Citrus Sinensis ID: 033697

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110---
Protein Sequence
MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTFFLRLLLFVFTRFQGFSLFTNSSLTQYRKII
Secondary Structure (PSIPRED)
cccccccccccccccccHHHHHHHHHHcccccccccHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccHHHcccccHHHHHHHHHHHcccccccHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEcccccHHHHHHcc
Coil and Loop (DISEMBL)
mnhnnnfqqssdgrhddDAALTEFLSSlmgytptipdELVEHYLaksgfqcpdVRLIRLVAVATQKFVAEVATDALQYATNTFFLRLLLFVFTRfqgfslftnssltQYRKII
Flexible Loop (DISEMBL)
mnhnnnfqqssdgrhDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTFFLRLLLFVFTRFQgfslftnssltqyrkii
Low Complexity Region (SEG)
MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNtfflrlllfvftrfQGFSLFTNSSLTQYRKII
Disordered region (IsUnstruct)
********************LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTFFLRLLLFVFTRFQGFSLFTNSSL*******
Disordered Region (DISOPRED)
***********************FLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQ************************************
Disordered Region (DISEMBL)
**************HDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTFFLRLLLFVFTRFQGFSLFTNSSLTQYRKII
Disordered Region (DISPRO)
*****************DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTFFLRLLLFVFTRFQGFSLFTNSSLTQY**II
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTFFLRLLLFVFTRFQGFSLFTNSSLTQYRKII
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	113	2.2.26 [Sep-21-2011]
Q12962	218	Transcription initiation	yes	no	0.513	0.266	0.5	1e-11
Q9XZT7	146	Transcription initiation	yes	no	0.522	0.404	0.457	1e-11
Q8K0H5	218	Transcription initiation	yes	no	0.513	0.266	0.5	2e-11
O60171	215	Transcription initiation	yes	no	0.548	0.288	0.467	3e-11
Q12030	206	Transcription initiation	yes	no	0.548	0.300	0.467	4e-11
Q9U5W9	167	Transcription initiation	no	no	0.548	0.371	0.419	6e-10

>sp|Q12962|TAF10_HUMAN Transcription initiation factor TFIID subunit 10 OS=Homo sapiens GN=TAF10 PE=1 SV=1

 Score = 68.6 bits (166), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 29/58 (50%), Positives = 44/58 (75%)

Query: 21  LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQY 78
           L +FL  L  YTPTIPD +  +YL ++GF+  D R+IRL+++A QKF++++A DALQ+
Sbjct: 116 LVDFLMQLEDYTPTIPDAVTGYYLNRAGFEASDPRIIRLISLAAQKFISDIANDALQH 173

TAFs are components of the transcription factor IID (TFIID) complex, PCAF histone acetylase complex and TBP-free TAFII complex (TFTC). TIIFD is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors.
Homo sapiens (taxid: 9606)

>sp|Q9XZT7|TAFAB_DROME Transcription initiation factor TFIID subunit 10b OS=Drosophila melanogaster GN=Taf10b PE=1 SV=1

 Score = 68.2 bits (165), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 27/59 (45%), Positives = 43/59 (72%)

Query: 21 LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYA 79
          L++F+S L  YTP IPD +  HYL   GFQ  D R++RL+++A QK+++++  DALQ++
Sbjct: 41 LSDFMSQLEDYTPLIPDAVTSHYLNMGGFQSDDKRIVRLISLAAQKYMSDIIDDALQHS 99

TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors.

Drosophila melanogaster (taxid: 7227)

>sp|Q8K0H5|TAF10_MOUSE Transcription initiation factor TFIID subunit 10 OS=Mus musculus GN=Taf10 PE=1 SV=1

 Score = 67.4 bits (163), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 29/58 (50%), Positives = 44/58 (75%)

Query: 21  LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQY 78
           L +FL  L  YTPTIPD +  +YL ++GF+  D R+IRL+++A QKF++++A DALQ+
Sbjct: 116 LVDFLMQLEDYTPTIPDAVTGYYLNRAGFEASDPRIIRLISLAAQKFISDIANDALQH 173

TAFs are components of the transcription factor IID (TFIID) complex, PCAF histone acetylase complex and TBP-free TAFII complex (TFTC). TIIFD is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. May regulate cyclin E expression.

Mus musculus (taxid: 10090)

>sp|O60171|TAF10_SCHPO Transcription initiation factor TFIID subunit 10 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=taf10 PE=3 SV=1

 Score = 67.0 bits (162), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 29/62 (46%), Positives = 44/62 (70%)

Query: 18  DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQ 77
           D  L  FL+ +  Y+P IPD L+++YL+ SGF+C D RL +L+ +  QKF+++VA DA Q
Sbjct: 90  DKTLENFLAQMDDYSPLIPDVLLDYYLSLSGFKCVDPRLKKLLGLTAQKFISDVAQDAYQ 149

Query: 78  YA 79
           Y+
Sbjct: 150 YS 151

Functions as a component of the DNA-binding general transcription factor complex TFIID and the transcription regulatory histone acetylation (HAT) complexes SAGA and SLIK. Binding of TFIID to a promoter (with or without TATA element) is the initial step in preinitiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation), facilitation of DNA opening and initiation of transcription. SAGA is involved in RNA polymerase II-dependent transcriptional regulation. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction and promoter selectivity, interaction with transcription activators, and chromatin modification through histone acetylation (gcn5) and deubiquitination (ubp8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3.

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

>sp|Q12030|TAF10_YEAST Transcription initiation factor TFIID subunit 10 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TAF10 PE=1 SV=1

 Score = 67.0 bits (162), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 29/62 (46%), Positives = 43/62 (69%)

Query: 18  DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQ 77
           D  L E L  +    P IPD ++++YL K+GF   DVR+ RL+A+ATQKFV+++A DA +
Sbjct: 71  DKTLEEILEMMDSTPPIIPDAVIDYYLTKNGFNVADVRVKRLLALATQKFVSDIAKDAYE 130

Query: 78  YA 79
           Y+
Sbjct: 131 YS 132

Functions as a component of the DNA-binding general transcription factor complex TFIID and the transcription regulatory histone acetylation (HAT) complexes SAGA and SLIK. Binding of TFIID to a promoter (with or without TATA element) is the initial step in preinitiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation by TAF1), facilitation of DNA opening and initiation of transcription. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus.

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

>sp|Q9U5W9|TAF10_DROME Transcription initiation factor TFIID subunit 10 OS=Drosophila melanogaster GN=Taf10 PE=1 SV=2

 Score = 62.8 bits (151), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 26/62 (41%), Positives = 43/62 (69%)

Query: 17  DDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDAL 76
           +++ + E +  L  Y+PTIPD L  H L  +GF   D +++RLV+V+ QKF++++A DAL
Sbjct: 53  EESEMDELIKQLEDYSPTIPDALTMHILKTAGFCTVDPKIVRLVSVSAQKFISDIANDAL 112

Query: 77  QY 78
           Q+
Sbjct: 113 QH 114

TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors.

Drosophila melanogaster (taxid: 7227)

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	113
449441834	136	PREDICTED: transcription initiation fact	0.663	0.551	0.820	2e-30
255548646	143	transcription factor, putative [Ricinus	0.584	0.461	0.939	9e-30
15236059	134	TBP-associated factor II 15 [Arabidopsis	0.663	0.559	0.807	1e-29
297798796	134	TAFII15 [Arabidopsis lyrata subsp. lyrat	0.663	0.559	0.807	2e-29
26450720	134	putative transcription factor II [Arabid	0.663	0.559	0.807	2e-29
356512077	136	PREDICTED: transcription initiation fact	0.663	0.551	0.820	2e-29
312281591	134	unnamed protein product [Thellungiella h	0.663	0.559	0.794	2e-29
225465621	136	PREDICTED: transcription initiation fact	0.654	0.544	0.818	2e-29
255638464	136	unknown [Glycine max]	0.663	0.551	0.807	7e-29
357507887	139	Transcription initiation factor TFIID su	0.690	0.561	0.782	2e-28

>gi|449441834|ref|XP_004138687.1| PREDICTED: transcription initiation factor TFIID subunit 10-like [Cucumis sativus] gi|449493281|ref|XP_004159243.1| PREDICTED: transcription initiation factor TFIID subunit 10-like [Cucumis sativus]

 Score =  136 bits (342), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 64/78 (82%), Positives = 71/78 (91%), Gaps = 3/78 (3%)

Query: 1  MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLV 60
          MNHN   QQ++  RHDDDAAL+EFL+SLM YTPTIPDELVEHYL KSGFQCPDVRLIRLV
Sbjct: 1  MNHN---QQATGSRHDDDAALSEFLASLMEYTPTIPDELVEHYLGKSGFQCPDVRLIRLV 57

Query: 61 AVATQKFVAEVATDALQY 78
          AVATQKFVA+VA+DALQ+
Sbjct: 58 AVATQKFVADVASDALQH 75

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255548646|ref|XP_002515379.1| transcription factor, putative [Ricinus communis] gi|223545323|gb|EEF46828.1| transcription factor, putative [Ricinus communis]

 Score =  134 bits (336), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 62/66 (93%), Positives = 63/66 (95%)

Query: 12 DGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEV 71
          DGRHDDDAALTEFLSSLM YTPTIPDELVEHYL KSGFQCPDVRL+RLVAVATQKFVAEV
Sbjct: 16 DGRHDDDAALTEFLSSLMDYTPTIPDELVEHYLGKSGFQCPDVRLVRLVAVATQKFVAEV 75

Query: 72 ATDALQ 77
          A DALQ
Sbjct: 76 ANDALQ 81

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15236059|ref|NP_194900.1| TBP-associated factor II 15 [Arabidopsis thaliana] gi|30689137|ref|NP_849481.1| TBP-associated factor II 15 [Arabidopsis thaliana] gi|13492648|gb|AAK28290.1|AF344879_1 putative TBP-associated 15 kDa subunit protein [Arabidopsis thaliana] gi|13549156|gb|AAK29671.1|AF352813_1 putative TBP associated factor 15kDa subunit [Arabidopsis thaliana] gi|2072626|emb|CAA73389.1| hypothetical protein [Arabidopsis thaliana] gi|3281856|emb|CAA19751.1| Transcription factor II homolog [Arabidopsis thaliana] gi|7270075|emb|CAB79890.1| Transcription factor II homolog [Arabidopsis thaliana] gi|21554584|gb|AAM63623.1| Transcription factor II homolog [Arabidopsis thaliana] gi|39545934|gb|AAR28030.1| TAF10 [Arabidopsis thaliana] gi|222424014|dbj|BAH19968.1| AT4G31720 [Arabidopsis thaliana] gi|332660549|gb|AEE85949.1| TBP-associated factor II 15 [Arabidopsis thaliana] gi|332660550|gb|AEE85950.1| TBP-associated factor II 15 [Arabidopsis thaliana]

 Score =  133 bits (334), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 63/78 (80%), Positives = 71/78 (91%), Gaps = 3/78 (3%)

Query: 1  MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLV 60
          MNH    QQS + +H+DDAALTEFL+SLM YTPTIPD+LVEHYLAKSGFQCPDVRLIRLV
Sbjct: 1  MNHG---QQSGEAKHEDDAALTEFLASLMDYTPTIPDDLVEHYLAKSGFQCPDVRLIRLV 57

Query: 61 AVATQKFVAEVATDALQY 78
          AVATQKFVA+VA+DALQ+
Sbjct: 58 AVATQKFVADVASDALQH 75

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297798796|ref|XP_002867282.1| TAFII15 [Arabidopsis lyrata subsp. lyrata] gi|297313118|gb|EFH43541.1| TAFII15 [Arabidopsis lyrata subsp. lyrata]

 Score =  133 bits (334), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 63/78 (80%), Positives = 71/78 (91%), Gaps = 3/78 (3%)

Query: 1  MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLV 60
          MNH    QQS + +H+DDAALTEFL+SLM YTPTIPD+LVEHYLAKSGFQCPDVRLIRLV
Sbjct: 1  MNHG---QQSGEAKHEDDAALTEFLASLMDYTPTIPDDLVEHYLAKSGFQCPDVRLIRLV 57

Query: 61 AVATQKFVAEVATDALQY 78
          AVATQKFVA+VA+DALQ+
Sbjct: 58 AVATQKFVADVASDALQH 75

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|26450720|dbj|BAC42469.1| putative transcription factor II [Arabidopsis thaliana] gi|28416879|gb|AAO42970.1| At4g31720 [Arabidopsis thaliana]

 Score =  133 bits (334), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 63/78 (80%), Positives = 71/78 (91%), Gaps = 3/78 (3%)

Query: 1  MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLV 60
          MNH    QQS + +H+DDAALTEFL+SLM YTPTIPD+LVEHYLAKSGFQCPDVRLIRLV
Sbjct: 1  MNHG---QQSGEAKHEDDAALTEFLASLMDYTPTIPDDLVEHYLAKSGFQCPDVRLIRLV 57

Query: 61 AVATQKFVAEVATDALQY 78
          AVATQKFVA+VA+DALQ+
Sbjct: 58 AVATQKFVADVASDALQH 75

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356512077|ref|XP_003524747.1| PREDICTED: transcription initiation factor TFIID subunit 10-like [Glycine max]

 Score =  132 bits (333), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 64/78 (82%), Positives = 70/78 (89%), Gaps = 3/78 (3%)

Query: 1  MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLV 60
          MN N    QSSDGR+DDD+AL++FL+SLM YTPTIPDELVEHYLAKSGFQCPDVRL RLV
Sbjct: 1  MNQN---PQSSDGRNDDDSALSDFLASLMDYTPTIPDELVEHYLAKSGFQCPDVRLTRLV 57

Query: 61 AVATQKFVAEVATDALQY 78
          AVATQKFVAEVA DALQ+
Sbjct: 58 AVATQKFVAEVAGDALQH 75

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|312281591|dbj|BAJ33661.1| unnamed protein product [Thellungiella halophila]

 Score =  132 bits (332), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 62/78 (79%), Positives = 71/78 (91%), Gaps = 3/78 (3%)

Query: 1  MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLV 60
          MNH    QQS + +H+DDAALTEFL+SLM YTPTIPD+LVEHYLAKSGFQCPDVRLIRLV
Sbjct: 1  MNHG---QQSGEAKHEDDAALTEFLASLMEYTPTIPDDLVEHYLAKSGFQCPDVRLIRLV 57

Query: 61 AVATQKFVAEVATDALQY 78
          +VATQKFVA+VA+DALQ+
Sbjct: 58 SVATQKFVADVASDALQH 75

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225465621|ref|XP_002267115.1| PREDICTED: transcription initiation factor TFIID subunit 10 [Vitis vinifera] gi|302143599|emb|CBI22352.3| unnamed protein product [Vitis vinifera]

 Score =  132 bits (332), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 63/77 (81%), Positives = 69/77 (89%), Gaps = 3/77 (3%)

Query: 1  MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLV 60
          MN N   Q  +D RHDDD+AL++FL+SLM YTPTIPDELVEHYLAKSGFQCPDVRLIRLV
Sbjct: 1  MNQN---QGGNDARHDDDSALSDFLASLMDYTPTIPDELVEHYLAKSGFQCPDVRLIRLV 57

Query: 61 AVATQKFVAEVATDALQ 77
          AVATQKFVAEVA+DALQ
Sbjct: 58 AVATQKFVAEVASDALQ 74

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255638464|gb|ACU19541.1| unknown [Glycine max]

 Score =  130 bits (328), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 63/78 (80%), Positives = 70/78 (89%), Gaps = 3/78 (3%)

Query: 1  MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLV 60
          MN N    QSSDGR+DDD+AL++FL+SLM YTPTIPDELVEHYLAKSGF+CPDVRL RLV
Sbjct: 1  MNQN---PQSSDGRNDDDSALSDFLASLMDYTPTIPDELVEHYLAKSGFRCPDVRLTRLV 57

Query: 61 AVATQKFVAEVATDALQY 78
          AVATQKFVAEVA DALQ+
Sbjct: 58 AVATQKFVAEVAGDALQH 75

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357507887|ref|XP_003624232.1| Transcription initiation factor TFIID subunit [Medicago truncatula] gi|355499247|gb|AES80450.1| Transcription initiation factor TFIID subunit [Medicago truncatula]

 Score =  129 bits (325), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 61/78 (78%), Positives = 68/78 (87%)

Query: 1  MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLV 60
          MN N     SS+GR DDD+AL++FL+SL+ YTPTIPDELVEHYLAKSGFQCPDVRL RLV
Sbjct: 1  MNQNQPQSSSSEGRADDDSALSDFLASLVDYTPTIPDELVEHYLAKSGFQCPDVRLTRLV 60

Query: 61 AVATQKFVAEVATDALQY 78
          AVATQKFVAEVA DALQ+
Sbjct: 61 AVATQKFVAEVAGDALQH 78

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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	113
TAIR|locus:2124884	134	TAFII15 "AT4G31720" [Arabidops	0.663	0.559	0.807	7.1e-29
ZFIN|ZDB-GENE-060526-334	181	taf10 "TAF10 RNA polymerase II	0.513	0.320	0.5	1.9e-12
UNIPROTKB|A5PJW1	218	TAF10 "TAF10 protein" [Bos tau	0.513	0.266	0.5	2.4e-12
UNIPROTKB|E2R5H1	218	TAF10 "Uncharacterized protein	0.513	0.266	0.5	2.4e-12
UNIPROTKB|Q12962	218	TAF10 "Transcription initiatio	0.513	0.266	0.5	2.4e-12
UNIPROTKB|I3LE15	218	TAF10 "Uncharacterized protein	0.513	0.266	0.5	2.4e-12
MGI|MGI:1346320	218	Taf10 "TAF10 RNA polymerase II	0.513	0.266	0.5	2.4e-12
RGD|1305907	218	Taf10 "TAF10 RNA polymerase II	0.513	0.266	0.5	2.4e-12
POMBASE|SPBC21H7.02	215	taf10 "SAGA complex/transcript	0.716	0.376	0.382	8.2e-12
FB|FBgn0026324	146	Taf10b "TBP-associated factor	0.522	0.404	0.457	1.3e-11

TAIR|locus:2124884 TAFII15 "AT4G31720" [Arabidopsis thaliana (taxid:3702)]

 Score = 321 (118.1 bits), Expect = 7.1e-29, P = 7.1e-29
 Identities = 63/78 (80%), Positives = 71/78 (91%)

Query:     1 MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLV 60
             MNH    QQS + +H+DDAALTEFL+SLM YTPTIPD+LVEHYLAKSGFQCPDVRLIRLV
Sbjct:     1 MNHG---QQSGEAKHEDDAALTEFLASLMDYTPTIPDDLVEHYLAKSGFQCPDVRLIRLV 57

Query:    61 AVATQKFVAEVATDALQY 78
             AVATQKFVA+VA+DALQ+
Sbjct:    58 AVATQKFVADVASDALQH 75

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

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA;ISS

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

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

ZFIN|ZDB-GENE-060526-334 taf10 "TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Danio rerio (taxid:7955)]

 Score = 166 (63.5 bits), Expect = 1.9e-12, P = 1.9e-12
 Identities = 29/58 (50%), Positives = 45/58 (77%)

Query:    21 LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQY 78
             L +FL  L  YTPTIPD +  +YL ++GF+  D R+IRL+++A+QKF++++A DALQ+
Sbjct:    79 LADFLMQLEDYTPTIPDAVTGYYLNRAGFEASDPRIIRLISLASQKFISDIANDALQH 136

GO:0005634 "nucleus" evidence=IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

UNIPROTKB|A5PJW1 TAF10 "TAF10 protein" [Bos taurus (taxid:9913)]

 Score = 165 (63.1 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 29/58 (50%), Positives = 44/58 (75%)

Query:    21 LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQY 78
             L +FL  L  YTPTIPD +  +YL ++GF+  D R+IRL+++A QKF++++A DALQ+
Sbjct:   116 LVDFLMQLEDYTPTIPDAVTGYYLNRAGFEASDPRIIRLISLAAQKFISDIANDALQH 173

GO:0070063 "RNA polymerase binding" evidence=IEA

GO:0051260 "protein homooligomerization" evidence=IEA

GO:0048471 "perinuclear region of cytoplasm" evidence=IEA

GO:0043966 "histone H3 acetylation" evidence=IEA

GO:0033276 "transcription factor TFTC complex" evidence=IEA

GO:0030914 "STAGA complex" evidence=IEA

GO:0030331 "estrogen receptor binding" evidence=IEA

GO:0016578 "histone deubiquitination" evidence=IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=IEA

GO:0004402 "histone acetyltransferase activity" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

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

GO:0000125 "PCAF complex" evidence=IEA

UNIPROTKB|E2R5H1 TAF10 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 165 (63.1 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 29/58 (50%), Positives = 44/58 (75%)

Query:    21 LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQY 78
             L +FL  L  YTPTIPD +  +YL ++GF+  D R+IRL+++A QKF++++A DALQ+
Sbjct:   116 LVDFLMQLEDYTPTIPDAVTGYYLNRAGFEASDPRIIRLISLAAQKFISDIANDALQH 173

GO:0070063 "RNA polymerase binding" evidence=IEA

GO:0051260 "protein homooligomerization" evidence=IEA

GO:0048471 "perinuclear region of cytoplasm" evidence=IEA

GO:0043966 "histone H3 acetylation" evidence=IEA

GO:0033276 "transcription factor TFTC complex" evidence=IEA

GO:0030914 "STAGA complex" evidence=IEA

GO:0030331 "estrogen receptor binding" evidence=IEA

GO:0016578 "histone deubiquitination" evidence=IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=IEA

GO:0004402 "histone acetyltransferase activity" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

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

GO:0000125 "PCAF complex" evidence=IEA

UNIPROTKB|Q12962 TAF10 "Transcription initiation factor TFIID subunit 10" [Homo sapiens (taxid:9606)]

 Score = 165 (63.1 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 29/58 (50%), Positives = 44/58 (75%)

Query:    21 LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQY 78
             L +FL  L  YTPTIPD +  +YL ++GF+  D R+IRL+++A QKF++++A DALQ+
Sbjct:   116 LVDFLMQLEDYTPTIPDAVTGYYLNRAGFEASDPRIIRLISLAAQKFISDIANDALQH 173

GO:0019899 "enzyme binding" evidence=IPI

GO:0005515 "protein binding" evidence=IPI

GO:0005669 "transcription factor TFIID complex" evidence=IDA

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

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

GO:0003713 "transcription coactivator activity" evidence=IDA

GO:0043966 "histone H3 acetylation" evidence=IDA

GO:0004402 "histone acetyltransferase activity" evidence=IDA

GO:0000125 "PCAF complex" evidence=IDA

GO:0033276 "transcription factor TFTC complex" evidence=IDA

GO:0070063 "RNA polymerase binding" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0016578 "histone deubiquitination" evidence=IDA

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

GO:0006352 "DNA-dependent transcription, initiation" evidence=IDA

GO:0051260 "protein homooligomerization" evidence=IDA

GO:0030331 "estrogen receptor binding" evidence=IDA

GO:0030914 "STAGA complex" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0048471 "perinuclear region of cytoplasm" evidence=IDA

GO:0005654 "nucleoplasm" evidence=TAS

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

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

UNIPROTKB|I3LE15 TAF10 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 165 (63.1 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 29/58 (50%), Positives = 44/58 (75%)

Query:    21 LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQY 78
             L +FL  L  YTPTIPD +  +YL ++GF+  D R+IRL+++A QKF++++A DALQ+
Sbjct:   116 LVDFLMQLEDYTPTIPDAVTGYYLNRAGFEASDPRIIRLISLAAQKFISDIANDALQH 173

GO:0070063 "RNA polymerase binding" evidence=IEA

GO:0051260 "protein homooligomerization" evidence=IEA

GO:0048471 "perinuclear region of cytoplasm" evidence=IEA

GO:0043966 "histone H3 acetylation" evidence=IEA

GO:0033276 "transcription factor TFTC complex" evidence=IEA

GO:0030914 "STAGA complex" evidence=IEA

GO:0030331 "estrogen receptor binding" evidence=IEA

GO:0016578 "histone deubiquitination" evidence=IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=IEA

GO:0004402 "histone acetyltransferase activity" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

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

GO:0000125 "PCAF complex" evidence=IEA

MGI|MGI:1346320 Taf10 "TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Mus musculus (taxid:10090)]

 Score = 165 (63.1 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 29/58 (50%), Positives = 44/58 (75%)

Query:    21 LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQY 78
             L +FL  L  YTPTIPD +  +YL ++GF+  D R+IRL+++A QKF++++A DALQ+
Sbjct:   116 LVDFLMQLEDYTPTIPDAVTGYYLNRAGFEASDPRIIRLISLAAQKFISDIANDALQH 173

GO:0000082 "G1/S transition of mitotic cell cycle" evidence=IMP

GO:0000125 "PCAF complex" evidence=ISO

GO:0001889 "liver development" evidence=IMP

GO:0003677 "DNA binding" evidence=IDA

GO:0003713 "transcription coactivator activity" evidence=ISO

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005669 "transcription factor TFIID complex" evidence=ISO;TAS

GO:0005737 "cytoplasm" evidence=ISO

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

GO:0006352 "DNA-dependent transcription, initiation" evidence=ISO

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

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

GO:0006915 "apoptotic process" evidence=IMP

GO:0009790 "embryo development" evidence=IMP

GO:0010468 "regulation of gene expression" evidence=IMP

GO:0016578 "histone deubiquitination" evidence=ISO

GO:0019899 "enzyme binding" evidence=ISO

GO:0030331 "estrogen receptor binding" evidence=ISO

GO:0030914 "STAGA complex" evidence=ISO

GO:0033276 "transcription factor TFTC complex" evidence=ISO

GO:0035264 "multicellular organism growth" evidence=IMP

GO:0043066 "negative regulation of apoptotic process" evidence=IMP

GO:0043623 "cellular protein complex assembly" evidence=IMP

GO:0043966 "histone H3 acetylation" evidence=ISO

GO:0048471 "perinuclear region of cytoplasm" evidence=ISO

GO:0051101 "regulation of DNA binding" evidence=IMP

GO:0051260 "protein homooligomerization" evidence=ISO

GO:0070063 "RNA polymerase binding" evidence=ISO

GO:0070365 "hepatocyte differentiation" evidence=IMP

RGD|1305907 Taf10 "TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Rattus norvegicus (taxid:10116)]

 Score = 165 (63.1 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 29/58 (50%), Positives = 44/58 (75%)

Query:    21 LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQY 78
             L +FL  L  YTPTIPD +  +YL ++GF+  D R+IRL+++A QKF++++A DALQ+
Sbjct:   116 LVDFLMQLEDYTPTIPDAVTGYYLNRAGFEASDPRIIRLISLAAQKFISDIANDALQH 173

GO:0000082 "G1/S transition of mitotic cell cycle" evidence=ISO

GO:0000125 "PCAF complex" evidence=IEA;ISO

GO:0001889 "liver development" evidence=ISO

GO:0003674 "molecular_function" evidence=ND

GO:0003677 "DNA binding" evidence=ISO

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA;ISO

GO:0003713 "transcription coactivator activity" evidence=IEA;ISO

GO:0004402 "histone acetyltransferase activity" evidence=IEA;ISO

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=ISO

GO:0005669 "transcription factor TFIID complex" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA;ISO

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

GO:0006915 "apoptotic process" evidence=ISO

GO:0008150 "biological_process" evidence=ND

GO:0009790 "embryo development" evidence=ISO

GO:0010468 "regulation of gene expression" evidence=ISO

GO:0016578 "histone deubiquitination" evidence=IEA;ISO

GO:0019899 "enzyme binding" evidence=ISO

GO:0030331 "estrogen receptor binding" evidence=IEA;ISO

GO:0030914 "STAGA complex" evidence=IEA;ISO

GO:0033276 "transcription factor TFTC complex" evidence=IEA;ISO

GO:0035264 "multicellular organism growth" evidence=ISO

GO:0043066 "negative regulation of apoptotic process" evidence=ISO

GO:0043623 "cellular protein complex assembly" evidence=ISO

GO:0043966 "histone H3 acetylation" evidence=IEA;ISO

GO:0048471 "perinuclear region of cytoplasm" evidence=IEA;ISO

GO:0051101 "regulation of DNA binding" evidence=ISO

GO:0051260 "protein homooligomerization" evidence=IEA;ISO

GO:0070063 "RNA polymerase binding" evidence=IEA;ISO

GO:0070365 "hepatocyte differentiation" evidence=ISO

POMBASE|SPBC21H7.02 taf10 "SAGA complex/transcription factor TFIID complex subunit Taf10" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 160 (61.4 bits), Expect = 8.2e-12, P = 8.2e-12
 Identities = 31/81 (38%), Positives = 46/81 (56%)

Query:    18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQ 77
             D  L  FL+ +  Y+P IPD L+++YL+ SGF+C D RL +L+ +  QKF+++VA DA Q
Sbjct:    90 DKTLENFLAQMDDYSPLIPDVLLDYYLSLSGFKCVDPRLKKLLGLTAQKFISDVAQDAYQ 149

Query:    78 YATNXXXXXXXXXXXXXXQGF 98
             Y+                Q F
Sbjct:   150 YSKIRTGSSNASSTTFGAQNF 170

GO:0000124 "SAGA complex" evidence=IDA

GO:0000790 "nuclear chromatin" evidence=IC

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

GO:0005634 "nucleus" evidence=IDA

GO:0005669 "transcription factor TFIID complex" evidence=ISO

GO:0005829 "cytosol" evidence=IDA

GO:0006338 "chromatin remodeling" evidence=IC

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

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

GO:0016573 "histone acetylation" evidence=ISO

FB|FBgn0026324 Taf10b "TBP-associated factor 10b" [Drosophila melanogaster (taxid:7227)]

 Score = 158 (60.7 bits), Expect = 1.3e-11, P = 1.3e-11
 Identities = 27/59 (45%), Positives = 43/59 (72%)

Query:    21 LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYA 79
             L++F+S L  YTP IPD +  HYL   GFQ  D R++RL+++A QK+++++  DALQ++
Sbjct:    41 LSDFMSQLEDYTPLIPDAVTSHYLNMGGFQSDDKRIVRLISLAAQKYMSDIIDDALQHS 99

GO:0005669 "transcription factor TFIID complex" evidence=ISS;IDA

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=ISS;IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0001075 "RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0000124 "SAGA complex" evidence=IDA

---

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:
	gw1.XVIII.2077.1	hypothetical protein (132 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	eugene3.00140678	hypothetical protein (129 aa)				•	•	•	•		0.825
	estExt_Genewise1_v1.C_LG_I9297	SubName- Full=Putative uncharacterized protein; (175 aa)					•	•	•		0.804
	GTF901	global transcription factor group (202 aa)					•	•	•		0.608
	GTF902	global transcription factor group (201 aa)					•	•	•		0.607
	gw1.XIV.649.1	hypothetical protein (739 aa)					•	•			0.582
	eugene3.00061942	hypothetical protein (675 aa)					•	•	•		0.579
	estExt_fgenesh4_pm.C_LG_V0264	SubName- Full=Putative uncharacterized protein; (107 aa)				•		•	•		0.578
	estExt_fgenesh4_pm.C_LG_XVIII0164	hypothetical protein (676 aa)					•	•	•		0.575
	gw1.XIV.3608.1	hypothetical protein (532 aa)					•	•	•		0.574
	estExt_Genewise1_v1.C_LG_I4516	hypothetical protein (529 aa)					•	•	•		0.571

---

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	113
cd07982	108	cd07982, TAF10, The TATA Binding Protein (TBP) Ass	7e-33
pfam03540	51	pfam03540, TFIID_30kDa, Transcription initiation f	6e-24
COG5162	197	COG5162, COG5162, Transcription initiation factor	6e-17

>gnl|CDD|187739 cd07982, TAF10, The TATA Binding Protein (TBP) Associated Factor 10

 Score =  110 bits (277), Expect = 7e-33
 Identities = 36/61 (59%), Positives = 48/61 (78%)

Query: 19 AALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQY 78
          A+L EFLS L  YTPTIPDE+ ++YL K+GF C D R+ RLV++A QKFV+++A DA+QY
Sbjct: 1  ASLAEFLSQLDDYTPTIPDEVTDYYLKKAGFDCSDPRVKRLVSLAAQKFVSDIANDAMQY 60

Query: 79 A 79
           
Sbjct: 61 C 61

The TATA Binding Protein (TBP) Associated Factor 10 (TAF 10) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of the seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and the assembly of the preinitiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. Several hypotheses are proposed for TAF functions, such as serving as activator-binding sites, being involved in core-promoter recognition, or to perform an essential catalytic activity. Each TAF - with the help of a specific activator - is required only for the expression of a subset of genes, and TAFs are not universally involved in transcription such as the GTFs. TAF10 regulates genes that are important for cell cycle progression and cell morphology. A lack of TAF10 leads to cell cycle arrest and cell death by apoptosis in mouse. In both yeast and human cells, TAFs have been found as components of other complexes besides TFIID. TAF10 is part of other transcription regulatory multiprotein complexes (e.g., SAGA, TBP-free TAF-containing complex [TFTC], STAGA, and PCAF/GCN5). Several TAFs interact via histone-fold motifs. The histone fold (HFD) is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamer. The minimal HFD contains three alpha-helices linked by two loops. The HFD is found in core histones, TAFs and many other transcription factors. Five HF-containing TAF pairs have been described in TFIID: TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10. Length = 108

>gnl|CDD|146270 pfam03540, TFIID_30kDa, Transcription initiation factor TFIID 23-30kDa subunit

 Score = 85.8 bits (213), Expect = 6e-24
 Identities = 27/47 (57%), Positives = 38/47 (80%)

Query: 33 PTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYA 79
          PTIPD + ++YL K+GFQ  D R+ RLV++A QKFV+++ATDA Q+A
Sbjct: 1  PTIPDAVTDYYLKKAGFQTSDPRVKRLVSLAAQKFVSDIATDAYQHA 47

Length = 51

>gnl|CDD|227491 COG5162, COG5162, Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]

 Score = 72.0 bits (176), Expect = 6e-17
 Identities = 27/61 (44%), Positives = 41/61 (67%)

Query: 18  DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQ 77
           D  L E L ++  YTP IPD + ++YL K+GF   D R+ +L+++  QKFV+++A DA Q
Sbjct: 72  DKTLEELLQNMDSYTPLIPDSVTDYYLEKAGFVTSDQRVKKLLSLLAQKFVSDIAVDAYQ 131

Query: 78  Y 78
           Y
Sbjct: 132 Y 132

Length = 197

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	113
KOG3423	176	consensus Transcription initiation factor TFIID, s	100.0
PF03540	51	TFIID_30kDa: Transcription initiation factor TFIID	99.98
COG5162	197	Transcription initiation factor TFIID, subunit TAF	99.96
smart00576	77	BTP Bromodomain transcription factors and PHD doma	95.09
PF07524	77	Bromo_TP: Bromodomain associated; InterPro: IPR006	94.25
PF02291	129	TFIID-31kDa: Transcription initiation factor IID,	93.24
cd07979	117	TAF9 TATA Binding Protein (TBP) Associated Factor	92.93
cd08045	212	TAF4 TATA Binding Protein (TBP) Associated Factor	92.44
PF05236	264	TAF4: Transcription initiation factor TFIID compon	91.89
PF00808	65	CBFD_NFYB_HMF: Histone-like transcription factor (	90.5
KOG1142	258	consensus Transcription initiation factor TFIID, s	89.79
PF03847	68	TFIID_20kDa: Transcription initiation factor TFIID	89.36
smart00803	65	TAF TATA box binding protein associated factor. TA	89.05
cd07981	72	TAF12 TATA Binding Protein (TBP) Associated Factor	88.31
PLN00035	103	histone H4; Provisional	85.44
PTZ00015	102	histone H4; Provisional	80.78

>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=100.00  E-value=1.2e-37  Score=240.99  Aligned_cols=76  Identities=46%  Similarity=0.703  Sum_probs=72.3

Q ss_pred             CCCCCCCCCCchHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697            8 QQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTF   83 (113)
Q Consensus         8 ~~~~~~~~~~d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r~   83 (113)
                      +.+......+|.+|+|||.+|+||+|||||+||+|||+++||+|+||||+|||||||||||||||+|||||||||-
T Consensus        60 ~~~~~~~~~~d~~l~efl~qLddYtP~IPDavt~~yL~~aGf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~  135 (176)
T KOG3423|consen   60 ANGELNPTTKDTHLEEFLAQLDDYTPTIPDAVTDHYLKKAGFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRT  135 (176)
T ss_pred             ccCCcCCCCcchHHHHHHHHHhcCCCCCcHHHHHHHHHhcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence            4556677889999999999999999999999999999999999999999999999999999999999999999985

>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors

Probab=99.98  E-value=5.2e-33  Score=179.15  Aligned_cols=50  Identities=52%  Similarity=0.895  Sum_probs=49.6

Q ss_pred             CCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           33 PTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNT   82 (113)
Q Consensus        33 PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r   82 (113)
                      |+|||+||+|||+++||+|+||||+|||||||||||+||++|||||||+|
T Consensus         1 P~IPD~v~~~yL~~~G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~r   50 (51)
T PF03540_consen    1 PTIPDEVTDYYLERSGFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKIR   50 (51)
T ss_pred             CCCCHHHHHHHHHHCCCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            99999999999999999999999999999999999999999999999998

The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus

>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=99.96  E-value=7.6e-30  Score=199.41  Aligned_cols=68  Identities=40%  Similarity=0.675  Sum_probs=66.5

Q ss_pred             CCchHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           16 DDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTF   83 (113)
Q Consensus        16 ~~d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r~   83 (113)
                      .+|++|+|||++||+|+|+|||+||+|||+++||.|.|+|||||+||+|||||||||.|||||+|+|-
T Consensus        70 ~Kdktlee~l~~mDsy~PliPd~v~DYyl~k~Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~  137 (197)
T COG5162          70 MKDKTLEELLQNMDSYTPLIPDSVTDYYLEKAGFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQ  137 (197)
T ss_pred             hhHHHHHHHHHhcccCCCCccHHHHHHHHHhcCceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            68999999999999999999999999999999999999999999999999999999999999999985

>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins

Probab=95.09  E-value=0.11  Score=34.34  Aligned_cols=44  Identities=20%  Similarity=0.283  Sum_probs=40.9

Q ss_pred             HHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           38 ELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATN   81 (113)
Q Consensus        38 aVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~   81 (113)
                      -++...|+.+||+...|...-.+.=..++|+..++..|.+||..
T Consensus        10 ~~Vaqil~~~Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~   53 (77)
T smart00576       10 IAVAQILESAGFDSFQESALETLTDILQSYIQELGRTAHSYAEL   53 (77)
T ss_pred             HHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46788999999999999999999999999999999999999965

subdomain of archael histone-like transcription factors

>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO)

Probab=94.25  E-value=0.23  Score=32.47  Aligned_cols=43  Identities=21%  Similarity=0.373  Sum_probs=39.6

Q ss_pred             HHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           38 ELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYAT   80 (113)
Q Consensus        38 aVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K   80 (113)
                      .++...|+.+||++..+-..-.++-.+++|+..+...+..||-
T Consensus        10 ~~va~il~~~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae   52 (77)
T PF07524_consen   10 RSVAQILKHAGFDSASPSALDTLTDILQRYLQELGRTAKRYAE   52 (77)
T ss_pred             HHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4677889999999999999999999999999999999999984

The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].

>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []

Probab=93.24  E-value=0.31  Score=36.23  Aligned_cols=45  Identities=18%  Similarity=0.299  Sum_probs=35.0

Q ss_pred             HHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           38 ELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNT   82 (113)
Q Consensus        38 aVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r   82 (113)
                      .++.-.|+..|++--+|||.-.+===+.++++||..||..|+..+
T Consensus        16 ~~i~~iL~~~Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA   60 (129)
T PF02291_consen   16 RVIHLILKSMGVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHA   60 (129)
T ss_dssp             HHHHHHHHHTT---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            467889999999888889887666667999999999999999765

TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.

>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=92.93  E-value=0.49  Score=34.16  Aligned_cols=45  Identities=18%  Similarity=0.301  Sum_probs=40.8

Q ss_pred             HHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           38 ELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNT   82 (113)
Q Consensus        38 aVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r   82 (113)
                      .++.-.|++.|.+.-+++++..+.=-+.++++||+.||..|++-.
T Consensus         5 ~~v~~iLk~~Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA   49 (117)
T cd07979           5 RVIAAILKSMGITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHA   49 (117)
T ss_pred             HHHHHHHHHCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            467889999999999999999999999999999999999999863

The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi

>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=92.44  E-value=0.53  Score=36.28  Aligned_cols=46  Identities=11%  Similarity=0.208  Sum_probs=40.8

Q ss_pred             HHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           40 VEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTFFL   85 (113)
Q Consensus        40 t~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r~~~   85 (113)
                      +..++.+.|+...|+.+..|||+|++-++.+|+.+....|+.|.-.
T Consensus        54 ~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~   99 (212)
T cd08045          54 IRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDS   99 (212)
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence            4456778888888999999999999999999999999999999643

The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are

>PF05236 TAF4: Transcription initiation factor TFIID component TAF4 family; InterPro: IPR007900 Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site

Probab=91.89  E-value=0.21  Score=39.56  Aligned_cols=54  Identities=15%  Similarity=0.252  Sum_probs=30.4

Q ss_pred             CCCCcHHHHHHHH----HhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           32 TPTIPDELVEHYL----AKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTFFL   85 (113)
Q Consensus        32 ~PtIPDaVt~yYL----~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r~~~   85 (113)
                      .|.+.-.+...++    .+.|....|+-+..|||+|+|-.+.+|+.++...|+.|.-.
T Consensus        41 ~~fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~   98 (264)
T PF05236_consen   41 EPFLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDS   98 (264)
T ss_dssp             ---S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH---------
T ss_pred             ccccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence            4445444444444    44576667899999999999999999999999999999764

Transcription factor TFIID is one of the general factors involved in this process. Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (IPR007124 from INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4 []. ; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_C.

>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin

Probab=90.50  E-value=1.5  Score=27.71  Aligned_cols=47  Identities=17%  Similarity=0.244  Sum_probs=34.7

Q ss_pred             CcHHHHHHHHHhC-CCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           35 IPDELVEHYLAKS-GFQCPDVRLIRLVAVATQKFVAEVATDALQYATN   81 (113)
Q Consensus        35 IPDaVt~yYL~~a-Gf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~   81 (113)
                      +|=+-+.-.++.. +..---..-.-+++.|++.|+..++.+|.++|+.
T Consensus         3 lP~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~   50 (65)
T PF00808_consen    3 LPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQR   50 (65)
T ss_dssp             S-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5777777777776 2221234456789999999999999999999985

The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....

>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=89.79  E-value=1.5  Score=36.50  Aligned_cols=37  Identities=16%  Similarity=0.141  Sum_probs=32.3

Q ss_pred             CCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           48 GFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTFF   84 (113)
Q Consensus        48 Gf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r~~   84 (113)
                      |=+.-|+.|..|+..-|..||+||.+-|-..||-|.-
T Consensus       169 ~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKs  205 (258)
T KOG1142|consen  169 GTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKS  205 (258)
T ss_pred             CcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            3334599999999999999999999999999998865

>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []

Probab=89.36  E-value=0.91  Score=30.32  Aligned_cols=33  Identities=21%  Similarity=0.168  Sum_probs=28.4

Q ss_pred             CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           52 PDVRLIRLVAVATQKFVAEVATDALQYATNTFF   84 (113)
Q Consensus        52 ~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r~~   84 (113)
                      -||-+..++.--|..||.+|++.|.+.||-|.-
T Consensus        18 ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s   50 (68)
T PF03847_consen   18 LDPDVEELLLELADDFVDDVVSFACRLAKHRKS   50 (68)
T ss_dssp             --HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence            488899999999999999999999999998853

; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.

>smart00803 TAF TATA box binding protein associated factor

Probab=89.05  E-value=3.3  Score=27.16  Aligned_cols=48  Identities=17%  Similarity=0.274  Sum_probs=42.2

Q ss_pred             CCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           34 TIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATN   81 (113)
Q Consensus        34 tIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~   81 (113)
                      .+|-+-+.-..+++|.+--..-+...++=....++.+|+.||..+++-
T Consensus         2 ~~p~~~i~ria~~~Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~h   49 (65)
T smart00803        2 WLPKETIKDVAESLGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRH   49 (65)
T ss_pred             CCCHHHHHHHHHHCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            478888899999999997666699999999999999999999988764

TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.

>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=88.31  E-value=3  Score=27.45  Aligned_cols=34  Identities=24%  Similarity=0.261  Sum_probs=31.2

Q ss_pred             CCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           50 QCPDVRLIRLVAVATQKFVAEVATDALQYATNTF   83 (113)
Q Consensus        50 ~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r~   83 (113)
                      ..-|+-+..++.=.+..|+.+|+.+|..+||-|.
T Consensus        18 ~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~   51 (72)
T cd07981          18 EQLDPDVEELLLEIADDFVDDVVEDACRLAKHRK   51 (72)
T ss_pred             CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            5678999999999999999999999999999775

The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind

>PLN00035 histone H4; Provisional

Probab=85.44  E-value=3.6  Score=29.91  Aligned_cols=56  Identities=14%  Similarity=0.180  Sum_probs=45.4

Q ss_pred             hcccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           27 SLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNT   82 (113)
Q Consensus        27 ~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r   82 (113)
                      .|.|...-||-+-+.-.+.++|.+---.-+.--+.-+...|+.+|+.||..|++-.
T Consensus        22 ~~~d~i~~ipk~~IrRLARr~GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA   77 (103)
T PLN00035         22 VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHA   77 (103)
T ss_pred             HHHhhhccCCHHHHHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            34567777999999999999998865444666667778899999999999998753

>PTZ00015 histone H4; Provisional

Probab=80.78  E-value=9.2  Score=27.71  Aligned_cols=54  Identities=13%  Similarity=0.166  Sum_probs=45.0

Q ss_pred             ccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           29 MGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNT   82 (113)
Q Consensus        29 dDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r   82 (113)
                      -|..+-||-+-+.-.+.++|..---.-+.--+.-+...|+.+|+.||..|++-.
T Consensus        25 r~~i~gI~k~~IrRLarr~GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA   78 (102)
T PTZ00015         25 RDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYA   78 (102)
T ss_pred             hhcccCCCHHHHHHHHHHcCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            588899999999999999999964333666667778899999999999988743

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	113
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	96.12
1taf_A	68	TFIID TBP associated factor 42; transcription init	94.84
2hue_C	84	Histone H4; mini beta sheet, elongated beta sandwh	91.58
1id3_B	102	Histone H4; nucleosome core particle, chromatin, p	91.07
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	90.94
1tzy_D	103	Histone H4-VI; histone-fold, tetramer-dimer-dimer,	89.4
2yfw_B	103	Histone H4, H4; cell cycle, kinetochore, centromer	88.35
1h3o_B	76	Transcription initiation factor TFIID 20/15 kDa su	86.54
1taf_B	70	TFIID TBP associated factor 62; transcription init	84.6
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	84.38
1n1j_A	93	NF-YB; histone-like PAIR, DNA binding protein; 1.6	80.08

>1ku5_A HPHA, archaeal histon; histone fold, DNA binding protein; 2.30A {Pyrococcus horikoshii} SCOP: a.22.1.2

Probab=96.12  E-value=0.02  Score=36.31  Aligned_cols=51  Identities=18%  Similarity=0.327  Sum_probs=45.6

Q ss_pred             CCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           31 YTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATN   81 (113)
Q Consensus        31 Y~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~   81 (113)
                      |.|.||-+.+.-.++++|..--.+.+.-.+.=++..|+.+|+.||..||+-
T Consensus         3 ~~~~lp~a~v~Rl~r~~g~~ris~~a~~~l~e~~~~~~~~v~~dA~~~a~h   53 (70)
T 1ku5_A            3 MMGELPIAPVDRLIRKAGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARH   53 (70)
T ss_dssp             --CCSCHHHHHHHHHHTTCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             ccccCChHHHHHHHHHcCcceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            678999999999999999877788899999999999999999999999874

>1taf_A TFIID TBP associated factor 42; transcription initiation, histone fold, complex (TWO transcr factors); 2.00A {Drosophila melanogaster} SCOP: a.22.1.3

Probab=94.84  E-value=0.1  Score=34.10  Aligned_cols=45  Identities=20%  Similarity=0.290  Sum_probs=40.7

Q ss_pred             HHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           38 ELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNT   82 (113)
Q Consensus        38 aVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r   82 (113)
                      .++.-.|+++|.+--+|+++-.+.=.+.+++++|+.||..|++-.
T Consensus         5 ~~i~~iLk~~G~~~~~~~v~~~L~e~~~ry~~~il~dA~~~a~HA   49 (68)
T 1taf_A            5 QVIMSILKELNVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHA   49 (68)
T ss_dssp             HHHHHHHHHTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            467889999999999999999999999999999999999998753

>2hue_C Histone H4; mini beta sheet, elongated beta sandwhich, DNA binding prote; 1.70A {Xenopus laevis} SCOP: a.22.1.1 PDB: 3nqj_B 1aoi_B 3kwq_B* 1hio_D 2yfv_B

Probab=91.58  E-value=0.66  Score=30.49  Aligned_cols=55  Identities=15%  Similarity=0.192  Sum_probs=46.3

Q ss_pred             cccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           28 LMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNT   82 (113)
Q Consensus        28 LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r   82 (113)
                      |.|...-||-+-+.-.++++|..---..+..-+.=....|+.+|+.||..||+-.
T Consensus         4 ~r~~~~~ip~~~I~Riar~~Gv~rIs~da~~~l~~~l~~~~~~I~~dA~~~a~ha   58 (84)
T 2hue_C            4 LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHA   58 (84)
T ss_dssp             GGGGCCSSCHHHHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             ccccCCCCCHHHHHHHHHHcCchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            4566778999999999999999744444788888889999999999999998753

>1id3_B Histone H4; nucleosome core particle, chromatin, protein/DNA interaction, nucleoprotein, supercoiled DNA; 3.10A {Saccharomyces cerevisiae} SCOP: a.22.1.1

Probab=91.07  E-value=0.47  Score=32.57  Aligned_cols=56  Identities=14%  Similarity=0.217  Sum_probs=45.8

Q ss_pred             hcccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           27 SLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNT   82 (113)
Q Consensus        27 ~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r   82 (113)
                      .|.|...-||-+-+.-.++++|...--..+..-+.=+...|+.+|+.||..||+-.
T Consensus        21 ~~r~~i~~ip~~~I~Rlar~~Gv~rIS~da~~~l~~~le~fi~~I~~dA~~~a~Ha   76 (102)
T 1id3_B           21 ILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHA   76 (102)
T ss_dssp             ---CCGGGSCHHHHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHhccCCCCHHHHHHHHHHcCchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            34566677999999999999999754455888889999999999999999998753

>3b0c_T CENP-T, centromere protein T; histone fold, DNA binding, DNA binding protein; HET: CIT; 2.20A {Gallus gallus} PDB: 3b0d_T* 3vh5_T 3vh6_T

Probab=90.94  E-value=0.4  Score=33.40  Aligned_cols=50  Identities=12%  Similarity=0.297  Sum_probs=41.8

Q ss_pred             CCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           33 PTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNT   82 (113)
Q Consensus        33 PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r   82 (113)
                      |-||-+.+.-.++++|..---+.+.-.+.=++..|+.+|+.||..||+-.
T Consensus         6 ~~lP~a~I~Ri~r~~g~~rIS~~a~~~l~e~l~~f~~~v~~da~~~A~HA   55 (111)
T 3b0c_T            6 PEIASSLIKQIFSHYVKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHA   55 (111)
T ss_dssp             ----CHHHHHHHHHHHCSCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            67999999999999998877777889999999999999999999999754

>1tzy_D Histone H4-VI; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1f66_B 1eqz_D 1hq3_D 1u35_B 2aro_D 2cv5_B* 2f8n_B 3nqu_B 3r45_B 3azg_B 3a6n_B 3an2_B 3av1_B 3av2_B 3ayw_B 3aze_B 3azf_B 3afa_B 3azh_B 3azk_B ...

Probab=89.40  E-value=0.95  Score=30.75  Aligned_cols=55  Identities=15%  Similarity=0.192  Sum_probs=44.1

Q ss_pred             cccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           28 LMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNT   82 (113)
Q Consensus        28 LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r   82 (113)
                      +.|-..-||-+-+.-++++.|+..--..+..-++=....|+.+|+.||..||+-.
T Consensus        23 ~r~~~~gip~~~I~Rlar~~G~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~ha   77 (103)
T 1tzy_D           23 LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHA   77 (103)
T ss_dssp             CCCGGGGSCHHHHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             hhhhcccCCHHHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            4444455999999999999999753345777777888999999999999998753

>2yfw_B Histone H4, H4; cell cycle, kinetochore, centromere, histone chaperone, BUDD; 2.60A {Kluyveromyces lactis nrrl y-1140}

Probab=88.35  E-value=1.3  Score=30.19  Aligned_cols=53  Identities=15%  Similarity=0.205  Sum_probs=40.8

Q ss_pred             ccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           29 MGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATN   81 (113)
Q Consensus        29 dDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~   81 (113)
                      .|-..-||-+-+.-++++.|+..--..+..-++=....|+.+|+.||..||+-
T Consensus        24 r~~~~gip~~~I~Rlar~~G~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~h   76 (103)
T 2yfw_B           24 RDNIQGITKPAIRRLARRGGVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEH   76 (103)
T ss_dssp             ------CCHHHHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhccCCHHHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44445599999999999999975444577778888999999999999999874

>1h3o_B Transcription initiation factor TFIID 20/15 kDa subunits; transcription/TBP-associated factors, TBP-associated factors; 2.3A {Homo sapiens} SCOP: a.22.1.3

Probab=86.54  E-value=2.8  Score=27.85  Aligned_cols=49  Identities=16%  Similarity=0.159  Sum_probs=40.7

Q ss_pred             chHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTFF   84 (113)
Q Consensus        18 d~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r~~   84 (113)
                      -..|.|++.+.+-                  =.+-||-+..++.=-|..||.+|++.|.+.||-|.-
T Consensus         8 k~~L~~Lv~~idp------------------~~~ld~~vee~ll~lADdFV~~V~~~ac~lAKhR~s   56 (76)
T 1h3o_B            8 KKKLQDLVREVDP------------------NEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKS   56 (76)
T ss_dssp             HHHHHHHHHHHCS------------------SCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHhcCC------------------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            4667888887752                  145699999999999999999999999999998863

>1taf_B TFIID TBP associated factor 62; transcription initiation, histone fold, complex (TWO transcr factors); 2.00A {Drosophila melanogaster} SCOP: a.22.1.3

Probab=84.60  E-value=6.3  Score=25.65  Aligned_cols=51  Identities=14%  Similarity=0.168  Sum_probs=45.6

Q ss_pred             CCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           31 YTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATN   81 (113)
Q Consensus        31 Y~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~   81 (113)
                      |...+|-+-+.-+.++.|.+.-..-+.+.++=-..--+.+|+++|..+.|-
T Consensus         3 ~~s~lp~~~v~~iaes~Gi~~lsddaa~~LA~dvEyr~~eI~qeA~kfmrH   53 (70)
T 1taf_B            3 YGSSISAESMKVIAESIGVGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNH   53 (70)
T ss_dssp             CSCCCCHHHHHHHHHHTTCCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            567899999999999999998888888999999999999999999887664

>1b67_A Protein (histone HMFA); DNA binding protein; 1.48A {Methanothermus fervidus} SCOP: a.22.1.2 PDB: 1hta_A 1a7w_A 1b6w_A 1bfm_A

Probab=84.38  E-value=3.9  Score=25.19  Aligned_cols=48  Identities=15%  Similarity=0.196  Sum_probs=36.2

Q ss_pred             CCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           34 TIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATN   81 (113)
Q Consensus        34 tIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~   81 (113)
                      .||-+-+.-.+++.|-..--..-.-+++=|+.-|+..|+.||..+|+-
T Consensus         2 ~lP~a~v~Ri~k~~~~~ris~~A~~~l~~a~e~fi~~l~~~A~~~a~~   49 (68)
T 1b67_A            2 ELPIAPIGRIIKNAGAERVSDDARIALAKVLEEMGEEIASEAVKLAKH   49 (68)
T ss_dssp             CSCHHHHHHHHHHTTCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCccHHHHHHhcCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            478888888888883222223345578889999999999999999874

>1n1j_A NF-YB; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3

Probab=80.08  E-value=10  Score=24.80  Aligned_cols=50  Identities=12%  Similarity=0.074  Sum_probs=39.6

Q ss_pred             CCCCcHHHHHHHHHhCCCCC--CChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           32 TPTIPDELVEHYLAKSGFQC--PDVRLIRLVAVATQKFVAEVATDALQYATN   81 (113)
Q Consensus        32 ~PtIPDaVt~yYL~~aGf~~--~D~RI~RLISLAAQKFISDIa~DA~Qy~K~   81 (113)
                      -..+|-+-+.-.++++|=+.  --.--.-+++-|+.-||..++.+|..+|+-
T Consensus         6 d~~LP~a~i~ri~K~~~~~~~~is~dA~~~l~~a~e~Fi~~l~~~A~~~a~~   57 (93)
T 1n1j_A            6 DIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQ   57 (93)
T ss_dssp             -CCCCHHHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccCChhHHHHHHHHhCCccceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35789999999999997432  123345688999999999999999999874

---

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	113
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	95.16
d1ku5a_	66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	93.34
d2huec1	82	Histone H4 {African clawed frog (Xenopus laevis) [	91.61
d1tafa_	68	TAF(II)42 {Fruit fly (Drosophila melanogaster) [Ta	91.18
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	81.84
d1h3ob_	74	TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom	80.99

>d1htaa_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanothermus fervidus, histone A [TaxId: 2180]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon Methanothermus fervidus, histone A [TaxId: 2180]

Probab=95.16  E-value=0.054  Score=32.43  Aligned_cols=48  Identities=15%  Similarity=0.196  Sum_probs=43.0

Q ss_pred             CCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           34 TIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATN   81 (113)
Q Consensus        34 tIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~   81 (113)
                      -+|-+.+...+++.|..---.-..-+++=++..||.+|+.+|.++|+-
T Consensus         3 eLP~a~I~ri~k~~~~~ris~ea~~~l~~~~e~fi~~l~~~a~~~a~~   50 (68)
T d1htaa_           3 ELPIAPIGRIIKNAGAERVSDDARIALAKVLEEMGEEIASEAVKLAKH   50 (68)
T ss_dssp             CSCHHHHHHHHHHTTCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCcHHHHHHHHHHCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            489999999999999876566788899999999999999999999874

>d1ku5a_ a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococcus horikoshii) [TaxId: 53953]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon (Pyrococcus horikoshii) [TaxId: 53953]

Probab=93.34  E-value=0.14  Score=30.51  Aligned_cols=47  Identities=19%  Similarity=0.372  Sum_probs=39.2

Q ss_pred             CcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           35 IPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATN   81 (113)
Q Consensus        35 IPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~   81 (113)
                      +|-+.+.-.+++.|-.---.-..-+++-|+..||.+++.+|..+|+-
T Consensus         3 LP~a~I~rI~k~~~~~ris~ea~~~l~~a~e~Fi~~l~~~a~~~a~~   49 (66)
T d1ku5a_           3 LPIAPVDRLIRKAGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARH   49 (66)
T ss_dssp             SCHHHHHHHHHHTTCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHhCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            78899999999987543344566799999999999999999999874

>d2huec1 a.22.1.1 (C:20-101) Histone H4 {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H4
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=91.61  E-value=0.23  Score=31.32  Aligned_cols=49  Identities=14%  Similarity=0.208  Sum_probs=43.9

Q ss_pred             CCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           33 PTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATN   81 (113)
Q Consensus        33 PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~   81 (113)
                      --||.+-+.-..+++|..--...+...++-....|+.+|+.||..+++-
T Consensus         8 ~gI~k~~i~Riar~~Gv~ris~d~~~~l~~~l~~~l~~i~~~a~~~~~h   56 (82)
T d2huec1           8 QGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEH   56 (82)
T ss_dssp             CSSCHHHHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCcCHHHHHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3599999999999999997677788889999999999999999999864

>d1tafa_ a.22.1.3 (A:) TAF(II)42 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)42
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=91.18  E-value=0.39  Score=30.23  Aligned_cols=44  Identities=20%  Similarity=0.292  Sum_probs=37.0

Q ss_pred             HHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           38 ELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATN   81 (113)
Q Consensus        38 aVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~   81 (113)
                      .++.-.|+..|.+.=+|||.-.+==-+-++++||..||.-|+.-
T Consensus         5 ~~i~~iL~~~GV~~yeprV~~qlLef~yRYtt~VL~DA~vys~H   48 (68)
T d1tafa_           5 QVIMSILKELNVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANH   48 (68)
T ss_dssp             HHHHHHHHHTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            36777899999999999988766666799999999999988754

>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon Methanopyrus kandleri [TaxId: 2320]

Probab=81.84  E-value=2.1  Score=28.99  Aligned_cols=51  Identities=16%  Similarity=0.208  Sum_probs=43.0

Q ss_pred             CCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           32 TPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNT   82 (113)
Q Consensus        32 ~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r   82 (113)
                      .-.+|-+-+.-+++++|..---.-..-+++-++.-|+.+|+.+|.++|+..
T Consensus        77 ~~~fp~a~IkRi~k~~g~~ris~dA~~~l~~~~E~fi~~l~~~A~~~a~~~  127 (151)
T d1f1ea_          77 GELFGRATVRRILKRAGIERASSDAVDLYNKLICRATEELGEKAAEYADED  127 (151)
T ss_dssp             SCCCCHHHHHHHHHHTTCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cCccCHHHHHHHHHcCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            446899999999999998744444577999999999999999999998753

>d1h3ob_ a.22.1.3 (B:) TAF(II)-20, (TAF(II)-15, hTAF12), histone fold domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)-20, (TAF(II)-15, hTAF12), histone fold domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.99  E-value=3.1  Score=26.01  Aligned_cols=47  Identities=17%  Similarity=0.182  Sum_probs=38.1

Q ss_pred             hHHHHHHHhcccCCCCCcHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033697           19 AALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLIRLVAVATQKFVAEVATDALQYATNTF   83 (113)
Q Consensus        19 ~~L~eFL~~LdDY~PtIPDaVt~yYL~~aGf~~~D~RI~RLISLAAQKFISDIa~DA~Qy~K~r~   83 (113)
                      ..|.||+.+.+-                  =..=||.+.-++.=-|..||.+|...|.+-||-|.
T Consensus         7 ~~L~eLv~~idp------------------~~~ld~~vee~ll~iADdFV~~V~~~ac~lAKhR~   53 (74)
T d1h3ob_           7 KKLQDLVREVDP------------------NEQLDEDVEEMLLQIADDFIESVVTAACQLARHRK   53 (74)
T ss_dssp             HHHHHHHHHHCS------------------SCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhCC------------------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            457777777642                  12358899999999999999999999999999886