Citrus Sinensis ID: 040211

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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
Protein Sequence
SNLWKHLINGGALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTIADSLETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTAEQQNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEFPSREDSKKMRLVVNAEIHMHMREFLRGQNK
Secondary Structure (PSIPRED)
cHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHccccccccccccccHHHHHHHcccccHHHHHHHHHHHHHHHHcHHHHHHHcccHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHcccEEEEccccccEEccccccccccccEEEEEcccHHHHHHHHHHHHHHHcccccEEEEEcHHHHHHHHHccccHHHHHccHHHHcccccccccHHHHHHHHHHHHccEEEcccEEccccccHHHHHHHEEEEcccccHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHcccccccccccEEcHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHccEEEEEcccccccccccEEEEEEEcEEEEEEcccHHHHHHHHHHHHHHHHcccEEEEEEcHHHHHHHHHccccHHHHHHcHHHccccccccccHHHHHHHHHHHHccEEEcccEEEcccccHHHHHHHHHHHHHcccHHHHHHHHHccc
Coil and Loop (DISEMBL)
snlwkhlinggalprepmpsgitarlptledLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRglliqrdkeaprltesGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKlqqgrkeswfipTIADSLETNFRMYAYSTSKLHCEILRLFSKIEyqlpnlivgaITKESLYNAVENgltaeqqnahprvadripsvLENVCDQIRLWESDlnrvemtpahyydefpsredskkMRLVVNAEIHMHMREFLRGQNK
Flexible Loop (DISEMBL)
snlwkhlinggalprepmpsGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLqqgrkeswfiptIADSLETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTAEQQNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHyydefpsredskKMRLVVNAEIHMHMreflrgqnk
Low Complexity Region (SEG)
SNLWKHLINGGALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTIADSLETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTAEQQNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEFPSREDSKKMRLVVNAEIHMHMREFLRGQNK
Disordered region (IsUnstruct)
*****HLI*************ITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTIADSLETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTAE***AHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDE***********LVVNAEIHM***********
Disordered Region (DISOPRED)
SNLWKHLINGGAL******************LEAYAIGQWERFLLQL*******************FQ***************ESGFQFLLMDTNAQLWYIVREYISNSQHDS******GINQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTIADSLETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTAEQQNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEFPSREDSKKMRLVVNAEIHMHMREFLRGQ**
Disordered Region (DISEMBL)
SNLWKHLINGGALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTIADSLETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTAEQQNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEFPSREDSKKMRLVVNAEIHMHMREFLRGQNK
Disordered Region (DISPRO)
*NL**HLINGGALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTIADSLETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTAEQQNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEFPSREDSKKMRLVVNAEIHMHMREFLRGQ**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
SNLWKHLINGGALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTIADSLETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTAEQQNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEFPSREDSKKMRLVVNAEIHMHMREFLRGQNK
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	310	2.2.26 [Sep-21-2011]
P60027	462	General transcription fac	yes	no	0.870	0.584	0.303	2e-35
Q92759	462	General transcription fac	yes	no	0.870	0.584	0.303	2e-35
O70422	463	General transcription fac	yes	no	0.870	0.583	0.303	5e-35
P87303	447	RNA polymerase II transcr	yes	no	0.790	0.548	0.299	8e-32
Q6BZX4	467	RNA polymerase II transcr	yes	no	0.796	0.528	0.286	3e-31
Q54C29	483	General transcription fac	yes	no	0.780	0.501	0.293	7e-27
Q6BGW8	515	RNA polymerase II transcr	yes	no	0.783	0.471	0.263	1e-24
Q6CLR2	496	RNA polymerase II transcr	yes	no	0.787	0.491	0.263	2e-24
Q6FP41	504	RNA polymerase II transcr	yes	no	0.783	0.482	0.251	6e-21
Q02939	513	RNA polymerase II transcr	yes	no	0.354	0.214	0.335	7e-12

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

 Score =  149 bits (376), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 99/326 (30%), Positives = 168/326 (51%), Gaps = 56/326 (17%)

Query: 29  LEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQRDK-EAPRLTESGF 87
           +  L+ YA  +WE  L  ++ S  A  S +       + Q GL+   +  E P +T +GF
Sbjct: 145 VPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQ---LLSQAGLMKSTEPGEPPCITSAGF 201

Query: 88  QFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTL 147
           QFLL+DT AQLWY + +Y+  +Q        RG++  +++SFL +LSF   G+ Y+++ +
Sbjct: 202 QFLLLDTPAQLWYFMLQYLQTAQ-------SRGMDLVEILSFLFQLSFSTLGKDYSVEGM 254

Query: 148 SEIQRSMIKDFADLGLVKLQQGRKESWFIPT-IADSL-------------------ETNF 187
           S+   + ++   + GLV  Q+ RK   + PT +A +L                   ETN+
Sbjct: 255 SDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGFIVVETNY 313

Query: 188 RMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTAEQ------QNAH 241
           R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A+ +G+TA+Q        AH
Sbjct: 314 RLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLRTRAH 373

Query: 242 PRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEFPSR------------------ 283
           P +  + P +   + DQIRLWE + +R+  T    Y++F S+                  
Sbjct: 374 PVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARELGVLVF 433

Query: 284 EDSKKMRLVVNAEIHMHMREFLRGQN 309
           E+S K  +VV    H  ++ F + Q 
Sbjct: 434 ENSAKRLMVVTPAGHSDVKRFWKRQK 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 =  149 bits (376), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 99/326 (30%), Positives = 168/326 (51%), Gaps = 56/326 (17%)

Query: 29  LEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQRDK-EAPRLTESGF 87
           +  L+ YA  +WE  L  ++ S  A  S +       + Q GL+   +  E P +T +GF
Sbjct: 145 VPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQ---LLSQAGLMKSTEPGEPPCITSAGF 201

Query: 88  QFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTL 147
           QFLL+DT AQLWY + +Y+  +Q        RG++  +++SFL +LSF   G+ Y+++ +
Sbjct: 202 QFLLLDTPAQLWYFMLQYLQTAQ-------SRGMDLVEILSFLFQLSFSTLGKDYSVEGM 254

Query: 148 SEIQRSMIKDFADLGLVKLQQGRKESWFIPT-IADSL-------------------ETNF 187
           S+   + ++   + GLV  Q+ RK   + PT +A +L                   ETN+
Sbjct: 255 SDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGFIVVETNY 313

Query: 188 RMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTAEQ------QNAH 241
           R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A+ +G+TA+Q        AH
Sbjct: 314 RLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLRTRAH 373

Query: 242 PRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEFPSR------------------ 283
           P +  + P +   + DQIRLWE + +R+  T    Y++F S+                  
Sbjct: 374 PVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARELGVLVF 433

Query: 284 EDSKKMRLVVNAEIHMHMREFLRGQN 309
           E+S K  +VV    H  ++ F + Q 
Sbjct: 434 ENSAKRLMVVTPAGHSDVKRFWKRQK 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 =  148 bits (373), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 99/326 (30%), Positives = 168/326 (51%), Gaps = 56/326 (17%)

Query: 29  LEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQRDK-EAPRLTESGF 87
           +  L+ YA  +WE  L  ++ S  A  S +       + Q GL+   +  E P +T +GF
Sbjct: 146 VPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQ---LLSQAGLMKSTEPGEPPCITSAGF 202

Query: 88  QFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTL 147
           QFLL+DT AQLWY + +Y+  +Q        RG++  +++SFL +LSF   G+ Y+++ +
Sbjct: 203 QFLLLDTPAQLWYFMLQYLQTAQ-------SRGMDLVEILSFLFQLSFSTLGKDYSVEGM 255

Query: 148 SEIQRSMIKDFADLGLVKLQQGRKESWFIPT-IADSL-------------------ETNF 187
           S+   + ++   + GLV  Q+ RK   + PT +A +L                   ETN+
Sbjct: 256 SDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGFIVVETNY 314

Query: 188 RMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTAEQ------QNAH 241
           R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A+ +G+TA+Q        AH
Sbjct: 315 RLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLRTRAH 374

Query: 242 PRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEFPSR------------------ 283
           P +  + P +   + DQIRLWE + +R+  T    Y++F S+                  
Sbjct: 375 PVMLKQNPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARELGVLVF 434

Query: 284 EDSKKMRLVVNAEIHMHMREFLRGQN 309
           E+S K  +VV    H  ++ F + Q 
Sbjct: 435 ENSAKRLMVVTPAGHSDVKRFWKRQK 460

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

Mus musculus (taxid: 10090)

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

 Score =  137 bits (346), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 85/284 (29%), Positives = 146/284 (51%), Gaps = 39/284 (13%)

Query: 26  LPTLEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQRDKEAPRLTES 85
           L T++ L+AYA   WE  L  ++ + +A+         + + +RG L+   K   R+T +
Sbjct: 125 LVTVDFLDAYAKETWETILHFMVGTPEAKFP---GEGVLSLLKRGGLMSGPKNQLRITRA 181

Query: 86  GFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLK 145
           GFQFLL D NAQ+W ++ +Y+  S+   M       +   ++ FL  L     G AY++ 
Sbjct: 182 GFQFLLQDINAQIWTLLLDYLKLSEDTHM-------DPVQVLHFLFMLGSLDLGRAYSVD 234

Query: 146 TLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTIADSL---------------------- 183
            L++ Q+ M++D  + GLV  ++   + ++   +A  L                      
Sbjct: 235 FLTDTQQIMLEDLREYGLVYQRKITSKRFYPTRLATGLTTDYRSLHGKQSENDDDKGFII 294

Query: 184 -ETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTAEQ----- 237
            ETN+R+YAY++S L   I+ LF+ +  +  NL+VG IT++S+  A+ NG+ AEQ     
Sbjct: 295 VETNYRLYAYTSSPLQIAIIGLFANLRARFSNLVVGVITRDSIRRALMNGIAAEQIITYL 354

Query: 238 -QNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEF 280
             +AHP++   +P +   + DQI LWE + NR+  TP   + +F
Sbjct: 355 TTHAHPQMRSNVPLLPPTLVDQIYLWELEKNRLRATPGILFRDF 398

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

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

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

 Score =  135 bits (341), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 86/300 (28%), Positives = 150/300 (50%), Gaps = 53/300 (17%)

Query: 32  LEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQRDKEAPRLTESGFQFLL 91
           L+A+A+ QWE  L  ++ ++            + + +   L++ ++   R+T +GFQFLL
Sbjct: 133 LDAHAVSQWEMILHFMVGTSIGRTP---SDGVLNLLKHSGLMEPERGGLRITNAGFQFLL 189

Query: 92  MDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQ 151
            D NAQ+W ++ +Y++ S++  M       +  D+++F+  L     G+ Y+L  LSE Q
Sbjct: 190 QDVNAQIWTLLLQYLNMSEYLQM-------DPVDVLNFIFMLGSLELGQDYSLSALSETQ 242

Query: 152 RSMIKDFADLGLVKLQQGRKESWFIPT--------------------------------I 179
           + M++D  D G+V  Q+      F PT                                 
Sbjct: 243 KHMLEDLRDYGIV-YQRKASSRRFYPTRLATTLTSETAALRTASQSMEAATQDTISSSVA 301

Query: 180 ADS----LETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTA 235
           ADS    LETNFR+YAY+ S L   +L LF  ++ +  N++ G I ++S+  A+ NG+TA
Sbjct: 302 ADSGFIILETNFRLYAYTESPLQIAVLNLFVNLKTRFANMVTGQINRDSVRFALSNGITA 361

Query: 236 EQ------QNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEFPSREDSKKM 289
           EQ       +AHPR+      +   V DQI+LW+ +++R+  T  + + EF + ++ K +
Sbjct: 362 EQIITYLSVHAHPRMKGMEHVLPPTVVDQIKLWQLEMDRIRATDGYLFSEFKNFDEYKDV 421

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

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

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

 Score =  121 bits (303), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 88/300 (29%), Positives = 148/300 (49%), Gaps = 58/300 (19%)

Query: 27  PTLEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQRDKEAPRLTESG 86
           P+++DL++Y+  QWE+ L  L     ++ ++       ++     L +++ +   +T  G
Sbjct: 156 PSIDDLDSYSKSQWEKVLYFL-----SDDTVQPSKLISELLLSSNLTKQEGDGLSITSEG 210

Query: 87  FQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQA---DLISFLLELSFHVAGEAYN 143
           F+FLL D   Q+W ++  Y+ +      L  ++G       DL+SFL  LSF   G  Y 
Sbjct: 211 FKFLLKDVYTQIWTLLIVYLDD------LEKKKGKGSGSRNDLLSFLFRLSFLNLGRGYL 264

Query: 144 LKTLSEIQRSMIKDFADLGLVKLQ---------------------------------QGR 170
           +  LSE Q+  +      GL+ ++                                 Q +
Sbjct: 265 VSELSEQQKEYLFALKQFGLIYMRTDSSILFYPTRLIISLTTGKTLSLIQSISSERTQTQ 324

Query: 171 KESWFIPTIADSLETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAVE 230
           KE  +I      LETN+R+YAY++S L   +L LF K+ Y+LPNL VG IT+ES+  A+ 
Sbjct: 325 KEQGYI-----VLETNYRLYAYTSSSLQISLLSLFVKMLYRLPNLAVGIITRESIRTALI 379

Query: 231 NGLTAEQ------QNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEFPSRE 284
           +G+TA+Q       N+HP  A+    + + V +QI LWE++ NR+  T +  Y+ FP+ +
Sbjct: 380 HGITADQIIDFVRHNSHPNAANSGQPIPDVVAEQILLWEAERNRITYTKSVLYNSFPTND 439

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 =  114 bits (285), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 91/346 (26%), Positives = 158/346 (45%), Gaps = 103/346 (29%)

Query: 32  LEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQ-RDKEAPRL--TESGFQ 88
           L+++A+ +WE  L  ++ +   E S+   +S + + + G L++  +K   RL  T SGFQ
Sbjct: 137 LDSFALQKWESILHFMVGT---ELSVTPSNSVLSLLKSGGLMEGTNKGGNRLNITNSGFQ 193

Query: 89  FLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLS 148
           FLL D NAQ+W ++ +Y++ +Q  +M       +  D+++F+  L     G+ Y + +LS
Sbjct: 194 FLLQDINAQIWTLLLQYLNLTQDLNM-------DPVDVLNFIFILGSLELGKGYTVSSLS 246

Query: 149 EIQRSMIKDFADLGLVKLQQGRKESWFIPT------IADS-------------------- 182
           E Q SM+ D  D GL+  Q+      F PT       +DS                    
Sbjct: 247 ETQISMLADLRDYGLI-YQRSENSERFYPTRLATTLTSDSAALKSPSMAMEQALESTTET 305

Query: 183 ----------------LETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLY 226
                           LETNF++YAY+ S L   IL LF  ++ +  N++ G IT+ES+ 
Sbjct: 306 EEQQNLASNSNQGTIILETNFKIYAYTNSPLEIAILNLFVHLKTRFSNMVCGQITRESIR 365

Query: 227 NAVENGLTAEQ------QNAHPRV----ADRIPSVLE----------------------- 253
           NA+ NG+TA+Q       +AH ++     +R+   +E                       
Sbjct: 366 NALYNGITADQIIKFLETHAHSQMKILAKERLDKKIEFDTSNNINTAGGAPQSQMMTNEN 425

Query: 254 --------------NVCDQIRLWESDLNRVEMTPAHYYDEFPSRED 285
                          V DQI+LW+ +L+R++    + + +F S+++
Sbjct: 426 GTTVAQHKLEVLPPTVVDQIKLWQLELDRIQTFEGYLFKDFASQQE 471

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

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

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

 Score =  113 bits (282), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 86/326 (26%), Positives = 145/326 (44%), Gaps = 82/326 (25%)

Query: 32  LEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQR-GLLIQRDKEAPRLTESGFQFL 90
           L+ Y+  +WE  L  ++ +             + + Q  GL+ + +    ++T  GFQFL
Sbjct: 137 LDQYSAEKWETILHYMVGTPNTNTP---GGKVLDLLQHSGLMEEAEYGELKITNQGFQFL 193

Query: 91  LMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEI 150
           L D NAQ+W ++ +Y+        +A    ++  D+++F+  L     G+AY    LS  
Sbjct: 194 LQDVNAQMWTLLLQYLK-------MAESLQMDPVDVLNFIFMLGALQLGKAYKCDQLSNT 246

Query: 151 QRSMIKDFADLGLVKLQQGRKESWFIPTIA------------------------------ 180
           QR+M++D  D GL+   Q     ++   +A                              
Sbjct: 247 QRTMLQDMRDYGLIYQNQSDYAKFYPTRLATLLTSDTKAFRSASVALDSVLNKANETTAV 306

Query: 181 --DS---------------LETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKE 223
             DS               +ETNF++Y+YS S L   IL LF  ++ +  N++ G +T+E
Sbjct: 307 EGDSGQDETTERTQDGALIIETNFKLYSYSNSPLQIAILSLFVHLKSRFANMVTGQLTRE 366

Query: 224 SLYNAVENGLTAEQ------QNAHPRV-----------ADRIPSVLE-------NVCDQI 259
           S+ NA+ NG+TAEQ       +AHPR+            +  P+V E        V DQI
Sbjct: 367 SVRNALLNGITAEQIIAYLETHAHPRMRRLAEENLSKKLELDPTVKETLQVLPPTVVDQI 426

Query: 260 RLWESDLNRVEMTPAHYYDEFPSRED 285
           RLW+ +L+R+     + Y +F S ++
Sbjct: 427 RLWQLELDRIISYDGYLYTDFESYQE 452

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|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 =  101 bits (252), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 83/330 (25%), Positives = 141/330 (42%), Gaps = 87/330 (26%)

Query: 32  LEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQR--DKEAPRLTESGFQF 89
           L+ YA  +WE  L  ++ +  A+       + + + +   L++   D     +T  GFQF
Sbjct: 139 LDEYAATKWETILHFMVGTPMAKMP---SENVLNLLKHSKLMEEVPDSSEFMITNEGFQF 195

Query: 90  LLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSE 149
           LL + N+Q+W ++ +Y+        LA    ++   +++F+  L     G+AY+ + LSE
Sbjct: 196 LLQEVNSQIWSLLLQYLK-------LAESLHMDPVHVLNFIFMLGALETGKAYSTENLSE 248

Query: 150 IQRSMIKDFADLGLVKLQQGRKESWFIPT------------------------------- 178
            Q  M+ D  D GLV  Q+    + F PT                               
Sbjct: 249 TQLKMLLDMRDYGLV-FQKTSNPNIFYPTRLAQMLTSDTKSMRTASGAMESVLNKPDDAA 307

Query: 179 ----------------IADS---LETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGA 219
                           I D    +ETNF++Y+Y  S L   IL LF  ++ +  N++ G 
Sbjct: 308 KSTDDKYDSLEGKAEDIQDGALIIETNFKLYSYCNSPLQIAILSLFVHLKSRFANMVAGQ 367

Query: 220 ITKESLYNAVENGLTAEQ------QNAHPRV------------------ADRIPSVLENV 255
           IT+ES+  A+ NG+TA+Q       +AHP++                   D +  +   V
Sbjct: 368 ITRESIRRALINGITADQVIAYLESHAHPQMRRLAEEKLQKKLELDPNCKDPLQVLPPTV 427

Query: 256 CDQIRLWESDLNRVEMTPAHYYDEFPSRED 285
            DQI+LW+ +L+RV       Y +F + +D
Sbjct: 428 VDQIKLWQLELDRVLTYEGSLYIDFDTAQD 457

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

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

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

 Score = 71.6 bits (174), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 45/134 (33%), Positives = 73/134 (54%), Gaps = 24/134 (17%)

Query: 176 IPTIADSLETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTA 235
           IP  +  +ETNF++Y+YS S L   +L LF  ++ +  N+++G IT+ES+  A+ NG+TA
Sbjct: 334 IPDGSLIVETNFKIYSYSNSPLQIAVLSLFVHLKARFVNMVLGQITRESIRRALTNGITA 393

Query: 236 EQ------QNAHP---RVADRI--------PSVLE-------NVCDQIRLWESDLNRVEM 271
           +Q       +AHP   R+A+          P+  E        V DQIRLW+ +L+RV  
Sbjct: 394 DQIIAYLETHAHPQMRRLAEEKLEKKLELDPNCKEPLQVLPPTVVDQIRLWQLELDRVIT 453

Query: 272 TPAHYYDEFPSRED 285
                Y +F + ++
Sbjct: 454 YEGSLYSDFETSQE 467

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

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

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	310
147854406	451	hypothetical protein VITISV_005315 [Viti	0.964	0.662	0.698	1e-133
255556021	451	tfiih, polypeptide, putative [Ricinus co	0.970	0.667	0.688	1e-133
449433857	451	PREDICTED: general transcription factor	0.970	0.667	0.694	1e-130
224077128	449	predicted protein [Populus trichocarpa]	0.964	0.665	0.665	1e-126
358346685	451	General transcription factor IIH subunit	0.967	0.665	0.661	1e-125
357461579	452	General transcription factor IIH subunit	0.951	0.652	0.662	1e-124
356521347	451	PREDICTED: general transcription factor	0.970	0.667	0.642	1e-121
356548733	451	PREDICTED: general transcription factor	0.970	0.667	0.645	1e-121
297800414	452	hypothetical protein ARALYDRAFT_493174 [	0.977	0.670	0.622	1e-119
42566894	452	transcription initiation factor TFIIH su	0.977	0.670	0.619	1e-119

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

 Score =  481 bits (1239), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 243/348 (69%), Positives = 271/348 (77%), Gaps = 49/348 (14%)

Query: 1   SNLWKHLINGGALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFC 60
           +NL KHLI GG LPREPMPS IT RLP+L+DLEAYA+GQWE FLLQLISS Q E+  NF 
Sbjct: 108 TNLQKHLIYGGVLPREPMPSNITVRLPSLDDLEAYALGQWECFLLQLISSTQTEKLTNFS 167

Query: 61  SSTMKVFQRGLLIQRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERG 120
           SS MKVFQRGLL QR+KEAPRLTESGFQFLLMDTNAQLWYI+REYISNS+       ERG
Sbjct: 168 SSLMKVFQRGLLTQREKEAPRLTESGFQFLLMDTNAQLWYIMREYISNSE-------ERG 220

Query: 121 INQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPT-- 178
           ++ ADLISFLLELSFHV GEAYN+ TL+E QR+ IKD  DLGLVKLQQGRKESWFIPT  
Sbjct: 221 VDPADLISFLLELSFHVTGEAYNINTLTEFQRNTIKDLVDLGLVKLQQGRKESWFIPTKL 280

Query: 179 -------IADS---------LETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITK 222
                  ++D+         +ETNFR+YAYS+SKLHCEILRLFS++EYQLPNLIVGAITK
Sbjct: 281 ATNLSMSLSDTSSRKQGFVVVETNFRLYAYSSSKLHCEILRLFSRVEYQLPNLIVGAITK 340

Query: 223 ESLYNAVENGLTAE------QQNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHY 276
           ESLYNA ENG+TAE      QQNAHPRVA+R P+V ENV DQIRLWE+DLNRVE  P+H 
Sbjct: 341 ESLYNAFENGITAEQIISFLQQNAHPRVAERTPAVPENVTDQIRLWETDLNRVETMPSHL 400

Query: 277 YDEFPSR------------------EDSKKMRLVVNAEIHMHMREFLR 306
           YDEFPSR                  EDSKKMRLVV AEIH+HMRE+LR
Sbjct: 401 YDEFPSRDVFEAACDFAREYGGLLWEDSKKMRLVVKAEIHLHMREYLR 448

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  480 bits (1235), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 241/350 (68%), Positives = 273/350 (78%), Gaps = 49/350 (14%)

Query: 1   SNLWKHLINGGALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFC 60
           +NL KHLI+GG LP EP+ S I  RLPTLE+L+ YA+GQWE FLL LI+S  AERS NF 
Sbjct: 108 TNLQKHLIDGGVLPGEPLASNIAVRLPTLEELDTYALGQWECFLLHLINSGHAERSTNFS 167

Query: 61  SSTMKVFQRGLLIQRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERG 120
           SS MK+FQRGLL QRDKEAPRLTESGFQFLLMDTNAQLWYI+REYISNS+       ERG
Sbjct: 168 SSMMKIFQRGLLTQRDKEAPRLTESGFQFLLMDTNAQLWYIIREYISNSE-------ERG 220

Query: 121 INQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPT-- 178
           ++ ADLISFLLELSFH+ GEAYN+  L+E QR+MIKD ADLGLVKLQQGRKESWFIPT  
Sbjct: 221 LDSADLISFLLELSFHITGEAYNMIMLTEFQRNMIKDLADLGLVKLQQGRKESWFIPTKL 280

Query: 179 -------IADS---------LETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITK 222
                  + DS         +ETNFRMYAYSTSKLHCEI+RLFS++EYQLPNL+VGA+TK
Sbjct: 281 ATNLSMSLTDSSSRKQGFVVVETNFRMYAYSTSKLHCEIMRLFSRVEYQLPNLVVGAMTK 340

Query: 223 ESLYNAVENGLTAE------QQNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHY 276
           ESLY+A ENG+TAE      QQNAHPRVA+RIPSV ENV DQIRLWESD+NRVEMTPAH 
Sbjct: 341 ESLYSAFENGITAEQIISFLQQNAHPRVAERIPSVPENVTDQIRLWESDMNRVEMTPAHL 400

Query: 277 YDEFPSR------------------EDSKKMRLVVNAEIHMHMREFLRGQ 308
           YDEFPSR                  EDSK+MR+VV AEIH++MRE+LRGQ
Sbjct: 401 YDEFPSRDVFEAACNFARDWNGLLWEDSKRMRMVVKAEIHLNMREYLRGQ 450

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  469 bits (1206), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 243/350 (69%), Positives = 270/350 (77%), Gaps = 49/350 (14%)

Query: 1   SNLWKHLINGGALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFC 60
           +NL K LI+G  L REPMPS IT RLP+LEDLEAYA+ QWE FLLQLI+S QAE+  N  
Sbjct: 108 ANLQKLLIHGEVLAREPMPSNITVRLPSLEDLEAYALDQWECFLLQLINSGQAEKPSNIS 167

Query: 61  SSTMKVFQRGLLIQRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERG 120
           SS MKVFQ+GLL QRDKEAPRLTESGFQFLLM+TNAQLWYI+REYISN++       ERG
Sbjct: 168 SSVMKVFQKGLLSQRDKEAPRLTESGFQFLLMETNAQLWYIIREYISNAE-------ERG 220

Query: 121 INQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPT-- 178
           ++ ADLISFLLELSFHV GEAY++ TLS+ QR  IKD ADLGLVKLQQGRKESWFIPT  
Sbjct: 221 VDPADLISFLLELSFHVTGEAYDIDTLSDEQRYAIKDLADLGLVKLQQGRKESWFIPTKL 280

Query: 179 -------IADS---------LETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITK 222
                  +ADS         +ETNFRMYAYSTSKLHCEILRLFS+IEYQLPNLIVGAITK
Sbjct: 281 ATNLSMSLADSSSRKLGFVVVETNFRMYAYSTSKLHCEILRLFSRIEYQLPNLIVGAITK 340

Query: 223 ESLYNAVENGLTAE------QQNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHY 276
           ESLYNA +NG+TAE      QQNAHPRVA+RIPSV ENV DQIRLWESDLNRV++TPAH+
Sbjct: 341 ESLYNAFKNGITAEQIVTFLQQNAHPRVAERIPSVPENVTDQIRLWESDLNRVDITPAHF 400

Query: 277 YDEFPSR------------------EDSKKMRLVVNAEIHMHMREFLRGQ 308
           YDEFPSR                  EDSK +RLVV A+IH HMRE LR Q
Sbjct: 401 YDEFPSREVFEAACDYAREWNGLLWEDSKNLRLVVKADIHTHMREHLRRQ 450

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  456 bits (1172), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 233/350 (66%), Positives = 268/350 (76%), Gaps = 51/350 (14%)

Query: 1   SNLWKHLINGGALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFC 60
           +NL KHL NGG LPRE M + +  +LP+LE+L+ YA+ QWE FLL LISS QAE+  +  
Sbjct: 108 ANLRKHLTNGGVLPRETMAAVV--KLPSLEELDTYALEQWECFLLLLISSGQAEKPTSLS 165

Query: 61  SSTMKVFQRGLLIQRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERG 120
           SS MK+FQRGLL QRD++APRLTE GFQFLLMDTNAQLWYI+REYI+NS+       ERG
Sbjct: 166 SSMMKIFQRGLLSQRDRDAPRLTEGGFQFLLMDTNAQLWYIIREYITNSE-------ERG 218

Query: 121 INQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPT-- 178
              ADLISFLLELSFHV GEAYN+ TL+EIQR+ IKD A+LGLVKLQQGRKESWFIPT  
Sbjct: 219 TEPADLISFLLELSFHVTGEAYNMNTLTEIQRNTIKDLAELGLVKLQQGRKESWFIPTKL 278

Query: 179 -------IADS---------LETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITK 222
                  + DS         +ETNFR+YAYS+SKLHCEILRLFSKIEYQLPNLIVGAITK
Sbjct: 279 ATNLSVSLTDSSSRKQGYVVVETNFRLYAYSSSKLHCEILRLFSKIEYQLPNLIVGAITK 338

Query: 223 ESLYNAVENGLTAE------QQNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHY 276
           ESLY A ENG+T++      QQNAHPRVA+R+PSV ENV DQIRLWE+DLNRVE+TP+H+
Sbjct: 339 ESLYTAFENGITSDQIISFLQQNAHPRVAERLPSVPENVTDQIRLWEADLNRVEITPSHF 398

Query: 277 YDEFPSR------------------EDSKKMRLVVNAEIHMHMREFLRGQ 308
           YDEFPSR                  EDSKKMR+VV AEIHM+MREFLRGQ
Sbjct: 399 YDEFPSRDTFEAACDFAREWNGLLWEDSKKMRVVVKAEIHMNMREFLRGQ 448

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  453 bits (1165), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 231/349 (66%), Positives = 267/349 (76%), Gaps = 49/349 (14%)

Query: 2   NLWKHLINGGALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFCS 61
           +L K L++GG LPRE MPS IT RLPTLEDLE YA+ QWE FLLQLIS +  ++++N  S
Sbjct: 109 SLQKLLVHGGTLPRESMPSNITVRLPTLEDLETYALEQWECFLLQLISPSHVDKTLNISS 168

Query: 62  STMKVFQRGLLIQRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGI 121
           S MKVFQR LL QRD+EAP+LTESGFQFLLMDTNAQLWYI+REYI+NS+       ERG+
Sbjct: 169 SLMKVFQRRLLSQRDREAPKLTESGFQFLLMDTNAQLWYIIREYITNSE-------ERGV 221

Query: 122 NQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPT-IA 180
           +  DLISF+LELSFHV GEAYN+ TL+E QR++IKD ADLGLVKLQQGRKESWFIPT +A
Sbjct: 222 DAGDLISFMLELSFHVIGEAYNINTLTEFQRNIIKDLADLGLVKLQQGRKESWFIPTKLA 281

Query: 181 DSL-----------------ETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKE 223
            +L                 ETNFR+YAYSTSKLHCEILRLFS++EYQLPNLIVGAITKE
Sbjct: 282 TNLSVSMTESSSRKEGFVVVETNFRVYAYSTSKLHCEILRLFSRVEYQLPNLIVGAITKE 341

Query: 224 SLYNAVENGLTAEQ------QNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYY 277
           SLYNA +NG+TA+Q      QNAHPRVA RIP+V ENV DQIRLWESDLNRVEMT A+YY
Sbjct: 342 SLYNAFDNGITADQIVSFFRQNAHPRVAQRIPAVPENVTDQIRLWESDLNRVEMTEAYYY 401

Query: 278 DEFPSR------------------EDSKKMRLVVNAEIHMHMREFLRGQ 308
           DEFPSR                  EDSKKM LVV +E+H ++R+FLR Q
Sbjct: 402 DEFPSRDVFEGACDCAREWSGLLWEDSKKMHLVVKSEVHTYVRDFLRRQ 450

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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 =  451 bits (1160), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 228/344 (66%), Positives = 264/344 (76%), Gaps = 49/344 (14%)

Query: 7   LINGGALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKV 66
           L++GG LPRE MPS IT RLPTLEDLE YA+ QWE FLLQLIS +  ++++N  SS MKV
Sbjct: 115 LVHGGTLPRESMPSNITVRLPTLEDLETYALEQWECFLLQLISPSHVDKTLNISSSLMKV 174

Query: 67  FQRGLLIQRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADL 126
           FQR LL QRD+EAP+LTESGFQFLLMDTNAQLWYI+REYI+NS+       ERG++  DL
Sbjct: 175 FQRRLLSQRDREAPKLTESGFQFLLMDTNAQLWYIIREYITNSE-------ERGVDAGDL 227

Query: 127 ISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPT-IADSL-- 183
           ISF+LELSFHV GEAYN+ TL+E QR++IKD ADLGLVKLQQGRKESWFIPT +A +L  
Sbjct: 228 ISFMLELSFHVIGEAYNINTLTEFQRNIIKDLADLGLVKLQQGRKESWFIPTKLATNLSV 287

Query: 184 ---------------ETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNA 228
                          ETNFR+YAYSTSKLHCEILRLFS++EYQLPNLIVGAITKESLYNA
Sbjct: 288 SMTESSSRKEGFVVVETNFRVYAYSTSKLHCEILRLFSRVEYQLPNLIVGAITKESLYNA 347

Query: 229 VENGLTAEQ------QNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEFPS 282
            +NG+TA+Q      QNAHPRVA R+P+V ENV DQIRLWESDLNRVEMT A+YYDEFPS
Sbjct: 348 FDNGITADQIVSFLRQNAHPRVAQRVPAVPENVTDQIRLWESDLNRVEMTEAYYYDEFPS 407

Query: 283 R------------------EDSKKMRLVVNAEIHMHMREFLRGQ 308
           R                  EDSKKM LVV +E+H ++R+FLR Q
Sbjct: 408 RDVFEGACDCAREWSGLLWEDSKKMHLVVKSEVHTYVRDFLRRQ 451

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  442 bits (1137), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 225/350 (64%), Positives = 264/350 (75%), Gaps = 49/350 (14%)

Query: 2   NLWKHLINGGALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFCS 61
           +L K L+ GG LPRE MPS IT RLPTLE+LEAYA+ QWE FLLQLIS +Q E+ +N  S
Sbjct: 109 SLQKLLVQGGTLPRESMPSNITVRLPTLENLEAYALEQWECFLLQLISPSQVEKPLNISS 168

Query: 62  STMKVFQRGLLIQRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGI 121
           S MKVFQR +L  RDKEAP+LTESGFQFLLMDTNAQLWYI+REYISNS+       +RG+
Sbjct: 169 SLMKVFQRRILSHRDKEAPKLTESGFQFLLMDTNAQLWYIIREYISNSE-------DRGV 221

Query: 122 NQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPT--- 178
           + ADLISF+LELSFHV GEAY++ TL+  QR++I D ADLGLVK+QQGRK SWFIPT   
Sbjct: 222 DAADLISFMLELSFHVIGEAYSVDTLTSFQRTIINDLADLGLVKIQQGRKGSWFIPTKLA 281

Query: 179 ------IADS---------LETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKE 223
                 +ADS         +ETNFR+YAYSTSKLHCEILRLFS++EYQLPNLIVGAITKE
Sbjct: 282 TNLSMSLADSSSRKQGFVVVETNFRVYAYSTSKLHCEILRLFSRVEYQLPNLIVGAITKE 341

Query: 224 SLYNAVENGLTAE------QQNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYY 277
           SLY+A ENG+TAE      QQNAHPRVA+R+PSV ENV +QIRLWE+DLNRVEMT  +YY
Sbjct: 342 SLYSAYENGITAEQIVTFLQQNAHPRVAERVPSVPENVTEQIRLWEADLNRVEMTDTYYY 401

Query: 278 DEFPSR------------------EDSKKMRLVVNAEIHMHMREFLRGQN 309
           DEFPSR                  EDSKKM +VV  E+H ++R++LR Q 
Sbjct: 402 DEFPSRDVFEGACDCAREWNGLLWEDSKKMHMVVKTEVHPYVRDYLRRQK 451

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  441 bits (1134), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 226/350 (64%), Positives = 264/350 (75%), Gaps = 49/350 (14%)

Query: 2   NLWKHLINGGALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFCS 61
           +L K L+ GG LPRE MPS IT RLPTLE+LEAYA+ QWE FLLQLIS +Q E+ +N  S
Sbjct: 109 SLQKLLVQGGTLPRESMPSNITVRLPTLENLEAYALEQWECFLLQLISPSQVEKPLNISS 168

Query: 62  STMKVFQRGLLIQRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGI 121
           S MKVFQR +L  RDKEAP+LTESGFQFLLMDTNAQLWYI+REYISNS+       +RG+
Sbjct: 169 SLMKVFQRRILSYRDKEAPKLTESGFQFLLMDTNAQLWYIIREYISNSE-------DRGV 221

Query: 122 NQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPT--- 178
           + ADLISF+LELSFH  GEAY++ TL+  QR++I D ADLGLVK+QQGRK SWFIPT   
Sbjct: 222 DAADLISFMLELSFHDIGEAYSVDTLTSFQRTIINDLADLGLVKIQQGRKGSWFIPTKLA 281

Query: 179 ------IADS---------LETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKE 223
                 +ADS         +ETNFR+YAYSTSKLHCEILRLFS++EYQLPNLIVGAITKE
Sbjct: 282 TNLSMSLADSSSRKQGFVVVETNFRVYAYSTSKLHCEILRLFSRVEYQLPNLIVGAITKE 341

Query: 224 SLYNAVENGLTAE------QQNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYY 277
           SLY+A ENG+TAE      QQNAHPRVA+RIPSV ENV +QIRLWE+DLNRVEMT A+YY
Sbjct: 342 SLYSAFENGITAEQIITFLQQNAHPRVAERIPSVPENVTEQIRLWEADLNRVEMTDAYYY 401

Query: 278 DEFPSR------------------EDSKKMRLVVNAEIHMHMREFLRGQN 309
           DEFPSR                  EDSKKM +VV  E+H ++R++LR Q 
Sbjct: 402 DEFPSRDVFEGACDCAREWNGLLWEDSKKMHMVVKTEVHQYVRDYLRRQK 451

Source: Glycine max

Species: Glycine max

Genus: Glycine

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 =  434 bits (1116), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 219/352 (62%), Positives = 259/352 (73%), Gaps = 49/352 (13%)

Query: 1   SNLWKHLINGGALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFC 60
           +NL KH+I+GG LPREPM S    +LP+L++LE YA+ QWE FLLQLI+S Q E+     
Sbjct: 108 NNLQKHIISGGVLPREPMHSDNAIKLPSLQELETYALKQWECFLLQLINSGQGEKLTGIS 167

Query: 61  SSTMKVFQRGLLIQRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERG 120
           SS M++FQRGLL QRDK+ PRLTESGFQFLLMDTNAQLWYI+REYISN++       ER 
Sbjct: 168 SSMMRIFQRGLLSQRDKDGPRLTESGFQFLLMDTNAQLWYIIREYISNAE-------ERD 220

Query: 121 INQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPT-- 178
           +  ADLISFLLELSFHV GEAYN  TL+E+Q + +KD ADLGLVKLQQGRK+SWFIPT  
Sbjct: 221 VEPADLISFLLELSFHVTGEAYNSNTLTEVQNNTLKDLADLGLVKLQQGRKDSWFIPTKL 280

Query: 179 -------IADS---------LETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITK 222
                  +ADS         +ETNFRMYAYSTSKL CEILRLF++IEYQLPNLI  AITK
Sbjct: 281 ATNLSVSLADSSARKEGFVVMETNFRMYAYSTSKLQCEILRLFARIEYQLPNLIACAITK 340

Query: 223 ESLYNAVENGLTAE------QQNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHY 276
           ESLYNA +NG+T++      QQN+HPR ADR+PS+ ENV DQIRLWE+DL R+EMT AH+
Sbjct: 341 ESLYNAFDNGITSDQIITFLQQNSHPRCADRVPSIPENVTDQIRLWETDLKRIEMTQAHF 400

Query: 277 YDEFPSR------------------EDSKKMRLVVNAEIHMHMREFLRGQNK 310
           YDEFPS+                  EDSK+MRLVV +E+H  MREFL  Q K
Sbjct: 401 YDEFPSKDVFEAACDFAREWGGLLWEDSKRMRLVVKSEVHNQMREFLHNQTK 452

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  434 bits (1116), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 218/352 (61%), Positives = 261/352 (74%), Gaps = 49/352 (13%)

Query: 1   SNLWKHLINGGALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFC 60
           +NL KH+I+GG LPREPM S    +LP+L++LE YA+ QWE FLLQLI+S Q E+     
Sbjct: 108 NNLQKHIISGGVLPREPMNSDNAIKLPSLQELETYALKQWECFLLQLINSGQGEKLTGIS 167

Query: 61  SSTMKVFQRGLLIQRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERG 120
           SS MK+FQRGLL QRDK+ PRLTESGFQFLLMDTNAQLWYI+REYI N++       ER 
Sbjct: 168 SSMMKIFQRGLLSQRDKDGPRLTESGFQFLLMDTNAQLWYIIREYILNAE-------ERD 220

Query: 121 INQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPT-- 178
           ++ ADLISFLLELSFHV G+AYNL TL+E+Q + +KD ADLGLVKLQQGRK+SWFIPT  
Sbjct: 221 VDPADLISFLLELSFHVTGQAYNLNTLTEVQNNTLKDLADLGLVKLQQGRKDSWFIPTKL 280

Query: 179 -------IADS---------LETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITK 222
                  +ADS         +ETNFRMYAYSTSKL CEILRLF++IEYQLPNLI  AITK
Sbjct: 281 ATNLSVSLADSSARKEGFVVMETNFRMYAYSTSKLQCEILRLFARIEYQLPNLIACAITK 340

Query: 223 ESLYNAVENGLTAE------QQNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHY 276
           ESLYNA +NG+T++      QQN+HPR ADR+PS+ ENV DQIRLWE+DL R+EMT AH+
Sbjct: 341 ESLYNAFDNGITSDQIITFLQQNSHPRCADRVPSIPENVTDQIRLWETDLQRIEMTQAHF 400

Query: 277 YDEFPSR------------------EDSKKMRLVVNAEIHMHMREFLRGQNK 310
           YDEFPS+                  EDSK+MRLVV +E+H  MREFL  Q++
Sbjct: 401 YDEFPSKDVFEAACDFAREWRGLLWEDSKRMRLVVKSEVHNQMREFLHTQSR 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	310
ZFIN|ZDB-GENE-030131-6779	466	gtf2h4 "general transcription	0.348	0.231	0.385	1.9e-38
FB|FBgn0261109	499	mrn "marionette" [Drosophila m	0.374	0.232	0.395	2.2e-29
ASPGD|ASPL0000068300	482	AN7015 [Emericella nidulans (t	0.480	0.309	0.296	5.5e-28
UNIPROTKB|Q767M2	463	TFIIH "Uncharacterized protein	0.896	0.600	0.299	1.3e-25
UNIPROTKB|Q92759	462	GTF2H4 "General transcription	0.896	0.601	0.299	2.2e-25
UNIPROTKB|P60027	462	GTF2H4 "General transcription	0.896	0.601	0.299	2.2e-25
RGD|1303309	463	Gtf2h4 "general transcription	0.896	0.600	0.299	2.2e-25
UNIPROTKB|F1PGI3	463	GTF2H4 "Uncharacterized protei	0.903	0.604	0.298	2.8e-25
MGI|MGI:1338799	463	Gtf2h4 "general transcription	0.896	0.600	0.299	3.7e-25
UNIPROTKB|A6H7G8	463	GTF2H4 "Uncharacterized protei	0.903	0.604	0.298	4.8e-25

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

 Score = 227 (85.0 bits), Expect = 1.9e-38, Sum P(2) = 1.9e-38
 Identities = 44/114 (38%), Positives = 74/114 (64%)

Query:   183 LETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTAEQ----- 237
             +ETN+R+YAY+ S+L   ++ LFS++ Y+ PNL+V  +T+ES+  A+ NG+TA+Q     
Sbjct:   313 VETNYRIYAYTNSELQIALVALFSEMLYRFPNLVVAQVTRESVQQAISNGITAQQIIHFL 372

Query:   238 -QNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEFPSREDSKKMR 290
                AHP +  + P +   + DQIRLWE + +R++ T    Y++F S+ D + +R
Sbjct:   373 RTRAHPVMLKQTPVLPPTITDQIRLWELEKDRLQFTEGVLYNQFLSQADFEVLR 426

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 = 205 (77.2 bits), Expect = 2.2e-29, Sum P(2) = 2.2e-29
 Identities = 51/129 (39%), Positives = 74/129 (57%)

Query:   183 LETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTAEQ----- 237
             +ETN+R+YAY+ S L   +L LF+++ Y+ PNL+VG +T++S+  A+  G+TAEQ     
Sbjct:   339 VETNYRVYAYTDSPLQVAVLGLFTELLYRFPNLVVGVLTRDSVRQALRGGITAEQIVSYL 398

Query:   238 -QNAHPRV-----ADRIPSVLE-NVCDQIRLWESDLNRVEMTPAHYYDEFPSREDSKKMR 290
              Q AHP +     A    S L   V DQI+LWE + NR   T    Y++F S  D   +R
Sbjct:   399 EQYAHPNMRMVESAIHSKSCLPPTVVDQIKLWELERNRFTYTEGVLYNQFLSHTDFVTLR 458

Query:   291 LVVNAEIHM 299
                 + IHM
Sbjct:   459 DYAQS-IHM 466

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

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

 Score = 185 (70.2 bits), Expect = 5.5e-28, Sum P(3) = 5.5e-28
 Identities = 48/162 (29%), Positives = 85/162 (52%)

Query:    29 LEDLEAYAIGQWERFLLQLI--SSAQAERSINFCSSTMKVFQRGLLIQ-RDKEAPRLTES 85
             + DL+ YA  QWE  L  ++  S    +R +N      ++ Q G L++ RD+    +T+ 
Sbjct:   139 IHDLDEYARRQWEGVLGYMVGTSGLGIQRDVNLSKGVKQLLQAGHLVEIRDRRV-EITQD 197

Query:    86 GFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLK 145
             GF F+L D   Q+W+I+  Y+ +++         G++  +++SF+  LS    G++Y  K
Sbjct:   198 GFAFVLQDVGTQVWHILILYVESAE-------AIGMDSVEVLSFIFLLSSLELGKSYEKK 250

Query:   146 TLSEIQRSMIKDFADLGLVKLQQGRKESWFIPT-IADSLETN 186
              L+  Q   + D AD G+V  Q   + S F PT +A +L ++
Sbjct:   251 HLTSNQLRTLTDLADFGIV-YQDSPEASHFYPTRLATTLTSD 291

GO:0006281 "DNA repair" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

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

 Score = 293 (108.2 bits), Expect = 1.3e-25, P = 1.3e-25
 Identities = 92/307 (29%), Positives = 153/307 (49%)

Query:     2 NLWKHLINGG-ALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFC 60
             NL   L+ GG A   +    G       +  L+ YA  +WE  L  ++ S  A  S +  
Sbjct:   118 NLRIALLGGGKAWSDDTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLA 177

Query:    61 SSTMKVFQRGLLIQRDK-EAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYER 119
                  + Q GL+   +  E P +T +GFQFLL+DT AQLWY + +Y+  +Q   M   E 
Sbjct:   178 QL---LSQAGLMKSAEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEI 234

Query:   120 GINQADLISF-LLELSFHVAGEAYNL----KTLSEI------QRSMIKDFADLGLVKLQQ 168
              ++    +SF  L   + V G + +L    + L E+      +R   + +     + L  
Sbjct:   235 -LSFLFQLSFSTLGKDYSVEGMSDSLLNFLQHLRELGLVFQRKRKSRRYYPTRLAINLSS 293

Query:   169 GRKESWFIPTIADS----LETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKES 224
             G   +    T+       +ETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES
Sbjct:   294 GVSGAG--GTVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRES 351

Query:   225 LYNAVENGLTAEQ------QNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYD 278
             +  A+ +G+TA+Q        AHP +  + P +   + DQIRLWE + +R+  T    Y+
Sbjct:   352 VQQAIASGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYN 411

Query:   279 EFPSRED 285
             +F S+ D
Sbjct:   412 QFLSQVD 418

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

 Score = 291 (107.5 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 92/307 (29%), Positives = 152/307 (49%)

Query:     2 NLWKHLINGG-ALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFC 60
             NL   L+ GG A   +    G       +  L+ YA  +WE  L  ++ S  A  S +  
Sbjct:   117 NLRIALLGGGKAWSDDTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLA 176

Query:    61 SSTMKVFQRGLLIQRDK-EAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYER 119
                  + Q GL+   +  E P +T +GFQFLL+DT AQLWY + +Y+  +Q   M   E 
Sbjct:   177 QL---LSQAGLMKSTEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEI 233

Query:   120 GINQADLISF-LLELSFHVAGEAYNL----KTLSEI------QRSMIKDFADLGLVKLQQ 168
              ++    +SF  L   + V G + +L    + L E       +R   + +     + L  
Sbjct:   234 -LSFLFQLSFSTLGKDYSVEGMSDSLLNFLQHLREFGLVFQRKRKSRRYYPTRLAINLSS 292

Query:   169 GRKESWFIPTIADS----LETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKES 224
             G   +    T+       +ETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES
Sbjct:   293 GVSGAG--GTVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRES 350

Query:   225 LYNAVENGLTAEQ------QNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYD 278
             +  A+ +G+TA+Q        AHP +  + P +   + DQIRLWE + +R+  T    Y+
Sbjct:   351 VQQAIASGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYN 410

Query:   279 EFPSRED 285
             +F S+ D
Sbjct:   411 QFLSQVD 417

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 = 291 (107.5 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 92/307 (29%), Positives = 152/307 (49%)

Query:     2 NLWKHLINGG-ALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFC 60
             NL   L+ GG A   +    G       +  L+ YA  +WE  L  ++ S  A  S +  
Sbjct:   117 NLRIALLGGGKAWSDDTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLA 176

Query:    61 SSTMKVFQRGLLIQRDK-EAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYER 119
                  + Q GL+   +  E P +T +GFQFLL+DT AQLWY + +Y+  +Q   M   E 
Sbjct:   177 QL---LSQAGLMKSTEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEI 233

Query:   120 GINQADLISF-LLELSFHVAGEAYNL----KTLSEI------QRSMIKDFADLGLVKLQQ 168
              ++    +SF  L   + V G + +L    + L E       +R   + +     + L  
Sbjct:   234 -LSFLFQLSFSTLGKDYSVEGMSDSLLNFLQHLREFGLVFQRKRKSRRYYPTRLAINLSS 292

Query:   169 GRKESWFIPTIADS----LETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKES 224
             G   +    T+       +ETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES
Sbjct:   293 GVSGAG--GTVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRES 350

Query:   225 LYNAVENGLTAEQ------QNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYD 278
             +  A+ +G+TA+Q        AHP +  + P +   + DQIRLWE + +R+  T    Y+
Sbjct:   351 VQQAIASGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYN 410

Query:   279 EFPSRED 285
             +F S+ D
Sbjct:   411 QFLSQVD 417

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 = 291 (107.5 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 92/307 (29%), Positives = 152/307 (49%)

Query:     2 NLWKHLINGG-ALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFC 60
             NL   L+ GG A   +    G       +  L+ YA  +WE  L  ++ S  A  S +  
Sbjct:   118 NLRIALLGGGKAWSDDTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLA 177

Query:    61 SSTMKVFQRGLLIQRDK-EAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYER 119
                  + Q GL+   +  E P +T +GFQFLL+DT AQLWY + +Y+  +Q   M   E 
Sbjct:   178 QL---LSQAGLMKSTEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEI 234

Query:   120 GINQADLISF-LLELSFHVAGEAYNL----KTLSEI------QRSMIKDFADLGLVKLQQ 168
              ++    +SF  L   + V G + +L    + L E       +R   + +     + L  
Sbjct:   235 -LSFLFQLSFSTLGKDYSVEGMSDSLLNFLQHLREFGLVFQRKRKSRRYYPTRLAINLSS 293

Query:   169 GRKESWFIPTIADS----LETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKES 224
             G   +    T+       +ETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES
Sbjct:   294 GVSGAG--GTVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRES 351

Query:   225 LYNAVENGLTAEQ------QNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYD 278
             +  A+ +G+TA+Q        AHP +  + P +   + DQIRLWE + +R+  T    Y+
Sbjct:   352 VQQAIASGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYN 411

Query:   279 EFPSRED 285
             +F S+ D
Sbjct:   412 QFLSQVD 418

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

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

 Score = 290 (107.1 bits), Expect = 2.8e-25, P = 2.8e-25
 Identities = 91/305 (29%), Positives = 150/305 (49%)

Query:     2 NLWKHLINGG-ALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFC 60
             NL   L+ GG A   +    G       +  L+ YA  +WE  L  ++ S  A  S +  
Sbjct:   118 NLRIALLGGGKAWSDDTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLA 177

Query:    61 SSTMKVFQRGLLIQRDK-EAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYER 119
                  + Q GL+   +  E P +T +GFQFLL+DT AQLWY + +Y+  +Q   M   E 
Sbjct:   178 QL---LSQAGLMKSTEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEI 234

Query:   120 GINQADLISF-LLELSFHVAGEAYNL----KTLSEI------QRSMIKDFADLGLVKLQQ 168
              ++    +SF  L   + V G + +L    + L E       +R   + +     + L  
Sbjct:   235 -LSFLFQLSFSTLGKDYSVEGMSDSLLNFLQHLREFGLVFQRKRKSRRYYPTRLAINLSS 293

Query:   169 GRKESWFIPTIADSL--ETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLY 226
             G   +         +  ETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+ 
Sbjct:   294 GVSGAGGTAHQPGFIIVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQ 353

Query:   227 NAVENGLTAEQ------QNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEF 280
              A+ +G+TA+Q        AHP +  + P +   + DQIRLWE + +R+  T    Y++F
Sbjct:   354 QAIASGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQF 413

Query:   281 PSRED 285
              S+ D
Sbjct:   414 LSQVD 418

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

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

GO:0000439 "core TFIIH complex" evidence=IEA

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

 Score = 289 (106.8 bits), Expect = 3.7e-25, P = 3.7e-25
 Identities = 92/307 (29%), Positives = 152/307 (49%)

Query:     2 NLWKHLINGG-ALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFC 60
             NL   L+ GG A   +    G       +  L+ YA  +WE  L  ++ S  A  S +  
Sbjct:   118 NLRIALLGGGKAWSDDTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLA 177

Query:    61 SSTMKVFQRGLLIQRDK-EAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYER 119
                  + Q GL+   +  E P +T +GFQFLL+DT AQLWY + +Y+  +Q   M   E 
Sbjct:   178 QL---LSQAGLMKSTEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEI 234

Query:   120 GINQADLISF-LLELSFHVAGEAYNL----KTLSEI------QRSMIKDFADLGLVKLQQ 168
              ++    +SF  L   + V G + +L    + L E       +R   + +     + L  
Sbjct:   235 -LSFLFQLSFSTLGKDYSVEGMSDSLLNFLQHLREFGLVFQRKRKSRRYYPTRLAINLSS 293

Query:   169 GRKESWFIPTIADS----LETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKES 224
             G   +    T+       +ETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES
Sbjct:   294 GVSGAG--GTVHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRES 351

Query:   225 LYNAVENGLTAEQ------QNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYD 278
             +  A+ +G+TA+Q        AHP +  + P +   + DQIRLWE + +R+  T    Y+
Sbjct:   352 VQQAIASGITAQQIIHFLRTRAHPVMLKQNPVLPPTITDQIRLWELERDRLRFTEGVLYN 411

Query:   279 EFPSRED 285
             +F S+ D
Sbjct:   412 QFLSQVD 418

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

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

 Score = 288 (106.4 bits), Expect = 4.8e-25, P = 4.8e-25
 Identities = 91/305 (29%), Positives = 150/305 (49%)

Query:     2 NLWKHLINGG-ALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFC 60
             NL   L+ GG A   +    G       +  L+ YA  +WE  L  ++ S  A  S +  
Sbjct:   118 NLRIALLGGGKAWSDDTSQLGPDKHARDVLSLDKYAEERWEVVLHFMVGSPSAAVSQDLA 177

Query:    61 SSTMKVFQRGLLIQRDK-EAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYER 119
                  + Q GL+   +  E P +T +GFQFLL+DT AQLWY + +Y+  +Q   M   E 
Sbjct:   178 QL---LSQAGLMKSAEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEI 234

Query:   120 GINQADLISF-LLELSFHVAGEAYNL----KTLSEI------QRSMIKDFADLGLVKLQQ 168
              ++    +SF  L   + V G + +L    + L E       +R   + +     + L  
Sbjct:   235 -LSFLFQLSFSTLGKDYSVEGMSDSLLNFLQHLREFGLVFQRKRKSRRYYPTRLAINLSS 293

Query:   169 GRKESWFIPTIADSL--ETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLY 226
             G   +         +  ETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+ 
Sbjct:   294 GVSGAGGTAHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQ 353

Query:   227 NAVENGLTAEQ------QNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEF 280
              A+ +G+TA+Q        AHP +  + P +   + DQIRLWE + +R+  T    Y++F
Sbjct:   354 QAIASGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQF 413

Query:   281 PSRED 285
              S+ D
Sbjct:   414 LSQVD 418

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

---

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	310
pfam03849	365	pfam03849, Tfb2, Transcription factor Tfb2	2e-90
TIGR00625	448	TIGR00625, tfb2, Transcription factor tfb2	3e-49
COG5144	447	COG5144, TFB2, RNA polymerase II transcription ini	2e-42

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

 Score =  273 bits (700), Expect = 2e-90
 Identities = 96/279 (34%), Positives = 150/279 (53%), Gaps = 48/279 (17%)

Query: 2   NLWKHLINGGALPREPMPSGIT-ARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFC 60
           NL + L  GG      +PS     +L  +  L++YA  +WE  L  ++ S++A+      
Sbjct: 97  NLRRALTGGGVNNSFGVPSDEPDKKLVDVAFLDSYAREKWETILHYMVGSSEAK--TQPS 154

Query: 61  SSTMKVFQRGLLIQRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERG 120
            S + + + G L++R     R+T  GFQFLL D NAQ+W ++ +Y+  ++       ERG
Sbjct: 155 KSVLNLLKHGGLMERSDGGLRITNEGFQFLLQDVNAQIWTLLLQYLKLAE-------ERG 207

Query: 121 INQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPT-- 178
           ++  D++SFL  L F   G+AY+   LSE QR+M++D  D GLV  ++ +   ++ PT  
Sbjct: 208 MDPVDVLSFLFMLGFLELGKAYSTDGLSETQRNMLQDLRDYGLVYQRKRKSRRFY-PTRL 266

Query: 179 ------------IADS-----------------LETNFRMYAYSTSKLHCEILRLFSKIE 209
                        A S                 +ETNFR+YAY++S L   IL LF +++
Sbjct: 267 ATTLTSDSSALRTASSAMEAATSSEAASKGFIIVETNFRLYAYTSSPLQIAILALFVELK 326

Query: 210 YQLPNLIVGAITKESLYNAVENGLTAEQ------QNAHP 242
           Y+ PNL+VG IT+ES+ NA+ENG+TA+Q       +AHP
Sbjct: 327 YRFPNLVVGQITRESIRNALENGITADQIISYLETHAHP 365

Length = 365

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

 Score =  169 bits (429), Expect = 3e-49
 Identities = 99/333 (29%), Positives = 166/333 (49%), Gaps = 60/333 (18%)

Query: 28  TLEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQ-RDKEAPRLTESG 86
            ++ L+ YA  +WE  L  ++ +  A+         +K  Q GL+      E P +T +G
Sbjct: 126 DVDSLDKYAEERWETILHFMVGTPSAKVPSEDVLQLLK--QAGLMKSTEPGEPPCITSAG 183

Query: 87  FQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKT 146
           FQFLL D NAQLW ++ +Y+  ++        RG++  +++ FL  L F   G+AY++  
Sbjct: 184 FQFLLQDINAQLWTLLLQYLKTAE-------SRGMDLVEVLHFLFMLGFLTLGKAYSVDG 236

Query: 147 LSEIQRSMIKDFADLGLVKLQQGRKESWFIPT-IADSL---------------------- 183
           LS+ Q  M++D  + GLV  Q+ RK   F PT +A +L                      
Sbjct: 237 LSDTQLIMLQDLREYGLV-FQRKRKSRRFYPTRLAINLTSDTKTVSGAGGTVDDDLGFII 295

Query: 184 -ETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTAEQ----- 237
            ETN+R+YAY+ S L   ++ LFS++  + PN++VG IT+ES+  A+ NG+TA+Q     
Sbjct: 296 VETNYRLYAYTESPLQIALIALFSELLARFPNMVVGQITRESIRRALANGITAQQIIHYL 355

Query: 238 -QNAHPRV-ADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEFPSR------------ 283
             +AHP++  ++ P +   + DQIRLWE + +R+  T    Y++F ++            
Sbjct: 356 RTHAHPQMRKEQTPVLPPTIVDQIRLWELERDRLRFTEGVLYNDFLTQVDFELLLAYARE 415

Query: 284 ------EDSKKMRLVVNAEIHMHMREFLRGQNK 310
                 E+S K    +    H  ++ F + Q  
Sbjct: 416 LGVLVWENSAKRLFFITPAGHSDVKRFWKRQKH 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 =  151 bits (383), Expect = 2e-42
 Identities = 92/335 (27%), Positives = 155/335 (46%), Gaps = 59/335 (17%)

Query: 20  SGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQRDKEA 79
             I  +L +++ L++Y+  +WE  L  ++ + +A+         +K    G L+ RD+  
Sbjct: 119 VCIGEKLVSVDMLDSYSSRKWETILHFMVGTPEAKIPAEGVLELLK---FGGLMGRDRNE 175

Query: 80  PRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAG 139
            ++T  GFQFLL   N QLW ++  Y+   +   M       ++  ++ FL  L     G
Sbjct: 176 FKITNRGFQFLLQTINEQLWTLLLLYLKYFEGSVM-------DEVAVLHFLFMLGALAVG 228

Query: 140 EAYNLKTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPT-IADSL--------------- 183
            AY +  LS+ Q+ M+ D    GLV+ Q G     F PT +A  L               
Sbjct: 229 TAYKIDALSDTQQIMLMDRRLYGLVE-QLGILRKIFYPTGLAIGLTFDQLFEASEQNRRE 287

Query: 184 --------ETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTA 235
                   ETN ++YAY+ S L   ++ LF  +  + PNL+ G IT+ES+  A++NG+TA
Sbjct: 288 DDKGFIIVETNNKIYAYTNSPLQIAVIHLFCNLTARFPNLVKGIITRESIRRALDNGITA 347

Query: 236 EQ------QNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEFPS------- 282
           +Q       +AHP++  ++  +   + DQI LWE + NR+ M P + Y +F +       
Sbjct: 348 KQIIHYLETHAHPQMRKKLELLPPTIVDQIVLWELERNRIFMVPGYLYSDFLTLSDYQKV 407

Query: 283 -----------REDSKKMRLVVNAEIHMHMREFLR 306
                        D  K    +  E H  ++EF++
Sbjct: 408 LEYAIRGGVLVWSDVDKRMFFIKLEGHSLVKEFVK 442

Length = 447

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	310
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	98.84
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	81.12

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

Probab=100.00  E-value=2.1e-107  Score=788.64  Aligned_cols=295  Identities=35%  Similarity=0.607  Sum_probs=282.0

Q ss_pred             ChhhhHHhhCC-----CCCCCCCCCCCCCCCCChHHHHHHHHhhHHHHHHHHhCCcccccccccchhHHHHHHhCCCccc
Q 040211            1 SNLWKHLINGG-----ALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQR   75 (310)
Q Consensus         1 ~~lr~aL~ggg-----~~~~~~~~~~~~~~~~~~~~Ld~ya~~~WE~iL~~mv~~~~~~~~~~~s~~v~~lL~~~~L~~~   75 (310)
                      +|+|.||+|||     |+++..++++.    .++++||+||.+|||||||||||++.+   ..+|+++.++|+++|||++
T Consensus       112 ~s~~~al~gg~~~~s~~s~~l~~~~~~----r~v~~ld~ya~~rwe~ILh~mvgt~~a---~~~se~v~~ll~~a~lm~~  184 (465)
T KOG3471|consen  112 RSLRDALTGGGKQNSFGSLVLGEDKHN----RDVDFLDKYASERWECILHFMVGTPEA---KAVSEGVLNLLKHAGLMSR  184 (465)
T ss_pred             HHHHHHHhcCCCcccCCCcccCCCcCc----ccchhhHHHHHHHHHHHHHHHhCCccc---cccChhHHHHHHhcCccCC
Confidence            48999999999     45667777777    999999999999999999999999765   7899999999999999998


Q ss_pred             CCCCCccccccchhcccccchHHHHHHHHHHHhcccchhhHHhhCCCHHHHHHHHHHhcccccCccccCCCCCHHHHHHH
Q 040211           76 DKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQRSMI  155 (310)
Q Consensus        76 ~~~~~~IT~~GFqFLL~d~~~QlW~lll~yL~~~e~~~~~~~~~g~~~~e~L~FLf~Ls~~~~g~~Y~~~~lt~~q~~~L  155 (310)
                      +...++||++||||||+|+++|+|+++++||++.+       ++|||++|||+|||+||++++|++|+++++|++|+.||
T Consensus       185 ~~~~~~IT~~GFQFLL~~~~aQlW~~~LqyLk~~~-------~~~~dlvevL~~LfqL~~~~~G~~Ysvd~~~~~~~~~l  257 (465)
T KOG3471|consen  185 DENQIEITNAGFQFLLLDINAQLWTLVLQYLKLFE-------SSGMDLVEVLEFLFQLSALALGRAYSVDALTETQRILL  257 (465)
T ss_pred             CCCCceEeecchhhhhcCcHHHHHHHHHHHHHHHH-------hcCCCHHHHHHHHHHHHHHHhcccceeehhhHHHHHHH
Confidence            87789999999999999999999999999999999       99999999999999999999999999999999999999


Q ss_pred             HHHhhcCeeeEeeCCCcceeecCC-----C------------------Cc---ccccceEEEecCChhHHHHHHHHHhhh
Q 040211          156 KDFADLGLVKLQQGRKESWFIPTI-----A------------------DS---LETNFRMYAYSTSKLHCEILRLFSKIE  209 (310)
Q Consensus       156 ~~L~~lGLVy~~~~~~~~fyipT~-----S------------------~g---vETNfRvYAYT~S~LqiaiL~lF~~l~  209 (310)
                      +||+|+|||||+|.+..+|| ||+     |                  -|   |||||||||||+||||||||+|||++.
T Consensus       258 q~Lre~GlvfQrk~k~~rfy-ptrla~~~ss~~~~~~~~~~~~~~edd~G~iIVETN~riYAYT~S~lQiAvi~LF~~l~  336 (465)
T KOG3471|consen  258 QHLRELGLVFQRKIKILRFY-PTRLAIGLSSDQLGAASLVHQNRNEDDVGFIIVETNYRIYAYTNSPLQIAVIALFTELT  336 (465)
T ss_pred             HHHHHhhHHHHhhhhhheec-chhhhhccchhhhhhhhhhhcccccccCceEEEEeccEEEEecCCHHHHHHHHHHHHHH
Confidence            99999999999999999999 999     1                  14   999999999999999999999999999


Q ss_pred             hccCceEEEEeCHHHHHHHHHcCCCccc------cccChhhhhcC--CCCChhHHHHHHHHHHhcCceeecCcEEeccCC
Q 040211          210 YQLPNLIVGAITKESLYNAVENGLTAEQ------QNAHPRVADRI--PSVLENVCDQIRLWESDLNRVEMTPAHYYDEFP  281 (310)
Q Consensus       210 ~rfPNlvvg~iTReSv~~Al~~GITA~Q------~hAHp~m~~~~--p~iP~tV~DQIrLWE~Er~Rl~~~~g~ly~~f~  281 (310)
                      |||||||||+|||||||+|+++||||+|      +||||||+...  |++||||+|||||||.||||+.++|||||++|.
T Consensus       337 ~rf~nlvvG~iTreSVr~Al~~GITa~QII~fLet~ahpqm~~~~~~~~LPpTv~dQIrLWElernR~~~~~g~LYs~Fl  416 (465)
T KOG3471|consen  337 YRFPNLVVGVITRESVRRALDNGITAEQIIHFLETHAHPQMRMLSPVPCLPPTVVDQIRLWELERNRLRMTEGYLYSDFL  416 (465)
T ss_pred             hhccccceeeeeHHHHHHHHhcCCcHHHHHHHHHhccCchhhhcCCCCCCCchHHhHHHHHHHhhcceecccchhHHhhh
Confidence            9999999999999999999999999999      99999999876  899999999999999999999999999999999


Q ss_pred             CC------------------ccccccEEEEecccchHHHHHHHhccC
Q 040211          282 SR------------------EDSKKMRLVVNAEIHMHMREFLRGQNK  310 (310)
Q Consensus       282 s~------------------~~~~kr~~~V~~~~h~~vr~f~k~~~~  310 (310)
                      |.                  +|+.||+|||+.+||++|++||||++|
T Consensus       417 s~~df~~l~eya~~~~vLvw~d~~kr~~vV~~~Ghs~Vk~f~Kr~~k  463 (465)
T KOG3471|consen  417 SLSDFQLLLEYAREIGVLVWSDSDKRMFVVTKEGHSLVKRFWKRKSK  463 (465)
T ss_pred             hhhhHHHHHHHHHHcCeEEEecCcceEEEEecCccHHHHHHHHHhhc
Confidence            98                  889999999999999999999999654

>TIGR00625 tfb2 Transcription factor tfb2

Probab=100.00  E-value=1.6e-105  Score=791.41  Aligned_cols=295  Identities=32%  Similarity=0.618  Sum_probs=278.0

Q ss_pred             ChhhhHHhhCC-----CCCCCCCCCCCCCCCCChHHHHHHHHhhHHHHHHHHhCCcccccccccchhHHHHHHhCCCccc
Q 040211            1 SNLWKHLINGG-----ALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQR   75 (310)
Q Consensus         1 ~~lr~aL~ggg-----~~~~~~~~~~~~~~~~~~~~Ld~ya~~~WE~iL~~mv~~~~~~~~~~~s~~v~~lL~~~~L~~~   75 (310)
                      +|||.||+|||     |+|+..++++.    +|+++||+||++|||+|||||||++..   ..+|++|+++|+++|||+.
T Consensus        98 ~~lr~aL~g~~~~~s~~v~~~~~d~~~----~~~~~Ld~yA~~~WE~IL~fmVgs~~~---~~~s~~v~~lL~~~~Lm~~  170 (448)
T TIGR00625        98 QNLRIALTGGGKANSFGVSQLGPDKHA----VDVDSLDKYAEERWETILHFMVGTPSA---KVPSEDVLQLLKQAGLMKS  170 (448)
T ss_pred             HHHHHHhcCCCCCCCCCCcccCCCCCC----CCHHHHHHHHHHHHHHHHHHHcCCCCc---CCCchHHHHHHHhCCCCcc
Confidence            48999999999     45565566555    999999999999999999999998753   5789999999999999987


Q ss_pred             C--CCCCccccccchhcccccchHHHHHHHHHHHhcccchhhHHhhCCCHHHHHHHHHHhcccccCccccCCCCCHHHHH
Q 040211           76 D--KEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQRS  153 (310)
Q Consensus        76 ~--~~~~~IT~~GFqFLL~d~~~QlW~lll~yL~~~e~~~~~~~~~g~~~~e~L~FLf~Ls~~~~g~~Y~~~~lt~~q~~  153 (310)
                      +  ++.+.||++||||||||+|+|||+||++||++++       ++|||++|+|+|||+||++++|++|++++||++|++
T Consensus       171 ~~~~~~~~IT~~GFqFLLqd~n~QvW~lll~YL~~~e-------~~g~d~vevLsFLf~Ls~l~lG~~Y~~~~Lt~tq~~  243 (448)
T TIGR00625       171 TEPGEPPCITSAGFQFLLQDINAQLWTLLLQYLKTAE-------SRGMDLVEVLHFLFMLGFLTLGKAYSVDGLSDTQLI  243 (448)
T ss_pred             cCCCCCccCchhhHHHHcCChhHHHHHHHHHHHHHHH-------hcCCCHHHHHHHHHHHhccccCCccCCCCCCHHHHH
Confidence            3  3358999999999999999999999999999999       999999999999999999999999999999999999


Q ss_pred             HHHHHhhcCeeeEeeCCCcceeecCC------C---------------Cc---ccccceEEEecCChhHHHHHHHHHhhh
Q 040211          154 MIKDFADLGLVKLQQGRKESWFIPTI------A---------------DS---LETNFRMYAYSTSKLHCEILRLFSKIE  209 (310)
Q Consensus       154 ~L~~L~~lGLVy~~~~~~~~fyipT~------S---------------~g---vETNfRvYAYT~S~LqiaiL~lF~~l~  209 (310)
                      ||+||+|+||||++++++++|| ||+      |               .|   |||||||||||+||||||||+|||+++
T Consensus       244 ~L~dL~dlGLVy~~~~~~~~fY-PTrLAt~Lts~~~~l~~~~~~~~~~~g~iivEtNfrvYaYt~s~l~~~il~lF~~~~  322 (448)
T TIGR00625       244 MLQDLREYGLVFQRKRKSRRFY-PTRLAINLTSDTKTVSGAGGTVDDDLGFIIVETNYRLYAYTESPLQIALIALFSELL  322 (448)
T ss_pred             HHHHHHHcCeEEEecCCCCccc-chHHHHHHhcCccccccccccccCCCceEEEEecceEEEecCCHHHHHHHHHHHHHH
Confidence            9999999999999999999999 999      1               13   999999999999999999999999999


Q ss_pred             hccCceEEEEeCHHHHHHHHHcCCCccc------cccChhhh-hcCCCCChhHHHHHHHHHHhcCceeecCcEEeccCCC
Q 040211          210 YQLPNLIVGAITKESLYNAVENGLTAEQ------QNAHPRVA-DRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEFPS  282 (310)
Q Consensus       210 ~rfPNlvvg~iTReSv~~Al~~GITA~Q------~hAHp~m~-~~~p~iP~tV~DQIrLWE~Er~Rl~~~~g~ly~~f~s  282 (310)
                      |||||||||+|||+||++|+++||||||      +||||+|+ +..|+|||||+|||||||.||||+++++||||++|+|
T Consensus       323 ~r~pnlvvg~iTr~Sv~~A~~~GITa~qIi~fl~~~ahp~~~~~~~~~lP~tv~dQi~lWe~e~~R~~~~~~~l~~~f~s  402 (448)
T TIGR00625       323 ARFPNMVVGQITRESIRRALANGITAQQIIHYLRTHAHPQMRKEQTPVLPPTIVDQIRLWELERDRLRFTEGVLYNDFLT  402 (448)
T ss_pred             hcCCceEEEEecHHHHHHHHHcCCCHHHHHHHHHhcCChhhhccCCCCCChHHHHHHHHHHHHhcceEeecceeeeecCC
Confidence            9999999999999999999999999999      99999998 4789999999999999999999999999999999999


Q ss_pred             C------------------ccccccEEEEecccchHHHHHHHhccC
Q 040211          283 R------------------EDSKKMRLVVNAEIHMHMREFLRGQNK  310 (310)
Q Consensus       283 ~------------------~~~~kr~~~V~~~~h~~vr~f~k~~~~  310 (310)
                      .                  +|++||+|||+.+||++||+|||++|+
T Consensus       403 ~~~y~~~~~ya~~~~~l~w~~~~kr~~~V~~~gh~~v~~f~k~~~~  448 (448)
T TIGR00625       403 QVDFELLLAYARELGVLVWENSAKRLFFITPAGHSDVKRFWKRQKH  448 (448)
T ss_pred             HHHHHHHHHHHHHcCEEEEecCCceEEEEeccchHHHHHHHHhhcC
Confidence            6                  899999999999999999999999986

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=6.1e-94  Score=679.09  Aligned_cols=290  Identities=30%  Similarity=0.526  Sum_probs=275.2

Q ss_pred             hhhhHHhhCC-----CCCCCCCCCCCCCCCCChHHHHHHHHhhHHHHHHHHhCCcccccccccchhHHHHHHhCCCcccC
Q 040211            2 NLWKHLINGG-----ALPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQRD   76 (310)
Q Consensus         2 ~lr~aL~ggg-----~~~~~~~~~~~~~~~~~~~~Ld~ya~~~WE~iL~~mv~~~~~~~~~~~s~~v~~lL~~~~L~~~~   76 (310)
                      +|+.|||||+     |+ |..+  +.    +|+++||+||.++||+|||||||+..+   .-|+++|.++|+++|||.++
T Consensus       103 sl~~altgg~~~nsfgv-~i~E--~l----vsvd~ld~ys~~kwEtILhfmVgtpea---kip~egVl~lLk~ggLm~~~  172 (447)
T COG5144         103 SLMDALTGGTMENSFGV-CIGE--KL----VSVDMLDSYSSRKWETILHFMVGTPEA---KIPAEGVLELLKFGGLMGRD  172 (447)
T ss_pred             HHHHHhhccccccccce-eecc--ce----eeeehhhhhhhhhHHHHHHHHhCCccc---cCcchhHHHHHHhcccccCC
Confidence            7899999999     55 3322  23    899999999999999999999998876   78999999999999999988


Q ss_pred             CCCCccccccchhcccccchHHHHHHHHHHHhcccchhhHHhhCCCHHHHHHHHHHhcccccCccccCCCCCHHHHHHHH
Q 040211           77 KEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQRSMIK  156 (310)
Q Consensus        77 ~~~~~IT~~GFqFLL~d~~~QlW~lll~yL~~~e~~~~~~~~~g~~~~e~L~FLf~Ls~~~~g~~Y~~~~lt~~q~~~L~  156 (310)
                      ....+||++|||||||+.|+|+|+++++||++.+       ..-||++++|.||||||.+++|++|++|.||++|+-||+
T Consensus       173 ~ne~kITn~GFqFLLq~in~QlWtLlL~yLK~~e-------~s~md~v~VLhflFmLgal~vG~aY~id~lsdtqqiml~  245 (447)
T COG5144         173 RNEFKITNRGFQFLLQTINEQLWTLLLLYLKYFE-------GSVMDEVAVLHFLFMLGALAVGTAYKIDALSDTQQIMLM  245 (447)
T ss_pred             cccceeehhHHHHHHHHHHHHHHHHHHHHHHHhc-------cccccHHHHHHHHHHhcchhhcceeeecccchHHHHHHH
Confidence            7789999999999999999999999999999999       888999999999999999999999999999999999999


Q ss_pred             HHhhcCeeeEeeCCCcceeecCC-------------C--------Cc---ccccceEEEecCChhHHHHHHHHHhhhhcc
Q 040211          157 DFADLGLVKLQQGRKESWFIPTI-------------A--------DS---LETNFRMYAYSTSKLHCEILRLFSKIEYQL  212 (310)
Q Consensus       157 ~L~~lGLVy~~~~~~~~fyipT~-------------S--------~g---vETNfRvYAYT~S~LqiaiL~lF~~l~~rf  212 (310)
                      |+|++||||+++-.+++|| ||+             |        .|   ||||||+||||+||||||+++|||++.+||
T Consensus       246 D~R~yglv~q~~i~~~~fY-pt~LA~glt~d~~~~~s~qnr~edd~gfiIVETN~kiYaYtnSplqiavi~LF~nl~arf  324 (447)
T COG5144         246 DRRLYGLVEQLGILRKIFY-PTGLAIGLTFDQLFEASEQNRREDDKGFIIVETNNKIYAYTNSPLQIAVIHLFCNLTARF  324 (447)
T ss_pred             HHHHhhHHHHhccchhhcc-ccccchhhhhHHHHHhhhhccccccCceEEEEecceEEEecCChHHHHHHHHhhhhhccc
Confidence            9999999999988888999 999             1        24   999999999999999999999999999999


Q ss_pred             CceEEEEeCHHHHHHHHHcCCCccc------cccChhhhhcCCCCChhHHHHHHHHHHhcCceeecCcEEeccCCCC---
Q 040211          213 PNLIVGAITKESLYNAVENGLTAEQ------QNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEFPSR---  283 (310)
Q Consensus       213 PNlvvg~iTReSv~~Al~~GITA~Q------~hAHp~m~~~~p~iP~tV~DQIrLWE~Er~Rl~~~~g~ly~~f~s~---  283 (310)
                      ||||+|+|||||||+|+.+||||+|      +||||||+++.|.+||||+|||+|||+||||+.+.||+||+||.+.   
T Consensus       325 ~Nlv~GiITreSirrAl~nGIta~QII~yLethahpqmr~~l~llPPtivdQI~lWele~nRi~~~pG~LysdFlt~s~y  404 (447)
T COG5144         325 PNLVKGIITRESIRRALDNGITAKQIIHYLETHAHPQMRKKLELLPPTIVDQIVLWELERNRIFMVPGYLYSDFLTLSDY  404 (447)
T ss_pred             chhhhhhccHHHHHHHHhcCccHHHHHHHHHhccChhhhhcCCCCChhhhhheeeeeeccCcEEeecchHHhhhhchhhH
Confidence            9999999999999999999999999      9999999999999999999999999999999999999999999987   


Q ss_pred             ---------------ccccccEEEEecccchHHHHHHHhcc
Q 040211          284 ---------------EDSKKMRLVVNAEIHMHMREFLRGQN  309 (310)
Q Consensus       284 ---------------~~~~kr~~~V~~~~h~~vr~f~k~~~  309 (310)
                                     +|+.||||||+.+||.+|++|.|++-
T Consensus       405 ~~~~eya~~~gvLvw~d~~Krmffi~~eG~s~v~~f~Kr~l  445 (447)
T COG5144         405 QKVLEYAIRGGVLVWSDVDKRMFFIKLEGHSLVKEFVKRIL  445 (447)
T ss_pred             HHHHHHHHhcCeEEeecccceEEEEEccCcHHHHHHHHHHh
Confidence                           78899999999999999999999864

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

Probab=100.00  E-value=1.3e-80  Score=604.72  Aligned_cols=229  Identities=39%  Similarity=0.723  Sum_probs=213.0

Q ss_pred             ChhhhHHhhCCC-----CCCCCCCCCCCCCCCChHHHHHHHHhhHHHHHHHHhCCcccccccccchhHHHHHHhCCCccc
Q 040211            1 SNLWKHLINGGA-----LPREPMPSGITARLPTLEDLEAYAIGQWERFLLQLISSAQAERSINFCSSTMKVFQRGLLIQR   75 (310)
Q Consensus         1 ~~lr~aL~ggg~-----~~~~~~~~~~~~~~~~~~~Ld~ya~~~WE~iL~~mv~~~~~~~~~~~s~~v~~lL~~~~L~~~   75 (310)
                      +|||.||+|||.     +|+..++++.    +++++||+||++|||+|||||||++.... ..||++|+++|+++|||+.
T Consensus        96 ~~Lr~aL~ggg~~~~~~~~~~~~~~~~----~~~~~Ld~yA~~rWE~IL~~mVgs~~~~~-~~~s~~v~~lL~~sgLm~~  170 (366)
T PF03849_consen   96 KNLRNALTGGGKPWSFGVPSEEPDKKA----PDVEFLDEYARERWESILHYMVGSSSSSN-SSPSQDVKQLLKRSGLMKR  170 (366)
T ss_pred             HHHHHHHhCCCCCcccCcccccccCCC----CCHHHHHHHHHHHHHHHHHHHhcCccccc-CCCCHHHHHHHHHcCCCcC
Confidence            489999999994     4455544455    99999999999999999999999987522 2299999999999999998


Q ss_pred             --CCCCCccccccchhcccccchHHHHHHHHHHHhcccchhhHHhhCCCHHHHHHHHHHhcccccCccccCCCCCHHHHH
Q 040211           76 --DKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQHDSMLAYERGINQADLISFLLELSFHVAGEAYNLKTLSEIQRS  153 (310)
Q Consensus        76 --~~~~~~IT~~GFqFLL~d~~~QlW~lll~yL~~~e~~~~~~~~~g~~~~e~L~FLf~Ls~~~~g~~Y~~~~lt~~q~~  153 (310)
                        ++++..||++||||||+|+|+|||++|++||++++       ++|+|++|+|+|||+||++++|++|++++||++|++
T Consensus       171 ~~~~~~~~IT~~GFqFLL~d~~~QlW~lll~yL~~~e-------~~~~~~~~~l~flf~L~~~~~g~~Y~~~~ls~~q~~  243 (366)
T PF03849_consen  171 SESGGSLKITSKGFQFLLQDTNAQLWTLLLQYLKMAE-------ARGMDLVEVLSFLFQLSFLELGKAYSTEGLSETQKN  243 (366)
T ss_pred             cCCCCCCcEehhheeeecCChHHHHHHHHHHHHHHHH-------hcCCCHHHHHHHHHHhcccccCCcCcCCCCCHHHHH
Confidence              45688999999999999999999999999999999       999999999999999999999999999999999999


Q ss_pred             HHHHHhhcCeeeEeeCCCcceeecCC------C--------------------Cc---ccccceEEEecCChhHHHHHHH
Q 040211          154 MIKDFADLGLVKLQQGRKESWFIPTI------A--------------------DS---LETNFRMYAYSTSKLHCEILRL  204 (310)
Q Consensus       154 ~L~~L~~lGLVy~~~~~~~~fyipT~------S--------------------~g---vETNfRvYAYT~S~LqiaiL~l  204 (310)
                      ||+||+|+||||++++++++|| |||      |                    .|   |||||||||||+||||||||+|
T Consensus       244 ~L~~l~~~GLvy~~~~~~~~fy-pT~La~~l~~~~~~~~~~~~~~~~~~~~~~~g~iivETNfrvYAYT~s~l~iaiL~l  322 (366)
T PF03849_consen  244 MLQDLRELGLVYQRKRKSRRFY-PTRLATNLTSGSSALRSASSALDSSSSSNKEGFIIVETNFRVYAYTNSPLQIAILSL  322 (366)
T ss_pred             HHHHHHHCCeEEEecCCCCeEe-chHHHHHHhcCCCcccccccccccccccccCceEEEEecceEEEecCCHHHHHHHHH
Confidence            9999999999999999999999 999      1                    12   9999999999999999999999


Q ss_pred             HHhhhhccCceEEEEeCHHHHHHHHHcCCCccc------cccCh
Q 040211          205 FSKIEYQLPNLIVGAITKESLYNAVENGLTAEQ------QNAHP  242 (310)
Q Consensus       205 F~~l~~rfPNlvvg~iTReSv~~Al~~GITA~Q------~hAHp  242 (310)
                      ||+++|||||||||+||||||++|+++||||||      +||||
T Consensus       323 F~~~~~r~pnlvvg~iTr~Sv~~A~~~GIta~qIi~fL~~~aHp  366 (366)
T PF03849_consen  323 FCELKYRFPNLVVGQITRESVRRALKNGITADQIISFLRSHAHP  366 (366)
T ss_pred             HHHHHhcCCCeEEEEEcHHHHHHHHHcCCCHHHHHHHHHhcCCC
Confidence            999999999999999999999999999999999      99998

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=98.84  E-value=1.9e-08  Score=84.76  Aligned_cols=92  Identities=22%  Similarity=0.307  Sum_probs=75.6

Q ss_pred             ccccceEEEecCCh--hHHHHHHHHHhhhhccCceEEEEeCHHHHHHHHHcCCCccccccChhhhhc-CCCCChhHHHHH
Q 040211          183 LETNFRMYAYSTSK--LHCEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTAEQQNAHPRVADR-IPSVLENVCDQI  259 (310)
Q Consensus       183 vETNfRvYAYT~S~--LqiaiL~lF~~l~~rfPNlvvg~iTReSv~~Al~~GITA~Q~hAHp~m~~~-~p~iP~tV~DQI  259 (310)
                      |+.||.|.+++.+|  -....|..|+++ .+..+|.+..||+.|+.+|++.|+|+++..+-  +.+. ..-||+||..+|
T Consensus         4 Vqpd~~I~v~~~~~~~~~~~~L~~fae~-~s~~~~~~yrlT~~Sl~~A~~~G~~~e~i~~~--L~~~S~~~lP~~v~~~i   80 (129)
T PF13625_consen    4 VQPDFEILVEPGHPSPADAWFLARFAEL-KSPDTMHVYRLTPASLWRAASAGLTAEEIIEF--LERYSKNPLPQNVEQSI   80 (129)
T ss_pred             ECCCCEEEEeCCCCCHHHHHHHHHHhcc-cccCceEEEEECHHHHHHHHHcCCCHHHHHHH--HHHHcCCCCCHHHHHHH
Confidence            78899999987775  456899999999 67799999999999999999999999992111  1111 234899999999


Q ss_pred             HHHHHhcCceeecCcEEe
Q 040211          260 RLWESDLNRVEMTPAHYY  277 (310)
Q Consensus       260 rLWE~Er~Rl~~~~g~ly  277 (310)
                      +-|...-.|+++.++.+|
T Consensus        81 ~~w~~~~g~v~l~~~~~~   98 (129)
T PF13625_consen   81 EDWARRYGRVRLYKGAYL   98 (129)
T ss_pred             HHHHHhcCCEEEecCeEE
Confidence            999999999999885433

>TIGR00603 rad25 DNA repair helicase rad25

Probab=81.12  E-value=2.4  Score=46.02  Aligned_cols=87  Identities=21%  Similarity=0.262  Sum_probs=67.4

Q ss_pred             ccccceEEEecCChhH---HHHHHHHHhhhhccCceEEEEeCHHHHHHHHHcCCCccc-cccChhhhhcCCCCChhHHHH
Q 040211          183 LETNFRMYAYSTSKLH---CEILRLFSKIEYQLPNLIVGAITKESLYNAVENGLTAEQ-QNAHPRVADRIPSVLENVCDQ  258 (310)
Q Consensus       183 vETNfRvYAYT~S~Lq---iaiL~lF~~l~~rfPNlvvg~iTReSv~~Al~~GITA~Q-~hAHp~m~~~~p~iP~tV~DQ  258 (310)
                      |..+=+|.-=|.||+-   -.-|.-|+|+..|--+|...+||-=|+-+|...|+++++ ...--...|  ..||++|++.
T Consensus        19 v~~d~~i~lE~~~p~~~~a~~fl~~~aEp~~rp~~iHeY~lT~~sl~~A~s~g~~~~~ii~~L~~~sk--~~~p~~i~~~   96 (732)
T TIGR00603        19 VAPDGHIFLESFSPLYKQAQDFLVAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLETEDIIEVLGRLSK--TPIPKGIIEF   96 (732)
T ss_pred             EcCCCeEEEEeCCccHHHHHHHHHHhcccccChhheEEEeccHHHHHHHHHcCCCHHHHHHHHHHHhC--CCCCHHHHHH
Confidence            3444444444556554   267899999999999999999999999999999999999 222222222  3699999999


Q ss_pred             HHHHHHhcCceee
Q 040211          259 IRLWESDLNRVEM  271 (310)
Q Consensus       259 IrLWE~Er~Rl~~  271 (310)
                      |+.+-.--.++++
T Consensus        97 i~~~~~~ygk~kl  109 (732)
T TIGR00603        97 IRLCTQSYGKVKL  109 (732)
T ss_pred             HHHHHHhcCcEEE
Confidence            9999998888776

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).

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	310
3dom_A	108	RNA polymerase II transcription factor B subunit;	2e-21
3dgp_A	80	RNA polymerase II transcription factor B subunit;	1e-16

>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 = 86.1 bits (213), Expect = 2e-21
 Identities = 19/92 (20%), Positives = 37/92 (40%), Gaps = 18/92 (19%)

Query: 237 QQNAHPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEFPSR------------- 283
           +    P   + +  +   V DQIRLW+ +L+RV       Y +F +              
Sbjct: 14  KLELDPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDI 73

Query: 284 -----EDSKKMRLVVNAEIHMHMREFLRGQNK 310
                +D KK +  ++ E +  + +F + + K
Sbjct: 74  GVLLWKDDKKKKFFISKEGNSQVLDFAKRKLK 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 = 72.5 bits (178), Expect = 1e-16
 Identities = 18/75 (24%), Positives = 32/75 (42%), Gaps = 18/75 (24%)

Query: 254 NVCDQIRLWESDLNRVEMTPAHYYDEFPSR------------------EDSKKMRLVVNA 295
            V DQIRLW+ +L+RV       Y +F +                   +D KK +  ++ 
Sbjct: 3   TVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISK 62

Query: 296 EIHMHMREFLRGQNK 310
           E +  + +F + + K
Sbjct: 63  EGNSQVLDFAKRKLK 77

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	310
3dom_A	108	RNA polymerase II transcription factor B subunit;	99.92
3dgp_A	80	RNA polymerase II transcription factor B subunit;	99.89

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

Probab=99.92  E-value=8.2e-27  Score=191.05  Aligned_cols=70  Identities=27%  Similarity=0.523  Sum_probs=53.9

Q ss_pred             ChhhhhcCCCCChhHHHHHHHHHHhcCceeecCcEEeccCCCC------------------ccccccEEEEecccchHHH
Q 040211          241 HPRVADRIPSVLENVCDQIRLWESDLNRVEMTPAHYYDEFPSR------------------EDSKKMRLVVNAEIHMHMR  302 (310)
Q Consensus       241 Hp~m~~~~p~iP~tV~DQIrLWE~Er~Rl~~~~g~ly~~f~s~------------------~~~~kr~~~V~~~~h~~vr  302 (310)
                      .|+++...|+|||||+|||||||+|||||++++||||++|+|+                  +|+.+|+|||+.+||++||
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            4555556899999999999999999999999999999999998                  8999999999999999999


Q ss_pred             HHHHhccC
Q 040211          303 EFLRGQNK  310 (310)
Q Consensus       303 ~f~k~~~~  310 (310)
                      +|||++++
T Consensus        98 ~f~Kr~~~  105 (108)
T 3dom_A           98 DFAKRKLK  105 (108)
T ss_dssp             HHHHHHC-
T ss_pred             HHHHHHHh
Confidence            99999874

>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=99.89  E-value=2.1e-24  Score=168.59  Aligned_cols=58  Identities=31%  Similarity=0.569  Sum_probs=43.2

Q ss_pred             hhHHHHHHHHHHhcCceeecCcEEeccCCCC------------------ccccccEEEEecccchHHHHHHHhccC
Q 040211          253 ENVCDQIRLWESDLNRVEMTPAHYYDEFPSR------------------EDSKKMRLVVNAEIHMHMREFLRGQNK  310 (310)
Q Consensus       253 ~tV~DQIrLWE~Er~Rl~~~~g~ly~~f~s~------------------~~~~kr~~~V~~~~h~~vr~f~k~~~~  310 (310)
                      |||+|||||||+|||||++++||||++|+|+                  +|+.+|+|||+.+||++||+|||++++
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            8999999999999999999999999999998                  899999999999999999999999874

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

No hit with probability above 80.00