Citrus Sinensis ID: 029030

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
Protein Sequence
MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK
Secondary Structure (PSIPRED)
cHHHHHHccEEEEEEccccccEEEEcHHHHHccccccccccccccEEEEEEcEEEEEEcccHHHHHHHHHHHHHHHccccEEEEEEcHHHHHHHHHccccHHHHHHHHHHccccccccccccccccHHHHHHHHHHHcccEEEcccEEEcccccHHHHHHHHHHHHHccEEEEEcccccEEEEEccccHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cHHHHHHccEEEEcccccccccEcccEEEEEEEccccccccccccEEEEEEcEEEEEEcccHHHHHHHHHHHHHHHHcccEEEEEEcHHHHHHHHHccccHHHHHHHHHHcccHHHHcccccccccHHHHHHHHHHHHccEEEcccEEEcccccHHHHHHHHHHHHHcccEEEcccccEEEEEccccHHHHHHHHHHccc
Coil and Loop (DISEMBL)
MIKDFADLGLVKLqqvgrkeswfiptklatnlsmsltdssarkegFVVVETNFRMYAYSTSKLHCEILRLFSKIEyqlpnlivgAITKESLYNAFENGITAEQIISFLQqnahprvadripsvpenvCDQIRLWESDlnrvemtpahyyeefpsrdvFEAACDYArdrsgllwedskKMRLVVNAEIHMHMREFLRGQNK
Flexible Loop (DISEMBL)
mikdfadlglvklqqvgrkeswfiptklatnlsmsltdssarkEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAhyyeefpsrdVFEAACDYARDrsgllwedskKMRLVVNAEIHMHMREFLRGQNK
Low Complexity Region (SEG)
MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK
Disordered region (IsUnstruct)
****FADLGLVKLQQVGRKESWFIPTKLATNLSMSLTD**ARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMR********
Disordered Region (DISOPRED)
MIKDFADLGLVKLQQVGRKESWFIPTKLAT*****************VVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPR*****PSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ**
Disordered Region (DISEMBL)
MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK
Disordered Region (DISPRO)
MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQ**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK
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	200	2.2.26 [Sep-21-2011]
P60027	462	General transcription fac	yes	no	0.98	0.424	0.38	9e-35
Q92759	462	General transcription fac	yes	no	0.98	0.424	0.38	9e-35
O70422	463	General transcription fac	yes	no	0.98	0.423	0.38	2e-34
P87303	447	RNA polymerase II transcr	yes	no	0.97	0.434	0.351	8e-34
Q6BZX4	467	RNA polymerase II transcr	yes	no	0.99	0.423	0.321	2e-31
Q54C29	483	General transcription fac	yes	no	0.87	0.360	0.378	1e-29
Q6CLR2	496	RNA polymerase II transcr	yes	no	0.97	0.391	0.315	3e-29
Q6FP41	504	RNA polymerase II transcr	yes	no	0.79	0.313	0.335	1e-26
Q75B51	514	RNA polymerase II transcr	yes	no	0.96	0.373	0.318	2e-26
Q6BGW8	515	RNA polymerase II transcr	yes	no	0.905	0.351	0.287	1e-25

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

 Score =  146 bits (368), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 76/200 (38%), Positives = 121/200 (60%), Gaps = 4/200 (2%)

Query: 2   IKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDSSA--RKEGFVVVETNFRMYAYS 59
           ++   + GLV   Q  RK   + PT+LA NLS  ++ +     + GF+VVETN+R+YAY+
Sbjct: 262 LQHLREFGLVF--QRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGFIVVETNYRLYAYT 319

Query: 60  TSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADR 119
            S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII FL+  AHP +  +
Sbjct: 320 ESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLRTRAHPVMLKQ 379

Query: 120 IPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKM 179
            P +P  + DQIRLWE + +R+  T    Y +F S+  FE    +AR+   L++E+S K 
Sbjct: 380 TPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARELGVLVFENSAKR 439

Query: 180 RLVVNAEIHMHMREFLRGQN 199
            +VV    H  ++ F + Q 
Sbjct: 440 LMVVTPAGHSDVKRFWKRQK 459

Component of the core-TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II.
Pan troglodytes (taxid: 9598)

>sp|Q92759|TF2H4_HUMAN General transcription factor IIH subunit 4 OS=Homo sapiens GN=GTF2H4 PE=2 SV=1

 Score =  146 bits (368), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 76/200 (38%), Positives = 121/200 (60%), Gaps = 4/200 (2%)

Query: 2   IKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDSSA--RKEGFVVVETNFRMYAYS 59
           ++   + GLV   Q  RK   + PT+LA NLS  ++ +     + GF+VVETN+R+YAY+
Sbjct: 262 LQHLREFGLVF--QRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGFIVVETNYRLYAYT 319

Query: 60  TSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADR 119
            S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII FL+  AHP +  +
Sbjct: 320 ESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLRTRAHPVMLKQ 379

Query: 120 IPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKM 179
            P +P  + DQIRLWE + +R+  T    Y +F S+  FE    +AR+   L++E+S K 
Sbjct: 380 TPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARELGVLVFENSAKR 439

Query: 180 RLVVNAEIHMHMREFLRGQN 199
            +VV    H  ++ F + Q 
Sbjct: 440 LMVVTPAGHSDVKRFWKRQK 459

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

Homo sapiens (taxid: 9606)

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

 Score =  145 bits (365), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 76/200 (38%), Positives = 121/200 (60%), Gaps = 4/200 (2%)

Query: 2   IKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDSSA--RKEGFVVVETNFRMYAYS 59
           ++   + GLV   Q  RK   + PT+LA NLS  ++ +     + GF+VVETN+R+YAY+
Sbjct: 263 LQHLREFGLVF--QRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGFIVVETNYRLYAYT 320

Query: 60  TSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADR 119
            S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII FL+  AHP +  +
Sbjct: 321 ESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLRTRAHPVMLKQ 380

Query: 120 IPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKM 179
            P +P  + DQIRLWE + +R+  T    Y +F S+  FE    +AR+   L++E+S K 
Sbjct: 381 NPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARELGVLVFENSAKR 440

Query: 180 RLVVNAEIHMHMREFLRGQN 199
            +VV    H  ++ F + Q 
Sbjct: 441 LMVVTPAGHSDVKRFWKRQK 460

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

Mus musculus (taxid: 10090)

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

 Score =  143 bits (360), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 71/202 (35%), Positives = 118/202 (58%), Gaps = 8/202 (3%)

Query: 1   MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDSSARK------EGFVVVETNFR 54
           M++D  + GLV  +++  K   F PT+LAT L+        ++      +GF++VETN+R
Sbjct: 243 MLEDLREYGLVYQRKITSKR--FYPTRLATGLTTDYRSLHGKQSENDDDKGFIIVETNYR 300

Query: 55  MYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHP 114
           +YAY++S L   I+ LF+ +  +  NL+VG IT++S+  A  NGI AEQII++L  +AHP
Sbjct: 301 LYAYTSSPLQIAIIGLFANLRARFSNLVVGVITRDSIRRALMNGIAAEQIITYLTTHAHP 360

Query: 115 RVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWE 174
           ++   +P +P  + DQI LWE + NR+  TP   + +F +   F+ A +YA++   L+W+
Sbjct: 361 QMRSNVPLLPPTLVDQIYLWELEKNRLRATPGILFRDFLTDSGFDQAVEYAKELGVLVWD 420

Query: 175 DSKKMRLVVNAEIHMHMREFLR 196
            S K    +       M  +L+
Sbjct: 421 SSLKRMFFITTTGAQPMIAYLK 442

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

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

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

 Score =  135 bits (339), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 70/218 (32%), Positives = 121/218 (55%), Gaps = 20/218 (9%)

Query: 1   MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSM------------------SLTDSSAR 42
           M++D  D G+V  ++   +   F PT+LAT L+                   +++ S A 
Sbjct: 245 MLEDLRDYGIVYQRKASSRR--FYPTRLATTLTSETAALRTASQSMEAATQDTISSSVAA 302

Query: 43  KEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAE 102
             GF+++ETNFR+YAY+ S L   +L LF  ++ +  N++ G I ++S+  A  NGITAE
Sbjct: 303 DSGFIILETNFRLYAYTESPLQIAVLNLFVNLKTRFANMVTGQINRDSVRFALSNGITAE 362

Query: 103 QIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAAC 162
           QII++L  +AHPR+      +P  V DQI+LW+ +++R+  T  + + EF + D ++   
Sbjct: 363 QIITYLSVHAHPRMKGMEHVLPPTVVDQIKLWQLEMDRIRATDGYLFSEFKNFDEYKDVS 422

Query: 163 DYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK 200
            YA++   LL+E+  K + V        + EF++ +N+
Sbjct: 423 TYAKELGVLLYENPGKRKFVSTLAGSQQIVEFVKRRNQ 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 =  129 bits (324), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 70/185 (37%), Positives = 114/185 (61%), Gaps = 11/185 (5%)

Query: 23  FIPTKLATNLS----MSLTDS-------SARKEGFVVVETNFRMYAYSTSKLHCEILRLF 71
           F PT+L  +L+    +SL  S       + +++G++V+ETN+R+YAY++S L   +L LF
Sbjct: 295 FYPTRLIISLTTGKTLSLIQSISSERTQTQKEQGYIVLETNYRLYAYTSSSLQISLLSLF 354

Query: 72  SKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQI 131
            K+ Y+LPNL VG IT+ES+  A  +GITA+QII F++ N+HP  A+    +P+ V +QI
Sbjct: 355 VKMLYRLPNLAVGIITRESIRTALIHGITADQIIDFVRHNSHPNAANSGQPIPDVVAEQI 414

Query: 132 RLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHM 191
            LWE++ NR+  T +  Y  FP+ D + A   +A+++   +W       LVV  E +  +
Sbjct: 415 LLWEAERNRITYTKSVLYNSFPTNDCYIATLKFAKEQDYYIWSHDPLKTLVVKEEGNDPI 474

Query: 192 REFLR 196
           R F++
Sbjct: 475 RNFIK 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|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 =  128 bits (321), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 77/244 (31%), Positives = 122/244 (50%), Gaps = 50/244 (20%)

Query: 1   MIKDFADLGLVKLQQVGRKESWFIPTKLAT-----------------------NLSMSLT 37
           M++D  D GL+   Q    +  F PT+LAT                       N + ++ 
Sbjct: 250 MLQDMRDYGLIYQNQSDYAK--FYPTRLATLLTSDTKAFRSASVALDSVLNKANETTAVE 307

Query: 38  DSSARKE-------GFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKES 90
             S + E       G +++ETNF++Y+YS S L   IL LF  ++ +  N++ G +T+ES
Sbjct: 308 GDSGQDETTERTQDGALIIETNFKLYSYSNSPLQIAILSLFVHLKSRFANMVTGQLTRES 367

Query: 91  LYNAFENGITAEQIISFLQQNAHPR------------------VADRIPSVPENVCDQIR 132
           + NA  NGITAEQII++L+ +AHPR                  V + +  +P  V DQIR
Sbjct: 368 VRNALLNGITAEQIIAYLETHAHPRMRRLAEENLSKKLELDPTVKETLQVLPPTVVDQIR 427

Query: 133 LWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMR 192
           LW+ +L+R+     + Y +F S   ++   DYA+D   LLW++ KK    V+ E +  + 
Sbjct: 428 LWQLELDRIISYDGYLYTDFESYQEYQTVADYAKDIGVLLWQNEKKKMFFVSTEGNSQVL 487

Query: 193 EFLR 196
           +F R
Sbjct: 488 DFHR 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|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 =  119 bits (298), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 59/176 (33%), Positives = 100/176 (56%), Gaps = 18/176 (10%)

Query: 43  KEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAE 102
           ++G +++ETNF++Y+Y  S L   IL LF  ++ +  N++ G IT+ES+  A  NGITA+
Sbjct: 325 QDGALIIETNFKLYSYCNSPLQIAILSLFVHLKSRFANMVAGQITRESIRRALINGITAD 384

Query: 103 QIISFLQQNAHPRV------------------ADRIPSVPENVCDQIRLWESDLNRVEMT 144
           Q+I++L+ +AHP++                   D +  +P  V DQI+LW+ +L+RV   
Sbjct: 385 QVIAYLESHAHPQMRRLAEEKLQKKLELDPNCKDPLQVLPPTVVDQIKLWQLELDRVLTY 444

Query: 145 PAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK 200
               Y +F +   F   C YA+D   LLW+D +K +L V+ E +  + E+ + + K
Sbjct: 445 EGSLYIDFDTAQDFNMLCKYAQDIGALLWKDDRKRKLFVSREGNAQVLEYAKRKIK 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 =  118 bits (296), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 81/254 (31%), Positives = 123/254 (48%), Gaps = 62/254 (24%)

Query: 1   MIKDFADLGLVKLQQVGRKESWFIPTKLATNLS---MSLTDSSA--------RKEGF--- 46
           M++D  D GLV  +Q     S F PT+LAT L+   +S+  +S         R EG    
Sbjct: 260 MLQDLRDYGLVFQKQ--SNLSKFYPTRLATMLTSDVVSIRSASGAVNSVLRQRAEGVDGK 317

Query: 47  -----------------------VVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIV 83
                                  ++VETNF++Y+YS S L   IL LF  ++ +  N++ 
Sbjct: 318 VLNGTALGDDDLQAGGEGALDGALIVETNFKLYSYSNSPLQIAILSLFIHLKTRFQNMVT 377

Query: 84  GAITKESLYNAFENGITAEQIISFLQQNAHP---RVA---------------DRIPSVPE 125
           G IT+ES+  A  NGITA+QII++++ +AHP   R+A               D +  +P 
Sbjct: 378 GQITRESIRRALHNGITADQIIAYMETHAHPQMRRLAGDNLEKKLELDPNCRDTLQVLPP 437

Query: 126 NVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNA 185
            V DQI+LW+ +L+R+     + + +F +   ++    YARD   LLW D KK    V+ 
Sbjct: 438 TVVDQIKLWQLELDRIISYDGYLFRDFDNLQEYQVLAQYARDIGVLLWSDDKKKMFFVSK 497

Query: 186 E-----IHMHMREF 194
           E     I  H R+F
Sbjct: 498 EGNAQVIDFHKRKF 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 =  116 bits (290), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 73/254 (28%), Positives = 117/254 (46%), Gaps = 73/254 (28%)

Query: 1   MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDSSARK----------------- 43
           M+ D  D GL+   Q       F PT+LAT L+   +DS+A K                 
Sbjct: 252 MLADLRDYGLI--YQRSENSERFYPTRLATTLT---SDSAALKSPSMAMEQALESTTETE 306

Query: 44  ----------EGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYN 93
                     +G +++ETNF++YAY+ S L   IL LF  ++ +  N++ G IT+ES+ N
Sbjct: 307 EQQNLASNSNQGTIILETNFKIYAYTNSPLEIAILNLFVHLKTRFSNMVCGQITRESIRN 366

Query: 94  AFENGITAEQIISFLQQNAHPRVA------------------------------------ 117
           A  NGITA+QII FL+ +AH ++                                     
Sbjct: 367 ALYNGITADQIIKFLETHAHSQMKILAKERLDKKIEFDTSNNINTAGGAPQSQMMTNENG 426

Query: 118 -----DRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLL 172
                 ++  +P  V DQI+LW+ +L+R++    + +++F S+  FEA  +YA +   LL
Sbjct: 427 TTVAQHKLEVLPPTVVDQIKLWQLELDRIQTFEGYLFKDFASQQEFEALSNYASEIGVLL 486

Query: 173 WEDSKKMRLVVNAE 186
           W +  KM+  V  +
Sbjct: 487 WSNKSKMKFFVTKD 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	200
255556021	451	tfiih, polypeptide, putative [Ricinus co	0.985	0.436	0.873	1e-101
224077128	449	predicted protein [Populus trichocarpa]	0.98	0.436	0.857	2e-98
449433857	451	PREDICTED: general transcription factor	0.98	0.434	0.868	7e-98
147854406	451	hypothetical protein VITISV_005315 [Viti	0.97	0.430	0.856	2e-97
357461579	452	General transcription factor IIH subunit	0.985	0.435	0.828	3e-94
358346685	451	General transcription factor IIH subunit	0.985	0.436	0.828	6e-94
356548733	451	PREDICTED: general transcription factor	0.985	0.436	0.813	1e-92
297800414	452	hypothetical protein ARALYDRAFT_493174 [	0.99	0.438	0.793	4e-92
42566894	452	transcription initiation factor TFIIH su	0.99	0.438	0.788	1e-91
42572935	462	transcription initiation factor TFIIH su	0.99	0.428	0.788	2e-91

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

 Score =  372 bits (954), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 173/198 (87%), Positives = 192/198 (96%), Gaps = 1/198 (0%)

Query: 1   MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYST 60
           MIKD ADLGLVKLQQ GRKESWFIPTKLATNLSMSLTDSS+RK+GFVVVETNFRMYAYST
Sbjct: 254 MIKDLADLGLVKLQQ-GRKESWFIPTKLATNLSMSLTDSSSRKQGFVVVETNFRMYAYST 312

Query: 61  SKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRI 120
           SKLHCEI+RLFS++EYQLPNL+VGA+TKESLY+AFENGITAEQIISFLQQNAHPRVA+RI
Sbjct: 313 SKLHCEIMRLFSRVEYQLPNLVVGAMTKESLYSAFENGITAEQIISFLQQNAHPRVAERI 372

Query: 121 PSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMR 180
           PSVPENV DQIRLWESD+NRVEMTPAH Y+EFPSRDVFEAAC++ARD +GLLWEDSK+MR
Sbjct: 373 PSVPENVTDQIRLWESDMNRVEMTPAHLYDEFPSRDVFEAACNFARDWNGLLWEDSKRMR 432

Query: 181 LVVNAEIHMHMREFLRGQ 198
           +VV AEIH++MRE+LRGQ
Sbjct: 433 MVVKAEIHLNMREYLRGQ 450

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  363 bits (933), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 169/197 (85%), Positives = 190/197 (96%), Gaps = 1/197 (0%)

Query: 2   IKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTS 61
           IKD A+LGLVKLQQ GRKESWFIPTKLATNLS+SLTDSS+RK+G+VVVETNFR+YAYS+S
Sbjct: 253 IKDLAELGLVKLQQ-GRKESWFIPTKLATNLSVSLTDSSSRKQGYVVVETNFRLYAYSSS 311

Query: 62  KLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIP 121
           KLHCEILRLFSKIEYQLPNLIVGAITKESLY AFENGIT++QIISFLQQNAHPRVA+R+P
Sbjct: 312 KLHCEILRLFSKIEYQLPNLIVGAITKESLYTAFENGITSDQIISFLQQNAHPRVAERLP 371

Query: 122 SVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRL 181
           SVPENV DQIRLWE+DLNRVE+TP+H+Y+EFPSRD FEAACD+AR+ +GLLWEDSKKMR+
Sbjct: 372 SVPENVTDQIRLWEADLNRVEITPSHFYDEFPSRDTFEAACDFAREWNGLLWEDSKKMRV 431

Query: 182 VVNAEIHMHMREFLRGQ 198
           VV AEIHM+MREFLRGQ
Sbjct: 432 VVKAEIHMNMREFLRGQ 448

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  362 bits (928), Expect = 7e-98,   Method: Compositional matrix adjust.
 Identities = 171/197 (86%), Positives = 186/197 (94%), Gaps = 1/197 (0%)

Query: 2   IKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTS 61
           IKD ADLGLVKLQQ GRKESWFIPTKLATNLSMSL DSS+RK GFVVVETNFRMYAYSTS
Sbjct: 255 IKDLADLGLVKLQQ-GRKESWFIPTKLATNLSMSLADSSSRKLGFVVVETNFRMYAYSTS 313

Query: 62  KLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIP 121
           KLHCEILRLFS+IEYQLPNLIVGAITKESLYNAF+NGITAEQI++FLQQNAHPRVA+RIP
Sbjct: 314 KLHCEILRLFSRIEYQLPNLIVGAITKESLYNAFKNGITAEQIVTFLQQNAHPRVAERIP 373

Query: 122 SVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRL 181
           SVPENV DQIRLWESDLNRV++TPAH+Y+EFPSR+VFEAACDYAR+ +GLLWEDSK +RL
Sbjct: 374 SVPENVTDQIRLWESDLNRVDITPAHFYDEFPSREVFEAACDYAREWNGLLWEDSKNLRL 433

Query: 182 VVNAEIHMHMREFLRGQ 198
           VV A+IH HMRE LR Q
Sbjct: 434 VVKADIHTHMREHLRRQ 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 =  360 bits (923), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 167/195 (85%), Positives = 184/195 (94%), Gaps = 1/195 (0%)

Query: 2   IKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTS 61
           IKD  DLGLVKLQQ GRKESWFIPTKLATNLSMSL+D+S+RK+GFVVVETNFR+YAYS+S
Sbjct: 255 IKDLVDLGLVKLQQ-GRKESWFIPTKLATNLSMSLSDTSSRKQGFVVVETNFRLYAYSSS 313

Query: 62  KLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIP 121
           KLHCEILRLFS++EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVA+R P
Sbjct: 314 KLHCEILRLFSRVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVAERTP 373

Query: 122 SVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRL 181
           +VPENV DQIRLWE+DLNRVE  P+H Y+EFPSRDVFEAACD+AR+  GLLWEDSKKMRL
Sbjct: 374 AVPENVTDQIRLWETDLNRVETMPSHLYDEFPSRDVFEAACDFAREYGGLLWEDSKKMRL 433

Query: 182 VVNAEIHMHMREFLR 196
           VV AEIH+HMRE+LR
Sbjct: 434 VVKAEIHLHMREYLR 448

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  350 bits (897), Expect = 3e-94,   Method: Compositional matrix adjust.
 Identities = 164/198 (82%), Positives = 186/198 (93%), Gaps = 1/198 (0%)

Query: 1   MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYST 60
           +IKD ADLGLVKLQQ GRKESWFIPTKLATNLS+S+T+SS+RKEGFVVVETNFR+YAYST
Sbjct: 255 IIKDLADLGLVKLQQ-GRKESWFIPTKLATNLSVSMTESSSRKEGFVVVETNFRVYAYST 313

Query: 61  SKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRI 120
           SKLHCEILRLFS++EYQLPNLIVGAITKESLYNAF+NGITA+QI+SFL+QNAHPRVA R+
Sbjct: 314 SKLHCEILRLFSRVEYQLPNLIVGAITKESLYNAFDNGITADQIVSFLRQNAHPRVAQRV 373

Query: 121 PSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMR 180
           P+VPENV DQIRLWESDLNRVEMT A+YY+EFPSRDVFE ACD AR+ SGLLWEDSKKM 
Sbjct: 374 PAVPENVTDQIRLWESDLNRVEMTEAYYYDEFPSRDVFEGACDCAREWSGLLWEDSKKMH 433

Query: 181 LVVNAEIHMHMREFLRGQ 198
           LVV +E+H ++R+FLR Q
Sbjct: 434 LVVKSEVHTYVRDFLRRQ 451

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  348 bits (893), Expect = 6e-94,   Method: Compositional matrix adjust.
 Identities = 164/198 (82%), Positives = 185/198 (93%), Gaps = 1/198 (0%)

Query: 1   MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYST 60
           +IKD ADLGLVKLQQ GRKESWFIPTKLATNLS+S+T+SS+RKEGFVVVETNFR+YAYST
Sbjct: 254 IIKDLADLGLVKLQQ-GRKESWFIPTKLATNLSVSMTESSSRKEGFVVVETNFRVYAYST 312

Query: 61  SKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRI 120
           SKLHCEILRLFS++EYQLPNLIVGAITKESLYNAF+NGITA+QI+SF +QNAHPRVA RI
Sbjct: 313 SKLHCEILRLFSRVEYQLPNLIVGAITKESLYNAFDNGITADQIVSFFRQNAHPRVAQRI 372

Query: 121 PSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMR 180
           P+VPENV DQIRLWESDLNRVEMT A+YY+EFPSRDVFE ACD AR+ SGLLWEDSKKM 
Sbjct: 373 PAVPENVTDQIRLWESDLNRVEMTEAYYYDEFPSRDVFEGACDCAREWSGLLWEDSKKMH 432

Query: 181 LVVNAEIHMHMREFLRGQ 198
           LVV +E+H ++R+FLR Q
Sbjct: 433 LVVKSEVHTYVRDFLRRQ 450

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  344 bits (882), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 161/198 (81%), Positives = 183/198 (92%), Gaps = 1/198 (0%)

Query: 1   MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYST 60
           +I D ADLGLVK+QQ GRK SWFIPTKLATNLSMSL DSS+RK+GFVVVETNFR+YAYST
Sbjct: 254 IINDLADLGLVKIQQ-GRKGSWFIPTKLATNLSMSLADSSSRKQGFVVVETNFRVYAYST 312

Query: 61  SKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRI 120
           SKLHCEILRLFS++EYQLPNLIVGAITKESLY+AFENGITAEQII+FLQQNAHPRVA+RI
Sbjct: 313 SKLHCEILRLFSRVEYQLPNLIVGAITKESLYSAFENGITAEQIITFLQQNAHPRVAERI 372

Query: 121 PSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMR 180
           PSVPENV +QIRLWE+DLNRVEMT A+YY+EFPSRDVFE ACD AR+ +GLLWEDSKKM 
Sbjct: 373 PSVPENVTEQIRLWEADLNRVEMTDAYYYDEFPSRDVFEGACDCAREWNGLLWEDSKKMH 432

Query: 181 LVVNAEIHMHMREFLRGQ 198
           +VV  E+H ++R++LR Q
Sbjct: 433 MVVKTEVHQYVRDYLRRQ 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 =  342 bits (878), Expect = 4e-92,   Method: Compositional matrix adjust.
 Identities = 158/199 (79%), Positives = 181/199 (90%), Gaps = 1/199 (0%)

Query: 2   IKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTS 61
           +KD ADLGLVKLQQ GRK+SWFIPTKLATNLS+SL DSSARKEGFVV+ETNFRMYAYSTS
Sbjct: 255 LKDLADLGLVKLQQ-GRKDSWFIPTKLATNLSVSLADSSARKEGFVVMETNFRMYAYSTS 313

Query: 62  KLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIP 121
           KL CEILRLF++IEYQLPNLI  AITKESLYNAF+NGIT++QII+FLQQN+HPR ADR+P
Sbjct: 314 KLQCEILRLFARIEYQLPNLIACAITKESLYNAFDNGITSDQIITFLQQNSHPRCADRVP 373

Query: 122 SVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRL 181
           S+PENV DQIRLWE+DL R+EMT AH+Y+EFPS+DVFEAACD+AR+  GLLWEDSK+MRL
Sbjct: 374 SIPENVTDQIRLWETDLKRIEMTQAHFYDEFPSKDVFEAACDFAREWGGLLWEDSKRMRL 433

Query: 182 VVNAEIHMHMREFLRGQNK 200
           VV +E+H  MREFL  Q K
Sbjct: 434 VVKSEVHNQMREFLHNQTK 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 =  341 bits (874), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 157/199 (78%), Positives = 182/199 (91%), Gaps = 1/199 (0%)

Query: 2   IKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTS 61
           +KD ADLGLVKLQQ GRK+SWFIPTKLATNLS+SL DSSARKEGFVV+ETNFRMYAYSTS
Sbjct: 255 LKDLADLGLVKLQQ-GRKDSWFIPTKLATNLSVSLADSSARKEGFVVMETNFRMYAYSTS 313

Query: 62  KLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIP 121
           KL CEILRLF++IEYQLPNLI  AITKESLYNAF+NGIT++QII+FLQQN+HPR ADR+P
Sbjct: 314 KLQCEILRLFARIEYQLPNLIACAITKESLYNAFDNGITSDQIITFLQQNSHPRCADRVP 373

Query: 122 SVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRL 181
           S+PENV DQIRLWE+DL R+EMT AH+Y+EFPS+DVFEAACD+AR+  GLLWEDSK+MRL
Sbjct: 374 SIPENVTDQIRLWETDLQRIEMTQAHFYDEFPSKDVFEAACDFAREWRGLLWEDSKRMRL 433

Query: 182 VVNAEIHMHMREFLRGQNK 200
           VV +E+H  MREFL  Q++
Sbjct: 434 VVKSEVHNQMREFLHTQSR 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 =  340 bits (873), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 157/199 (78%), Positives = 182/199 (91%), Gaps = 1/199 (0%)

Query: 2   IKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTS 61
           +KD ADLGLVKLQQ GRK+SWFIPTKLATNLS+SL DSSARKEGFVV+ETNFRMYAYSTS
Sbjct: 255 LKDLADLGLVKLQQ-GRKDSWFIPTKLATNLSVSLADSSARKEGFVVMETNFRMYAYSTS 313

Query: 62  KLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIP 121
           KL CEILRLF++IEYQLPNLI  AITKESLYNAF+NGIT++QII+FLQQN+HPR ADR+P
Sbjct: 314 KLQCEILRLFARIEYQLPNLIACAITKESLYNAFDNGITSDQIITFLQQNSHPRCADRVP 373

Query: 122 SVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRL 181
           S+PENV DQIRLWE+DL R+EMT AH+Y+EFPS+DVFEAACD+AR+  GLLWEDSK+MRL
Sbjct: 374 SIPENVTDQIRLWETDLQRIEMTQAHFYDEFPSKDVFEAACDFAREWRGLLWEDSKRMRL 433

Query: 182 VVNAEIHMHMREFLRGQNK 200
           VV +E+H  MREFL  Q++
Sbjct: 434 VVKSEVHNQMREFLHTQSR 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	200
WB|WBGene00013529	481	Y73F8A.24 [Caenorhabditis eleg	0.97	0.403	0.403	3.1e-35
UNIPROTKB|A6H7G8	463	GTF2H4 "Uncharacterized protei	0.975	0.421	0.381	1.5e-33
UNIPROTKB|Q767M2	463	TFIIH "Uncharacterized protein	0.975	0.421	0.381	2e-33
UNIPROTKB|F1PGI3	463	GTF2H4 "Uncharacterized protei	0.975	0.421	0.376	2.5e-33
UNIPROTKB|Q92759	462	GTF2H4 "General transcription	0.975	0.422	0.376	5.2e-33
UNIPROTKB|P60027	462	GTF2H4 "General transcription	0.975	0.422	0.376	5.2e-33
RGD|1303309	463	Gtf2h4 "general transcription	0.975	0.421	0.376	5.2e-33
MGI|MGI:1338799	463	Gtf2h4 "general transcription	0.975	0.421	0.376	8.5e-33
POMBASE|SPBC13G1.13	447	tfb2 "transcription factor TFI	0.97	0.434	0.361	6e-32
DICTYBASE|DDB_G0293228	483	gtf2h4 "TFIIH subunit" [Dictyo	0.87	0.360	0.378	8.8e-31

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

 Score = 381 (139.2 bits), Expect = 3.1e-35, P = 3.1e-35
 Identities = 82/203 (40%), Positives = 131/203 (64%)

Query:     1 MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLT--DSSARK--EGFVVVETNFRMY 56
             ++    +LG++ +++  RK+  F  T+L T+L+ + T  D SA K   G V+VETNFR+Y
Sbjct:   262 LLNHLRELGVIFIRK--RKDGVFFLTQLLTHLATNETIDDVSAEKVSNGKVIVETNFRVY 319

Query:    57 AYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPR- 115
             AY++S L   I+ LF+++ Y+  ++ VG IT+ES+  A ++GITA QIISFL+ NAHP+ 
Sbjct:   320 AYTSSLLQLAIIALFTEMTYRFQDMSVGMITRESVRGALQHGITAAQIISFLRANAHPQC 379

Query:   116 VADRIP--SVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLW 173
             +A   P   +P  V DQIRLWE +  R+ +  A+ Y  F S D F   C+YAR ++ LLW
Sbjct:   380 IATSGPVNCLPITVADQIRLWEDERRRMNLKDAYIYSHFESEDEFHGVCEYARQQNILLW 439

Query:   174 EDSKKMRLVVNAEIHMHMREFLR 196
              D+++  ++VN + H  +R++ +
Sbjct:   440 SDNQQKLVIVNEDGHELVRQWYK 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

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

 Score = 365 (133.5 bits), Expect = 1.5e-33, P = 1.5e-33
 Identities = 76/199 (38%), Positives = 124/199 (62%)

Query:     2 IKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDS--SARKEGFVVVETNFRMYAYS 59
             ++   + GLV  ++  RK   + PT+LA NLS  ++ +  +A + GF+VVETN+R+YAY+
Sbjct:   263 LQHLREFGLVFQRK--RKSRRYYPTRLAINLSSGVSGAGGTAHQPGFIVVETNYRLYAYT 320

Query:    60 TSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADR 119
              S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII FL+  AHP +  +
Sbjct:   321 ESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLRTRAHPVMLKQ 380

Query:   120 IPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKM 179
              P +P  + DQIRLWE + +R+  T    Y +F S+  FE    +AR+   L++E+S K 
Sbjct:   381 TPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARELGVLMFENSAKR 440

Query:   180 RLVVNAEIHMHMREFLRGQ 198
              +VV    H  ++ F + Q
Sbjct:   441 LMVVTPAGHSDVKRFWKRQ 459

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

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

GO:0005675 "holo TFIIH complex" evidence=IEA

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

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

GO:0000439 "core TFIIH complex" evidence=IEA

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

 Score = 364 (133.2 bits), Expect = 2.0e-33, P = 2.0e-33
 Identities = 76/199 (38%), Positives = 124/199 (62%)

Query:     2 IKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDS--SARKEGFVVVETNFRMYAYS 59
             ++   +LGLV  ++  RK   + PT+LA NLS  ++ +  +  + GF+VVETN+R+YAY+
Sbjct:   263 LQHLRELGLVFQRK--RKSRRYYPTRLAINLSSGVSGAGGTVHQPGFIVVETNYRLYAYT 320

Query:    60 TSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADR 119
              S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII FL+  AHP +  +
Sbjct:   321 ESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLRTRAHPVMLKQ 380

Query:   120 IPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKM 179
              P +P  + DQIRLWE + +R+  T    Y +F S+  FE    +AR+   L++E+S K 
Sbjct:   381 TPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARELGVLVFENSAKR 440

Query:   180 RLVVNAEIHMHMREFLRGQ 198
              +VV    H  ++ F + Q
Sbjct:   441 LMVVTPAGHSDVKRFWKRQ 459

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

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

GO:0005675 "holo TFIIH complex" evidence=IEA

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

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

GO:0000439 "core TFIIH complex" evidence=IEA

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

 Score = 363 (132.8 bits), Expect = 2.5e-33, P = 2.5e-33
 Identities = 75/199 (37%), Positives = 124/199 (62%)

Query:     2 IKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDS--SARKEGFVVVETNFRMYAYS 59
             ++   + GLV  ++  RK   + PT+LA NLS  ++ +  +A + GF++VETN+R+YAY+
Sbjct:   263 LQHLREFGLVFQRK--RKSRRYYPTRLAINLSSGVSGAGGTAHQPGFIIVETNYRLYAYT 320

Query:    60 TSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADR 119
              S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII FL+  AHP +  +
Sbjct:   321 ESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLRTRAHPVMLKQ 380

Query:   120 IPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKM 179
              P +P  + DQIRLWE + +R+  T    Y +F S+  FE    +AR+   L++E+S K 
Sbjct:   381 TPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARELGVLVFENSAKR 440

Query:   180 RLVVNAEIHMHMREFLRGQ 198
              +VV    H  ++ F + Q
Sbjct:   441 LMVVTPAGHSDVKRFWKRQ 459

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

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

GO:0000439 "core TFIIH complex" evidence=IEA

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

 Score = 360 (131.8 bits), Expect = 5.2e-33, P = 5.2e-33
 Identities = 75/199 (37%), Positives = 123/199 (61%)

Query:     2 IKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDS--SARKEGFVVVETNFRMYAYS 59
             ++   + GLV  ++  RK   + PT+LA NLS  ++ +  +  + GF+VVETN+R+YAY+
Sbjct:   262 LQHLREFGLVFQRK--RKSRRYYPTRLAINLSSGVSGAGGTVHQPGFIVVETNYRLYAYT 319

Query:    60 TSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADR 119
              S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII FL+  AHP +  +
Sbjct:   320 ESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLRTRAHPVMLKQ 379

Query:   120 IPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKM 179
              P +P  + DQIRLWE + +R+  T    Y +F S+  FE    +AR+   L++E+S K 
Sbjct:   380 TPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARELGVLVFENSAKR 439

Query:   180 RLVVNAEIHMHMREFLRGQ 198
              +VV    H  ++ F + Q
Sbjct:   440 LMVVTPAGHSDVKRFWKRQ 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 = 360 (131.8 bits), Expect = 5.2e-33, P = 5.2e-33
 Identities = 75/199 (37%), Positives = 123/199 (61%)

Query:     2 IKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDS--SARKEGFVVVETNFRMYAYS 59
             ++   + GLV  ++  RK   + PT+LA NLS  ++ +  +  + GF+VVETN+R+YAY+
Sbjct:   262 LQHLREFGLVFQRK--RKSRRYYPTRLAINLSSGVSGAGGTVHQPGFIVVETNYRLYAYT 319

Query:    60 TSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADR 119
              S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII FL+  AHP +  +
Sbjct:   320 ESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLRTRAHPVMLKQ 379

Query:   120 IPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKM 179
              P +P  + DQIRLWE + +R+  T    Y +F S+  FE    +AR+   L++E+S K 
Sbjct:   380 TPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARELGVLVFENSAKR 439

Query:   180 RLVVNAEIHMHMREFLRGQ 198
              +VV    H  ++ F + Q
Sbjct:   440 LMVVTPAGHSDVKRFWKRQ 458

GO:0005675 "holo TFIIH complex" evidence=ISS

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

GO:0004672 "protein kinase activity" evidence=ISS

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

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

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

 Score = 360 (131.8 bits), Expect = 5.2e-33, P = 5.2e-33
 Identities = 75/199 (37%), Positives = 123/199 (61%)

Query:     2 IKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDS--SARKEGFVVVETNFRMYAYS 59
             ++   + GLV  ++  RK   + PT+LA NLS  ++ +  +  + GF+VVETN+R+YAY+
Sbjct:   263 LQHLREFGLVFQRK--RKSRRYYPTRLAINLSSGVSGAGGTVHQPGFIVVETNYRLYAYT 320

Query:    60 TSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADR 119
              S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII FL+  AHP +  +
Sbjct:   321 ESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLRTRAHPVMLKQ 380

Query:   120 IPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKM 179
              P +P  + DQIRLWE + +R+  T    Y +F S+  FE    +AR+   L++E+S K 
Sbjct:   381 TPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARELGVLVFENSAKR 440

Query:   180 RLVVNAEIHMHMREFLRGQ 198
              +VV    H  ++ F + Q
Sbjct:   441 LMVVTPAGHSDVKRFWKRQ 459

GO:0000439 "core TFIIH complex" evidence=IEA

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

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

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

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

GO:0004672 "protein kinase activity" evidence=ISO

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

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

 Score = 358 (131.1 bits), Expect = 8.5e-33, P = 8.5e-33
 Identities = 75/199 (37%), Positives = 123/199 (61%)

Query:     2 IKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDS--SARKEGFVVVETNFRMYAYS 59
             ++   + GLV  ++  RK   + PT+LA NLS  ++ +  +  + GF+VVETN+R+YAY+
Sbjct:   263 LQHLREFGLVFQRK--RKSRRYYPTRLAINLSSGVSGAGGTVHQPGFIVVETNYRLYAYT 320

Query:    60 TSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADR 119
              S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII FL+  AHP +  +
Sbjct:   321 ESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHFLRTRAHPVMLKQ 380

Query:   120 IPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKM 179
              P +P  + DQIRLWE + +R+  T    Y +F S+  FE    +AR+   L++E+S K 
Sbjct:   381 NPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARELGVLVFENSAKR 440

Query:   180 RLVVNAEIHMHMREFLRGQ 198
              +VV    H  ++ F + Q
Sbjct:   441 LMVVTPAGHSDVKRFWKRQ 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

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

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 73/202 (36%), Positives = 119/202 (58%)

Query:     1 MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSM---SLTDSSARKE---GFVVVETNFR 54
             M++D  + GLV  +++  K   F PT+LAT L+    SL    +  +   GF++VETN+R
Sbjct:   243 MLEDLREYGLVYQRKITSKR--FYPTRLATGLTTDYRSLHGKQSENDDDKGFIIVETNYR 300

Query:    55 MYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHP 114
             +YAY++S L   I+ LF+ +  +  NL+VG IT++S+  A  NGI AEQII++L  +AHP
Sbjct:   301 LYAYTSSPLQIAIIGLFANLRARFSNLVVGVITRDSIRRALMNGIAAEQIITYLTTHAHP 360

Query:   115 RVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWE 174
             ++   +P +P  + DQI LWE + NR+  TP   + +F +   F+ A +YA++   L+W+
Sbjct:   361 QMRSNVPLLPPTLVDQIYLWELEKNRLRATPGILFRDFLTDSGFDQAVEYAKELGVLVWD 420

Query:   175 DSKKMRLVVNAEIHMHMREFLR 196
              S K    +       M  +L+
Sbjct:   421 SSLKRMFFITTTGAQPMIAYLK 442

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

GO:0000439 "core TFIIH complex" evidence=ISO

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

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

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

GO:0005675 "holo TFIIH complex" evidence=ISO

GO:0005737 "cytoplasm" evidence=IDA

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

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

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

 Score = 339 (124.4 bits), Expect = 8.8e-31, P = 8.8e-31
 Identities = 70/185 (37%), Positives = 114/185 (61%)

Query:    23 FIPTKLATNLS----MSLTDS-------SARKEGFVVVETNFRMYAYSTSKLHCEILRLF 71
             F PT+L  +L+    +SL  S       + +++G++V+ETN+R+YAY++S L   +L LF
Sbjct:   295 FYPTRLIISLTTGKTLSLIQSISSERTQTQKEQGYIVLETNYRLYAYTSSSLQISLLSLF 354

Query:    72 SKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQI 131
              K+ Y+LPNL VG IT+ES+  A  +GITA+QII F++ N+HP  A+    +P+ V +QI
Sbjct:   355 VKMLYRLPNLAVGIITRESIRTALIHGITADQIIDFVRHNSHPNAANSGQPIPDVVAEQI 414

Query:   132 RLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHM 191
              LWE++ NR+  T +  Y  FP+ D + A   +A+++   +W       LVV  E +  +
Sbjct:   415 LLWEAERNRITYTKSVLYNSFPTNDCYIATLKFAKEQDYYIWSHDPLKTLVVKEEGNDPI 474

Query:   192 REFLR 196
             R F++
Sbjct:   475 RNFIK 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

---

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	200
pfam03849	365	pfam03849, Tfb2, Transcription factor Tfb2	1e-56
TIGR00625	448	TIGR00625, tfb2, Transcription factor tfb2	2e-51
COG5144	447	COG5144, TFB2, RNA polymerase II transcription ini	2e-48
pfam13625	128	pfam13625, Helicase_C_3, Helicase conserved C-term	5e-05

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

 Score =  182 bits (464), Expect = 1e-56
 Identities = 56/127 (44%), Positives = 83/127 (65%), Gaps = 15/127 (11%)

Query: 1   MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTDSS-------------ARKEGFV 47
           M++D  D GLV  ++  +   ++ PT+LAT L+   +                A  +GF+
Sbjct: 241 MLQDLRDYGLVYQRK-RKSRRFY-PTRLATTLTSDSSALRTASSAMEAATSSEAASKGFI 298

Query: 48  VVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISF 107
           +VETNFR+YAY++S L   IL LF +++Y+ PNL+VG IT+ES+ NA ENGITA+QIIS+
Sbjct: 299 IVETNFRLYAYTSSPLQIAILALFVELKYRFPNLVVGQITRESIRNALENGITADQIISY 358

Query: 108 LQQNAHP 114
           L+ +AHP
Sbjct: 359 LETHAHP 365

Length = 365

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

 Score =  170 bits (433), Expect = 2e-51
 Identities = 80/207 (38%), Positives = 123/207 (59%), Gaps = 9/207 (4%)

Query: 1   MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSM-SLTDSSARKE-----GFVVVETNFR 54
           M++D  + GLV   Q  RK   F PT+LA NL+  + T S A        GF++VETN+R
Sbjct: 244 MLQDLREYGLV--FQRKRKSRRFYPTRLAINLTSDTKTVSGAGGTVDDDLGFIIVETNYR 301

Query: 55  MYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHP 114
           +YAY+ S L   ++ LFS++  + PN++VG IT+ES+  A  NGITA+QII +L+ +AHP
Sbjct: 302 LYAYTESPLQIALIALFSELLARFPNMVVGQITRESIRRALANGITAQQIIHYLRTHAHP 361

Query: 115 RV-ADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLW 173
           ++  ++ P +P  + DQIRLWE + +R+  T    Y +F ++  FE    YAR+   L+W
Sbjct: 362 QMRKEQTPVLPPTIVDQIRLWELERDRLRFTEGVLYNDFLTQVDFELLLAYARELGVLVW 421

Query: 174 EDSKKMRLVVNAEIHMHMREFLRGQNK 200
           E+S K    +    H  ++ F + Q  
Sbjct: 422 ENSAKRLFFITPAGHSDVKRFWKRQKH 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 =  163 bits (413), Expect = 2e-48
 Identities = 72/202 (35%), Positives = 116/202 (57%), Gaps = 8/202 (3%)

Query: 1   MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSM-SLTDSSARKE-----GFVVVETNFR 54
           M+ D    GLV  +Q+G     F PT LA  L+   L ++S +       GF++VETN +
Sbjct: 243 MLMDRRLYGLV--EQLGILRKIFYPTGLAIGLTFDQLFEASEQNRREDDKGFIIVETNNK 300

Query: 55  MYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHP 114
           +YAY+ S L   ++ LF  +  + PNL+ G IT+ES+  A +NGITA+QII +L+ +AHP
Sbjct: 301 IYAYTNSPLQIAVIHLFCNLTARFPNLVKGIITRESIRRALDNGITAKQIIHYLETHAHP 360

Query: 115 RVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWE 174
           ++  ++  +P  + DQI LWE + NR+ M P + Y +F +   ++   +YA     L+W 
Sbjct: 361 QMRKKLELLPPTIVDQIVLWELERNRIFMVPGYLYSDFLTLSDYQKVLEYAIRGGVLVWS 420

Query: 175 DSKKMRLVVNAEIHMHMREFLR 196
           D  K    +  E H  ++EF++
Sbjct: 421 DVDKRMFFIKLEGHSLVKEFVK 442

Length = 447

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

 Score = 41.0 bits (97), Expect = 5e-05
 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 9/65 (13%)

Query: 86  ITKESLYNAFENGITAEQIISFLQQNA-HPRVADRIPSVPENVCDQIRLWESDLNRVEMT 144
           +T  SL  A + G+TAE+II FL++++  P        VP+++   IR       R+ + 
Sbjct: 41  LTPLSLRRALDAGLTAEEIIEFLERHSRTP--------VPQSLLYLIRDVARRHGRLRLG 92

Query: 145 PAHYY 149
            A  Y
Sbjct: 93  KAGLY 97

This domain family is found in a wide variety of helicases and helicase-related proteins. Length = 128

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	200
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	99.73
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	97.68
PF08671	30	SinI: Anti-repressor SinI; InterPro: IPR010981 The	94.04
PRK06015	201	keto-hydroxyglutarate-aldolase/keto-deoxy-phosphog	88.0
TIGR01615	131	A_thal_3542 uncharacterized plant-specific domain	86.65
PRK05718	212	keto-hydroxyglutarate-aldolase/keto-deoxy-phosphog	84.32
TIGR01182	204	eda Entner-Doudoroff aldolase. 2-deydro-3-deoxypho	82.25
PRK07114	222	keto-hydroxyglutarate-aldolase/keto-deoxy-phosphog	81.35

>TIGR00625 tfb2 Transcription factor tfb2

Probab=100.00  E-value=9.7e-81  Score=577.87  Aligned_cols=198  Identities=37%  Similarity=0.698  Sum_probs=189.3

Q ss_pred             CcccccccceeEEeecCCCCccccchhhhhhhcccCCc----cc--ccccceEEEeeCceEEEecCCHhHHHHHHHhhhh
Q 029030            1 MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTD----SS--ARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKI   74 (200)
Q Consensus         1 ~L~~l~~~GLvy~~~~~~~~~fy~pT~La~~l~~~~~~----~~--~~~~g~IIvETNFrvYAYT~s~l~iaiL~lF~~l   74 (200)
                      ||+||+|+||||++ ++++++|| |||||++|++++++    ++  +.++|+|||||||||||||+||||++||++||++
T Consensus       244 ~L~dL~dlGLVy~~-~~~~~~fY-PTrLAt~Lts~~~~l~~~~~~~~~~~g~iivEtNfrvYaYt~s~l~~~il~lF~~~  321 (448)
T TIGR00625       244 MLQDLREYGLVFQR-KRKSRRFY-PTRLAINLTSDTKTVSGAGGTVDDDLGFIIVETNYRLYAYTESPLQIALIALFSEL  321 (448)
T ss_pred             HHHHHHHcCeEEEe-cCCCCccc-chHHHHHHhcCccccccccccccCCCceEEEEecceEEEecCCHHHHHHHHHHHHH
Confidence            68999999999999 88999999 99999999887553    11  2567999999999999999999999999999999


Q ss_pred             hhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCcccc-ccCCCCCccHHHHHHHHHHhcCceEecceeeeccCC
Q 029030           75 EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVA-DRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFP  153 (200)
Q Consensus        75 ~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~-~~~~~iP~tV~dQI~lWe~Er~R~~~~~g~L~~~f~  153 (200)
                      .||||||+||.|||+||++|+++||||||||+||++||||+|+ ++.|+|||||+|||+|||.||||+++++|+||++|.
T Consensus       322 ~~r~pnlvvg~iTr~Sv~~A~~~GITa~qIi~fl~~~ahp~~~~~~~~~lP~tv~dQi~lWe~e~~R~~~~~~~l~~~f~  401 (448)
T TIGR00625       322 LARFPNMVVGQITRESIRRALANGITAQQIIHYLRTHAHPQMRKEQTPVLPPTIVDQIRLWELERDRLRFTEGVLYNDFL  401 (448)
T ss_pred             HhcCCceEEEEecHHHHHHHHHcCCCHHHHHHHHHhcCChhhhccCCCCCChHHHHHHHHHHHHhcceEeecceeeeecC
Confidence            9999999999999999999999999999999999999999998 478999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHcCeEeeecCCcceEEEeccccHHHHHHHhhccC
Q 029030          154 SRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK  200 (200)
Q Consensus       154 s~~~f~~v~~ya~~~g~llw~~~~~r~~~V~~~~~~~v~~f~k~~~~  200 (200)
                      |+++|+++++||++.|+|+|+|+.||+|||+.+||++|++|||++|+
T Consensus       402 s~~~y~~~~~ya~~~~~l~w~~~~kr~~~V~~~gh~~v~~f~k~~~~  448 (448)
T TIGR00625       402 TQVDFELLLAYARELGVLVWENSAKRLFFITPAGHSDVKRFWKRQKH  448 (448)
T ss_pred             CHHHHHHHHHHHHHcCEEEEecCCceEEEEeccchHHHHHHHHhhcC
Confidence            99999999999999999999999999999999999999999999985

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-80  Score=569.18  Aligned_cols=198  Identities=41%  Similarity=0.711  Sum_probs=188.1

Q ss_pred             CcccccccceeEEeecCCCCccccchhhhhhhcccCCc--------ccccccceEEEeeCceEEEecCCHhHHHHHHHhh
Q 029030            1 MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTD--------SSARKEGFVVVETNFRMYAYSTSKLHCEILRLFS   72 (200)
Q Consensus         1 ~L~~l~~~GLvy~~~~~~~~~fy~pT~La~~l~~~~~~--------~~~~~~g~IIvETNFrvYAYT~s~l~iaiL~lF~   72 (200)
                      ||+||+|+|||||| |.+..+|| ||+||+++|++..+        ...++.||||||||||||||||||||+|+++|||
T Consensus       256 ~lq~Lre~GlvfQr-k~k~~rfy-ptrla~~~ss~~~~~~~~~~~~~~edd~G~iIVETN~riYAYT~S~lQiAvi~LF~  333 (465)
T KOG3471|consen  256 LLQHLRELGLVFQR-KIKILRFY-PTRLAIGLSSDQLGAASLVHQNRNEDDVGFIIVETNYRIYAYTNSPLQIAVIALFT  333 (465)
T ss_pred             HHHHHHHhhHHHHh-hhhhheec-chhhhhccchhhhhhhhhhhcccccccCceEEEEeccEEEEecCCHHHHHHHHHHH
Confidence            68999999999999 99999999 99999999886442        1224569999999999999999999999999999


Q ss_pred             hhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccC--CCCCccHHHHHHHHHHhcCceEecceeeec
Q 029030           73 KIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRI--PSVPENVCDQIRLWESDLNRVEMTPAHYYE  150 (200)
Q Consensus        73 ~l~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~~~--~~iP~tV~dQI~lWe~Er~R~~~~~g~L~~  150 (200)
                      ++.|||||||||+|||||||+|+++||||+|||+||++||||||+...  |++||||+|||+|||.||||+.++||+||+
T Consensus       334 ~l~~rf~nlvvG~iTreSVr~Al~~GITa~QII~fLet~ahpqm~~~~~~~~LPpTv~dQIrLWElernR~~~~~g~LYs  413 (465)
T KOG3471|consen  334 ELTYRFPNLVVGVITRESVRRALDNGITAEQIIHFLETHAHPQMRMLSPVPCLPPTVVDQIRLWELERNRLRMTEGYLYS  413 (465)
T ss_pred             HHHhhccccceeeeeHHHHHHHHhcCCcHHHHHHHHHhccCchhhhcCCCCCCCchHHhHHHHHHHhhcceecccchhHH
Confidence            999999999999999999999999999999999999999999998865  999999999999999999999999999999


Q ss_pred             cCCCHHHHHHHHHHHHHcCeEeeecCCcceEEEeccccHHHHHHHhhccC
Q 029030          151 EFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK  200 (200)
Q Consensus       151 ~f~s~~~f~~v~~ya~~~g~llw~~~~~r~~~V~~~~~~~v~~f~k~~~~  200 (200)
                      +|.|..||+.+++||++.|+|+|+|+.||+|||+.+||++|++|||+++|
T Consensus       414 ~Fls~~df~~l~eya~~~~vLvw~d~~kr~~vV~~~Ghs~Vk~f~Kr~~k  463 (465)
T KOG3471|consen  414 DFLSLSDFQLLLEYAREIGVLVWSDSDKRMFVVTKEGHSLVKRFWKRKSK  463 (465)
T ss_pred             hhhhhhhHHHHHHHHHHcCeEEEecCcceEEEEecCccHHHHHHHHHhhc
Confidence            99999999999999999999999999999999999999999999999654

>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=3.3e-71  Score=496.89  Aligned_cols=197  Identities=34%  Similarity=0.611  Sum_probs=187.8

Q ss_pred             CcccccccceeEEeecCCCCccccchhhhhhhcccCC----c--ccccccceEEEeeCceEEEecCCHhHHHHHHHhhhh
Q 029030            1 MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLT----D--SSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKI   74 (200)
Q Consensus         1 ~L~~l~~~GLvy~~~~~~~~~fy~pT~La~~l~~~~~----~--~~~~~~g~IIvETNFrvYAYT~s~l~iaiL~lF~~l   74 (200)
                      ||+|+|++||||++ +-.+++|| ||+||+.||++--    .  ...++.||||||||||||||||||||+|+++|||++
T Consensus       243 ml~D~R~yglv~q~-~i~~~~fY-pt~LA~glt~d~~~~~s~qnr~edd~gfiIVETN~kiYaYtnSplqiavi~LF~nl  320 (447)
T COG5144         243 MLMDRRLYGLVEQL-GILRKIFY-PTGLAIGLTFDQLFEASEQNRREDDKGFIIVETNNKIYAYTNSPLQIAVIHLFCNL  320 (447)
T ss_pred             HHHHHHHhhHHHHh-ccchhhcc-ccccchhhhhHHHHHhhhhccccccCceEEEEecceEEEecCChHHHHHHHHhhhh
Confidence            68999999999999 77888999 9999999987532    1  233667999999999999999999999999999999


Q ss_pred             hhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCCccHHHHHHHHHHhcCceEecceeeeccCCC
Q 029030           75 EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPS  154 (200)
Q Consensus        75 ~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~~~~~iP~tV~dQI~lWe~Er~R~~~~~g~L~~~f~s  154 (200)
                      ..||||||+|+|||||||+|+.+||||+|||.||++||||+|+++.+.+||||+|||+|||.|+||+...||+||+||.+
T Consensus       321 ~arf~Nlv~GiITreSirrAl~nGIta~QII~yLethahpqmr~~l~llPPtivdQI~lWele~nRi~~~pG~LysdFlt  400 (447)
T COG5144         321 TARFPNLVKGIITRESIRRALDNGITAKQIIHYLETHAHPQMRKKLELLPPTIVDQIVLWELERNRIFMVPGYLYSDFLT  400 (447)
T ss_pred             hcccchhhhhhccHHHHHHHHhcCccHHHHHHHHHhccChhhhhcCCCCChhhhhheeeeeeccCcEEeecchHHhhhhc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHcCeEeeecCCcceEEEeccccHHHHHHHhhcc
Q 029030          155 RDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQN  199 (200)
Q Consensus       155 ~~~f~~v~~ya~~~g~llw~~~~~r~~~V~~~~~~~v~~f~k~~~  199 (200)
                      .++|+.+++||++.|+|+|++..||||||+.+||.+|++|.|++-
T Consensus       401 ~s~y~~~~eya~~~gvLvw~d~~Krmffi~~eG~s~v~~f~Kr~l  445 (447)
T COG5144         401 LSDYQKVLEYAIRGGVLVWSDVDKRMFFIKLEGHSLVKEFVKRIL  445 (447)
T ss_pred             hhhHHHHHHHHHhcCeEEeecccceEEEEEccCcHHHHHHHHHHh
Confidence            999999999999999999999999999999999999999999864

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

Probab=100.00  E-value=1.8e-49  Score=361.39  Aligned_cols=112  Identities=53%  Similarity=0.908  Sum_probs=106.1

Q ss_pred             CcccccccceeEEeecCCCCccccchhhhhhhcccCCc-----------ccccccceEEEeeCceEEEecCCHhHHHHHH
Q 029030            1 MIKDFADLGLVKLQQVGRKESWFIPTKLATNLSMSLTD-----------SSARKEGFVVVETNFRMYAYSTSKLHCEILR   69 (200)
Q Consensus         1 ~L~~l~~~GLvy~~~~~~~~~fy~pT~La~~l~~~~~~-----------~~~~~~g~IIvETNFrvYAYT~s~l~iaiL~   69 (200)
                      ||+||+|+||||++ ++++++|| |||||++|+++.++           ....++|||||||||||||||+||||+|||+
T Consensus       244 ~L~~l~~~GLvy~~-~~~~~~fy-pT~La~~l~~~~~~~~~~~~~~~~~~~~~~~g~iivETNfrvYAYT~s~l~iaiL~  321 (366)
T PF03849_consen  244 MLQDLRELGLVYQR-KRKSRRFY-PTRLATNLTSGSSALRSASSALDSSSSSNKEGFIIVETNFRVYAYTNSPLQIAILS  321 (366)
T ss_pred             HHHHHHHCCeEEEe-cCCCCeEe-chHHHHHHhcCCCcccccccccccccccccCceEEEEecceEEEecCCHHHHHHHH
Confidence            68999999999999 88999999 99999999987663           2346789999999999999999999999999


Q ss_pred             HhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCc
Q 029030           70 LFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHP  114 (200)
Q Consensus        70 lF~~l~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp  114 (200)
                      +||++.||||||+||+||||||++|+++||||||||+||++||||
T Consensus       322 lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GIta~qIi~fL~~~aHp  366 (366)
T PF03849_consen  322 LFCELKYRFPNLVVGQITRESVRRALKNGITADQIISFLRSHAHP  366 (366)
T ss_pred             HHHHHHhcCCCeEEEEEcHHHHHHHHHcCCCHHHHHHHHHhcCCC
Confidence            999999999999999999999999999999999999999999998

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=99.73  E-value=4.3e-17  Score=128.28  Aligned_cols=118  Identities=23%  Similarity=0.363  Sum_probs=105.2

Q ss_pred             EEEeeCceEEEecCCH--hHHHHHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCC
Q 029030           47 VVVETNFRMYAYSTSK--LHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVP  124 (200)
Q Consensus        47 IIvETNFrvYAYT~s~--l~iaiL~lF~~l~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~~~~~iP  124 (200)
                      +||++||.|.+.+.+|  -..+.|..||++ .+..+|.+++||+.|+.+|++.|+|+++|++||+.|+.       ..||
T Consensus         2 liVqpd~~I~v~~~~~~~~~~~~L~~fae~-~s~~~~~~yrlT~~Sl~~A~~~G~~~e~i~~~L~~~S~-------~~lP   73 (129)
T PF13625_consen    2 LIVQPDFEILVEPGHPSPADAWFLARFAEL-KSPDTMHVYRLTPASLWRAASAGLTAEEIIEFLERYSK-------NPLP   73 (129)
T ss_pred             EEECCCCEEEEeCCCCCHHHHHHHHHHhcc-cccCceEEEEECHHHHHHHHHcCCCHHHHHHHHHHHcC-------CCCC
Confidence            7999999999977666  344999999999 56799999999999999999999999999999999994       5799


Q ss_pred             ccHHHHHHHHHHhcCceEecceeeeccCCCHHHHHHHHHHHHHcCeEe
Q 029030          125 ENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLL  172 (200)
Q Consensus       125 ~tV~dQI~lWe~Er~R~~~~~g~L~~~f~s~~~f~~v~~ya~~~g~ll  172 (200)
                      +||..+|+.|+...+|+++.++.++-.+.+.+..+.+.+..+-.++.+
T Consensus        74 ~~v~~~i~~w~~~~g~v~l~~~~~~l~~~d~~~l~~l~~~~~~~~~~~  121 (129)
T PF13625_consen   74 QNVEQSIEDWARRYGRVRLYKGAYLLECDDPELLDELLADPELAKLIL  121 (129)
T ss_pred             HHHHHHHHHHHHhcCCEEEecCeEEEEECCHHHHHHHHhChhhhhhhc
Confidence            999999999999999999999777779999999999888776655443

>TIGR00603 rad25 DNA repair helicase rad25

Probab=97.68  E-value=0.00043  Score=69.22  Aligned_cols=106  Identities=23%  Similarity=0.378  Sum_probs=85.4

Q ss_pred             cceEEEeeCceEEEecCCHhH--H-HHHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccC
Q 029030           44 EGFVVVETNFRMYAYSTSKLH--C-EILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRI  120 (200)
Q Consensus        44 ~g~IIvETNFrvYAYT~s~l~--i-aiL~lF~~l~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~~~  120 (200)
                      +|.|++||        .+|+-  . ..|.-|+|+.+|--+|..++||-=|+-.|...|+++++||++|...+-       
T Consensus        22 d~~i~lE~--------~~p~~~~a~~fl~~~aEp~~rp~~iHeY~lT~~sl~~A~s~g~~~~~ii~~L~~~sk-------   86 (732)
T TIGR00603        22 DGHIFLES--------FSPLYKQAQDFLVAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLETEDIIEVLGRLSK-------   86 (732)
T ss_pred             CCeEEEEe--------CCccHHHHHHHHHHhcccccChhheEEEeccHHHHHHHHHcCCCHHHHHHHHHHHhC-------
Confidence            45566665        45443  3 889999999999999999999999999999999999999999999984       


Q ss_pred             CCCCccHHHHHHHHHHhcCceEec--ceeeeccCCCHHHHHHHHHH
Q 029030          121 PSVPENVCDQIRLWESDLNRVEMT--PAHYYEEFPSRDVFEAACDY  164 (200)
Q Consensus       121 ~~iP~tV~dQI~lWe~Er~R~~~~--~g~L~~~f~s~~~f~~v~~y  164 (200)
                      ..||++|.+.|+.+-.-.+++++.  +.--|-+-.+.+..+.+.+-
T Consensus        87 ~~~p~~i~~~i~~~~~~ygk~klv~~~~~~~~es~~~~~l~~l~~~  132 (732)
T TIGR00603        87 TPIPKGIIEFIRLCTQSYGKVKLVLKHNRYFVESPHPEVLQRLLKD  132 (732)
T ss_pred             CCCCHHHHHHHHHHHHhcCcEEEEEcCCceEEecCCHHHHHHHHhc
Confidence            589999999999999999999883  22223344556666666543

All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []

Probab=94.04  E-value=0.053  Score=33.58  Aligned_cols=22  Identities=36%  Similarity=0.525  Sum_probs=17.7

Q ss_pred             HHHHHHHcCCCHHHHHHHHhhc
Q 029030           90 SLYNAFENGITAEQIISFLQQN  111 (200)
Q Consensus        90 Sv~~Al~~GITA~QII~fL~~h  111 (200)
                      =|++|...|||.+||-.||+.+
T Consensus         8 Li~eA~~~Gls~eeir~FL~~~   29 (30)
T PF08671_consen    8 LIKEAKESGLSKEEIREFLEFN   29 (30)
T ss_dssp             HHHHHHHTT--HHHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHhC
Confidence            3689999999999999999864

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

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

Probab=88.00  E-value=4.4  Score=34.83  Aligned_cols=125  Identities=15%  Similarity=0.249  Sum_probs=85.6

Q ss_pred             cceEEEeeCceEEEecCCHhHHHHHHHhhhhhhccCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHhhcCC
Q 029030           44 EGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAH  113 (200)
Q Consensus        44 ~g~IIvETNFrvYAYT~s~l~iaiL~lF~~l~~r~Pnlvvg---~lTR~Sv~~Al~~GI-------TA~QII~fL~~haH  113 (200)
                      .|.=.+|-.++      +|--.   ..+.++..++|++.||   ++|.+.+++|.+.|-       .-+.++++.+.+-.
T Consensus        28 gGi~~iEit~~------tp~a~---~~I~~l~~~~~~~~vGAGTVl~~e~a~~ai~aGA~FivSP~~~~~vi~~a~~~~i   98 (201)
T PRK06015         28 GGLPAIEITLR------TPAAL---DAIRAVAAEVEEAIVGAGTILNAKQFEDAAKAGSRFIVSPGTTQELLAAANDSDV   98 (201)
T ss_pred             CCCCEEEEeCC------CccHH---HHHHHHHHHCCCCEEeeEeCcCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCC
Confidence            46667777775      44333   3444566678999999   899999999999995       45788888877765


Q ss_pred             ccccccCCCCCc--cHHHHHHHHHHhcCceEecceeeeccCCCHHHHHHHHHHHHHcCeEeeecCCcceEEEeccccHHH
Q 029030          114 PRVADRIPSVPE--NVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHM  191 (200)
Q Consensus       114 p~m~~~~~~iP~--tV~dQI~lWe~Er~R~~~~~g~L~~~f~s~~~f~~v~~ya~~~g~llw~~~~~r~~~V~~~~~~~v  191 (200)
                             |.+|=  |..+=..-|+.--+-+|+.|+-++-   .       .+|.+.+...+   +.-+++-+..=.-+++
T Consensus        99 -------~~iPG~~TptEi~~A~~~Ga~~vK~FPa~~~G---G-------~~yikal~~pl---p~~~l~ptGGV~~~n~  158 (201)
T PRK06015         99 -------PLLPGAATPSEVMALREEGYTVLKFFPAEQAG---G-------AAFLKALSSPL---AGTFFCPTGGISLKNA  158 (201)
T ss_pred             -------CEeCCCCCHHHHHHHHHCCCCEEEECCchhhC---C-------HHHHHHHHhhC---CCCcEEecCCCCHHHH
Confidence                   45664  7788888999999999999865441   0       24555554444   3444444333344778


Q ss_pred             HHHHhh
Q 029030          192 REFLRG  197 (200)
Q Consensus       192 ~~f~k~  197 (200)
                      .+|++.
T Consensus       159 ~~~l~a  164 (201)
T PRK06015        159 RDYLSL  164 (201)
T ss_pred             HHHHhC
Confidence            888764

>TIGR01615 A_thal_3542 uncharacterized plant-specific domain TIGR01615

Probab=86.65  E-value=0.34  Score=39.36  Aligned_cols=65  Identities=18%  Similarity=0.385  Sum_probs=50.3

Q ss_pred             ccceEEEeeCceEEEecCCHhHHH-HHHHhhhhhhccCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCC
Q 029030           43 KEGFVVVETNFRMYAYSTSKLHCE-ILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIP  121 (200)
Q Consensus        43 ~~g~IIvETNFrvYAYT~s~l~ia-iL~lF~~l~~r~Pnlvvg~lTR~Sv~~Al~~GITA~QII~fL~~haHp~m~~~~~  121 (200)
                      ....+|||.|||      +.+.|| ==.-+..+...+|.+.||...|            -.||++.+...|--.|++++-
T Consensus        47 ~~~R~iVd~dFr------~~FeiARpt~~Y~~ll~~LP~vFVG~~~r------------L~~iV~~mc~Aak~Slk~~gm  108 (131)
T TIGR01615        47 QEMRVIIDLDFR------SEFEIARPTEEYKRLLESLPEVFVGTTER------------LRQLVRLMCDAAKKSLKKKGM  108 (131)
T ss_pred             CcceEEEeccch------hhceecCCCHHHHHHHHhCCcceECCHHH------------HHHHHHHHHHHHHHHHHHcCC
Confidence            445899999999      666652 2233566777899999996554            368999999999888998888


Q ss_pred             CCCc
Q 029030          122 SVPE  125 (200)
Q Consensus       122 ~iP~  125 (200)
                      -+||
T Consensus       109 hlPP  112 (131)
T TIGR01615       109 PLPP  112 (131)
T ss_pred             CCCC
Confidence            8888

of a number of uncharacterized plant proteins. The domain is strongly conserved (greater than 30 % sequence identity between most pairs of members) but flanked by highly divergent regions including stretches of low-complexity sequence.

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

Probab=84.32  E-value=12  Score=32.28  Aligned_cols=125  Identities=18%  Similarity=0.270  Sum_probs=82.5

Q ss_pred             cceEEEeeCceEEEecCCHhHHHHHHHhhhhhhccCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHhhcCC
Q 029030           44 EGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAH  113 (200)
Q Consensus        44 ~g~IIvETNFrvYAYT~s~l~iaiL~lF~~l~~r~Pnlvvg---~lTR~Sv~~Al~~GI-------TA~QII~fL~~haH  113 (200)
                      .|.=++|--++      +|--   +..+.++..++|++.||   ++|.+.++.|++.|-       ..+.++++-..+-.
T Consensus        39 ~Gi~~iEitl~------~~~~---~~~I~~l~~~~p~~~IGAGTVl~~~~a~~a~~aGA~FivsP~~~~~vi~~a~~~~i  109 (212)
T PRK05718         39 GGLPVLEVTLR------TPAA---LEAIRLIAKEVPEALIGAGTVLNPEQLAQAIEAGAQFIVSPGLTPPLLKAAQEGPI  109 (212)
T ss_pred             cCCCEEEEecC------CccH---HHHHHHHHHHCCCCEEEEeeccCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCC
Confidence            35567776643      4433   34445555679999999   899999999999984       35588888777554


Q ss_pred             ccccccCCCCCc--cHHHHHHHHHHhcCceEecceeeeccCCCHHHHHHHHHHHHHcCeEeeecCCcceEEEeccccHHH
Q 029030          114 PRVADRIPSVPE--NVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHM  191 (200)
Q Consensus       114 p~m~~~~~~iP~--tV~dQI~lWe~Er~R~~~~~g~L~~~f~s~~~f~~v~~ya~~~g~llw~~~~~r~~~V~~~~~~~v  191 (200)
                             +.+|-  |..+=...|+.--+-+++.|+-.+-          =.+|-+.+...+   +.-+.+.+..=.-+.+
T Consensus       110 -------~~iPG~~TptEi~~a~~~Ga~~vKlFPa~~~g----------g~~~lk~l~~p~---p~~~~~ptGGV~~~ni  169 (212)
T PRK05718        110 -------PLIPGVSTPSELMLGMELGLRTFKFFPAEASG----------GVKMLKALAGPF---PDVRFCPTGGISPANY  169 (212)
T ss_pred             -------CEeCCCCCHHHHHHHHHCCCCEEEEccchhcc----------CHHHHHHHhccC---CCCeEEEeCCCCHHHH
Confidence                   56665  4466445888888888886643220          145556655444   4455555444445789


Q ss_pred             HHHHhh
Q 029030          192 REFLRG  197 (200)
Q Consensus       192 ~~f~k~  197 (200)
                      ++|++.
T Consensus       170 ~~~l~a  175 (212)
T PRK05718        170 RDYLAL  175 (212)
T ss_pred             HHHHhC
Confidence            999874

>TIGR01182 eda Entner-Doudoroff aldolase

Probab=82.25  E-value=15  Score=31.65  Aligned_cols=124  Identities=15%  Similarity=0.311  Sum_probs=84.4

Q ss_pred             ceEEEeeCceEEEecCCHhHHHHHHHhhhhhhccCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHhhcCCc
Q 029030           45 GFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAHP  114 (200)
Q Consensus        45 g~IIvETNFrvYAYT~s~l~iaiL~lF~~l~~r~Pnlvvg---~lTR~Sv~~Al~~GI-------TA~QII~fL~~haHp  114 (200)
                      |.=.+|--++      +|--...+   .++..++|++.||   ++|.+.+++|.+.|-       .-..++.+.+.+-- 
T Consensus        33 Gi~~iEit~~------t~~a~~~i---~~l~~~~~~~~vGAGTVl~~~~a~~a~~aGA~FivsP~~~~~v~~~~~~~~i-  102 (204)
T TIGR01182        33 GLRVLEVTLR------TPVALDAI---RLLRKEVPDALIGAGTVLNPEQLRQAVDAGAQFIVSPGLTPELAKHAQDHGI-  102 (204)
T ss_pred             CCCEEEEeCC------CccHHHHH---HHHHHHCCCCEEEEEeCCCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCC-
Confidence            5456676663      55544444   4445578999999   899999999999994       34577777666543 


Q ss_pred             cccccCCCCCc--cHHHHHHHHHHhcCceEecceeeeccCCCHHHHHHHHHHHHHcCeEeeecCCcceEEEeccccHHHH
Q 029030          115 RVADRIPSVPE--NVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMR  192 (200)
Q Consensus       115 ~m~~~~~~iP~--tV~dQI~lWe~Er~R~~~~~g~L~~~f~s~~~f~~v~~ya~~~g~llw~~~~~r~~~V~~~~~~~v~  192 (200)
                            |.+|=  |-.+=..-|+.--+-+|+.|+-.+-   .       .+|-+++...+   +.-+++-+..=.-+++.
T Consensus       103 ------~~iPG~~TptEi~~A~~~Ga~~vKlFPA~~~G---G-------~~yikal~~pl---p~i~~~ptGGV~~~N~~  163 (204)
T TIGR01182       103 ------PIIPGVATPSEIMLALELGITALKLFPAEVSG---G-------VKMLKALAGPF---PQVRFCPTGGINLANVR  163 (204)
T ss_pred             ------cEECCCCCHHHHHHHHHCCCCEEEECCchhcC---C-------HHHHHHHhccC---CCCcEEecCCCCHHHHH
Confidence                  55663  7778888999999999999866541   0       35666666555   44555544444447899


Q ss_pred             HHHhh
Q 029030          193 EFLRG  197 (200)
Q Consensus       193 ~f~k~  197 (200)
                      +|++.
T Consensus       164 ~~l~a  168 (204)
T TIGR01182       164 DYLAA  168 (204)
T ss_pred             HHHhC
Confidence            99874

2-deydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14) is an enzyme of the Entner-Doudoroff pathway. This aldolase has another function, 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) shown experimentally in Escherichia coli and Pseudomonas putida

>PRK07114 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional

Probab=81.35  E-value=27  Score=30.42  Aligned_cols=125  Identities=14%  Similarity=0.188  Sum_probs=84.8

Q ss_pred             cceEEEeeCceEEEecCCHhHHHHHHHhh-hhhhccCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHhhcC
Q 029030           44 EGFVVVETNFRMYAYSTSKLHCEILRLFS-KIEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNA  112 (200)
Q Consensus        44 ~g~IIvETNFrvYAYT~s~l~iaiL~lF~-~l~~r~Pnlvvg---~lTR~Sv~~Al~~GI-------TA~QII~fL~~ha  112 (200)
                      .|.=.+|-=|+      +|--...+.... +...++|++.||   ++|.+.++.|.+.|-       .-..++++.+.+-
T Consensus        39 gGi~~iEiT~~------tp~a~~~i~~l~~~~~~~~p~~~vGaGTVl~~e~a~~a~~aGA~FiVsP~~~~~v~~~~~~~~  112 (222)
T PRK07114         39 GGARVFEFTNR------GDFAHEVFAELVKYAAKELPGMILGVGSIVDAATAALYIQLGANFIVTPLFNPDIAKVCNRRK  112 (222)
T ss_pred             CCCCEEEEeCC------CCcHHHHHHHHHHHHHhhCCCeEEeeEeCcCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcC
Confidence            45566776664      444444443333 444579999999   899999999999995       3568888888776


Q ss_pred             CccccccCCCCCc--cHHHHHHHHHHhcCceEecceeeeccCCCHHHHHHHHHHHHHcCeEeeecCCcceEEEecccc--
Q 029030          113 HPRVADRIPSVPE--NVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIH--  188 (200)
Q Consensus       113 Hp~m~~~~~~iP~--tV~dQI~lWe~Er~R~~~~~g~L~~~f~s~~~f~~v~~ya~~~g~llw~~~~~r~~~V~~~~~--  188 (200)
                      .       |.+|=  |..+=...|+.--+-+|+.|+-.+    .       ..|-+.+...+   +.-+++-  ..|-  
T Consensus       113 i-------~~iPG~~TpsEi~~A~~~Ga~~vKlFPA~~~----G-------~~~ikal~~p~---p~i~~~p--tGGV~~  169 (222)
T PRK07114        113 V-------PYSPGCGSLSEIGYAEELGCEIVKLFPGSVY----G-------PGFVKAIKGPM---PWTKIMP--TGGVEP  169 (222)
T ss_pred             C-------CEeCCCCCHHHHHHHHHCCCCEEEECccccc----C-------HHHHHHHhccC---CCCeEEe--CCCCCc
Confidence            5       45664  777888899999999999986543    1       45666655444   3333333  3333  


Q ss_pred             --HHHHHHHhh
Q 029030          189 --MHMREFLRG  197 (200)
Q Consensus       189 --~~v~~f~k~  197 (200)
                        +++.+|++.
T Consensus       170 ~~~n~~~yl~a  180 (222)
T PRK07114        170 TEENLKKWFGA  180 (222)
T ss_pred             chhcHHHHHhC
Confidence              578888863

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	200
3dom_A	108	Crystal Structure Of The Complex Between Tfb5 And T		6e-05
3dgp_A	80	Crystal Structure Of The Complex Between Tfb5 And T		5e-04

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 43/83 (51%)
Query: 114 PRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLW 173
           P   + +  +P  V DQIRLW+ +L+RV       Y +F +   +     YA+D   LLW
Sbjct: 19  PNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLW 78
Query: 174 EDSKKMRLVVNAEIHMHMREFLR 196
           +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 = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 38/71 (53%)
Query: 126 NVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNA 185
            V DQIRLW+ +L+RV       Y +F +   +     YA+D   LLW+D KK +  ++ 
Sbjct: 3   TVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISK 62
Query: 186 EIHMHMREFLR 196
           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	200
3dom_A	108	RNA polymerase II transcription factor B subunit;	1e-38
3dgp_A	80	RNA polymerase II transcription factor B subunit;	9e-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 =  128 bits (322), Expect = 1e-38
 Identities = 28/100 (28%), Positives = 50/100 (50%), Gaps = 1/100 (1%)

Query: 101 AEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEA 160
           AE+ +   +    P   + +  +P  V DQIRLW+ +L+RV       Y +F +   +  
Sbjct: 7   AEEKLEK-KLELDPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNL 65

Query: 161 ACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK 200
              YA+D   LLW+D KK +  ++ E +  + +F + + K
Sbjct: 66  LSKYAQDIGVLLWKDDKKKKFFISKEGNSQVLDFAKRKLK 105

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

 Score =  106 bits (267), Expect = 9e-31
 Identities = 24/75 (32%), Positives = 40/75 (53%)

Query: 126 NVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNA 185
            V DQIRLW+ +L+RV       Y +F +   +     YA+D   LLW+D KK +  ++ 
Sbjct: 3   TVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISK 62

Query: 186 EIHMHMREFLRGQNK 200
           E +  + +F + + K
Sbjct: 63  EGNSQVLDFAKRKLK 77

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	200
3dom_A	108	RNA polymerase II transcription factor B subunit;	100.0
3dgp_A	80	RNA polymerase II transcription factor B subunit;	99.98

>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=3.2e-35  Score=227.37  Aligned_cols=88  Identities=30%  Similarity=0.591  Sum_probs=72.3

Q ss_pred             CccccccCCCCCccHHHHHHHHHHhcCceEecceeeeccCCCHHHHHHHHHHHHHcCeEeeecCCcceEEEeccccHHHH
Q 029030          113 HPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMR  192 (200)
Q Consensus       113 Hp~m~~~~~~iP~tV~dQI~lWe~Er~R~~~~~g~L~~~f~s~~~f~~v~~ya~~~g~llw~~~~~r~~~V~~~~~~~v~  192 (200)
                      .|+++...|+|||||+|||||||.||||+++++|+||++|.|+++|+++++||+++|+|||+++.+|+|||+.+||++|+
T Consensus        18 ~~~~~~~~p~lPpTVvDQIrLWE~ErnRl~~~~G~LY~dF~s~~efe~v~~yA~e~gvLlW~d~~kr~~~Vs~egh~~vk   97 (108)
T 3dom_A           18 DPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISKEGNSQVL   97 (108)
T ss_dssp             --------------CCCHHHHHHHHHTTCEEEEEEEEECCSCHHHHHHHHHHHHHHTCEEEEEGGGTEEEEEGGGHHHHH
T ss_pred             CcccccCCCCCCCcHHHHHHHHHHhhCceeccceEEEecCCCHHHHHHHHHHHHHcCeEEEecCCccEEEEeccchHHHH
Confidence            34555567999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhccC
Q 029030          193 EFLRGQNK  200 (200)
Q Consensus       193 ~f~k~~~~  200 (200)
                      +|||++++
T Consensus        98 ~f~Kr~~~  105 (108)
T 3dom_A           98 DFAKRKLK  105 (108)
T ss_dssp             HHHHHHC-
T ss_pred             HHHHHHHh
Confidence            99999874

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

Probab=99.98  E-value=4.1e-33  Score=205.66  Aligned_cols=76  Identities=32%  Similarity=0.593  Sum_probs=61.6

Q ss_pred             ccHHHHHHHHHHhcCceEecceeeeccCCCHHHHHHHHHHHHHcCeEeeecCCcceEEEeccccHHHHHHHhhccC
Q 029030          125 ENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK  200 (200)
Q Consensus       125 ~tV~dQI~lWe~Er~R~~~~~g~L~~~f~s~~~f~~v~~ya~~~g~llw~~~~~r~~~V~~~~~~~v~~f~k~~~~  200 (200)
                      |||+|||||||.|||||++++|+||++|.|+++|+++++||+++|+|||+|+.+|+|||+.+||++|++|||++++
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

---

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	200
d1b0na1	35	SinR repressor dimerisation domain {Bacillus subti	85.24
d1wbha1	213	KDPG aldolase {Escherichia coli [TaxId: 562]}	85.17

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

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

Probab=85.24  E-value=0.37  Score=28.29  Aligned_cols=21  Identities=24%  Similarity=0.455  Sum_probs=19.0

Q ss_pred             HHHHHHHcCCCHHHHHHHHhh
Q 029030           90 SLYNAFENGITAEQIISFLQQ  110 (200)
Q Consensus        90 Sv~~Al~~GITA~QII~fL~~  110 (200)
                      =|+.|+.+||+-+|.-.||+-
T Consensus         8 lVkeAM~SGvSK~QFrEflef   28 (35)
T d1b0na1           8 LVRDAMTSGVSKKQFREFLDY   28 (35)
T ss_dssp             HHHHHHHSCCCHHHHHHHHHH
T ss_pred             HHHHHHHccCCHHHHHHHHHH
Confidence            479999999999999999974

>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=85.17  E-value=0.87  Score=36.17  Aligned_cols=124  Identities=18%  Similarity=0.270  Sum_probs=83.4

Q ss_pred             ceEEEeeCceEEEecCCHhHHHHHHHhhhhhhccCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHhhcCCc
Q 029030           45 GFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAHP  114 (200)
Q Consensus        45 g~IIvETNFrvYAYT~s~l~iaiL~lF~~l~~r~Pnlvvg---~lTR~Sv~~Al~~GI-------TA~QII~fL~~haHp  114 (200)
                      |.=.+|-=+|      +|--   +..+.++..++|++.+|   ++|.+.+++|.+.|.       .-..++++...+-. 
T Consensus        40 Gi~~iEitl~------tp~a---~~~I~~l~~~~p~~~vGaGTV~~~~~~~~a~~aGa~FivSP~~~~~v~~~a~~~~i-  109 (213)
T d1wbha1          40 GVRVLNVTLR------TECA---VDAIRAIAKEVPEAIVGAGTVLNPQQLAEVTEAGAQFAISPGLTEPLLKAATEGTI-  109 (213)
T ss_dssp             TCCEEEEESC------STTH---HHHHHHHHHHCTTSEEEEESCCSHHHHHHHHHHTCSCEEESSCCHHHHHHHHHSSS-
T ss_pred             CCCEEEEeCC------ChhH---HHHHHHHHHHCCCCeeeccccccHHHHHHHHHCCCcEEECCCCCHHHHHHHHhcCC-
Confidence            4445555444      3433   44445556689999999   899999999999996       45678888888765 


Q ss_pred             cccccCCCCCc--cHHHHHHHHHHhcCceEecceeeeccCCCHHHHHHHHHHHHHcCeEeeecCCcceEEEeccccHHHH
Q 029030          115 RVADRIPSVPE--NVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMR  192 (200)
Q Consensus       115 ~m~~~~~~iP~--tV~dQI~lWe~Er~R~~~~~g~L~~~f~s~~~f~~v~~ya~~~g~llw~~~~~r~~~V~~~~~~~v~  192 (200)
                            |.+|-  |..+=...|+.-.+-+++.|+-.+    .      -.+|.+.+...+   +.-+++-...=.-++++
T Consensus       110 ------~~iPGv~TpsEi~~A~~~G~~~vKlFPA~~~----G------g~~~lkal~~p~---p~~~~~ptGGV~~~n~~  170 (213)
T d1wbha1         110 ------PLIPGISTVSELMLGMDYGLKEFKFFPAEAN----G------GVKALQAIAGPF---SQVRFCPTGGISPANYR  170 (213)
T ss_dssp             ------CEEEEESSHHHHHHHHHTTCCEEEETTTTTT----T------HHHHHHHHHTTC---TTCEEEEBSSCCTTTHH
T ss_pred             ------CccCCcCCHHHHHHHHHCCCCEEEeccchhc----C------hHHHHHHhcCcc---cCCceeeeCCCCHHHHH
Confidence                  46664  788888899999999999987433    1      134445544333   33444443444456788


Q ss_pred             HHHhh
Q 029030          193 EFLRG  197 (200)
Q Consensus       193 ~f~k~  197 (200)
                      +|++.
T Consensus       171 ~yl~~  175 (213)
T d1wbha1         171 DYLAL  175 (213)
T ss_dssp             HHHTS
T ss_pred             HHHhC
Confidence            88764