTNF------SSSMMKVFQRGLLIQSILRSL 185
             +  L+A+A+ QWE  L  ++ ++    P++        S +M+  + GL I +     
Sbjct: 128 VDVAFLDAHAVSQWEMILHFMVGTSIGRTPSDGVLNLLKHSGLMEPERGGLRITNA--GF 185

Query: 186 KFLCQ----------------------------------GILEA---YNLNTLSEIQRSM 208
           +FL Q                                  G LE    Y+L+ LSE Q+ M
Sbjct: 186 QFLLQDVNAQIWTLLLQYLNMSEYLQMDPVDVLNFIFMLGSLELGQDYSLSALSETQKHM 245

Query: 209 IKDFADLGLVKLQQGRKESWFIPTKLATNLSM------------------SLTDSSARKE 250
           ++D  D G+V  Q+      F PT+LAT L+                   +++ S A   
Sbjct: 246 LEDLRDYGIV-YQRKASSRRFYPTRLATTLTSETAALRTASQSMEAATQDTISSSVAADS 304

Query: 251 GFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQI 310
           GF+++ETNFR+YAY+ S L   +L LF  ++ +  N++ G I ++S+  A  NGITAEQI
Sbjct: 305 GFIILETNFRLYAYTESPLQIAVLNLFVNLKTRFANMVTGQINRDSVRFALSNGITAEQI 364

Query: 311 ISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDY 370
           I++L  +AHPR+      +P  V DQI+LW+ +++R+  T  + + EF + D ++    Y
Sbjct: 365 ITYLSVHAHPRMKGMEHVLPPTVVDQIKLWQLEMDRIRATDGYLFSEFKNFDEYKDVSTY 424

Query: 371 ARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK 406
           A++   LL+E+  K + V        + EF++ +N+
Sbjct: 425 AKELGVLLYENPGKRKFVSTLAGSQQIVEFVKRRNQ 460

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|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 =  172 bits (436), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 130/492 (26%), Positives = 215/492 (43%), Gaps = 138/492 (28%)

Query: 24  NKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLV 83
           ++LYE P  C +I R LPP+AK Y+  ML+ +  +  K +++W  P   T  K   D L 
Sbjct: 24  SRLYEAPATCLSIYRLLPPIAKFYIMTMLFYETPVALKDLDKWCKP---TSRKFQFDSLK 80

Query: 84  QLRLFS--EEKKKETTYRLNSTFQSNLQKHLING------GALPREPMPSGITARLPTLE 135
           +LR     EE    +  RL+ TF+ N +  L         G L   P    ++ +     
Sbjct: 81  RLRALHLIEEDSSGSHIRLHPTFRQNFRDCLTGSQARNAFGNLSTTPDEQSVSIKF---- 136

Query: 136 DLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQSILRS----------L 185
            L+++A+ +WE  L  ++ +  +  P+N   S++ + + G L++   +            
Sbjct: 137 -LDSFALQKWESILHFMVGTELSVTPSN---SVLSLLKSGGLMEGTNKGGNRLNITNSGF 192

Query: 186 KFLCQ----------------------------------GILE---AYNLNTLSEIQRSM 208
           +FL Q                                  G LE    Y +++LSE Q SM
Sbjct: 193 QFLLQDINAQIWTLLLQYLNLTQDLNMDPVDVLNFIFILGSLELGKGYTVSSLSETQISM 252

Query: 209 IKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARK------------------- 249
           + D  D GL+  Q+      F PT+LAT L+   +DS+A K                   
Sbjct: 253 LADLRDYGLI-YQRSENSERFYPTRLATTLT---SDSAALKSPSMAMEQALESTTETEEQ 308

Query: 250 --------EGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAF 301
                   +G +++ETNF++YAY+ S L   IL LF  ++ +  N++ G IT+ES+ NA 
Sbjct: 309 QNLASNSNQGTIILETNFKIYAYTNSPLEIAILNLFVHLKTRFSNMVCGQITRESIRNAL 368

Query: 302 ENGITAEQIISFLQQNAHPRVA-------------------------------------- 323
            NGITA+QII FL+ +AH ++                                       
Sbjct: 369 YNGITADQIIKFLETHAHSQMKILAKERLDKKIEFDTSNNINTAGGAPQSQMMTNENGTT 428

Query: 324 ---DRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWE 380
               ++  +P  V DQI+LW+ +L+R++    + +++F S+  FEA  +YA +   LLW 
Sbjct: 429 VAQHKLEVLPPTVVDQIKLWQLELDRIQTFEGYLFKDFASQQEFEALSNYASEIGVLLWS 488

Query: 381 DSKKMRLVVNAE 392
           +  KM+  V  +
Sbjct: 489 NKSKMKFFVTKD 500

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|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 =  169 bits (428), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 136/488 (27%), Positives = 219/488 (44%), Gaps = 119/488 (24%)

Query: 24  NKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLV 83
           ++LY++P  C AI R L P+AK ++  M++ D  +  + ++ WV PD   +   AI  + 
Sbjct: 32  SRLYQSPATCLAIYRLLSPMAKFFIMSMIFQDEEVSLRDLDRWVKPDAKFQLHDAIKSMK 91

Query: 84  QLRLFSEEKKKE-TTYRLNSTFQSNLQKHLING-------GALPREPMPSGITARLPTLE 135
            L L +E +  +    +LNS F+ + +  L  G         +  E  P        T+ 
Sbjct: 92  LLHLITEGRSGQPLMVQLNSIFKESFKNALTGGEVKNSFGNVVEEENDPV-------TMA 144

Query: 136 DLEAYAIGQWECFLLQLISSAQAERP---------------TNFSSSMMKVFQRG----- 175
            L++YA  +WE  L  ++ +   + P                + SS  +K+   G     
Sbjct: 145 MLDSYAADKWETILHFMVGTPLTKSPGKNVLSLLRHSKLMEVDESSKELKITNEGFQFLL 204

Query: 176 ---------LLIQSILRSLKFLCQ-----------GILE---AYNLNTLSEIQRSMIKDF 212
                    LL+Q +  +  F              G LE   AY++  LSE Q++M++D 
Sbjct: 205 QDANAQIWTLLLQYLTMAETFQMDPVDVLNLIFMIGALELGKAYSVVGLSETQKTMLQDL 264

Query: 213 ADLGLVKLQQGRKESWFIPTKLATNLS---MSLTDSSA--------RKEGF--------- 252
            D GLV  Q+    S F PT+LAT L+   +S+  +S         R EG          
Sbjct: 265 RDYGLV-FQKQSNLSKFYPTRLATMLTSDVVSIRSASGAVNSVLRQRAEGVDGKVLNGTA 323

Query: 253 -----------------VVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKE 295
                            ++VETNF++Y+YS S L   IL LF  ++ +  N++ G IT+E
Sbjct: 324 LGDDDLQAGGEGALDGALIVETNFKLYSYSNSPLQIAILSLFIHLKTRFQNMVTGQITRE 383

Query: 296 SLYNAFENGITAEQIISFLQQNAHP---RVA---------------DRIPSVPENVCDQI 337
           S+  A  NGITA+QII++++ +AHP   R+A               D +  +P  V DQI
Sbjct: 384 SIRRALHNGITADQIIAYMETHAHPQMRRLAGDNLEKKLELDPNCRDTLQVLPPTVVDQI 443

Query: 338 RLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAE----- 392
           +LW+ +L+R+     + + +F +   ++    YARD   LLW D KK    V+ E     
Sbjct: 444 KLWQLELDRIISYDGYLFRDFDNLQEYQVLAQYARDIGVLLWSDDKKKMFFVSKEGNAQV 503

Query: 393 IHMHMREF 400
           I  H R+F
Sbjct: 504 IDFHKRKF 511

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)

>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 =  162 bits (409), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 134/487 (27%), Positives = 219/487 (44%), Gaps = 111/487 (22%)

Query: 24  NKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLV 83
           N+LY +P  C AI R LPPLAK ++  M++ +  +P   +++WV  +G  + + AI  + 
Sbjct: 23  NRLYTSPATCLAIYRILPPLAKFFIMAMVFNENEVPLLDLDKWVNSNGKLQFQNAIKSMK 82

Query: 84  QLRLFSEEKKKET-TYRLNSTFQSNLQKHLINGGALPREPMPSGITARLPTLEDLEAYAI 142
            L L    K   T    LN TF+ +L+  L  G    +      +   + +L+ L+ Y+ 
Sbjct: 83  SLHLLIPNKSSGTLMINLNPTFKISLRNALTGGEV--QNSFGVVVEENVVSLDLLDEYSA 140

Query: 143 GQWECFLLQLISSAQAERPTN---------------FSSSMMKVFQRGL--LIQSI---- 181
            +WE  L  ++ +  A+ P+                 S+   K+   G   L+Q I    
Sbjct: 141 NKWETILHFMVGTPLAKIPSEKVLNLLKHSKLMEEVNSTGEFKITNEGFQFLLQEINSQL 200

Query: 182 ----LRSLKFL---------------CQGILE---AYNLNTLSEIQRSMIKDFADLGLVK 219
               L+ LK +                 G LE   AY ++ LSE QR M++D  D GLV 
Sbjct: 201 WTLLLQYLKMIETSKMDLVDVLHFIFMLGALEVGKAYKIDALSETQRIMLQDMRDYGLV- 259

Query: 220 LQQGRKESWFIPTKLATNLSM---------SLTDSSARK--------------------- 249
            Q+   +S F PTKLA  L+          +  DS  R+                     
Sbjct: 260 FQKHSNDSIFYPTKLALMLTSDTKTIRSASNAMDSVLRQNREEPSVNEDGANGKSTTDIT 319

Query: 250 ----------------EGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAIT 293
                           +G ++VETNF++Y+YS S L   +L LF  ++ +  N+++G IT
Sbjct: 320 TSDDLNKAGLKNQDIPDGSLIVETNFKIYSYSNSPLQIAVLSLFVHLKARFVNMVLGQIT 379

Query: 294 KESLYNAFENGITAEQIISFLQQNAHPRV------------------ADRIPSVPENVCD 335
           +ES+  A  NGITA+QII++L+ +AHP++                   + +  +P  V D
Sbjct: 380 RESIRRALTNGITADQIIAYLETHAHPQMRRLAEEKLEKKLELDPNCKEPLQVLPPTVVD 439

Query: 336 QIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHM 395
           QIRLW+ +L+RV       Y +F +   +     YA+D   LLW+D KK +  ++ E + 
Sbjct: 440 QIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISKEGNS 499

Query: 396 HMREFLR 402
            + +F +
Sbjct: 500 QVLDFAK 506

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)

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	406
147854406	451	hypothetical protein VITISV_005315 [Viti	0.985	0.886	0.717	0.0
255556021	451	tfiih, polypeptide, putative [Ricinus co	0.990	0.891	0.703	0.0
449433857	451	PREDICTED: general transcription factor	0.990	0.891	0.710	0.0
224077128	449	predicted protein [Populus trichocarpa]	0.985	0.890	0.681	1e-177
357461579	452	General transcription factor IIH subunit	0.990	0.889	0.671	1e-174
42566894	452	transcription initiation factor TFIIH su	0.995	0.893	0.660	1e-172
42572935	462	transcription initiation factor TFIIH su	0.995	0.874	0.660	1e-172
334186626	482	transcription initiation factor TFIIH su	0.992	0.836	0.662	1e-172
51969958	452	unnamed protein product [Arabidopsis tha	0.995	0.893	0.660	1e-171
358346685	451	General transcription factor IIH subunit	0.990	0.891	0.665	1e-171

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

 Score =  660 bits (1704), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 323/450 (71%), Positives = 360/450 (80%), Gaps = 50/450 (11%)

Query: 1   MPQVKIIAKNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPA 60
           MPQVKIIAKNFMDMVASL A  L+ LY N FICEAILRSLPPLAKKY+ QMLYID  + A
Sbjct: 1   MPQVKIIAKNFMDMVASLPAMKLDALYHNTFICEAILRSLPPLAKKYILQMLYIDVPVTA 60

Query: 61  KTMEEWVLPDGFTKHKVAIDRLVQLRLFSE--EKKKETTYRLNSTFQSNLQKHLINGGAL 118
           K MEEWVL DGF+KH+VAIDRL+QLR+F+E  ++KKET+YRLN TFQ+NLQKHLI GG L
Sbjct: 61  KAMEEWVLADGFSKHRVAIDRLIQLRVFTETSDRKKETSYRLNPTFQTNLQKHLIYGGVL 120

Query: 119 PREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLI 178
           PREPMPS IT RLP+L+DLEAYA+GQWECFLLQLISS Q E+ TNFSSS+MKVFQRGLL 
Sbjct: 121 PREPMPSNITVRLPSLDDLEAYALGQWECFLLQLISSTQTEKLTNFSSSLMKVFQRGLLT 180

Query: 179 Q----------------------------------------------SILRSLKFLCQGI 192
           Q                                              S L  L F   G 
Sbjct: 181 QREKEAPRLTESGFQFLLMDTNAQLWYIMREYISNSEERGVDPADLISFLLELSFHVTG- 239

Query: 193 LEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGF 252
            EAYN+NTL+E QR+ IKD  DLGLVKLQQGRKESWFIPTKLATNLSMSL+D+S+RK+GF
Sbjct: 240 -EAYNINTLTEFQRNTIKDLVDLGLVKLQQGRKESWFIPTKLATNLSMSLSDTSSRKQGF 298

Query: 253 VVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIIS 312
           VVVETNFR+YAYS+SKLHCEILRLFS++EYQLPNLIVGAITKESLYNAFENGITAEQIIS
Sbjct: 299 VVVETNFRLYAYSSSKLHCEILRLFSRVEYQLPNLIVGAITKESLYNAFENGITAEQIIS 358

Query: 313 FLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYAR 372
           FLQQNAHPRVA+R P+VPENV DQIRLWE+DLNRVE  P+H Y+EFPSRDVFEAACD+AR
Sbjct: 359 FLQQNAHPRVAERTPAVPENVTDQIRLWETDLNRVETMPSHLYDEFPSRDVFEAACDFAR 418

Query: 373 DRSGLLWEDSKKMRLVVNAEIHMHMREFLR 402
           +  GLLWEDSKKMRLVV AEIH+HMRE+LR
Sbjct: 419 EYGGLLWEDSKKMRLVVKAEIHLHMREYLR 448

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 =  653 bits (1685), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 318/452 (70%), Positives = 363/452 (80%), Gaps = 50/452 (11%)

Query: 1   MPQVKIIAKNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPA 60
           MPQV+IIAKNFMDMVASL A  L+KLY NPFIC+AILRSLPPLAKKYV Q+LYIDG +  
Sbjct: 1   MPQVRIIAKNFMDMVASLPAMKLDKLYTNPFICQAILRSLPPLAKKYVVQILYIDGPVAD 60

Query: 61  KTMEEWVLPDGFTKHKVAIDRLVQLRLFSE--EKKKETTYRLNSTFQSNLQKHLINGGAL 118
           KT+EEW+LPDG +KH+VAIDRL QLR+F+E  ++KKE +Y+LN TFQ+NLQKHLI+GG L
Sbjct: 61  KTLEEWLLPDGSSKHRVAIDRLTQLRIFTEIVDRKKEISYKLNPTFQTNLQKHLIDGGVL 120

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

Query: 179 Q----------------------------------------------SILRSLKFLCQGI 192
           Q                                              S L  L F   G 
Sbjct: 181 QRDKEAPRLTESGFQFLLMDTNAQLWYIIREYISNSEERGLDSADLISFLLELSFHITG- 239

Query: 193 LEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGF 252
            EAYN+  L+E QR+MIKD ADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSS+RK+GF
Sbjct: 240 -EAYNMIMLTEFQRNMIKDLADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSSRKQGF 298

Query: 253 VVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIIS 312
           VVVETNFRMYAYSTSKLHCEI+RLFS++EYQLPNL+VGA+TKESLY+AFENGITAEQIIS
Sbjct: 299 VVVETNFRMYAYSTSKLHCEIMRLFSRVEYQLPNLVVGAMTKESLYSAFENGITAEQIIS 358

Query: 313 FLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYAR 372
           FLQQNAHPRVA+RIPSVPENV DQIRLWESD+NRVEMTPAH Y+EFPSRDVFEAAC++AR
Sbjct: 359 FLQQNAHPRVAERIPSVPENVTDQIRLWESDMNRVEMTPAHLYDEFPSRDVFEAACNFAR 418

Query: 373 DRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 404
           D +GLLWEDSK+MR+VV AEIH++MRE+LRGQ
Sbjct: 419 DWNGLLWEDSKRMRMVVKAEIHLNMREYLRGQ 450

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 =  646 bits (1667), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 321/452 (71%), Positives = 362/452 (80%), Gaps = 50/452 (11%)

Query: 1   MPQVKIIAKNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPA 60
           MPQVKIIAKNFMDMVASL A  L++LYEN FICEAILRSLPPLAKK+V QMLYIDG + A
Sbjct: 1   MPQVKIIAKNFMDMVASLPAMKLDQLYENAFICEAILRSLPPLAKKFVLQMLYIDGPVSA 60

Query: 61  KTMEEWVLPDGFTKHKVAIDRLVQLRLFSE--EKKKETTYRLNSTFQSNLQKHLINGGAL 118
           K+MEEWVLPDG +K+KVA+DRL+QLR+F E  ++K+ETTYRLN TFQ+NLQK LI+G  L
Sbjct: 61  KSMEEWVLPDGVSKYKVAVDRLIQLRVFIETADRKRETTYRLNPTFQANLQKLLIHGEVL 120

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

Query: 179 Q----------------------------------------------SILRSLKFLCQGI 192
           Q                                              S L  L F   G 
Sbjct: 181 QRDKEAPRLTESGFQFLLMETNAQLWYIIREYISNAEERGVDPADLISFLLELSFHVTG- 239

Query: 193 LEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGF 252
            EAY+++TLS+ QR  IKD ADLGLVKLQQGRKESWFIPTKLATNLSMSL DSS+RK GF
Sbjct: 240 -EAYDIDTLSDEQRYAIKDLADLGLVKLQQGRKESWFIPTKLATNLSMSLADSSSRKLGF 298

Query: 253 VVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIIS 312
           VVVETNFRMYAYSTSKLHCEILRLFS+IEYQLPNLIVGAITKESLYNAF+NGITAEQI++
Sbjct: 299 VVVETNFRMYAYSTSKLHCEILRLFSRIEYQLPNLIVGAITKESLYNAFKNGITAEQIVT 358

Query: 313 FLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYAR 372
           FLQQNAHPRVA+RIPSVPENV DQIRLWESDLNRV++TPAH+Y+EFPSR+VFEAACDYAR
Sbjct: 359 FLQQNAHPRVAERIPSVPENVTDQIRLWESDLNRVDITPAHFYDEFPSREVFEAACDYAR 418

Query: 373 DRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 404
           + +GLLWEDSK +RLVV A+IH HMRE LR Q
Sbjct: 419 EWNGLLWEDSKNLRLVVKADIHTHMREHLRRQ 450

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  629 bits (1621), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 308/452 (68%), Positives = 360/452 (79%), Gaps = 52/452 (11%)

Query: 1   MPQVKIIAKNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPA 60
           MPQV+IIAKNFMDMVASL A  L+ LY+N FICEAILRSLPPLAKKYV Q+L+ DG +  
Sbjct: 1   MPQVRIIAKNFMDMVASLPAMKLDTLYQNAFICEAILRSLPPLAKKYVVQILFFDGPVSG 60

Query: 61  KTMEEWVLPDGFTKHKVAIDRLVQLRLFSE--EKKKETTYRLNSTFQSNLQKHLINGGAL 118
           K +E+WVL DG TKH+VAIDRL+QLR+F E  +KK+E++Y+LN TFQ+NL+KHL NGG L
Sbjct: 61  KLLEQWVLADGVTKHRVAIDRLIQLRIFIEVSDKKRESSYKLNQTFQANLRKHLTNGGVL 120

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

Query: 179 Q----------------------------------------------SILRSLKFLCQGI 192
           Q                                              S L  L F   G 
Sbjct: 179 QRDRDAPRLTEGGFQFLLMDTNAQLWYIIREYITNSEERGTEPADLISFLLELSFHVTG- 237

Query: 193 LEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGF 252
            EAYN+NTL+EIQR+ IKD A+LGLVKLQQGRKESWFIPTKLATNLS+SLTDSS+RK+G+
Sbjct: 238 -EAYNMNTLTEIQRNTIKDLAELGLVKLQQGRKESWFIPTKLATNLSVSLTDSSSRKQGY 296

Query: 253 VVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIIS 312
           VVVETNFR+YAYS+SKLHCEILRLFSKIEYQLPNLIVGAITKESLY AFENGIT++QIIS
Sbjct: 297 VVVETNFRLYAYSSSKLHCEILRLFSKIEYQLPNLIVGAITKESLYTAFENGITSDQIIS 356

Query: 313 FLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYAR 372
           FLQQNAHPRVA+R+PSVPENV DQIRLWE+DLNRVE+TP+H+Y+EFPSRD FEAACD+AR
Sbjct: 357 FLQQNAHPRVAERLPSVPENVTDQIRLWEADLNRVEITPSHFYDEFPSRDTFEAACDFAR 416

Query: 373 DRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 404
           + +GLLWEDSKKMR+VV AEIHM+MREFLRGQ
Sbjct: 417 EWNGLLWEDSKKMRVVVKAEIHMNMREFLRGQ 448

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  617 bits (1590), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 304/453 (67%), Positives = 353/453 (77%), Gaps = 51/453 (11%)

Query: 1   MPQVKIIAKNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPA 60
           MP+V+IIAKNFMDMVAS+ A  L+KLY+N FICEAILRSLPPLAKKYV Q+L+IDG +PA
Sbjct: 1   MPEVRIIAKNFMDMVASMPAIKLDKLYQNGFICEAILRSLPPLAKKYVLQLLHIDGPVPA 60

Query: 61  KTMEEWVLPDGFTKHKVAIDRLVQLRLFSE---EKKKETTYRLNSTFQSNLQKHLINGGA 117
           K + EWVLPDG +KHKVAIDRLVQLR+F E    +K E TY++NST+Q +LQ  L++GG 
Sbjct: 61  KLLAEWVLPDGLSKHKVAIDRLVQLRVFVEAFDNRKNEKTYQVNSTYQKSLQNLLVHGGT 120

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

Query: 178 IQ----------------------------------------------SILRSLKFLCQG 191
            Q                                              S +  L F   G
Sbjct: 181 SQRDREAPKLTESGFQFLLMDTNAQLWYIIREYITNSEERGVDAGDLISFMLELSFHVIG 240

Query: 192 ILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEG 251
             EAYN+NTL+E QR++IKD ADLGLVKLQQGRKESWFIPTKLATNLS+S+T+SS+RKEG
Sbjct: 241 --EAYNINTLTEFQRNIIKDLADLGLVKLQQGRKESWFIPTKLATNLSVSMTESSSRKEG 298

Query: 252 FVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQII 311
           FVVVETNFR+YAYSTSKLHCEILRLFS++EYQLPNLIVGAITKESLYNAF+NGITA+QI+
Sbjct: 299 FVVVETNFRVYAYSTSKLHCEILRLFSRVEYQLPNLIVGAITKESLYNAFDNGITADQIV 358

Query: 312 SFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYA 371
           SFL+QNAHPRVA R+P+VPENV DQIRLWESDLNRVEMT A+YY+EFPSRDVFE ACD A
Sbjct: 359 SFLRQNAHPRVAQRVPAVPENVTDQIRLWESDLNRVEMTEAYYYDEFPSRDVFEGACDCA 418

Query: 372 RDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 404
           R+ SGLLWEDSKKM LVV +E+H ++R+FLR Q
Sbjct: 419 REWSGLLWEDSKKMHLVVKSEVHTYVRDFLRRQ 451

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

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 =  610 bits (1574), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 300/454 (66%), Positives = 350/454 (77%), Gaps = 50/454 (11%)

Query: 1   MPQVKIIAKNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPA 60
           MPQVKIIAKNFMDMVASL A  L+KLY N FICEAILRSLPPLAKKYV QMLYID  +PA
Sbjct: 1   MPQVKIIAKNFMDMVASLPAIKLDKLYNNVFICEAILRSLPPLAKKYVLQMLYIDVPVPA 60

Query: 61  KTMEEWVLPDGFTKHKVAIDRLVQLRLFSE--EKKKETTYRLNSTFQSNLQKHLINGGAL 118
             MEEWVL DG +KH+VAIDRL+QLR+FSE  ++K+ T+Y LN TFQ+NLQKH+I+GG L
Sbjct: 61  TMMEEWVLADGTSKHRVAIDRLIQLRIFSEISDRKRGTSYSLNPTFQNNLQKHIISGGVL 120

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

Query: 179 Q----------------------------------------------SILRSLKFLCQGI 192
           Q                                              S L  L F   G 
Sbjct: 181 QRDKDGPRLTESGFQFLLMDTNAQLWYIIREYILNAEERDVDPADLISFLLELSFHVTG- 239

Query: 193 LEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGF 252
            +AYNLNTL+E+Q + +KD ADLGLVKLQQGRK+SWFIPTKLATNLS+SL DSSARKEGF
Sbjct: 240 -QAYNLNTLTEVQNNTLKDLADLGLVKLQQGRKDSWFIPTKLATNLSVSLADSSARKEGF 298

Query: 253 VVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIIS 312
           VV+ETNFRMYAYSTSKL CEILRLF++IEYQLPNLI  AITKESLYNAF+NGIT++QII+
Sbjct: 299 VVMETNFRMYAYSTSKLQCEILRLFARIEYQLPNLIACAITKESLYNAFDNGITSDQIIT 358

Query: 313 FLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYAR 372
           FLQQN+HPR ADR+PS+PENV DQIRLWE+DL R+EMT AH+Y+EFPS+DVFEAACD+AR
Sbjct: 359 FLQQNSHPRCADRVPSIPENVTDQIRLWETDLQRIEMTQAHFYDEFPSKDVFEAACDFAR 418

Query: 373 DRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK 406
           +  GLLWEDSK+MRLVV +E+H  MREFL  Q++
Sbjct: 419 EWRGLLWEDSKRMRLVVKSEVHNQMREFLHTQSR 452

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42572935|ref|NP_974564.1| transcription initiation factor TFIIH subunit H4 [Arabidopsis thaliana] gi|332658438|gb|AEE83838.1| transcription initiation factor TFIIH subunit H4 [Arabidopsis thaliana]

 Score =  609 bits (1571), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 300/454 (66%), Positives = 350/454 (77%), Gaps = 50/454 (11%)

Query: 1   MPQVKIIAKNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPA 60
           MPQVKIIAKNFMDMVASL A  L+KLY N FICEAILRSLPPLAKKYV QMLYID  +PA
Sbjct: 1   MPQVKIIAKNFMDMVASLPAIKLDKLYNNVFICEAILRSLPPLAKKYVLQMLYIDVPVPA 60

Query: 61  KTMEEWVLPDGFTKHKVAIDRLVQLRLFSE--EKKKETTYRLNSTFQSNLQKHLINGGAL 118
             MEEWVL DG +KH+VAIDRL+QLR+FSE  ++K+ T+Y LN TFQ+NLQKH+I+GG L
Sbjct: 61  TMMEEWVLADGTSKHRVAIDRLIQLRIFSEISDRKRGTSYSLNPTFQNNLQKHIISGGVL 120

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

Query: 179 Q----------------------------------------------SILRSLKFLCQGI 192
           Q                                              S L  L F   G 
Sbjct: 181 QRDKDGPRLTESGFQFLLMDTNAQLWYIIREYILNAEERDVDPADLISFLLELSFHVTG- 239

Query: 193 LEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGF 252
            +AYNLNTL+E+Q + +KD ADLGLVKLQQGRK+SWFIPTKLATNLS+SL DSSARKEGF
Sbjct: 240 -QAYNLNTLTEVQNNTLKDLADLGLVKLQQGRKDSWFIPTKLATNLSVSLADSSARKEGF 298

Query: 253 VVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIIS 312
           VV+ETNFRMYAYSTSKL CEILRLF++IEYQLPNLI  AITKESLYNAF+NGIT++QII+
Sbjct: 299 VVMETNFRMYAYSTSKLQCEILRLFARIEYQLPNLIACAITKESLYNAFDNGITSDQIIT 358

Query: 313 FLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYAR 372
           FLQQN+HPR ADR+PS+PENV DQIRLWE+DL R+EMT AH+Y+EFPS+DVFEAACD+AR
Sbjct: 359 FLQQNSHPRCADRVPSIPENVTDQIRLWETDLQRIEMTQAHFYDEFPSKDVFEAACDFAR 418

Query: 373 DRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK 406
           +  GLLWEDSK+MRLVV +E+H  MREFL  Q++
Sbjct: 419 EWRGLLWEDSKRMRLVVKSEVHNQMREFLHTQSR 452

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 =  609 bits (1570), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 300/453 (66%), Positives = 349/453 (77%), Gaps = 50/453 (11%)

Query: 1   MPQVKIIAKNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPA 60
           MPQVKIIAKNFMDMVASL A  L+KLY N FICEAILRSLPPLAKKYV QMLYID  +PA
Sbjct: 1   MPQVKIIAKNFMDMVASLPAIKLDKLYNNVFICEAILRSLPPLAKKYVLQMLYIDVPVPA 60

Query: 61  KTMEEWVLPDGFTKHKVAIDRLVQLRLFSE--EKKKETTYRLNSTFQSNLQKHLINGGAL 118
             MEEWVL DG +KH+VAIDRL+QLR+FSE  ++K+ T+Y LN TFQ+NLQKH+I+GG L
Sbjct: 61  TMMEEWVLADGTSKHRVAIDRLIQLRIFSEISDRKRGTSYSLNPTFQNNLQKHIISGGVL 120

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

Query: 179 Q----------------------------------------------SILRSLKFLCQGI 192
           Q                                              S L  L F   G 
Sbjct: 181 QRDKDGPRLTESGFQFLLMDTNAQLWYIIREYILNAEERDVDPADLISFLLELSFHVTG- 239

Query: 193 LEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGF 252
            +AYNLNTL+E+Q + +KD ADLGLVKLQQGRK+SWFIPTKLATNLS+SL DSSARKEGF
Sbjct: 240 -QAYNLNTLTEVQNNTLKDLADLGLVKLQQGRKDSWFIPTKLATNLSVSLADSSARKEGF 298

Query: 253 VVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIIS 312
           VV+ETNFRMYAYSTSKL CEILRLF++IEYQLPNLI  AITKESLYNAF+NGIT++QII+
Sbjct: 299 VVMETNFRMYAYSTSKLQCEILRLFARIEYQLPNLIACAITKESLYNAFDNGITSDQIIT 358

Query: 313 FLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYAR 372
           FLQQN+HPR ADR+PS+PENV DQIRLWE+DL R+EMT AH+Y+EFPS+DVFEAACD+AR
Sbjct: 359 FLQQNSHPRCADRVPSIPENVTDQIRLWETDLQRIEMTQAHFYDEFPSKDVFEAACDFAR 418

Query: 373 DRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQN 405
           +  GLLWEDSK+MRLVV +E+H  MREFL  Q+
Sbjct: 419 EWRGLLWEDSKRMRLVVKSEVHNQMREFLHTQS 451

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|51969958|dbj|BAD43671.1| unnamed protein product [Arabidopsis thaliana]

 Score =  608 bits (1569), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 300/454 (66%), Positives = 349/454 (76%), Gaps = 50/454 (11%)

Query: 1   MPQVKIIAKNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPA 60
           MPQVKIIAKNFMDMVASL A  L+KLY N FICEAILRSLPPLAKKYV QMLYID  +PA
Sbjct: 1   MPQVKIIAKNFMDMVASLPAIKLDKLYNNVFICEAILRSLPPLAKKYVLQMLYIDVPVPA 60

Query: 61  KTMEEWVLPDGFTKHKVAIDRLVQLRLFSE--EKKKETTYRLNSTFQSNLQKHLINGGAL 118
             MEEWVL DG +KH+VAIDRL+QLR+FSE  ++K+ T+Y LN TFQ+NLQKH+I+GG L
Sbjct: 61  TMMEEWVLADGTSKHRVAIDRLIQLRIFSEISDRKRGTSYSLNPTFQNNLQKHIISGGVL 120

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

Query: 179 Q----------------------------------------------SILRSLKFLCQGI 192
           Q                                              S L  L F   G 
Sbjct: 181 QRDKDGPRLTESGFQFLLMDTNAQLWYIIREYILNAEERDVDPADLISFLLELSFHVTG- 239

Query: 193 LEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGF 252
            +AYNLNTL+E+Q + +KD ADLGLVKLQQGRK+SWFIPTKLATNLS+SL DSSARKEGF
Sbjct: 240 -QAYNLNTLTEVQNNTLKDLADLGLVKLQQGRKDSWFIPTKLATNLSVSLADSSARKEGF 298

Query: 253 VVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIIS 312
           VV+ETNFRMYAYSTSKL CEILRLF++IEYQLPNLI  AITKESLYNAF NGIT++QII+
Sbjct: 299 VVMETNFRMYAYSTSKLQCEILRLFARIEYQLPNLIACAITKESLYNAFGNGITSDQIIT 358

Query: 313 FLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYAR 372
           FLQQN+HPR ADR+PS+PENV DQIRLWE+DL R+EMT AH+Y+EFPS+DVFEAACD+AR
Sbjct: 359 FLQQNSHPRCADRVPSIPENVTDQIRLWETDLQRIEMTQAHFYDEFPSKDVFEAACDFAR 418

Query: 373 DRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK 406
           +  GLLWEDSK+MRLVV +E+H  MREFL  Q++
Sbjct: 419 EWRGLLWEDSKRMRLVVKSEVHNQMREFLHTQSR 452

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  608 bits (1568), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 301/452 (66%), Positives = 348/452 (76%), Gaps = 50/452 (11%)

Query: 1   MPQVKIIAKNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPA 60
           MP+V+IIAKNFMDMVAS+    L+KLYEN FICEAILRSLPPLAKKYV Q+ +IDG +PA
Sbjct: 1   MPEVRIIAKNFMDMVASMPTIKLDKLYENGFICEAILRSLPPLAKKYVLQLFHIDGPVPA 60

Query: 61  KTMEEWVLPDGFTKHKVAIDRLVQLRLFSE--EKKKETTYRLNSTFQSNLQKHLINGGAL 118
           K + EWVLPDG +KHKVAIDRLVQL +F E  + K   TY++N T+Q +LQK L++GG L
Sbjct: 61  KLLAEWVLPDGLSKHKVAIDRLVQLGVFVEALDSKNGKTYKVNPTYQRSLQKLLVHGGTL 120

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

Query: 179 Q----------------------------------------------SILRSLKFLCQGI 192
           Q                                              S +  L F   G 
Sbjct: 181 QRDREAPKLTESGFQFLLMDTNAQLWYIIREYITNSEERGVDAGDLISFMLELSFHVIG- 239

Query: 193 LEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGF 252
            EAYN+NTL+E QR++IKD ADLGLVKLQQGRKESWFIPTKLATNLS+S+T+SS+RKEGF
Sbjct: 240 -EAYNINTLTEFQRNIIKDLADLGLVKLQQGRKESWFIPTKLATNLSVSMTESSSRKEGF 298

Query: 253 VVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIIS 312
           VVVETNFR+YAYSTSKLHCEILRLFS++EYQLPNLIVGAITKESLYNAF+NGITA+QI+S
Sbjct: 299 VVVETNFRVYAYSTSKLHCEILRLFSRVEYQLPNLIVGAITKESLYNAFDNGITADQIVS 358

Query: 313 FLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYAR 372
           F +QNAHPRVA RIP+VPENV DQIRLWESDLNRVEMT A+YY+EFPSRDVFE ACD AR
Sbjct: 359 FFRQNAHPRVAQRIPAVPENVTDQIRLWESDLNRVEMTEAYYYDEFPSRDVFEGACDCAR 418

Query: 373 DRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 404
           + SGLLWEDSKKM LVV +E+H ++R+FLR Q
Sbjct: 419 EWSGLLWEDSKKMHLVVKSEVHTYVRDFLRRQ 450

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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	406
ZFIN|ZDB-GENE-030131-6779	466	gtf2h4 "general transcription	0.586	0.510	0.347	6.9e-53
UNIPROTKB|A6H7G8	463	GTF2H4 "Uncharacterized protei	0.551	0.483	0.371	4.7e-50
UNIPROTKB|Q767M2	463	TFIIH "Uncharacterized protein	0.551	0.483	0.371	4.7e-50
UNIPROTKB|F1PGI3	463	GTF2H4 "Uncharacterized protei	0.551	0.483	0.366	9.8e-50
UNIPROTKB|Q92759	462	GTF2H4 "General transcription	0.551	0.484	0.366	9.8e-50
UNIPROTKB|P60027	462	GTF2H4 "General transcription	0.551	0.484	0.366	9.8e-50
RGD|1303309	463	Gtf2h4 "general transcription	0.551	0.483	0.366	1.6e-49
MGI|MGI:1338799	463	Gtf2h4 "general transcription	0.551	0.483	0.366	2.6e-49
DICTYBASE|DDB_G0293228	483	gtf2h4 "TFIIH subunit" [Dictyo	0.541	0.455	0.354	1.1e-48
POMBASE|SPBC13G1.13	447	tfb2 "transcription factor TFI	0.509	0.463	0.359	2.6e-47

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

 Score = 364 (133.2 bits), Expect = 6.9e-53, Sum P(2) = 6.9e-53
 Identities = 90/259 (34%), Positives = 142/259 (54%)

Query:   164 FSSSMMKVFQ-RGL-LIQ--SILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVK 219
             F+   +K  Q RG+ L++  S L  L F   G    Y++  +SE   + ++   + GLV 
Sbjct:   207 FTLQYLKTAQSRGMDLVEILSFLFQLSFSTLG--RDYSVEGMSESLLTFLQHLREFGLV- 263

Query:   220 LQQGRKESWFIPTKLATNLSMSLTDSSARKE--------------GFVVVETNFRMYAYS 265
              Q+ RK   + PT+LA  L+  +T + A                 GF+VVETN+R+YAY+
Sbjct:   264 FQRKRKSRRYYPTRLAITLAAGVTANPASGSASSALGAIPGTGDTGFIVVETNYRIYAYT 323

Query:   266 TSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADR 325
              S+L   ++ LFS++ Y+ PNL+V  +T+ES+  A  NGITA+QII FL+  AHP +  +
Sbjct:   324 NSELQIALVALFSEMLYRFPNLVVAQVTRESVQQAISNGITAQQIIHFLRTRAHPVMLKQ 383

Query:   326 IPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKM 385
              P +P  + DQIRLWE + +R++ T    Y +F S+  FE   D A+    L+W++    
Sbjct:   384 TPVLPPTITDQIRLWELEKDRLQFTEGVLYNQFLSQADFEVLRDRAQGLGVLVWQNPAHR 443

Query:   386 RLVVNAEIHMHMREFLRGQ 404
              +VV    H  ++ F + Q
Sbjct:   444 VMVVTPHGHSEVKRFWKRQ 462

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

 Score = 390 (142.3 bits), Expect = 4.7e-50, Sum P(2) = 4.7e-50
 Identities = 85/229 (37%), Positives = 138/229 (60%)

Query:   178 IQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATN 237
             I S L  L F   G  + Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA N
Sbjct:   234 ILSFLFQLSFSTLG--KDYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAIN 290

Query:   238 LSMSLTDS--SARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKE 295
             LS  ++ +  +A + GF+VVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+E
Sbjct:   291 LSSGVSGAGGTAHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRE 350

Query:   296 SLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYY 355
             S+  A  +GITA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y
Sbjct:   351 SVQQAIASGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLY 410

Query:   356 EEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 404
              +F S+  FE    +AR+   L++E+S K  +VV    H  ++ F + Q
Sbjct:   411 NQFLSQVDFELLLAHARELGVLMFENSAKRLMVVTPAGHSDVKRFWKRQ 459

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

 Score = 389 (142.0 bits), Expect = 4.7e-50, Sum P(2) = 4.7e-50
 Identities = 85/229 (37%), Positives = 138/229 (60%)

Query:   178 IQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATN 237
             I S L  L F   G  + Y++  +S+   + ++   +LGLV  Q+ RK   + PT+LA N
Sbjct:   234 ILSFLFQLSFSTLG--KDYSVEGMSDSLLNFLQHLRELGLV-FQRKRKSRRYYPTRLAIN 290

Query:   238 LSMSLTDS--SARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKE 295
             LS  ++ +  +  + GF+VVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+E
Sbjct:   291 LSSGVSGAGGTVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRE 350

Query:   296 SLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYY 355
             S+  A  +GITA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y
Sbjct:   351 SVQQAIASGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLY 410

Query:   356 EEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 404
              +F S+  FE    +AR+   L++E+S K  +VV    H  ++ F + Q
Sbjct:   411 NQFLSQVDFELLLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQ 459

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 = 388 (141.6 bits), Expect = 9.8e-50, Sum P(2) = 9.8e-50
 Identities = 84/229 (36%), Positives = 138/229 (60%)

Query:   178 IQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATN 237
             I S L  L F   G  + Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA N
Sbjct:   234 ILSFLFQLSFSTLG--KDYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAIN 290

Query:   238 LSMSLTDS--SARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKE 295
             LS  ++ +  +A + GF++VETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+E
Sbjct:   291 LSSGVSGAGGTAHQPGFIIVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRE 350

Query:   296 SLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYY 355
             S+  A  +GITA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y
Sbjct:   351 SVQQAIASGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLY 410

Query:   356 EEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 404
              +F S+  FE    +AR+   L++E+S K  +VV    H  ++ F + Q
Sbjct:   411 NQFLSQVDFELLLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQ 459

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 = 385 (140.6 bits), Expect = 9.8e-50, Sum P(2) = 9.8e-50
 Identities = 84/229 (36%), Positives = 137/229 (59%)

Query:   178 IQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATN 237
             I S L  L F   G  + Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA N
Sbjct:   233 ILSFLFQLSFSTLG--KDYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAIN 289

Query:   238 LSMSLTDS--SARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKE 295
             LS  ++ +  +  + GF+VVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+E
Sbjct:   290 LSSGVSGAGGTVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRE 349

Query:   296 SLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYY 355
             S+  A  +GITA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y
Sbjct:   350 SVQQAIASGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLY 409

Query:   356 EEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 404
              +F S+  FE    +AR+   L++E+S K  +VV    H  ++ F + Q
Sbjct:   410 NQFLSQVDFELLLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQ 458

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 = 385 (140.6 bits), Expect = 9.8e-50, Sum P(2) = 9.8e-50
 Identities = 84/229 (36%), Positives = 137/229 (59%)

Query:   178 IQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATN 237
             I S L  L F   G  + Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA N
Sbjct:   233 ILSFLFQLSFSTLG--KDYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAIN 289

Query:   238 LSMSLTDS--SARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKE 295
             LS  ++ +  +  + GF+VVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+E
Sbjct:   290 LSSGVSGAGGTVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRE 349

Query:   296 SLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYY 355
             S+  A  +GITA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y
Sbjct:   350 SVQQAIASGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLY 409

Query:   356 EEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 404
              +F S+  FE    +AR+   L++E+S K  +VV    H  ++ F + Q
Sbjct:   410 NQFLSQVDFELLLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQ 458

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 = 385 (140.6 bits), Expect = 1.6e-49, Sum P(2) = 1.6e-49
 Identities = 84/229 (36%), Positives = 137/229 (59%)

Query:   178 IQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATN 237
             I S L  L F   G  + Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA N
Sbjct:   234 ILSFLFQLSFSTLG--KDYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAIN 290

Query:   238 LSMSLTDS--SARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKE 295
             LS  ++ +  +  + GF+VVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+E
Sbjct:   291 LSSGVSGAGGTVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRE 350

Query:   296 SLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYY 355
             S+  A  +GITA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y
Sbjct:   351 SVQQAIASGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLY 410

Query:   356 EEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 404
              +F S+  FE    +AR+   L++E+S K  +VV    H  ++ F + Q
Sbjct:   411 NQFLSQVDFELLLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQ 459

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 = 383 (139.9 bits), Expect = 2.6e-49, Sum P(2) = 2.6e-49
 Identities = 84/229 (36%), Positives = 137/229 (59%)

Query:   178 IQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATN 237
             I S L  L F   G  + Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA N
Sbjct:   234 ILSFLFQLSFSTLG--KDYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAIN 290

Query:   238 LSMSLTDS--SARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKE 295
             LS  ++ +  +  + GF+VVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+E
Sbjct:   291 LSSGVSGAGGTVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRE 350

Query:   296 SLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYY 355
             S+  A  +GITA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y
Sbjct:   351 SVQQAIASGITAQQIIHFLRTRAHPVMLKQNPVLPPTITDQIRLWELERDRLRFTEGVLY 410

Query:   356 EEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 404
              +F S+  FE    +AR+   L++E+S K  +VV    H  ++ F + Q
Sbjct:   411 NQFLSQVDFELLLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQ 459

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 = 363 (132.8 bits), Expect = 1.1e-48, Sum P(2) = 1.1e-48
 Identities = 83/234 (35%), Positives = 134/234 (57%)

Query:   180 SILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLS 239
             S L  L FL  G    Y ++ LSE Q+  +      GL+ ++       F PT+L  +L+
Sbjct:   249 SFLFRLSFLNLG--RGYLVSELSEQQKEYLFALKQFGLIYMRTD-SSILFYPTRLIISLT 305

Query:   240 ----MSLTDS-------SARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLI 288
                 +SL  S       + +++G++V+ETN+R+YAY++S L   +L LF K+ Y+LPNL 
Sbjct:   306 TGKTLSLIQSISSERTQTQKEQGYIVLETNYRLYAYTSSSLQISLLSLFVKMLYRLPNLA 365

Query:   289 VGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVE 348
             VG IT+ES+  A  +GITA+QII F++ N+HP  A+    +P+ V +QI LWE++ NR+ 
Sbjct:   366 VGIITRESIRTALIHGITADQIIDFVRHNSHPNAANSGQPIPDVVAEQILLWEAERNRIT 425

Query:   349 MTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLR 402
              T +  Y  FP+ D + A   +A+++   +W       LVV  E +  +R F++
Sbjct:   426 YTKSVLYNSFPTNDCYIATLKFAKEQDYYIWSHDPLKTLVVKEEGNDPIRNFIK 479

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

POMBASE|SPBC13G1.13 tfb2 "transcription factor TFIIH complex subunit Tfb2" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 367 (134.2 bits), Expect = 2.6e-47, Sum P(2) = 2.6e-47
 Identities = 77/214 (35%), Positives = 127/214 (59%)

Query:   195 AYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSM---SLTDSSARKE- 250
             AY+++ L++ Q+ M++D  + GLV  Q+      F PT+LAT L+    SL    +  + 
Sbjct:   230 AYSVDFLTDTQQIMLEDLREYGLV-YQRKITSKRFYPTRLATGLTTDYRSLHGKQSENDD 288

Query:   251 --GFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAE 308
               GF++VETN+R+YAY++S L   I+ LF+ +  +  NL+VG IT++S+  A  NGI AE
Sbjct:   289 DKGFIIVETNYRLYAYTSSPLQIAIIGLFANLRARFSNLVVGVITRDSIRRALMNGIAAE 348

Query:   309 QIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAAC 368
             QII++L  +AHP++   +P +P  + DQI LWE + NR+  TP   + +F +   F+ A 
Sbjct:   349 QIITYLTTHAHPQMRSNVPLLPPTLVDQIYLWELEKNRLRATPGILFRDFLTDSGFDQAV 408

Query:   369 DYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLR 402
             +YA++   L+W+ S K    +       M  +L+
Sbjct:   409 EYAKELGVLVWDSSLKRMFFITTTGAQPMIAYLK 442

GO:0000112 "nucleotide-excision repair factor 3 complex" evidence=ISO

GO:0000439 "core TFIIH complex" evidence=ISO

GO:0000717 "nucleotide-excision repair, DNA duplex unwinding" evidence=ISO

GO:0000991 "core RNA polymerase II binding transcription factor activity" evidence=ISO

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

GO:0005675 "holo TFIIH complex" evidence=ISO

GO:0005737 "cytoplasm" evidence=IDA

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

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

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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!

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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

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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	406
pfam03849	365	pfam03849, Tfb2, Transcription factor Tfb2	1e-124
TIGR00625	448	TIGR00625, tfb2, Transcription factor tfb2	3e-72
COG5144	447	COG5144, TFB2, RNA polymerase II transcription ini	8e-67
pfam13625	128	pfam13625, Helicase_C_3, Helicase conserved C-term	1e-04

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

 Score =  363 bits (934), Expect = e-124
 Identities = 128/368 (34%), Positives = 201/368 (54%), Gaps = 63/368 (17%)

Query: 13  DMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGF 72
           D + SL    L++LY++P  C AI R LPPLAK+++ +ML++D  +PA  +++WV P+  
Sbjct: 1   DYLESLPPTVLDRLYQSPATCLAIFRLLPPLAKQFIMRMLFVDQPVPAADLDKWVKPESK 60

Query: 73  TKHKVAIDRLVQLRLF--SEEKKKETTYRLNSTFQSNLQKHLINGGALPREPMPSGIT-A 129
            +H+ AI RL  L +   +    K+ + RLN TF+ NL++ L  GG      +PS     
Sbjct: 61  KQHEEAIKRLKSLHIITETPSGGKKQSIRLNPTFKKNLRRALTGGGVNNSFGVPSDEPDK 120

Query: 130 RLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQ------SILR 183
           +L  +  L++YA  +WE  L  ++ S++A+  T  S S++ + + G L++       I  
Sbjct: 121 KLVDVAFLDSYAREKWETILHYMVGSSEAK--TQPSKSVLNLLKHGGLMERSDGGLRITN 178

Query: 184 S-LKFLCQ----------------------------------GILE---AYNLNTLSEIQ 205
              +FL Q                                  G LE   AY+ + LSE Q
Sbjct: 179 EGFQFLLQDVNAQIWTLLLQYLKLAEERGMDPVDVLSFLFMLGFLELGKAYSTDGLSETQ 238

Query: 206 RSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSS-------------ARKEGF 252
           R+M++D  D GLV  ++ +   ++ PT+LAT L+   +                A  +GF
Sbjct: 239 RNMLQDLRDYGLVYQRKRKSRRFY-PTRLATTLTSDSSALRTASSAMEAATSSEAASKGF 297

Query: 253 VVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIIS 312
           ++VETNFR+YAY++S L   IL LF +++Y+ PNL+VG IT+ES+ NA ENGITA+QIIS
Sbjct: 298 IIVETNFRLYAYTSSPLQIAILALFVELKYRFPNLVVGQITRESIRNALENGITADQIIS 357

Query: 313 FLQQNAHP 320
           +L+ +AHP
Sbjct: 358 YLETHAHP 365

Length = 365

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

 Score =  232 bits (594), Expect = 3e-72
 Identities = 135/451 (29%), Positives = 219/451 (48%), Gaps = 57/451 (12%)

Query: 10  NFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLP 69
           +  + +  L    L++LY +P  C A+ R LP LAK +V +ML+ +  +P   ++ WV  
Sbjct: 1   SLQEFLEGLPPGVLDRLYGHPATCLAVFRELPSLAKNWVMRMLFNEQPVPLADVDLWVKK 60

Query: 70  DGFTKHKVAIDRLVQLRLFSEEKKKETTY-RLNSTFQSNLQKHLINGGALPREPMP-SGI 127
           +     + +   L  L ++  +         LN  F+ NL+  L  GG      +   G 
Sbjct: 61  EFKKAQEESTGLLSGLHIWHTQLLPGLQGIILNPIFRQNLRIALTGGGKANSFGVSQLGP 120

Query: 128 TARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGL----------- 176
                 ++ L+ YA  +WE  L  ++ +  A+ P+     ++K  Q GL           
Sbjct: 121 DKHAVDVDSLDKYAEERWETILHFMVGTPSAKVPSEDVLQLLK--QAGLMKSTEPGEPPC 178

Query: 177 --------LIQSI----------------------LRSLKFLCQ-GILE---AYNLNTLS 202
                   L+Q I                      +  L FL   G L    AY+++ LS
Sbjct: 179 ITSAGFQFLLQDINAQLWTLLLQYLKTAESRGMDLVEVLHFLFMLGFLTLGKAYSVDGLS 238

Query: 203 EIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSM-SLTDSSARKE-----GFVVVE 256
           + Q  M++D  + GLV  Q+ RK   F PT+LA NL+  + T S A        GF++VE
Sbjct: 239 DTQLIMLQDLREYGLV-FQRKRKSRRFYPTRLAINLTSDTKTVSGAGGTVDDDLGFIIVE 297

Query: 257 TNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQ 316
           TN+R+YAY+ S L   ++ LFS++  + PN++VG IT+ES+  A  NGITA+QII +L+ 
Sbjct: 298 TNYRLYAYTESPLQIALIALFSELLARFPNMVVGQITRESIRRALANGITAQQIIHYLRT 357

Query: 317 NAHPRV-ADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRS 375
           +AHP++  ++ P +P  + DQIRLWE + +R+  T    Y +F ++  FE    YAR+  
Sbjct: 358 HAHPQMRKEQTPVLPPTIVDQIRLWELERDRLRFTEGVLYNDFLTQVDFELLLAYARELG 417

Query: 376 GLLWEDSKKMRLVVNAEIHMHMREFLRGQNK 406
            L+WE+S K    +    H  ++ F + Q  
Sbjct: 418 VLVWENSAKRLFFITPAGHSDVKRFWKRQKH 448

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 =  218 bits (557), Expect = 8e-67
 Identities = 120/426 (28%), Positives = 204/426 (47%), Gaps = 53/426 (12%)

Query: 24  NKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLV 83
            +LY  P  C A LR LP LA K+V  ML+   ++     +EW+        ++ +    
Sbjct: 23  TRLYGAPAFCLAFLRVLPELATKFVMDMLFNSHSVSLLDEDEWIKETLKILLRIQVIGKK 82

Query: 84  QLRLFSEEKKKETTYRLNSTFQSNLQKHLINGGALPREPMPSGITARLPTLEDLEAYAIG 143
              ++ +E       RLN  F+ +L   L  G           I  +L +++ L++Y+  
Sbjct: 83  GNHIYLDEGL---MIRLNPEFKISLMDALTGGTM--ENSFGVCIGEKLVSVDMLDSYSSR 137

Query: 144 QWECFLLQLISSAQAERPTNFSSSMMK-------------VFQRGL--LIQSI------- 181
           +WE  L  ++ + +A+ P      ++K             +  RG   L+Q+I       
Sbjct: 138 KWETILHFMVGTPEAKIPAEGVLELLKFGGLMGRDRNEFKITNRGFQFLLQTINEQLWTL 197

Query: 182 -LRSLKFLCQGILE------------------AYNLNTLSEIQRSMIKDFADLGLVKLQQ 222
            L  LK+    +++                  AY ++ LS+ Q+ M+ D    GLV+ Q 
Sbjct: 198 LLLYLKYFEGSVMDEVAVLHFLFMLGALAVGTAYKIDALSDTQQIMLMDRRLYGLVE-QL 256

Query: 223 GRKESWFIPTKLATNLSM-SLTDSSARKE-----GFVVVETNFRMYAYSTSKLHCEILRL 276
           G     F PT LA  L+   L ++S +       GF++VETN ++YAY+ S L   ++ L
Sbjct: 257 GILRKIFYPTGLAIGLTFDQLFEASEQNRREDDKGFIIVETNNKIYAYTNSPLQIAVIHL 316

Query: 277 FSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQ 336
           F  +  + PNL+ G IT+ES+  A +NGITA+QII +L+ +AHP++  ++  +P  + DQ
Sbjct: 317 FCNLTARFPNLVKGIITRESIRRALDNGITAKQIIHYLETHAHPQMRKKLELLPPTIVDQ 376

Query: 337 IRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMH 396
           I LWE + NR+ M P + Y +F +   ++   +YA     L+W D  K    +  E H  
Sbjct: 377 IVLWELERNRIFMVPGYLYSDFLTLSDYQKVLEYAIRGGVLVWSDVDKRMFFIKLEGHSL 436

Query: 397 MREFLR 402
           ++EF++
Sbjct: 437 VKEFVK 442

Length = 447

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

 Score = 41.0 bits (97), Expect = 1e-04
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 9/65 (13%)

Query: 292 ITKESLYNAFENGITAEQIISFLQQNA-HPRVADRIPSVPENVCDQIRLWESDLNRVEMT 350
           +T  SL  A + G+TAE+II FL++++  P        VP+++   IR       R+ + 
Sbjct: 41  LTPLSLRRALDAGLTAEEIIEFLERHSRTP--------VPQSLLYLIRDVARRHGRLRLG 92

Query: 351 PAHYY 355
            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	406
TIGR00625	448	tfb2 Transcription factor tfb2. This family is bas	100.0
KOG3471	465	consensus RNA polymerase II transcription initiati	100.0
COG5144	447	TFB2 RNA polymerase II transcription initiation/nu	100.0
PF03849	366	Tfb2: Transcription factor Tfb2; InterPro: IPR0045	100.0
PF13625	129	Helicase_C_3: Helicase conserved C-terminal domain	99.59
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	97.04
PF08671	30	SinI: Anti-repressor SinI; InterPro: IPR010981 The	90.7
PRK05718	212	keto-hydroxyglutarate-aldolase/keto-deoxy-phosphog	86.31

>TIGR00625 tfb2 Transcription factor tfb2

Probab=100.00  E-value=4.1e-132  Score=1015.43  Aligned_cols=387  Identities=31%  Similarity=0.576  Sum_probs=366.2

Q ss_pred             hHHHHHhhcCHHHHHHhhCChhhHHHHHhcCChhHHHHHHHHhcCCCCCChhHHHhhcCCcchhHHHHHHHHHHcCceee
Q 015440           10 NFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFS   89 (406)
Q Consensus        10 ~~~~yL~~Lp~~~~~~LY~~p~tclaIfR~LP~lak~~VmrlL~~~~~vp~~~l~~Wv~~~~~~~~~~al~~L~~L~I~~   89 (406)
                      +++|||++||+.++++||++||||+||||+||||||+|||||||+++|||.++++.|+++++++++++|+++|++||||+
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            47899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ec-CCCceeEEeCHHHHHHHHHHHhcCC-----CCCCCCCCCCCCCCCCChHHHHHHHhhhHHHHHHHHhCCcCCCCCCC
Q 015440           90 EE-KKKETTYRLNSTFQSNLQKHLINGG-----ALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTN  163 (406)
Q Consensus        90 ~~-~~~~~~~~Ln~~F~~~lr~aL~ggg-----~~~~~~~~~~~~~~~~~~~~Ld~ya~~kWE~IL~~mVgs~~~~~~~~  163 (406)
                      +. .+|.+.|.||++||+|||.||+|||     ++|++.++++    .+++++||+||++|||+|||||||++..   ..
T Consensus        81 ~~~~~~~~~~~Ln~~F~~~lr~aL~g~~~~~s~~v~~~~~d~~----~~~~~~Ld~yA~~~WE~IL~fmVgs~~~---~~  153 (448)
T TIGR00625        81 TQLLPGLQGIILNPIFRQNLRIALTGGGKANSFGVSQLGPDKH----AVDVDSLDKYAEERWETILHFMVGTPSA---KV  153 (448)
T ss_pred             ecCCCCceeEEECHHHHHHHHHHhcCCCCCCCCCCcccCCCCC----CCCHHHHHHHHHHHHHHHHHHHcCCCCc---CC
Confidence            73 3355789999999999999999998     4667777765    8999999999999999999999998753   57


Q ss_pred             CChhHHHHHHhcCCccc-c-----------------------------------------------hhhhccchhhhhcc
Q 015440          164 FSSSMMKVFQRGLLIQS-I-----------------------------------------------LRSLKFLCQGILEA  195 (406)
Q Consensus       164 ~s~~v~~lL~~~gLm~~-~-----------------------------------------------lf~Ls~l~~~lG~~  195 (406)
                      +|++|+++|+++|||++ +                                               ||+|||++  +|++
T Consensus       154 ~s~~v~~lL~~~~Lm~~~~~~~~~~IT~~GFqFLLqd~n~QvW~lll~YL~~~e~~g~d~vevLsFLf~Ls~l~--lG~~  231 (448)
T TIGR00625       154 PSEDVLQLLKQAGLMKSTEPGEPPCITSAGFQFLLQDINAQLWTLLLQYLKTAESRGMDLVEVLHFLFMLGFLT--LGKA  231 (448)
T ss_pred             CchHHHHHHHhCCCCcccCCCCCccCchhhHHHHcCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHhccc--cCCc
Confidence            99999999999999976 1                                               59999999  9999


Q ss_pred             ccCCCCCHHHHHHHHHhhhcCeeeEeeCCCcceecchhhhhhhccCCCc----cc--ccccceEEEeeCceEEeecCChh
Q 015440          196 YNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTD----SS--ARKEGFVVVETNFRMYAYSTSKL  269 (406)
Q Consensus       196 Ys~~~Lt~tq~~~L~~L~~lGLVy~~~~~~~~fy~pT~La~~Lt~~~~~----~~--~~~~g~iivETNfrvYAYt~s~l  269 (406)
                      |++++||++|++||+||+|+||||++++++++|| |||||++||++.++    ++  +.++|||||||||||||||+|||
T Consensus       232 Y~~~~Lt~tq~~~L~dL~dlGLVy~~~~~~~~fY-PTrLAt~Lts~~~~l~~~~~~~~~~~g~iivEtNfrvYaYt~s~l  310 (448)
T TIGR00625       232 YSVDGLSDTQLIMLQDLREYGLVFQRKRKSRRFY-PTRLAINLTSDTKTVSGAGGTVDDDLGFIIVETNYRLYAYTESPL  310 (448)
T ss_pred             cCCCCCCHHHHHHHHHHHHcCeEEEecCCCCccc-chHHHHHHhcCccccccccccccCCCceEEEEecceEEEecCCHH
Confidence            9999999999999999999999999999999999 99999999887542    11  25679999999999999999999


Q ss_pred             HHHHHHHHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCcccc-ccCCCCChhHHHHHHHHHHhcCcee
Q 015440          270 HCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVA-DRIPSVPENVCDQIRLWESDLNRVE  348 (406)
Q Consensus       270 ~iaiL~lF~~l~~r~pnmvvg~iTreSv~~A~~~GITA~QIi~fL~~hahp~m~-~~~p~iP~tV~dQIrlWe~E~~R~~  348 (406)
                      |++||++||++.||||||+||+|||+||++|+++||||||||+||++||||+|+ ++.|+|||||+|||||||.||||++
T Consensus       311 ~~~il~lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GITa~qIi~fl~~~ahp~~~~~~~~~lP~tv~dQi~lWe~e~~R~~  390 (448)
T TIGR00625       311 QIALIALFSELLARFPNMVVGQITRESIRRALANGITAQQIIHYLRTHAHPQMRKEQTPVLPPTIVDQIRLWELERDRLR  390 (448)
T ss_pred             HHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHcCCCHHHHHHHHHhcCChhhhccCCCCCChHHHHHHHHHHHHhcceE
Confidence            999999999999999999999999999999999999999999999999999998 4789999999999999999999999


Q ss_pred             eccceeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhhccC
Q 015440          349 MTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK  406 (406)
Q Consensus       349 ~~~g~L~~~f~s~~~f~~~~~ya~~~g~llW~~~~kr~~~V~~~~h~~v~~f~k~~~~  406 (406)
                      +++|+||++|+|+++|+++++||+++|+|+|+|+.||+|||+.+||++||+|||++|+
T Consensus       391 ~~~~~l~~~f~s~~~y~~~~~ya~~~~~l~w~~~~kr~~~V~~~gh~~v~~f~k~~~~  448 (448)
T TIGR00625       391 FTEGVLYNDFLTQVDFELLLAYARELGVLVWENSAKRLFFITPAGHSDVKRFWKRQKH  448 (448)
T ss_pred             eecceeeeecCCHHHHHHHHHHHHHcCEEEEecCCceEEEEeccchHHHHHHHHhhcC
Confidence            9999999999999999999999999999999999999999999999999999999986

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=7e-132  Score=989.84  Aligned_cols=396  Identities=36%  Similarity=0.615  Sum_probs=372.4

Q ss_pred             CCchhcchhhHHHHHhhcCH--HHHHHhhCChhhHHHHHhcCChhHHHHHHHHhcCCCCCChhHHHhhcCCcchhHHHHH
Q 015440            1 MPQVKIIAKNFMDMVASLTA--RDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVA   78 (406)
Q Consensus         1 m~~~~~~~~~~~~yL~~Lp~--~~~~~LY~~p~tclaIfR~LP~lak~~VmrlL~~~~~vp~~~l~~Wv~~~~~~~~~~a   78 (406)
                      ||+....++++.+||+.||.  .+++|||++|++|+||||+|||+||+|||+|||.++|||.+++++|++.++.+++++|
T Consensus         5 ~~~~~~~~~~~c~~leeLp~~~~~l~RLY~~Pa~ClAIfR~LPpLAkqfVm~MLf~~~pVP~a~~~~Wv~~~~tk~q~ea   84 (465)
T KOG3471|consen    5 PSQGWPYAKNICDYLEELPRIPHSLDRLYGKPAICLAIFRELPPLAKQFVMQMLFKDQPVPLADVDLWVKVEETKEQEEA   84 (465)
T ss_pred             ccccCcccchHHHHHHHhhccchHHHHHhCCchHHHHHHHhCcHHHHHHHHHHHhcCCCccHHHHHHHhhhhhHHHHHHH
Confidence            45556688999999999999  5899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHcCceeeecCCCceeEEeCHHHHHHHHHHHhcCC-----CCCCCCCCCCCCCCCCChHHHHHHHhhhHHHHHHHHh
Q 015440           79 IDRLVQLRLFSEEKKKETTYRLNSTFQSNLQKHLINGG-----ALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLI  153 (406)
Q Consensus        79 l~~L~~L~I~~~~~~~~~~~~Ln~~F~~~lr~aL~ggg-----~~~~~~~~~~~~~~~~~~~~Ld~ya~~kWE~IL~~mV  153 (406)
                      ++.|.+||||+.....++.+.|||+||+|+|.||+|||     ++++.++|++    .+++++||+||.+||||||||||
T Consensus        85 ik~L~~L~I~~~~~~~g~~i~Lnp~fr~s~~~al~gg~~~~s~~s~~l~~~~~----~r~v~~ld~ya~~rwe~ILh~mv  160 (465)
T KOG3471|consen   85 IKLLKRLRIFHKQGTPGQAINLNPTFRRSLRDALTGGGKQNSFGSLVLGEDKH----NRDVDFLDKYASERWECILHFMV  160 (465)
T ss_pred             HHHHhheeeEeecCCCCceEEeCHHHHHHHHHHHhcCCCcccCCCcccCCCcC----cccchhhHHHHHHHHHHHHHHHh
Confidence            99999999998853222778999999999999999999     4666777877    89999999999999999999999


Q ss_pred             CCcCCCCCCCCChhHHHHHHhcCCcccc----------------------------------------------hhhhcc
Q 015440          154 SSAQAERPTNFSSSMMKVFQRGLLIQSI----------------------------------------------LRSLKF  187 (406)
Q Consensus       154 gs~~~~~~~~~s~~v~~lL~~~gLm~~~----------------------------------------------lf~Ls~  187 (406)
                      |++..   ..+|++|.+||+++|||+++                                              |||||+
T Consensus       161 gt~~a---~~~se~v~~ll~~a~lm~~~~~~~~IT~~GFQFLL~~~~aQlW~~~LqyLk~~~~~~~dlvevL~~LfqL~~  237 (465)
T KOG3471|consen  161 GTPEA---KAVSEGVLNLLKHAGLMSRDENQIEITNAGFQFLLLDINAQLWTLVLQYLKLFESSGMDLVEVLEFLFQLSA  237 (465)
T ss_pred             CCccc---cccChhHHHHHHhcCccCCCCCCceEeecchhhhhcCcHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence            99755   78999999999999999976                                              599999


Q ss_pred             chhhhhccccCCCCCHHHHHHHHHhhhcCeeeEeeCCCcceecchhhhhhhccCCCc--------ccccccceEEEeeCc
Q 015440          188 LCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTD--------SSARKEGFVVVETNF  259 (406)
Q Consensus       188 l~~~lG~~Ys~~~Lt~tq~~~L~~L~~lGLVy~~~~~~~~fy~pT~La~~Lt~~~~~--------~~~~~~g~iivETNf  259 (406)
                      ++  +|++|++++||++|+.||+||||+|||||+|.+..+|| ||+||+++|++..+        ..+++.|||||||||
T Consensus       238 ~~--~G~~Ysvd~~~~~~~~~lq~Lre~GlvfQrk~k~~rfy-ptrla~~~ss~~~~~~~~~~~~~~edd~G~iIVETN~  314 (465)
T KOG3471|consen  238 LA--LGRAYSVDALTETQRILLQHLRELGLVFQRKIKILRFY-PTRLAIGLSSDQLGAASLVHQNRNEDDVGFIIVETNY  314 (465)
T ss_pred             HH--hcccceeehhhHHHHHHHHHHHHhhHHHHhhhhhheec-chhhhhccchhhhhhhhhhhcccccccCceEEEEecc
Confidence            99  99999999999999999999999999999999999999 99999999886442        122455999999999


Q ss_pred             eEEeecCChhHHHHHHHHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccC--CCCChhHHHHH
Q 015440          260 RMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRI--PSVPENVCDQI  337 (406)
Q Consensus       260 rvYAYt~s~l~iaiL~lF~~l~~r~pnmvvg~iTreSv~~A~~~GITA~QIi~fL~~hahp~m~~~~--p~iP~tV~dQI  337 (406)
                      ||||||+||||+|+++|||++.|||||||||+|||||||+|+++||||+|||+||++||||||+...  |.+||||+|||
T Consensus       315 riYAYT~S~lQiAvi~LF~~l~~rf~nlvvG~iTreSVr~Al~~GITa~QII~fLet~ahpqm~~~~~~~~LPpTv~dQI  394 (465)
T KOG3471|consen  315 RIYAYTNSPLQIAVIALFTELTYRFPNLVVGVITRESVRRALDNGITAEQIIHFLETHAHPQMRMLSPVPCLPPTVVDQI  394 (465)
T ss_pred             EEEEecCCHHHHHHHHHHHHHHhhccccceeeeeHHHHHHHHhcCCcHHHHHHHHHhccCchhhhcCCCCCCCchHHhHH
Confidence            9999999999999999999999999999999999999999999999999999999999999998776  88999999999


Q ss_pred             HHHHHhcCceeeccceeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhhccC
Q 015440          338 RLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK  406 (406)
Q Consensus       338 rlWe~E~~R~~~~~g~L~~~f~s~~~f~~~~~ya~~~g~llW~~~~kr~~~V~~~~h~~v~~f~k~~~~  406 (406)
                      ||||.||||+.+++|+||++|.|..||+.+++||+++|+|+|+|+.||+|||+.+||++|++||||++|
T Consensus       395 rLWElernR~~~~~g~LYs~Fls~~df~~l~eya~~~~vLvw~d~~kr~~vV~~~Ghs~Vk~f~Kr~~k  463 (465)
T KOG3471|consen  395 RLWELERNRLRMTEGYLYSDFLSLSDFQLLLEYAREIGVLVWSDSDKRMFVVTKEGHSLVKRFWKRKSK  463 (465)
T ss_pred             HHHHHhhcceecccchhHHhhhhhhhHHHHHHHHHHcCeEEEecCcceEEEEecCccHHHHHHHHHhhc
Confidence            999999999999999999999999999999999999999999999999999999999999999999764

>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=1e-112  Score=831.24  Aligned_cols=382  Identities=29%  Similarity=0.505  Sum_probs=360.4

Q ss_pred             hhhHHHHHhhcCHHHHHHhhCChhhHHHHHhcCChhHHHHHHHHhcCCCCCChhHHHhhcCCcchhHHHHHHHHHHcCce
Q 015440            8 AKNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRL   87 (406)
Q Consensus         8 ~~~~~~yL~~Lp~~~~~~LY~~p~tclaIfR~LP~lak~~VmrlL~~~~~vp~~~l~~Wv~~~~~~~~~~al~~L~~L~I   87 (406)
                      ..++.+||+.||.....|||+.|++|+|+||.||++|++|||.|||.+.|||..+.+.|++.+.+-.+.+++..+.++||
T Consensus         7 k~si~~ylE~lP~~~~~rLY~~Pa~cla~~rvlp~la~~fvm~mlfn~~~v~lld~d~wik~~~Ki~~~~~v~~~k~~hi   86 (447)
T COG5144           7 KISIIEYLEMLPRHSKTRLYGAPAFCLAFLRVLPELATKFVMDMLFNSHSVSLLDEDEWIKETLKILLRIQVIGKKGNHI   86 (447)
T ss_pred             cccHHHHHHHhhhhhhhhhhcCcHHHHHHHHhccHHHHHHHHHHHcCCCCcchhhHHHHHhhhhHHHHHHHHhhhccceE
Confidence            45788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeecCCCceeEEeCHHHHHHHHHHHhcCC-----CCCCCCCCCCCCCCCCChHHHHHHHhhhHHHHHHHHhCCcCCCCCC
Q 015440           88 FSEEKKKETTYRLNSTFQSNLQKHLINGG-----ALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPT  162 (406)
Q Consensus        88 ~~~~~~~~~~~~Ln~~F~~~lr~aL~ggg-----~~~~~~~~~~~~~~~~~~~~Ld~ya~~kWE~IL~~mVgs~~~~~~~  162 (406)
                      ....   ...+.|||+||.+|++|||||+     |+ |..+  +    .++++.||.||.++||+|||||||+...   .
T Consensus        87 ~~~~---g~~i~ln~~fk~sl~~altgg~~~nsfgv-~i~E--~----lvsvd~ld~ys~~kwEtILhfmVgtpea---k  153 (447)
T COG5144          87 YLDE---GLMIRLNPEFKISLMDALTGGTMENSFGV-CIGE--K----LVSVDMLDSYSSRKWETILHFMVGTPEA---K  153 (447)
T ss_pred             EecC---CceEEeChHHHHHHHHHhhccccccccce-eecc--c----eeeeehhhhhhhhhHHHHHHHHhCCccc---c
Confidence            9764   2678999999999999999998     34 3332  2    6899999999999999999999998775   6


Q ss_pred             CCChhHHHHHHhcCCcccc----------------------------------------------hhhhccchhhhhccc
Q 015440          163 NFSSSMMKVFQRGLLIQSI----------------------------------------------LRSLKFLCQGILEAY  196 (406)
Q Consensus       163 ~~s~~v~~lL~~~gLm~~~----------------------------------------------lf~Ls~l~~~lG~~Y  196 (406)
                      -|+.+|+++|+++|||.++                                              +||||.++  +|++|
T Consensus       154 ip~egVl~lLk~ggLm~~~~ne~kITn~GFqFLLq~in~QlWtLlL~yLK~~e~s~md~v~VLhflFmLgal~--vG~aY  231 (447)
T COG5144         154 IPAEGVLELLKFGGLMGRDRNEFKITNRGFQFLLQTINEQLWTLLLLYLKYFEGSVMDEVAVLHFLFMLGALA--VGTAY  231 (447)
T ss_pred             CcchhHHHHHHhcccccCCcccceeehhHHHHHHHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHhcchh--hccee
Confidence            7899999999999999976                                              59999999  99999


Q ss_pred             cCCCCCHHHHHHHHHhhhcCeeeEeeCCCcceecchhhhhhhccCCC----c--ccccccceEEEeeCceEEeecCChhH
Q 015440          197 NLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLT----D--SSARKEGFVVVETNFRMYAYSTSKLH  270 (406)
Q Consensus       197 s~~~Lt~tq~~~L~~L~~lGLVy~~~~~~~~fy~pT~La~~Lt~~~~----~--~~~~~~g~iivETNfrvYAYt~s~l~  270 (406)
                      +++.||+||+.||+|+|++||||+++-.+.+|| ||+||+.||++..    .  ...++.||||||||||||||||||||
T Consensus       232 ~id~lsdtqqiml~D~R~yglv~q~~i~~~~fY-pt~LA~glt~d~~~~~s~qnr~edd~gfiIVETN~kiYaYtnSplq  310 (447)
T COG5144         232 KIDALSDTQQIMLMDRRLYGLVEQLGILRKIFY-PTGLAIGLTFDQLFEASEQNRREDDKGFIIVETNNKIYAYTNSPLQ  310 (447)
T ss_pred             eecccchHHHHHHHHHHHhhHHHHhccchhhcc-ccccchhhhhHHHHHhhhhccccccCceEEEEecceEEEecCChHH
Confidence            999999999999999999999999988888999 9999999987533    1  22356799999999999999999999


Q ss_pred             HHHHHHHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCChhHHHHHHHHHHhcCceeec
Q 015440          271 CEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMT  350 (406)
Q Consensus       271 iaiL~lF~~l~~r~pnmvvg~iTreSv~~A~~~GITA~QIi~fL~~hahp~m~~~~p~iP~tV~dQIrlWe~E~~R~~~~  350 (406)
                      +|++.|||++..||||||+|+|||||||+|+.+||||+|||.||++||||||+++.|.+||||+|||+|||.|+||+.+.
T Consensus       311 iavi~LF~nl~arf~Nlv~GiITreSirrAl~nGIta~QII~yLethahpqmr~~l~llPPtivdQI~lWele~nRi~~~  390 (447)
T COG5144         311 IAVIHLFCNLTARFPNLVKGIITRESIRRALDNGITAKQIIHYLETHAHPQMRKKLELLPPTIVDQIVLWELERNRIFMV  390 (447)
T ss_pred             HHHHHHhhhhhcccchhhhhhccHHHHHHHHhcCccHHHHHHHHHhccChhhhhcCCCCChhhhhheeeeeeccCcEEee
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cceeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhhcc
Q 015440          351 PAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQN  405 (406)
Q Consensus       351 ~g~L~~~f~s~~~f~~~~~ya~~~g~llW~~~~kr~~~V~~~~h~~v~~f~k~~~  405 (406)
                      +|+||+||.+..+|+.+.+||++.|||+|+|+.||||||+.+||.+|++|.||+-
T Consensus       391 pG~LysdFlt~s~y~~~~eya~~~gvLvw~d~~Krmffi~~eG~s~v~~f~Kr~l  445 (447)
T COG5144         391 PGYLYSDFLTLSDYQKVLEYAIRGGVLVWSDVDKRMFFIKLEGHSLVKEFVKRIL  445 (447)
T ss_pred             cchHHhhhhchhhHHHHHHHHHhcCeEEeecccceEEEEEccCcHHHHHHHHHHh
Confidence            9999999999999999999999999999999999999999999999999999964

>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=7.6e-102  Score=782.27  Aligned_cols=300  Identities=41%  Similarity=0.744  Sum_probs=279.9

Q ss_pred             HHHhhcCHHHHHHhhCChhhHHHHHhcCChhHHHHHHHHhcCCCCCChhHHHhhcCCcchhHHHHHHHHHHcCceeeecC
Q 015440           13 DMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFSEEK   92 (406)
Q Consensus        13 ~yL~~Lp~~~~~~LY~~p~tclaIfR~LP~lak~~VmrlL~~~~~vp~~~l~~Wv~~~~~~~~~~al~~L~~L~I~~~~~   92 (406)
                      |||++||++++++||++||||+||||+||++||+|||||||+++|||++++++||++++++++++|+++|.+||||++.+
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            69999999999999999999999999999999999999999999999999999999999999999999999999998743


Q ss_pred             --CCceeEEeCHHHHHHHHHHHhcCC-----CCCCCCCCCCCCCCCCChHHHHHHHhhhHHHHHHHHhCCcCCCCCCCCC
Q 015440           93 --KKETTYRLNSTFQSNLQKHLINGG-----ALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFS  165 (406)
Q Consensus        93 --~~~~~~~Ln~~F~~~lr~aL~ggg-----~~~~~~~~~~~~~~~~~~~~Ld~ya~~kWE~IL~~mVgs~~~~~~~~~s  165 (406)
                        ++.+.|.|||+||+|||.||+|||     ++|++.++++    .+++++||+||++|||+|||||||++.... ..||
T Consensus        81 ~~~~~~~~~Ln~~F~~~Lr~aL~ggg~~~~~~~~~~~~~~~----~~~~~~Ld~yA~~rWE~IL~~mVgs~~~~~-~~~s  155 (366)
T PF03849_consen   81 SPGGKQQYQLNPIFRKNLRNALTGGGKPWSFGVPSEEPDKK----APDVEFLDEYARERWESILHYMVGSSSSSN-SSPS  155 (366)
T ss_pred             CCCCceeEEeCHHHHHHHHHHHhCCCCCcccCcccccccCC----CCCHHHHHHHHHHHHHHHHHHHhcCccccc-CCCC
Confidence              334889999999999999999999     4556655555    899999999999999999999999987521 2299


Q ss_pred             hhHHHHHHhcCCcccc------------------------------------------------hhhhccchhhhhcccc
Q 015440          166 SSMMKVFQRGLLIQSI------------------------------------------------LRSLKFLCQGILEAYN  197 (406)
Q Consensus       166 ~~v~~lL~~~gLm~~~------------------------------------------------lf~Ls~l~~~lG~~Ys  197 (406)
                      ++|+++|+++|||+.+                                                ||+||+++  +|++|+
T Consensus       156 ~~v~~lL~~sgLm~~~~~~~~~~IT~~GFqFLL~d~~~QlW~lll~yL~~~e~~~~~~~~~l~flf~L~~~~--~g~~Y~  233 (366)
T PF03849_consen  156 QDVKQLLKRSGLMKRSESGGSLKITSKGFQFLLQDTNAQLWTLLLQYLKMAEARGMDLVEVLSFLFQLSFLE--LGKAYS  233 (366)
T ss_pred             HHHHHHHHHcCCCcCcCCCCCCcEehhheeeecCChHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhcccc--cCCcCc
Confidence            9999999999999982                                                59999999  999999


Q ss_pred             CCCCCHHHHHHHHHhhhcCeeeEeeCCCcceecchhhhhhhccCCCc-----------ccccccceEEEeeCceEEeecC
Q 015440          198 LNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTD-----------SSARKEGFVVVETNFRMYAYST  266 (406)
Q Consensus       198 ~~~Lt~tq~~~L~~L~~lGLVy~~~~~~~~fy~pT~La~~Lt~~~~~-----------~~~~~~g~iivETNfrvYAYt~  266 (406)
                      +++||++|++||+||+|+||||++++++++|| |||||++|+++.+.           ....++|||||||||||||||+
T Consensus       234 ~~~ls~~q~~~L~~l~~~GLvy~~~~~~~~fy-pT~La~~l~~~~~~~~~~~~~~~~~~~~~~~g~iivETNfrvYAYT~  312 (366)
T PF03849_consen  234 TEGLSETQKNMLQDLRELGLVYQRKRKSRRFY-PTRLATNLTSGSSALRSASSALDSSSSSNKEGFIIVETNFRVYAYTN  312 (366)
T ss_pred             CCCCCHHHHHHHHHHHHCCeEEEecCCCCeEe-chHHHHHHhcCCCcccccccccccccccccCceEEEEecceEEEecC
Confidence            99999999999999999999999999999999 99999999887662           1246789999999999999999


Q ss_pred             ChhHHHHHHHHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCc
Q 015440          267 SKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHP  320 (406)
Q Consensus       267 s~l~iaiL~lF~~l~~r~pnmvvg~iTreSv~~A~~~GITA~QIi~fL~~hahp  320 (406)
                      ||||||||++||++.|||||||||+||||||++|+++||||||||+||++||||
T Consensus       313 s~l~iaiL~lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GIta~qIi~fL~~~aHp  366 (366)
T PF03849_consen  313 SPLQIAILSLFCELKYRFPNLVVGQITRESVRRALKNGITADQIISFLRSHAHP  366 (366)
T ss_pred             CHHHHHHHHHHHHHHhcCCCeEEEEEcHHHHHHHHHcCCCHHHHHHHHHhcCCC
Confidence            999999999999999999999999999999999999999999999999999998

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

>PF13625 Helicase_C_3: Helicase conserved C-terminal domain

Probab=99.59  E-value=1.1e-14  Score=127.45  Aligned_cols=116  Identities=22%  Similarity=0.350  Sum_probs=103.4

Q ss_pred             EEEeeCceEEeecCCh--hHHHHHHHHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCC
Q 015440          253 VVVETNFRMYAYSTSK--LHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVP  330 (406)
Q Consensus       253 iivETNfrvYAYt~s~--l~iaiL~lF~~l~~r~pnmvvg~iTreSv~~A~~~GITA~QIi~fL~~hahp~m~~~~p~iP  330 (406)
                      +||++||.|.+.+.+|  -..+.|..|+++ .+..+|.+++||+.|+.+|++.|+|+++|+.||+.|+..       .||
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-KSPDTMHVYRLTPASLWRAASAGLTAEEIIEFLERYSKN-------PLP   73 (129)
T ss_pred             EEECCCCEEEEeCCCCCHHHHHHHHHHhcc-cccCceEEEEECHHHHHHHHHcCCCHHHHHHHHHHHcCC-------CCC
Confidence            7999999999977665  345999999999 667999999999999999999999999999999999944       699


Q ss_pred             hhHHHHHHHHHHhcCceeeccceeecCCCCHHHHHHHHHHHHHcCe
Q 015440          331 ENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSG  376 (406)
Q Consensus       331 ~tV~dQIrlWe~E~~R~~~~~g~L~~~f~s~~~f~~~~~ya~~~g~  376 (406)
                      +||..+|+-|+...+|+++.++.+|-.+.+.+..+.+.+..+-.++
T Consensus        74 ~~v~~~i~~w~~~~g~v~l~~~~~~l~~~d~~~l~~l~~~~~~~~~  119 (129)
T PF13625_consen   74 QNVEQSIEDWARRYGRVRLYKGAYLLECDDPELLDELLADPELAKL  119 (129)
T ss_pred             HHHHHHHHHHHHhcCCEEEecCeEEEEECCHHHHHHHHhChhhhhh
Confidence            9999999999999999999996666699999999988877665443

>TIGR00603 rad25 DNA repair helicase rad25

Probab=97.04  E-value=0.0052  Score=68.40  Aligned_cols=105  Identities=23%  Similarity=0.398  Sum_probs=84.1

Q ss_pred             cceEEEeeCceEEeecCChh--HH-HHHHHHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccC
Q 015440          250 EGFVVVETNFRMYAYSTSKL--HC-EILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRI  326 (406)
Q Consensus       250 ~g~iivETNfrvYAYt~s~l--~i-aiL~lF~~l~~r~pnmvvg~iTreSv~~A~~~GITA~QIi~fL~~hahp~m~~~~  326 (406)
                      +|.|++||-        +|+  |. ..|.-|+|+..|--+|..++||-=|+-.|...|+++++||++|...+-.      
T Consensus        22 d~~i~lE~~--------~p~~~~a~~fl~~~aEp~~rp~~iHeY~lT~~sl~~A~s~g~~~~~ii~~L~~~sk~------   87 (732)
T TIGR00603        22 DGHIFLESF--------SPLYKQAQDFLVAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLETEDIIEVLGRLSKT------   87 (732)
T ss_pred             CCeEEEEeC--------CccHHHHHHHHHHhcccccChhheEEEeccHHHHHHHHHcCCCHHHHHHHHHHHhCC------
Confidence            466666663        443  33 7899999999999999999999999999999999999999999999843      


Q ss_pred             CCCChhHHHHHHHHHHhcCceeec--cceeecCCCCHHHHHHHHH
Q 015440          327 PSVPENVCDQIRLWESDLNRVEMT--PAHYYEEFPSRDVFEAACD  369 (406)
Q Consensus       327 p~iP~tV~dQIrlWe~E~~R~~~~--~g~L~~~f~s~~~f~~~~~  369 (406)
                       .||++|.+.|+.+-.-.+++++.  ++--|-+-.+.+..+.+.+
T Consensus        88 -~~p~~i~~~i~~~~~~ygk~klv~~~~~~~~es~~~~~l~~l~~  131 (732)
T TIGR00603        88 -PIPKGIIEFIRLCTQSYGKVKLVLKHNRYFVESPHPEVLQRLLK  131 (732)
T ss_pred             -CCCHHHHHHHHHHHHhcCcEEEEEcCCceEEecCCHHHHHHHHh
Confidence             79999999999999999999883  2211334455555555553

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=90.70  E-value=0.24  Score=33.63  Aligned_cols=22  Identities=36%  Similarity=0.525  Sum_probs=17.7

Q ss_pred             HHHHHHHcCCCHHHHHHHHhhc
Q 015440          296 SLYNAFENGITAEQIISFLQQN  317 (406)
Q Consensus       296 Sv~~A~~~GITA~QIi~fL~~h  317 (406)
                      =|++|...|||.+||..||+.+
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            3689999999999999999864

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.

>PRK05718 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional

Probab=86.31  E-value=18  Score=34.79  Aligned_cols=162  Identities=18%  Similarity=0.214  Sum_probs=104.5

Q ss_pred             CCHHHHHHHHHhhhcCeeeEeeCC-CcceecchhhhhhhccCCCcccccccceEEEeeCceEEeecCChhHHHHHHHHHh
Q 015440          201 LSEIQRSMIKDFADLGLVKLQQGR-KESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSK  279 (406)
Q Consensus       201 Lt~tq~~~L~~L~~lGLVy~~~~~-~~~fy~pT~La~~Lt~~~~~~~~~~~g~iivETNfrvYAYt~s~l~iaiL~lF~~  279 (406)
                      +++++..+++.|.+-|+|-.-+.. .....   +++-.|         .+.|.=++|--++      +|-   =+..+.+
T Consensus         1 ~~~~~~~~~~~l~~~~~iaV~r~~~~~~a~---~i~~al---------~~~Gi~~iEitl~------~~~---~~~~I~~   59 (212)
T PRK05718          1 MKNWKTSIEEILRAGPVVPVIVINKLEDAV---PLAKAL---------VAGGLPVLEVTLR------TPA---ALEAIRL   59 (212)
T ss_pred             CchhHHHHHHHHHHCCEEEEEEcCCHHHHH---HHHHHH---------HHcCCCEEEEecC------Ccc---HHHHHHH
Confidence            468888999999999999665432 22211   222222         2236667776643      343   3344455


Q ss_pred             hHhcCCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHhhcCCccccccCCCCCh--hHHHHHHHHHHhcCce
Q 015440          280 IEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAHPRVADRIPSVPE--NVCDQIRLWESDLNRV  347 (406)
Q Consensus       280 l~~r~pnmvvg---~iTreSv~~A~~~GI-------TA~QIi~fL~~hahp~m~~~~p~iP~--tV~dQIrlWe~E~~R~  347 (406)
                      +..+||++.||   ++|.+.++.|++.|-       ..+.+|++-..+-.|       .+|-  |..+=...|+.--+-+
T Consensus        60 l~~~~p~~~IGAGTVl~~~~a~~a~~aGA~FivsP~~~~~vi~~a~~~~i~-------~iPG~~TptEi~~a~~~Ga~~v  132 (212)
T PRK05718         60 IAKEVPEALIGAGTVLNPEQLAQAIEAGAQFIVSPGLTPPLLKAAQEGPIP-------LIPGVSTPSELMLGMELGLRTF  132 (212)
T ss_pred             HHHHCCCCEEEEeeccCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCCC-------EeCCCCCHHHHHHHHHCCCCEE
Confidence            66679999999   899999999999984       455899988876544       6665  4466444888888888


Q ss_pred             eeccceeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhh
Q 015440          348 EMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRG  403 (406)
Q Consensus       348 ~~~~g~L~~~f~s~~~f~~~~~ya~~~g~llW~~~~kr~~~V~~~~h~~v~~f~k~  403 (406)
                      ++.|+-.+-          =.+|-+.+...+   +.-+.+.+..=.-+++++|++.
T Consensus       133 KlFPa~~~g----------g~~~lk~l~~p~---p~~~~~ptGGV~~~ni~~~l~a  175 (212)
T PRK05718        133 KFFPAEASG----------GVKMLKALAGPF---PDVRFCPTGGISPANYRDYLAL  175 (212)
T ss_pred             EEccchhcc----------CHHHHHHHhccC---CCCeEEEeCCCCHHHHHHHHhC
Confidence            886533220          145556655444   3455555444445789999874

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	406
3dom_A	108	Crystal Structure Of The Complex Between Tfb5 And T		2e-04

>pdb|3DOM|A Chain A, Crystal Structure Of The Complex Between Tfb5 And The C-Terminal Domain Of Tfb2 Length = 108

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 43/83 (51%)
Query: 320 PRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLW 379
           P   + +  +P  V DQIRLW+ +L+RV       Y +F +   +     YA+D   LLW
Sbjct: 19  PNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLW 78
Query: 380 EDSKKMRLVVNAEIHMHMREFLR 402
           +D KK +  ++ E +  + +F +
Sbjct: 79  KDDKKKKFFISKEGNSQVLDFAK 101

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	406
3dom_A	108	RNA polymerase II transcription factor B subunit;	3e-37
3dgp_A	80	RNA polymerase II transcription factor B subunit;	8e-30
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-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 =  130 bits (327), Expect = 3e-37
 Identities = 28/100 (28%), Positives = 50/100 (50%), Gaps = 1/100 (1%)

Query: 307 AEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEA 366
           AE+ +   +    P   + +  +P  V DQIRLW+ +L+RV       Y +F +   +  
Sbjct: 7   AEEKLEK-KLELDPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNL 65

Query: 367 ACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK 406
              YA+D   LLW+D KK +  ++ E +  + +F + + K
Sbjct: 66  LSKYAQDIGVLLWKDDKKKKFFISKEGNSQVLDFAKRKLK 105

>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 =  109 bits (274), Expect = 8e-30
 Identities = 24/75 (32%), Positives = 40/75 (53%)

Query: 332 NVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNA 391
            V DQIRLW+ +L+RV       Y +F +   +     YA+D   LLW+D KK +  ++ 
Sbjct: 3   TVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISK 62

Query: 392 EIHMHMREFLRGQNK 406
           E +  + +F + + K
Sbjct: 63  EGNSQVLDFAKRKLK 77

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 59.9 bits (144), Expect = 9e-10
 Identities = 58/314 (18%), Positives = 105/314 (33%), Gaps = 76/314 (24%)

Query: 2   PQ-VKIIAKNFMDMVASLT---ARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYI--- 54
           P+ + IIA++  D +A+       + +KL     I E+ L  L P   + +F  L +   
Sbjct: 327 PRRLSIIAESIRDGLATWDNWKHVNCDKLTT---IIESSLNVLEPAEYRKMFDRLSVFPP 383

Query: 55  DGAIPAKTMEE-WVLPDGFTKHKVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLQK--- 110
              IP   +   W          V  ++L +  L  E++ KE+T  + S +     K   
Sbjct: 384 SAHIPTILLSLIWFDVIKSDVMVVV-NKLHKYSLV-EKQPKESTISIPSIYLELKVKLEN 441

Query: 111 ----H--LINGGALPREPMPSGITARLPTLEDLEAYAIGQWECFLL-QLISSAQAERPTN 163
               H  +++   +P+      +    P   D   Y    +   +   L +    ER T 
Sbjct: 442 EYALHRSIVDHYNIPKTFDSDDLI---PPYLD--QY----FYSHIGHHLKNIEHPERMTL 492

Query: 164 FSSSMMKVFQRGLLIQSILRSLKFLCQGI-LEAYNLNTLSEIQRSMIKDFADLGLVKLQQ 222
           F      VF             +FL Q I  ++   N    I         +     LQQ
Sbjct: 493 FR----MVFL----------DFRFLEQKIRHDSTAWNASGSI--------LNT----LQQ 526

Query: 223 GRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEY 282
            +    +I             D+  + E  V    +F +     + +  +   L  +I  
Sbjct: 527 LKFYKPYI------------CDNDPKYERLVNAILDF-LPKIEENLICSKYTDLL-RIAL 572

Query: 283 QLPNLIVGAITKES 296
              +    AI +E+
Sbjct: 573 MAED---EAIFEEA 583

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	406
3dom_A	108	RNA polymerase II transcription factor B subunit;	99.97
3dgp_A	80	RNA polymerase II transcription factor B subunit;	99.97
3jth_A	98	Transcription activator HLYU; transcription factor	82.52
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	82.23
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	80.18

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

Probab=99.97  E-value=3.2e-33  Score=236.55  Aligned_cols=87  Identities=30%  Similarity=0.596  Sum_probs=72.4

Q ss_pred             ccccccCCCCChhHHHHHHHHHHhcCceeeccceeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHH
Q 015440          320 PRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMRE  399 (406)
Q Consensus       320 p~m~~~~p~iP~tV~dQIrlWe~E~~R~~~~~g~L~~~f~s~~~f~~~~~ya~~~g~llW~~~~kr~~~V~~~~h~~v~~  399 (406)
                      |+++...|+|||||+|||||||.||||+++++||||++|.|+++|+.+++||+++|+|+|+|+.+|+|||+.+||++|++
T Consensus        19 ~~~~~~~p~lPpTVvDQIrLWE~ErnRl~~~~G~LY~dF~s~~efe~v~~yA~e~gvLlW~d~~kr~~~Vs~egh~~vk~   98 (108)
T 3dom_A           19 PNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISKEGNSQVLD   98 (108)
T ss_dssp             -------------CCCHHHHHHHHHTTCEEEEEEEEECCSCHHHHHHHHHHHHHHTCEEEEEGGGTEEEEEGGGHHHHHH
T ss_pred             cccccCCCCCCCcHHHHHHHHHHhhCceeccceEEEecCCCHHHHHHHHHHHHHcCeEEEecCCccEEEEeccchHHHHH
Confidence            45555679999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhccC
Q 015440          400 FLRGQNK  406 (406)
Q Consensus       400 f~k~~~~  406 (406)
                      |||++++
T Consensus        99 f~Kr~~~  105 (108)
T 3dom_A           99 FAKRKLK  105 (108)
T ss_dssp             HHHHHC-
T ss_pred             HHHHHHh
Confidence            9999875

>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=99.97  E-value=2.9e-31  Score=214.31  Aligned_cols=76  Identities=32%  Similarity=0.593  Sum_probs=61.7

Q ss_pred             hhHHHHHHHHHHhcCceeeccceeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhhccC
Q 015440          331 ENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK  406 (406)
Q Consensus       331 ~tV~dQIrlWe~E~~R~~~~~g~L~~~f~s~~~f~~~~~ya~~~g~llW~~~~kr~~~V~~~~h~~v~~f~k~~~~  406 (406)
                      |||+|||||||.|||||++++||||++|+|+++|+.+++||+++|+|+|+|+.+|+|||+.+||++||+|||++++
T Consensus         2 pTV~DQIrLWe~ErnRl~~~~g~Ly~~F~s~~efe~~~~yA~e~gvLlW~~~~kr~~~V~~~gh~~vk~f~k~~~~   77 (80)
T 3dgp_A            2 PTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISKEGNSQVLDFAKRKLK   77 (80)
T ss_dssp             ------------CGGGCEEEEEEEEECCSCHHHHHHHHHHHHHTTCEEEEETTTTEEEEEGGGHHHHHHHHTTC--
T ss_pred             CchHHHHHHHHHhhCceeccceEEEecCCCHHHHHHHHHHHHHcCeEEEecCCccEEEEeccchHHHHHHHHHHHh
Confidence            7999999999999999999999999999999999999999999999999999999999999999999999999875

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=82.52  E-value=4.8  Score=31.38  Aligned_cols=81  Identities=14%  Similarity=0.073  Sum_probs=62.9

Q ss_pred             hhHHHHHhcCChhHHHHHHHHhcCCCCCChhHHHhhcCCcchhHHHHHHHHHHcCceeeecCCC-ceeEEeCHHHHHHHH
Q 015440           31 FICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFSEEKKK-ETTYRLNSTFQSNLQ  109 (406)
Q Consensus        31 ~tclaIfR~LP~lak~~VmrlL~~~~~vp~~~l~~Wv~~~~~~~~~~al~~L~~L~I~~~~~~~-~~~~~Ln~~F~~~lr  109 (406)
                      .....+|+.|..-.+.-|+.+|.. ++++..++..-+. -++......++.|.+.+++...+.| ...|.+++..-..+.
T Consensus        11 ~~~~~~~~~l~~~~r~~Il~~L~~-~~~~~~ela~~l~-is~~tvs~~L~~L~~~Glv~~~~~g~~~~y~l~~~~~~~l~   88 (98)
T 3jth_A           11 AKAVVLLKAMANERRLQILCMLHN-QELSVGELCAKLQ-LSQSALSQHLAWLRRDGLVTTRKEAQTVYYTLKSEEVKAMI   88 (98)
T ss_dssp             HHHHHHHHHHCSHHHHHHHHHTTT-SCEEHHHHHHHHT-CCHHHHHHHHHHHHHTTSEEEECCTTCCEEEECCHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHhc-CCCCHHHHHHHHC-cCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEECHHHHHHHH
Confidence            345677888877788888888875 8999999999885 4477888999999999999865433 467899998776666


Q ss_pred             HHHh
Q 015440          110 KHLI  113 (406)
Q Consensus       110 ~aL~  113 (406)
                      ..+.
T Consensus        89 ~~l~   92 (98)
T 3jth_A           89 KLLH   92 (98)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5543

>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A

Probab=82.23  E-value=4.1  Score=32.13  Aligned_cols=79  Identities=16%  Similarity=0.234  Sum_probs=60.3

Q ss_pred             hHHHHHhcCChhHHHHHHHHhcCCCCCChhHHHhhcCCcchhHHHHHHHHHHcCceeeecCC-CceeEEeCHHHHHHHHH
Q 015440           32 ICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFSEEKK-KETTYRLNSTFQSNLQK  110 (406)
Q Consensus        32 tclaIfR~LP~lak~~VmrlL~~~~~vp~~~l~~Wv~~~~~~~~~~al~~L~~L~I~~~~~~-~~~~~~Ln~~F~~~lr~  110 (406)
                      ....+|+.|..-.+.-|+++|. ++|.+..++..-+. -++......++.|.+.+++...+. ....|.|++..-..+..
T Consensus        12 ~~~~~~~~l~~~~r~~Il~~L~-~~~~~~~ela~~l~-is~~tvs~~L~~L~~~Glv~~~~~g~~~~y~l~~~~~~~~~~   89 (102)
T 3pqk_A           12 EVANLLKTLSHPVRLMLVCTLV-EGEFSVGELEQQIG-IGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVN   89 (102)
T ss_dssp             HHHHHHHHHCSHHHHHHHHHHH-TCCBCHHHHHHHHT-CCTTHHHHHHHHHHHTTSEEEECSSSCCEEEECSSTHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHH-hCCCCHHHHHHHHC-cCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEECcHHHHHHHH
Confidence            3456778777777888888884 68899999998874 457788899999999999986433 44779999966555555


Q ss_pred             HH
Q 015440          111 HL  112 (406)
Q Consensus       111 aL  112 (406)
                      +|
T Consensus        90 ~l   91 (102)
T 3pqk_A           90 AL   91 (102)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=80.18  E-value=6.5  Score=32.04  Aligned_cols=80  Identities=13%  Similarity=0.085  Sum_probs=62.6

Q ss_pred             hhHHHHHhcCChhHHHHHHHHhcCCCCCChhHHHhhcCCcchhHHHHHHHHHHcCceeeecC-CCceeEEeCHHHHHHHH
Q 015440           31 FICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFSEEK-KKETTYRLNSTFQSNLQ  109 (406)
Q Consensus        31 ~tclaIfR~LP~lak~~VmrlL~~~~~vp~~~l~~Wv~~~~~~~~~~al~~L~~L~I~~~~~-~~~~~~~Ln~~F~~~lr  109 (406)
                      .....+|+.|..-.+.-|+.+|. ++|++..++..-+. -++......++.|.+.+++...+ +....|.|++.....+.
T Consensus         6 ~~~~~~~~al~~~~R~~Il~~L~-~~~~~~~eLa~~l~-is~~tvs~hL~~L~~~GlV~~~~~gr~~~y~l~~~~~~~l~   83 (118)
T 3f6o_A            6 EQLNGIFQALADPTRRAVLGRLS-RGPATVSELAKPFD-MALPSFMKHIHFLEDSGWIRTHKQGRVRTCAIEKEPFTAVE   83 (118)
T ss_dssp             HHHHHHHHHHTSHHHHHHHHHHH-TCCEEHHHHHTTCC-SCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECSHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHH-hCCCCHHHHHHHhC-cCHHHHHHHHHHHHHCCCeEEEecCCEEEEEECHHHHHHHH
Confidence            44567889888888888999887 78999999998775 44777888999999999997643 34477999998766665


Q ss_pred             HHH
Q 015440          110 KHL  112 (406)
Q Consensus       110 ~aL  112 (406)
                      ..+
T Consensus        84 ~~~   86 (118)
T 3f6o_A           84 AWL   86 (118)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            444

---

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

ID	Length	Definition	Probability
Query	406
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	86.09

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=86.09  E-value=1.6  Score=33.48  Aligned_cols=84  Identities=14%  Similarity=0.167  Sum_probs=62.9

Q ss_pred             hhcCHHHHHHhhCChhhHHHHHhcCChhHHHHHHHHhcCCCCCChhHHHhhcCCcchhHHHHHHHHHHcCceeeecCCC-
Q 015440           16 ASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFSEEKKK-   94 (406)
Q Consensus        16 ~~Lp~~~~~~LY~~p~tclaIfR~LP~lak~~VmrlL~~~~~vp~~~l~~Wv~~~~~~~~~~al~~L~~L~I~~~~~~~-   94 (406)
                      ..+++++++.|       -.+|+.|.+=.+.-|+++| .++|....++..-+.- +.......++.|++.+|+...+.| 
T Consensus         3 ~~~~pe~~~~l-------a~~~kaL~~p~Rl~Il~~L-~~~~~~v~ela~~l~i-s~stvS~HL~~L~~aglV~~~r~G~   73 (98)
T d1r1ta_           3 QAIAPEVAQSL-------AEFFAVLADPNRLRLLSLL-ARSELCVGDLAQAIGV-SESAVSHQLRSLRNLRLVSYRKQGR   73 (98)
T ss_dssp             CCCCHHHHHHH-------HHHHHHHCCHHHHHHHHHH-TTCCBCHHHHHHHHTC-CHHHHHHHHHHHHHTTSEEEEEETT
T ss_pred             ccCCHHHHHHH-------HHHHHHhCCHHHHHHHHHH-HcCCcCHHHHHHHHCc-CHHHHHHHHHHHHHCCceEEEEECC
Confidence            34566666544       4688888777777788888 4788999999998875 477888889999999999875434 


Q ss_pred             ceeEEeCHHHHHHH
Q 015440           95 ETTYRLNSTFQSNL  108 (406)
Q Consensus        95 ~~~~~Ln~~F~~~l  108 (406)
                      ...|.||+..-..+
T Consensus        74 ~~~Y~l~~~~i~~l   87 (98)
T d1r1ta_          74 HVYYQLQDHHIVAL   87 (98)
T ss_dssp             EEEEEESSHHHHHH
T ss_pred             EEEEEEChHHHHHH
Confidence            46788987654443