Citrus Sinensis ID: 036799

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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------
Protein Sequence
MPSGIIARLPTSEDLEAYAIGQWELMDTNAQLWYIVREYISNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQQNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDRSGLL
Secondary Structure (PSIPRED)
cccccccccccHHHHHHHHHcHHHHHccHHHHHHHHHHHccccccEEEEEEccEEEEEcccHHHHHHHHHHHHHHHHcccEEEEEEcHHHHHHHHHccccHHHHHcccccccccccccccHHHHHHHHHHHcccccccccEEEcccccHHHHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
ccccEEEEccccHHHHHHHHHHHHHHHccccHHHHHHHcccccccEEEEEEcEEEEEEcccHHHHHHHHHHHHHHHHcccEEEEEEcHHHHHHHHHccccHHHHHccHHHccccccccccHHHHHHHHHHHHccEEEcccEEEcccccHHHHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
mpsgiiarlptsedleAYAIGQWELMDTNAQLWYIVREYISNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIeyqlpnlivgaTTKESLNNAFENgitaeqqnahprvadripsipenvCDQIRLWESDlnrvemtpahyydefpsrdvFEAACDYardrsgll
Flexible Loop (DISEMBL)
mpsgiiarlptsedLEAYAIGQWELMDTNAQLWYIVREYISNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQQNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPahyydefpsrdVFEAACDYARDRSGLL
Low Complexity Region (SEG)
MPSGIIARLPTSEDLEAYAIGQWELMDTNAQLWYIVREYISNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQQNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDRSGLL
Disordered region (IsUnstruct)
************EDLEAYAIGQWELMDTNAQLWYIVREYISNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGI************DRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDY********
Disordered Region (DISOPRED)
********LPTSEDLEAYAIGQWELMDTNAQLWYIVREYISNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQQNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDRSGLL
Disordered Region (DISEMBL)
MPSGIIARLPTSEDLEAYAIGQWELMDTNAQLWYIVREYISNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQQNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDRSGLL
Disordered Region (DISPRO)
*PSGIIARLPTSEDLEAYAIGQWELMDTNAQLWYIVREYISNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQQNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDRSGLL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPSGIIARLPTSEDLEAYAIGQWELMDTNAQLWYIVREYISNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQQNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDRSGLL
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	166	2.2.26 [Sep-21-2011]
P87303	447	RNA polymerase II transcr	yes	no	0.722	0.268	0.380	7e-23
P60027	462	General transcription fac	yes	no	0.704	0.253	0.406	8e-23
Q92759	462	General transcription fac	yes	no	0.704	0.253	0.406	8e-23
O70422	463	General transcription fac	yes	no	0.704	0.252	0.406	2e-22
Q54C29	483	General transcription fac	yes	no	0.759	0.260	0.409	1e-21
Q6BZX4	467	RNA polymerase II transcr	yes	no	0.765	0.271	0.345	1e-20
Q6CLR2	496	RNA polymerase II transcr	yes	no	0.734	0.245	0.356	9e-20
Q6FP41	504	RNA polymerase II transcr	yes	no	0.734	0.242	0.328	3e-17
Q75B51	514	RNA polymerase II transcr	yes	no	0.734	0.237	0.321	9e-17
Q02939	513	RNA polymerase II transcr	yes	no	0.734	0.237	0.321	4e-16

>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 =  106 bits (265), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 48/126 (38%), Positives = 79/126 (62%), Gaps = 6/126 (4%)

Query: 42  NSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITA 101
           + +GF++VETN+R+YAY++S L   I+ LF+ +  +  NL+VG  T++S+  A  NGI A
Sbjct: 288 DDKGFIIVETNYRLYAYTSSPLQIAIIGLFANLRARFSNLVVGVITRDSIRRALMNGIAA 347

Query: 102 EQ------QNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAA 155
           EQ       +AHP++   +P +P  + DQI LWE + NR+  TP   + +F +   F+ A
Sbjct: 348 EQIITYLTTHAHPQMRSNVPLLPPTLVDQIYLWELEKNRLRATPGILFRDFLTDSGFDQA 407

Query: 156 CDYARD 161
            +YA++
Sbjct: 408 VEYAKE 413

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

 Score =  106 bits (264), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 50/123 (40%), Positives = 78/123 (63%), Gaps = 6/123 (4%)

Query: 45  GFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQ- 103
           GF+VVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V   T+ES+  A  +GITA+Q 
Sbjct: 305 GFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQI 364

Query: 104 -----QNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDY 158
                  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE    +
Sbjct: 365 IHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAH 424

Query: 159 ARD 161
           AR+
Sbjct: 425 ARE 427

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 =  106 bits (264), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 50/123 (40%), Positives = 78/123 (63%), Gaps = 6/123 (4%)

Query: 45  GFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQ- 103
           GF+VVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V   T+ES+  A  +GITA+Q 
Sbjct: 305 GFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQI 364

Query: 104 -----QNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDY 158
                  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE    +
Sbjct: 365 IHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAH 424

Query: 159 ARD 161
           AR+
Sbjct: 425 ARE 427

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 =  105 bits (261), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 50/123 (40%), Positives = 78/123 (63%), Gaps = 6/123 (4%)

Query: 45  GFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQ- 103
           GF+VVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V   T+ES+  A  +GITA+Q 
Sbjct: 306 GFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQI 365

Query: 104 -----QNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDY 158
                  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE    +
Sbjct: 366 IHFLRTRAHPVMLKQNPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAH 425

Query: 159 ARD 161
           AR+
Sbjct: 426 ARE 428

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

 Score =  102 bits (254), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 54/132 (40%), Positives = 83/132 (62%), Gaps = 6/132 (4%)

Query: 37  REYISNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFE 96
           R      QG++V+ETN+R+YAY++S L   +L LF K+ Y+LPNL VG  T+ES+  A  
Sbjct: 320 RTQTQKEQGYIVLETNYRLYAYTSSSLQISLLSLFVKMLYRLPNLAVGIITRESIRTALI 379

Query: 97  NGITAEQ------QNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRD 150
           +GITA+Q       N+HP  A+    IP+ V +QI LWE++ NR+  T +  Y+ FP+ D
Sbjct: 380 HGITADQIIDFVRHNSHPNAANSGQPIPDVVAEQILLWEAERNRITYTKSVLYNSFPTND 439

Query: 151 VFEAACDYARDR 162
            + A   +A+++
Sbjct: 440 CYIATLKFAKEQ 451

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|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 = 99.0 bits (245), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 46/133 (34%), Positives = 78/133 (58%), Gaps = 6/133 (4%)

Query: 40  ISNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGI 99
           ++   GF+++ETNFR+YAY+ S L   +L LF  ++ +  N++ G   ++S+  A  NGI
Sbjct: 300 VAADSGFIILETNFRLYAYTESPLQIAVLNLFVNLKTRFANMVTGQINRDSVRFALSNGI 359

Query: 100 TAEQ------QNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFE 153
           TAEQ       +AHPR+      +P  V DQI+LW+ +++R+  T  + + EF + D ++
Sbjct: 360 TAEQIITYLSVHAHPRMKGMEHVLPPTVVDQIKLWQLEMDRIRATDGYLFSEFKNFDEYK 419

Query: 154 AACDYARDRSGLL 166
               YA++   LL
Sbjct: 420 DVSTYAKELGVLL 432

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

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

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

 Score = 95.9 bits (237), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 52/146 (35%), Positives = 78/146 (53%), Gaps = 24/146 (16%)

Query: 45  GFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQ- 103
           G +++ETNF++Y+YS S L   IL LF  ++ +  N++ G  T+ES+ NA  NGITAEQ 
Sbjct: 322 GALIIETNFKLYSYSNSPLQIAILSLFVHLKSRFANMVTGQLTRESVRNALLNGITAEQI 381

Query: 104 -----QNAHPR------------------VADRIPSIPENVCDQIRLWESDLNRVEMTPA 140
                 +AHPR                  V + +  +P  V DQIRLW+ +L+R+     
Sbjct: 382 IAYLETHAHPRMRRLAEENLSKKLELDPTVKETLQVLPPTVVDQIRLWQLELDRIISYDG 441

Query: 141 HYYDEFPSRDVFEAACDYARDRSGLL 166
           + Y +F S   ++   DYA+D   LL
Sbjct: 442 YLYTDFESYQEYQTVADYAKDIGVLL 467

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 = 87.8 bits (216), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 48/146 (32%), Positives = 74/146 (50%), Gaps = 24/146 (16%)

Query: 45  GFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQ- 103
           G +++ETNF++Y+Y  S L   IL LF  ++ +  N++ G  T+ES+  A  NGITA+Q 
Sbjct: 327 GALIIETNFKLYSYCNSPLQIAILSLFVHLKSRFANMVAGQITRESIRRALINGITADQV 386

Query: 104 -----QNAHPRV------------------ADRIPSIPENVCDQIRLWESDLNRVEMTPA 140
                 +AHP++                   D +  +P  V DQI+LW+ +L+RV     
Sbjct: 387 IAYLESHAHPQMRRLAEEKLQKKLELDPNCKDPLQVLPPTVVDQIKLWQLELDRVLTYEG 446

Query: 141 HYYDEFPSRDVFEAACDYARDRSGLL 166
             Y +F +   F   C YA+D   LL
Sbjct: 447 SLYIDFDTAQDFNMLCKYAQDIGALL 472

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 = 86.3 bits (212), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 47/146 (32%), Positives = 76/146 (52%), Gaps = 24/146 (16%)

Query: 45  GFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQ- 103
           G ++VETNF++Y+YS S L   IL LF  ++ +  N++ G  T+ES+  A  NGITA+Q 
Sbjct: 339 GALIVETNFKLYSYSNSPLQIAILSLFIHLKTRFQNMVTGQITRESIRRALHNGITADQI 398

Query: 104 -----QNAHPRV------------------ADRIPSIPENVCDQIRLWESDLNRVEMTPA 140
                 +AHP++                   D +  +P  V DQI+LW+ +L+R+     
Sbjct: 399 IAYMETHAHPQMRRLAGDNLEKKLELDPNCRDTLQVLPPTVVDQIKLWQLELDRIISYDG 458

Query: 141 HYYDEFPSRDVFEAACDYARDRSGLL 166
           + + +F +   ++    YARD   LL
Sbjct: 459 YLFRDFDNLQEYQVLAQYARDIGVLL 484

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

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

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

 Score = 84.0 bits (206), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 47/146 (32%), Positives = 75/146 (51%), Gaps = 24/146 (16%)

Query: 45  GFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQ- 103
           G ++VETNF++Y+YS S L   +L LF  ++ +  N+++G  T+ES+  A  NGITA+Q 
Sbjct: 337 GSLIVETNFKIYSYSNSPLQIAVLSLFVHLKARFVNMVLGQITRESIRRALTNGITADQI 396

Query: 104 -----QNAHPRV------------------ADRIPSIPENVCDQIRLWESDLNRVEMTPA 140
                 +AHP++                   + +  +P  V DQIRLW+ +L+RV     
Sbjct: 397 IAYLETHAHPQMRRLAEEKLEKKLELDPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEG 456

Query: 141 HYYDEFPSRDVFEAACDYARDRSGLL 166
             Y +F +   +     YA+D   LL
Sbjct: 457 SLYSDFETSQEYNLLSKYAQDIGVLL 482

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	166
255556021	451	tfiih, polypeptide, putative [Ricinus co	0.759	0.279	0.810	3e-57
449433857	451	PREDICTED: general transcription factor	0.759	0.279	0.818	1e-56
224077128	449	predicted protein [Populus trichocarpa]	0.759	0.280	0.772	5e-55
147854406	451	hypothetical protein VITISV_005315 [Viti	0.759	0.279	0.780	5e-55
356548733	451	PREDICTED: general transcription factor	0.759	0.279	0.795	1e-54
358346685	451	General transcription factor IIH subunit	0.885	0.325	0.670	2e-54
357461579	452	General transcription factor IIH subunit	0.885	0.325	0.664	2e-54
115461368	444	Os04g0680000 [Oryza sativa Japonica Grou	0.879	0.328	0.541	5e-54
90399251	470	B0213E10.4 [Oryza sativa Indica Group]	0.873	0.308	0.549	6e-54
356521347	451	PREDICTED: general transcription factor	0.759	0.279	0.772	3e-53

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

 Score =  226 bits (575), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 107/132 (81%), Positives = 118/132 (89%), Gaps = 6/132 (4%)

Query: 41  SNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGIT 100
           S  QGFVVVETNFRMYAYSTSKLH EI+RLFS++EYQLPNL+VGA TKESL +AFENGIT
Sbjct: 293 SRKQGFVVVETNFRMYAYSTSKLHCEIMRLFSRVEYQLPNLVVGAMTKESLYSAFENGIT 352

Query: 101 AEQ------QNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEA 154
           AEQ      QNAHPRVA+RIPS+PENV DQIRLWESD+NRVEMTPAH YDEFPSRDVFEA
Sbjct: 353 AEQIISFLQQNAHPRVAERIPSVPENVTDQIRLWESDMNRVEMTPAHLYDEFPSRDVFEA 412

Query: 155 ACDYARDRSGLL 166
           AC++ARD +GLL
Sbjct: 413 ACNFARDWNGLL 424

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 =  224 bits (571), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 108/132 (81%), Positives = 118/132 (89%), Gaps = 6/132 (4%)

Query: 41  SNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGIT 100
           S   GFVVVETNFRMYAYSTSKLH EILRLFS+IEYQLPNLIVGA TKESL NAF+NGIT
Sbjct: 293 SRKLGFVVVETNFRMYAYSTSKLHCEILRLFSRIEYQLPNLIVGAITKESLYNAFKNGIT 352

Query: 101 AEQ------QNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEA 154
           AEQ      QNAHPRVA+RIPS+PENV DQIRLWESDLNRV++TPAH+YDEFPSR+VFEA
Sbjct: 353 AEQIVTFLQQNAHPRVAERIPSVPENVTDQIRLWESDLNRVDITPAHFYDEFPSREVFEA 412

Query: 155 ACDYARDRSGLL 166
           ACDYAR+ +GLL
Sbjct: 413 ACDYAREWNGLL 424

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 =  218 bits (556), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 102/132 (77%), Positives = 117/132 (88%), Gaps = 6/132 (4%)

Query: 41  SNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGIT 100
           S  QG+VVVETNFR+YAYS+SKLH EILRLFSKIEYQLPNLIVGA TKESL  AFENGIT
Sbjct: 291 SRKQGYVVVETNFRLYAYSSSKLHCEILRLFSKIEYQLPNLIVGAITKESLYTAFENGIT 350

Query: 101 AEQ------QNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEA 154
           ++Q      QNAHPRVA+R+PS+PENV DQIRLWE+DLNRVE+TP+H+YDEFPSRD FEA
Sbjct: 351 SDQIISFLQQNAHPRVAERLPSVPENVTDQIRLWEADLNRVEITPSHFYDEFPSRDTFEA 410

Query: 155 ACDYARDRSGLL 166
           ACD+AR+ +GLL
Sbjct: 411 ACDFAREWNGLL 422

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  218 bits (556), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 103/132 (78%), Positives = 114/132 (86%), Gaps = 6/132 (4%)

Query: 41  SNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGIT 100
           S  QGFVVVETNFR+YAYS+SKLH EILRLFS++EYQLPNLIVGA TKESL NAFENGIT
Sbjct: 293 SRKQGFVVVETNFRLYAYSSSKLHCEILRLFSRVEYQLPNLIVGAITKESLYNAFENGIT 352

Query: 101 AEQ------QNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEA 154
           AEQ      QNAHPRVA+R P++PENV DQIRLWE+DLNRVE  P+H YDEFPSRDVFEA
Sbjct: 353 AEQIISFLQQNAHPRVAERTPAVPENVTDQIRLWETDLNRVETMPSHLYDEFPSRDVFEA 412

Query: 155 ACDYARDRSGLL 166
           ACD+AR+  GLL
Sbjct: 413 ACDFAREYGGLL 424

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  217 bits (552), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 105/132 (79%), Positives = 116/132 (87%), Gaps = 6/132 (4%)

Query: 41  SNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGIT 100
           S  QGFVVVETNFR+YAYSTSKLH EILRLFS++EYQLPNLIVGA TKESL +AFENGIT
Sbjct: 293 SRKQGFVVVETNFRVYAYSTSKLHCEILRLFSRVEYQLPNLIVGAITKESLYSAFENGIT 352

Query: 101 AEQ------QNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEA 154
           AEQ      QNAHPRVA+RIPS+PENV +QIRLWE+DLNRVEMT A+YYDEFPSRDVFE 
Sbjct: 353 AEQIITFLQQNAHPRVAERIPSVPENVTEQIRLWEADLNRVEMTDAYYYDEFPSRDVFEG 412

Query: 155 ACDYARDRSGLL 166
           ACD AR+ +GLL
Sbjct: 413 ACDCAREWNGLL 424

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 110/164 (67%), Positives = 125/164 (76%), Gaps = 17/164 (10%)

Query: 20  IGQWELMDTNAQLWYI-----------VREYISNSQGFVVVETNFRMYAYSTSKLHYEIL 68
           +G  +L     + W+I           + E  S  +GFVVVETNFR+YAYSTSKLH EIL
Sbjct: 261 LGLVKLQQGRKESWFIPTKLATNLSVSMTESSSRKEGFVVVETNFRVYAYSTSKLHCEIL 320

Query: 69  RLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQ------QNAHPRVADRIPSIPENVC 122
           RLFS++EYQLPNLIVGA TKESL NAF+NGITA+Q      QNAHPRVA RIP++PENV 
Sbjct: 321 RLFSRVEYQLPNLIVGAITKESLYNAFDNGITADQIVSFFRQNAHPRVAQRIPAVPENVT 380

Query: 123 DQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDRSGLL 166
           DQIRLWESDLNRVEMT A+YYDEFPSRDVFE ACD AR+ SGLL
Sbjct: 381 DQIRLWESDLNRVEMTEAYYYDEFPSRDVFEGACDCAREWSGLL 424

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 =  216 bits (551), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 109/164 (66%), Positives = 125/164 (76%), Gaps = 17/164 (10%)

Query: 20  IGQWELMDTNAQLWYI-----------VREYISNSQGFVVVETNFRMYAYSTSKLHYEIL 68
           +G  +L     + W+I           + E  S  +GFVVVETNFR+YAYSTSKLH EIL
Sbjct: 262 LGLVKLQQGRKESWFIPTKLATNLSVSMTESSSRKEGFVVVETNFRVYAYSTSKLHCEIL 321

Query: 69  RLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQ------QNAHPRVADRIPSIPENVC 122
           RLFS++EYQLPNLIVGA TKESL NAF+NGITA+Q      QNAHPRVA R+P++PENV 
Sbjct: 322 RLFSRVEYQLPNLIVGAITKESLYNAFDNGITADQIVSFLRQNAHPRVAQRVPAVPENVT 381

Query: 123 DQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDRSGLL 166
           DQIRLWESDLNRVEMT A+YYDEFPSRDVFE ACD AR+ SGLL
Sbjct: 382 DQIRLWESDLNRVEMTEAYYYDEFPSRDVFEGACDCAREWSGLL 425

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115461368|ref|NP_001054284.1| Os04g0680000 [Oryza sativa Japonica Group] gi|113565855|dbj|BAF16198.1| Os04g0680000 [Oryza sativa Japonica Group]

 Score =  215 bits (548), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 110/203 (54%), Positives = 132/203 (65%), Gaps = 57/203 (28%)

Query: 21  GQWELMDTNAQLWYIVREYISNS------------------------------------- 43
            +++LM+TNAQLWYI+REYIS++                                     
Sbjct: 213 SEFKLMETNAQLWYIMREYISSAEERGVDPTELISFLLELSFHTLGEAYSLNTLTDVQRN 272

Query: 44  --------------QGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKE 89
                         QGFVVVETNFRMYAYSTS+LH EILRLFS++EYQLPNLIVG+ TKE
Sbjct: 273 AIRDLAELGLVKLQQGFVVVETNFRMYAYSTSRLHCEILRLFSRVEYQLPNLIVGSITKE 332

Query: 90  SLNNAFENGITAE------QQNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYY 143
           SL  AFENGITAE      QQNAHPRVAD+IP++PENV DQIRLWE+D NRV+MT +H Y
Sbjct: 333 SLYGAFENGITAEQIISFLQQNAHPRVADKIPAVPENVTDQIRLWETDRNRVDMTLSHLY 392

Query: 144 DEFPSRDVFEAACDYARDRSGLL 166
           ++FPS+D+F+  CDYARD   LL
Sbjct: 393 EDFPSKDMFDQCCDYARDHGCLL 415

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|90399251|emb|CAJ86205.1| B0213E10.4 [Oryza sativa Indica Group]

 Score =  215 bits (547), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 111/202 (54%), Positives = 131/202 (64%), Gaps = 57/202 (28%)

Query: 22  QWELMDTNAQLWYIVREYISNS-------------------------------------- 43
           Q+ LM+TNAQLWYI+REYIS++                                      
Sbjct: 242 QFLLMETNAQLWYIMREYISSAEERGVDPTELISFLLELSFHTLGEAYSLNTLTDVQRNA 301

Query: 44  -------------QGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKES 90
                        QGFVVVETNFRMYAYSTS+LH EILRLFS++EYQLPNLIVG+ TKES
Sbjct: 302 IRDLAELGLVKLQQGFVVVETNFRMYAYSTSRLHCEILRLFSRVEYQLPNLIVGSITKES 361

Query: 91  LNNAFENGITAE------QQNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYD 144
           L  AFENGITAE      QQNAHPRVAD+IP++PENV DQIRLWE+D NRV+MT +H Y+
Sbjct: 362 LYGAFENGITAEQIISFLQQNAHPRVADKIPAVPENVTDQIRLWETDRNRVDMTLSHLYE 421

Query: 145 EFPSRDVFEAACDYARDRSGLL 166
           +FPS+D+F+  CDYARD   LL
Sbjct: 422 DFPSKDMFDQCCDYARDHGCLL 443

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  213 bits (541), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 102/132 (77%), Positives = 115/132 (87%), Gaps = 6/132 (4%)

Query: 41  SNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGIT 100
           S  QGFVVVETNFR+YAYSTSKLH EILRLFS++EYQLPNLIVGA TKESL +A+ENGIT
Sbjct: 293 SRKQGFVVVETNFRVYAYSTSKLHCEILRLFSRVEYQLPNLIVGAITKESLYSAYENGIT 352

Query: 101 AEQ------QNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEA 154
           AEQ      QNAHPRVA+R+PS+PENV +QIRLWE+DLNRVEMT  +YYDEFPSRDVFE 
Sbjct: 353 AEQIVTFLQQNAHPRVAERVPSVPENVTEQIRLWEADLNRVEMTDTYYYDEFPSRDVFEG 412

Query: 155 ACDYARDRSGLL 166
           ACD AR+ +GLL
Sbjct: 413 ACDCAREWNGLL 424

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	166
DICTYBASE|DDB_G0293228	483	gtf2h4 "TFIIH subunit" [Dictyo	0.759	0.260	0.409	2.4e-26
POMBASE|SPBC13G1.13	447	tfb2 "transcription factor TFI	0.722	0.268	0.380	5.7e-25
ZFIN|ZDB-GENE-030131-6779	466	gtf2h4 "general transcription	0.698	0.248	0.426	8.1e-24
WB|WBGene00013529	481	Y73F8A.24 [Caenorhabditis eleg	0.825	0.284	0.412	1e-22
ASPGD|ASPL0000068300	482	AN7015 [Emericella nidulans (t	0.397	0.136	0.416	1.2e-22
UNIPROTKB|A6H7G8	463	GTF2H4 "Uncharacterized protei	0.759	0.272	0.386	3.2e-21
UNIPROTKB|Q92759	462	GTF2H4 "General transcription	0.704	0.253	0.406	5.2e-21
UNIPROTKB|P60027	462	GTF2H4 "General transcription	0.704	0.253	0.406	5.2e-21
UNIPROTKB|F1PGI3	463	GTF2H4 "Uncharacterized protei	0.728	0.261	0.385	5.3e-21
UNIPROTKB|Q767M2	463	TFIIH "Uncharacterized protein	0.704	0.252	0.406	5.3e-21

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

 Score = 274 (101.5 bits), Expect = 2.4e-26, Sum P(2) = 2.4e-26
 Identities = 54/132 (40%), Positives = 83/132 (62%)

Query:    37 REYISNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFE 96
             R      QG++V+ETN+R+YAY++S L   +L LF K+ Y+LPNL VG  T+ES+  A  
Sbjct:   320 RTQTQKEQGYIVLETNYRLYAYTSSSLQISLLSLFVKMLYRLPNLAVGIITRESIRTALI 379

Query:    97 NGITAEQ------QNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRD 150
             +GITA+Q       N+HP  A+    IP+ V +QI LWE++ NR+  T +  Y+ FP+ D
Sbjct:   380 HGITADQIIDFVRHNSHPNAANSGQPIPDVVAEQILLWEAERNRITYTKSVLYNSFPTND 439

Query:   151 VFEAACDYARDR 162
              + A   +A+++
Sbjct:   440 CYIATLKFAKEQ 451

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0000439 "core TFIIH complex" evidence=IEA

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

GO:0005675 "holo TFIIH complex" evidence=ISS

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

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

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

GO:0006281 "DNA repair" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

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

 Score = 255 (94.8 bits), Expect = 5.7e-25, Sum P(2) = 5.7e-25
 Identities = 48/126 (38%), Positives = 79/126 (62%)

Query:    42 NSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITA 101
             + +GF++VETN+R+YAY++S L   I+ LF+ +  +  NL+VG  T++S+  A  NGI A
Sbjct:   288 DDKGFIIVETNYRLYAYTSSPLQIAIIGLFANLRARFSNLVVGVITRDSIRRALMNGIAA 347

Query:   102 EQ------QNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAA 155
             EQ       +AHP++   +P +P  + DQI LWE + NR+  TP   + +F +   F+ A
Sbjct:   348 EQIITYLTTHAHPQMRSNVPLLPPTLVDQIYLWELEKNRLRATPGILFRDFLTDSGFDQA 407

Query:   156 CDYARD 161
              +YA++
Sbjct:   408 VEYAKE 413

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

GO:0000439 "core TFIIH complex" evidence=ISO

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

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

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

GO:0005675 "holo TFIIH complex" evidence=ISO

GO:0005737 "cytoplasm" evidence=IDA

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

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

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

 Score = 259 (96.2 bits), Expect = 8.1e-24, Sum P(2) = 8.1e-24
 Identities = 52/122 (42%), Positives = 78/122 (63%)

Query:    45 GFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQ- 103
             GF+VVETN+R+YAY+ S+L   ++ LFS++ Y+ PNL+V   T+ES+  A  NGITA+Q 
Sbjct:   309 GFIVVETNYRIYAYTNSELQIALVALFSEMLYRFPNLVVAQVTRESVQQAISNGITAQQI 368

Query:   104 -----QNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDY 158
                    AHP +  + P +P  + DQIRLWE + +R++ T    Y++F S+  FE   D 
Sbjct:   369 IHFLRTRAHPVMLKQTPVLPPTITDQIRLWELEKDRLQFTEGVLYNQFLSQADFEVLRDR 428

Query:   159 AR 160
             A+
Sbjct:   429 AQ 430

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

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

 Score = 268 (99.4 bits), Expect = 1.0e-22, P = 1.0e-22
 Identities = 61/148 (41%), Positives = 89/148 (60%)

Query:    28 TNAQLWYIVREYISNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATT 87
             TN  +  +  E +SN  G V+VETNFR+YAY++S L   I+ LF+++ Y+  ++ VG  T
Sbjct:   293 TNETIDDVSAEKVSN--GKVIVETNFRVYAYTSSLLQLAIIALFTEMTYRFQDMSVGMIT 350

Query:    88 KESLNNAFENGITAEQ------QNAHPR-VADRIP--SIPENVCDQIRLWESDLNRVEMT 138
             +ES+  A ++GITA Q       NAHP+ +A   P   +P  V DQIRLWE +  R+ + 
Sbjct:   351 RESVRGALQHGITAAQIISFLRANAHPQCIATSGPVNCLPITVADQIRLWEDERRRMNLK 410

Query:   139 PAHYYDEFPSRDVFEAACDYARDRSGLL 166
              A+ Y  F S D F   C+YAR ++ LL
Sbjct:   411 DAYIYSHFESEDEFHGVCEYARQQNILL 438

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

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

 Score = 172 (65.6 bits), Expect = 1.2e-22, Sum P(3) = 1.2e-22
 Identities = 30/72 (41%), Positives = 51/72 (70%)

Query:    45 GFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQ- 103
             GF+++ETN+R+YAY++S L   ++ LF+ ++Y+ PNL+ G  T++S+  A E GITA+Q 
Sbjct:   317 GFIIIETNYRLYAYTSSPLQISLIALFTTLKYRFPNLVTGKVTRQSIRRAIEMGITADQI 376

Query:   104 -----QNAHPRV 110
                   +AHP++
Sbjct:   377 ISYLATHAHPQM 388

GO:0006281 "DNA repair" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

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

 Score = 254 (94.5 bits), Expect = 3.2e-21, P = 3.2e-21
 Identities = 51/132 (38%), Positives = 82/132 (62%)

Query:    41 SNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGIT 100
             ++  GF+VVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V   T+ES+  A  +GIT
Sbjct:   302 AHQPGFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGIT 361

Query:   101 AEQ------QNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEA 154
             A+Q        AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE 
Sbjct:   362 AQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFEL 421

Query:   155 ACDYARDRSGLL 166
                +AR+   L+
Sbjct:   422 LLAHARELGVLM 433

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 = 252 (93.8 bits), Expect = 5.2e-21, P = 5.2e-21
 Identities = 50/123 (40%), Positives = 78/123 (63%)

Query:    45 GFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQ- 103
             GF+VVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V   T+ES+  A  +GITA+Q 
Sbjct:   305 GFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQI 364

Query:   104 -----QNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDY 158
                    AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE    +
Sbjct:   365 IHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAH 424

Query:   159 ARD 161
             AR+
Sbjct:   425 ARE 427

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 = 252 (93.8 bits), Expect = 5.2e-21, P = 5.2e-21
 Identities = 50/123 (40%), Positives = 78/123 (63%)

Query:    45 GFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQ- 103
             GF+VVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V   T+ES+  A  +GITA+Q 
Sbjct:   305 GFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQI 364

Query:   104 -----QNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDY 158
                    AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE    +
Sbjct:   365 IHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAH 424

Query:   159 ARD 161
             AR+
Sbjct:   425 ARE 427

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

 Score = 252 (93.8 bits), Expect = 5.3e-21, P = 5.3e-21
 Identities = 49/127 (38%), Positives = 80/127 (62%)

Query:    41 SNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGIT 100
             ++  GF++VETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V   T+ES+  A  +GIT
Sbjct:   302 AHQPGFIIVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGIT 361

Query:   101 AEQ------QNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEA 154
             A+Q        AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE 
Sbjct:   362 AQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFEL 421

Query:   155 ACDYARD 161
                +AR+
Sbjct:   422 LLAHARE 428

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

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

GO:0000439 "core TFIIH complex" evidence=IEA

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

 Score = 252 (93.8 bits), Expect = 5.3e-21, P = 5.3e-21
 Identities = 50/123 (40%), Positives = 78/123 (63%)

Query:    45 GFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQ- 103
             GF+VVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V   T+ES+  A  +GITA+Q 
Sbjct:   306 GFIVVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQI 365

Query:   104 -----QNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDY 158
                    AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE    +
Sbjct:   366 IHFLRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAH 425

Query:   159 ARD 161
             AR+
Sbjct:   426 ARE 428

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	166
pfam03849	365	pfam03849, Tfb2, Transcription factor Tfb2	1e-32
TIGR00625	448	TIGR00625, tfb2, Transcription factor tfb2	1e-31
COG5144	447	COG5144, TFB2, RNA polymerase II transcription ini	1e-31
pfam03849	365	pfam03849, Tfb2, Transcription factor Tfb2	6e-04

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

 Score =  118 bits (298), Expect = 1e-32
 Identities = 39/74 (52%), Positives = 55/74 (74%), Gaps = 6/74 (8%)

Query: 41  SNSQGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGIT 100
           + S+GF++VETNFR+YAY++S L   IL LF +++Y+ PNL+VG  T+ES+ NA ENGIT
Sbjct: 292 AASKGFIIVETNFRLYAYTSSPLQIAILALFVELKYRFPNLVVGQITRESIRNALENGIT 351

Query: 101 AEQ------QNAHP 108
           A+Q       +AHP
Sbjct: 352 ADQIISYLETHAHP 365

Length = 365

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

 Score =  117 bits (294), Expect = 1e-31
 Identities = 50/124 (40%), Positives = 80/124 (64%), Gaps = 7/124 (5%)

Query: 45  GFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQ- 103
           GF++VETN+R+YAY+ S L   ++ LFS++  + PN++VG  T+ES+  A  NGITA+Q 
Sbjct: 292 GFIIVETNYRLYAYTESPLQIALIALFSELLARFPNMVVGQITRESIRRALANGITAQQI 351

Query: 104 -----QNAHPRV-ADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACD 157
                 +AHP++  ++ P +P  + DQIRLWE + +R+  T    Y++F ++  FE    
Sbjct: 352 IHYLRTHAHPQMRKEQTPVLPPTIVDQIRLWELERDRLRFTEGVLYNDFLTQVDFELLLA 411

Query: 158 YARD 161
           YAR+
Sbjct: 412 YARE 415

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 =  116 bits (293), Expect = 1e-31
 Identities = 46/128 (35%), Positives = 76/128 (59%), Gaps = 6/128 (4%)

Query: 45  GFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQ- 103
           GF++VETN ++YAY+ S L   ++ LF  +  + PNL+ G  T+ES+  A +NGITA+Q 
Sbjct: 291 GFIIVETNNKIYAYTNSPLQIAVIHLFCNLTARFPNLVKGIITRESIRRALDNGITAKQI 350

Query: 104 -----QNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDY 158
                 +AHP++  ++  +P  + DQI LWE + NR+ M P + Y +F +   ++   +Y
Sbjct: 351 IHYLETHAHPQMRKKLELLPPTIVDQIVLWELERNRIFMVPGYLYSDFLTLSDYQKVLEY 410

Query: 159 ARDRSGLL 166
           A     L+
Sbjct: 411 AIRGGVLV 418

Length = 447

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

 Score = 38.8 bits (91), Expect = 6e-04
 Identities = 8/23 (34%), Positives = 16/23 (69%)

Query: 22  QWELMDTNAQLWYIVREYISNSQ 44
           Q+ L D NAQ+W ++ +Y+  ++
Sbjct: 182 QFLLQDVNAQIWTLLLQYLKLAE 204

Length = 365

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	166
TIGR00625	448	tfb2 Transcription factor tfb2. This family is bas	100.0
KOG3471	465	consensus RNA polymerase II transcription initiati	100.0
COG5144	447	TFB2 RNA polymerase II transcription initiation/nu	100.0
PF03849	366	Tfb2: Transcription factor Tfb2; InterPro: IPR0045	100.0
PF13625	129	Helicase_C_3: Helicase conserved C-terminal domain	99.18
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	86.73

>TIGR00625 tfb2 Transcription factor tfb2

Probab=100.00  E-value=2e-62  Score=443.78  Aligned_cols=122  Identities=42%  Similarity=0.795  Sum_probs=120.1

Q ss_pred             ceEEEEecceEEEEcCCHhHHHHHHHHHhhHhhcCceEEEEeCHHHHHHHHHcCCChhh------hhcChhhh-hcCCCC
Q 036799           45 GFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQ------QNAHPRVA-DRIPSI  117 (166)
Q Consensus        45 gfIIvETNFRvYAYT~S~LqiaiL~lF~~l~~r~PNlvvG~iTR~Sv~~Al~~GITA~Q------~~AHp~m~-~~~p~i  117 (166)
                      |||||||||||||||+||||++||++||+++||||||+||+|||+||++|+++||||||      +||||+|+ +..|+|
T Consensus       292 g~iivEtNfrvYaYt~s~l~~~il~lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GITa~qIi~fl~~~ahp~~~~~~~~~l  371 (448)
T TIGR00625       292 GFIIVETNYRLYAYTESPLQIALIALFSELLARFPNMVVGQITRESIRRALANGITAQQIIHYLRTHAHPQMRKEQTPVL  371 (448)
T ss_pred             ceEEEEecceEEEecCCHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHcCCCHHHHHHHHHhcCChhhhccCCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999      99999998 478999


Q ss_pred             CHHHHHHHHHHHHhcCceeeccceeecCCCCHHHHHHHHHHHHHcCCCC
Q 036799          118 PENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDRSGLL  166 (166)
Q Consensus       118 P~tV~DQIrLWE~ErnRl~~~~g~Ly~~F~s~~~f~~~~~yA~~~g~Ll  166 (166)
                      ||||+|||||||.||||+++++|+||++|+|+.+|+++++||+++|+|+
T Consensus       372 P~tv~dQi~lWe~e~~R~~~~~~~l~~~f~s~~~y~~~~~ya~~~~~l~  420 (448)
T TIGR00625       372 PPTIVDQIRLWELERDRLRFTEGVLYNDFLTQVDFELLLAYARELGVLV  420 (448)
T ss_pred             ChHHHHHHHHHHHHhcceEeecceeeeecCCHHHHHHHHHHHHHcCEEE
Confidence            9999999999999999999999999999999999999999999999985

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

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

Probab=100.00  E-value=1.1e-61  Score=435.67  Aligned_cols=122  Identities=46%  Similarity=0.828  Sum_probs=119.8

Q ss_pred             ceEEEEecceEEEEcCCHhHHHHHHHHHhhHhhcCceEEEEeCHHHHHHHHHcCCChhh------hhcChhhhhcC--CC
Q 036799           45 GFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQ------QNAHPRVADRI--PS  116 (166)
Q Consensus        45 gfIIvETNFRvYAYT~S~LqiaiL~lF~~l~~r~PNlvvG~iTR~Sv~~Al~~GITA~Q------~~AHp~m~~~~--p~  116 (166)
                      |||||||||||||||+||||+||++|||++.||||||+||+|||||||+|+++||||+|      +||||+|+...  |+
T Consensus       306 G~iIVETN~riYAYT~S~lQiAvi~LF~~l~~rf~nlvvG~iTreSVr~Al~~GITa~QII~fLet~ahpqm~~~~~~~~  385 (465)
T KOG3471|consen  306 GFIIVETNYRIYAYTNSPLQIAVIALFTELTYRFPNLVVGVITRESVRRALDNGITAEQIIHFLETHAHPQMRMLSPVPC  385 (465)
T ss_pred             ceEEEEeccEEEEecCCHHHHHHHHHHHHHHhhccccceeeeeHHHHHHHHhcCCcHHHHHHHHHhccCchhhhcCCCCC
Confidence            79999999999999999999999999999999999999999999999999999999999      99999998865  99


Q ss_pred             CCHHHHHHHHHHHHhcCceeeccceeecCCCCHHHHHHHHHHHHHcCCCC
Q 036799          117 IPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDRSGLL  166 (166)
Q Consensus       117 iP~tV~DQIrLWE~ErnRl~~~~g~Ly~~F~s~~~f~~~~~yA~~~g~Ll  166 (166)
                      +||||+|||||||.||||+.+++|+||++|.|..||+.+++||+++|+||
T Consensus       386 LPpTv~dQIrLWElernR~~~~~g~LYs~Fls~~df~~l~eya~~~~vLv  435 (465)
T KOG3471|consen  386 LPPTVVDQIRLWELERNRLRMTEGYLYSDFLSLSDFQLLLEYAREIGVLV  435 (465)
T ss_pred             CCchHHhHHHHHHHhhcceecccchhHHhhhhhhhHHHHHHHHHHcCeEE
Confidence            99999999999999999999999999999999999999999999999986

>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=3.7e-56  Score=393.44  Aligned_cols=123  Identities=37%  Similarity=0.720  Sum_probs=121.5

Q ss_pred             CceEEEEecceEEEEcCCHhHHHHHHHHHhhHhhcCceEEEEeCHHHHHHHHHcCCChhh------hhcChhhhhcCCCC
Q 036799           44 QGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQ------QNAHPRVADRIPSI  117 (166)
Q Consensus        44 ~gfIIvETNFRvYAYT~S~LqiaiL~lF~~l~~r~PNlvvG~iTR~Sv~~Al~~GITA~Q------~~AHp~m~~~~p~i  117 (166)
                      .||||||||||+||||+||+|+|+++|||++..||||||+|+|||||||+|+.+||||+|      +||||+|+++.|.+
T Consensus       290 ~gfiIVETN~kiYaYtnSplqiavi~LF~nl~arf~Nlv~GiITreSirrAl~nGIta~QII~yLethahpqmr~~l~ll  369 (447)
T COG5144         290 KGFIIVETNNKIYAYTNSPLQIAVIHLFCNLTARFPNLVKGIITRESIRRALDNGITAKQIIHYLETHAHPQMRKKLELL  369 (447)
T ss_pred             CceEEEEecceEEEecCChHHHHHHHHhhhhhcccchhhhhhccHHHHHHHHhcCccHHHHHHHHHhccChhhhhcCCCC
Confidence            589999999999999999999999999999999999999999999999999999999999      99999999999999


Q ss_pred             CHHHHHHHHHHHHhcCceeeccceeecCCCCHHHHHHHHHHHHHcCCCC
Q 036799          118 PENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDRSGLL  166 (166)
Q Consensus       118 P~tV~DQIrLWE~ErnRl~~~~g~Ly~~F~s~~~f~~~~~yA~~~g~Ll  166 (166)
                      |||++|||+|||.||||+...||+||+||.+..+|+++++||++.|+|+
T Consensus       370 PPtivdQI~lWele~nRi~~~pG~LysdFlt~s~y~~~~eya~~~gvLv  418 (447)
T COG5144         370 PPTIVDQIVLWELERNRIFMVPGYLYSDFLTLSDYQKVLEYAIRGGVLV  418 (447)
T ss_pred             ChhhhhheeeeeeccCcEEeecchHHhhhhchhhHHHHHHHHHhcCeEE
Confidence            9999999999999999999999999999999999999999999999985

>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=4.3e-41  Score=296.95  Aligned_cols=65  Identities=55%  Similarity=1.016  Sum_probs=64.1

Q ss_pred             CceEEEEecceEEEEcCCHhHHHHHHHHHhhHhhcCceEEEEeCHHHHHHHHHcCCChhh------hhcCh
Q 036799           44 QGFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQ------QNAHP  108 (166)
Q Consensus        44 ~gfIIvETNFRvYAYT~S~LqiaiL~lF~~l~~r~PNlvvG~iTR~Sv~~Al~~GITA~Q------~~AHp  108 (166)
                      +|||||||||||||||+||||+|||++||+++||||||+||+||||||++|+++||||||      +||||
T Consensus       296 ~g~iivETNfrvYAYT~s~l~iaiL~lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GIta~qIi~fL~~~aHp  366 (366)
T PF03849_consen  296 EGFIIVETNFRVYAYTNSPLQIAILSLFCELKYRFPNLVVGQITRESVRRALKNGITADQIISFLRSHAHP  366 (366)
T ss_pred             CceEEEEecceEEEecCCHHHHHHHHHHHHHHhcCCCeEEEEEcHHHHHHHHHcCCCHHHHHHHHHhcCCC
Confidence            689999999999999999999999999999999999999999999999999999999999      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=99.18  E-value=3.9e-10  Score=85.89  Aligned_cols=110  Identities=20%  Similarity=0.243  Sum_probs=89.2

Q ss_pred             EEEEecceEEEEcCCH--hHHHHHHHHHhhHhhcCceEEEEeCHHHHHHHHHcCCChhhhhcChhhhhcCCCCCHHHHHH
Q 036799           47 VVVETNFRMYAYSTSK--LHYEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQQNAHPRVADRIPSIPENVCDQ  124 (166)
Q Consensus        47 IIvETNFRvYAYT~S~--LqiaiL~lF~~l~~r~PNlvvG~iTR~Sv~~Al~~GITA~Q~~AHp~m~~~~p~iP~tV~DQ  124 (166)
                      +||+.||.|.+.+.+|  -....|..|+++ .+..++.+..||+.|+.+|++.|+|+++..+-=.-.. ..-||++|..+
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 6779999999999999999999999999222100011 23589999999


Q ss_pred             HHHHHHhcCceeeccceeecCCCCHHHHHHHHHH
Q 036799          125 IRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDY  158 (166)
Q Consensus       125 IrLWE~ErnRl~~~~g~Ly~~F~s~~~f~~~~~y  158 (166)
                      |+-|.....|+++.++.++-...+.+..+.+.+.
T Consensus        80 i~~w~~~~g~v~l~~~~~~l~~~d~~~l~~l~~~  113 (129)
T PF13625_consen   80 IEDWARRYGRVRLYKGAYLLECDDPELLDELLAD  113 (129)
T ss_pred             HHHHHHhcCCEEEecCeEEEEECCHHHHHHHHhC
Confidence            9999999999999997777688887777666554

>TIGR00603 rad25 DNA repair helicase rad25

Probab=86.73  E-value=7.3  Score=38.62  Aligned_cols=87  Identities=20%  Similarity=0.282  Sum_probs=68.8

Q ss_pred             CCceEEEEecceEEEEcCCHhH-HHHHHHHHhhHhhcCceEEEEeCHHHHHHHHHcCCChhh-hhcChhhhhcCCCCCHH
Q 036799           43 SQGFVVVETNFRMYAYSTSKLH-YEILRLFSKIEYQLPNLIVGATTKESLNNAFENGITAEQ-QNAHPRVADRIPSIPEN  120 (166)
Q Consensus        43 ~~gfIIvETNFRvYAYT~S~Lq-iaiL~lF~~l~~r~PNlvvG~iTR~Sv~~Al~~GITA~Q-~~AHp~m~~~~p~iP~t  120 (166)
                      ++|.|++||--.+|      -+ -..|.-|+|+..|--++..-.||.=|+-.|...|+++++ ...--...  ...||++
T Consensus        21 ~d~~i~lE~~~p~~------~~a~~fl~~~aEp~~rp~~iHeY~lT~~sl~~A~s~g~~~~~ii~~L~~~s--k~~~p~~   92 (732)
T TIGR00603        21 PDGHIFLESFSPLY------KQAQDFLVAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLETEDIIEVLGRLS--KTPIPKG   92 (732)
T ss_pred             CCCeEEEEeCCccH------HHHHHHHHHhcccccChhheEEEeccHHHHHHHHHcCCCHHHHHHHHHHHh--CCCCCHH
Confidence            36788888743322      12 278899999999999999999999999999999999999 22211222  2379999


Q ss_pred             HHHHHHHHHHhcCceee
Q 036799          121 VCDQIRLWESDLNRVEM  137 (166)
Q Consensus       121 V~DQIrLWE~ErnRl~~  137 (166)
                      |.+.|+.+-.--.++++
T Consensus        93 i~~~i~~~~~~ygk~kl  109 (732)
T TIGR00603        93 IIEFIRLCTQSYGKVKL  109 (732)
T ss_pred             HHHHHHHHHHhcCcEEE
Confidence            99999999999888877

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	166
3dom_A	108	RNA polymerase II transcription factor B subunit;	1e-25
3dgp_A	80	RNA polymerase II transcription factor B subunit;	2e-18

>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 = 93.5 bits (232), Expect = 1e-25
 Identities = 19/64 (29%), Positives = 30/64 (46%)

Query: 103 QQNAHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDR 162
           +    P   + +  +P  V DQIRLW+ +L+RV       Y +F +   +     YA+D 
Sbjct: 14  KLELDPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDI 73

Query: 163 SGLL 166
             LL
Sbjct: 74  GVLL 77

>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 = 74.1 bits (182), Expect = 2e-18
 Identities = 17/47 (36%), Positives = 24/47 (51%)

Query: 120 NVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDRSGLL 166
            V DQIRLW+ +L+RV       Y +F +   +     YA+D   LL
Sbjct: 3   TVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLL 49

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	166
3dom_A	108	RNA polymerase II transcription factor B subunit;	99.89
3dgp_A	80	RNA polymerase II transcription factor B subunit;	99.84

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

Probab=99.89  E-value=1.1e-24  Score=165.29  Aligned_cols=61  Identities=31%  Similarity=0.604  Sum_probs=45.4

Q ss_pred             cChhhhhcCCCCCHHHHHHHHHHHHhcCceeeccceeecCCCCHHHHHHHHHHHHHcCCCC
Q 036799          106 AHPRVADRIPSIPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDRSGLL  166 (166)
Q Consensus       106 AHp~m~~~~p~iP~tV~DQIrLWE~ErnRl~~~~g~Ly~~F~s~~~f~~~~~yA~~~g~Ll  166 (166)
                      ..|+++.+.|+|||||+|||||||.|||||++++|+||++|.|+++|+++++||+++|+||
T Consensus        17 ~~~~~~~~~p~lPpTVvDQIrLWE~ErnRl~~~~G~LY~dF~s~~efe~v~~yA~e~gvLl   77 (108)
T 3dom_A           17 LDPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLL   77 (108)
T ss_dssp             ---------------CCCHHHHHHHHHTTCEEEEEEEEECCSCHHHHHHHHHHHHHHTCEE
T ss_pred             cCcccccCCCCCCCcHHHHHHHHHHhhCceeccceEEEecCCCHHHHHHHHHHHHHcCeEE
Confidence            4566667789999999999999999999999999999999999999999999999999986

>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=99.84  E-value=4.5e-22  Score=143.92  Aligned_cols=48  Identities=35%  Similarity=0.625  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHhcCceeeccceeecCCCCHHHHHHHHHHHHHcCCCC
Q 036799          119 ENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDRSGLL  166 (166)
Q Consensus       119 ~tV~DQIrLWE~ErnRl~~~~g~Ly~~F~s~~~f~~~~~yA~~~g~Ll  166 (166)
                      |||+|||||||.|||||++++|+||++|+|+++|+++++||+++|+||
T Consensus         2 pTV~DQIrLWe~ErnRl~~~~g~Ly~~F~s~~efe~~~~yA~e~gvLl   49 (80)
T 3dgp_A            2 PTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLL   49 (80)
T ss_dssp             ------------CGGGCEEEEEEEEECCSCHHHHHHHHHHHHHTTCEE
T ss_pred             CchHHHHHHHHHhhCceeccceEEEecCCCHHHHHHHHHHHHHcCeEE
Confidence            799999999999999999999999999999999999999999999986

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	166
d1wbha1	213	KDPG aldolase {Escherichia coli [TaxId: 562]}	81.9
d1mxsa_	216	KDPG aldolase {Pseudomonas putida [TaxId: 303]}	81.41
d1vhca_	212	Hypothetical protein HI0047 {Haemophilus influenza	80.17

>d1wbha1 c.1.10.1 (A:1-213) KDPG aldolase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Aldolase
family: Class I aldolase
domain: KDPG aldolase
species: Escherichia coli [TaxId: 562]

Probab=81.90  E-value=0.96  Score=34.97  Aligned_cols=74  Identities=22%  Similarity=0.326  Sum_probs=56.2

Q ss_pred             HHHHHhhHhhcCceEEE---EeCHHHHHHHHHcCCChhh-hhcChhhhh-----cCCCCC--HHHHHHHHHHHHhcCcee
Q 036799           68 LRLFSKIEYQLPNLIVG---ATTKESLNNAFENGITAEQ-QNAHPRVAD-----RIPSIP--ENVCDQIRLWESDLNRVE  136 (166)
Q Consensus        68 L~lF~~l~~r~PNlvvG---~iTR~Sv~~Al~~GITA~Q-~~AHp~m~~-----~~p~iP--~tV~DQIrLWE~ErnRl~  136 (166)
                      +..+.++..+||++++|   ++|.+.+++|.+.|..-== -+.+|.+.+     ..|.+|  -|..+=...|+.=-+-+|
T Consensus        54 ~~~I~~l~~~~p~~~vGaGTV~~~~~~~~a~~aGa~FivSP~~~~~v~~~a~~~~i~~iPGv~TpsEi~~A~~~G~~~vK  133 (213)
T d1wbha1          54 VDAIRAIAKEVPEAIVGAGTVLNPQQLAEVTEAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELMLGMDYGLKEFK  133 (213)
T ss_dssp             HHHHHHHHHHCTTSEEEEESCCSHHHHHHHHHHTCSCEEESSCCHHHHHHHHHSSSCEEEEESSHHHHHHHHHTTCCEEE
T ss_pred             HHHHHHHHHHCCCCeeeccccccHHHHHHHHHCCCcEEECCCCCHHHHHHHHhcCCCccCCcCCHHHHHHHHHCCCCEEE
Confidence            44555667799999999   8999999999999975433 334444432     367888  677787889999999999


Q ss_pred             eccce
Q 036799          137 MTPAH  141 (166)
Q Consensus       137 ~~~g~  141 (166)
                      +.|+-
T Consensus       134 lFPA~  138 (213)
T d1wbha1         134 FFPAE  138 (213)
T ss_dssp             ETTTT
T ss_pred             eccch
Confidence            99873

>d1mxsa_ c.1.10.1 (A:) KDPG aldolase {Pseudomonas putida [TaxId: 303]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Aldolase
family: Class I aldolase
domain: KDPG aldolase
species: Pseudomonas putida [TaxId: 303]

Probab=81.41  E-value=0.91  Score=35.23  Aligned_cols=87  Identities=18%  Similarity=0.287  Sum_probs=62.0

Q ss_pred             ceEEEEecceEEEEcCCHhHHHHHHHHHhhHhhcCceEEE---EeCHHHHHHHHHcCCChhh-hhcChhhh-----hcCC
Q 036799           45 GFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVG---ATTKESLNNAFENGITAEQ-QNAHPRVA-----DRIP  115 (166)
Q Consensus        45 gfIIvETNFRvYAYT~S~LqiaiL~lF~~l~~r~PNlvvG---~iTR~Sv~~Al~~GITA~Q-~~AHp~m~-----~~~p  115 (166)
                      |+=++|-=+|      +|--+.   .+..+..++|++.+|   ++|++.+++|.+.|..-== -+..|.+.     +..|
T Consensus        42 Gi~~iEitl~------~p~a~~---~i~~l~~~~p~~~vGaGTV~~~~~~~~a~~aGa~FivsP~~~~~v~~~a~~~~i~  112 (216)
T d1mxsa_          42 GIRTLEVTLR------SQHGLK---AIQVLREQRPELCVGAGTVLDRSMFAAVEAAGAQFVVTPGITEDILEAGVDSEIP  112 (216)
T ss_dssp             TCCEEEEESS------STHHHH---HHHHHHHHCTTSEEEEECCCSHHHHHHHHHHTCSSEECSSCCHHHHHHHHHCSSC
T ss_pred             CCCEEEEeCC------ChhHHH---HHHHHHHhCCCcceeeeeeecHHHHHHHHhCCCCEEECCCCcHHHHHHHHhcCCC
Confidence            4445554443      454444   445666799999999   8999999999999974322 34444443     2468


Q ss_pred             CCC--HHHHHHHHHHHHhcCceeeccc
Q 036799          116 SIP--ENVCDQIRLWESDLNRVEMTPA  140 (166)
Q Consensus       116 ~iP--~tV~DQIrLWE~ErnRl~~~~g  140 (166)
                      .+|  -|..+=...|+.--+-+|+.|+
T Consensus       113 ~iPGv~TpsEi~~A~~~G~~~vKlFPA  139 (216)
T d1mxsa_         113 LLPGISTPSEIMMGYALGYRRFKLFPA  139 (216)
T ss_dssp             EECEECSHHHHHHHHTTTCCEEEETTH
T ss_pred             ccCCcCCHHHHHHHHHCCCCEEEeccc
Confidence            888  6778888899999999999886

>d1vhca_ c.1.10.1 (A:) Hypothetical protein HI0047 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Aldolase
family: Class I aldolase
domain: Hypothetical protein HI0047
species: Haemophilus influenzae [TaxId: 727]

Probab=80.17  E-value=1  Score=34.67  Aligned_cols=87  Identities=22%  Similarity=0.304  Sum_probs=61.7

Q ss_pred             ceEEEEecceEEEEcCCHhHHHHHHHHHhhHhhcCceEEE---EeCHHHHHHHHHcCCChhh-hhcChhhh-----hcCC
Q 036799           45 GFVVVETNFRMYAYSTSKLHYEILRLFSKIEYQLPNLIVG---ATTKESLNNAFENGITAEQ-QNAHPRVA-----DRIP  115 (166)
Q Consensus        45 gfIIvETNFRvYAYT~S~LqiaiL~lF~~l~~r~PNlvvG---~iTR~Sv~~Al~~GITA~Q-~~AHp~m~-----~~~p  115 (166)
                      |.-++|-=+|      +|--   +....++..++|++.+|   ++|.+.+++|.+.|..-== -+..|.+.     ...|
T Consensus        39 Gi~~iEitl~------~~~a---~~~I~~l~~~~p~~~vGaGTV~~~~~~~~a~~aGa~FivSP~~~~~v~~~a~~~~i~  109 (212)
T d1vhca_          39 GLSVAEITFR------SEAA---ADAIRLLRANRPDFLIAAGTVLTAEQVVLAKSSGADFVVTPGLNPKIVKLCQDLNFP  109 (212)
T ss_dssp             TCCEEEEETT------STTH---HHHHHHHHHHCTTCEEEEESCCSHHHHHHHHHHTCSEEECSSCCHHHHHHHHHTTCC
T ss_pred             CCCEEEEeCC------ChhH---HHHHHHHHhcCCCceEeeeecccHHHHHHHHhhCCcEEECCCCCHHHHHHHHhcCCC
Confidence            5555565444      3433   34455667789999999   8999999999999964322 23333332     2468


Q ss_pred             CCC--HHHHHHHHHHHHhcCceeeccc
Q 036799          116 SIP--ENVCDQIRLWESDLNRVEMTPA  140 (166)
Q Consensus       116 ~iP--~tV~DQIrLWE~ErnRl~~~~g  140 (166)
                      .+|  .|..+=...|+.-.+-+|+.|+
T Consensus       110 ~iPGv~TpsEi~~A~~~G~~~vK~FPA  136 (212)
T d1vhca_         110 ITPGVNNPMAIEIALEMGISAVKFFPA  136 (212)
T ss_dssp             EECEECSHHHHHHHHHTTCCEEEETTT
T ss_pred             ccCCcCCHHHHHHHHHCCCCEEEEccc
Confidence            888  6788888899999999999986