Citrus Sinensis ID: 023328

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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----
Protein Sequence
MPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK
Secondary Structure (PSIPRED)
cccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHccHHHHHHHHHHHHEEcccccccccccccHHHHHHHHHHHHcccEEEEccccccEEEccHHHHHHHccccccccccccEEEEEEccEEEEccccHHHHHHHHHHHHHHHcccccEEEEEcHHHHHHHHHccccHHHHHHHHHHccccccccccccccccHHHHHHHHHHHcccEEEcccEEEcccccHHHHHHHHHHHHHccEEEEEcccccEEEEEccccHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHcccHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHcccEEEEcccccccEcccEEEEEEEccccccccccccEEEEEEcEEEEEEcccHHHHHHHHHHHHHHHHcccEEEEEEcHHHHHHHHHccccHHHHHHHHHHcccHHHccccccccccHHHHHHHHHHHHccEEEcccEEEcccccHHHHHHHHHHHHHcccEEEEccccEEEEEccccHHHHHHHHHHccc
Coil and Loop (DISEMBL)
mpsgitarlptledLEAYAIGQWECFLLQLISSaqaerptnfssSMMKVFQRGLLIQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLqqgrkeswfiptklatnlsmsltdssarkegFVVVETNFRMYAYSTSKLHCEILRLFSKIEyqlpnlivgAITKESLYNAFENGITAEQIISFLQqnahprvadripsvpenvCDQIRLWESDlnrvemtpahyyeefpsrdvFEAACDYArdrsgllwedskKMRLVVNAEIHMHMREFLRGQNK
Flexible Loop (DISEMBL)
mpsgitarlptLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLatnlsmsltdssarkEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAhyyeefpsrdVFEAACDYARDrsgllwedskKMRLVVNAEIHMHMREFLRGQNK
Low Complexity Region (SEG)
MPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK
Disordered region (IsUnstruct)
********LPTLEDLEAYAIGQWECFLLQLISSA**********SMMKVFQRGLLIQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTD*SARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMR********
Disordered Region (DISOPRED)
*********PTLEDLEAYAIGQWECFLLQLIS********************GLLIQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATN****************VVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPR*****PSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ**
Disordered Region (DISEMBL)
MPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK
Disordered Region (DISPRO)
****ITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK
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	284	2.2.26 [Sep-21-2011]
P60027	462	General transcription fac	yes	no	0.855	0.525	0.353	1e-36
Q92759	462	General transcription fac	yes	no	0.855	0.525	0.353	1e-36
O70422	463	General transcription fac	yes	no	0.855	0.524	0.353	2e-36
P87303	447	RNA polymerase II transcr	yes	no	0.943	0.599	0.295	4e-36
Q6BZX4	467	RNA polymerase II transcr	yes	no	0.940	0.571	0.290	2e-35
Q6CLR2	496	RNA polymerase II transcr	yes	no	0.732	0.419	0.322	1e-32
Q54C29	483	General transcription fac	yes	no	0.767	0.451	0.360	2e-31
Q75B51	514	RNA polymerase II transcr	yes	no	0.725	0.400	0.325	2e-30
Q6FP41	504	RNA polymerase II transcr	yes	no	0.746	0.420	0.304	5e-30
Q6BGW8	515	RNA polymerase II transcr	yes	no	0.686	0.378	0.295	2e-29

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

 Score =  153 bits (387), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 92/260 (35%), Positives = 148/260 (56%), Gaps = 17/260 (6%)

Query: 26  FLLQLISSAQAERPTNFSSSMMKVFQRGLLIQSILRSLKFLCQGILEAYNLNTLSEIQRS 85
           F+LQ + +AQ        S  M + +    I S L  L F   G  + Y++  +S+   +
Sbjct: 215 FMLQYLQTAQ--------SRGMDLVE----ILSFLFQLSFSTLG--KDYSVEGMSDSLLN 260

Query: 86  MIKDFADLGLVKLQQGRKESWFIPTKLATNLS--MSLTDSSARKEGFVVVETNFRMYAYS 143
            ++   + GLV  Q+ RK   + PT+LA NLS  +S    +  + GF+VVETN+R+YAY+
Sbjct: 261 FLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGFIVVETNYRLYAYT 319

Query: 144 TSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADR 203
            S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII FL+  AHP +  +
Sbjct: 320 ESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLRTRAHPVMLKQ 379

Query: 204 IPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKM 263
            P +P  + DQIRLWE + +R+  T    Y +F S+  FE    +AR+   L++E+S K 
Sbjct: 380 TPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARELGVLVFENSAKR 439

Query: 264 RLVVNAEIHMHMREFLRGQN 283
            +VV    H  ++ F + Q 
Sbjct: 440 LMVVTPAGHSDVKRFWKRQK 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 =  153 bits (387), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 92/260 (35%), Positives = 148/260 (56%), Gaps = 17/260 (6%)

Query: 26  FLLQLISSAQAERPTNFSSSMMKVFQRGLLIQSILRSLKFLCQGILEAYNLNTLSEIQRS 85
           F+LQ + +AQ        S  M + +    I S L  L F   G  + Y++  +S+   +
Sbjct: 215 FMLQYLQTAQ--------SRGMDLVE----ILSFLFQLSFSTLG--KDYSVEGMSDSLLN 260

Query: 86  MIKDFADLGLVKLQQGRKESWFIPTKLATNLS--MSLTDSSARKEGFVVVETNFRMYAYS 143
            ++   + GLV  Q+ RK   + PT+LA NLS  +S    +  + GF+VVETN+R+YAY+
Sbjct: 261 FLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGFIVVETNYRLYAYT 319

Query: 144 TSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADR 203
            S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII FL+  AHP +  +
Sbjct: 320 ESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLRTRAHPVMLKQ 379

Query: 204 IPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKM 263
            P +P  + DQIRLWE + +R+  T    Y +F S+  FE    +AR+   L++E+S K 
Sbjct: 380 TPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARELGVLVFENSAKR 439

Query: 264 RLVVNAEIHMHMREFLRGQN 283
            +VV    H  ++ F + Q 
Sbjct: 440 LMVVTPAGHSDVKRFWKRQK 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|O70422|TF2H4_MOUSE General transcription factor IIH subunit 4 OS=Mus musculus GN=Gtf2h4 PE=2 SV=1

 Score =  152 bits (385), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 92/260 (35%), Positives = 148/260 (56%), Gaps = 17/260 (6%)

Query: 26  FLLQLISSAQAERPTNFSSSMMKVFQRGLLIQSILRSLKFLCQGILEAYNLNTLSEIQRS 85
           F+LQ + +AQ        S  M + +    I S L  L F   G  + Y++  +S+   +
Sbjct: 216 FMLQYLQTAQ--------SRGMDLVE----ILSFLFQLSFSTLG--KDYSVEGMSDSLLN 261

Query: 86  MIKDFADLGLVKLQQGRKESWFIPTKLATNLS--MSLTDSSARKEGFVVVETNFRMYAYS 143
            ++   + GLV  Q+ RK   + PT+LA NLS  +S    +  + GF+VVETN+R+YAY+
Sbjct: 262 FLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGFIVVETNYRLYAYT 320

Query: 144 TSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADR 203
            S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII FL+  AHP +  +
Sbjct: 321 ESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLRTRAHPVMLKQ 380

Query: 204 IPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKM 263
            P +P  + DQIRLWE + +R+  T    Y +F S+  FE    +AR+   L++E+S K 
Sbjct: 381 NPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARELGVLVFENSAKR 440

Query: 264 RLVVNAEIHMHMREFLRGQN 283
            +VV    H  ++ F + Q 
Sbjct: 441 LMVVTPAGHSDVKRFWKRQK 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 =  151 bits (382), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 95/322 (29%), Positives = 161/322 (50%), Gaps = 54/322 (16%)

Query: 9   LPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQS------ILRS 62
           L T++ L+AYA   WE  L  ++ + +A+ P      ++ + +RG L+        I R+
Sbjct: 125 LVTVDFLDAYAKETWETILHFMVGTPEAKFP---GEGVLSLLKRGGLMSGPKNQLRITRA 181

Query: 63  -LKFLCQGI-------------------------------------LEAYNLNTLSEIQR 84
             +FL Q I                                       AY+++ L++ Q+
Sbjct: 182 GFQFLLQDINAQIWTLLLDYLKLSEDTHMDPVQVLHFLFMLGSLDLGRAYSVDFLTDTQQ 241

Query: 85  SMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARK------EGFVVVETNFR 138
            M++D  + GLV  Q+      F PT+LAT L+        ++      +GF++VETN+R
Sbjct: 242 IMLEDLREYGLV-YQRKITSKRFYPTRLATGLTTDYRSLHGKQSENDDDKGFIIVETNYR 300

Query: 139 MYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHP 198
           +YAY++S L   I+ LF+ +  +  NL+VG IT++S+  A  NGI AEQII++L  +AHP
Sbjct: 301 LYAYTSSPLQIAIIGLFANLRARFSNLVVGVITRDSIRRALMNGIAAEQIITYLTTHAHP 360

Query: 199 RVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWE 258
           ++   +P +P  + DQI LWE + NR+  TP   + +F +   F+ A +YA++   L+W+
Sbjct: 361 QMRSNVPLLPPTLVDQIYLWELEKNRLRATPGILFRDFLTDSGFDQAVEYAKELGVLVWD 420

Query: 259 DSKKMRLVVNAEIHMHMREFLR 280
            S K    +       M  +L+
Sbjct: 421 SSLKRMFFITTTGAQPMIAYLK 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|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 =  149 bits (376), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 96/331 (29%), Positives = 162/331 (48%), Gaps = 64/331 (19%)

Query: 15  LEAYAIGQWECFLLQLISSAQAERPTNF------SSSMMKVFQRGLLIQSILRSLKFLCQ 68
           L+A+A+ QWE  L  ++ ++    P++        S +M+  + GL I +     +FL Q
Sbjct: 133 LDAHAVSQWEMILHFMVGTSIGRTPSDGVLNLLKHSGLMEPERGGLRITNA--GFQFLLQ 190

Query: 69  ----------------------------------GILEA---YNLNTLSEIQRSMIKDFA 91
                                             G LE    Y+L+ LSE Q+ M++D  
Sbjct: 191 DVNAQIWTLLLQYLNMSEYLQMDPVDVLNFIFMLGSLELGQDYSLSALSETQKHMLEDLR 250

Query: 92  DLGLVKLQQGRKESWFIPTKLATNLSM------------------SLTDSSARKEGFVVV 133
           D G+V  Q+      F PT+LAT L+                   +++ S A   GF+++
Sbjct: 251 DYGIV-YQRKASSRRFYPTRLATTLTSETAALRTASQSMEAATQDTISSSVAADSGFIIL 309

Query: 134 ETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQ 193
           ETNFR+YAY+ S L   +L LF  ++ +  N++ G I ++S+  A  NGITAEQII++L 
Sbjct: 310 ETNFRLYAYTESPLQIAVLNLFVNLKTRFANMVTGQINRDSVRFALSNGITAEQIITYLS 369

Query: 194 QNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRS 253
            +AHPR+      +P  V DQI+LW+ +++R+  T  + + EF + D ++    YA++  
Sbjct: 370 VHAHPRMKGMEHVLPPTVVDQIKLWQLEMDRIRATDGYLFSEFKNFDEYKDVSTYAKELG 429

Query: 254 GLLWEDSKKMRLVVNAEIHMHMREFLRGQNK 284
            LL+E+  K + V        + EF++ +N+
Sbjct: 430 VLLYENPGKRKFVSTLAGSQQIVEFVKRRNQ 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|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 =  140 bits (353), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 83/257 (32%), Positives = 131/257 (50%), Gaps = 49/257 (19%)

Query: 72  EAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLAT----------------- 114
           +AY  + LS  QR+M++D  D GL+  Q     + F PT+LAT                 
Sbjct: 236 KAYKCDQLSNTQRTMLQDMRDYGLI-YQNQSDYAKFYPTRLATLLTSDTKAFRSASVALD 294

Query: 115 ------NLSMSLTDSSARKE-------GFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQ 161
                 N + ++   S + E       G +++ETNF++Y+YS S L   IL LF  ++ +
Sbjct: 295 SVLNKANETTAVEGDSGQDETTERTQDGALIIETNFKLYSYSNSPLQIAILSLFVHLKSR 354

Query: 162 LPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPR------------------VADR 203
             N++ G +T+ES+ NA  NGITAEQII++L+ +AHPR                  V + 
Sbjct: 355 FANMVTGQLTRESVRNALLNGITAEQIIAYLETHAHPRMRRLAEENLSKKLELDPTVKET 414

Query: 204 IPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKM 263
           +  +P  V DQIRLW+ +L+R+     + Y +F S   ++   DYA+D   LLW++ KK 
Sbjct: 415 LQVLPPTVVDQIRLWQLELDRIISYDGYLYTDFESYQEYQTVADYAKDIGVLLWQNEKKK 474

Query: 264 RLVVNAEIHMHMREFLR 280
              V+ E +  + +F R
Sbjct: 475 MFFVSTEGNSQVLDFHR 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|Q54C29|TF2H4_DICDI General transcription factor IIH subunit 4 OS=Dictyostelium discoideum GN=gtf2h4 PE=3 SV=1

 Score =  136 bits (342), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 85/236 (36%), Positives = 136/236 (57%), Gaps = 18/236 (7%)

Query: 58  SILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKES--WFIPTKLATN 115
           S L  L FL  G    Y ++ LSE Q+  +      GL+ +   R +S   F PT+L  +
Sbjct: 249 SFLFRLSFLNLG--RGYLVSELSEQQKEYLFALKQFGLIYM---RTDSSILFYPTRLIIS 303

Query: 116 LS----MSLTDS-------SARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPN 164
           L+    +SL  S       + +++G++V+ETN+R+YAY++S L   +L LF K+ Y+LPN
Sbjct: 304 LTTGKTLSLIQSISSERTQTQKEQGYIVLETNYRLYAYTSSSLQISLLSLFVKMLYRLPN 363

Query: 165 LIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNR 224
           L VG IT+ES+  A  +GITA+QII F++ N+HP  A+    +P+ V +QI LWE++ NR
Sbjct: 364 LAVGIITRESIRTALIHGITADQIIDFVRHNSHPNAANSGQPIPDVVAEQILLWEAERNR 423

Query: 225 VEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLR 280
           +  T +  Y  FP+ D + A   +A+++   +W       LVV  E +  +R F++
Sbjct: 424 ITYTKSVLYNSFPTNDCYIATLKFAKEQDYYIWSHDPLKTLVVKEEGNDPIRNFIK 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|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 =  132 bits (333), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 87/267 (32%), Positives = 134/267 (50%), Gaps = 61/267 (22%)

Query: 72  EAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLS---MSLTDSSA--- 125
           +AY++  LSE Q++M++D  D GLV  Q+    S F PT+LAT L+   +S+  +S    
Sbjct: 246 KAYSVVGLSETQKTMLQDLRDYGLV-FQKQSNLSKFYPTRLATMLTSDVVSIRSASGAVN 304

Query: 126 -----RKEGF--------------------------VVVETNFRMYAYSTSKLHCEILRL 154
                R EG                           ++VETNF++Y+YS S L   IL L
Sbjct: 305 SVLRQRAEGVDGKVLNGTALGDDDLQAGGEGALDGALIVETNFKLYSYSNSPLQIAILSL 364

Query: 155 FSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHP---RVA---------- 201
           F  ++ +  N++ G IT+ES+  A  NGITA+QII++++ +AHP   R+A          
Sbjct: 365 FIHLKTRFQNMVTGQITRESIRRALHNGITADQIIAYMETHAHPQMRRLAGDNLEKKLEL 424

Query: 202 -----DRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLL 256
                D +  +P  V DQI+LW+ +L+R+     + + +F +   ++    YARD   LL
Sbjct: 425 DPNCRDTLQVLPPTVVDQIKLWQLELDRIISYDGYLFRDFDNLQEYQVLAQYARDIGVLL 484

Query: 257 WEDSKKMRLVVNAE-----IHMHMREF 278
           W D KK    V+ E     I  H R+F
Sbjct: 485 WSDDKKKMFFVSKEGNAQVIDFHKRKF 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|Q6FP41|TFB2_CANGA RNA polymerase II transcription factor B subunit 2 OS=Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) GN=TFB2 PE=3 SV=1

 Score =  131 bits (330), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 80/263 (30%), Positives = 132/263 (50%), Gaps = 51/263 (19%)

Query: 72  EAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLS-------------- 117
           +AY+   LSE Q  M+ D  D GLV  Q+    + F PT+LA  L+              
Sbjct: 239 KAYSTENLSETQLKMLLDMRDYGLV-FQKTSNPNIFYPTRLAQMLTSDTKSMRTASGAME 297

Query: 118 --MSLTDSSAR----------------KEGFVVVETNFRMYAYSTSKLHCEILRLFSKIE 159
             ++  D +A+                ++G +++ETNF++Y+Y  S L   IL LF  ++
Sbjct: 298 SVLNKPDDAAKSTDDKYDSLEGKAEDIQDGALIIETNFKLYSYCNSPLQIAILSLFVHLK 357

Query: 160 YQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRV------------------A 201
            +  N++ G IT+ES+  A  NGITA+Q+I++L+ +AHP++                   
Sbjct: 358 SRFANMVAGQITRESIRRALINGITADQVIAYLESHAHPQMRRLAEEKLQKKLELDPNCK 417

Query: 202 DRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSK 261
           D +  +P  V DQI+LW+ +L+RV       Y +F +   F   C YA+D   LLW+D +
Sbjct: 418 DPLQVLPPTVVDQIKLWQLELDRVLTYEGSLYIDFDTAQDFNMLCKYAQDIGALLWKDDR 477

Query: 262 KMRLVVNAEIHMHMREFLRGQNK 284
           K +L V+ E +  + E+ + + K
Sbjct: 478 KRKLFVSREGNAQVLEYAKRKIK 500

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

Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (taxid: 284593)

>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 =  129 bits (324), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 79/267 (29%), Positives = 128/267 (47%), Gaps = 72/267 (26%)

Query: 72  EAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARK---- 127
           + Y +++LSE Q SM+ D  D GL+  Q+      F PT+LAT L+   +DS+A K    
Sbjct: 238 KGYTVSSLSETQISMLADLRDYGLI-YQRSENSERFYPTRLATTLT---SDSAALKSPSM 293

Query: 128 -----------------------EGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPN 164
                                  +G +++ETNF++YAY+ S L   IL LF  ++ +  N
Sbjct: 294 AMEQALESTTETEEQQNLASNSNQGTIILETNFKIYAYTNSPLEIAILNLFVHLKTRFSN 353

Query: 165 LIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVA----------------------- 201
           ++ G IT+ES+ NA  NGITA+QII FL+ +AH ++                        
Sbjct: 354 MVCGQITRESIRNALYNGITADQIIKFLETHAHSQMKILAKERLDKKIEFDTSNNINTAG 413

Query: 202 ------------------DRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFE 243
                              ++  +P  V DQI+LW+ +L+R++    + +++F S+  FE
Sbjct: 414 GAPQSQMMTNENGTTVAQHKLEVLPPTVVDQIKLWQLELDRIQTFEGYLFKDFASQQEFE 473

Query: 244 AACDYARDRSGLLWEDSKKMRLVVNAE 270
           A  +YA +   LLW +  KM+  V  +
Sbjct: 474 ALSNYASEIGVLLWSNKSKMKFFVTKD 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)

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	284
147854406	451	hypothetical protein VITISV_005315 [Viti	0.978	0.616	0.699	1e-128
255556021	451	tfiih, polypeptide, putative [Ricinus co	0.985	0.620	0.692	1e-127
449433857	451	PREDICTED: general transcription factor	0.985	0.620	0.695	1e-126
224077128	449	predicted protein [Populus trichocarpa]	0.968	0.612	0.684	1e-124
357461579	452	General transcription factor IIH subunit	0.985	0.619	0.664	1e-120
358346685	451	General transcription factor IIH subunit	0.985	0.620	0.664	1e-120
356548733	451	PREDICTED: general transcription factor	0.992	0.625	0.653	1e-118
356521347	451	PREDICTED: general transcription factor	0.985	0.620	0.637	1e-116
42566894	452	transcription initiation factor TFIIH su	0.992	0.623	0.627	1e-115
297800414	452	hypothetical protein ARALYDRAFT_493174 [	0.992	0.623	0.627	1e-114

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

 Score =  464 bits (1193), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 228/326 (69%), Positives = 253/326 (77%), Gaps = 48/326 (14%)

Query: 1   MPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQ--- 57
           MPS IT RLP+L+DLEAYA+GQWECFLLQLISS Q E+ TNFSSS+MKVFQRGLL Q   
Sbjct: 125 MPSNITVRLPSLDDLEAYALGQWECFLLQLISSTQTEKLTNFSSSLMKVFQRGLLTQREK 184

Query: 58  -------------------------------------------SILRSLKFLCQGILEAY 74
                                                      S L  L F   G  EAY
Sbjct: 185 EAPRLTESGFQFLLMDTNAQLWYIMREYISNSEERGVDPADLISFLLELSFHVTG--EAY 242

Query: 75  NLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVE 134
           N+NTL+E QR+ IKD  DLGLVKLQQGRKESWFIPTKLATNLSMSL+D+S+RK+GFVVVE
Sbjct: 243 NINTLTEFQRNTIKDLVDLGLVKLQQGRKESWFIPTKLATNLSMSLSDTSSRKQGFVVVE 302

Query: 135 TNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQ 194
           TNFR+YAYS+SKLHCEILRLFS++EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQ
Sbjct: 303 TNFRLYAYSSSKLHCEILRLFSRVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQ 362

Query: 195 NAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSG 254
           NAHPRVA+R P+VPENV DQIRLWE+DLNRVE  P+H Y+EFPSRDVFEAACD+AR+  G
Sbjct: 363 NAHPRVAERTPAVPENVTDQIRLWETDLNRVETMPSHLYDEFPSRDVFEAACDFAREYGG 422

Query: 255 LLWEDSKKMRLVVNAEIHMHMREFLR 280
           LLWEDSKKMRLVV AEIH+HMRE+LR
Sbjct: 423 LLWEDSKKMRLVVKAEIHLHMREYLR 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 =  461 bits (1186), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 227/328 (69%), Positives = 255/328 (77%), Gaps = 48/328 (14%)

Query: 1   MPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQ--- 57
           + S I  RLPTLE+L+ YA+GQWECFLL LI+S  AER TNFSSSMMK+FQRGLL Q   
Sbjct: 125 LASNIAVRLPTLEELDTYALGQWECFLLHLINSGHAERSTNFSSSMMKIFQRGLLTQRDK 184

Query: 58  -------------------------------------------SILRSLKFLCQGILEAY 74
                                                      S L  L F   G  EAY
Sbjct: 185 EAPRLTESGFQFLLMDTNAQLWYIIREYISNSEERGLDSADLISFLLELSFHITG--EAY 242

Query: 75  NLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVE 134
           N+  L+E QR+MIKD ADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSS+RK+GFVVVE
Sbjct: 243 NMIMLTEFQRNMIKDLADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSSRKQGFVVVE 302

Query: 135 TNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQ 194
           TNFRMYAYSTSKLHCEI+RLFS++EYQLPNL+VGA+TKESLY+AFENGITAEQIISFLQQ
Sbjct: 303 TNFRMYAYSTSKLHCEIMRLFSRVEYQLPNLVVGAMTKESLYSAFENGITAEQIISFLQQ 362

Query: 195 NAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSG 254
           NAHPRVA+RIPSVPENV DQIRLWESD+NRVEMTPAH Y+EFPSRDVFEAAC++ARD +G
Sbjct: 363 NAHPRVAERIPSVPENVTDQIRLWESDMNRVEMTPAHLYDEFPSRDVFEAACNFARDWNG 422

Query: 255 LLWEDSKKMRLVVNAEIHMHMREFLRGQ 282
           LLWEDSK+MR+VV AEIH++MRE+LRGQ
Sbjct: 423 LLWEDSKRMRMVVKAEIHLNMREYLRGQ 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 =  456 bits (1173), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 228/328 (69%), Positives = 254/328 (77%), Gaps = 48/328 (14%)

Query: 1   MPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQ--- 57
           MPS IT RLP+LEDLEAYA+ QWECFLLQLI+S QAE+P+N SSS+MKVFQ+GLL Q   
Sbjct: 125 MPSNITVRLPSLEDLEAYALDQWECFLLQLINSGQAEKPSNISSSVMKVFQKGLLSQRDK 184

Query: 58  -------------------------------------------SILRSLKFLCQGILEAY 74
                                                      S L  L F   G  EAY
Sbjct: 185 EAPRLTESGFQFLLMETNAQLWYIIREYISNAEERGVDPADLISFLLELSFHVTG--EAY 242

Query: 75  NLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVE 134
           +++TLS+ QR  IKD ADLGLVKLQQGRKESWFIPTKLATNLSMSL DSS+RK GFVVVE
Sbjct: 243 DIDTLSDEQRYAIKDLADLGLVKLQQGRKESWFIPTKLATNLSMSLADSSSRKLGFVVVE 302

Query: 135 TNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQ 194
           TNFRMYAYSTSKLHCEILRLFS+IEYQLPNLIVGAITKESLYNAF+NGITAEQI++FLQQ
Sbjct: 303 TNFRMYAYSTSKLHCEILRLFSRIEYQLPNLIVGAITKESLYNAFKNGITAEQIVTFLQQ 362

Query: 195 NAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSG 254
           NAHPRVA+RIPSVPENV DQIRLWESDLNRV++TPAH+Y+EFPSR+VFEAACDYAR+ +G
Sbjct: 363 NAHPRVAERIPSVPENVTDQIRLWESDLNRVDITPAHFYDEFPSREVFEAACDYAREWNG 422

Query: 255 LLWEDSKKMRLVVNAEIHMHMREFLRGQ 282
           LLWEDSK +RLVV A+IH HMRE LR Q
Sbjct: 423 LLWEDSKNLRLVVKADIHTHMREHLRRQ 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 =  449 bits (1156), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 221/323 (68%), Positives = 253/323 (78%), Gaps = 48/323 (14%)

Query: 6   TARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQ-------- 57
             +LP+LE+L+ YA+ QWECFLL LISS QAE+PT+ SSSMMK+FQRGLL Q        
Sbjct: 128 VVKLPSLEELDTYALEQWECFLLLLISSGQAEKPTSLSSSMMKIFQRGLLSQRDRDAPRL 187

Query: 58  --------------------------------------SILRSLKFLCQGILEAYNLNTL 79
                                                 S L  L F   G  EAYN+NTL
Sbjct: 188 TEGGFQFLLMDTNAQLWYIIREYITNSEERGTEPADLISFLLELSFHVTG--EAYNMNTL 245

Query: 80  SEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRM 139
           +EIQR+ IKD A+LGLVKLQQGRKESWFIPTKLATNLS+SLTDSS+RK+G+VVVETNFR+
Sbjct: 246 TEIQRNTIKDLAELGLVKLQQGRKESWFIPTKLATNLSVSLTDSSSRKQGYVVVETNFRL 305

Query: 140 YAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPR 199
           YAYS+SKLHCEILRLFSKIEYQLPNLIVGAITKESLY AFENGIT++QIISFLQQNAHPR
Sbjct: 306 YAYSSSKLHCEILRLFSKIEYQLPNLIVGAITKESLYTAFENGITSDQIISFLQQNAHPR 365

Query: 200 VADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWED 259
           VA+R+PSVPENV DQIRLWE+DLNRVE+TP+H+Y+EFPSRD FEAACD+AR+ +GLLWED
Sbjct: 366 VAERLPSVPENVTDQIRLWEADLNRVEITPSHFYDEFPSRDTFEAACDFAREWNGLLWED 425

Query: 260 SKKMRLVVNAEIHMHMREFLRGQ 282
           SKKMR+VV AEIHM+MREFLRGQ
Sbjct: 426 SKKMRVVVKAEIHMNMREFLRGQ 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 =  437 bits (1124), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 218/328 (66%), Positives = 249/328 (75%), Gaps = 48/328 (14%)

Query: 1   MPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQ--- 57
           MPS IT RLPTLEDLE YA+ QWECFLLQLIS +  ++  N SSS+MKVFQR LL Q   
Sbjct: 126 MPSNITVRLPTLEDLETYALEQWECFLLQLISPSHVDKTLNISSSLMKVFQRRLLSQRDR 185

Query: 58  -------------------------------------------SILRSLKFLCQGILEAY 74
                                                      S +  L F   G  EAY
Sbjct: 186 EAPKLTESGFQFLLMDTNAQLWYIIREYITNSEERGVDAGDLISFMLELSFHVIG--EAY 243

Query: 75  NLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVE 134
           N+NTL+E QR++IKD ADLGLVKLQQGRKESWFIPTKLATNLS+S+T+SS+RKEGFVVVE
Sbjct: 244 NINTLTEFQRNIIKDLADLGLVKLQQGRKESWFIPTKLATNLSVSMTESSSRKEGFVVVE 303

Query: 135 TNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQ 194
           TNFR+YAYSTSKLHCEILRLFS++EYQLPNLIVGAITKESLYNAF+NGITA+QI+SFL+Q
Sbjct: 304 TNFRVYAYSTSKLHCEILRLFSRVEYQLPNLIVGAITKESLYNAFDNGITADQIVSFLRQ 363

Query: 195 NAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSG 254
           NAHPRVA R+P+VPENV DQIRLWESDLNRVEMT A+YY+EFPSRDVFE ACD AR+ SG
Sbjct: 364 NAHPRVAQRVPAVPENVTDQIRLWESDLNRVEMTEAYYYDEFPSRDVFEGACDCAREWSG 423

Query: 255 LLWEDSKKMRLVVNAEIHMHMREFLRGQ 282
           LLWEDSKKM LVV +E+H ++R+FLR Q
Sbjct: 424 LLWEDSKKMHLVVKSEVHTYVRDFLRRQ 451

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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 =  436 bits (1120), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 218/328 (66%), Positives = 248/328 (75%), Gaps = 48/328 (14%)

Query: 1   MPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQ--- 57
           MPS IT RLPTLEDLE YA+ QWECFLLQLIS +  ++  N SSS+MKVFQR LL Q   
Sbjct: 125 MPSNITVRLPTLEDLETYALEQWECFLLQLISPSHVDKTLNISSSLMKVFQRRLLSQRDR 184

Query: 58  -------------------------------------------SILRSLKFLCQGILEAY 74
                                                      S +  L F   G  EAY
Sbjct: 185 EAPKLTESGFQFLLMDTNAQLWYIIREYITNSEERGVDAGDLISFMLELSFHVIG--EAY 242

Query: 75  NLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVE 134
           N+NTL+E QR++IKD ADLGLVKLQQGRKESWFIPTKLATNLS+S+T+SS+RKEGFVVVE
Sbjct: 243 NINTLTEFQRNIIKDLADLGLVKLQQGRKESWFIPTKLATNLSVSMTESSSRKEGFVVVE 302

Query: 135 TNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQ 194
           TNFR+YAYSTSKLHCEILRLFS++EYQLPNLIVGAITKESLYNAF+NGITA+QI+SF +Q
Sbjct: 303 TNFRVYAYSTSKLHCEILRLFSRVEYQLPNLIVGAITKESLYNAFDNGITADQIVSFFRQ 362

Query: 195 NAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSG 254
           NAHPRVA RIP+VPENV DQIRLWESDLNRVEMT A+YY+EFPSRDVFE ACD AR+ SG
Sbjct: 363 NAHPRVAQRIPAVPENVTDQIRLWESDLNRVEMTEAYYYDEFPSRDVFEGACDCAREWSG 422

Query: 255 LLWEDSKKMRLVVNAEIHMHMREFLRGQ 282
           LLWEDSKKM LVV +E+H ++R+FLR Q
Sbjct: 423 LLWEDSKKMHLVVKSEVHTYVRDFLRRQ 450

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  429 bits (1104), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 213/326 (65%), Positives = 249/326 (76%), Gaps = 44/326 (13%)

Query: 1   MPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLL----- 55
           MPS IT RLPTLE+LEAYA+ QWECFLLQLIS +Q E+P N SSS+MKVFQR +L     
Sbjct: 125 MPSNITVRLPTLENLEAYALEQWECFLLQLISPSQVEKPLNISSSLMKVFQRRILSYRDK 184

Query: 56  --------------------IQSILRS-------------------LKFLCQGILEAYNL 76
                               +  I+R                    L+     I EAY++
Sbjct: 185 EAPKLTESGFQFLLMDTNAQLWYIIREYISNSEDRGVDAADLISFMLELSFHDIGEAYSV 244

Query: 77  NTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETN 136
           +TL+  QR++I D ADLGLVK+QQGRK SWFIPTKLATNLSMSL DSS+RK+GFVVVETN
Sbjct: 245 DTLTSFQRTIINDLADLGLVKIQQGRKGSWFIPTKLATNLSMSLADSSSRKQGFVVVETN 304

Query: 137 FRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNA 196
           FR+YAYSTSKLHCEILRLFS++EYQLPNLIVGAITKESLY+AFENGITAEQII+FLQQNA
Sbjct: 305 FRVYAYSTSKLHCEILRLFSRVEYQLPNLIVGAITKESLYSAFENGITAEQIITFLQQNA 364

Query: 197 HPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLL 256
           HPRVA+RIPSVPENV +QIRLWE+DLNRVEMT A+YY+EFPSRDVFE ACD AR+ +GLL
Sbjct: 365 HPRVAERIPSVPENVTEQIRLWEADLNRVEMTDAYYYDEFPSRDVFEGACDCAREWNGLL 424

Query: 257 WEDSKKMRLVVNAEIHMHMREFLRGQ 282
           WEDSKKM +VV  E+H ++R++LR Q
Sbjct: 425 WEDSKKMHMVVKTEVHQYVRDYLRRQ 450

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  424 bits (1091), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 209/328 (63%), Positives = 247/328 (75%), Gaps = 48/328 (14%)

Query: 1   MPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLL----- 55
           MPS IT RLPTLE+LEAYA+ QWECFLLQLIS +Q E+P N SSS+MKVFQR +L     
Sbjct: 125 MPSNITVRLPTLENLEAYALEQWECFLLQLISPSQVEKPLNISSSLMKVFQRRILSHRDK 184

Query: 56  -----------------------------------------IQSILRSLKFLCQGILEAY 74
                                                    + S +  L F   G  EAY
Sbjct: 185 EAPKLTESGFQFLLMDTNAQLWYIIREYISNSEDRGVDAADLISFMLELSFHVIG--EAY 242

Query: 75  NLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVE 134
           +++TL+  QR++I D ADLGLVK+QQGRK SWFIPTKLATNLSMSL DSS+RK+GFVVVE
Sbjct: 243 SVDTLTSFQRTIINDLADLGLVKIQQGRKGSWFIPTKLATNLSMSLADSSSRKQGFVVVE 302

Query: 135 TNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQ 194
           TNFR+YAYSTSKLHCEILRLFS++EYQLPNLIVGAITKESLY+A+ENGITAEQI++FLQQ
Sbjct: 303 TNFRVYAYSTSKLHCEILRLFSRVEYQLPNLIVGAITKESLYSAYENGITAEQIVTFLQQ 362

Query: 195 NAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSG 254
           NAHPRVA+R+PSVPENV +QIRLWE+DLNRVEMT  +YY+EFPSRDVFE ACD AR+ +G
Sbjct: 363 NAHPRVAERVPSVPENVTEQIRLWEADLNRVEMTDTYYYDEFPSRDVFEGACDCAREWNG 422

Query: 255 LLWEDSKKMRLVVNAEIHMHMREFLRGQ 282
           LLWEDSKKM +VV  E+H ++R++LR Q
Sbjct: 423 LLWEDSKKMHMVVKTEVHPYVRDYLRRQ 450

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  419 bits (1077), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 207/330 (62%), Positives = 244/330 (73%), Gaps = 48/330 (14%)

Query: 1   MPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQ--- 57
           M S    +LP+L++LE YA+ QWECFLLQLI+S Q E+ T  SSSMMK+FQRGLL Q   
Sbjct: 125 MNSDNAIKLPSLQELETYALKQWECFLLQLINSGQGEKLTGISSSMMKIFQRGLLSQRDK 184

Query: 58  -------------------------------------------SILRSLKFLCQGILEAY 74
                                                      S L  L F   G  +AY
Sbjct: 185 DGPRLTESGFQFLLMDTNAQLWYIIREYILNAEERDVDPADLISFLLELSFHVTG--QAY 242

Query: 75  NLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVE 134
           NLNTL+E+Q + +KD ADLGLVKLQQGRK+SWFIPTKLATNLS+SL DSSARKEGFVV+E
Sbjct: 243 NLNTLTEVQNNTLKDLADLGLVKLQQGRKDSWFIPTKLATNLSVSLADSSARKEGFVVME 302

Query: 135 TNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQ 194
           TNFRMYAYSTSKL CEILRLF++IEYQLPNLI  AITKESLYNAF+NGIT++QII+FLQQ
Sbjct: 303 TNFRMYAYSTSKLQCEILRLFARIEYQLPNLIACAITKESLYNAFDNGITSDQIITFLQQ 362

Query: 195 NAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSG 254
           N+HPR ADR+PS+PENV DQIRLWE+DL R+EMT AH+Y+EFPS+DVFEAACD+AR+  G
Sbjct: 363 NSHPRCADRVPSIPENVTDQIRLWETDLQRIEMTQAHFYDEFPSKDVFEAACDFAREWRG 422

Query: 255 LLWEDSKKMRLVVNAEIHMHMREFLRGQNK 284
           LLWEDSK+MRLVV +E+H  MREFL  Q++
Sbjct: 423 LLWEDSKRMRLVVKSEVHNQMREFLHTQSR 452

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297800414|ref|XP_002868091.1| hypothetical protein ARALYDRAFT_493174 [Arabidopsis lyrata subsp. lyrata] gi|297313927|gb|EFH44350.1| hypothetical protein ARALYDRAFT_493174 [Arabidopsis lyrata subsp. lyrata]

 Score =  418 bits (1075), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 207/330 (62%), Positives = 242/330 (73%), Gaps = 48/330 (14%)

Query: 1   MPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQ--- 57
           M S    +LP+L++LE YA+ QWECFLLQLI+S Q E+ T  SSSMM++FQRGLL Q   
Sbjct: 125 MHSDNAIKLPSLQELETYALKQWECFLLQLINSGQGEKLTGISSSMMRIFQRGLLSQRDK 184

Query: 58  -------------------------------------------SILRSLKFLCQGILEAY 74
                                                      S L  L F   G  EAY
Sbjct: 185 DGPRLTESGFQFLLMDTNAQLWYIIREYISNAEERDVEPADLISFLLELSFHVTG--EAY 242

Query: 75  NLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVE 134
           N NTL+E+Q + +KD ADLGLVKLQQGRK+SWFIPTKLATNLS+SL DSSARKEGFVV+E
Sbjct: 243 NSNTLTEVQNNTLKDLADLGLVKLQQGRKDSWFIPTKLATNLSVSLADSSARKEGFVVME 302

Query: 135 TNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQ 194
           TNFRMYAYSTSKL CEILRLF++IEYQLPNLI  AITKESLYNAF+NGIT++QII+FLQQ
Sbjct: 303 TNFRMYAYSTSKLQCEILRLFARIEYQLPNLIACAITKESLYNAFDNGITSDQIITFLQQ 362

Query: 195 NAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSG 254
           N+HPR ADR+PS+PENV DQIRLWE+DL R+EMT AH+Y+EFPS+DVFEAACD+AR+  G
Sbjct: 363 NSHPRCADRVPSIPENVTDQIRLWETDLKRIEMTQAHFYDEFPSKDVFEAACDFAREWGG 422

Query: 255 LLWEDSKKMRLVVNAEIHMHMREFLRGQNK 284
           LLWEDSK+MRLVV +E+H  MREFL  Q K
Sbjct: 423 LLWEDSKRMRLVVKSEVHNQMREFLHNQTK 452

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	284
WB|WBGene00013529	481	Y73F8A.24 [Caenorhabditis eleg	0.732	0.432	0.396	5.8e-40
POMBASE|SPBC13G1.13	447	tfb2 "transcription factor TFI	0.728	0.463	0.359	4.5e-38
DICTYBASE|DDB_G0293228	483	gtf2h4 "TFIIH subunit" [Dictyo	0.774	0.455	0.354	9.3e-38
ZFIN|ZDB-GENE-030131-6779	466	gtf2h4 "general transcription	0.838	0.510	0.347	1e-36
ASPGD|ASPL0000068300	482	AN7015 [Emericella nidulans (t	0.732	0.431	0.354	2.2e-36
UNIPROTKB|A6H7G8	463	GTF2H4 "Uncharacterized protei	0.788	0.483	0.371	3.5e-36
UNIPROTKB|Q767M2	463	TFIIH "Uncharacterized protein	0.788	0.483	0.371	4.4e-36
UNIPROTKB|F1PGI3	463	GTF2H4 "Uncharacterized protei	0.788	0.483	0.366	5.7e-36
UNIPROTKB|Q92759	462	GTF2H4 "General transcription	0.788	0.484	0.366	1.2e-35
UNIPROTKB|P60027	462	GTF2H4 "General transcription	0.788	0.484	0.366	1.2e-35

WB|WBGene00013529 Y73F8A.24 [Caenorhabditis elegans (taxid:6239)]

 Score = 395 (144.1 bits), Expect = 5.8e-40, Sum P(2) = 5.8e-40
 Identities = 86/217 (39%), Positives = 138/217 (63%)

Query:    72 EAYNLNT-LSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLT--DSSARK- 127
             E Y ++   +E Q  ++    +LG++ +++ RK+  F  T+L T+L+ + T  D SA K 
Sbjct:   247 ECYQIDANWTEPQNELLNHLRELGVIFIRK-RKDGVFFLTQLLTHLATNETIDDVSAEKV 305

Query:   128 -EGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAE 186
               G V+VETNFR+YAY++S L   I+ LF+++ Y+  ++ VG IT+ES+  A ++GITA 
Sbjct:   306 SNGKVIVETNFRVYAYTSSLLQLAIIALFTEMTYRFQDMSVGMITRESVRGALQHGITAA 365

Query:   187 QIISFLQQNAHPR-VADRIP--SVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFE 243
             QIISFL+ NAHP+ +A   P   +P  V DQIRLWE +  R+ +  A+ Y  F S D F 
Sbjct:   366 QIISFLRANAHPQCIATSGPVNCLPITVADQIRLWEDERRRMNLKDAYIYSHFESEDEFH 425

Query:   244 AACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLR 280
               C+YAR ++ LLW D+++  ++VN + H  +R++ +
Sbjct:   426 GVCEYARQQNILLWSDNQQKLVIVNEDGHELVRQWYK 462

GO:0005634 "nucleus" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

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

GO:0000003 "reproduction" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

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

 Score = 367 (134.2 bits), Expect = 4.5e-38, Sum P(2) = 4.5e-38
 Identities = 77/214 (35%), Positives = 127/214 (59%)

Query:    73 AYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSM---SLTDSSARKE- 128
             AY+++ L++ Q+ M++D  + GLV  Q+      F PT+LAT L+    SL    +  + 
Sbjct:   230 AYSVDFLTDTQQIMLEDLREYGLV-YQRKITSKRFYPTRLATGLTTDYRSLHGKQSENDD 288

Query:   129 --GFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAE 186
               GF++VETN+R+YAY++S L   I+ LF+ +  +  NL+VG IT++S+  A  NGI AE
Sbjct:   289 DKGFIIVETNYRLYAYTSSPLQIAIIGLFANLRARFSNLVVGVITRDSIRRALMNGIAAE 348

Query:   187 QIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAAC 246
             QII++L  +AHP++   +P +P  + DQI LWE + NR+  TP   + +F +   F+ A 
Sbjct:   349 QIITYLTTHAHPQMRSNVPLLPPTLVDQIYLWELEKNRLRATPGILFRDFLTDSGFDQAV 408

Query:   247 DYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLR 280
             +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

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

 Score = 363 (132.8 bits), Expect = 9.3e-38, Sum P(2) = 9.3e-38
 Identities = 83/234 (35%), Positives = 134/234 (57%)

Query:    58 SILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLS 117
             S L  L FL  G    Y ++ LSE Q+  +      GL+ ++       F PT+L  +L+
Sbjct:   249 SFLFRLSFLNLG--RGYLVSELSEQQKEYLFALKQFGLIYMRTD-SSILFYPTRLIISLT 305

Query:   118 ----MSLTDS-------SARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLI 166
                 +SL  S       + +++G++V+ETN+R+YAY++S L   +L LF K+ Y+LPNL 
Sbjct:   306 TGKTLSLIQSISSERTQTQKEQGYIVLETNYRLYAYTSSSLQISLLSLFVKMLYRLPNLA 365

Query:   167 VGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVE 226
             VG IT+ES+  A  +GITA+QII F++ N+HP  A+    +P+ V +QI LWE++ NR+ 
Sbjct:   366 VGIITRESIRTALIHGITADQIIDFVRHNSHPNAANSGQPIPDVVAEQILLWEAERNRIT 425

Query:   227 MTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLR 280
              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

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

 Score = 364 (133.2 bits), Expect = 1.0e-36, Sum P(2) = 1.0e-36
 Identities = 90/259 (34%), Positives = 142/259 (54%)

Query:    42 FSSSMMKVFQ-RGL-LIQ--SILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVK 97
             F+   +K  Q RG+ L++  S L  L F   G    Y++  +SE   + ++   + GLV 
Sbjct:   207 FTLQYLKTAQSRGMDLVEILSFLFQLSFSTLG--RDYSVEGMSESLLTFLQHLREFGLV- 263

Query:    98 LQQGRKESWFIPTKLATNLSMSLTDSSARKE--------------GFVVVETNFRMYAYS 143
              Q+ RK   + PT+LA  L+  +T + A                 GF+VVETN+R+YAY+
Sbjct:   264 FQRKRKSRRYYPTRLAITLAAGVTANPASGSASSALGAIPGTGDTGFIVVETNYRIYAYT 323

Query:   144 TSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADR 203
              S+L   ++ LFS++ Y+ PNL+V  +T+ES+  A  NGITA+QII FL+  AHP +  +
Sbjct:   324 NSELQIALVALFSEMLYRFPNLVVAQVTRESVQQAISNGITAQQIIHFLRTRAHPVMLKQ 383

Query:   204 IPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKM 263
              P +P  + DQIRLWE + +R++ T    Y +F S+  FE   D A+    L+W++    
Sbjct:   384 TPVLPPTITDQIRLWELEKDRLQFTEGVLYNQFLSQADFEVLRDRAQGLGVLVWQNPAHR 443

Query:   264 RLVVNAEIHMHMREFLRGQ 282
              +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

ASPGD|ASPL0000068300 AN7015 [Emericella nidulans (taxid:162425)]

 Score = 345 (126.5 bits), Expect = 2.2e-36, Sum P(2) = 2.2e-36
 Identities = 85/240 (35%), Positives = 132/240 (55%)

Query:    72 EAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNL---SMSLT------- 121
             ++Y    L+  Q   + D AD G+V  Q   + S F PT+LAT L   S +L+       
Sbjct:   245 KSYEKKHLTSNQLRTLTDLADFGIV-YQDSPEASHFYPTRLATTLTSDSSALSNPISGAL 303

Query:   122 ------DSSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESL 175
                   DS+    GF+++ETN+R+YAY++S L   ++ LF+ ++Y+ PNL+ G +T++S+
Sbjct:   304 SDPDGGDSNQPGSGFIIIETNYRLYAYTSSPLQISLIALFTTLKYRFPNLVTGKVTRQSI 363

Query:   176 YNAFENGITAEQIISFLQQNAHPRV------------ADRIPSV-PENVCDQIRLWESDL 222
               A E GITA+QIIS+L  +AHP++            A   PSV P  V DQIRLW+ + 
Sbjct:   364 RRAIEMGITADQIISYLATHAHPQMRKHNVARSTSNQAGMPPSVLPPTVVDQIRLWQLER 423

Query:   223 NRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 282
             +RV+ T    +++F S   +EA C YA +   L+W+  +K    V    H  +  FLR +
Sbjct:   424 DRVKATAGFLFKDFVSLAEYEAPCRYAEEIGVLIWKSDRKRMFFVTR--HEQVAAFLRSR 481

GO:0006281 "DNA repair" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

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

 Score = 390 (142.3 bits), Expect = 3.5e-36, P = 3.5e-36
 Identities = 85/229 (37%), Positives = 138/229 (60%)

Query:    56 IQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATN 115
             I S L  L F   G  + Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA N
Sbjct:   234 ILSFLFQLSFSTLG--KDYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAIN 290

Query:   116 LSMSLTDS--SARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKE 173
             LS  ++ +  +A + GF+VVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+E
Sbjct:   291 LSSGVSGAGGTAHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRE 350

Query:   174 SLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYY 233
             S+  A  +GITA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y
Sbjct:   351 SVQQAIASGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLY 410

Query:   234 EEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 282
              +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 = 4.4e-36, P = 4.4e-36
 Identities = 85/229 (37%), Positives = 138/229 (60%)

Query:    56 IQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATN 115
             I S L  L F   G  + Y++  +S+   + ++   +LGLV  Q+ RK   + PT+LA N
Sbjct:   234 ILSFLFQLSFSTLG--KDYSVEGMSDSLLNFLQHLRELGLV-FQRKRKSRRYYPTRLAIN 290

Query:   116 LSMSLTDS--SARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKE 173
             LS  ++ +  +  + GF+VVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+E
Sbjct:   291 LSSGVSGAGGTVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRE 350

Query:   174 SLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYY 233
             S+  A  +GITA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y
Sbjct:   351 SVQQAIASGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLY 410

Query:   234 EEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 282
              +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 = 5.7e-36, P = 5.7e-36
 Identities = 84/229 (36%), Positives = 138/229 (60%)

Query:    56 IQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATN 115
             I S L  L F   G  + Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA N
Sbjct:   234 ILSFLFQLSFSTLG--KDYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAIN 290

Query:   116 LSMSLTDS--SARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKE 173
             LS  ++ +  +A + GF++VETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+E
Sbjct:   291 LSSGVSGAGGTAHQPGFIIVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRE 350

Query:   174 SLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYY 233
             S+  A  +GITA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y
Sbjct:   351 SVQQAIASGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLY 410

Query:   234 EEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 282
              +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 = 1.2e-35, P = 1.2e-35
 Identities = 84/229 (36%), Positives = 137/229 (59%)

Query:    56 IQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATN 115
             I S L  L F   G  + Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA N
Sbjct:   233 ILSFLFQLSFSTLG--KDYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAIN 289

Query:   116 LSMSLTDS--SARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKE 173
             LS  ++ +  +  + GF+VVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+E
Sbjct:   290 LSSGVSGAGGTVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRE 349

Query:   174 SLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYY 233
             S+  A  +GITA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y
Sbjct:   350 SVQQAIASGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLY 409

Query:   234 EEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 282
              +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 = 1.2e-35, P = 1.2e-35
 Identities = 84/229 (36%), Positives = 137/229 (59%)

Query:    56 IQSILRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATN 115
             I S L  L F   G  + Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA N
Sbjct:   233 ILSFLFQLSFSTLG--KDYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAIN 289

Query:   116 LSMSLTDS--SARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKE 173
             LS  ++ +  +  + GF+VVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+E
Sbjct:   290 LSSGVSGAGGTVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRE 349

Query:   174 SLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYY 233
             S+  A  +GITA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y
Sbjct:   350 SVQQAIASGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLY 409

Query:   234 EEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 282
              +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

---

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!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	284
pfam03849	365	pfam03849, Tfb2, Transcription factor Tfb2	5e-75
TIGR00625	448	TIGR00625, tfb2, Transcription factor tfb2	9e-55
COG5144	447	COG5144, TFB2, RNA polymerase II transcription ini	1e-51
pfam13625	128	pfam13625, Helicase_C_3, Helicase conserved C-term	1e-04

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

 Score =  232 bits (595), Expect = 5e-75
 Identities = 84/249 (33%), Positives = 131/249 (52%), Gaps = 60/249 (24%)

Query: 7   ARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQSILRSLK-- 64
            +L  +  L++YA  +WE  L  ++ S++A+  T  S S++ + + G L++     L+  
Sbjct: 120 KKLVDVAFLDSYAREKWETILHYMVGSSEAK--TQPSKSVLNLLKHGGLMERSDGGLRIT 177

Query: 65  -----FLCQ----------------------------------GILE---AYNLNTLSEI 82
                FL Q                                  G LE   AY+ + LSE 
Sbjct: 178 NEGFQFLLQDVNAQIWTLLLQYLKLAEERGMDPVDVLSFLFMLGFLELGKAYSTDGLSET 237

Query: 83  QRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTDSS-------------ARKEG 129
           QR+M++D  D GLV  ++ +   ++ PT+LAT L+   +                A  +G
Sbjct: 238 QRNMLQDLRDYGLVYQRKRKSRRFY-PTRLATTLTSDSSALRTASSAMEAATSSEAASKG 296

Query: 130 FVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQII 189
           F++VETNFR+YAY++S L   IL LF +++Y+ PNL+VG IT+ES+ NA ENGITA+QII
Sbjct: 297 FIIVETNFRLYAYTSSPLQIAILALFVELKYRFPNLVVGQITRESIRNALENGITADQII 356

Query: 190 SFLQQNAHP 198
           S+L+ +AHP
Sbjct: 357 SYLETHAHP 365

Length = 365

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

 Score =  183 bits (465), Expect = 9e-55
 Identities = 96/266 (36%), Positives = 151/266 (56%), Gaps = 22/266 (8%)

Query: 26  FLLQLISSAQAERPTNFSSSMMKVFQRGLLIQSILRSLKFLCQGILEAYNLNTLSEIQRS 85
            LLQ + +A+        S  M + +    +   L  L FL  G  +AY+++ LS+ Q  
Sbjct: 198 LLLQYLKTAE--------SRGMDLVE----VLHFLFMLGFLTLG--KAYSVDGLSDTQLI 243

Query: 86  MIKDFADLGLVKLQQGRKESWFIPTKLATNLSM-SLTDSSARKE-----GFVVVETNFRM 139
           M++D  + GLV  Q+ RK   F PT+LA NL+  + T S A        GF++VETN+R+
Sbjct: 244 MLQDLREYGLV-FQRKRKSRRFYPTRLAINLTSDTKTVSGAGGTVDDDLGFIIVETNYRL 302

Query: 140 YAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPR 199
           YAY+ S L   ++ LFS++  + PN++VG IT+ES+  A  NGITA+QII +L+ +AHP+
Sbjct: 303 YAYTESPLQIALIALFSELLARFPNMVVGQITRESIRRALANGITAQQIIHYLRTHAHPQ 362

Query: 200 V-ADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWE 258
           +  ++ P +P  + DQIRLWE + +R+  T    Y +F ++  FE    YAR+   L+WE
Sbjct: 363 MRKEQTPVLPPTIVDQIRLWELERDRLRFTEGVLYNDFLTQVDFELLLAYARELGVLVWE 422

Query: 259 DSKKMRLVVNAEIHMHMREFLRGQNK 284
           +S K    +    H  ++ F + Q  
Sbjct: 423 NSAKRLFFITPAGHSDVKRFWKRQKH 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 =  174 bits (443), Expect = 1e-51
 Identities = 95/325 (29%), Positives = 164/325 (50%), Gaps = 48/325 (14%)

Query: 3   SGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMK-------------V 49
             I  +L +++ L++Y+  +WE  L  ++ + +A+ P      ++K             +
Sbjct: 119 VCIGEKLVSVDMLDSYSSRKWETILHFMVGTPEAKIPAEGVLELLKFGGLMGRDRNEFKI 178

Query: 50  FQRGL--LIQSI--------LRSLKFLCQGILE------------------AYNLNTLSE 81
             RG   L+Q+I        L  LK+    +++                  AY ++ LS+
Sbjct: 179 TNRGFQFLLQTINEQLWTLLLLYLKYFEGSVMDEVAVLHFLFMLGALAVGTAYKIDALSD 238

Query: 82  IQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSM-SLTDSSARKE-----GFVVVET 135
            Q+ M+ D    GLV+ Q G     F PT LA  L+   L ++S +       GF++VET
Sbjct: 239 TQQIMLMDRRLYGLVE-QLGILRKIFYPTGLAIGLTFDQLFEASEQNRREDDKGFIIVET 297

Query: 136 NFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQN 195
           N ++YAY+ S L   ++ LF  +  + PNL+ G IT+ES+  A +NGITA+QII +L+ +
Sbjct: 298 NNKIYAYTNSPLQIAVIHLFCNLTARFPNLVKGIITRESIRRALDNGITAKQIIHYLETH 357

Query: 196 AHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGL 255
           AHP++  ++  +P  + DQI LWE + NR+ M P + Y +F +   ++   +YA     L
Sbjct: 358 AHPQMRKKLELLPPTIVDQIVLWELERNRIFMVPGYLYSDFLTLSDYQKVLEYAIRGGVL 417

Query: 256 LWEDSKKMRLVVNAEIHMHMREFLR 280
           +W D  K    +  E H  ++EF++
Sbjct: 418 VWSDVDKRMFFIKLEGHSLVKEFVK 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: 170 ITKESLYNAFENGITAEQIISFLQQNA-HPRVADRIPSVPENVCDQIRLWESDLNRVEMT 228
           +T  SL  A + G+TAE+II FL++++  P        VP+++   IR       R+ + 
Sbjct: 41  LTPLSLRRALDAGLTAEEIIEFLERHSRTP--------VPQSLLYLIRDVARRHGRLRLG 92

Query: 229 PAHYY 233
            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	284
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	99.67
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	97.39
PF08671	30	SinI: Anti-repressor SinI; InterPro: IPR010981 The	92.11
PRK05718	212	keto-hydroxyglutarate-aldolase/keto-deoxy-phosphog	85.14

>TIGR00625 tfb2 Transcription factor tfb2

Probab=100.00  E-value=1.1e-100  Score=748.37  Aligned_cols=277  Identities=33%  Similarity=0.604  Sum_probs=259.9

Q ss_pred             CCCCCCC-CCChhHHHHHHhhhHHHHHHHHhCCCCCCCCCCCChhHHHHHHhcCCccc---c------------------
Q 023328            2 PSGITAR-LPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQS---I------------------   59 (284)
Q Consensus         2 ~~~~~~~-~~~~~~Ld~ya~~~WE~IL~~mVgs~~~~~~~~~s~~v~~lL~~~~Lm~~---~------------------   59 (284)
                      |....++ .+++++||+||.+|||+|||||||++..   ..+|++|+++|+++|||++   +                  
T Consensus       116 ~~~~~d~~~~~~~~Ld~yA~~~WE~IL~fmVgs~~~---~~~s~~v~~lL~~~~Lm~~~~~~~~~~IT~~GFqFLLqd~n  192 (448)
T TIGR00625       116 SQLGPDKHAVDVDSLDKYAEERWETILHFMVGTPSA---KVPSEDVLQLLKQAGLMKSTEPGEPPCITSAGFQFLLQDIN  192 (448)
T ss_pred             cccCCCCCCCCHHHHHHHHHHHHHHHHHHHcCCCCc---CCCchHHHHHHHhCCCCcccCCCCCccCchhhHHHHcCChh
Confidence            3333443 8899999999999999999999998754   5789999999999999976   1                  


Q ss_pred             ---------------------------hhhhccccccccccccCCCCCHHHHHHHHHhhhcCeeeEeeCCCcceecchhh
Q 023328           60 ---------------------------LRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKL  112 (284)
Q Consensus        60 ---------------------------lf~L~~~~~~lG~~Y~~~~Lt~~q~~~L~~l~~~GLvy~~~~~~~~fy~pT~L  112 (284)
                                                 ||+|||++  +|++|++++||++|++||+||+|+||||++++++++|| ||||
T Consensus       193 ~QvW~lll~YL~~~e~~g~d~vevLsFLf~Ls~l~--lG~~Y~~~~Lt~tq~~~L~dL~dlGLVy~~~~~~~~fY-PTrL  269 (448)
T TIGR00625       193 AQLWTLLLQYLKTAESRGMDLVEVLHFLFMLGFLT--LGKAYSVDGLSDTQLIMLQDLREYGLVFQRKRKSRRFY-PTRL  269 (448)
T ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHhccc--cCCccCCCCCCHHHHHHHHHHHHcCeEEEecCCCCccc-chHH
Confidence                                       59999999  99999999999999999999999999999999999999 9999


Q ss_pred             HHhhhcCCCc----cc--ccCcceEEEeeCceEEEecCChhHHHHHHHHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHH
Q 023328          113 ATNLSMSLTD----SS--ARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAE  186 (284)
Q Consensus       113 a~~L~~~~~~----~~--~~~~g~IIvETNFrvYAYT~S~lqiaiL~lF~~l~~r~Pnlvvg~iTReSv~~Al~~GITA~  186 (284)
                      |++|+++.++    ++  ..++|+|||||||||||||+||||++||++||++.||||||+||+|||+||++|+++|||||
T Consensus       270 At~Lts~~~~l~~~~~~~~~~~g~iivEtNfrvYaYt~s~l~~~il~lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GITa~  349 (448)
T TIGR00625       270 AINLTSDTKTVSGAGGTVDDDLGFIIVETNYRLYAYTESPLQIALIALFSELLARFPNMVVGQITRESIRRALANGITAQ  349 (448)
T ss_pred             HHHHhcCccccccccccccCCCceEEEEecceEEEecCCHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHcCCCHH
Confidence            9999887542    11  25679999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhcCCcccc-ccCCCCChhHHHHHHHHHHhcCceeeccceeeccCCCHHHHHHHHHHHHHcCeEeeecCCCceE
Q 023328          187 QIISFLQQNAHPRVA-DRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRL  265 (284)
Q Consensus       187 QIi~fL~~hAHp~m~-~~~p~lP~tV~dQIrLWe~E~~R~~~~~g~Ly~~f~s~~~fe~~~~yA~~~g~llw~~~~kr~~  265 (284)
                      |||+||++||||+|+ ++.|+|||||+|||||||.||||+++++|+||++|+|+++|+++++||+++|+|+|+|+.||+|
T Consensus       350 qIi~fl~~~ahp~~~~~~~~~lP~tv~dQi~lWe~e~~R~~~~~~~l~~~f~s~~~y~~~~~ya~~~~~l~w~~~~kr~~  429 (448)
T TIGR00625       350 QIIHYLRTHAHPQMRKEQTPVLPPTIVDQIRLWELERDRLRFTEGVLYNDFLTQVDFELLLAYARELGVLVWENSAKRLF  429 (448)
T ss_pred             HHHHHHHhcCChhhhccCCCCCChHHHHHHHHHHHHhcceEeecceeeeecCCHHHHHHHHHHHHHcCEEEEecCCceEE
Confidence            999999999999998 4789999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeccccHHHHHHHhhccC
Q 023328          266 VVNAEIHMHMREFLRGQNK  284 (284)
Q Consensus       266 ~V~~~~h~~v~~f~k~~~~  284 (284)
                      ||+.+||++||+|||++|+
T Consensus       430 ~V~~~gh~~v~~f~k~~~~  448 (448)
T TIGR00625       430 FITPAGHSDVKRFWKRQKH  448 (448)
T ss_pred             EEeccchHHHHHHHHhhcC
Confidence            9999999999999999986

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=2.3e-101  Score=739.48  Aligned_cols=271  Identities=37%  Similarity=0.649  Sum_probs=257.7

Q ss_pred             CCCChhHHHHHHhhhHHHHHHHHhCCCCCCCCCCCChhHHHHHHhcCCcccc----------------------------
Q 023328            8 RLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQSI----------------------------   59 (284)
Q Consensus         8 ~~~~~~~Ld~ya~~~WE~IL~~mVgs~~~~~~~~~s~~v~~lL~~~~Lm~~~----------------------------   59 (284)
                      +.+++++||+||.+|||||||||||++.+   ..+|++|.+||+++|||+++                            
T Consensus       137 ~~r~v~~ld~ya~~rwe~ILh~mvgt~~a---~~~se~v~~ll~~a~lm~~~~~~~~IT~~GFQFLL~~~~aQlW~~~Lq  213 (465)
T KOG3471|consen  137 HNRDVDFLDKYASERWECILHFMVGTPEA---KAVSEGVLNLLKHAGLMSRDENQIEITNAGFQFLLLDINAQLWTLVLQ  213 (465)
T ss_pred             CcccchhhHHHHHHHHHHHHHHHhCCccc---cccChhHHHHHHhcCccCCCCCCceEeecchhhhhcCcHHHHHHHHHH
Confidence            46789999999999999999999999765   89999999999999999975                            


Q ss_pred             ------------------hhhhccccccccccccCCCCCHHHHHHHHHhhhcCeeeEeeCCCcceecchhhHHhhhcCCC
Q 023328           60 ------------------LRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLT  121 (284)
Q Consensus        60 ------------------lf~L~~~~~~lG~~Y~~~~Lt~~q~~~L~~l~~~GLvy~~~~~~~~fy~pT~La~~L~~~~~  121 (284)
                                        |||||+++  +|++|++++||++|+.||+||||+|||||||.+..+|| ||+||+++|++-.
T Consensus       214 yLk~~~~~~~dlvevL~~LfqL~~~~--~G~~Ysvd~~~~~~~~~lq~Lre~GlvfQrk~k~~rfy-ptrla~~~ss~~~  290 (465)
T KOG3471|consen  214 YLKLFESSGMDLVEVLEFLFQLSALA--LGRAYSVDALTETQRILLQHLRELGLVFQRKIKILRFY-PTRLAIGLSSDQL  290 (465)
T ss_pred             HHHHHHhcCCCHHHHHHHHHHHHHHH--hcccceeehhhHHHHHHHHHHHHhhHHHHhhhhhheec-chhhhhccchhhh
Confidence                              59999999  99999999999999999999999999999999999999 9999999988644


Q ss_pred             c--------ccccCcceEEEeeCceEEEecCChhHHHHHHHHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHh
Q 023328          122 D--------SSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQ  193 (284)
Q Consensus       122 ~--------~~~~~~g~IIvETNFrvYAYT~S~lqiaiL~lF~~l~~r~Pnlvvg~iTReSv~~Al~~GITA~QIi~fL~  193 (284)
                      +        ...++.|||||||||||||||+||||+|+++|||++.|||||||||+|||||||+|+++||||+|||+||+
T Consensus       291 ~~~~~~~~~~~edd~G~iIVETN~riYAYT~S~lQiAvi~LF~~l~~rf~nlvvG~iTreSVr~Al~~GITa~QII~fLe  370 (465)
T KOG3471|consen  291 GAASLVHQNRNEDDVGFIIVETNYRIYAYTNSPLQIAVIALFTELTYRFPNLVVGVITRESVRRALDNGITAEQIIHFLE  370 (465)
T ss_pred             hhhhhhhcccccccCceEEEEeccEEEEecCCHHHHHHHHHHHHHHhhccccceeeeeHHHHHHHHhcCCcHHHHHHHHH
Confidence            2        12245699999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCCccccccC--CCCChhHHHHHHHHHHhcCceeeccceeeccCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccc
Q 023328          194 QNAHPRVADRI--PSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEI  271 (284)
Q Consensus       194 ~hAHp~m~~~~--p~lP~tV~dQIrLWe~E~~R~~~~~g~Ly~~f~s~~~fe~~~~yA~~~g~llw~~~~kr~~~V~~~~  271 (284)
                      +||||||+...  |++||||+|||||||.||||+.+++|+||++|.|..||+.+++||+++|+|+|+|+.||+|||+.+|
T Consensus       371 t~ahpqm~~~~~~~~LPpTv~dQIrLWElernR~~~~~g~LYs~Fls~~df~~l~eya~~~~vLvw~d~~kr~~vV~~~G  450 (465)
T KOG3471|consen  371 THAHPQMRMLSPVPCLPPTVVDQIRLWELERNRLRMTEGYLYSDFLSLSDFQLLLEYAREIGVLVWSDSDKRMFVVTKEG  450 (465)
T ss_pred             hccCchhhhcCCCCCCCchHHhHHHHHHHhhcceecccchhHHhhhhhhhHHHHHHHHHHcCeEEEecCcceEEEEecCc
Confidence            99999998876  8999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHhhccC
Q 023328          272 HMHMREFLRGQNK  284 (284)
Q Consensus       272 h~~v~~f~k~~~~  284 (284)
                      |++|++||||++|
T Consensus       451 hs~Vk~f~Kr~~k  463 (465)
T KOG3471|consen  451 HSLVKRFWKRKSK  463 (465)
T ss_pred             cHHHHHHHHHhhc
Confidence            9999999999764

>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=2.8e-90  Score=648.72  Aligned_cols=273  Identities=31%  Similarity=0.558  Sum_probs=259.5

Q ss_pred             CCCCCCChhHHHHHHhhhHHHHHHHHhCCCCCCCCCCCChhHHHHHHhcCCcccc-------------------------
Q 023328            5 ITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQSI-------------------------   59 (284)
Q Consensus         5 ~~~~~~~~~~Ld~ya~~~WE~IL~~mVgs~~~~~~~~~s~~v~~lL~~~~Lm~~~-------------------------   59 (284)
                      +..+.+++++||+||.++||+|||||||+.++   .-|+.+|.++|+++|||.++                         
T Consensus       121 i~E~lvsvd~ld~ys~~kwEtILhfmVgtpea---kip~egVl~lLk~ggLm~~~~ne~kITn~GFqFLLq~in~QlWtL  197 (447)
T COG5144         121 IGEKLVSVDMLDSYSSRKWETILHFMVGTPEA---KIPAEGVLELLKFGGLMGRDRNEFKITNRGFQFLLQTINEQLWTL  197 (447)
T ss_pred             eccceeeeehhhhhhhhhHHHHHHHHhCCccc---cCcchhHHHHHHhcccccCCcccceeehhHHHHHHHHHHHHHHHH
Confidence            44568899999999999999999999999886   78999999999999999865                         


Q ss_pred             ---------------------hhhhccccccccccccCCCCCHHHHHHHHHhhhcCeeeEeeCCCcceecchhhHHhhhc
Q 023328           60 ---------------------LRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSM  118 (284)
Q Consensus        60 ---------------------lf~L~~~~~~lG~~Y~~~~Lt~~q~~~L~~l~~~GLvy~~~~~~~~fy~pT~La~~L~~  118 (284)
                                           +||||.++  +|++|+++.||+||+.||+|+|++||||+++-.+.+|| ||+||+.||+
T Consensus       198 lL~yLK~~e~s~md~v~VLhflFmLgal~--vG~aY~id~lsdtqqiml~D~R~yglv~q~~i~~~~fY-pt~LA~glt~  274 (447)
T COG5144         198 LLLYLKYFEGSVMDEVAVLHFLFMLGALA--VGTAYKIDALSDTQQIMLMDRRLYGLVEQLGILRKIFY-PTGLAIGLTF  274 (447)
T ss_pred             HHHHHHHhccccccHHHHHHHHHHhcchh--hcceeeecccchHHHHHHHHHHHhhHHHHhccchhhcc-ccccchhhhh
Confidence                                 59999999  99999999999999999999999999999998899999 9999999987


Q ss_pred             CCC----c--ccccCcceEEEeeCceEEEecCChhHHHHHHHHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHH
Q 023328          119 SLT----D--SSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFL  192 (284)
Q Consensus       119 ~~~----~--~~~~~~g~IIvETNFrvYAYT~S~lqiaiL~lF~~l~~r~Pnlvvg~iTReSv~~Al~~GITA~QIi~fL  192 (284)
                      +..    .  ...++.||||||||||||||||||||+|+++|||++..||||||+|+|||||||+|+.+||||+|||.||
T Consensus       275 d~~~~~s~qnr~edd~gfiIVETN~kiYaYtnSplqiavi~LF~nl~arf~Nlv~GiITreSirrAl~nGIta~QII~yL  354 (447)
T COG5144         275 DQLFEASEQNRREDDKGFIIVETNNKIYAYTNSPLQIAVIHLFCNLTARFPNLVKGIITRESIRRALDNGITAKQIIHYL  354 (447)
T ss_pred             HHHHHhhhhccccccCceEEEEecceEEEecCChHHHHHHHHhhhhhcccchhhhhhccHHHHHHHHhcCccHHHHHHHH
Confidence            532    1  1235679999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCCccccccCCCCChhHHHHHHHHHHhcCceeeccceeeccCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEecccc
Q 023328          193 QQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIH  272 (284)
Q Consensus       193 ~~hAHp~m~~~~p~lP~tV~dQIrLWe~E~~R~~~~~g~Ly~~f~s~~~fe~~~~yA~~~g~llw~~~~kr~~~V~~~~h  272 (284)
                      ++||||||+++.|.+||||+|||+|||.|+||+...+|+||+||.+..+|+.+.+||++.|+|+|++..||||||+.+||
T Consensus       355 ethahpqmr~~l~llPPtivdQI~lWele~nRi~~~pG~LysdFlt~s~y~~~~eya~~~gvLvw~d~~Krmffi~~eG~  434 (447)
T COG5144         355 ETHAHPQMRKKLELLPPTIVDQIVLWELERNRIFMVPGYLYSDFLTLSDYQKVLEYAIRGGVLVWSDVDKRMFFIKLEGH  434 (447)
T ss_pred             HhccChhhhhcCCCCChhhhhheeeeeeccCcEEeecchHHhhhhchhhHHHHHHHHHhcCeEEeecccceEEEEEccCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcc
Q 023328          273 MHMREFLRGQN  283 (284)
Q Consensus       273 ~~v~~f~k~~~  283 (284)
                      .+|++|.||+-
T Consensus       435 s~v~~f~Kr~l  445 (447)
T COG5144         435 SLVKEFVKRIL  445 (447)
T ss_pred             HHHHHHHHHHh
Confidence            99999999964

>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=9e-70  Score=521.69  Aligned_cols=188  Identities=43%  Similarity=0.739  Sum_probs=176.1

Q ss_pred             CCCCChhHHHHHHhhhHHHHHHHHhCCCCCCCCCCCChhHHHHHHhcCCcccc---------------------------
Q 023328            7 ARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFSSSMMKVFQRGLLIQSI---------------------------   59 (284)
Q Consensus         7 ~~~~~~~~Ld~ya~~~WE~IL~~mVgs~~~~~~~~~s~~v~~lL~~~~Lm~~~---------------------------   59 (284)
                      .+.+++++||+||++|||+|||||||++.... ..||++|+++|+++|||+..                           
T Consensus       120 ~~~~~~~~Ld~yA~~rWE~IL~~mVgs~~~~~-~~~s~~v~~lL~~sgLm~~~~~~~~~~IT~~GFqFLL~d~~~QlW~l  198 (366)
T PF03849_consen  120 KKAPDVEFLDEYARERWESILHYMVGSSSSSN-SSPSQDVKQLLKRSGLMKRSESGGSLKITSKGFQFLLQDTNAQLWTL  198 (366)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHhcCccccc-CCCCHHHHHHHHHcCCCcCcCCCCCCcEehhheeeecCChHHHHHHH
Confidence            67899999999999999999999999987521 22999999999999999982                           


Q ss_pred             ---------------------hhhhccccccccccccCCCCCHHHHHHHHHhhhcCeeeEeeCCCcceecchhhHHhhhc
Q 023328           60 ---------------------LRSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSM  118 (284)
Q Consensus        60 ---------------------lf~L~~~~~~lG~~Y~~~~Lt~~q~~~L~~l~~~GLvy~~~~~~~~fy~pT~La~~L~~  118 (284)
                                           ||+||+++  +|++|++++||++|++||+||+|+||||++++++++|| |||||++|++
T Consensus       199 ll~yL~~~e~~~~~~~~~l~flf~L~~~~--~g~~Y~~~~ls~~q~~~L~~l~~~GLvy~~~~~~~~fy-pT~La~~l~~  275 (366)
T PF03849_consen  199 LLQYLKMAEARGMDLVEVLSFLFQLSFLE--LGKAYSTEGLSETQKNMLQDLRELGLVYQRKRKSRRFY-PTRLATNLTS  275 (366)
T ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHhcccc--cCCcCcCCCCCHHHHHHHHHHHHCCeEEEecCCCCeEe-chHHHHHHhc
Confidence                                 59999999  99999999999999999999999999999999999999 9999999988


Q ss_pred             CCCc-----------ccccCcceEEEeeCceEEEecCChhHHHHHHHHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHHH
Q 023328          119 SLTD-----------SSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQ  187 (284)
Q Consensus       119 ~~~~-----------~~~~~~g~IIvETNFrvYAYT~S~lqiaiL~lF~~l~~r~Pnlvvg~iTReSv~~Al~~GITA~Q  187 (284)
                      +.+.           ....++|||||||||||||||+||||||||++||++.||||||+||+||||||++|+++||||||
T Consensus       276 ~~~~~~~~~~~~~~~~~~~~~g~iivETNfrvYAYT~s~l~iaiL~lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GIta~q  355 (366)
T PF03849_consen  276 GSSALRSASSALDSSSSSNKEGFIIVETNFRVYAYTNSPLQIAILSLFCELKYRFPNLVVGQITRESVRRALKNGITADQ  355 (366)
T ss_pred             CCCcccccccccccccccccCceEEEEecceEEEecCCHHHHHHHHHHHHHHhcCCCeEEEEEcHHHHHHHHHcCCCHHH
Confidence            7652           12467899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhcCCc
Q 023328          188 IISFLQQNAHP  198 (284)
Q Consensus       188 Ii~fL~~hAHp  198 (284)
                      ||+||++||||
T Consensus       356 Ii~fL~~~aHp  366 (366)
T PF03849_consen  356 IISFLRSHAHP  366 (366)
T ss_pred             HHHHHHhcCCC
Confidence            99999999999

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=99.67  E-value=6.8e-16  Score=128.14  Aligned_cols=117  Identities=22%  Similarity=0.355  Sum_probs=104.5

Q ss_pred             EEEeeCceEEEecCCh--hHHHHHHHHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCC
Q 023328          131 VVVETNFRMYAYSTSK--LHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVP  208 (284)
Q Consensus       131 IIvETNFrvYAYT~S~--lqiaiL~lF~~l~~r~Pnlvvg~iTReSv~~Al~~GITA~QIi~fL~~hAHp~m~~~~p~lP  208 (284)
                      +||++||.|.+.+.+|  -..+.|..||++ .+..+|.+++||+.|+.+|++.|+|+++|+.||+.|+..       .||
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 567999999999999999999999999999999999944       699


Q ss_pred             hhHHHHHHHHHHhcCceeeccceeeccCCCHHHHHHHHHHHHHcCeE
Q 023328          209 ENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGL  255 (284)
Q Consensus       209 ~tV~dQIrLWe~E~~R~~~~~g~Ly~~f~s~~~fe~~~~yA~~~g~l  255 (284)
                      ++|..+|+-|+...+|+++.++.++-.+.+.+..+.+.+..+-.++.
T Consensus        74 ~~v~~~i~~w~~~~g~v~l~~~~~~l~~~d~~~l~~l~~~~~~~~~~  120 (129)
T PF13625_consen   74 QNVEQSIEDWARRYGRVRLYKGAYLLECDDPELLDELLADPELAKLI  120 (129)
T ss_pred             HHHHHHHHHHHHhcCCEEEecCeEEEEECCHHHHHHHHhChhhhhhh
Confidence            99999999999999999999977777999999999988876655543

>TIGR00603 rad25 DNA repair helicase rad25

Probab=97.39  E-value=0.0014  Score=69.19  Aligned_cols=106  Identities=23%  Similarity=0.378  Sum_probs=84.5

Q ss_pred             cceEEEeeCceEEEecCChhH--H-HHHHHHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccC
Q 023328          128 EGFVVVETNFRMYAYSTSKLH--C-EILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRI  204 (284)
Q Consensus       128 ~g~IIvETNFrvYAYT~S~lq--i-aiL~lF~~l~~r~Pnlvvg~iTReSv~~Al~~GITA~QIi~fL~~hAHp~m~~~~  204 (284)
                      +|.|++||        .+|+-  . ..|.-|+|+..|--+|..++||-=|+-.|...|+++++||++|...+-.      
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 DGHIFLES--------FSPLYKQAQDFLVAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLETEDIIEVLGRLSKT------   87 (732)
T ss_pred             CCeEEEEe--------CCccHHHHHHHHHHhcccccChhheEEEeccHHHHHHHHHcCCCHHHHHHHHHHHhCC------
Confidence            46666666        34443  3 7899999999999999999999999999999999999999999999843      


Q ss_pred             CCCChhHHHHHHHHHHhcCceeec--cceeeccCCCHHHHHHHHHH
Q 023328          205 PSVPENVCDQIRLWESDLNRVEMT--PAHYYEEFPSRDVFEAACDY  248 (284)
Q Consensus       205 p~lP~tV~dQIrLWe~E~~R~~~~--~g~Ly~~f~s~~~fe~~~~y  248 (284)
                       .||++|++.|+.+-.-.+++++.  +.--|-+-.+.+..+.+.+.
T Consensus        88 -~~p~~i~~~i~~~~~~ygk~klv~~~~~~~~es~~~~~l~~l~~~  132 (732)
T TIGR00603        88 -PIPKGIIEFIRLCTQSYGKVKLVLKHNRYFVESPHPEVLQRLLKD  132 (732)
T ss_pred             -CCCHHHHHHHHHHHHhcCcEEEEEcCCceEEecCCHHHHHHHHhc
Confidence             79999999999999999999872  22223344555666655543

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=92.11  E-value=0.15  Score=33.22  Aligned_cols=22  Identities=36%  Similarity=0.525  Sum_probs=17.7

Q ss_pred             HHHHHHHcCCCHHHHHHHHhhc
Q 023328          174 SLYNAFENGITAEQIISFLQQN  195 (284)
Q Consensus       174 Sv~~Al~~GITA~QIi~fL~~h  195 (284)
                      =|++|...|||.+||-.||+.+
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=85.14  E-value=12  Score=34.17  Aligned_cols=162  Identities=18%  Similarity=0.220  Sum_probs=102.9

Q ss_pred             CCHHHHHHHHHhhhcCeeeEeeC-CCcceecchhhHHhhhcCCCcccccCcceEEEeeCceEEEecCChhHHHHHHHHHh
Q 023328           79 LSEIQRSMIKDFADLGLVKLQQG-RKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSK  157 (284)
Q Consensus        79 Lt~~q~~~L~~l~~~GLvy~~~~-~~~~fy~pT~La~~L~~~~~~~~~~~~g~IIvETNFrvYAYT~S~lqiaiL~lF~~  157 (284)
                      +++++..+++.|.+-|+|-.-+. +.....   +++-.|..         .|.=++|--++      +|--   +..+.+
T Consensus         1 ~~~~~~~~~~~l~~~~~iaV~r~~~~~~a~---~i~~al~~---------~Gi~~iEitl~------~~~~---~~~I~~   59 (212)
T PRK05718          1 MKNWKTSIEEILRAGPVVPVIVINKLEDAV---PLAKALVA---------GGLPVLEVTLR------TPAA---LEAIRL   59 (212)
T ss_pred             CchhHHHHHHHHHHCCEEEEEEcCCHHHHH---HHHHHHHH---------cCCCEEEEecC------CccH---HHHHHH
Confidence            47888999999999999966543 222222   22222222         35667776643      3433   344455


Q ss_pred             hHhcCCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHhhcCCccccccCCCCCh--hHHHHHHHHHHhcCce
Q 023328          158 IEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAHPRVADRIPSVPE--NVCDQIRLWESDLNRV  225 (284)
Q Consensus       158 l~~r~Pnlvvg---~iTReSv~~Al~~GI-------TA~QIi~fL~~hAHp~m~~~~p~lP~--tV~dQIrLWe~E~~R~  225 (284)
                      +..+||++.||   ++|.+.++.|++.|-       ..+.+|++-..+-.|       .+|-  |..+=...|+.-.+-+
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            56679999999   899999999999984       355899888876544       6665  4466444888888888


Q ss_pred             eeccceeeccCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhh
Q 023328          226 EMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRG  281 (284)
Q Consensus       226 ~~~~g~Ly~~f~s~~~fe~~~~yA~~~g~llw~~~~kr~~~V~~~~h~~v~~f~k~  281 (284)
                      ++.|+-.+-          =.+|-+.+...+   +.-+.+.+.-=.-+.+++|++.
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            885533220          134555544332   3344444434444778888874

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	284
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 = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 43/83 (51%)
Query: 198 PRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLW 257
           P   + +  +P  V DQIRLW+ +L+RV       Y +F +   +     YA+D   LLW
Sbjct: 19  PNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLW 78
Query: 258 EDSKKMRLVVNAEIHMHMREFLR 280
           +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	284
3dom_A	108	RNA polymerase II transcription factor B subunit;	1e-38
3dgp_A	80	RNA polymerase II transcription factor B subunit;	1e-30

>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 (328), Expect = 1e-38
 Identities = 28/100 (28%), Positives = 50/100 (50%), Gaps = 1/100 (1%)

Query: 185 AEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEA 244
           AE+ +   +    P   + +  +P  V DQIRLW+ +L+RV       Y +F +   +  
Sbjct: 7   AEEKLEK-KLELDPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNL 65

Query: 245 ACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK 284
              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 =  108 bits (272), Expect = 1e-30
 Identities = 24/75 (32%), Positives = 40/75 (53%)

Query: 210 NVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNA 269
            V DQIRLW+ +L+RV       Y +F +   +     YA+D   LLW+D KK +  ++ 
Sbjct: 3   TVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISK 62

Query: 270 EIHMHMREFLRGQNK 284
           E +  + +F + + K
Sbjct: 63  EGNSQVLDFAKRKLK 77

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	284
3dom_A	108	RNA polymerase II transcription factor B subunit;	100.0
3dgp_A	80	RNA polymerase II transcription factor B subunit;	99.97

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

Probab=100.00  E-value=2e-34  Score=233.92  Aligned_cols=88  Identities=30%  Similarity=0.591  Sum_probs=72.4

Q ss_pred             CccccccCCCCChhHHHHHHHHHHhcCceeeccceeeccCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHH
Q 023328          197 HPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMR  276 (284)
Q Consensus       197 Hp~m~~~~p~lP~tV~dQIrLWe~E~~R~~~~~g~Ly~~f~s~~~fe~~~~yA~~~g~llw~~~~kr~~~V~~~~h~~v~  276 (284)
                      .|++....|+|||||+|||||||.||||+++++||||++|.|+++|+.+++||+++|+|+|+|+.+|+|||+.+||++|+
T Consensus        18 ~~~~~~~~p~lPpTVvDQIrLWE~ErnRl~~~~G~LY~dF~s~~efe~v~~yA~e~gvLlW~d~~kr~~~Vs~egh~~vk   97 (108)
T 3dom_A           18 DPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISKEGNSQVL   97 (108)
T ss_dssp             --------------CCCHHHHHHHHHTTCEEEEEEEEECCSCHHHHHHHHHHHHHHTCEEEEEGGGTEEEEEGGGHHHHH
T ss_pred             CcccccCCCCCCCcHHHHHHHHHHhhCceeccceEEEecCCCHHHHHHHHHHHHHcCeEEEecCCccEEEEeccchHHHH
Confidence            35555567999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhccC
Q 023328          277 EFLRGQNK  284 (284)
Q Consensus       277 ~f~k~~~~  284 (284)
                      +|||++++
T Consensus        98 ~f~Kr~~~  105 (108)
T 3dom_A           98 DFAKRKLK  105 (108)
T ss_dssp             HHHHHHC-
T ss_pred             HHHHHHHh
Confidence            99999875

>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=2.2e-32  Score=211.72  Aligned_cols=76  Identities=32%  Similarity=0.593  Sum_probs=61.7

Q ss_pred             hhHHHHHHHHHHhcCceeeccceeeccCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhhccC
Q 023328          209 ENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK  284 (284)
Q Consensus       209 ~tV~dQIrLWe~E~~R~~~~~g~Ly~~f~s~~~fe~~~~yA~~~g~llw~~~~kr~~~V~~~~h~~v~~f~k~~~~  284 (284)
                      |||+|||||||.|||||++++|+||++|+|+++|+.+++||+++|+|||+|+.+|+|||+.+||++||+|||++++
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

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

No hit with probability above 80.00