Citrus Sinensis ID: 041357

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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-------17
Protein Sequence
MAIQSRKESWFIPTIADNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQQNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK
Secondary Structure (PSIPRED)
ccccccccccccccccccccEEEEEEccEEEEEcccHHHHHHHHHHHHHHHccccEEEEEEcHHHHHHHHHcccccHHHHcccccccccccccccHHHHHHHHHHHcccEEEcccEEEcccccHHHHHHHHHHHHHccEEEEEcccccEEEEEcccHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccccccEEEEcccccccEEEEEEcEEEEEEcccHHHHHHHHHHHHHHHHcccEEEEEEcHHHHHHHHHccccHHHHHccHHHccccccccccHHHHHHHHHHHHccEEEcccEEEcccccHHHHHHHHHHHHHcccEEEcccccEEEEEccccHHHHHHHHHHccc
Coil and Loop (DISEMBL)
maiqsrkeswfiptiadncgfvVVETNFKMYAYSTSKLHCEILRLFSKIEyqlpnlivgAITKESLYNAFENgitteqqnahprvadkipsvpknvCDQIRLWESdlnrvettpahyydefpsrdvFEAACDYArdqsgllwedskKMRLVVNAEIHMHMREFLRGQNK
Flexible Loop (DISEMBL)
maiqsrkeswfiptiadnCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQQNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTpahyydefpsrDVFEAACDYARDqsgllwedskKMRLVVNAEIHMHMREFLRGQNK
Low Complexity Region (SEG)
MAIQSRKESWFIPTIADNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQQNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK
Disordered region (IsUnstruct)
********SWFIPTIADNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTE*******VADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMR********
Disordered Region (DISOPRED)
****************DNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQQNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ**
Disordered Region (DISEMBL)
********SWFIPTIADNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQQNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK
Disordered Region (DISPRO)
*****RKESWFIPTIADNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQQNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAIQSRKESWFIPTIADNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQQNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK
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	169	2.2.26 [Sep-21-2011]
P60027	462	General transcription fac	yes	no	0.881	0.322	0.367	6e-26
Q92759	462	General transcription fac	yes	no	0.881	0.322	0.367	6e-26
P87303	447	RNA polymerase II transcr	yes	no	0.881	0.333	0.348	9e-26
O70422	463	General transcription fac	yes	no	0.881	0.321	0.367	2e-25
Q6CLR2	496	RNA polymerase II transcr	yes	no	0.863	0.294	0.347	2e-24
Q6BZX4	467	RNA polymerase II transcr	yes	no	0.923	0.334	0.320	3e-24
Q54C29	483	General transcription fac	yes	no	0.863	0.302	0.381	2e-23
Q6FP41	504	RNA polymerase II transcr	yes	no	0.887	0.297	0.333	6e-23
Q75B51	514	RNA polymerase II transcr	yes	no	0.852	0.280	0.346	4e-22
Q6BGW8	515	RNA polymerase II transcr	yes	no	0.816	0.267	0.291	5e-20

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

 Score =  116 bits (291), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 57/155 (36%), Positives = 94/155 (60%), Gaps = 6/155 (3%)

Query: 20  GFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQ- 78
           GF+VVETN+++YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GIT +Q 
Sbjct: 305 GFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQI 364

Query: 79  -----QNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDY 133
                  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE    +
Sbjct: 365 IHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAH 424

Query: 134 ARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQN 168
           AR+   L++E+S K  +VV    H  ++ F + Q 
Sbjct: 425 ARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQK 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 =  116 bits (291), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 57/155 (36%), Positives = 94/155 (60%), Gaps = 6/155 (3%)

Query: 20  GFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQ- 78
           GF+VVETN+++YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GIT +Q 
Sbjct: 305 GFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQI 364

Query: 79  -----QNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDY 133
                  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE    +
Sbjct: 365 IHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAH 424

Query: 134 ARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQN 168
           AR+   L++E+S K  +VV    H  ++ F + Q 
Sbjct: 425 ARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQK 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|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 =  115 bits (289), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 54/155 (34%), Positives = 90/155 (58%), Gaps = 6/155 (3%)

Query: 17  DNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITT 76
           D+ GF++VETN+++YAY++S L   I+ LF+ +  +  NL+VG IT++S+  A  NGI  
Sbjct: 288 DDKGFIIVETNYRLYAYTSSPLQIAIIGLFANLRARFSNLVVGVITRDSIRRALMNGIAA 347

Query: 77  EQ------QNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAA 130
           EQ       +AHP++   +P +P  + DQI LWE + NR+  TP   + +F +   F+ A
Sbjct: 348 EQIITYLTTHAHPQMRSNVPLLPPTLVDQIYLWELEKNRLRATPGILFRDFLTDSGFDQA 407

Query: 131 CDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFLR 165
            +YA++   L+W+ S K    +       M  +L+
Sbjct: 408 VEYAKELGVLVWDSSLKRMFFITTTGAQPMIAYLK 442

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

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

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

 Score =  115 bits (287), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 57/155 (36%), Positives = 94/155 (60%), Gaps = 6/155 (3%)

Query: 20  GFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQ- 78
           GF+VVETN+++YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GIT +Q 
Sbjct: 306 GFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQI 365

Query: 79  -----QNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDY 133
                  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE    +
Sbjct: 366 IHFLRTRAHPVMLKQNPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAH 425

Query: 134 ARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQN 168
           AR+   L++E+S K  +VV    H  ++ F + Q 
Sbjct: 426 ARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQK 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|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 =  111 bits (278), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 59/170 (34%), Positives = 92/170 (54%), Gaps = 24/170 (14%)

Query: 20  GFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQ- 78
           G +++ETNFK+Y+YS S L   IL LF  ++ +  N++ G +T+ES+ NA  NGIT EQ 
Sbjct: 322 GALIIETNFKLYSYSNSPLQIAILSLFVHLKSRFANMVTGQLTRESVRNALLNGITAEQI 381

Query: 79  -----QNAHPR------------------VADKIPSVPKNVCDQIRLWESDLNRVETTPA 115
                 +AHPR                  V + +  +P  V DQIRLW+ +L+R+ +   
Sbjct: 382 IAYLETHAHPRMRRLAEENLSKKLELDPTVKETLQVLPPTVVDQIRLWQLELDRIISYDG 441

Query: 116 HYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFLR 165
           + Y +F S   ++   DYA+D   LLW++ KK    V+ E +  + +F R
Sbjct: 442 YLYTDFESYQEYQTVADYAKDIGVLLWQNEKKKMFFVSTEGNSQVLDFHR 491

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

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

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

 Score =  110 bits (276), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 52/162 (32%), Positives = 94/162 (58%), Gaps = 6/162 (3%)

Query: 14  TIADNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENG 73
           ++A + GF+++ETNF++YAY+ S L   +L LF  ++ +  N++ G I ++S+  A  NG
Sbjct: 299 SVAADSGFIILETNFRLYAYTESPLQIAVLNLFVNLKTRFANMVTGQINRDSVRFALSNG 358

Query: 74  ITTEQ------QNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVF 127
           IT EQ       +AHPR+      +P  V DQI+LW+ +++R+  T  + + EF + D +
Sbjct: 359 ITAEQIITYLSVHAHPRMKGMEHVLPPTVVDQIKLWQLEMDRIRATDGYLFSEFKNFDEY 418

Query: 128 EAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK 169
           +    YA++   LL+E+  K + V        + EF++ +N+
Sbjct: 419 KDVSTYAKELGVLLYENPGKRKFVSTLAGSQQIVEFVKRRNQ 460

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

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

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

 Score =  108 bits (269), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 58/152 (38%), Positives = 92/152 (60%), Gaps = 6/152 (3%)

Query: 20  GFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQ- 78
           G++V+ETN+++YAY++S L   +L LF K+ Y+LPNL VG IT+ES+  A  +GIT +Q 
Sbjct: 328 GYIVLETNYRLYAYTSSSLQISLLSLFVKMLYRLPNLAVGIITRESIRTALIHGITADQI 387

Query: 79  -----QNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDY 133
                 N+HP  A+    +P  V +QI LWE++ NR+  T +  Y+ FP+ D + A   +
Sbjct: 388 IDFVRHNSHPNAANSGQPIPDVVAEQILLWEAERNRITYTKSVLYNSFPTNDCYIATLKF 447

Query: 134 ARDQSGLLWEDSKKMRLVVNAEIHMHMREFLR 165
           A++Q   +W       LVV  E +  +R F++
Sbjct: 448 AKEQDYYIWSHDPLKTLVVKEEGNDPIRNFIK 479

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

Dictyostelium discoideum (taxid: 44689)

>sp|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 =  106 bits (265), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 58/174 (33%), Positives = 92/174 (52%), Gaps = 24/174 (13%)

Query: 20  GFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQ- 78
           G +++ETNFK+Y+Y  S L   IL LF  ++ +  N++ G IT+ES+  A  NGIT +Q 
Sbjct: 327 GALIIETNFKLYSYCNSPLQIAILSLFVHLKSRFANMVAGQITRESIRRALINGITADQV 386

Query: 79  -----QNAHPRV------------------ADKIPSVPKNVCDQIRLWESDLNRVETTPA 115
                 +AHP++                   D +  +P  V DQI+LW+ +L+RV T   
Sbjct: 387 IAYLESHAHPQMRRLAEEKLQKKLELDPNCKDPLQVLPPTVVDQIKLWQLELDRVLTYEG 446

Query: 116 HYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK 169
             Y +F +   F   C YA+D   LLW+D +K +L V+ E +  + E+ + + K
Sbjct: 447 SLYIDFDTAQDFNMLCKYAQDIGALLWKDDRKRKLFVSREGNAQVLEYAKRKIK 500

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

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

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

 Score =  103 bits (258), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 60/173 (34%), Positives = 90/173 (52%), Gaps = 29/173 (16%)

Query: 20  GFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQ- 78
           G ++VETNFK+Y+YS S L   IL LF  ++ +  N++ G IT+ES+  A  NGIT +Q 
Sbjct: 339 GALIVETNFKLYSYSNSPLQIAILSLFIHLKTRFQNMVTGQITRESIRRALHNGITADQI 398

Query: 79  -----QNAHP---RVA---------------DKIPSVPKNVCDQIRLWESDLNRVETTPA 115
                 +AHP   R+A               D +  +P  V DQI+LW+ +L+R+ +   
Sbjct: 399 IAYMETHAHPQMRRLAGDNLEKKLELDPNCRDTLQVLPPTVVDQIKLWQLELDRIISYDG 458

Query: 116 HYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAE-----IHMHMREF 163
           + + +F +   ++    YARD   LLW D KK    V+ E     I  H R+F
Sbjct: 459 YLFRDFDNLQEYQVLAQYARDIGVLLWSDDKKKMFFVSKEGNAQVIDFHKRKF 511

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

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

>sp|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 = 97.1 bits (240), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 54/185 (29%), Positives = 85/185 (45%), Gaps = 47/185 (25%)

Query: 18  NCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTE 77
           N G +++ETNFK+YAY+ S L   IL LF  ++ +  N++ G IT+ES+ NA  NGIT +
Sbjct: 316 NQGTIILETNFKIYAYTNSPLEIAILNLFVHLKTRFSNMVCGQITRESIRNALYNGITAD 375

Query: 78  Q-----------------------------------------------QNAHPRVADKIP 90
           Q                                               +N       K+ 
Sbjct: 376 QIIKFLETHAHSQMKILAKERLDKKIEFDTSNNINTAGGAPQSQMMTNENGTTVAQHKLE 435

Query: 91  SVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRL 150
            +P  V DQI+LW+ +L+R++T   + + +F S+  FEA  +YA +   LLW +  KM+ 
Sbjct: 436 VLPPTVVDQIKLWQLELDRIQTFEGYLFKDFASQQEFEALSNYASEIGVLLWSNKSKMKF 495

Query: 151 VVNAE 155
            V  +
Sbjct: 496 FVTKD 500

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

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

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	169
224077128	449	predicted protein [Populus trichocarpa]	0.970	0.365	0.743	3e-75
255556021	451	tfiih, polypeptide, putative [Ricinus co	0.970	0.363	0.737	6e-75
449433857	451	PREDICTED: general transcription factor	0.970	0.363	0.754	2e-74
147854406	451	hypothetical protein VITISV_005315 [Viti	0.958	0.359	0.745	2e-74
358346685	451	General transcription factor IIH subunit	0.970	0.363	0.721	3e-70
357461579	452	General transcription factor IIH subunit	0.970	0.362	0.715	4e-70
356548733	451	PREDICTED: general transcription factor	0.970	0.363	0.699	1e-68
297800414	452	hypothetical protein ARALYDRAFT_493174 [	0.982	0.367	0.670	4e-68
42566894	452	transcription initiation factor TFIIH su	0.982	0.367	0.664	1e-67
42572935	462	transcription initiation factor TFIIH su	0.982	0.359	0.664	2e-67

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

 Score =  285 bits (730), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 136/183 (74%), Positives = 155/183 (84%), Gaps = 19/183 (10%)

Query: 4   QSRKESWFIPT-IADNC------------GFVVVETNFKMYAYSTSKLHCEILRLFSKIE 50
           Q RKESWFIPT +A N             G+VVVETNF++YAYS+SKLHCEILRLFSKIE
Sbjct: 266 QGRKESWFIPTKLATNLSVSLTDSSSRKQGYVVVETNFRLYAYSSSKLHCEILRLFSKIE 325

Query: 51  YQLPNLIVGAITKESLYNAFENGITTEQ------QNAHPRVADKIPSVPKNVCDQIRLWE 104
           YQLPNLIVGAITKESLY AFENGIT++Q      QNAHPRVA+++PSVP+NV DQIRLWE
Sbjct: 326 YQLPNLIVGAITKESLYTAFENGITSDQIISFLQQNAHPRVAERLPSVPENVTDQIRLWE 385

Query: 105 SDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFL 164
           +DLNRVE TP+H+YDEFPSRD FEAACD+AR+ +GLLWEDSKKMR+VV AEIHM+MREFL
Sbjct: 386 ADLNRVEITPSHFYDEFPSRDTFEAACDFAREWNGLLWEDSKKMRVVVKAEIHMNMREFL 445

Query: 165 RGQ 167
           RGQ
Sbjct: 446 RGQ 448

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  285 bits (728), Expect = 6e-75,   Method: Compositional matrix adjust.
 Identities = 135/183 (73%), Positives = 155/183 (84%), Gaps = 19/183 (10%)

Query: 4   QSRKESWFIPT-IADNC------------GFVVVETNFKMYAYSTSKLHCEILRLFSKIE 50
           Q RKESWFIPT +A N             GFVVVETNF+MYAYSTSKLHCEI+RLFS++E
Sbjct: 268 QGRKESWFIPTKLATNLSMSLTDSSSRKQGFVVVETNFRMYAYSTSKLHCEIMRLFSRVE 327

Query: 51  YQLPNLIVGAITKESLYNAFENGITTEQ------QNAHPRVADKIPSVPKNVCDQIRLWE 104
           YQLPNL+VGA+TKESLY+AFENGIT EQ      QNAHPRVA++IPSVP+NV DQIRLWE
Sbjct: 328 YQLPNLVVGAMTKESLYSAFENGITAEQIISFLQQNAHPRVAERIPSVPENVTDQIRLWE 387

Query: 105 SDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFL 164
           SD+NRVE TPAH YDEFPSRDVFEAAC++ARD +GLLWEDSK+MR+VV AEIH++MRE+L
Sbjct: 388 SDMNRVEMTPAHLYDEFPSRDVFEAACNFARDWNGLLWEDSKRMRMVVKAEIHLNMREYL 447

Query: 165 RGQ 167
           RGQ
Sbjct: 448 RGQ 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 =  283 bits (724), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 138/183 (75%), Positives = 153/183 (83%), Gaps = 19/183 (10%)

Query: 4   QSRKESWFIPT---------IADN----CGFVVVETNFKMYAYSTSKLHCEILRLFSKIE 50
           Q RKESWFIPT         +AD+     GFVVVETNF+MYAYSTSKLHCEILRLFS+IE
Sbjct: 268 QGRKESWFIPTKLATNLSMSLADSSSRKLGFVVVETNFRMYAYSTSKLHCEILRLFSRIE 327

Query: 51  YQLPNLIVGAITKESLYNAFENGITTEQ------QNAHPRVADKIPSVPKNVCDQIRLWE 104
           YQLPNLIVGAITKESLYNAF+NGIT EQ      QNAHPRVA++IPSVP+NV DQIRLWE
Sbjct: 328 YQLPNLIVGAITKESLYNAFKNGITAEQIVTFLQQNAHPRVAERIPSVPENVTDQIRLWE 387

Query: 105 SDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFL 164
           SDLNRV+ TPAH+YDEFPSR+VFEAACDYAR+ +GLLWEDSK +RLVV A+IH HMRE L
Sbjct: 388 SDLNRVDITPAHFYDEFPSREVFEAACDYAREWNGLLWEDSKNLRLVVKADIHTHMREHL 447

Query: 165 RGQ 167
           R Q
Sbjct: 448 RRQ 450

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  283 bits (724), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 135/181 (74%), Positives = 151/181 (83%), Gaps = 19/181 (10%)

Query: 4   QSRKESWFIPT-IADNC------------GFVVVETNFKMYAYSTSKLHCEILRLFSKIE 50
           Q RKESWFIPT +A N             GFVVVETNF++YAYS+SKLHCEILRLFS++E
Sbjct: 268 QGRKESWFIPTKLATNLSMSLSDTSSRKQGFVVVETNFRLYAYSSSKLHCEILRLFSRVE 327

Query: 51  YQLPNLIVGAITKESLYNAFENGITTEQ------QNAHPRVADKIPSVPKNVCDQIRLWE 104
           YQLPNLIVGAITKESLYNAFENGIT EQ      QNAHPRVA++ P+VP+NV DQIRLWE
Sbjct: 328 YQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVAERTPAVPENVTDQIRLWE 387

Query: 105 SDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFL 164
           +DLNRVET P+H YDEFPSRDVFEAACD+AR+  GLLWEDSKKMRLVV AEIH+HMRE+L
Sbjct: 388 TDLNRVETMPSHLYDEFPSRDVFEAACDFAREYGGLLWEDSKKMRLVVKAEIHLHMREYL 447

Query: 165 R 165
           R
Sbjct: 448 R 448

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  269 bits (687), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 132/183 (72%), Positives = 149/183 (81%), Gaps = 19/183 (10%)

Query: 4   QSRKESWFIPT-IADNC------------GFVVVETNFKMYAYSTSKLHCEILRLFSKIE 50
           Q RKESWFIPT +A N             GFVVVETNF++YAYSTSKLHCEILRLFS++E
Sbjct: 268 QGRKESWFIPTKLATNLSVSMTESSSRKEGFVVVETNFRVYAYSTSKLHCEILRLFSRVE 327

Query: 51  YQLPNLIVGAITKESLYNAFENGITTEQ------QNAHPRVADKIPSVPKNVCDQIRLWE 104
           YQLPNLIVGAITKESLYNAF+NGIT +Q      QNAHPRVA +IP+VP+NV DQIRLWE
Sbjct: 328 YQLPNLIVGAITKESLYNAFDNGITADQIVSFFRQNAHPRVAQRIPAVPENVTDQIRLWE 387

Query: 105 SDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFL 164
           SDLNRVE T A+YYDEFPSRDVFE ACD AR+ SGLLWEDSKKM LVV +E+H ++R+FL
Sbjct: 388 SDLNRVEMTEAYYYDEFPSRDVFEGACDCAREWSGLLWEDSKKMHLVVKSEVHTYVRDFL 447

Query: 165 RGQ 167
           R Q
Sbjct: 448 RRQ 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 =  269 bits (687), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 131/183 (71%), Positives = 149/183 (81%), Gaps = 19/183 (10%)

Query: 4   QSRKESWFIPT-IADNC------------GFVVVETNFKMYAYSTSKLHCEILRLFSKIE 50
           Q RKESWFIPT +A N             GFVVVETNF++YAYSTSKLHCEILRLFS++E
Sbjct: 269 QGRKESWFIPTKLATNLSVSMTESSSRKEGFVVVETNFRVYAYSTSKLHCEILRLFSRVE 328

Query: 51  YQLPNLIVGAITKESLYNAFENGITTEQ------QNAHPRVADKIPSVPKNVCDQIRLWE 104
           YQLPNLIVGAITKESLYNAF+NGIT +Q      QNAHPRVA ++P+VP+NV DQIRLWE
Sbjct: 329 YQLPNLIVGAITKESLYNAFDNGITADQIVSFLRQNAHPRVAQRVPAVPENVTDQIRLWE 388

Query: 105 SDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFL 164
           SDLNRVE T A+YYDEFPSRDVFE ACD AR+ SGLLWEDSKKM LVV +E+H ++R+FL
Sbjct: 389 SDLNRVEMTEAYYYDEFPSRDVFEGACDCAREWSGLLWEDSKKMHLVVKSEVHTYVRDFL 448

Query: 165 RGQ 167
           R Q
Sbjct: 449 RRQ 451

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  264 bits (674), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 128/183 (69%), Positives = 149/183 (81%), Gaps = 19/183 (10%)

Query: 4   QSRKESWFIPT---------IADNC----GFVVVETNFKMYAYSTSKLHCEILRLFSKIE 50
           Q RK SWFIPT         +AD+     GFVVVETNF++YAYSTSKLHCEILRLFS++E
Sbjct: 268 QGRKGSWFIPTKLATNLSMSLADSSSRKQGFVVVETNFRVYAYSTSKLHCEILRLFSRVE 327

Query: 51  YQLPNLIVGAITKESLYNAFENGITTEQ------QNAHPRVADKIPSVPKNVCDQIRLWE 104
           YQLPNLIVGAITKESLY+AFENGIT EQ      QNAHPRVA++IPSVP+NV +QIRLWE
Sbjct: 328 YQLPNLIVGAITKESLYSAFENGITAEQIITFLQQNAHPRVAERIPSVPENVTEQIRLWE 387

Query: 105 SDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFL 164
           +DLNRVE T A+YYDEFPSRDVFE ACD AR+ +GLLWEDSKKM +VV  E+H ++R++L
Sbjct: 388 ADLNRVEMTDAYYYDEFPSRDVFEGACDCAREWNGLLWEDSKKMHMVVKTEVHQYVRDYL 447

Query: 165 RGQ 167
           R Q
Sbjct: 448 RRQ 450

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 =  262 bits (669), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 124/185 (67%), Positives = 148/185 (80%), Gaps = 19/185 (10%)

Query: 4   QSRKESWFIPT---------IADNC----GFVVVETNFKMYAYSTSKLHCEILRLFSKIE 50
           Q RK+SWFIPT         +AD+     GFVV+ETNF+MYAYSTSKL CEILRLF++IE
Sbjct: 268 QGRKDSWFIPTKLATNLSVSLADSSARKEGFVVMETNFRMYAYSTSKLQCEILRLFARIE 327

Query: 51  YQLPNLIVGAITKESLYNAFENGITTEQ------QNAHPRVADKIPSVPKNVCDQIRLWE 104
           YQLPNLI  AITKESLYNAF+NGIT++Q      QN+HPR AD++PS+P+NV DQIRLWE
Sbjct: 328 YQLPNLIACAITKESLYNAFDNGITSDQIITFLQQNSHPRCADRVPSIPENVTDQIRLWE 387

Query: 105 SDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFL 164
           +DL R+E T AH+YDEFPS+DVFEAACD+AR+  GLLWEDSK+MRLVV +E+H  MREFL
Sbjct: 388 TDLKRIEMTQAHFYDEFPSKDVFEAACDFAREWGGLLWEDSKRMRLVVKSEVHNQMREFL 447

Query: 165 RGQNK 169
             Q K
Sbjct: 448 HNQTK 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 =  260 bits (665), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 123/185 (66%), Positives = 149/185 (80%), Gaps = 19/185 (10%)

Query: 4   QSRKESWFIPT---------IADNC----GFVVVETNFKMYAYSTSKLHCEILRLFSKIE 50
           Q RK+SWFIPT         +AD+     GFVV+ETNF+MYAYSTSKL CEILRLF++IE
Sbjct: 268 QGRKDSWFIPTKLATNLSVSLADSSARKEGFVVMETNFRMYAYSTSKLQCEILRLFARIE 327

Query: 51  YQLPNLIVGAITKESLYNAFENGITTEQ------QNAHPRVADKIPSVPKNVCDQIRLWE 104
           YQLPNLI  AITKESLYNAF+NGIT++Q      QN+HPR AD++PS+P+NV DQIRLWE
Sbjct: 328 YQLPNLIACAITKESLYNAFDNGITSDQIITFLQQNSHPRCADRVPSIPENVTDQIRLWE 387

Query: 105 SDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFL 164
           +DL R+E T AH+YDEFPS+DVFEAACD+AR+  GLLWEDSK+MRLVV +E+H  MREFL
Sbjct: 388 TDLQRIEMTQAHFYDEFPSKDVFEAACDFAREWRGLLWEDSKRMRLVVKSEVHNQMREFL 447

Query: 165 RGQNK 169
             Q++
Sbjct: 448 HTQSR 452

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  260 bits (664), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 123/185 (66%), Positives = 149/185 (80%), Gaps = 19/185 (10%)

Query: 4   QSRKESWFIPT---------IADNC----GFVVVETNFKMYAYSTSKLHCEILRLFSKIE 50
           Q RK+SWFIPT         +AD+     GFVV+ETNF+MYAYSTSKL CEILRLF++IE
Sbjct: 268 QGRKDSWFIPTKLATNLSVSLADSSARKEGFVVMETNFRMYAYSTSKLQCEILRLFARIE 327

Query: 51  YQLPNLIVGAITKESLYNAFENGITTEQ------QNAHPRVADKIPSVPKNVCDQIRLWE 104
           YQLPNLI  AITKESLYNAF+NGIT++Q      QN+HPR AD++PS+P+NV DQIRLWE
Sbjct: 328 YQLPNLIACAITKESLYNAFDNGITSDQIITFLQQNSHPRCADRVPSIPENVTDQIRLWE 387

Query: 105 SDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFL 164
           +DL R+E T AH+YDEFPS+DVFEAACD+AR+  GLLWEDSK+MRLVV +E+H  MREFL
Sbjct: 388 TDLQRIEMTQAHFYDEFPSKDVFEAACDFAREWRGLLWEDSKRMRLVVKSEVHNQMREFL 447

Query: 165 RGQNK 169
             Q++
Sbjct: 448 HTQSR 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	169
WB|WBGene00013529	481	Y73F8A.24 [Caenorhabditis eleg	0.863	0.303	0.4	5.8e-26
DICTYBASE|DDB_G0293228	483	gtf2h4 "TFIIH subunit" [Dictyo	0.863	0.302	0.381	3.7e-25
ZFIN|ZDB-GENE-030131-6779	466	gtf2h4 "general transcription	0.917	0.332	0.370	8.5e-25
UNIPROTKB|A6H7G8	463	GTF2H4 "Uncharacterized protei	0.875	0.319	0.370	5.1e-24
UNIPROTKB|Q92759	462	GTF2H4 "General transcription	0.875	0.320	0.370	6.5e-24
UNIPROTKB|P60027	462	GTF2H4 "General transcription	0.875	0.320	0.370	6.5e-24
UNIPROTKB|Q767M2	463	TFIIH "Uncharacterized protein	0.875	0.319	0.370	6.6e-24
RGD|1303309	463	Gtf2h4 "general transcription	0.875	0.319	0.370	6.6e-24
UNIPROTKB|F1PGI3	463	GTF2H4 "Uncharacterized protei	0.875	0.319	0.363	8.5e-24
MGI|MGI:1338799	463	Gtf2h4 "general transcription	0.875	0.319	0.370	1.1e-23

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

 Score = 297 (109.6 bits), Expect = 5.8e-26, P = 5.8e-26
 Identities = 62/155 (40%), Positives = 96/155 (61%)

Query:    20 GFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQ- 78
             G V+VETNF++YAY++S L   I+ LF+++ Y+  ++ VG IT+ES+  A ++GIT  Q 
Sbjct:   308 GKVIVETNFRVYAYTSSLLQLAIIALFTEMTYRFQDMSVGMITRESVRGALQHGITAAQI 367

Query:    79 -----QNAHPR-VADKIP--SVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAA 130
                   NAHP+ +A   P   +P  V DQIRLWE +  R+    A+ Y  F S D F   
Sbjct:   368 ISFLRANAHPQCIATSGPVNCLPITVADQIRLWEDERRRMNLKDAYIYSHFESEDEFHGV 427

Query:   131 CDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFLR 165
             C+YAR Q+ LLW D+++  ++VN + H  +R++ +
Sbjct:   428 CEYARQQNILLWSDNQQKLVIVNEDGHELVRQWYK 462

GO:0005634 "nucleus" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

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

GO:0000003 "reproduction" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

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

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

 Score = 290 (107.1 bits), Expect = 3.7e-25, P = 3.7e-25
 Identities = 58/152 (38%), Positives = 92/152 (60%)

Query:    20 GFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQ- 78
             G++V+ETN+++YAY++S L   +L LF K+ Y+LPNL VG IT+ES+  A  +GIT +Q 
Sbjct:   328 GYIVLETNYRLYAYTSSSLQISLLSLFVKMLYRLPNLAVGIITRESIRTALIHGITADQI 387

Query:    79 -----QNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDY 133
                   N+HP  A+    +P  V +QI LWE++ NR+  T +  Y+ FP+ D + A   +
Sbjct:   388 IDFVRHNSHPNAANSGQPIPDVVAEQILLWEAERNRITYTKSVLYNSFPTNDCYIATLKF 447

Query:   134 ARDQSGLLWEDSKKMRLVVNAEIHMHMREFLR 165
             A++Q   +W       LVV  E +  +R F++
Sbjct:   448 AKEQDYYIWSHDPLKTLVVKEEGNDPIRNFIK 479

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0000439 "core TFIIH complex" evidence=IEA

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

GO:0005675 "holo TFIIH complex" evidence=ISS

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

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

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

GO:0006281 "DNA repair" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

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

 Score = 286 (105.7 bits), Expect = 8.5e-25, P = 8.5e-25
 Identities = 60/162 (37%), Positives = 95/162 (58%)

Query:    12 IPTIADNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFE 71
             IP   D  GF+VVETN+++YAY+ S+L   ++ LFS++ Y+ PNL+V  +T+ES+  A  
Sbjct:   302 IPGTGDT-GFIVVETNYRIYAYTNSELQIALVALFSEMLYRFPNLVVAQVTRESVQQAIS 360

Query:    72 NGITTEQ------QNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRD 125
             NGIT +Q        AHP +  + P +P  + DQIRLWE + +R++ T    Y++F S+ 
Sbjct:   361 NGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELEKDRLQFTEGVLYNQFLSQA 420

Query:   126 VFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 167
              FE   D A+    L+W++     +VV    H  ++ F + Q
Sbjct:   421 DFEVLRDRAQGLGVLVWQNPAHRVMVVTPHGHSEVKRFWKRQ 462

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0000439 "core TFIIH complex" evidence=IEA

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

 Score = 279 (103.3 bits), Expect = 5.1e-24, P = 5.1e-24
 Identities = 57/154 (37%), Positives = 94/154 (61%)

Query:    20 GFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQ- 78
             GF+VVETN+++YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GIT +Q 
Sbjct:   306 GFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQI 365

Query:    79 -----QNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDY 133
                    AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE    +
Sbjct:   366 IHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAH 425

Query:   134 ARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 167
             AR+   L++E+S K  +VV    H  ++ F + Q
Sbjct:   426 ARELGVLMFENSAKRLMVVTPAGHSDVKRFWKRQ 459

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

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

GO:0005675 "holo TFIIH complex" evidence=IEA

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

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

GO:0000439 "core TFIIH complex" evidence=IEA

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

 Score = 278 (102.9 bits), Expect = 6.5e-24, P = 6.5e-24
 Identities = 57/154 (37%), Positives = 94/154 (61%)

Query:    20 GFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQ- 78
             GF+VVETN+++YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GIT +Q 
Sbjct:   305 GFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQI 364

Query:    79 -----QNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDY 133
                    AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE    +
Sbjct:   365 IHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAH 424

Query:   134 ARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 167
             AR+   L++E+S K  +VV    H  ++ F + Q
Sbjct:   425 ARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQ 458

GO:0000439 "core TFIIH complex" evidence=IEA

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

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

GO:0004672 "protein kinase activity" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005675 "holo TFIIH complex" evidence=IDA

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

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

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

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

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

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

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

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

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

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

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

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

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

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

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

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

GO:0006468 "protein phosphorylation" evidence=IDA

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

 Score = 278 (102.9 bits), Expect = 6.5e-24, P = 6.5e-24
 Identities = 57/154 (37%), Positives = 94/154 (61%)

Query:    20 GFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQ- 78
             GF+VVETN+++YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GIT +Q 
Sbjct:   305 GFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQI 364

Query:    79 -----QNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDY 133
                    AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE    +
Sbjct:   365 IHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAH 424

Query:   134 ARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 167
             AR+   L++E+S K  +VV    H  ++ F + Q
Sbjct:   425 ARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQ 458

GO:0005675 "holo TFIIH complex" evidence=ISS

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

GO:0004672 "protein kinase activity" evidence=ISS

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

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

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

 Score = 278 (102.9 bits), Expect = 6.6e-24, P = 6.6e-24
 Identities = 57/154 (37%), Positives = 94/154 (61%)

Query:    20 GFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQ- 78
             GF+VVETN+++YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GIT +Q 
Sbjct:   306 GFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQI 365

Query:    79 -----QNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDY 133
                    AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE    +
Sbjct:   366 IHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAH 425

Query:   134 ARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 167
             AR+   L++E+S K  +VV    H  ++ F + Q
Sbjct:   426 ARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQ 459

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

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

GO:0005675 "holo TFIIH complex" evidence=IEA

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

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

GO:0000439 "core TFIIH complex" evidence=IEA

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

 Score = 278 (102.9 bits), Expect = 6.6e-24, P = 6.6e-24
 Identities = 57/154 (37%), Positives = 94/154 (61%)

Query:    20 GFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQ- 78
             GF+VVETN+++YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GIT +Q 
Sbjct:   306 GFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQI 365

Query:    79 -----QNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDY 133
                    AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE    +
Sbjct:   366 IHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAH 425

Query:   134 ARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 167
             AR+   L++E+S K  +VV    H  ++ F + Q
Sbjct:   426 ARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQ 459

GO:0000439 "core TFIIH complex" evidence=IEA

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

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

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

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

GO:0004672 "protein kinase activity" evidence=ISO

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

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

 Score = 277 (102.6 bits), Expect = 8.5e-24, P = 8.5e-24
 Identities = 56/154 (36%), Positives = 94/154 (61%)

Query:    20 GFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQ- 78
             GF++VETN+++YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GIT +Q 
Sbjct:   306 GFIIVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQI 365

Query:    79 -----QNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDY 133
                    AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE    +
Sbjct:   366 IHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAH 425

Query:   134 ARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 167
             AR+   L++E+S K  +VV    H  ++ F + Q
Sbjct:   426 ARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQ 459

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 = 276 (102.2 bits), Expect = 1.1e-23, P = 1.1e-23
 Identities = 57/154 (37%), Positives = 94/154 (61%)

Query:    20 GFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQ- 78
             GF+VVETN+++YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GIT +Q 
Sbjct:   306 GFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQI 365

Query:    79 -----QNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDY 133
                    AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE    +
Sbjct:   366 IHFLRTRAHPVMLKQNPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAH 425

Query:   134 ARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ 167
             AR+   L++E+S K  +VV    H  ++ F + Q
Sbjct:   426 ARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQ 459

GO:0000439 "core TFIIH complex" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0005675 "holo TFIIH complex" evidence=ISO

GO:0006281 "DNA repair" evidence=IEA

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

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

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

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

---

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	169
TIGR00625	448	TIGR00625, tfb2, Transcription factor tfb2	9e-41
COG5144	447	COG5144, TFB2, RNA polymerase II transcription ini	2e-39
pfam03849	365	pfam03849, Tfb2, Transcription factor Tfb2	4e-34

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

 Score =  141 bits (358), Expect = 9e-41
 Identities = 59/163 (36%), Positives = 98/163 (60%), Gaps = 7/163 (4%)

Query: 14  TIADNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENG 73
           T+ D+ GF++VETN+++YAY+ S L   ++ LFS++  + PN++VG IT+ES+  A  NG
Sbjct: 286 TVDDDLGFIIVETNYRLYAYTESPLQIALIALFSELLARFPNMVVGQITRESIRRALANG 345

Query: 74  ITTEQ------QNAHPRV-ADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDV 126
           IT +Q       +AHP++  ++ P +P  + DQIRLWE + +R+  T    Y++F ++  
Sbjct: 346 ITAQQIIHYLRTHAHPQMRKEQTPVLPPTIVDQIRLWELERDRLRFTEGVLYNDFLTQVD 405

Query: 127 FEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK 169
           FE    YAR+   L+WE+S K    +    H  ++ F + Q  
Sbjct: 406 FELLLAYARELGVLVWENSAKRLFFITPAGHSDVKRFWKRQKH 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 =  138 bits (348), Expect = 2e-39
 Identities = 58/168 (34%), Positives = 94/168 (55%), Gaps = 14/168 (8%)

Query: 4   QSRKESWFIPTIADNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITK 63
           Q+R+E        D+ GF++VETN K+YAY+ S L   ++ LF  +  + PNL+ G IT+
Sbjct: 283 QNRRE--------DDKGFIIVETNNKIYAYTNSPLQIAVIHLFCNLTARFPNLVKGIITR 334

Query: 64  ESLYNAFENGITTEQ------QNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHY 117
           ES+  A +NGIT +Q       +AHP++  K+  +P  + DQI LWE + NR+   P + 
Sbjct: 335 ESIRRALDNGITAKQIIHYLETHAHPQMRKKLELLPPTIVDQIVLWELERNRIFMVPGYL 394

Query: 118 YDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFLR 165
           Y +F +   ++   +YA     L+W D  K    +  E H  ++EF++
Sbjct: 395 YSDFLTLSDYQKVLEYAIRGGVLVWSDVDKRMFFIKLEGHSLVKEFVK 442

Length = 447

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

 Score =  122 bits (309), Expect = 4e-34
 Identities = 37/70 (52%), Positives = 52/70 (74%), Gaps = 6/70 (8%)

Query: 20  GFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQ- 78
           GF++VETNF++YAY++S L   IL LF +++Y+ PNL+VG IT+ES+ NA ENGIT +Q 
Sbjct: 296 GFIIVETNFRLYAYTSSPLQIAILALFVELKYRFPNLVVGQITRESIRNALENGITADQI 355

Query: 79  -----QNAHP 83
                 +AHP
Sbjct: 356 ISYLETHAHP 365

Length = 365

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	169
KOG3471	465	consensus RNA polymerase II transcription initiati	100.0
TIGR00625	448	tfb2 Transcription factor tfb2. This family is bas	100.0
COG5144	447	TFB2 RNA polymerase II transcription initiation/nu	100.0
PF03849	366	Tfb2: Transcription factor Tfb2; InterPro: IPR0045	100.0
PF13625	129	Helicase_C_3: Helicase conserved C-terminal domain	99.22
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	88.04

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

Probab=100.00  E-value=2.3e-73  Score=509.87  Aligned_cols=167  Identities=41%  Similarity=0.722  Sum_probs=161.5

Q ss_pred             ccccCccceeece---------------------eCCCceEEEEeCceEEEEcCCHhHHHHHHHHHhhhhccCceEEEEe
Q 041357            3 IQSRKESWFIPTI---------------------ADNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAI   61 (169)
Q Consensus         3 ~~k~k~~~f~pT~---------------------~~~~g~IIvETNfRvYAYT~S~LqiaiL~lF~~l~~r~PNlvvg~i   61 (169)
                      +||+|+++||||+                     .++.|||||||||||||||+||||+|||+|||++.|||||||||+|
T Consensus       268 Qrk~k~~rfyptrla~~~ss~~~~~~~~~~~~~~edd~G~iIVETN~riYAYT~S~lQiAvi~LF~~l~~rf~nlvvG~i  347 (465)
T KOG3471|consen  268 QRKIKILRFYPTRLAIGLSSDQLGAASLVHQNRNEDDVGFIIVETNYRIYAYTNSPLQIAVIALFTELTYRFPNLVVGVI  347 (465)
T ss_pred             HhhhhhheecchhhhhccchhhhhhhhhhhcccccccCceEEEEeccEEEEecCCHHHHHHHHHHHHHHhhccccceeee
Confidence            6899999999999                     3456999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHcCCCccc------cccChhhhhcC--CCCChhHHHHHHHHHHhcCceeecCceeecCCCCHHHHHHHHHH
Q 041357           62 TKESLYNAFENGITTEQ------QNAHPRVADKI--PSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDY  133 (169)
Q Consensus        62 TR~Sv~~Al~~GITA~Q------~~aHp~m~~~~--p~iP~tV~dQIrLWE~Er~Rl~~~~g~ly~~f~s~~~f~~~~~y  133 (169)
                      ||||||+||++||||+|      +||||||+...  |+|||||+|||+|||+||||+.+++|+||++|+|..||+.+++|
T Consensus       348 TreSVr~Al~~GITa~QII~fLet~ahpqm~~~~~~~~LPpTv~dQIrLWElernR~~~~~g~LYs~Fls~~df~~l~ey  427 (465)
T KOG3471|consen  348 TRESVRRALDNGITAEQIIHFLETHAHPQMRMLSPVPCLPPTVVDQIRLWELERNRLRMTEGYLYSDFLSLSDFQLLLEY  427 (465)
T ss_pred             eHHHHHHHHhcCCcHHHHHHHHHhccCchhhhcCCCCCCCchHHhHHHHHHHhhcceecccchhHHhhhhhhhHHHHHHH
Confidence            99999999999999999      99999998876  89999999999999999999999999999999999999999999


Q ss_pred             HHHcCeEEeecCCccEEEEecccchHHHHHHhhccC
Q 041357          134 ARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK  169 (169)
Q Consensus       134 A~~~g~llw~~~~kr~~~V~~~~h~~vr~f~k~~~~  169 (169)
                      |+++|+|+|+|+.||+|||+.+||++|++|||+++|
T Consensus       428 a~~~~vLvw~d~~kr~~vV~~~Ghs~Vk~f~Kr~~k  463 (465)
T KOG3471|consen  428 AREIGVLVWSDSDKRMFVVTKEGHSLVKRFWKRKSK  463 (465)
T ss_pred             HHHcCeEEEecCcceEEEEecCccHHHHHHHHHhhc
Confidence            999999999999999999999999999999999654

>TIGR00625 tfb2 Transcription factor tfb2

Probab=100.00  E-value=1.7e-70  Score=496.97  Aligned_cols=167  Identities=38%  Similarity=0.711  Sum_probs=161.4

Q ss_pred             ccccCccceeece------------e-------CCCceEEEEeCceEEEEcCCHhHHHHHHHHHhhhhccCceEEEEeCH
Q 041357            3 IQSRKESWFIPTI------------A-------DNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITK   63 (169)
Q Consensus         3 ~~k~k~~~f~pT~------------~-------~~~g~IIvETNfRvYAYT~S~LqiaiL~lF~~l~~r~PNlvvg~iTR   63 (169)
                      ++++++++|||||            +       .++|||||||||||||||+||||+|||+|||++.||||||+||.|||
T Consensus       256 ~~~~~~~~fYPTrLAt~Lts~~~~l~~~~~~~~~~~g~iivEtNfrvYaYt~s~l~~~il~lF~~~~~r~pnlvvg~iTr  335 (448)
T TIGR00625       256 QRKRKSRRFYPTRLAINLTSDTKTVSGAGGTVDDDLGFIIVETNYRLYAYTESPLQIALIALFSELLARFPNMVVGQITR  335 (448)
T ss_pred             EecCCCCcccchHHHHHHhcCccccccccccccCCCceEEEEecceEEEecCCHHHHHHHHHHHHHHhcCCceEEEEecH
Confidence            5788999999999            1       35799999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHcCCCccc------cccChhhh-hcCCCCChhHHHHHHHHHHhcCceeecCceeecCCCCHHHHHHHHHHHHH
Q 041357           64 ESLYNAFENGITTEQ------QNAHPRVA-DKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARD  136 (169)
Q Consensus        64 ~Sv~~Al~~GITA~Q------~~aHp~m~-~~~p~iP~tV~dQIrLWE~Er~Rl~~~~g~ly~~f~s~~~f~~~~~yA~~  136 (169)
                      +||++|+++||||||      +||||+|+ +..|+|||||+|||+|||.||||+++++|+||++|.|+.||+++++||++
T Consensus       336 ~Sv~~A~~~GITa~qIi~fl~~~ahp~~~~~~~~~lP~tv~dQi~lWe~e~~R~~~~~~~l~~~f~s~~~y~~~~~ya~~  415 (448)
T TIGR00625       336 ESIRRALANGITAQQIIHYLRTHAHPQMRKEQTPVLPPTIVDQIRLWELERDRLRFTEGVLYNDFLTQVDFELLLAYARE  415 (448)
T ss_pred             HHHHHHHHcCCCHHHHHHHHHhcCChhhhccCCCCCChHHHHHHHHHHHHhcceEeecceeeeecCCHHHHHHHHHHHHH
Confidence            999999999999999      99999998 47899999999999999999999999999999999999999999999999


Q ss_pred             cCeEEeecCCccEEEEecccchHHHHHHhhccC
Q 041357          137 QSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK  169 (169)
Q Consensus       137 ~g~llw~~~~kr~~~V~~~~h~~vr~f~k~~~~  169 (169)
                      +|+|+|+|+.||+|||+.+||++||+|||++|+
T Consensus       416 ~~~l~w~~~~kr~~~V~~~gh~~v~~f~k~~~~  448 (448)
T TIGR00625       416 LGVLVWENSAKRLFFITPAGHSDVKRFWKRQKH  448 (448)
T ss_pred             cCEEEEecCCceEEEEeccchHHHHHHHHhhcC
Confidence            999999999999999999999999999999985

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

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

Probab=100.00  E-value=1.2e-63  Score=439.21  Aligned_cols=165  Identities=35%  Similarity=0.621  Sum_probs=159.5

Q ss_pred             cccCccceeece-------------------eCCCceEEEEeCceEEEEcCCHhHHHHHHHHHhhhhccCceEEEEeCHH
Q 041357            4 QSRKESWFIPTI-------------------ADNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKE   64 (169)
Q Consensus         4 ~k~k~~~f~pT~-------------------~~~~g~IIvETNfRvYAYT~S~LqiaiL~lF~~l~~r~PNlvvg~iTR~   64 (169)
                      ++-.+.+||||+                   .++.||||||||||+|||||||||+|+++|||++.+||||||+|+||||
T Consensus       256 ~~i~~~~fYpt~LA~glt~d~~~~~s~qnr~edd~gfiIVETN~kiYaYtnSplqiavi~LF~nl~arf~Nlv~GiITre  335 (447)
T COG5144         256 LGILRKIFYPTGLAIGLTFDQLFEASEQNRREDDKGFIIVETNNKIYAYTNSPLQIAVIHLFCNLTARFPNLVKGIITRE  335 (447)
T ss_pred             hccchhhccccccchhhhhHHHHHhhhhccccccCceEEEEecceEEEecCChHHHHHHHHhhhhhcccchhhhhhccHH
Confidence            456677899999                   4567999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHcCCCccc------cccChhhhhcCCCCChhHHHHHHHHHHhcCceeecCceeecCCCCHHHHHHHHHHHHHcC
Q 041357           65 SLYNAFENGITTEQ------QNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQS  138 (169)
Q Consensus        65 Sv~~Al~~GITA~Q------~~aHp~m~~~~p~iP~tV~dQIrLWE~Er~Rl~~~~g~ly~~f~s~~~f~~~~~yA~~~g  138 (169)
                      ||++||.+||||+|      +||||||+++.|.+|||++|||+|||+||||+...||+||+||.+.++|+.+++||.+.|
T Consensus       336 SirrAl~nGIta~QII~yLethahpqmr~~l~llPPtivdQI~lWele~nRi~~~pG~LysdFlt~s~y~~~~eya~~~g  415 (447)
T COG5144         336 SIRRALDNGITAKQIIHYLETHAHPQMRKKLELLPPTIVDQIVLWELERNRIFMVPGYLYSDFLTLSDYQKVLEYAIRGG  415 (447)
T ss_pred             HHHHHHhcCccHHHHHHHHHhccChhhhhcCCCCChhhhhheeeeeeccCcEEeecchHHhhhhchhhHHHHHHHHHhcC
Confidence            99999999999999      999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEeecCCccEEEEecccchHHHHHHhhcc
Q 041357          139 GLLWEDSKKMRLVVNAEIHMHMREFLRGQN  168 (169)
Q Consensus       139 ~llw~~~~kr~~~V~~~~h~~vr~f~k~~~  168 (169)
                      +|+|+|..||||||+.+||.+|++|.|++-
T Consensus       416 vLvw~d~~Krmffi~~eG~s~v~~f~Kr~l  445 (447)
T COG5144         416 VLVWSDVDKRMFFIKLEGHSLVKEFVKRIL  445 (447)
T ss_pred             eEEeecccceEEEEEccCcHHHHHHHHHHh
Confidence            999999999999999999999999999864

>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=4.6e-38  Score=278.93  Aligned_cols=81  Identities=49%  Similarity=0.889  Sum_probs=77.4

Q ss_pred             ccccCccceeece------------------------eCCCceEEEEeCceEEEEcCCHhHHHHHHHHHhhhhccCceEE
Q 041357            3 IQSRKESWFIPTI------------------------ADNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIV   58 (169)
Q Consensus         3 ~~k~k~~~f~pT~------------------------~~~~g~IIvETNfRvYAYT~S~LqiaiL~lF~~l~~r~PNlvv   58 (169)
                      ++|+++++|||||                        +.++|||||||||||||||+||||+|||+|||++.||||||+|
T Consensus       256 ~~~~~~~~fypT~La~~l~~~~~~~~~~~~~~~~~~~~~~~g~iivETNfrvYAYT~s~l~iaiL~lF~~~~~r~pnlvv  335 (366)
T PF03849_consen  256 QRKRKSRRFYPTRLATNLTSGSSALRSASSALDSSSSSNKEGFIIVETNFRVYAYTNSPLQIAILSLFCELKYRFPNLVV  335 (366)
T ss_pred             EecCCCCeEechHHHHHHhcCCCcccccccccccccccccCceEEEEecceEEEecCCHHHHHHHHHHHHHHhcCCCeEE
Confidence            5788999999999                        1358999999999999999999999999999999999999999


Q ss_pred             EEeCHHHHHHHHHcCCCccc------cccCh
Q 041357           59 GAITKESLYNAFENGITTEQ------QNAHP   83 (169)
Q Consensus        59 g~iTR~Sv~~Al~~GITA~Q------~~aHp   83 (169)
                      |+||||||++|+++||||||      +||||
T Consensus       336 g~iTr~Sv~~A~~~GIta~qIi~fL~~~aHp  366 (366)
T PF03849_consen  336 GQITRESVRRALKNGITADQIISFLRSHAHP  366 (366)
T ss_pred             EEEcHHHHHHHHHcCCCHHHHHHHHHhcCCC
Confidence            99999999999999999999      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=99.22  E-value=1.3e-10  Score=88.95  Aligned_cols=112  Identities=19%  Similarity=0.265  Sum_probs=91.5

Q ss_pred             EEEEeCceEEEEcCCH--hHHHHHHHHHhhhhccCceEEEEeCHHHHHHHHHcCCCccccccChhhhhcCCCCChhHHHH
Q 041357           22 VVVETNFKMYAYSTSK--LHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQQNAHPRVADKIPSVPKNVCDQ   99 (169)
Q Consensus        22 IIvETNfRvYAYT~S~--LqiaiL~lF~~l~~r~PNlvvg~iTR~Sv~~Al~~GITA~Q~~aHp~m~~~~p~iP~tV~dQ   99 (169)
                      +||+.||.|.+.+.+|  -+...|..|+++ .+..+|.+..||+.|+.+|++.|+|+++..+-=+-.. ..-||+||..+
T Consensus         2 liVqpd~~I~v~~~~~~~~~~~~L~~fae~-~s~~~~~~yrlT~~Sl~~A~~~G~~~e~i~~~L~~~S-~~~lP~~v~~~   79 (129)
T PF13625_consen    2 LIVQPDFEILVEPGHPSPADAWFLARFAEL-KSPDTMHVYRLTPASLWRAASAGLTAEEIIEFLERYS-KNPLPQNVEQS   79 (129)
T ss_pred             EEECCCCEEEEeCCCCCHHHHHHHHHHhcc-cccCceEEEEECHHHHHHHHHcCCCHHHHHHHHHHHc-CCCCCHHHHHH
Confidence            6899999999977766  455899999999 6779999999999999999999999999222111111 23589999999


Q ss_pred             HHHHHHhcCceeecCceeecCCCCHHHHHHHHHHHH
Q 041357          100 IRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYAR  135 (169)
Q Consensus       100 IrLWE~Er~Rl~~~~g~ly~~f~s~~~f~~~~~yA~  135 (169)
                      |+-|...-.++++.++.++-...+.+..+.+.+..+
T Consensus        80 i~~w~~~~g~v~l~~~~~~l~~~d~~~l~~l~~~~~  115 (129)
T PF13625_consen   80 IEDWARRYGRVRLYKGAYLLECDDPELLDELLADPE  115 (129)
T ss_pred             HHHHHHhcCCEEEecCeEEEEECCHHHHHHHHhChh
Confidence            999999999999999777778888887777665433

>TIGR00603 rad25 DNA repair helicase rad25

Probab=88.04  E-value=5.6  Score=39.42  Aligned_cols=90  Identities=20%  Similarity=0.230  Sum_probs=69.4

Q ss_pred             CCCceEEEEeCceEEEEcCCHhHHHHHHHHHhhhhccCceEEEEeCHHHHHHHHHcCCCccccccChhhhhcCCCCChhH
Q 041357           17 DNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQQNAHPRVADKIPSVPKNV   96 (169)
Q Consensus        17 ~~~g~IIvETNfRvYAYT~S~LqiaiL~lF~~l~~r~PNlvvg~iTR~Sv~~Al~~GITA~Q~~aHp~m~~~~p~iP~tV   96 (169)
                      ..+|.|++||--.+|.     -=-..|.-|+|+..|--+|-...||-=|+-+|...|+++++...--.-.+ ...||++|
T Consensus        20 ~~d~~i~lE~~~p~~~-----~a~~fl~~~aEp~~rp~~iHeY~lT~~sl~~A~s~g~~~~~ii~~L~~~s-k~~~p~~i   93 (732)
T TIGR00603        20 APDGHIFLESFSPLYK-----QAQDFLVAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLETEDIIEVLGRLS-KTPIPKGI   93 (732)
T ss_pred             cCCCeEEEEeCCccHH-----HHHHHHHHhcccccChhheEEEeccHHHHHHHHHcCCCHHHHHHHHHHHh-CCCCCHHH
Confidence            3468888888433321     11378899999999999999999999999999999999999222111111 24799999


Q ss_pred             HHHHHHHHHhcCceee
Q 041357           97 CDQIRLWESDLNRVET  112 (169)
Q Consensus        97 ~dQIrLWE~Er~Rl~~  112 (169)
                      ++.|+.+-.--.++++
T Consensus        94 ~~~i~~~~~~ygk~kl  109 (732)
T TIGR00603        94 IEFIRLCTQSYGKVKL  109 (732)
T ss_pred             HHHHHHHHHhcCcEEE
Confidence            9999999999888777

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).

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Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	169
3dom_A	108	Crystal Structure Of The Complex Between Tfb5 And T		7e-06
3dgp_A	80	Crystal Structure Of The Complex Between Tfb5 And T		8e-05

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 26/83 (31%), Positives = 44/83 (53%)
Query: 83  PRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLW 142
           P   + +  +P  V DQIRLW+ +L+RV T     Y +F +   +     YA+D   LLW
Sbjct: 19  PNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLW 78
Query: 143 EDSKKMRLVVNAEIHMHMREFLR 165
           +D KK +  ++ E +  + +F +
Sbjct: 79  KDDKKKKFFISKEGNSQVLDFAK 101

>pdb|3DGP|A Chain A, Crystal Structure Of The Complex Between Tfb5 And The C-Terminal Domain Of Tfb2 Length = 80

Iteration: 1
 Score = 43.1 bits (100), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 39/71 (54%)
Query: 95  NVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNA 154
            V DQIRLW+ +L+RV T     Y +F +   +     YA+D   LLW+D KK +  ++ 
Sbjct: 3   TVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISK 62
Query: 155 EIHMHMREFLR 165
           E +  + +F +
Sbjct: 63  EGNSQVLDFAK 73

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	169
3dom_A	108	RNA polymerase II transcription factor B subunit;	2e-37
3dgp_A	80	RNA polymerase II transcription factor B subunit;	2e-31

>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 =  123 bits (311), Expect = 2e-37
 Identities = 27/96 (28%), Positives = 48/96 (50%)

Query: 74  ITTEQQNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDY 133
              ++    P   + +  +P  V DQIRLW+ +L+RV T     Y +F +   +     Y
Sbjct: 10  KLEKKLELDPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKY 69

Query: 134 ARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK 169
           A+D   LLW+D KK +  ++ E +  + +F + + K
Sbjct: 70  AQDIGVLLWKDDKKKKFFISKEGNSQVLDFAKRKLK 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 =  107 bits (269), Expect = 2e-31
 Identities = 25/75 (33%), Positives = 41/75 (54%)

Query: 95  NVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNA 154
            V DQIRLW+ +L+RV T     Y +F +   +     YA+D   LLW+D KK +  ++ 
Sbjct: 3   TVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISK 62

Query: 155 EIHMHMREFLRGQNK 169
           E +  + +F + + K
Sbjct: 63  EGNSQVLDFAKRKLK 77

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	169
3dom_A	108	RNA polymerase II transcription factor B subunit;	100.0
3dgp_A	80	RNA polymerase II transcription factor B subunit;	100.0

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

Probab=100.00  E-value=1.1e-37  Score=236.04  Aligned_cols=89  Identities=30%  Similarity=0.595  Sum_probs=72.3

Q ss_pred             cChhhhhcCCCCChhHHHHHHHHHHhcCceeecCceeecCCCCHHHHHHHHHHHHHcCeEEeecCCccEEEEecccchHH
Q 041357           81 AHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHM  160 (169)
Q Consensus        81 aHp~m~~~~p~iP~tV~dQIrLWE~Er~Rl~~~~g~ly~~f~s~~~f~~~~~yA~~~g~llw~~~~kr~~~V~~~~h~~v  160 (169)
                      ..|++....|+|||||+|||||||.|||||++++||||++|.|+++|+.+++||+++|+|||+|+.+|+|||+.+||++|
T Consensus        17 ~~~~~~~~~p~lPpTVvDQIrLWE~ErnRl~~~~G~LY~dF~s~~efe~v~~yA~e~gvLlW~d~~kr~~~Vs~egh~~v   96 (108)
T 3dom_A           17 LDPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISKEGNSQV   96 (108)
T ss_dssp             ---------------CCCHHHHHHHHHTTCEEEEEEEEECCSCHHHHHHHHHHHHHHTCEEEEEGGGTEEEEEGGGHHHH
T ss_pred             cCcccccCCCCCCCcHHHHHHHHHHhhCceeccceEEEecCCCHHHHHHHHHHHHHcCeEEEecCCccEEEEeccchHHH
Confidence            34555555899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhccC
Q 041357          161 REFLRGQNK  169 (169)
Q Consensus       161 r~f~k~~~~  169 (169)
                      ++|||++++
T Consensus        97 k~f~Kr~~~  105 (108)
T 3dom_A           97 LDFAKRKLK  105 (108)
T ss_dssp             HHHHHHHC-
T ss_pred             HHHHHHHHh
Confidence            999999874

>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=100.00  E-value=1.4e-35  Score=214.29  Aligned_cols=76  Identities=33%  Similarity=0.610  Sum_probs=61.6

Q ss_pred             hhHHHHHHHHHHhcCceeecCceeecCCCCHHHHHHHHHHHHHcCeEEeecCCccEEEEecccchHHHHHHhhccC
Q 041357           94 KNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK  169 (169)
Q Consensus        94 ~tV~dQIrLWE~Er~Rl~~~~g~ly~~f~s~~~f~~~~~yA~~~g~llw~~~~kr~~~V~~~~h~~vr~f~k~~~~  169 (169)
                      |||+|||||||+|||||++++|+||++|+|+++|+++++||+++|+|||+|+.+|+|||+.+||++|++|||++++
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            7999999999999999999999999999999999999999999999999999999999999999999999999874

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Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

No hit with probability above 80.00