Citrus Sinensis ID: 020247

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------33
Protein Sequence
MVELCQGNQCLLVLLQGFQPWRTLRPMPLDNGSSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQNK
Secondary Structure (PSIPRED)
ccccccccccccccccccccccEEEcccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHcccEEEEccccccEEEccHHHHHHHccccccccccccEEEEEEccEEEEccccHHHHHHHHHHHHHHHcccccEEEEEcHHHHHHHHHccccHHHHHHHHHHccccccccccccccccHHHHHHHHHHHcccEEEcccEEEcccccHHHHHHHHHHHHHccEEEEEcccccEEEEEccccHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccEEcccccEEEEEEccHcHHHHHHHHEccccccccccccccccHHHHHHHHHcccccccccccEEcHHHHHHHHccHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHcccEEEEcccccccEcccEEEEEEEccccccccccccEEEEEEcEEEEEEcccHHHHHHHHHHHHHHHHcccEEEEEEcHHHHHHHHHccccHHHHHHHHHHcccHHHHcccccccccHHHHHHHHHHHHccEEEcccEEEcccccHHHHHHHHHHHHHcccEEEEccccEEEEEccccHHHHHHHHHHccc
Coil and Loop (DISEMBL)
mvelcqgnQCLLVLLQgfqpwrtlrpmpldngsstqaerptnfssSMMKVFQRGllsrrdkeaprltesGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLqqgrkenwfiptklatnlsmsltdssarkegFIVVETNFRMYAYSTSKLHCEILRLFSKVeyqlpnlivgAITKESLYNAFENGITAEQIISFLQqnahprvadrmpsvpenvCDQIRLWESDlnrvemtpahyydefpsrdvFEAACDYArdqsgllwedpkkMRLVVKAEIHMHMREFLRGQNK
Flexible Loop (DISEMBL)
MVELCQGNQCLLVLLQGFQPWRTLRPMPLDNGSStqaerptnfsssMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLatnlsmsltdssarkEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPahyydefpsrDVFEAACDYARdqsgllwedpkKMRLVVKAEIHMHMREFLRGQNK
Low Complexity Region (SEG)
MVELCQGNQCLLVLLQGFQPWRTLRPMPLDNGSSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQNK
Disordered region (IsUnstruct)
***LCQGNQCLLVLLQGFQPWRTL********************************************SGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMR********
Disordered Region (DISOPRED)
*******NQCLLVLLQGFQPWRTLRPMP********************KVFQRG***************GFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLAT*****************VVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPR*****PSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ**
Disordered Region (DISEMBL)
MVELCQGNQCLLVLLQGFQPWRTLRPMPLDNGSSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQNK
Disordered Region (DISPRO)
MVELCQGNQCLLVLLQGFQPWRTLRPMPLDN**********NFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVELCQGNQCLLVLLQGFQPWRTLRPMPLDNGSSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQNK
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	329	2.2.26 [Sep-21-2011]
P60027	462	General transcription fac	yes	no	0.838	0.597	0.389	1e-54
Q92759	462	General transcription fac	yes	no	0.838	0.597	0.389	1e-54
O70422	463	General transcription fac	yes	no	0.838	0.596	0.389	2e-54
Q6BZX4	467	RNA polymerase II transcr	yes	no	0.866	0.610	0.332	2e-48
P87303	447	RNA polymerase II transcr	yes	no	0.848	0.624	0.342	4e-47
Q6CLR2	496	RNA polymerase II transcr	yes	no	0.823	0.546	0.315	3e-43
Q54C29	483	General transcription fac	yes	no	0.814	0.554	0.363	1e-42
Q6BGW8	515	RNA polymerase II transcr	yes	no	0.820	0.524	0.312	2e-42
Q75B51	514	RNA polymerase II transcr	yes	no	0.784	0.501	0.319	6e-40
Q6FP41	504	RNA polymerase II transcr	yes	no	0.799	0.521	0.302	2e-39

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

 Score =  213 bits (543), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 109/280 (38%), Positives = 176/280 (62%), Gaps = 4/280 (1%)

Query: 52  QRGLL-SRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLEL 110
           Q GL+ S    E P +T +GFQFLL+DT AQLWY + +Y+  +Q RG++  +++SFL +L
Sbjct: 181 QAGLMKSTEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQL 240

Query: 111 SFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS-- 168
           SF   G+ Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +  
Sbjct: 241 SFSTLGKDYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGG 299

Query: 169 SARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGI 228
           +  + GFIVVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GI
Sbjct: 300 TVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGI 359

Query: 229 TAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFE 288
           TA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE
Sbjct: 360 TAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFE 419

Query: 289 AACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQN 328
               +AR+   L++E+  K  +VV    H  ++ F + Q 
Sbjct: 420 LLLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQK 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 =  213 bits (543), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 109/280 (38%), Positives = 176/280 (62%), Gaps = 4/280 (1%)

Query: 52  QRGLL-SRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLEL 110
           Q GL+ S    E P +T +GFQFLL+DT AQLWY + +Y+  +Q RG++  +++SFL +L
Sbjct: 181 QAGLMKSTEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQL 240

Query: 111 SFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS-- 168
           SF   G+ Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +  
Sbjct: 241 SFSTLGKDYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGG 299

Query: 169 SARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGI 228
           +  + GFIVVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GI
Sbjct: 300 TVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGI 359

Query: 229 TAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFE 288
           TA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE
Sbjct: 360 TAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFE 419

Query: 289 AACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQN 328
               +AR+   L++E+  K  +VV    H  ++ F + Q 
Sbjct: 420 LLLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQK 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 =  213 bits (541), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 109/280 (38%), Positives = 176/280 (62%), Gaps = 4/280 (1%)

Query: 52  QRGLL-SRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLEL 110
           Q GL+ S    E P +T +GFQFLL+DT AQLWY + +Y+  +Q RG++  +++SFL +L
Sbjct: 182 QAGLMKSTEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQL 241

Query: 111 SFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS-- 168
           SF   G+ Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +  
Sbjct: 242 SFSTLGKDYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGG 300

Query: 169 SARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGI 228
           +  + GFIVVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GI
Sbjct: 301 TVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGI 360

Query: 229 TAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFE 288
           TA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE
Sbjct: 361 TAQQIIHFLRTRAHPVMLKQNPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFE 420

Query: 289 AACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQN 328
               +AR+   L++E+  K  +VV    H  ++ F + Q 
Sbjct: 421 LLLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQK 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|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 =  193 bits (490), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 101/304 (33%), Positives = 173/304 (56%), Gaps = 19/304 (6%)

Query: 44  SSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADL 103
           S  ++ + +   L   ++   R+T +GFQFLL D NAQ+W ++ +Y++ S+   ++  D+
Sbjct: 158 SDGVLNLLKHSGLMEPERGGLRITNAGFQFLLQDVNAQIWTLLLQYLNMSEYLQMDPVDV 217

Query: 104 ISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSM 163
           ++F+  L     G+ Y+L+ LSE QK M++D  D G+V  Q+      F PT+LAT L+ 
Sbjct: 218 LNFIFMLGSLELGQDYSLSALSETQKHMLEDLRDYGIV-YQRKASSRRFYPTRLATTLTS 276

Query: 164 ------------------SLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEY 205
                             +++ S A   GFI++ETNFR+YAY+ S L   +L LF  ++ 
Sbjct: 277 ETAALRTASQSMEAATQDTISSSVAADSGFIILETNFRLYAYTESPLQIAVLNLFVNLKT 336

Query: 206 QLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWES 265
           +  N++ G I ++S+  A  NGITAEQII++L  +AHPR+      +P  V DQI+LW+ 
Sbjct: 337 RFANMVTGQINRDSVRFALSNGITAEQIITYLSVHAHPRMKGMEHVLPPTVVDQIKLWQL 396

Query: 266 DLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLR 325
           +++R+  T  + + EF + D ++    YA++   LL+E+P K + V        + EF++
Sbjct: 397 EMDRIRATDGYLFSEFKNFDEYKDVSTYAKELGVLLYENPGKRKFVSTLAGSQQIVEFVK 456

Query: 326 GQNK 329
            +N+
Sbjct: 457 RRNQ 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|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 =  188 bits (478), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 98/286 (34%), Positives = 165/286 (57%), Gaps = 7/286 (2%)

Query: 46  SMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLIS 105
            ++ + +RG L    K   R+T +GFQFLL D NAQ+W ++ +Y+  S++  ++   ++ 
Sbjct: 158 GVLSLLKRGGLMSGPKNQLRITRAGFQFLLQDINAQIWTLLLDYLKLSEDTHMDPVQVLH 217

Query: 106 FLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSL 165
           FL  L     G AY+++ L++ Q+ M++D  + GLV  Q+      F PT+LAT L+   
Sbjct: 218 FLFMLGSLDLGRAYSVDFLTDTQQIMLEDLREYGLV-YQRKITSKRFYPTRLATGLTTDY 276

Query: 166 TDSSARK------EGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKES 219
                ++      +GFI+VETN+R+YAY++S L   I+ LF+ +  +  NL+VG IT++S
Sbjct: 277 RSLHGKQSENDDDKGFIIVETNYRLYAYTSSPLQIAIIGLFANLRARFSNLVVGVITRDS 336

Query: 220 LYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYD 279
           +  A  NGI AEQII++L  +AHP++   +P +P  + DQI LWE + NR+  TP   + 
Sbjct: 337 IRRALMNGIAAEQIITYLTTHAHPQMRSNVPLLPPTLVDQIYLWELEKNRLRATPGILFR 396

Query: 280 EFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLR 325
           +F +   F+ A +YA++   L+W+   K    +       M  +L+
Sbjct: 397 DFLTDSGFDQAVEYAKELGVLVWDSSLKRMFFITTTGAQPMIAYLK 442

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

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

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

 Score =  176 bits (445), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 101/320 (31%), Positives = 165/320 (51%), Gaps = 49/320 (15%)

Query: 54  GLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFH 113
           GL+   +    ++T  GFQFLL D NAQ+W ++ +Y+  ++   ++  D+++F+  L   
Sbjct: 173 GLMEEAEYGELKITNQGFQFLLQDVNAQMWTLLLQYLKMAESLQMDPVDVLNFIFMLGAL 232

Query: 114 VAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLAT-------------- 159
             G+AY  + LS  Q++M++D  D GL+   Q      F PT+LAT              
Sbjct: 233 QLGKAYKCDQLSNTQRTMLQDMRDYGLIYQNQSDYAK-FYPTRLATLLTSDTKAFRSASV 291

Query: 160 ---------NLSMSLTDSSARKE-------GFIVVETNFRMYAYSTSKLHCEILRLFSKV 203
                    N + ++   S + E       G +++ETNF++Y+YS S L   IL LF  +
Sbjct: 292 ALDSVLNKANETTAVEGDSGQDETTERTQDGALIIETNFKLYSYSNSPLQIAILSLFVHL 351

Query: 204 EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPR------------------V 245
           + +  N++ G +T+ES+ NA  NGITAEQII++L+ +AHPR                  V
Sbjct: 352 KSRFANMVTGQLTRESVRNALLNGITAEQIIAYLETHAHPRMRRLAEENLSKKLELDPTV 411

Query: 246 ADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDP 305
            + +  +P  V DQIRLW+ +L+R+     + Y +F S   ++   DYA+D   LLW++ 
Sbjct: 412 KETLQVLPPTVVDQIRLWQLELDRIISYDGYLYTDFESYQEYQTVADYAKDIGVLLWQNE 471

Query: 306 KKMRLVVKAEIHMHMREFLR 325
           KK    V  E +  + +F R
Sbjct: 472 KKKMFFVSTEGNSQVLDFHR 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 =  174 bits (440), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 104/286 (36%), Positives = 171/286 (59%), Gaps = 18/286 (6%)

Query: 56  LSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQER----GINQADLISFLLELS 111
           L++++ +   +T  GF+FLL D   Q+W ++  Y+ + +++      ++ DL+SFL  LS
Sbjct: 196 LTKQEGDGLSITSEGFKFLLKDVYTQIWTLLIVYLDDLEKKKGKGSGSRNDLLSFLFRLS 255

Query: 112 FHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLS----MSLTD 167
           F   G  Y ++ LSE QK  +      GL+ ++       F PT+L  +L+    +SL  
Sbjct: 256 FLNLGRGYLVSELSEQQKEYLFALKQFGLIYMRTD-SSILFYPTRLIISLTTGKTLSLIQ 314

Query: 168 S-------SARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESL 220
           S       + +++G+IV+ETN+R+YAY++S L   +L LF K+ Y+LPNL VG IT+ES+
Sbjct: 315 SISSERTQTQKEQGYIVLETNYRLYAYTSSSLQISLLSLFVKMLYRLPNLAVGIITRESI 374

Query: 221 YNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDE 280
             A  +GITA+QII F++ N+HP  A+    +P+ V +QI LWE++ NR+  T +  Y+ 
Sbjct: 375 RTALIHGITADQIIDFVRHNSHPNAANSGQPIPDVVAEQILLWEAERNRITYTKSVLYNS 434

Query: 281 FPSRDVFEAACDYARDQSGLLW-EDPKKMRLVVKAEIHMHMREFLR 325
           FP+ D + A   +A++Q   +W  DP K  LVVK E +  +R F++
Sbjct: 435 FPTNDCYIATLKFAKEQDYYIWSHDPLKT-LVVKEEGNDPIRNFIK 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|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 =  173 bits (438), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 108/346 (31%), Positives = 174/346 (50%), Gaps = 76/346 (21%)

Query: 40  PTNFSSSMMKVFQRGLLSRRDKEAPRL--TESGFQFLLMDTNAQLWYIVREYISNSQERG 97
           P+N   S++K    GL+   +K   RL  T SGFQFLL D NAQ+W ++ +Y++ +Q+  
Sbjct: 161 PSNSVLSLLK--SGGLMEGTNKGGNRLNITNSGFQFLLQDINAQIWTLLLQYLNLTQDLN 218

Query: 98  INQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKL 157
           ++  D+++F+  L     G+ Y +++LSE Q SM+ D  D GL+  Q+      F PT+L
Sbjct: 219 MDPVDVLNFIFILGSLELGKGYTVSSLSETQISMLADLRDYGLI-YQRSENSERFYPTRL 277

Query: 158 ATNLSMSLTDSSARK---------------------------EGFIVVETNFRMYAYSTS 190
           AT L+   +DS+A K                           +G I++ETNF++YAY+ S
Sbjct: 278 ATTLT---SDSAALKSPSMAMEQALESTTETEEQQNLASNSNQGTIILETNFKIYAYTNS 334

Query: 191 KLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVA---- 246
            L   IL LF  ++ +  N++ G IT+ES+ NA  NGITA+QII FL+ +AH ++     
Sbjct: 335 PLEIAILNLFVHLKTRFSNMVCGQITRESIRNALYNGITADQIIKFLETHAHSQMKILAK 394

Query: 247 -------------------------------------DRMPSVPENVCDQIRLWESDLNR 269
                                                 ++  +P  V DQI+LW+ +L+R
Sbjct: 395 ERLDKKIEFDTSNNINTAGGAPQSQMMTNENGTTVAQHKLEVLPPTVVDQIKLWQLELDR 454

Query: 270 VEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAE 315
           ++    + + +F S+  FEA  +YA +   LLW +  KM+  V  +
Sbjct: 455 IQTFEGYLFKDFASQQEFEALSNYASEIGVLLWSNKSKMKFFVTKD 500

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

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

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

 Score =  164 bits (416), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 102/319 (31%), Positives = 165/319 (51%), Gaps = 61/319 (19%)

Query: 65  RLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTL 124
           ++T  GFQFLL D NAQ+W ++ +Y++ ++   ++  D+++ +  +     G+AY++  L
Sbjct: 194 KITNEGFQFLLQDANAQIWTLLLQYLTMAETFQMDPVDVLNLIFMIGALELGKAYSVVGL 253

Query: 125 SEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLS---MSLTDSSA--------RKE 173
           SE QK+M++D  D GLV  Q+    + F PT+LAT L+   +S+  +S         R E
Sbjct: 254 SETQKTMLQDLRDYGLV-FQKQSNLSKFYPTRLATMLTSDVVSIRSASGAVNSVLRQRAE 312

Query: 174 GF--------------------------IVVETNFRMYAYSTSKLHCEILRLFSKVEYQL 207
           G                           ++VETNF++Y+YS S L   IL LF  ++ + 
Sbjct: 313 GVDGKVLNGTALGDDDLQAGGEGALDGALIVETNFKLYSYSNSPLQIAILSLFIHLKTRF 372

Query: 208 PNLIVGAITKESLYNAFENGITAEQIISFLQQNAHP---RVA---------------DRM 249
            N++ G IT+ES+  A  NGITA+QII++++ +AHP   R+A               D +
Sbjct: 373 QNMVTGQITRESIRRALHNGITADQIIAYMETHAHPQMRRLAGDNLEKKLELDPNCRDTL 432

Query: 250 PSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMR 309
             +P  V DQI+LW+ +L+R+     + + +F +   ++    YARD   LLW D KK  
Sbjct: 433 QVLPPTVVDQIKLWQLELDRIISYDGYLFRDFDNLQEYQVLAQYARDIGVLLWSDDKKKM 492

Query: 310 LVVKAE-----IHMHMREF 323
             V  E     I  H R+F
Sbjct: 493 FFVSKEGNAQVIDFHKRKF 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 =  162 bits (411), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 95/314 (30%), Positives = 161/314 (51%), Gaps = 51/314 (16%)

Query: 66  LTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLS 125
           +T  GFQFLL + N+Q+W ++ +Y+  ++   ++   +++F+  L     G+AY+   LS
Sbjct: 188 ITNEGFQFLLQEVNSQIWSLLLQYLKLAESLHMDPVHVLNFIFMLGALETGKAYSTENLS 247

Query: 126 EIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLS----------------MSLTDSS 169
           E Q  M+ D  D GLV  Q+    N F PT+LA  L+                ++  D +
Sbjct: 248 ETQLKMLLDMRDYGLV-FQKTSNPNIFYPTRLAQMLTSDTKSMRTASGAMESVLNKPDDA 306

Query: 170 AR----------------KEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVG 213
           A+                ++G +++ETNF++Y+Y  S L   IL LF  ++ +  N++ G
Sbjct: 307 AKSTDDKYDSLEGKAEDIQDGALIIETNFKLYSYCNSPLQIAILSLFVHLKSRFANMVAG 366

Query: 214 AITKESLYNAFENGITAEQIISFLQQNAHPRV------------------ADRMPSVPEN 255
            IT+ES+  A  NGITA+Q+I++L+ +AHP++                   D +  +P  
Sbjct: 367 QITRESIRRALINGITADQVIAYLESHAHPQMRRLAEEKLQKKLELDPNCKDPLQVLPPT 426

Query: 256 VCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAE 315
           V DQI+LW+ +L+RV       Y +F +   F   C YA+D   LLW+D +K +L V  E
Sbjct: 427 VVDQIKLWQLELDRVLTYEGSLYIDFDTAQDFNMLCKYAQDIGALLWKDDRKRKLFVSRE 486

Query: 316 IHMHMREFLRGQNK 329
            +  + E+ + + K
Sbjct: 487 GNAQVLEYAKRKIK 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)

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	329
255556021	451	tfiih, polypeptide, putative [Ricinus co	0.896	0.654	0.844	1e-150
224077128	449	predicted protein [Populus trichocarpa]	0.896	0.657	0.830	1e-149
147854406	451	hypothetical protein VITISV_005315 [Viti	0.890	0.649	0.843	1e-149
449433857	451	PREDICTED: general transcription factor	0.896	0.654	0.823	1e-146
357461579	452	General transcription factor IIH subunit	0.896	0.652	0.793	1e-141
358346685	451	General transcription factor IIH subunit	0.896	0.654	0.789	1e-140
297800414	452	hypothetical protein ARALYDRAFT_493174 [	0.902	0.657	0.771	1e-138
356548733	451	PREDICTED: general transcription factor	0.896	0.654	0.779	1e-138
356521347	451	PREDICTED: general transcription factor	0.896	0.654	0.772	1e-138
42566894	452	transcription initiation factor TFIIH su	0.902	0.657	0.767	1e-138

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

 Score =  538 bits (1385), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 249/295 (84%), Positives = 282/295 (95%)

Query: 33  SSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISN 92
           +S  AER TNFSSSMMK+FQRGLL++RDKEAPRLTESGFQFLLMDTNAQLWYI+REYISN
Sbjct: 156 NSGHAERSTNFSSSMMKIFQRGLLTQRDKEAPRLTESGFQFLLMDTNAQLWYIIREYISN 215

Query: 93  SQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWF 152
           S+ERG++ ADLISFLLELSFH+ GEAYN+  L+E Q++MIKD ADLGLVKLQQGRKE+WF
Sbjct: 216 SEERGLDSADLISFLLELSFHITGEAYNMIMLTEFQRNMIKDLADLGLVKLQQGRKESWF 275

Query: 153 IPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIV 212
           IPTKLATNLSMSLTDSS+RK+GF+VVETNFRMYAYSTSKLHCEI+RLFS+VEYQLPNL+V
Sbjct: 276 IPTKLATNLSMSLTDSSSRKQGFVVVETNFRMYAYSTSKLHCEIMRLFSRVEYQLPNLVV 335

Query: 213 GAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEM 272
           GA+TKESLY+AFENGITAEQIISFLQQNAHPRVA+R+PSVPENV DQIRLWESD+NRVEM
Sbjct: 336 GAMTKESLYSAFENGITAEQIISFLQQNAHPRVAERIPSVPENVTDQIRLWESDMNRVEM 395

Query: 273 TPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ 327
           TPAH YDEFPSRDVFEAAC++ARD +GLLWED K+MR+VVKAEIH++MRE+LRGQ
Sbjct: 396 TPAHLYDEFPSRDVFEAACNFARDWNGLLWEDSKRMRMVVKAEIHLNMREYLRGQ 450

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  533 bits (1373), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 245/295 (83%), Positives = 281/295 (95%)

Query: 33  SSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISN 92
           SS QAE+PT+ SSSMMK+FQRGLLS+RD++APRLTE GFQFLLMDTNAQLWYI+REYI+N
Sbjct: 154 SSGQAEKPTSLSSSMMKIFQRGLLSQRDRDAPRLTEGGFQFLLMDTNAQLWYIIREYITN 213

Query: 93  SQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWF 152
           S+ERG   ADLISFLLELSFHV GEAYN+NTL+EIQ++ IKD A+LGLVKLQQGRKE+WF
Sbjct: 214 SEERGTEPADLISFLLELSFHVTGEAYNMNTLTEIQRNTIKDLAELGLVKLQQGRKESWF 273

Query: 153 IPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIV 212
           IPTKLATNLS+SLTDSS+RK+G++VVETNFR+YAYS+SKLHCEILRLFSK+EYQLPNLIV
Sbjct: 274 IPTKLATNLSVSLTDSSSRKQGYVVVETNFRLYAYSSSKLHCEILRLFSKIEYQLPNLIV 333

Query: 213 GAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEM 272
           GAITKESLY AFENGIT++QIISFLQQNAHPRVA+R+PSVPENV DQIRLWE+DLNRVE+
Sbjct: 334 GAITKESLYTAFENGITSDQIISFLQQNAHPRVAERLPSVPENVTDQIRLWEADLNRVEI 393

Query: 273 TPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ 327
           TP+H+YDEFPSRD FEAACD+AR+ +GLLWED KKMR+VVKAEIHM+MREFLRGQ
Sbjct: 394 TPSHFYDEFPSRDTFEAACDFAREWNGLLWEDSKKMRVVVKAEIHMNMREFLRGQ 448

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  532 bits (1370), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 247/293 (84%), Positives = 277/293 (94%)

Query: 33  SSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISN 92
           SSTQ E+ TNFSSS+MKVFQRGLL++R+KEAPRLTESGFQFLLMDTNAQLWYI+REYISN
Sbjct: 156 SSTQTEKLTNFSSSLMKVFQRGLLTQREKEAPRLTESGFQFLLMDTNAQLWYIMREYISN 215

Query: 93  SQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWF 152
           S+ERG++ ADLISFLLELSFHV GEAYN+NTL+E Q++ IKD  DLGLVKLQQGRKE+WF
Sbjct: 216 SEERGVDPADLISFLLELSFHVTGEAYNINTLTEFQRNTIKDLVDLGLVKLQQGRKESWF 275

Query: 153 IPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIV 212
           IPTKLATNLSMSL+D+S+RK+GF+VVETNFR+YAYS+SKLHCEILRLFS+VEYQLPNLIV
Sbjct: 276 IPTKLATNLSMSLSDTSSRKQGFVVVETNFRLYAYSSSKLHCEILRLFSRVEYQLPNLIV 335

Query: 213 GAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEM 272
           GAITKESLYNAFENGITAEQIISFLQQNAHPRVA+R P+VPENV DQIRLWE+DLNRVE 
Sbjct: 336 GAITKESLYNAFENGITAEQIISFLQQNAHPRVAERTPAVPENVTDQIRLWETDLNRVET 395

Query: 273 TPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLR 325
            P+H YDEFPSRDVFEAACD+AR+  GLLWED KKMRLVVKAEIH+HMRE+LR
Sbjct: 396 MPSHLYDEFPSRDVFEAACDFAREYGGLLWEDSKKMRLVVKAEIHLHMREYLR 448

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  523 bits (1347), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 243/295 (82%), Positives = 278/295 (94%)

Query: 33  SSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISN 92
           +S QAE+P+N SSS+MKVFQ+GLLS+RDKEAPRLTESGFQFLLM+TNAQLWYI+REYISN
Sbjct: 156 NSGQAEKPSNISSSVMKVFQKGLLSQRDKEAPRLTESGFQFLLMETNAQLWYIIREYISN 215

Query: 93  SQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWF 152
           ++ERG++ ADLISFLLELSFHV GEAY+++TLS+ Q+  IKD ADLGLVKLQQGRKE+WF
Sbjct: 216 AEERGVDPADLISFLLELSFHVTGEAYDIDTLSDEQRYAIKDLADLGLVKLQQGRKESWF 275

Query: 153 IPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIV 212
           IPTKLATNLSMSL DSS+RK GF+VVETNFRMYAYSTSKLHCEILRLFS++EYQLPNLIV
Sbjct: 276 IPTKLATNLSMSLADSSSRKLGFVVVETNFRMYAYSTSKLHCEILRLFSRIEYQLPNLIV 335

Query: 213 GAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEM 272
           GAITKESLYNAF+NGITAEQI++FLQQNAHPRVA+R+PSVPENV DQIRLWESDLNRV++
Sbjct: 336 GAITKESLYNAFKNGITAEQIVTFLQQNAHPRVAERIPSVPENVTDQIRLWESDLNRVDI 395

Query: 273 TPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ 327
           TPAH+YDEFPSR+VFEAACDYAR+ +GLLWED K +RLVVKA+IH HMRE LR Q
Sbjct: 396 TPAHFYDEFPSREVFEAACDYAREWNGLLWEDSKNLRLVVKADIHTHMREHLRRQ 450

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  506 bits (1302), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 234/295 (79%), Positives = 273/295 (92%)

Query: 33  SSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISN 92
           S +  ++  N SSS+MKVFQR LLS+RD+EAP+LTESGFQFLLMDTNAQLWYI+REYI+N
Sbjct: 157 SPSHVDKTLNISSSLMKVFQRRLLSQRDREAPKLTESGFQFLLMDTNAQLWYIIREYITN 216

Query: 93  SQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWF 152
           S+ERG++  DLISF+LELSFHV GEAYN+NTL+E Q+++IKD ADLGLVKLQQGRKE+WF
Sbjct: 217 SEERGVDAGDLISFMLELSFHVIGEAYNINTLTEFQRNIIKDLADLGLVKLQQGRKESWF 276

Query: 153 IPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIV 212
           IPTKLATNLS+S+T+SS+RKEGF+VVETNFR+YAYSTSKLHCEILRLFS+VEYQLPNLIV
Sbjct: 277 IPTKLATNLSVSMTESSSRKEGFVVVETNFRVYAYSTSKLHCEILRLFSRVEYQLPNLIV 336

Query: 213 GAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEM 272
           GAITKESLYNAF+NGITA+QI+SFL+QNAHPRVA R+P+VPENV DQIRLWESDLNRVEM
Sbjct: 337 GAITKESLYNAFDNGITADQIVSFLRQNAHPRVAQRVPAVPENVTDQIRLWESDLNRVEM 396

Query: 273 TPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ 327
           T A+YYDEFPSRDVFE ACD AR+ SGLLWED KKM LVVK+E+H ++R+FLR Q
Sbjct: 397 TEAYYYDEFPSRDVFEGACDCAREWSGLLWEDSKKMHLVVKSEVHTYVRDFLRRQ 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 =  504 bits (1298), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 233/295 (78%), Positives = 272/295 (92%)

Query: 33  SSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISN 92
           S +  ++  N SSS+MKVFQR LLS+RD+EAP+LTESGFQFLLMDTNAQLWYI+REYI+N
Sbjct: 156 SPSHVDKTLNISSSLMKVFQRRLLSQRDREAPKLTESGFQFLLMDTNAQLWYIIREYITN 215

Query: 93  SQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWF 152
           S+ERG++  DLISF+LELSFHV GEAYN+NTL+E Q+++IKD ADLGLVKLQQGRKE+WF
Sbjct: 216 SEERGVDAGDLISFMLELSFHVIGEAYNINTLTEFQRNIIKDLADLGLVKLQQGRKESWF 275

Query: 153 IPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIV 212
           IPTKLATNLS+S+T+SS+RKEGF+VVETNFR+YAYSTSKLHCEILRLFS+VEYQLPNLIV
Sbjct: 276 IPTKLATNLSVSMTESSSRKEGFVVVETNFRVYAYSTSKLHCEILRLFSRVEYQLPNLIV 335

Query: 213 GAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEM 272
           GAITKESLYNAF+NGITA+QI+SF +QNAHPRVA R+P+VPENV DQIRLWESDLNRVEM
Sbjct: 336 GAITKESLYNAFDNGITADQIVSFFRQNAHPRVAQRIPAVPENVTDQIRLWESDLNRVEM 395

Query: 273 TPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ 327
           T A+YYDEFPSRDVFE ACD AR+ SGLLWED KKM LVVK+E+H ++R+FLR Q
Sbjct: 396 TEAYYYDEFPSRDVFEGACDCAREWSGLLWEDSKKMHLVVKSEVHTYVRDFLRRQ 450

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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 =  498 bits (1283), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 229/297 (77%), Positives = 267/297 (89%)

Query: 33  SSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISN 92
           +S Q E+ T  SSSMM++FQRGLLS+RDK+ PRLTESGFQFLLMDTNAQLWYI+REYISN
Sbjct: 156 NSGQGEKLTGISSSMMRIFQRGLLSQRDKDGPRLTESGFQFLLMDTNAQLWYIIREYISN 215

Query: 93  SQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWF 152
           ++ER +  ADLISFLLELSFHV GEAYN NTL+E+Q + +KD ADLGLVKLQQGRK++WF
Sbjct: 216 AEERDVEPADLISFLLELSFHVTGEAYNSNTLTEVQNNTLKDLADLGLVKLQQGRKDSWF 275

Query: 153 IPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIV 212
           IPTKLATNLS+SL DSSARKEGF+V+ETNFRMYAYSTSKL CEILRLF+++EYQLPNLI 
Sbjct: 276 IPTKLATNLSVSLADSSARKEGFVVMETNFRMYAYSTSKLQCEILRLFARIEYQLPNLIA 335

Query: 213 GAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEM 272
            AITKESLYNAF+NGIT++QII+FLQQN+HPR ADR+PS+PENV DQIRLWE+DL R+EM
Sbjct: 336 CAITKESLYNAFDNGITSDQIITFLQQNSHPRCADRVPSIPENVTDQIRLWETDLKRIEM 395

Query: 273 TPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQNK 329
           T AH+YDEFPS+DVFEAACD+AR+  GLLWED K+MRLVVK+E+H  MREFL  Q K
Sbjct: 396 TQAHFYDEFPSKDVFEAACDFAREWGGLLWEDSKRMRLVVKSEVHNQMREFLHNQTK 452

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  498 bits (1281), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 230/295 (77%), Positives = 270/295 (91%)

Query: 33  SSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISN 92
           S +Q E+P N SSS+MKVFQR +LS RDKEAP+LTESGFQFLLMDTNAQLWYI+REYISN
Sbjct: 156 SPSQVEKPLNISSSLMKVFQRRILSYRDKEAPKLTESGFQFLLMDTNAQLWYIIREYISN 215

Query: 93  SQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWF 152
           S++RG++ ADLISF+LELSFH  GEAY+++TL+  Q+++I D ADLGLVK+QQGRK +WF
Sbjct: 216 SEDRGVDAADLISFMLELSFHDIGEAYSVDTLTSFQRTIINDLADLGLVKIQQGRKGSWF 275

Query: 153 IPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIV 212
           IPTKLATNLSMSL DSS+RK+GF+VVETNFR+YAYSTSKLHCEILRLFS+VEYQLPNLIV
Sbjct: 276 IPTKLATNLSMSLADSSSRKQGFVVVETNFRVYAYSTSKLHCEILRLFSRVEYQLPNLIV 335

Query: 213 GAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEM 272
           GAITKESLY+AFENGITAEQII+FLQQNAHPRVA+R+PSVPENV +QIRLWE+DLNRVEM
Sbjct: 336 GAITKESLYSAFENGITAEQIITFLQQNAHPRVAERIPSVPENVTEQIRLWEADLNRVEM 395

Query: 273 TPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ 327
           T A+YYDEFPSRDVFE ACD AR+ +GLLWED KKM +VVK E+H ++R++LR Q
Sbjct: 396 TDAYYYDEFPSRDVFEGACDCAREWNGLLWEDSKKMHMVVKTEVHQYVRDYLRRQ 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 =  497 bits (1279), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 228/295 (77%), Positives = 270/295 (91%)

Query: 33  SSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISN 92
           S +Q E+P N SSS+MKVFQR +LS RDKEAP+LTESGFQFLLMDTNAQLWYI+REYISN
Sbjct: 156 SPSQVEKPLNISSSLMKVFQRRILSHRDKEAPKLTESGFQFLLMDTNAQLWYIIREYISN 215

Query: 93  SQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWF 152
           S++RG++ ADLISF+LELSFHV GEAY+++TL+  Q+++I D ADLGLVK+QQGRK +WF
Sbjct: 216 SEDRGVDAADLISFMLELSFHVIGEAYSVDTLTSFQRTIINDLADLGLVKIQQGRKGSWF 275

Query: 153 IPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIV 212
           IPTKLATNLSMSL DSS+RK+GF+VVETNFR+YAYSTSKLHCEILRLFS+VEYQLPNLIV
Sbjct: 276 IPTKLATNLSMSLADSSSRKQGFVVVETNFRVYAYSTSKLHCEILRLFSRVEYQLPNLIV 335

Query: 213 GAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEM 272
           GAITKESLY+A+ENGITAEQI++FLQQNAHPRVA+R+PSVPENV +QIRLWE+DLNRVEM
Sbjct: 336 GAITKESLYSAYENGITAEQIVTFLQQNAHPRVAERVPSVPENVTEQIRLWEADLNRVEM 395

Query: 273 TPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ 327
           T  +YYDEFPSRDVFE ACD AR+ +GLLWED KKM +VVK E+H ++R++LR Q
Sbjct: 396 TDTYYYDEFPSRDVFEGACDCAREWNGLLWEDSKKMHMVVKTEVHPYVRDYLRRQ 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 =  497 bits (1279), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 228/297 (76%), Positives = 269/297 (90%)

Query: 33  SSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISN 92
           +S Q E+ T  SSSMMK+FQRGLLS+RDK+ PRLTESGFQFLLMDTNAQLWYI+REYI N
Sbjct: 156 NSGQGEKLTGISSSMMKIFQRGLLSQRDKDGPRLTESGFQFLLMDTNAQLWYIIREYILN 215

Query: 93  SQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWF 152
           ++ER ++ ADLISFLLELSFHV G+AYNLNTL+E+Q + +KD ADLGLVKLQQGRK++WF
Sbjct: 216 AEERDVDPADLISFLLELSFHVTGQAYNLNTLTEVQNNTLKDLADLGLVKLQQGRKDSWF 275

Query: 153 IPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIV 212
           IPTKLATNLS+SL DSSARKEGF+V+ETNFRMYAYSTSKL CEILRLF+++EYQLPNLI 
Sbjct: 276 IPTKLATNLSVSLADSSARKEGFVVMETNFRMYAYSTSKLQCEILRLFARIEYQLPNLIA 335

Query: 213 GAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEM 272
            AITKESLYNAF+NGIT++QII+FLQQN+HPR ADR+PS+PENV DQIRLWE+DL R+EM
Sbjct: 336 CAITKESLYNAFDNGITSDQIITFLQQNSHPRCADRVPSIPENVTDQIRLWETDLQRIEM 395

Query: 273 TPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQNK 329
           T AH+YDEFPS+DVFEAACD+AR+  GLLWED K+MRLVVK+E+H  MREFL  Q++
Sbjct: 396 TQAHFYDEFPSKDVFEAACDFAREWRGLLWEDSKRMRLVVKSEVHNQMREFLHTQSR 452

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	329
UNIPROTKB|A6H7G8	463	GTF2H4 "Uncharacterized protei	0.835	0.593	0.394	2.1e-52
UNIPROTKB|Q767M2	463	TFIIH "Uncharacterized protein	0.835	0.593	0.394	2.7e-52
UNIPROTKB|F1PGI3	463	GTF2H4 "Uncharacterized protei	0.835	0.593	0.390	3.5e-52
UNIPROTKB|Q92759	462	GTF2H4 "General transcription	0.835	0.595	0.390	7.2e-52
UNIPROTKB|P60027	462	GTF2H4 "General transcription	0.835	0.595	0.390	7.2e-52
RGD|1303309	463	Gtf2h4 "general transcription	0.835	0.593	0.390	7.2e-52
MGI|MGI:1338799	463	Gtf2h4 "general transcription	0.835	0.593	0.390	9.2e-52
ZFIN|ZDB-GENE-030131-6779	466	gtf2h4 "general transcription	0.841	0.594	0.380	3.1e-51
FB|FBgn0261109	499	mrn "marionette" [Drosophila m	0.893	0.589	0.343	5.4e-47
CGD|CAL0002355	494	orf19.5846 [Candida albicans (	0.665	0.443	0.379	8.6e-45

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

 Score = 543 (196.2 bits), Expect = 2.1e-52, P = 2.1e-52
 Identities = 110/279 (39%), Positives = 177/279 (63%)

Query:    52 QRGLL-SRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLEL 110
             Q GL+ S    E P +T +GFQFLL+DT AQLWY + +Y+  +Q RG++  +++SFL +L
Sbjct:   182 QAGLMKSAEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQL 241

Query:   111 SFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS-- 168
             SF   G+ Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +  
Sbjct:   242 SFSTLGKDYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGG 300

Query:   169 SARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGI 228
             +A + GFIVVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GI
Sbjct:   301 TAHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGI 360

Query:   229 TAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFE 288
             TA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE
Sbjct:   361 TAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFE 420

Query:   289 AACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ 327
                 +AR+   L++E+  K  +VV    H  ++ F + Q
Sbjct:   421 LLLAHARELGVLMFENSAKRLMVVTPAGHSDVKRFWKRQ 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 = 542 (195.9 bits), Expect = 2.7e-52, P = 2.7e-52
 Identities = 110/279 (39%), Positives = 177/279 (63%)

Query:    52 QRGLL-SRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLEL 110
             Q GL+ S    E P +T +GFQFLL+DT AQLWY + +Y+  +Q RG++  +++SFL +L
Sbjct:   182 QAGLMKSAEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQL 241

Query:   111 SFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS-- 168
             SF   G+ Y++  +S+   + ++   +LGLV  Q+ RK   + PT+LA NLS  ++ +  
Sbjct:   242 SFSTLGKDYSVEGMSDSLLNFLQHLRELGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGG 300

Query:   169 SARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGI 228
             +  + GFIVVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GI
Sbjct:   301 TVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGI 360

Query:   229 TAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFE 288
             TA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE
Sbjct:   361 TAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFE 420

Query:   289 AACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ 327
                 +AR+   L++E+  K  +VV    H  ++ F + Q
Sbjct:   421 LLLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQ 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 = 541 (195.5 bits), Expect = 3.5e-52, P = 3.5e-52
 Identities = 109/279 (39%), Positives = 177/279 (63%)

Query:    52 QRGLL-SRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLEL 110
             Q GL+ S    E P +T +GFQFLL+DT AQLWY + +Y+  +Q RG++  +++SFL +L
Sbjct:   182 QAGLMKSTEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQL 241

Query:   111 SFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS-- 168
             SF   G+ Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +  
Sbjct:   242 SFSTLGKDYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGG 300

Query:   169 SARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGI 228
             +A + GFI+VETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GI
Sbjct:   301 TAHQPGFIIVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGI 360

Query:   229 TAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFE 288
             TA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE
Sbjct:   361 TAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFE 420

Query:   289 AACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ 327
                 +AR+   L++E+  K  +VV    H  ++ F + Q
Sbjct:   421 LLLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQ 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 = 538 (194.4 bits), Expect = 7.2e-52, P = 7.2e-52
 Identities = 109/279 (39%), Positives = 176/279 (63%)

Query:    52 QRGLL-SRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLEL 110
             Q GL+ S    E P +T +GFQFLL+DT AQLWY + +Y+  +Q RG++  +++SFL +L
Sbjct:   181 QAGLMKSTEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQL 240

Query:   111 SFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS-- 168
             SF   G+ Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +  
Sbjct:   241 SFSTLGKDYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGG 299

Query:   169 SARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGI 228
             +  + GFIVVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GI
Sbjct:   300 TVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGI 359

Query:   229 TAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFE 288
             TA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE
Sbjct:   360 TAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFE 419

Query:   289 AACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ 327
                 +AR+   L++E+  K  +VV    H  ++ F + Q
Sbjct:   420 LLLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQ 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 = 538 (194.4 bits), Expect = 7.2e-52, P = 7.2e-52
 Identities = 109/279 (39%), Positives = 176/279 (63%)

Query:    52 QRGLL-SRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLEL 110
             Q GL+ S    E P +T +GFQFLL+DT AQLWY + +Y+  +Q RG++  +++SFL +L
Sbjct:   181 QAGLMKSTEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQL 240

Query:   111 SFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS-- 168
             SF   G+ Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +  
Sbjct:   241 SFSTLGKDYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGG 299

Query:   169 SARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGI 228
             +  + GFIVVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GI
Sbjct:   300 TVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGI 359

Query:   229 TAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFE 288
             TA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE
Sbjct:   360 TAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFE 419

Query:   289 AACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ 327
                 +AR+   L++E+  K  +VV    H  ++ F + Q
Sbjct:   420 LLLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQ 458

GO:0005675 "holo TFIIH complex" evidence=ISS

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

GO:0004672 "protein kinase activity" evidence=ISS

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

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

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

 Score = 538 (194.4 bits), Expect = 7.2e-52, P = 7.2e-52
 Identities = 109/279 (39%), Positives = 176/279 (63%)

Query:    52 QRGLL-SRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLEL 110
             Q GL+ S    E P +T +GFQFLL+DT AQLWY + +Y+  +Q RG++  +++SFL +L
Sbjct:   182 QAGLMKSTEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQL 241

Query:   111 SFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS-- 168
             SF   G+ Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +  
Sbjct:   242 SFSTLGKDYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGG 300

Query:   169 SARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGI 228
             +  + GFIVVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GI
Sbjct:   301 TVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGI 360

Query:   229 TAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFE 288
             TA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE
Sbjct:   361 TAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFE 420

Query:   289 AACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ 327
                 +AR+   L++E+  K  +VV    H  ++ F + Q
Sbjct:   421 LLLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQ 459

GO:0000439 "core TFIIH complex" evidence=IEA

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

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

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

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

GO:0004672 "protein kinase activity" evidence=ISO

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

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

 Score = 537 (194.1 bits), Expect = 9.2e-52, P = 9.2e-52
 Identities = 109/279 (39%), Positives = 176/279 (63%)

Query:    52 QRGLL-SRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLEL 110
             Q GL+ S    E P +T +GFQFLL+DT AQLWY + +Y+  +Q RG++  +++SFL +L
Sbjct:   182 QAGLMKSTEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQL 241

Query:   111 SFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS-- 168
             SF   G+ Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +  
Sbjct:   242 SFSTLGKDYSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGG 300

Query:   169 SARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGI 228
             +  + GFIVVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GI
Sbjct:   301 TVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGI 360

Query:   229 TAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFE 288
             TA+QII FL+  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE
Sbjct:   361 TAQQIIHFLRTRAHPVMLKQNPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFE 420

Query:   289 AACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ 327
                 +AR+   L++E+  K  +VV    H  ++ F + Q
Sbjct:   421 LLLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQ 459

GO:0000439 "core TFIIH complex" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0005675 "holo TFIIH complex" evidence=ISO

GO:0006281 "DNA repair" evidence=IEA

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

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

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

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

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

 Score = 532 (192.3 bits), Expect = 3.1e-51, P = 3.1e-51
 Identities = 111/292 (38%), Positives = 173/292 (59%)

Query:    50 VFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLE 109
             + Q GL+     EAP +T +GFQFLL+DT +QLWY   +Y+  +Q RG++  +++SFL +
Sbjct:   172 LIQAGLMKSETGEAPCITSAGFQFLLLDTASQLWYFTLQYLKTAQSRGMDLVEILSFLFQ 231

Query:   110 LSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSS 169
             LSF   G  Y++  +SE   + ++   + GLV  Q+ RK   + PT+LA  L+  +T + 
Sbjct:   232 LSFSTLGRDYSVEGMSESLLTFLQHLREFGLV-FQRKRKSRRYYPTRLAITLAAGVTANP 290

Query:   170 ARKE--------------GFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAI 215
             A                 GFIVVETN+R+YAY+ S+L   ++ LFS++ Y+ PNL+V  +
Sbjct:   291 ASGSASSALGAIPGTGDTGFIVVETNYRIYAYTNSELQIALVALFSEMLYRFPNLVVAQV 350

Query:   216 TKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPA 275
             T+ES+  A  NGITA+QII FL+  AHP +  + P +P  + DQIRLWE + +R++ T  
Sbjct:   351 TRESVQQAISNGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELEKDRLQFTEG 410

Query:   276 HYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ 327
               Y++F S+  FE   D A+    L+W++P    +VV    H  ++ F + Q
Sbjct:   411 VLYNQFLSQADFEVLRDRAQGLGVLVWQNPAHRVMVVTPHGHSEVKRFWKRQ 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

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

 Score = 492 (178.3 bits), Expect = 5.4e-47, P = 5.4e-47
 Identities = 108/314 (34%), Positives = 180/314 (57%)

Query:    31 NGSSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYI 90
             NG+  +A  P     ++  +    L+ R +++   +T  GFQFLL+DT AQ+W+ + +Y+
Sbjct:   188 NGTDAEAISP----DAVRILLHANLMKRDERDGITITRQGFQFLLLDTRAQVWHFMLQYL 243

Query:    91 SNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKEN 150
                +ERGI+  + +S L +LSF   G  Y+   ++    + ++   + GLV  Q+ RKE 
Sbjct:   244 DTCEERGISLPECLSMLFQLSFSTLGRDYSSEGMNSQMLTFLQHLREFGLV-FQRKRKEG 302

Query:   151 WFIPTKLATNL---------SMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFS 201
              F PT+LA N+         S+++ + + +  G+IVVETN+R+YAY+ S L   +L LF+
Sbjct:   303 RFYPTRLALNVTSKEAAATASVAMDEEATQDCGYIVVETNYRVYAYTDSPLQVAVLGLFT 362

Query:   202 KVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPR---VADRMPS---VPEN 255
             ++ Y+ PNL+VG +T++S+  A   GITAEQI+S+L+Q AHP    V   + S   +P  
Sbjct:   363 ELLYRFPNLVVGVLTRDSVRQALRGGITAEQIVSYLEQYAHPNMRMVESAIHSKSCLPPT 422

Query:   256 VCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAE 315
             V DQI+LWE + NR   T    Y++F S   F    DYA+    L+W++ +   +VV+  
Sbjct:   423 VVDQIKLWELERNRFTYTEGVLYNQFLSHTDFVTLRDYAQSIHMLVWQNERTRTMVVQKN 482

Query:   316 IHMHMREFLRGQNK 329
              H  ++ + +  +K
Sbjct:   483 GHDDVKRYWKKYSK 496

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

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

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

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

GO:0001671 "ATPase activator activity" evidence=IDA

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

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

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

GO:0005634 "nucleus" evidence=IDA

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

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

CGD|CAL0002355 orf19.5846 [Candida albicans (taxid:5476)]

 Score = 377 (137.8 bits), Expect = 8.6e-45, Sum P(2) = 8.6e-45
 Identities = 91/240 (37%), Positives = 144/240 (60%)

Query:    19 QPWRTLRPMPLDNGSSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDT 78
             Q W T+    +  G+ + A  P++   S++K+   GL+   + +  R+T SGFQFLL D 
Sbjct:   142 QKWETILHFMV--GTESTAT-PSDSVLSLLKL--GGLMEGPNNDL-RITNSGFQFLLQDV 195

Query:    79 NAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADL 138
             NAQ+W ++ +Y++ +QE  ++  D+++F+  L     G++Y++ +LSE Q SM+ D  D 
Sbjct:   196 NAQIWTLLLQYLNLTQELNMDPVDVLNFIFVLGSLELGKSYSVLSLSETQVSMLADLKDY 255

Query:   139 GLVKLQQGRKENWFIPTKLATNL----------SMSLTDSS---ARKEGFIVVETNFRMY 185
             GLV  Q+      F PT+LAT L          SM++ +     A KE  I++ETNF++Y
Sbjct:   256 GLV-YQRSDTSGRFYPTRLATTLTSDSAALKTPSMAMDEEEQQVATKES-IIIETNFKIY 313

Query:   186 AYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRV 245
             AY+ S L   IL LF   + +  N++ G IT+ES+ NA  NGITA+QII FL+ +AHP++
Sbjct:   314 AYTKSPLEIAILNLFVHFKTRFANMVCGQITRESIRNALYNGITADQIIKFLETHAHPQM 373

GO:0005675 "holo TFIIH complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0000439 "core TFIIH complex" evidence=IEA

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

GO:0003690 "double-stranded DNA binding" evidence=IEA

GO:0070816 "phosphorylation of RNA polymerase II C-terminal domain" evidence=IEA

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

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

---

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	329
pfam03849	365	pfam03849, Tfb2, Transcription factor Tfb2	1e-103
TIGR00625	448	TIGR00625, tfb2, Transcription factor tfb2	3e-74
COG5144	447	COG5144, TFB2, RNA polymerase II transcription ini	4e-67
pfam13625	128	pfam13625, Helicase_C_3, Helicase conserved C-term	8e-05

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

 Score =  306 bits (787), Expect = e-103
 Identities = 95/223 (42%), Positives = 145/223 (65%), Gaps = 16/223 (7%)

Query: 34  STQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNS 93
           S++A+  T  S S++ + + G L  R     R+T  GFQFLL D NAQ+W ++ +Y+  +
Sbjct: 146 SSEAK--TQPSKSVLNLLKHGGLMERSDGGLRITNEGFQFLLQDVNAQIWTLLLQYLKLA 203

Query: 94  QERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFI 153
           +ERG++  D++SFL  L F   G+AY+ + LSE Q++M++D  D GLV  ++ +   ++ 
Sbjct: 204 EERGMDPVDVLSFLFMLGFLELGKAYSTDGLSETQRNMLQDLRDYGLVYQRKRKSRRFY- 262

Query: 154 PTKLATNLSMSLTDSS-------------ARKEGFIVVETNFRMYAYSTSKLHCEILRLF 200
           PT+LAT L+   +                A  +GFI+VETNFR+YAY++S L   IL LF
Sbjct: 263 PTRLATTLTSDSSALRTASSAMEAATSSEAASKGFIIVETNFRLYAYTSSPLQIAILALF 322

Query: 201 SKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHP 243
            +++Y+ PNL+VG IT+ES+ NA ENGITA+QIIS+L+ +AHP
Sbjct: 323 VELKYRFPNLVVGQITRESIRNALENGITADQIISYLETHAHP 365

Length = 365

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

 Score =  235 bits (601), Expect = 3e-74
 Identities = 111/286 (38%), Positives = 174/286 (60%), Gaps = 9/286 (3%)

Query: 52  QRGLLSR-RDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLEL 110
           Q GL+      E P +T +GFQFLL D NAQLW ++ +Y+  ++ RG++  +++ FL  L
Sbjct: 164 QAGLMKSTEPGEPPCITSAGFQFLLQDINAQLWTLLLQYLKTAESRGMDLVEVLHFLFML 223

Query: 111 SFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSM-SLTDSS 169
            F   G+AY+++ LS+ Q  M++D  + GLV  Q+ RK   F PT+LA NL+  + T S 
Sbjct: 224 GFLTLGKAYSVDGLSDTQLIMLQDLREYGLV-FQRKRKSRRFYPTRLAINLTSDTKTVSG 282

Query: 170 ARKE-----GFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAF 224
           A        GFI+VETN+R+YAY+ S L   ++ LFS++  + PN++VG IT+ES+  A 
Sbjct: 283 AGGTVDDDLGFIIVETNYRLYAYTESPLQIALIALFSELLARFPNMVVGQITRESIRRAL 342

Query: 225 ENGITAEQIISFLQQNAHPRV-ADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPS 283
            NGITA+QII +L+ +AHP++  ++ P +P  + DQIRLWE + +R+  T    Y++F +
Sbjct: 343 ANGITAQQIIHYLRTHAHPQMRKEQTPVLPPTIVDQIRLWELERDRLRFTEGVLYNDFLT 402

Query: 284 RDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQNK 329
           +  FE    YAR+   L+WE+  K    +    H  ++ F + Q  
Sbjct: 403 QVDFELLLAYARELGVLVWENSAKRLFFITPAGHSDVKRFWKRQKH 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 =  216 bits (552), Expect = 4e-67
 Identities = 99/288 (34%), Positives = 163/288 (56%), Gaps = 7/288 (2%)

Query: 44  SSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADL 103
           +  ++++ + G L  RD+   ++T  GFQFLL   N QLW ++  Y+   +   +++  +
Sbjct: 156 AEGVLELLKFGGLMGRDRNEFKITNRGFQFLLQTINEQLWTLLLLYLKYFEGSVMDEVAV 215

Query: 104 ISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSM 163
           + FL  L     G AY ++ LS+ Q+ M+ D    GLV+ Q G     F PT LA  L+ 
Sbjct: 216 LHFLFMLGALAVGTAYKIDALSDTQQIMLMDRRLYGLVE-QLGILRKIFYPTGLAIGLTF 274

Query: 164 -SLTDSSARKE-----GFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITK 217
             L ++S +       GFI+VETN ++YAY+ S L   ++ LF  +  + PNL+ G IT+
Sbjct: 275 DQLFEASEQNRREDDKGFIIVETNNKIYAYTNSPLQIAVIHLFCNLTARFPNLVKGIITR 334

Query: 218 ESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHY 277
           ES+  A +NGITA+QII +L+ +AHP++  ++  +P  + DQI LWE + NR+ M P + 
Sbjct: 335 ESIRRALDNGITAKQIIHYLETHAHPQMRKKLELLPPTIVDQIVLWELERNRIFMVPGYL 394

Query: 278 YDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLR 325
           Y +F +   ++   +YA     L+W D  K    +K E H  ++EF++
Sbjct: 395 YSDFLTLSDYQKVLEYAIRGGVLVWSDVDKRMFFIKLEGHSLVKEFVK 442

Length = 447

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

 Score = 41.4 bits (98), Expect = 8e-05
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 9/65 (13%)

Query: 215 ITKESLYNAFENGITAEQIISFLQQNA-HPRVADRMPSVPENVCDQIRLWESDLNRVEMT 273
           +T  SL  A + G+TAE+II FL++++  P        VP+++   IR       R+ + 
Sbjct: 41  LTPLSLRRALDAGLTAEEIIEFLERHSRTP--------VPQSLLYLIRDVARRHGRLRLG 92

Query: 274 PAHYY 278
            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	329
KOG3471	465	consensus RNA polymerase II transcription initiati	100.0
TIGR00625	448	tfb2 Transcription factor tfb2. This family is bas	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	99.68
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	97.39
PF08671	30	SinI: Anti-repressor SinI; InterPro: IPR010981 The	92.48
PRK06015	201	keto-hydroxyglutarate-aldolase/keto-deoxy-phosphog	84.22
PRK05718	212	keto-hydroxyglutarate-aldolase/keto-deoxy-phosphog	80.25

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

Probab=100.00  E-value=1.9e-111  Score=822.37  Aligned_cols=307  Identities=36%  Similarity=0.661  Sum_probs=292.6

Q ss_pred             cccCccceecceeccCCCCCCCCCCCCCcHHHHHHHHhCCCccCCCCCCccchhchhhhccChhhHHHHHHHHHHHHHHH
Q 020247           16 QGFQPWRTLRPMPLDNGSSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQE   95 (329)
Q Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~v~~lL~~~gL~~~~~~~~~IT~~GfqFLL~d~~~Q~W~lll~yl~~~e~   95 (329)
                      -+.+|||||+||||+++.+      ..+|+++.++|+++|||+.+...+.||++||||||+|+++|+|+++++||++.+.
T Consensus       147 ya~~rwe~ILh~mvgt~~a------~~~se~v~~ll~~a~lm~~~~~~~~IT~~GFQFLL~~~~aQlW~~~LqyLk~~~~  220 (465)
T KOG3471|consen  147 YASERWECILHFMVGTPEA------KAVSEGVLNLLKHAGLMSRDENQIEITNAGFQFLLLDINAQLWTLVLQYLKLFES  220 (465)
T ss_pred             HHHHHHHHHHHHHhCCccc------cccChhHHHHHHhcCccCCCCCCceEeecchhhhhcCcHHHHHHHHHHHHHHHHh
Confidence            3689999999999955533      7899999999999999998888999999999999999999999999999999999


Q ss_pred             cCCChHHHHHHHHHhcccccCccccCCCCCHHHHHHHHHHhhcCceeeecCCCccccccchhhhhcccccCC--------
Q 020247           96 RGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTD--------  167 (329)
Q Consensus        96 ~g~~~~e~L~fLf~Ls~~~~G~~Y~~~~lt~~q~~~L~~L~d~GLVy~~~~~~~~fy~pT~La~~L~~~~~~--------  167 (329)
                      +|+|++|+|+|||+||++++|++|+++++|++|+.||+||+|+|||||+|.+..+|| ||+||++++++-.+        
T Consensus       221 ~~~dlvevL~~LfqL~~~~~G~~Ysvd~~~~~~~~~lq~Lre~GlvfQrk~k~~rfy-ptrla~~~ss~~~~~~~~~~~~  299 (465)
T KOG3471|consen  221 SGMDLVEVLEFLFQLSALALGRAYSVDALTETQRILLQHLRELGLVFQRKIKILRFY-PTRLAIGLSSDQLGAASLVHQN  299 (465)
T ss_pred             cCCCHHHHHHHHHHHHHHHhcccceeehhhHHHHHHHHHHHHhhHHHHhhhhhheec-chhhhhccchhhhhhhhhhhcc
Confidence            999999999999999999999999999999999999999999999999999999999 99999999875431        


Q ss_pred             ccccccceEEEeeceeEEeecCChhHHHHHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccc
Q 020247          168 SSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVAD  247 (329)
Q Consensus       168 ~~~~~~g~IIVETNFrvYAYT~S~lqiaiL~lF~el~~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~~  247 (329)
                      ..+++.|||||||||||||||+||||+|+|+||||+.|||||||||+|||||||+|+++||||+|||+||++||||||+.
T Consensus       300 ~~edd~G~iIVETN~riYAYT~S~lQiAvi~LF~~l~~rf~nlvvG~iTreSVr~Al~~GITa~QII~fLet~ahpqm~~  379 (465)
T KOG3471|consen  300 RNEDDVGFIIVETNYRIYAYTNSPLQIAVIALFTELTYRFPNLVVGVITRESVRRALDNGITAEQIIHFLETHAHPQMRM  379 (465)
T ss_pred             cccccCceEEEEeccEEEEecCCHHHHHHHHHHHHHHhhccccceeeeeHHHHHHHHhcCCcHHHHHHHHHhccCchhhh
Confidence            12355699999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             cC--CCCChhHHHHHHHHHHhcCceeeeceeeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHh
Q 020247          248 RM--PSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLR  325 (329)
Q Consensus       248 ~~--~~iP~tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s~~~fe~v~~yA~~~g~llw~~~~kr~~~V~~~~h~~vr~f~k  325 (329)
                      ..  |++||||+|||||||.||||+.++||+||++|.|..||+.+++||+++|+|+|+|+.||+|||+.+||++||+|||
T Consensus       380 ~~~~~~LPpTv~dQIrLWElernR~~~~~g~LYs~Fls~~df~~l~eya~~~~vLvw~d~~kr~~vV~~~Ghs~Vk~f~K  459 (465)
T KOG3471|consen  380 LSPVPCLPPTVVDQIRLWELERNRLRMTEGYLYSDFLSLSDFQLLLEYAREIGVLVWSDSDKRMFVVTKEGHSLVKRFWK  459 (465)
T ss_pred             cCCCCCCCchHHhHHHHHHHhhcceecccchhHHhhhhhhhHHHHHHHHHHcCeEEEecCcceEEEEecCccHHHHHHHH
Confidence            76  9999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccC
Q 020247          326 GQNK  329 (329)
Q Consensus       326 ~~~~  329 (329)
                      +++|
T Consensus       460 r~~k  463 (465)
T KOG3471|consen  460 RKSK  463 (465)
T ss_pred             Hhhc
Confidence            9764

>TIGR00625 tfb2 Transcription factor tfb2

Probab=100.00  E-value=3.2e-109  Score=824.10  Aligned_cols=306  Identities=35%  Similarity=0.663  Sum_probs=289.5

Q ss_pred             ccCccceecceeccCCCCCCCCCCCCCcHHHHHHHHhCCCccCC--CCCCccchhchhhhccChhhHHHHHHHHHHHHHH
Q 020247           17 GFQPWRTLRPMPLDNGSSTQAERPTNFSSSMMKVFQRGLLSRRD--KEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQ   94 (329)
Q Consensus        17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~v~~lL~~~gL~~~~--~~~~~IT~~GfqFLL~d~~~Q~W~lll~yl~~~e   94 (329)
                      +.++||||+||||++++.      ..||++|+++|+++|||+.+  ++.+.||++||||||+|+++|+|+||++||+++|
T Consensus       134 A~~~WE~IL~fmVgs~~~------~~~s~~v~~lL~~~~Lm~~~~~~~~~~IT~~GFqFLLqd~n~QvW~lll~YL~~~e  207 (448)
T TIGR00625       134 AEERWETILHFMVGTPSA------KVPSEDVLQLLKQAGLMKSTEPGEPPCITSAGFQFLLQDINAQLWTLLLQYLKTAE  207 (448)
T ss_pred             HHHHHHHHHHHHcCCCCc------CCCchHHHHHHHhCCCCcccCCCCCccCchhhHHHHcCChhHHHHHHHHHHHHHHH
Confidence            568999999999944322      56899999999999999873  3358999999999999999999999999999999


Q ss_pred             HcCCChHHHHHHHHHhcccccCccccCCCCCHHHHHHHHHHhhcCceeeecCCCccccccchhhhhcccccCC----cc-
Q 020247           95 ERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTD----SS-  169 (329)
Q Consensus        95 ~~g~~~~e~L~fLf~Ls~~~~G~~Y~~~~lt~~q~~~L~~L~d~GLVy~~~~~~~~fy~pT~La~~L~~~~~~----~~-  169 (329)
                      ++|+|.+|+|+|||+||++++|++|++++||++|++||+||+|+||||++++++++|| |||||++|+++.++    ++ 
T Consensus       208 ~~g~d~vevLsFLf~Ls~l~lG~~Y~~~~Lt~tq~~~L~dL~dlGLVy~~~~~~~~fY-PTrLAt~Lts~~~~l~~~~~~  286 (448)
T TIGR00625       208 SRGMDLVEVLHFLFMLGFLTLGKAYSVDGLSDTQLIMLQDLREYGLVFQRKRKSRRFY-PTRLAINLTSDTKTVSGAGGT  286 (448)
T ss_pred             hcCCCHHHHHHHHHHHhccccCCccCCCCCCHHHHHHHHHHHHcCeEEEecCCCCccc-chHHHHHHhcCcccccccccc
Confidence            9999999999999999999999999999999999999999999999999999999999 99999999876542    11 


Q ss_pred             -ccccceEEEeeceeEEeecCChhHHHHHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCcccc-c
Q 020247          170 -ARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVA-D  247 (329)
Q Consensus       170 -~~~~g~IIVETNFrvYAYT~S~lqiaiL~lF~el~~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~-~  247 (329)
                       ..++|||||||||||||||+||||++||++||++.||||||+||+|||+||++|+++||||||||+||++||||+|+ +
T Consensus       287 ~~~~~g~iivEtNfrvYaYt~s~l~~~il~lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GITa~qIi~fl~~~ahp~~~~~  366 (448)
T TIGR00625       287 VDDDLGFIIVETNYRLYAYTESPLQIALIALFSELLARFPNMVVGQITRESIRRALANGITAQQIIHYLRTHAHPQMRKE  366 (448)
T ss_pred             ccCCCceEEEEecceEEEecCCHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHcCCCHHHHHHHHHhcCChhhhcc
Confidence             25679999999999999999999999999999999999999999999999999999999999999999999999998 4


Q ss_pred             cCCCCChhHHHHHHHHHHhcCceeeeceeeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhhc
Q 020247          248 RMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ  327 (329)
Q Consensus       248 ~~~~iP~tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s~~~fe~v~~yA~~~g~llw~~~~kr~~~V~~~~h~~vr~f~k~~  327 (329)
                      +.|+|||||+|||||||.||||+++++|+||++|.|++||+++++||+++|+|+|+|+.||+|||+.+||++||+|||++
T Consensus       367 ~~~~lP~tv~dQi~lWe~e~~R~~~~~~~l~~~f~s~~~y~~~~~ya~~~~~l~w~~~~kr~~~V~~~gh~~v~~f~k~~  446 (448)
T TIGR00625       367 QTPVLPPTIVDQIRLWELERDRLRFTEGVLYNDFLTQVDFELLLAYARELGVLVWENSAKRLFFITPAGHSDVKRFWKRQ  446 (448)
T ss_pred             CCCCCChHHHHHHHHHHHHhcceEeecceeeeecCCHHHHHHHHHHHHHcCEEEEecCCceEEEEeccchHHHHHHHHhh
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cC
Q 020247          328 NK  329 (329)
Q Consensus       328 ~~  329 (329)
                      |+
T Consensus       447 ~~  448 (448)
T TIGR00625       447 KH  448 (448)
T ss_pred             cC
Confidence            86

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

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

Probab=100.00  E-value=1.4e-98  Score=715.27  Aligned_cols=305  Identities=32%  Similarity=0.574  Sum_probs=291.2

Q ss_pred             ccCccceecceeccCCCCCCCCCCCCCcHHHHHHHHhCCCccCCCCCCccchhchhhhccChhhHHHHHHHHHHHHHHHc
Q 020247           17 GFQPWRTLRPMPLDNGSSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQER   96 (329)
Q Consensus        17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~v~~lL~~~gL~~~~~~~~~IT~~GfqFLL~d~~~Q~W~lll~yl~~~e~~   96 (329)
                      +-++|||++|+||  |++.+    .-|++.|+++|+++|||..+...++||++|||||||+.|+|+|++++.||++.|..
T Consensus       135 s~~kwEtILhfmV--gtpea----kip~egVl~lLk~ggLm~~~~ne~kITn~GFqFLLq~in~QlWtLlL~yLK~~e~s  208 (447)
T COG5144         135 SSRKWETILHFMV--GTPEA----KIPAEGVLELLKFGGLMGRDRNEFKITNRGFQFLLQTINEQLWTLLLLYLKYFEGS  208 (447)
T ss_pred             hhhhHHHHHHHHh--CCccc----cCcchhHHHHHHhcccccCCcccceeehhHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            4578999999999  66544    77999999999999999988889999999999999999999999999999999999


Q ss_pred             CCChHHHHHHHHHhcccccCccccCCCCCHHHHHHHHHHhhcCceeeecCCCccccccchhhhhcccccC----C--ccc
Q 020247           97 GINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLT----D--SSA  170 (329)
Q Consensus        97 g~~~~e~L~fLf~Ls~~~~G~~Y~~~~lt~~q~~~L~~L~d~GLVy~~~~~~~~fy~pT~La~~L~~~~~----~--~~~  170 (329)
                      -||++++|+|||+||.+++|++|+++.||++|+-+|+|+|++|||++++-.+++|| ||+||+.++++--    .  ...
T Consensus       209 ~md~v~VLhflFmLgal~vG~aY~id~lsdtqqiml~D~R~yglv~q~~i~~~~fY-pt~LA~glt~d~~~~~s~qnr~e  287 (447)
T COG5144         209 VMDEVAVLHFLFMLGALAVGTAYKIDALSDTQQIMLMDRRLYGLVEQLGILRKIFY-PTGLAIGLTFDQLFEASEQNRRE  287 (447)
T ss_pred             cccHHHHHHHHHHhcchhhcceeeecccchHHHHHHHHHHHhhHHHHhccchhhcc-ccccchhhhhHHHHHhhhhcccc
Confidence            99999999999999999999999999999999999999999999999998889999 9999999876422    1  233


Q ss_pred             cccceEEEeeceeEEeecCChhHHHHHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCC
Q 020247          171 RKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMP  250 (329)
Q Consensus       171 ~~~g~IIVETNFrvYAYT~S~lqiaiL~lF~el~~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~~~~~  250 (329)
                      ++.|||||||||||||||+||+|+|+++|||++.+||||||+|+|||||||+|+.+||||+|||.||++||||+|+++.|
T Consensus       288 dd~gfiIVETN~kiYaYtnSplqiavi~LF~nl~arf~Nlv~GiITreSirrAl~nGIta~QII~yLethahpqmr~~l~  367 (447)
T COG5144         288 DDKGFIIVETNNKIYAYTNSPLQIAVIHLFCNLTARFPNLVKGIITRESIRRALDNGITAKQIIHYLETHAHPQMRKKLE  367 (447)
T ss_pred             ccCceEEEEecceEEEecCChHHHHHHHHhhhhhcccchhhhhhccHHHHHHHHhcCccHHHHHHHHHhccChhhhhcCC
Confidence            66799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCChhHHHHHHHHHHhcCceeeeceeeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhhcc
Q 020247          251 SVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQN  328 (329)
Q Consensus       251 ~iP~tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s~~~fe~v~~yA~~~g~llw~~~~kr~~~V~~~~h~~vr~f~k~~~  328 (329)
                      .+||||+|||++||.|+||+...||+||+||.+..+|+.+.+||++.|+|+|++..||+|||+.+||..|++|.|++-
T Consensus       368 llPPtivdQI~lWele~nRi~~~pG~LysdFlt~s~y~~~~eya~~~gvLvw~d~~Krmffi~~eG~s~v~~f~Kr~l  445 (447)
T COG5144         368 LLPPTIVDQIVLWELERNRIFMVPGYLYSDFLTLSDYQKVLEYAIRGGVLVWSDVDKRMFFIKLEGHSLVKEFVKRIL  445 (447)
T ss_pred             CCChhhhhheeeeeeccCcEEeecchHHhhhhchhhHHHHHHHHHhcCeEEeecccceEEEEEccCcHHHHHHHHHHh
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999999964

>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=2.3e-78  Score=593.97  Aligned_cols=222  Identities=44%  Similarity=0.770  Sum_probs=207.8

Q ss_pred             ccCccceecceeccCCCCCCCCCCCCCcHHHHHHHHhCCCccC--CCCCCccchhchhhhccChhhHHHHHHHHHHHHHH
Q 020247           17 GFQPWRTLRPMPLDNGSSTQAERPTNFSSSMMKVFQRGLLSRR--DKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQ   94 (329)
Q Consensus        17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~v~~lL~~~gL~~~--~~~~~~IT~~GfqFLL~d~~~Q~W~lll~yl~~~e   94 (329)
                      +.++||||+||||++++...    ..||++|+++|+++|||+.  ++++..||++||||||+|+++|+|+||++||+++|
T Consensus       132 A~~rWE~IL~~mVgs~~~~~----~~~s~~v~~lL~~sgLm~~~~~~~~~~IT~~GFqFLL~d~~~QlW~lll~yL~~~e  207 (366)
T PF03849_consen  132 ARERWESILHYMVGSSSSSN----SSPSQDVKQLLKRSGLMKRSESGGSLKITSKGFQFLLQDTNAQLWTLLLQYLKMAE  207 (366)
T ss_pred             HHHHHHHHHHHHhcCccccc----CCCCHHHHHHHHHcCCCcCcCCCCCCcEehhheeeecCChHHHHHHHHHHHHHHHH
Confidence            67899999999995444322    2299999999999999998  55689999999999999999999999999999999


Q ss_pred             HcCCChHHHHHHHHHhcccccCccccCCCCCHHHHHHHHHHhhcCceeeecCCCccccccchhhhhcccccCC-------
Q 020247           95 ERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTD-------  167 (329)
Q Consensus        95 ~~g~~~~e~L~fLf~Ls~~~~G~~Y~~~~lt~~q~~~L~~L~d~GLVy~~~~~~~~fy~pT~La~~L~~~~~~-------  167 (329)
                      ++|++.+|+|+|||+||++++|++|++++||++|++||+||+|+||||++++++++|| |||||++|+++.+.       
T Consensus       208 ~~~~~~~~~l~flf~L~~~~~g~~Y~~~~ls~~q~~~L~~l~~~GLvy~~~~~~~~fy-pT~La~~l~~~~~~~~~~~~~  286 (366)
T PF03849_consen  208 ARGMDLVEVLSFLFQLSFLELGKAYSTEGLSETQKNMLQDLRELGLVYQRKRKSRRFY-PTRLATNLTSGSSALRSASSA  286 (366)
T ss_pred             hcCCCHHHHHHHHHHhcccccCCcCcCCCCCHHHHHHHHHHHHCCeEEEecCCCCeEe-chHHHHHHhcCCCcccccccc
Confidence            9999999999999999999999999999999999999999999999999999999999 99999999887652       


Q ss_pred             ----ccccccceEEEeeceeEEeecCChhHHHHHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCc
Q 020247          168 ----SSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHP  243 (329)
Q Consensus       168 ----~~~~~~g~IIVETNFrvYAYT~S~lqiaiL~lF~el~~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp  243 (329)
                          ....++|||||||||||||||+||||||||++||++.|||||||||+||||||++|+++||||||||+||++||||
T Consensus       287 ~~~~~~~~~~g~iivETNfrvYAYT~s~l~iaiL~lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GIta~qIi~fL~~~aHp  366 (366)
T PF03849_consen  287 LDSSSSSNKEGFIIVETNFRVYAYTNSPLQIAILSLFCELKYRFPNLVVGQITRESVRRALKNGITADQIISFLRSHAHP  366 (366)
T ss_pred             cccccccccCceEEEEecceEEEecCCHHHHHHHHHHHHHHhcCCCeEEEEEcHHHHHHHHHcCCCHHHHHHHHHhcCCC
Confidence                1346789999999999999999999999999999999999999999999999999999999999999999999999

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=99.68  E-value=4.7e-16  Score=132.01  Aligned_cols=118  Identities=23%  Similarity=0.361  Sum_probs=105.3

Q ss_pred             EEEeeceeEEeecCCh--hHHHHHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCCCCC
Q 020247          176 IVVETNFRMYAYSTSK--LHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVP  253 (329)
Q Consensus       176 IIVETNFrvYAYT~S~--lqiaiL~lF~el~~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~~~~~~iP  253 (329)
                      +||++||.|.+++.+|  -..+.|..|+++ .+..+|.+++||+.|+.+|++.|+|+++|++||+.|+..       .||
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            7999999999977766  344999999999 567999999999999999999999999999999999954       699


Q ss_pred             hhHHHHHHHHHHhcCceeeeceeeecCCCCHHHHHHHHHHHHHcCeEe
Q 020247          254 ENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLL  301 (329)
Q Consensus       254 ~tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s~~~fe~v~~yA~~~g~ll  301 (329)
                      ++|..+|+-|+...+|+++.++..|-.+.+.+..+.+.+..+-.++.+
T Consensus        74 ~~v~~~i~~w~~~~g~v~l~~~~~~l~~~d~~~l~~l~~~~~~~~~~~  121 (129)
T PF13625_consen   74 QNVEQSIEDWARRYGRVRLYKGAYLLECDDPELLDELLADPELAKLIL  121 (129)
T ss_pred             HHHHHHHHHHHHhcCCEEEecCeEEEEECCHHHHHHHHhChhhhhhhc
Confidence            999999999999999999999676669999999999988877665443

>TIGR00603 rad25 DNA repair helicase rad25

Probab=97.39  E-value=0.0016  Score=70.36  Aligned_cols=106  Identities=24%  Similarity=0.380  Sum_probs=84.3

Q ss_pred             cceEEEeeceeEEeecCChhH--H-HHHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccC
Q 020247          173 EGFIVVETNFRMYAYSTSKLH--C-EILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRM  249 (329)
Q Consensus       173 ~g~IIVETNFrvYAYT~S~lq--i-aiL~lF~el~~r~PNlvvg~iTReSV~~Al~~GITA~QII~fL~~hAHp~m~~~~  249 (329)
                      +|.|++||        .||+-  . .-|..|+|+.+|--+|..++||-=|+-.|...|+++++||++|..++-.      
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            45666666        34443  3 7899999999999999999999999999999999999999999999844      


Q ss_pred             CCCChhHHHHHHHHHHhcCceeee--ceeeecCCCCHHHHHHHHHH
Q 020247          250 PSVPENVCDQIRLWESDLNRVEMT--PAHYYDEFPSRDVFEAACDY  293 (329)
Q Consensus       250 ~~iP~tV~dQI~lWe~Er~Rl~~~--~g~Ly~~f~s~~~fe~v~~y  293 (329)
                       .||++|.+.|+.+-.-.+++++.  +.--|-+-.+.+..+.+.+.
T Consensus        88 -~~p~~i~~~i~~~~~~ygk~klv~~~~~~~~es~~~~~l~~l~~~  132 (732)
T TIGR00603        88 -PIPKGIIEFIRLCTQSYGKVKLVLKHNRYFVESPHPEVLQRLLKD  132 (732)
T ss_pred             -CCCHHHHHHHHHHHHhcCcEEEEEcCCceEEecCCHHHHHHHHhc
Confidence             79999999999999999999883  22113244555555555543

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=92.48  E-value=0.12  Score=34.08  Aligned_cols=22  Identities=36%  Similarity=0.525  Sum_probs=17.7

Q ss_pred             HHHHHHHcCCCHHHHHHHHHhc
Q 020247          219 SLYNAFENGITAEQIISFLQQN  240 (329)
Q Consensus       219 SV~~Al~~GITA~QII~fL~~h  240 (329)
                      =|++|...|||.+||-+||+.+
T Consensus         8 Li~eA~~~Gls~eeir~FL~~~   29 (30)
T PF08671_consen    8 LIKEAKESGLSKEEIREFLEFN   29 (30)
T ss_dssp             HHHHHHHTT--HHHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHhC
Confidence            3789999999999999999864

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

>PRK06015 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional

Probab=84.22  E-value=7.2  Score=36.16  Aligned_cols=126  Identities=16%  Similarity=0.242  Sum_probs=87.5

Q ss_pred             ccceEEEeeceeEEeecCChhHHHHHHHhhhhhhccCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHHhcC
Q 020247          172 KEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNA  241 (329)
Q Consensus       172 ~~g~IIVETNFrvYAYT~S~lqiaiL~lF~el~~r~PNlvvg---~iTReSV~~Al~~GI-------TA~QII~fL~~hA  241 (329)
                      +.|.=++|-.|+      +|--.   ..+.++..++|++.||   ++|.|.+++|.+.|-       .-+.++++-+.+-
T Consensus        27 ~gGi~~iEit~~------tp~a~---~~I~~l~~~~~~~~vGAGTVl~~e~a~~ai~aGA~FivSP~~~~~vi~~a~~~~   97 (201)
T PRK06015         27 AGGLPAIEITLR------TPAAL---DAIRAVAAEVEEAIVGAGTILNAKQFEDAAKAGSRFIVSPGTTQELLAAANDSD   97 (201)
T ss_pred             HCCCCEEEEeCC------CccHH---HHHHHHHHHCCCCEEeeEeCcCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcC
Confidence            346667777765      44333   3344566678999999   899999999999995       4678888888776


Q ss_pred             CccccccCCCCCh--hHHHHHHHHHHhcCceeeeceeeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHH
Q 020247          242 HPRVADRMPSVPE--NVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMH  319 (329)
Q Consensus       242 Hp~m~~~~~~iP~--tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s~~~fe~v~~yA~~~g~llw~~~~kr~~~V~~~~h~~  319 (329)
                      .|       .+|=  |..+=..-|+.=-+-+|+.|+-.+-   .       .+|.+.+...+   +.-++|-+.-=.-++
T Consensus        98 i~-------~iPG~~TptEi~~A~~~Ga~~vK~FPa~~~G---G-------~~yikal~~pl---p~~~l~ptGGV~~~n  157 (201)
T PRK06015         98 VP-------LLPGAATPSEVMALREEGYTVLKFFPAEQAG---G-------AAFLKALSSPL---AGTFFCPTGGISLKN  157 (201)
T ss_pred             CC-------EeCCCCCHHHHHHHHHCCCCEEEECCchhhC---C-------HHHHHHHHhhC---CCCcEEecCCCCHHH
Confidence            66       7775  7788888999999999998864441   0       34556655444   344444433333478


Q ss_pred             HHHHHhh
Q 020247          320 MREFLRG  326 (329)
Q Consensus       320 vr~f~k~  326 (329)
                      +.+|++.
T Consensus       158 ~~~~l~a  164 (201)
T PRK06015        158 ARDYLSL  164 (201)
T ss_pred             HHHHHhC
Confidence            8888874

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

Probab=80.25  E-value=20  Score=33.40  Aligned_cols=162  Identities=18%  Similarity=0.229  Sum_probs=103.6

Q ss_pred             CCHHHHHHHHHHhhcCceeeecCC-CccccccchhhhhcccccCCccccccceEEEeeceeEEeecCChhHHHHHHHhhh
Q 020247          124 LSEIQKSMIKDFADLGLVKLQQGR-KENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSK  202 (329)
Q Consensus       124 lt~~q~~~L~~L~d~GLVy~~~~~-~~~fy~pT~La~~L~~~~~~~~~~~~g~IIVETNFrvYAYT~S~lqiaiL~lF~e  202 (329)
                      +++++..+++.|.+.|+|-.-+.. .....   +++-.+         .+.|.=++|--++      +|--   +..+.+
T Consensus         1 ~~~~~~~~~~~l~~~~~iaV~r~~~~~~a~---~i~~al---------~~~Gi~~iEitl~------~~~~---~~~I~~   59 (212)
T PRK05718          1 MKNWKTSIEEILRAGPVVPVIVINKLEDAV---PLAKAL---------VAGGLPVLEVTLR------TPAA---LEAIRL   59 (212)
T ss_pred             CchhHHHHHHHHHHCCEEEEEEcCCHHHHH---HHHHHH---------HHcCCCEEEEecC------CccH---HHHHHH
Confidence            367888899999999999665432 11111   111111         2335556776643      4433   344455


Q ss_pred             hhhccCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHHhcCCccccccCCCCCh--hHHHHHHHHHHhcCce
Q 020247          203 VEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAHPRVADRMPSVPE--NVCDQIRLWESDLNRV  270 (329)
Q Consensus       203 l~~r~PNlvvg---~iTReSV~~Al~~GI-------TA~QII~fL~~hAHp~m~~~~~~iP~--tV~dQI~lWe~Er~Rl  270 (329)
                      +..+||++.||   ++|.+.++.|++.|-       ..+.+|++-..+-.|       .+|-  |..+=...|+.--+-+
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            55679999999   899999999999984       456899988876555       7775  4466445888888888


Q ss_pred             eeeceeeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhh
Q 020247          271 EMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRG  326 (329)
Q Consensus       271 ~~~~g~Ly~~f~s~~~fe~v~~yA~~~g~llw~~~~kr~~~V~~~~h~~vr~f~k~  326 (329)
                      ++.|+-.+-          =.+|-+.+...+   +.-+.+.+.-=.-+++++|++.
T Consensus       133 KlFPa~~~g----------g~~~lk~l~~p~---p~~~~~ptGGV~~~ni~~~l~a  175 (212)
T PRK05718        133 KFFPAEASG----------GVKMLKALAGPF---PDVRFCPTGGISPANYRDYLAL  175 (212)
T ss_pred             EEccchhcc----------CHHHHHHHhccC---CCCeEEEeCCCCHHHHHHHHhC
Confidence            886533220          145666655444   4455555444445889999874

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	329
3dom_A	108	Crystal Structure Of The Complex Between Tfb5 And T		3e-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 = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 42/83 (50%)
Query: 243 PRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLW 302
           P   + +  +P  V DQIRLW+ +L+RV       Y +F +   +     YA+D   LLW
Sbjct: 19  PNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLW 78
Query: 303 EDPKKMRLVVKAEIHMHMREFLR 325
           +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	329
3dom_A	108	RNA polymerase II transcription factor B subunit;	7e-38
3dgp_A	80	RNA polymerase II transcription factor B subunit;	2e-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 (327), Expect = 7e-38
 Identities = 28/100 (28%), Positives = 49/100 (49%), Gaps = 1/100 (1%)

Query: 230 AEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEA 289
           AE+ +   +    P   + +  +P  V DQIRLW+ +L+RV       Y +F +   +  
Sbjct: 7   AEEKLEK-KLELDPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNL 65

Query: 290 ACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQNK 329
              YA+D   LLW+D KK +  +  E +  + +F + + K
Sbjct: 66  LSKYAQDIGVLLWKDDKKKKFFISKEGNSQVLDFAKRKLK 105

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

 Score =  109 bits (274), Expect = 2e-30
 Identities = 24/75 (32%), Positives = 39/75 (52%)

Query: 255 NVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKA 314
            V DQIRLW+ +L+RV       Y +F +   +     YA+D   LLW+D KK +  +  
Sbjct: 3   TVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISK 62

Query: 315 EIHMHMREFLRGQNK 329
           E +  + +F + + K
Sbjct: 63  EGNSQVLDFAKRKLK 77

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	329
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=8.2e-34  Score=234.09  Aligned_cols=88  Identities=30%  Similarity=0.586  Sum_probs=72.4

Q ss_pred             CccccccCCCCChhHHHHHHHHHHhcCceeeeceeeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHH
Q 020247          242 HPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMR  321 (329)
Q Consensus       242 Hp~m~~~~~~iP~tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s~~~fe~v~~yA~~~g~llw~~~~kr~~~V~~~~h~~vr  321 (329)
                      .|+++.+.|+|||||+|||||||.||||+++++||||++|.|+++|+++++||+++|+|+|+|+.+|+|||+.+||++||
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            35555668999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhccC
Q 020247          322 EFLRGQNK  329 (329)
Q Consensus       322 ~f~k~~~~  329 (329)
                      +|||++++
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=9.2e-32  Score=211.69  Aligned_cols=76  Identities=32%  Similarity=0.588  Sum_probs=61.7

Q ss_pred             hhHHHHHHHHHHhcCceeeeceeeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhhccC
Q 020247          254 ENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQNK  329 (329)
Q Consensus       254 ~tV~dQI~lWe~Er~Rl~~~~g~Ly~~f~s~~~fe~v~~yA~~~g~llw~~~~kr~~~V~~~~h~~vr~f~k~~~~  329 (329)
                      |||+|||||||.|||||++++|+||++|+|+++|+++++||+++|+|+|+|+.+|+|||+.+||++||+|||++|+
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

ID	Length	Definition	Probability
Query	329
d1b0na1	35	SinR repressor dimerisation domain {Bacillus subti	80.11

>d1b0na1 a.34.1.1 (A:74-108) SinR repressor dimerisation domain {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: Dimerisation interlock
superfamily: SinR repressor dimerisation domain-like
family: SinR repressor dimerisation domain-like
domain: SinR repressor dimerisation domain
species: Bacillus subtilis [TaxId: 1423]

Probab=80.11  E-value=0.71  Score=28.71  Aligned_cols=21  Identities=24%  Similarity=0.455  Sum_probs=19.0

Q ss_pred             HHHHHHHcCCCHHHHHHHHHh
Q 020247          219 SLYNAFENGITAEQIISFLQQ  239 (329)
Q Consensus       219 SV~~Al~~GITA~QII~fL~~  239 (329)
                      =|+.|+..||+-+|.-.||+-
T Consensus         8 lVkeAM~SGvSK~QFrEflef   28 (35)
T d1b0na1           8 LVRDAMTSGVSKKQFREFLDY   28 (35)
T ss_dssp             HHHHHHHSCCCHHHHHHHHHH
T ss_pred             HHHHHHHccCCHHHHHHHHHH
Confidence            489999999999999999973