Citrus Sinensis ID: 035227

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70
Protein Sequence
MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEFRDQNSYEKPA
Secondary Structure (PSIPRED)
cccccEEEEEEEcHHHHHHHHHHHccccccccEEEEEccccEEEEcccHHHHHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
cccEEEEEEEEccHHHHHHHHHHccccccccEEEEEEccccEEEEcHHHHHHHHHHHHHHHHcccccccc
Coil and Loop (DISEMBL)
MVNAIKGLFISCDIPMAQFIInmnasmpqsQKFIIHILdsthlfvqpNMAEMIRSAIAEfrdqnsyekpa
Flexible Loop (DISEMBL)
MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAefrdqnsyekpa
Low Complexity Region (SEG)
MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEFRDQNSYEKPA
Disordered region (IsUnstruct)
***AIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAI*************
Disordered Region (DISOPRED)
**NAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEFRD*N******
Disordered Region (DISEMBL)
MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEFR*********
Disordered Region (DISPRO)
*VNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEFRDQNSY****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEFRDQNSYEKPA
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	70	2.2.26 [Sep-21-2011]
Q5ZKH0	71	General transcription fac	yes	no	0.942	0.929	0.409	8e-10
Q6ZYL4	71	General transcription fac	yes	no	0.942	0.929	0.378	3e-09
Q2T9Z5	71	General transcription fac	yes	no	0.942	0.929	0.378	3e-09
Q8K2X8	71	General transcription fac	yes	no	0.942	0.929	0.363	7e-09
Q55CT8	72	General transcription fac	yes	no	0.885	0.861	0.362	1e-05
Q6C1B5	75	RNA polymerase II transcr	yes	no	0.9	0.84	0.303	7e-05
Q4P985	62	RNA polymerase II transcr	N/A	no	0.742	0.838	0.321	0.0003

>sp|Q5ZKH0|TF2H5_CHICK General transcription factor IIH subunit 5 OS=Gallus gallus GN=GTF2H5 PE=3 SV=1

 Score = 62.4 bits (150), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 27/66 (40%), Positives = 40/66 (60%)

Query: 1  MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
          MVN +KG+ I CD  M QF++ ++ S    +KFII  LD TH+FV   +   ++  + E 
Sbjct: 1  MVNVLKGVLIECDPAMKQFLLYLDESNALGKKFIIQDLDETHVFVLAELVNFLQERVGEL 60

Query: 61 RDQNSY 66
           DQNS+
Sbjct: 61 MDQNSF 66

Component of the TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. Necessary for the stability of the TFIIH complex and for the presence of normal levels of TFIIH in the cell.
Gallus gallus (taxid: 9031)

>sp|Q6ZYL4|TF2H5_HUMAN General transcription factor IIH subunit 5 OS=Homo sapiens GN=GTF2H5 PE=1 SV=1

 Score = 60.5 bits (145), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 41/66 (62%)

Query: 1  MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
          MVN +KG+ I CD  M QF++ ++ S    +KFII  +D TH+FV   +  +++  + E 
Sbjct: 1  MVNVLKGVLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGEL 60

Query: 61 RDQNSY 66
           DQN++
Sbjct: 61 MDQNAF 66

Component of the TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. Necessary for the stability of the TFIIH complex and for the presence of normal levels of TFIIH in the cell.

Homo sapiens (taxid: 9606)

>sp|Q2T9Z5|TF2H5_BOVIN General transcription factor IIH subunit 5 OS=Bos taurus GN=GTF2H5 PE=3 SV=1

 Score = 60.5 bits (145), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 41/66 (62%)

Query: 1  MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
          MVN +KG+ I CD  M QF++ ++ S    +KFII  +D TH+FV   +  +++  + E 
Sbjct: 1  MVNVLKGVLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGEL 60

Query: 61 RDQNSY 66
           DQN++
Sbjct: 61 MDQNAF 66

Component of the TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. Necessary for the stability of the TFIIH complex and for the presence of normal levels of TFIIH in the cell.

Bos taurus (taxid: 9913)

>sp|Q8K2X8|TF2H5_MOUSE General transcription factor IIH subunit 5 OS=Mus musculus GN=Gtf2h5 PE=1 SV=1

 Score = 59.3 bits (142), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 41/66 (62%)

Query: 1  MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
          MVN +KG+ I CD  M QF++ ++ +    +KFII  +D TH+FV   +  +++  + E 
Sbjct: 1  MVNVLKGVLIECDPAMKQFLLYLDEANALGKKFIIQDIDDTHVFVIAELVNVLQERVGEL 60

Query: 61 RDQNSY 66
           DQN++
Sbjct: 61 MDQNAF 66

Component of the TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. Necessary for the stability of the TFIIH complex and for the presence of normal levels of TFIIH in the cell.

Mus musculus (taxid: 10090)

>sp|Q55CT8|TF2H5_DICDI General transcription factor IIH subunit 5 OS=Dictyostelium discoideum GN=gtf2h5 PE=3 SV=1

 Score = 48.5 bits (114), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 40/69 (57%), Gaps = 7/69 (10%)

Query: 1  MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRS---AI 57
          MV+  KGLF+ CD P  QF+      + + + F + +LD THLF+Q    ++I S    I
Sbjct: 1  MVHVYKGLFLECDPPTKQFV----EYISKQEHFEVIVLDETHLFLQGGDEKVINSIQRRI 56

Query: 58 AEFRDQNSY 66
           + ++QN+Y
Sbjct: 57 DDLQNQNTY 65

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|Q6C1B5|TFB5_YARLI RNA polymerase II transcription factor B subunit 5 OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=TFB5 PE=3 SV=1

 Score = 45.8 bits (107), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 20/66 (30%), Positives = 37/66 (56%), Gaps = 3/66 (4%)

Query: 1  MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
          M  A +G+ I CD  +   I+N+++S       I+  LD THL + P+M E+++  + + 
Sbjct: 1  MPKATRGVLIECDPSIKALIVNIDSS---QHNIILDELDDTHLMIHPSMVEVVKQKLNKM 57

Query: 61 RDQNSY 66
            +N+Y
Sbjct: 58 LAENTY 63

Component of the general transcription and DNA repair factor IIH (TFIIH), which is essential for both basal and activated transcription, as well as for nucleotide excision repair (NER) of DNA. TFB5 is required for stable recruitment of TFIIH to a promoter, but not for stability of TFIIH subunits.

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

>sp|Q4P985|TFB5_USTMA RNA polymerase II transcription factor B subunit 5 OS=Ustilago maydis (strain 521 / FGSC 9021) GN=TFB5 PE=3 SV=2

 Score = 43.9 bits (102), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/56 (32%), Positives = 33/56 (58%), Gaps = 4/56 (7%)

Query: 2  VNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAI 57
          + A KG+ ++CD  + Q I+    S+ +  +FII  LD THL + P+  + +R+ +
Sbjct: 1  MKAYKGMLLTCDAAVKQLIL----SLDERNRFIIMDLDETHLLISPDRIDWLRAEL 52

Component of the general transcription and DNA repair factor IIH (TFIIH), which is essential for both basal and activated transcription, as well as for nucleotide excision repair (NER) of DNA. TFB5 is required for stable recruitment of TFIIH to a promoter, but not for stability of TFIIH subunits.

Ustilago maydis (strain 521 / FGSC 9021) (taxid: 237631)

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	70
225470287	70	PREDICTED: general transcription factor	1.0	1.0	0.9	7e-30
357130141	457	PREDICTED: xylem cysteine proteinase 1-l	0.985	0.150	0.811	2e-29
115472939	131	Os07g0573600 [Oryza sativa Japonica Grou	1.0	0.534	0.8	1e-27
224125074	70	predicted protein [Populus trichocarpa]	1.0	1.0	0.814	2e-27
297844104	71	hypothetical protein ARALYDRAFT_471390 [	1.0	0.985	0.814	3e-27
8778626	113	F5O11.12 [Arabidopsis thaliana]	1.0	0.619	0.8	3e-27
15221323	71	basal transcription factor complex TTD-A	1.0	0.985	0.8	4e-27
326515518	71	predicted protein [Hordeum vulgare subsp	1.0	0.985	0.8	4e-27
242090297	70	hypothetical protein SORBIDRAFT_09g01833	0.985	0.985	0.797	1e-26
218196244	81	hypothetical protein OsI_18797 [Oryza sa	1.0	0.864	0.785	1e-26

>gi|225470287|ref|XP_002266482.1| PREDICTED: general transcription factor IIH subunit 5 [Vitis vinifera] gi|297742669|emb|CBI34818.3| unnamed protein product [Vitis vinifera]

 Score =  134 bits (337), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 63/70 (90%), Positives = 68/70 (97%)

Query: 1  MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
          MVNA KGLFISCDIPMAQFIINMNASMP SQKFIIH+LDSTHLFVQP++AEMIRSAI+EF
Sbjct: 1  MVNATKGLFISCDIPMAQFIINMNASMPASQKFIIHVLDSTHLFVQPHVAEMIRSAISEF 60

Query: 61 RDQNSYEKPA 70
          R+QNSYEKPA
Sbjct: 61 REQNSYEKPA 70

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357130141|ref|XP_003566711.1| PREDICTED: xylem cysteine proteinase 1-like [Brachypodium distachyon]

 Score =  132 bits (332), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 56/69 (81%), Positives = 65/69 (94%)

Query: 1  MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
          MVNAIKGLFISCD+PMAQFI+N+NASMP S+KFI+H+LD TH+FVQP++ EMIRS IAEF
Sbjct: 1  MVNAIKGLFISCDVPMAQFIVNLNASMPASEKFIVHMLDPTHMFVQPHVGEMIRSKIAEF 60

Query: 61 RDQNSYEKP 69
          RDQNSYEKP
Sbjct: 61 RDQNSYEKP 69

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115472939|ref|NP_001060068.1| Os07g0573600 [Oryza sativa Japonica Group] gi|34393555|dbj|BAC83153.1| unknown protein [Oryza sativa Japonica Group] gi|113611604|dbj|BAF21982.1| Os07g0573600 [Oryza sativa Japonica Group] gi|215707252|dbj|BAG93712.1| unnamed protein product [Oryza sativa Japonica Group] gi|218199880|gb|EEC82307.1| hypothetical protein OsI_26568 [Oryza sativa Indica Group] gi|222637319|gb|EEE67451.1| hypothetical protein OsJ_24828 [Oryza sativa Japonica Group]

 Score =  126 bits (317), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 56/70 (80%), Positives = 65/70 (92%)

Query: 1   MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
           MVNAIKGLFISCD+PMAQFI+N+NASMP S KFI+H+LD TH+FVQP++AEMIRS I+EF
Sbjct: 62  MVNAIKGLFISCDVPMAQFIVNLNASMPASDKFILHMLDPTHMFVQPHVAEMIRSKISEF 121

Query: 61  RDQNSYEKPA 70
           RDQNSYEKP 
Sbjct: 122 RDQNSYEKPT 131

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224125074|ref|XP_002329886.1| predicted protein [Populus trichocarpa] gi|222871123|gb|EEF08254.1| predicted protein [Populus trichocarpa]

 Score =  126 bits (316), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 57/70 (81%), Positives = 68/70 (97%)

Query: 1  MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
          MVNA KGLFISCDIPMAQFIIN+NAS+P SQKFIIHILDSTH+FVQP++++MIRSAI++F
Sbjct: 1  MVNATKGLFISCDIPMAQFIINLNASLPASQKFIIHILDSTHMFVQPHVSDMIRSAISDF 60

Query: 61 RDQNSYEKPA 70
          R+QNSYEKP+
Sbjct: 61 REQNSYEKPS 70

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297844104|ref|XP_002889933.1| hypothetical protein ARALYDRAFT_471390 [Arabidopsis lyrata subsp. lyrata] gi|297335775|gb|EFH66192.1| hypothetical protein ARALYDRAFT_471390 [Arabidopsis lyrata subsp. lyrata]

 Score =  125 bits (314), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 57/70 (81%), Positives = 65/70 (92%)

Query: 1  MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
          MVNAIKG+FISCDIPM QFI+NMN SMP SQKFIIH+LDSTHLFVQP++ +MIRSAI++F
Sbjct: 1  MVNAIKGVFISCDIPMTQFIVNMNNSMPPSQKFIIHVLDSTHLFVQPHVEQMIRSAISDF 60

Query: 61 RDQNSYEKPA 70
          RDQNSYEKP 
Sbjct: 61 RDQNSYEKPT 70

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|8778626|gb|AAF79634.1|AC025416_8 F5O11.12 [Arabidopsis thaliana]

 Score =  125 bits (314), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 56/70 (80%), Positives = 65/70 (92%)

Query: 1   MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
           MVNAIKG+F+SCDIPM QFI+NMN SMP SQKFIIH+LDSTHLFVQP++ +MIRSAI++F
Sbjct: 43  MVNAIKGVFVSCDIPMTQFIVNMNNSMPPSQKFIIHVLDSTHLFVQPHVEQMIRSAISDF 102

Query: 61  RDQNSYEKPA 70
           RDQNSYEKP 
Sbjct: 103 RDQNSYEKPT 112

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15221323|ref|NP_172702.1| basal transcription factor complex TTD-A subunit [Arabidopsis thaliana] gi|38566546|gb|AAR24163.1| At1g12400 [Arabidopsis thaliana] gi|40823747|gb|AAR92302.1| At1g12400 [Arabidopsis thaliana] gi|332190754|gb|AEE28875.1| basal transcription factor complex TTD-A subunit [Arabidopsis thaliana]

 Score =  125 bits (314), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 56/70 (80%), Positives = 65/70 (92%)

Query: 1  MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
          MVNAIKG+F+SCDIPM QFI+NMN SMP SQKFIIH+LDSTHLFVQP++ +MIRSAI++F
Sbjct: 1  MVNAIKGVFVSCDIPMTQFIVNMNNSMPPSQKFIIHVLDSTHLFVQPHVEQMIRSAISDF 60

Query: 61 RDQNSYEKPA 70
          RDQNSYEKP 
Sbjct: 61 RDQNSYEKPT 70

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326515518|dbj|BAK07005.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  125 bits (313), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 56/70 (80%), Positives = 63/70 (90%)

Query: 1  MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
          MVNAIKGLFISCDIPMAQFI+NMNASMP S KFI+HILD TH+F+QPNM + I+S +AEF
Sbjct: 2  MVNAIKGLFISCDIPMAQFIVNMNASMPASDKFIVHILDPTHMFIQPNMGDYIKSKMAEF 61

Query: 61 RDQNSYEKPA 70
          RDQNSYEKP 
Sbjct: 62 RDQNSYEKPT 71

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242090297|ref|XP_002440981.1| hypothetical protein SORBIDRAFT_09g018330 [Sorghum bicolor] gi|241946266|gb|EES19411.1| hypothetical protein SORBIDRAFT_09g018330 [Sorghum bicolor]

 Score =  123 bits (309), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 55/69 (79%), Positives = 65/69 (94%)

Query: 1  MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
          MVNAIKGLFISCD+PMAQFI+N+NASMP S++FI+H+LD TH+FVQP++AEMIRS IAEF
Sbjct: 1  MVNAIKGLFISCDVPMAQFIVNLNASMPASERFIVHMLDPTHMFVQPHVAEMIRSKIAEF 60

Query: 61 RDQNSYEKP 69
           DQNSYEKP
Sbjct: 61 WDQNSYEKP 69

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|218196244|gb|EEC78671.1| hypothetical protein OsI_18797 [Oryza sativa Indica Group] gi|222630525|gb|EEE62657.1| hypothetical protein OsJ_17460 [Oryza sativa Japonica Group]

 Score =  123 bits (309), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 55/70 (78%), Positives = 64/70 (91%)

Query: 1  MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
          MVNAIKGLFISCD+PMAQFI+N+NASMP S KFI+H+LD TH+FVQP++AEMIR  I+EF
Sbjct: 12 MVNAIKGLFISCDVPMAQFIVNLNASMPASDKFILHMLDPTHMFVQPHVAEMIRGKISEF 71

Query: 61 RDQNSYEKPA 70
          RDQNSYEKP 
Sbjct: 72 RDQNSYEKPT 81

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	70
TAIR|locus:2034685	71	AT1G12400 [Arabidopsis thalian	0.985	0.971	0.811	2.2e-27
TAIR|locus:4515102707	72	AT1G62886 [Arabidopsis thalian	0.971	0.944	0.628	3.1e-19
UNIPROTKB|Q5ZKH0	71	GTF2H5 "General transcription	0.942	0.929	0.409	3.2e-10
ZFIN|ZDB-GENE-041001-144	71	gtf2h5 "general transcription	0.942	0.929	0.363	5.2e-10
UNIPROTKB|Q2T9Z5	71	GTF2H5 "General transcription	0.942	0.929	0.378	1.1e-09
UNIPROTKB|E2RRJ1	71	GTF2H5 "Uncharacterized protei	0.942	0.929	0.378	1.1e-09
UNIPROTKB|Q6ZYL4	71	GTF2H5 "General transcription	0.942	0.929	0.378	1.1e-09
UNIPROTKB|F2Z5A9	71	GTF2H5 "Uncharacterized protei	0.942	0.929	0.378	1.1e-09
RGD|1560991	71	Gtf2h5 "general transcription	0.942	0.929	0.378	1.1e-09
MGI|MGI:107227	71	Gtf2h5 "general transcription	0.942	0.929	0.363	2.2e-09

TAIR|locus:2034685 AT1G12400 [Arabidopsis thaliana (taxid:3702)]

 Score = 307 (113.1 bits), Expect = 2.2e-27, P = 2.2e-27
 Identities = 56/69 (81%), Positives = 65/69 (94%)

Query:     1 MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
             MVNAIKG+F+SCDIPM QFI+NMN SMP SQKFIIH+LDSTHLFVQP++ +MIRSAI++F
Sbjct:     1 MVNAIKGVFVSCDIPMTQFIVNMNNSMPPSQKFIIHVLDSTHLFVQPHVEQMIRSAISDF 60

Query:    61 RDQNSYEKP 69
             RDQNSYEKP
Sbjct:    61 RDQNSYEKP 69

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:4515102707 AT1G62886 [Arabidopsis thaliana (taxid:3702)]

 Score = 230 (86.0 bits), Expect = 3.1e-19, P = 3.1e-19
 Identities = 44/70 (62%), Positives = 57/70 (81%)

Query:     1 MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHIL--DSTHLFVQPNMAEMIRSAIA 58
             MVN+IKG+FISCD+PMAQFI ++N S+P SQKFII +L  D+T +FV+P   EMIR A+ 
Sbjct:     1 MVNSIKGVFISCDVPMAQFIAHLNNSLPASQKFIIQVLKLDTTSMFVKPYAEEMIRDAVI 60

Query:    59 EFRDQNSYEK 68
             +FRD+NSY K
Sbjct:    61 KFRDENSYAK 70

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

UNIPROTKB|Q5ZKH0 GTF2H5 "General transcription factor IIH subunit 5" [Gallus gallus (taxid:9031)]

 Score = 145 (56.1 bits), Expect = 3.2e-10, P = 3.2e-10
 Identities = 27/66 (40%), Positives = 40/66 (60%)

Query:     1 MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
             MVN +KG+ I CD  M QF++ ++ S    +KFII  LD TH+FV   +   ++  + E 
Sbjct:     1 MVNVLKGVLIECDPAMKQFLLYLDESNALGKKFIIQDLDETHVFVLAELVNFLQERVGEL 60

Query:    61 RDQNSY 66
              DQNS+
Sbjct:    61 MDQNSF 66

GO:0000439 "core TFIIH complex" 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:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

ZFIN|ZDB-GENE-041001-144 gtf2h5 "general transcription factor IIH, polypeptide 5" [Danio rerio (taxid:7955)]

 Score = 143 (55.4 bits), Expect = 5.2e-10, P = 5.2e-10
 Identities = 24/66 (36%), Positives = 42/66 (63%)

Query:     1 MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
             MVN +KG+ + CD  M QF++ ++ +    +KFII  LD TH+F+   + ++++  + E 
Sbjct:     1 MVNVLKGVLVECDPAMKQFLLYLDETSALGKKFIIQDLDDTHVFILAEVVQILQERVGEL 60

Query:    61 RDQNSY 66
              DQNS+
Sbjct:    61 MDQNSF 66

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

GO:0000439 "core TFIIH complex" evidence=IEA

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

UNIPROTKB|Q2T9Z5 GTF2H5 "General transcription factor IIH subunit 5" [Bos taurus (taxid:9913)]

 Score = 140 (54.3 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 25/66 (37%), Positives = 41/66 (62%)

Query:     1 MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
             MVN +KG+ I CD  M QF++ ++ S    +KFII  +D TH+FV   +  +++  + E 
Sbjct:     1 MVNVLKGVLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGEL 60

Query:    61 RDQNSY 66
              DQN++
Sbjct:    61 MDQNAF 66

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

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

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

GO:0000439 "core TFIIH complex" evidence=IEA

UNIPROTKB|E2RRJ1 GTF2H5 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 140 (54.3 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 25/66 (37%), Positives = 41/66 (62%)

Query:     1 MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
             MVN +KG+ I CD  M QF++ ++ S    +KFII  +D TH+FV   +  +++  + E 
Sbjct:     1 MVNVLKGVLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGEL 60

Query:    61 RDQNSY 66
              DQN++
Sbjct:    61 MDQNAF 66

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

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

GO:0000439 "core TFIIH complex" evidence=IEA

UNIPROTKB|Q6ZYL4 GTF2H5 "General transcription factor IIH subunit 5" [Homo sapiens (taxid:9606)]

 Score = 140 (54.3 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 25/66 (37%), Positives = 41/66 (62%)

Query:     1 MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
             MVN +KG+ I CD  M QF++ ++ S    +KFII  +D TH+FV   +  +++  + E 
Sbjct:     1 MVNVLKGVLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGEL 60

Query:    61 RDQNSY 66
              DQN++
Sbjct:    61 MDQNAF 66

GO:0000439 "core TFIIH complex" 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

UNIPROTKB|F2Z5A9 GTF2H5 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 140 (54.3 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 25/66 (37%), Positives = 41/66 (62%)

Query:     1 MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
             MVN +KG+ I CD  M QF++ ++ S    +KFII  +D TH+FV   +  +++  + E 
Sbjct:     1 MVNVLKGVLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGEL 60

Query:    61 RDQNSY 66
              DQN++
Sbjct:    61 MDQNAF 66

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

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

GO:0000439 "core TFIIH complex" evidence=IEA

RGD|1560991 Gtf2h5 "general transcription factor IIH, polypeptide 5" [Rattus norvegicus (taxid:10116)]

 Score = 140 (54.3 bits), Expect = 1.1e-09, P = 1.1e-09
 Identities = 25/66 (37%), Positives = 41/66 (62%)

Query:     1 MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
             MVN +KG+ I CD  M QF++ ++ S    +KFII  +D TH+FV   +  +++  + E 
Sbjct:     1 MVNVLKGVLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGEL 60

Query:    61 RDQNSY 66
              DQN++
Sbjct:    61 MDQNAF 66

GO:0000439 "core TFIIH complex" evidence=IEA

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

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

MGI|MGI:107227 Gtf2h5 "general transcription factor IIH, polypeptide 5" [Mus musculus (taxid:10090)]

 Score = 137 (53.3 bits), Expect = 2.2e-09, P = 2.2e-09
 Identities = 24/66 (36%), Positives = 41/66 (62%)

Query:     1 MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
             MVN +KG+ I CD  M QF++ ++ +    +KFII  +D TH+FV   +  +++  + E 
Sbjct:     1 MVNVLKGVLIECDPAMKQFLLYLDEANALGKKFIIQDIDDTHVFVIAELVNVLQERVGEL 60

Query:    61 RDQNSY 66
              DQN++
Sbjct:    61 MDQNAF 66

GO:0000439 "core TFIIH complex" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

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

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q6C1B5	TFB5_YARLI	No assigned EC number	0.3030	0.9	0.84	yes	no
Q5ZKH0	TF2H5_CHICK	No assigned EC number	0.4090	0.9428	0.9295	yes	no
Q6ZYL4	TF2H5_HUMAN	No assigned EC number	0.3787	0.9428	0.9295	yes	no
Q8K2X8	TF2H5_MOUSE	No assigned EC number	0.3636	0.9428	0.9295	yes	no
Q2T9Z5	TF2H5_BOVIN	No assigned EC number	0.3787	0.9428	0.9295	yes	no
Q55CT8	TF2H5_DICDI	No assigned EC number	0.3623	0.8857	0.8611	yes	no

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:
	GSVIVG00010308001	SubName- Full=Chromosome undetermined scaffold_254, whole genome shotgun sequence; (70 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00002569001	SubName- Full=Chromosome chr2 scaffold_132, whole genome shotgun sequence; (779 aa)					•	•	•		0.801
	GSVIVG00023710001	SubName- Full=Chromosome chr7 scaffold_31, whole genome shotgun sequence; (758 aa)					•		•		0.549
	GSVIVG00028385001	SubName- Full=Chromosome chr10 scaffold_43, whole genome shotgun sequence; (1089 aa)						•	•		0.542

---

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	70
pfam06331	68	pfam06331, Tbf5, Transcription factor TFIIH comple	1e-18

>gnl|CDD|218993 pfam06331, Tbf5, Transcription factor TFIIH complex subunit Tfb5

 Score = 71.1 bits (175), Expect = 1e-18
 Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 2/69 (2%)

Query: 1  MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
          MV AIKG+ + CD  + Q I++++        FII  LD THL V+ ++ E ++  +   
Sbjct: 1  MVRAIKGVLVECDPSIKQIILHIDEQEHHG--FIIEDLDDTHLLVKESVVEFLKEELERL 58

Query: 61 RDQNSYEKP 69
           ++N Y   
Sbjct: 59 LEENIYNPT 67

This family is a component of the general transcription and DNA repair factor IIH. TFB5 has been shown to be required for efficient recruitment of TFIIH to a promoter. Length = 68

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	70
PF06331	68	Tbf5: Transcription factor TFIIH complex subunit T	100.0
KOG3451	71	consensus Uncharacterized conserved protein [Funct	100.0

>PF06331 Tbf5: Transcription factor TFIIH complex subunit Tfb5; InterPro: IPR009400 This entry represents nucleotide excision repair (NER) proteins, such as TTDA subunit of TFIIH basal transcription factor complex (also known as subunit 5 of RNA polymerase II transcription factor B), and Rex1

Probab=100.00  E-value=2.8e-39  Score=196.46  Aligned_cols=68  Identities=50%  Similarity=0.909  Sum_probs=60.1

Q ss_pred             CccceeeeEEeeCHHHHHHHHHhhcCCCCCCCeEEEeccCceeEEccchHHHHHHHHHHHHHhcCCCCCC
Q 035227            1 MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEFRDQNSYEKPA   70 (70)
Q Consensus         1 Mv~a~kGvLi~CDpaiKq~il~lde~~~~~~~FIIedLDdthlfV~~~~v~~lk~~l~~~l~~n~~~~~~   70 (70)
                      ||||+|||||+|||||||||++||++++.+  |||+|||||||||+++++++||+||+++|++|+|++++
T Consensus         1 Mv~a~kGvLv~CDpa~Kq~il~ld~~~~~~--FIIedLDdthlfV~~~~v~~lk~~l~~~l~~n~~~~~~   68 (68)
T PF06331_consen    1 MVNAIKGVLVECDPAIKQFILHLDESMPHG--FIIEDLDDTHLFVKPDVVEMLKEELDELLDQNSYPPTE   68 (68)
T ss_dssp             --EEEEEEEEES-HHHHHHHHHHHHHCCTS--SEEEEECTTEEEE-CCCHHHHHHHHHHCCCC-TTTTS-
T ss_pred             CCceeeeEEEEcCHHHHHHHHHHhcCCCCC--eEEEEcCCCeEEEcHhHHHHHHHHHHHHHHhcCCCCCC
Confidence            999999999999999999999999987666  99999999999999999999999999999999999974

These proteins have a structural motif consisting of a 2-layer sandwich structure with an alpha/beta plait topology. Nucleotide excision repair is a major pathway for repairing UV light-induced DNA damage in most organisms. Transcription/repair factor IIH (TFIIH) is essential for RNA polymerase II transcription and nucleotide excision repair. The TFIIH complex consists of ten subunits: ERCC2, ERCC3, GTF2H1, GTF2H2, GTF2H3, GTF2H4, GTF2H5, MNAT1, CDK7 and CCNH. Defects in GTF2H5 cause the disease trichothiodystrophy (TTD), therefore GTF2H5 (general transcription factor 2H subunit 5) is also known as the TTD group A (TTDA) subunit (and as Tfb5) []. The TTDA subunit is responsible for the DNA repair function of the complex. TTDA is present both bound to TFIIH, and as a free fraction that shuffles between the cytoplasm and nucleus; induction of NER-type DNA lesions shifts the balance towards TTDA's more stable association with TFIIH []. TTDA is also required for the stability of the TFIIH complex and for the presence of normal levels of TFIIH in the cell. REX1 (required for excision 1) is required for DNA repair in the single-celled, photosynthetic algae Chlamydomonas reinhardtii [], and has homologues in other eukaryotes.; GO: 0003677 DNA binding, 0006289 nucleotide-excision repair; PDB: 2JNJ_B 1YDL_A 3DGP_B 3DOM_B.

>KOG3451 consensus Uncharacterized conserved protein [Function unknown]

Probab=100.00  E-value=2.7e-36  Score=184.19  Aligned_cols=69  Identities=45%  Similarity=0.800  Sum_probs=68.3

Q ss_pred             CccceeeeEEeeCHHHHHHHHHhhcCCCCCCCeEEEeccCceeEEccchHHHHHHHHHHHHHhcCCCCC
Q 035227            1 MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEFRDQNSYEKP   69 (70)
Q Consensus         1 Mv~a~kGvLi~CDpaiKq~il~lde~~~~~~~FIIedLDdthlfV~~~~v~~lk~~l~~~l~~n~~~~~   69 (70)
                      ||||.||+||+||||+||+|+++|++++++.+|||++||||||||+++.++++|.+|+++|++|+|+|+
T Consensus         1 Mvna~KGvlV~cDp~~kqlilnmd~sm~~~skfii~eLDdthLfV~p~~vemvk~~le~~le~n~ye~~   69 (71)
T KOG3451|consen    1 MVNAKKGVLVTCDPAFKQLILNMDDSMQLGSKFIIEELDDTHLFVNPSIVEMVKNELERILENNNYEAV   69 (71)
T ss_pred             CCccccceEEecChhHHHHhhhccccCCCCCCeeEEEeccceeeecHHHHHHHHHHHHHHHHhcCCCcC
Confidence            999999999999999999999999999999999999999999999999999999999999999999987

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	70
2jnj_A	74	Solution Structure Of The P8 Tfiih Subunit Length =		3e-10
1ydl_A	79	Crystal Structure Of The Human Tfiih, Northeast Str		1e-07

>pdb|2JNJ|A Chain A, Solution Structure Of The P8 Tfiih Subunit Length = 74

Iteration: 1
 Score = 60.1 bits (144), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 41/66 (62%)
Query: 1  MVNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEF 60
          MVN +KG+ I CD  M QF++ ++ S    +KFII  +D TH+FV   +  +++  + E 
Sbjct: 4  MVNVLKGVLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGEL 63
Query: 61 RDQNSY 66
           DQN++
Sbjct: 64 MDQNAF 69

>pdb|1YDL|A Chain A, Crystal Structure Of The Human Tfiih, Northeast Structural Genomics Target Hr2045 Length = 79

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 21/61 (34%), Positives = 35/61 (57%)
Query: 6  KGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEFRDQNS 65
          KG  I CD    QF++ ++ S    +KFII  +D TH+FV   +  +++  + E  DQN+
Sbjct: 14 KGXLIECDPAXKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELXDQNA 73
Query: 66 Y 66
          +
Sbjct: 74 F 74

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	70
1ydl_A	79	TFIIH, general transcription factor IIH, polypepti	4e-27
3dgp_B	71	RNA polymerase II transcription factor B subunit;	3e-23

>1ydl_A TFIIH, general transcription factor IIH, polypeptide 5; alpha-beta protein, structural genomics, PSI, protein structure initiative; 2.30A {Homo sapiens} SCOP: d.295.1.1 PDB: 2jnj_A Length = 79

 Score = 92.5 bits (230), Expect = 4e-27
 Identities = 22/64 (34%), Positives = 37/64 (57%)

Query: 6  KGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEFRDQNS 65
          KG+ I CD  M QF++ ++ S    +KFII  +D TH+FV   +  +++  + E  DQN+
Sbjct: 14 KGMLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQNA 73

Query: 66 YEKP 69
          +   
Sbjct: 74 FSLT 77

>3dgp_B RNA polymerase II transcription factor B subunit; protein-protein complex, beta-alpha-beta spilt, heterodimer, damage, DNA excision; 1.80A {Saccharomyces cerevisiae} PDB: 3dom_B Length = 71

 Score = 82.5 bits (204), Expect = 3e-23
 Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 3/65 (4%)

Query: 3  NAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEFRD 62
           A KG  + CD  +   I+ ++A M      ++  LD THL V P+  E ++  +     
Sbjct: 2  RARKGALVQCDPSIKALILQIDAKMS---DIVLEELDDTHLLVNPSKVEFVKHELNRLLS 58

Query: 63 QNSYE 67
          +N Y 
Sbjct: 59 KNIYN 63

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	70
3dgp_B	71	RNA polymerase II transcription factor B subunit;	100.0
1ydl_A	79	TFIIH, general transcription factor IIH, polypepti	100.0

>3dgp_B RNA polymerase II transcription factor B subunit; protein-protein complex, beta-alpha-beta spilt, heterodimer, damage, DNA excision; 1.80A {Saccharomyces cerevisiae} SCOP: d.295.1.0 PDB: 3dom_B

Probab=100.00  E-value=5.9e-38  Score=191.39  Aligned_cols=65  Identities=26%  Similarity=0.560  Sum_probs=61.9

Q ss_pred             ccceeeeEEeeCHHHHHHHHHhhcCCCCCCCeEEEeccCceeEEccchHHHHHHHHHHHHHhcCCCCC
Q 035227            2 VNAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEFRDQNSYEKP   69 (70)
Q Consensus         2 v~a~kGvLi~CDpaiKq~il~lde~~~~~~~FIIedLDdthlfV~~~~v~~lk~~l~~~l~~n~~~~~   69 (70)
                      +||+|||||+|||||||||++||++   +++|||+|||||||||+++++++||++|+++|++|+|+||
T Consensus         1 ~~A~kGvLi~CDpa~Kq~il~lde~---~~~FIIedLDdtHl~V~~~~v~~lk~~l~~~l~~n~~~~~   65 (71)
T 3dgp_B            1 ARARKGALVQCDPSIKALILQIDAK---MSDIVLEELDDTHLLVNPSKVEFVKHELNRLLSKNIYNPM   65 (71)
T ss_dssp             CEEEEEEEEECCHHHHHHHHHHHHH---HCSSEEEEEETTEEEECGGGHHHHHHHHHHHHHSCSCC--
T ss_pred             CCceeEEEEEcCHHHHHHHHHHcCC---CCCEEEEEcCCceEEEcHHHHHHHHHHHHHHHHhcCCCCc
Confidence            6999999999999999999999997   8999999999999999999999999999999999999998

>1ydl_A TFIIH, general transcription factor IIH, polypeptide 5; alpha-beta protein, structural genomics, PSI, protein structure initiative; 2.30A {Homo sapiens} SCOP: d.295.1.1 PDB: 2jnj_A

Probab=100.00  E-value=7.7e-38  Score=194.18  Aligned_cols=68  Identities=32%  Similarity=0.640  Sum_probs=66.3

Q ss_pred             cceeeeEEeeCHHHHHHHHHhhcCCCCCCCeEEEeccCceeEEccchHHHHHHHHHHHHHhcCCCCCC
Q 035227            3 NAIKGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEFRDQNSYEKPA   70 (70)
Q Consensus         3 ~a~kGvLi~CDpaiKq~il~lde~~~~~~~FIIedLDdthlfV~~~~v~~lk~~l~~~l~~n~~~~~~   70 (70)
                      ||+|||||+|||||||||++|||++|++++|||+|||||||||+++++++||+||+++|++|+|++++
T Consensus        11 ~~~kGvLI~CDpa~Kq~Il~lde~~~~~~kFIIedLDdtHLfV~~~~v~~lk~~l~~~ld~ns~~~~~   78 (79)
T 1ydl_A           11 GTRKGMLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQNAFSLTQ   78 (79)
T ss_dssp             CCCCCEEEECCHHHHHHHHHHHHTTTTSSCCEEEECSSSEEEECTTHHHHHHHHHHHTSCCCTTTTTT
T ss_pred             ccccceEEEeCHHHHHHHHHHhccCCcCCCEEEEEcCCceEEEcHHHHHHHHHHHHHHHHhcCCCccc
Confidence            79999999999999999999999999999999999999999999999999999999999999999863

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	70
d1ydla1	66	d.295.1.1 (A:6-71) General transcription factor II	4e-27

>d1ydla1 d.295.1.1 (A:6-71) General transcription factor IIH polypeptide 5, TFB5 {Human (Homo sapiens) [TaxId: 9606]} Length = 66

class: Alpha and beta proteins (a+b)
fold: TFB5-like
superfamily: TFB5-like
family: TFB5-like
domain: General transcription factor IIH polypeptide 5, TFB5
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 90.9 bits (226), Expect = 4e-27
 Identities = 22/61 (36%), Positives = 37/61 (60%)

Query: 6  KGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEFRDQNS 65
          KG+ I CD  M QF++ ++ S    +KFII  +D TH+FV   +  +++  + E  DQN+
Sbjct: 1  KGMLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQNA 60

Query: 66 Y 66
          +
Sbjct: 61 F 61

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	70
d1ydla1	66	General transcription factor IIH polypeptide 5, TF	100.0

>d1ydla1 d.295.1.1 (A:6-71) General transcription factor IIH polypeptide 5, TFB5 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: TFB5-like
superfamily: TFB5-like
family: TFB5-like
domain: General transcription factor IIH polypeptide 5, TFB5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=8.9e-38  Score=186.94  Aligned_cols=64  Identities=34%  Similarity=0.688  Sum_probs=62.8

Q ss_pred             eeeEEeeCHHHHHHHHHhhcCCCCCCCeEEEeccCceeEEccchHHHHHHHHHHHHHhcCCCCC
Q 035227            6 KGLFISCDIPMAQFIINMNASMPQSQKFIIHILDSTHLFVQPNMAEMIRSAIAEFRDQNSYEKP   69 (70)
Q Consensus         6 kGvLi~CDpaiKq~il~lde~~~~~~~FIIedLDdthlfV~~~~v~~lk~~l~~~l~~n~~~~~   69 (70)
                      |||||+|||||||||+|||+++|++++|||+|||||||||+++++++||+||+++|++|+|++-
T Consensus         1 KGvLv~CDp~~Kq~il~ld~~~~~~~kFII~dLDdtHl~V~~~~~~~lk~~l~~l~d~nsy~~~   64 (66)
T d1ydla1           1 KGMLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQNAFSLT   64 (66)
T ss_dssp             CCEEEECCHHHHHHHHHHHHTTTTSSCCEEEECSSSEEEECTTHHHHHHHHHHHTSCCCTTTTT
T ss_pred             CcEEEEcCHHHHHHHHHhccCCccCCCEEEEEcCCceEEEcHHHHHHHHHHHHHHHHhcCCCcc
Confidence            7999999999999999999999999999999999999999999999999999999999999974