Citrus Sinensis ID: 032126

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------
Protein Sequence
MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREYGVNVKHQEYFADNPSTGMDPASKEE
Secondary Structure (PSIPRED)
ccccccccccccccccccHHHHHHHHHcccccccccHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccHHHHccccHHHHHHHHHHHcccccccHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccEEEEEHHHHHHHHHHcccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mnhnnnfqqssdgrhddDAALTEFLSSlmgytptipdELVEHYLAksgfqcpdvrlncclcfcrIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREYGvnvkhqeyfadnpstgmdpaskee
Flexible Loop (DISEMBL)
mnhnnnfqqssdgrhDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKArqaavvkdkrdkqqkdkrliLTMEDLSKALREYGVnvkhqeyfadnpstgmdpaskee
Low Complexity Region (SEG)
MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVkdkrdkqqkdkrLILTMEDLSKALREYGVNVKHQEYFADNPSTGMDPASKEE
Disordered region (IsUnstruct)
********************LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAV*************LILTMEDLSKALREYGVNVKHQEY****************
Disordered Region (DISOPRED)
***********************FLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDAL**************************TMEDLSKALREYGVNVKHQEYFA**************
Disordered Region (DISEMBL)
**************HDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQC*****************DKRLILTMEDLSKALREYGVNVKHQEYFADNP***********
Disordered Region (DISPRO)
*****************DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQA************DKRLILTMEDLSKALREYGVNVKHQEYF***************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREYGVNVKHQEYFADNPSTGMDPASKEE
Positional Conservation
no confident homologs detected

---

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	147	2.2.26 [Sep-21-2011]
Q8K0H5	218	Transcription initiation	yes	no	0.693	0.467	0.446	2e-22
Q12962	218	Transcription initiation	yes	no	0.693	0.467	0.446	2e-22
Q9XZT7	146	Transcription initiation	yes	no	0.700	0.705	0.401	2e-18
Q9U5W9	167	Transcription initiation	no	no	0.721	0.634	0.362	2e-16
O60171	215	Transcription initiation	yes	no	0.727	0.497	0.323	2e-14
Q12030	206	Transcription initiation	yes	no	0.727	0.519	0.286	2e-13

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

 Score =  104 bits (260), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 50/112 (44%), Positives = 71/112 (63%), Gaps = 10/112 (8%)

Query: 21  LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVA 80
           L +FL  L  YTPTIPD +  +YL ++GF+  D R+        IRL+++A QKF++++A
Sbjct: 116 LVDFLMQLEDYTPTIPDAVTGYYLNRAGFEASDPRI--------IRLISLAAQKFISDIA 167

Query: 81  TDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREYGVNVKHQEYF 132
            DALQ CK +  A    +   + KD++  LTMEDL+ AL EYG+NVK   YF
Sbjct: 168 NDALQHCKMKGTASGSSR--SKSKDRKYTLTMEDLTPALSEYGINVKKPHYF 217

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

 Score =  104 bits (259), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 50/112 (44%), Positives = 71/112 (63%), Gaps = 10/112 (8%)

Query: 21  LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVA 80
           L +FL  L  YTPTIPD +  +YL ++GF+  D R+        IRL+++A QKF++++A
Sbjct: 116 LVDFLMQLEDYTPTIPDAVTGYYLNRAGFEASDPRI--------IRLISLAAQKFISDIA 167

Query: 81  TDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREYGVNVKHQEYF 132
            DALQ CK +  A    +   + KD++  LTMEDL+ AL EYG+NVK   YF
Sbjct: 168 NDALQHCKMKGTASGSSR--SKSKDRKYTLTMEDLTPALSEYGINVKKPHYF 217

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 = 91.3 bits (225), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/112 (40%), Positives = 66/112 (58%), Gaps = 9/112 (8%)

Query: 21  LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVA 80
           L++F+S L  YTP IPD +  HYL   GFQ  D R+        +RL+++A QK+++++ 
Sbjct: 41  LSDFMSQLEDYTPLIPDAVTSHYLNMGGFQSDDKRI--------VRLISLAAQKYMSDII 92

Query: 81  TDALQQCKAR-QAAVVKDKRDKQQKDKRLILTMEDLSKALREYGVNVKHQEY 131
            DALQ  KAR            + KD++  LTMEDL  AL +YG+NV+  +Y
Sbjct: 93  DDALQHSKARTHMQTTNTPGGSKAKDRKFTLTMEDLQPALADYGINVRKVDY 144

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

 Score = 84.3 bits (207), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 45/124 (36%), Positives = 69/124 (55%), Gaps = 18/124 (14%)

Query: 17  DDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFV 76
           +++ + E +  L  Y+PTIPD L  H L  +GF        C +    +RLV+V+ QKF+
Sbjct: 53  EESEMDELIKQLEDYSPTIPDALTMHILKTAGF--------CTVDPKIVRLVSVSAQKFI 104

Query: 77  AEVATDALQQCKARQAAV--------VKDKRDKQQKDKRLILTMEDLSKALREYGVNVKH 128
           +++A DALQ CK R   +         KDK  K  KD++  L MEDL  AL ++G+ ++ 
Sbjct: 105 SDIANDALQHCKTRTTNIQHSSGHSSSKDK--KNPKDRKYTLAMEDLVPALADHGITMRK 162

Query: 129 QEYF 132
            +YF
Sbjct: 163 PQYF 166

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

 Score = 78.2 bits (191), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 43/133 (32%), Positives = 68/133 (51%), Gaps = 26/133 (19%)

Query: 18  DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVA 77
           D  L  FL+ +  Y+P IPD L+++YL+ SGF+C D RL         +L+ +  QKF++
Sbjct: 90  DKTLENFLAQMDDYSPLIPDVLLDYYLSLSGFKCVDPRLK--------KLLGLTAQKFIS 141

Query: 78  EVATDALQQCKARQAA------------------VVKDKRDKQQKDKRLILTMEDLSKAL 119
           +VA DA Q  K R  +                         ++    + +LT++DLS AL
Sbjct: 142 DVAQDAYQYSKIRTGSSNASSTTFGAQNFGAGGASGIGSSGRRGDRGKTVLTVDDLSAAL 201

Query: 120 REYGVNVKHQEYF 132
            EYG+N+K  ++F
Sbjct: 202 NEYGINLKRPDFF 214

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 = 74.7 bits (182), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 41/143 (28%), Positives = 70/143 (48%), Gaps = 36/143 (25%)

Query: 18  DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVA 77
           D  L E L  +    P IPD ++++YL K+GF   DVR+         RL+A+ATQKFV+
Sbjct: 71  DKTLEEILEMMDSTPPIIPDAVIDYYLTKNGFNVADVRVK--------RLLALATQKFVS 122

Query: 78  EVATDALQQCKARQAAVVKDKRDKQQKDK----------------------------RLI 109
           ++A DA +  + R +  V +  + Q + +                            +++
Sbjct: 123 DIAKDAYEYSRIRSSVAVSNANNSQARARQLLQGQQQPGVQQISQQQHQQNEKTTASKVV 182

Query: 110 LTMEDLSKALREYGVNVKHQEYF 132
           LT+ DLS A+ EYG+N+   +++
Sbjct: 183 LTVNDLSSAVAEYGLNIGRPDFY 205

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)

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	147
255548646	143	transcription factor, putative [Ricinus	0.870	0.895	0.867	1e-61
449441834	136	PREDICTED: transcription initiation fact	0.925	1.0	0.809	3e-61
225465617	136	PREDICTED: transcription initiation fact	0.925	1.0	0.802	4e-61
225465621	136	PREDICTED: transcription initiation fact	0.925	1.0	0.816	5e-61
356512077	136	PREDICTED: transcription initiation fact	0.925	1.0	0.789	6e-60
224142025	144	predicted protein [Populus trichocarpa]	0.870	0.888	0.845	1e-59
351727012	136	uncharacterized protein LOC100500618 [Gl	0.891	0.963	0.812	2e-59
255638464	136	unknown [Glycine max]	0.925	1.0	0.782	2e-59
388512029	139	unknown [Medicago truncatula]	0.945	1.0	0.755	1e-58
357507887	139	Transcription initiation factor TFIID su	0.945	1.0	0.748	2e-58

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

 Score =  240 bits (613), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 118/136 (86%), Positives = 124/136 (91%), Gaps = 8/136 (5%)

Query: 12  DGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVA 71
           DGRHDDDAALTEFLSSLM YTPTIPDELVEHYL KSGFQCPDVRL        +RLVAVA
Sbjct: 16  DGRHDDDAALTEFLSSLMDYTPTIPDELVEHYLGKSGFQCPDVRL--------VRLVAVA 67

Query: 72  TQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREYGVNVKHQEY 131
           TQKFVAEVA DALQQCKARQ+AVVKDKR+KQQKDKRLILTMEDLSKAL EYGVNVKHQEY
Sbjct: 68  TQKFVAEVANDALQQCKARQSAVVKDKREKQQKDKRLILTMEDLSKALHEYGVNVKHQEY 127

Query: 132 FADNPSTGMDPASKEE 147
           FAD+PSTGMDPAS++E
Sbjct: 128 FADSPSTGMDPASRDE 143

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>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 =  239 bits (610), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 119/147 (80%), Positives = 129/147 (87%), Gaps = 11/147 (7%)

Query: 1   MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCL 60
           MNHN   QQ++  RHDDDAAL+EFL+SLM YTPTIPDELVEHYL KSGFQCPDVRL    
Sbjct: 1   MNHN---QQATGSRHDDDAALSEFLASLMEYTPTIPDELVEHYLGKSGFQCPDVRL---- 53

Query: 61  CFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALR 120
               IRLVAVATQKFVA+VA+DALQ CKARQAAVVKDKRDKQQKDKRLILTM+DLSKALR
Sbjct: 54  ----IRLVAVATQKFVADVASDALQHCKARQAAVVKDKRDKQQKDKRLILTMDDLSKALR 109

Query: 121 EYGVNVKHQEYFADNPSTGMDPASKEE 147
           EYGVNVKHQEYFAD+PSTG+D  S+EE
Sbjct: 110 EYGVNVKHQEYFADSPSTGVDSTSREE 136

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225465617|ref|XP_002266754.1| PREDICTED: transcription initiation factor TFIID subunit 10 [Vitis vinifera] gi|302143597|emb|CBI22350.3| unnamed protein product [Vitis vinifera]

 Score =  238 bits (608), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 118/147 (80%), Positives = 130/147 (88%), Gaps = 11/147 (7%)

Query: 1   MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCL 60
           MN N   Q  +D RHDDD+AL++FL+SL+ YTPTIPDELVEHYLAKSGFQCPDVRL    
Sbjct: 1   MNQN---QGGNDARHDDDSALSDFLASLVDYTPTIPDELVEHYLAKSGFQCPDVRL---- 53

Query: 61  CFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALR 120
               IRLVAVATQKFV EVA+DALQQCKARQ+AVVKDKRDKQQKDKRLILTMEDLSKALR
Sbjct: 54  ----IRLVAVATQKFVTEVASDALQQCKARQSAVVKDKRDKQQKDKRLILTMEDLSKALR 109

Query: 121 EYGVNVKHQEYFADNPSTGMDPASKEE 147
           EYGVNVKHQEYFAD+PS+GMDPAS++E
Sbjct: 110 EYGVNVKHQEYFADSPSSGMDPASRDE 136

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  238 bits (608), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 120/147 (81%), Positives = 130/147 (88%), Gaps = 11/147 (7%)

Query: 1   MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCL 60
           MN N   Q  +D RHDDD+AL++FL+SLM YTPTIPDELVEHYLAKSGFQCPDVRL    
Sbjct: 1   MNQN---QGGNDARHDDDSALSDFLASLMDYTPTIPDELVEHYLAKSGFQCPDVRL---- 53

Query: 61  CFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALR 120
               IRLVAVATQKFVAEVA+DALQQCKARQ+AVVKDKRDKQQKDKRLILTMEDLSKALR
Sbjct: 54  ----IRLVAVATQKFVAEVASDALQQCKARQSAVVKDKRDKQQKDKRLILTMEDLSKALR 109

Query: 121 EYGVNVKHQEYFADNPSTGMDPASKEE 147
           E GVNVKHQEYFAD+PSTGMDPAS++E
Sbjct: 110 ECGVNVKHQEYFADSPSTGMDPASRDE 136

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  235 bits (599), Expect = 6e-60,   Method: Compositional matrix adjust.
 Identities = 116/147 (78%), Positives = 128/147 (87%), Gaps = 11/147 (7%)

Query: 1   MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCL 60
           MN N    QSSDGR+DDD+AL++FL+SLM YTPTIPDELVEHYLAKSGFQCPDVRL    
Sbjct: 1   MNQN---PQSSDGRNDDDSALSDFLASLMDYTPTIPDELVEHYLAKSGFQCPDVRLT--- 54

Query: 61  CFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALR 120
                RLVAVATQKFVAEVA DALQ CKARQA + KDKRDKQQKDKRL+LTMEDLSKALR
Sbjct: 55  -----RLVAVATQKFVAEVAGDALQHCKARQATIPKDKRDKQQKDKRLVLTMEDLSKALR 109

Query: 121 EYGVNVKHQEYFADNPSTGMDPASKEE 147
           EYGVN++HQEYFAD+PSTGMDPA++EE
Sbjct: 110 EYGVNLRHQEYFADSPSTGMDPATREE 136

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224142025|ref|XP_002324360.1| predicted protein [Populus trichocarpa] gi|222865794|gb|EEF02925.1| predicted protein [Populus trichocarpa]

 Score =  234 bits (597), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 115/136 (84%), Positives = 122/136 (89%), Gaps = 8/136 (5%)

Query: 12  DGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVA 71
           + RHDDDA LTEFL+SLM YTPTIPDELVEHYLAKSGFQCPDVRL        +RLVAVA
Sbjct: 17  EARHDDDAVLTEFLASLMDYTPTIPDELVEHYLAKSGFQCPDVRL--------VRLVAVA 68

Query: 72  TQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREYGVNVKHQEY 131
           TQKFVA+VATDALQQCKAR A VVKDKRDKQQK+KRLILTMEDLSKAL EYGVNVKHQEY
Sbjct: 69  TQKFVADVATDALQQCKARPAPVVKDKRDKQQKEKRLILTMEDLSKALSEYGVNVKHQEY 128

Query: 132 FADNPSTGMDPASKEE 147
           FAD+PSTGMDPAS+EE
Sbjct: 129 FADSPSTGMDPASREE 144

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351727012|ref|NP_001236890.1| uncharacterized protein LOC100500618 [Glycine max] gi|255630766|gb|ACU15744.1| unknown [Glycine max]

 Score =  233 bits (594), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 113/139 (81%), Positives = 125/139 (89%), Gaps = 8/139 (5%)

Query: 9   QSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLV 68
           QSS+GR+DDD+AL++FL+SLM YTPTIPDELVEHYLAKSGFQCPDVRL         RLV
Sbjct: 6   QSSEGRNDDDSALSDFLASLMDYTPTIPDELVEHYLAKSGFQCPDVRLT--------RLV 57

Query: 69  AVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREYGVNVKH 128
           AVATQKFVAEVA DALQ CKARQA + KDKRDKQQKDKRL+LTMEDLSKALREYGVN+KH
Sbjct: 58  AVATQKFVAEVAGDALQHCKARQATIPKDKRDKQQKDKRLVLTMEDLSKALREYGVNLKH 117

Query: 129 QEYFADNPSTGMDPASKEE 147
           QEYFAD+PSTGMDPA++EE
Sbjct: 118 QEYFADSPSTGMDPATREE 136

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  233 bits (594), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 115/147 (78%), Positives = 128/147 (87%), Gaps = 11/147 (7%)

Query: 1   MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCL 60
           MN N    QSSDGR+DDD+AL++FL+SLM YTPTIPDELVEHYLAKSGF+CPDVRL    
Sbjct: 1   MNQN---PQSSDGRNDDDSALSDFLASLMDYTPTIPDELVEHYLAKSGFRCPDVRLT--- 54

Query: 61  CFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALR 120
                RLVAVATQKFVAEVA DALQ CKARQA + KDKRDKQQKDKRL+LTMEDLSKALR
Sbjct: 55  -----RLVAVATQKFVAEVAGDALQHCKARQATIPKDKRDKQQKDKRLVLTMEDLSKALR 109

Query: 121 EYGVNVKHQEYFADNPSTGMDPASKEE 147
           EYGVN++HQEYFAD+PSTGMDPA++EE
Sbjct: 110 EYGVNLRHQEYFADSPSTGMDPATREE 136

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388512029|gb|AFK44076.1| unknown [Medicago truncatula]

 Score =  230 bits (587), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 111/147 (75%), Positives = 126/147 (85%), Gaps = 8/147 (5%)

Query: 1   MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCL 60
           MN N     SS+GR DDD+AL++FL+SL+ YTPTIPDELVEHYLAKSGFQCPDVRL    
Sbjct: 1   MNQNQPQSSSSEGRADDDSALSDFLASLVDYTPTIPDELVEHYLAKSGFQCPDVRLT--- 57

Query: 61  CFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALR 120
                RLVAVATQKFVAEVA DALQ CKARQA V KDKRD+QQKD+RL+LTMEDLSKALR
Sbjct: 58  -----RLVAVATQKFVAEVAGDALQHCKARQATVPKDKRDRQQKDRRLVLTMEDLSKALR 112

Query: 121 EYGVNVKHQEYFADNPSTGMDPASKEE 147
           EYGVN++HQEYFAD+PSTGMDPA+++E
Sbjct: 113 EYGVNIRHQEYFADSPSTGMDPATRDE 139

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

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 =  230 bits (586), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 110/147 (74%), Positives = 126/147 (85%), Gaps = 8/147 (5%)

Query: 1   MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCL 60
           MN N     SS+GR DDD+AL++FL+SL+ YTPTIPDELVEHYLAKSGFQCPDVRL    
Sbjct: 1   MNQNQPQSSSSEGRADDDSALSDFLASLVDYTPTIPDELVEHYLAKSGFQCPDVRLT--- 57

Query: 61  CFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALR 120
                RLVAVATQKFVAEVA DALQ CKARQA + KDKRD+QQKD+RL+LTMEDLSKALR
Sbjct: 58  -----RLVAVATQKFVAEVAGDALQHCKARQATIPKDKRDRQQKDRRLVLTMEDLSKALR 112

Query: 121 EYGVNVKHQEYFADNPSTGMDPASKEE 147
           EYGVN++HQEYFAD+PSTGMDPA+++E
Sbjct: 113 EYGVNIRHQEYFADSPSTGMDPATRDE 139

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	147
TAIR|locus:2124884	134	TAFII15 "AT4G31720" [Arabidops	0.911	1.0	0.707	4.2e-47
UNIPROTKB|A5PJW1	218	TAF10 "TAF10 protein" [Bos tau	0.693	0.467	0.428	3.6e-18
UNIPROTKB|E2R5H1	218	TAF10 "Uncharacterized protein	0.693	0.467	0.428	3.6e-18
UNIPROTKB|Q12962	218	TAF10 "Transcription initiatio	0.693	0.467	0.428	3.6e-18
UNIPROTKB|I3LE15	218	TAF10 "Uncharacterized protein	0.693	0.467	0.428	3.6e-18
MGI|MGI:1346320	218	Taf10 "TAF10 RNA polymerase II	0.693	0.467	0.428	3.6e-18
RGD|1305907	218	Taf10 "TAF10 RNA polymerase II	0.693	0.467	0.428	3.6e-18
ZFIN|ZDB-GENE-060526-334	181	taf10 "TAF10 RNA polymerase II	0.693	0.563	0.428	3.6e-18
CGD|CAL0003312	244	orf19.3242 [Candida albicans (	0.476	0.286	0.379	5.2e-16
FB|FBgn0026324	146	Taf10b "TBP-associated factor	0.700	0.705	0.383	2e-15

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

 Score = 493 (178.6 bits), Expect = 4.2e-47, P = 4.2e-47
 Identities = 104/147 (70%), Positives = 116/147 (78%)

Query:     1 MNHNNNFQQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCL 60
             MNH    QQS + +H+DDAALTEFL+SLM YTPTIPD+LVEHYLAKSGFQCPDVRL    
Sbjct:     1 MNHG---QQSGEAKHEDDAALTEFLASLMDYTPTIPDDLVEHYLAKSGFQCPDVRL---- 53

Query:    61 CFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVXXXXXXXXXXXXLILTMEDLSKALR 120
                 IRLVAVATQKFVA+VA+DALQ CKAR A VV            L+LTMEDLSKALR
Sbjct:    54 ----IRLVAVATQKFVADVASDALQHCKARPAPVVKDKKQQKDKR--LVLTMEDLSKALR 107

Query:   121 EYGVNVKHQEYFADNPSTGMDPASKEE 147
             EYGVNVKH EYFAD+PSTGMDPA+++E
Sbjct:   108 EYGVNVKHPEYFADSPSTGMDPATRDE 134

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

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

 Score = 220 (82.5 bits), Expect = 3.6e-18, P = 3.6e-18
 Identities = 48/112 (42%), Positives = 65/112 (58%)

Query:    21 LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVA 80
             L +FL  L  YTPTIPD +  +YL ++GF+  D R+        IRL+++A QKF++++A
Sbjct:   116 LVDFLMQLEDYTPTIPDAVTGYYLNRAGFEASDPRI--------IRLISLAAQKFISDIA 167

Query:    81 TDALQQCKARQAAVVXXXXXXXXXXXXLILTMEDLSKALREYGVNVKHQEYF 132
              DALQ CK +  A                LTMEDL+ AL EYG+NVK   YF
Sbjct:   168 NDALQHCKMKGTA--SGSSRSKSKDRKYTLTMEDLTPALSEYGINVKKPHYF 217

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 = 220 (82.5 bits), Expect = 3.6e-18, P = 3.6e-18
 Identities = 48/112 (42%), Positives = 65/112 (58%)

Query:    21 LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVA 80
             L +FL  L  YTPTIPD +  +YL ++GF+  D R+        IRL+++A QKF++++A
Sbjct:   116 LVDFLMQLEDYTPTIPDAVTGYYLNRAGFEASDPRI--------IRLISLAAQKFISDIA 167

Query:    81 TDALQQCKARQAAVVXXXXXXXXXXXXLILTMEDLSKALREYGVNVKHQEYF 132
              DALQ CK +  A                LTMEDL+ AL EYG+NVK   YF
Sbjct:   168 NDALQHCKMKGTA--SGSSRSKSKDRKYTLTMEDLTPALSEYGINVKKPHYF 217

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 = 220 (82.5 bits), Expect = 3.6e-18, P = 3.6e-18
 Identities = 48/112 (42%), Positives = 65/112 (58%)

Query:    21 LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVA 80
             L +FL  L  YTPTIPD +  +YL ++GF+  D R+        IRL+++A QKF++++A
Sbjct:   116 LVDFLMQLEDYTPTIPDAVTGYYLNRAGFEASDPRI--------IRLISLAAQKFISDIA 167

Query:    81 TDALQQCKARQAAVVXXXXXXXXXXXXLILTMEDLSKALREYGVNVKHQEYF 132
              DALQ CK +  A                LTMEDL+ AL EYG+NVK   YF
Sbjct:   168 NDALQHCKMKGTA--SGSSRSKSKDRKYTLTMEDLTPALSEYGINVKKPHYF 217

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 = 220 (82.5 bits), Expect = 3.6e-18, P = 3.6e-18
 Identities = 48/112 (42%), Positives = 65/112 (58%)

Query:    21 LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVA 80
             L +FL  L  YTPTIPD +  +YL ++GF+  D R+        IRL+++A QKF++++A
Sbjct:   116 LVDFLMQLEDYTPTIPDAVTGYYLNRAGFEASDPRI--------IRLISLAAQKFISDIA 167

Query:    81 TDALQQCKARQAAVVXXXXXXXXXXXXLILTMEDLSKALREYGVNVKHQEYF 132
              DALQ CK +  A                LTMEDL+ AL EYG+NVK   YF
Sbjct:   168 NDALQHCKMKGTA--SGSSRSKSKDRKYTLTMEDLTPALSEYGINVKKPHYF 217

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 = 220 (82.5 bits), Expect = 3.6e-18, P = 3.6e-18
 Identities = 48/112 (42%), Positives = 65/112 (58%)

Query:    21 LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVA 80
             L +FL  L  YTPTIPD +  +YL ++GF+  D R+        IRL+++A QKF++++A
Sbjct:   116 LVDFLMQLEDYTPTIPDAVTGYYLNRAGFEASDPRI--------IRLISLAAQKFISDIA 167

Query:    81 TDALQQCKARQAAVVXXXXXXXXXXXXLILTMEDLSKALREYGVNVKHQEYF 132
              DALQ CK +  A                LTMEDL+ AL EYG+NVK   YF
Sbjct:   168 NDALQHCKMKGTA--SGSSRSKSKDRKYTLTMEDLTPALSEYGINVKKPHYF 217

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 = 220 (82.5 bits), Expect = 3.6e-18, P = 3.6e-18
 Identities = 48/112 (42%), Positives = 65/112 (58%)

Query:    21 LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVA 80
             L +FL  L  YTPTIPD +  +YL ++GF+  D R+        IRL+++A QKF++++A
Sbjct:   116 LVDFLMQLEDYTPTIPDAVTGYYLNRAGFEASDPRI--------IRLISLAAQKFISDIA 167

Query:    81 TDALQQCKARQAAVVXXXXXXXXXXXXLILTMEDLSKALREYGVNVKHQEYF 132
              DALQ CK +  A                LTMEDL+ AL EYG+NVK   YF
Sbjct:   168 NDALQHCKMKGTA--SGSSRSKSKDRKYTLTMEDLTPALSEYGINVKKPHYF 217

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

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

 Score = 220 (82.5 bits), Expect = 3.6e-18, P = 3.6e-18
 Identities = 48/112 (42%), Positives = 66/112 (58%)

Query:    21 LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVA 80
             L +FL  L  YTPTIPD +  +YL ++GF+  D R+        IRL+++A+QKF++++A
Sbjct:    79 LADFLMQLEDYTPTIPDAVTGYYLNRAGFEASDPRI--------IRLISLASQKFISDIA 130

Query:    81 TDALQQCKARQAAVVXXXXXXXXXXXXLILTMEDLSKALREYGVNVKHQEYF 132
              DALQ CK +  A                LTMEDL+ AL EYG+NVK   YF
Sbjct:   131 NDALQHCKMKGTA--SGSSRNKAKDKKYTLTMEDLTPALAEYGINVKKPHYF 180

GO:0005634 "nucleus" evidence=IEA

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

CGD|CAL0003312 orf19.3242 [Candida albicans (taxid:5476)]

 Score = 140 (54.3 bits), Expect = 5.2e-16, Sum P(2) = 5.2e-16
 Identities = 30/79 (37%), Positives = 50/79 (63%)

Query:    18 DAALTEFLSSLMG-YTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFV 76
             D +L E L  + G + P IPD + ++YLAK+GF+  D+++         RL+A+ATQKF+
Sbjct:    95 DKSLKEVLDLMDGDFAPIIPDAVTDYYLAKNGFETSDIKIK--------RLLALATQKFI 146

Query:    77 AEVATDALQQCKARQAAVV 95
             +++A DA +  + R A+ V
Sbjct:   147 SDIAQDAYEYSRIRSASAV 165

GO:0000124 "SAGA complex" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0046695 "SLIK (SAGA-like) complex" evidence=IEA

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

GO:0016573 "histone acetylation" evidence=IEA

GO:0051123 "RNA polymerase II transcriptional preinitiation complex assembly" evidence=IEA

GO:0032947 "protein complex scaffold" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

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

 Score = 194 (73.4 bits), Expect = 2.0e-15, P = 2.0e-15
 Identities = 43/112 (38%), Positives = 61/112 (54%)

Query:    21 LTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVA 80
             L++F+S L  YTP IPD +  HYL   GFQ  D R+        +RL+++A QK+++++ 
Sbjct:    41 LSDFMSQLEDYTPLIPDAVTSHYLNMGGFQSDDKRI--------VRLISLAAQKYMSDII 92

Query:    81 TDALQQCKAR-QAAVVXXXXXXXXXXXXLILTMEDLSKALREYGVNVKHQEY 131
              DALQ  KAR                    LTMEDL  AL +YG+NV+  +Y
Sbjct:    93 DDALQHSKARTHMQTTNTPGGSKAKDRKFTLTMEDLQPALADYGINVRKVDY 144

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	147
cd07982	108	cd07982, TAF10, The TATA Binding Protein (TBP) Ass	2e-53
pfam03540	51	pfam03540, TFIID_30kDa, Transcription initiation f	2e-21
COG5162	197	COG5162, COG5162, Transcription initiation factor	5e-21

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

 Score =  163 bits (415), Expect = 2e-53
 Identities = 60/116 (51%), Positives = 78/116 (67%), Gaps = 10/116 (8%)

Query: 19  AALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAE 78
           A+L EFLS L  YTPTIPDE+ ++YL K+GF C D R+         RLV++A QKFV++
Sbjct: 1   ASLAEFLSQLDDYTPTIPDEVTDYYLKKAGFDCSDPRV--------KRLVSLAAQKFVSD 52

Query: 79  VATDALQQCKARQAAVVKDKR--DKQQKDKRLILTMEDLSKALREYGVNVKHQEYF 132
           +A DA+Q CK R +A  K+     K  KDKR +LTMEDLS AL EYG+N+K   Y+
Sbjct: 53  IANDAMQYCKMRGSAQTKNLSEDKKGPKDKRYVLTMEDLSAALAEYGINIKRPPYY 108

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 = 80.8 bits (200), Expect = 2e-21
 Identities = 28/59 (47%), Positives = 38/59 (64%), Gaps = 8/59 (13%)

Query: 33 PTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQ 91
          PTIPD + ++YL K+GFQ  D R+         RLV++A QKFV+++ATDA Q  K R 
Sbjct: 1  PTIPDAVTDYYLKKAGFQTSDPRV--------KRLVSLAAQKFVSDIATDAYQHAKIRT 51

Length = 51

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

 Score = 83.9 bits (207), Expect = 5e-21
 Identities = 44/135 (32%), Positives = 68/135 (50%), Gaps = 30/135 (22%)

Query: 18  DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVA 77
           D  L E L ++  YTP IPD + ++YL K+GF   D R+         +L+++  QKFV+
Sbjct: 72  DKTLEELLQNMDSYTPLIPDSVTDYYLEKAGFVTSDQRVK--------KLLSLLAQKFVS 123

Query: 78  EVATDALQQCKARQAAVVKDKRDKQQKDKRL--------------------ILTMEDLSK 117
           ++A DA Q  + RQ     + +   QK KR                     +LT+ DLSK
Sbjct: 124 DIAVDAYQYSRIRQG--SSNAKATAQKAKRFAKGGASGIGSSGRRGDRKKPVLTVVDLSK 181

Query: 118 ALREYGVNVKHQEYF 132
           AL EYG+N+   +++
Sbjct: 182 ALEEYGINISRPDFY 196

Length = 197

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	147
KOG3423	176	consensus Transcription initiation factor TFIID, s	100.0
COG5162	197	Transcription initiation factor TFIID, subunit TAF	100.0
PF03540	51	TFIID_30kDa: Transcription initiation factor TFIID	99.97
PF07524	77	Bromo_TP: Bromodomain associated; InterPro: IPR006	97.83
smart00576	77	BTP Bromodomain transcription factors and PHD doma	97.82
PF00808	65	CBFD_NFYB_HMF: Histone-like transcription factor (	96.68
smart00803	65	TAF TATA box binding protein associated factor. TA	96.68
PF02969	66	TAF: TATA box binding protein associated factor (T	96.49
cd07979	117	TAF9 TATA Binding Protein (TBP) Associated Factor	96.2
PLN00035	103	histone H4; Provisional	95.83
cd00076	85	H4 Histone H4, one of the four histones, along wit	95.66
COG2036	91	HHT1 Histones H3 and H4 [Chromatin structure and d	95.54
cd08050	343	TAF6 TATA Binding Protein (TBP) Associated Factor	95.5
PTZ00015	102	histone H4; Provisional	95.31
PF03847	68	TFIID_20kDa: Transcription initiation factor TFIID	94.82
PF02291	129	TFIID-31kDa: Transcription initiation factor IID,	94.47
cd07981	72	TAF12 TATA Binding Protein (TBP) Associated Factor	93.04
KOG1142	258	consensus Transcription initiation factor TFIID, s	91.44
PF05236	264	TAF4: Transcription initiation factor TFIID compon	91.35
cd08045	212	TAF4 TATA Binding Protein (TBP) Associated Factor	89.65
KOG3334	148	consensus Transcription initiation factor TFIID, s	85.13
KOG4336	323	consensus TBP-associated transcription factor Prod	80.19

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

Probab=100.00  E-value=3.9e-54  Score=344.48  Aligned_cols=116  Identities=54%  Similarity=0.825  Sum_probs=108.0

Q ss_pred             CCCCCCCCCCchHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHH
Q 032126            8 QQSSDGRHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQC   87 (147)
Q Consensus         8 ~~~~~~~~~~d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~   87 (147)
                      +.+....+.+|..|.|||.+|+||+|+|||+||+|||+++||+|+||||        +|||||||||||||||+||||||
T Consensus        60 ~~~~~~~~~~d~~l~efl~qLddYtP~IPDavt~~yL~~aGf~~~D~rv--------~RLvsLaAQKfvSDIa~DA~Q~~  131 (176)
T KOG3423|consen   60 ANGELNPTTKDTHLEEFLAQLDDYTPTIPDAVTDHYLKKAGFQTSDPRV--------KRLVSLAAQKFVSDIANDALQHS  131 (176)
T ss_pred             ccCCcCCCCcchHHHHHHHHHhcCCCCCcHHHHHHHHHhcCCCcCcHHH--------HHHHHHHHHHHHHHHHHHHHHHh
Confidence            4556667789999999999999999999999999999999999999999        99999999999999999999999


Q ss_pred             HHhhh-hhhhchhcccccccceeeeHHHHHHHHHHhCcccCCCCccc
Q 032126           88 KARQA-AVVKDKRDKQQKDKRLILTMEDLSKALREYGVNVKHQEYFA  133 (147)
Q Consensus        88 kiR~~-~~~~~k~~~~~kd~r~vLTmEDLs~AL~EyGInvkrP~Yy~  133 (147)
                      |||++ +.+++|  +++||+|+|||||||++||+||||||+||+||+
T Consensus       132 k~r~~~~~~~~k--~~~kdkK~tLtmeDL~~AL~EyGinv~rP~y~~  176 (176)
T KOG3423|consen  132 KIRTKTAIGKDK--KQAKDKKYTLTMEDLSPALAEYGINVKRPDYFT  176 (176)
T ss_pred             hhcccccccccc--ccccccceeeeHHHHHHHHHHhCcccCCCCCCC
Confidence            99995 455554  678999999999999999999999999999995

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

Probab=100.00  E-value=4.5e-43  Score=282.48  Aligned_cols=110  Identities=39%  Similarity=0.687  Sum_probs=98.4

Q ss_pred             CCchHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 032126           16 DDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVV   95 (147)
Q Consensus        16 ~~d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~   95 (147)
                      .+|++|+|||++||+|+|+|||+||+|||.++||.|+|+||        +||+||+|||||||||.|||||+|||+..+.
T Consensus        70 ~Kdktlee~l~~mDsy~PliPd~v~DYyl~k~Gf~~~D~rv--------KkLl~L~aqKFvsDiA~dayqYsrIr~~~sn  141 (197)
T COG5162          70 MKDKTLEELLQNMDSYTPLIPDSVTDYYLEKAGFVTSDQRV--------KKLLSLLAQKFVSDIAVDAYQYSRIRQGSSN  141 (197)
T ss_pred             hhHHHHHHHHHhcccCCCCccHHHHHHHHHhcCceeccHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence            68999999999999999999999999999999999999999        9999999999999999999999999994332


Q ss_pred             hc------hh------------cccccccceeeeHHHHHHHHHHhCcccCCCCccc
Q 032126           96 KD------KR------------DKQQKDKRLILTMEDLSKALREYGVNVKHQEYFA  133 (147)
Q Consensus        96 ~~------k~------------~~~~kd~r~vLTmEDLs~AL~EyGInvkrP~Yy~  133 (147)
                      ..      ++            +++...+|.|||+.||++||.||||||+||+||+
T Consensus       142 a~~t~~~a~~f~~gg~~~i~~~~~~~dr~K~vltv~DLs~Al~EyGini~RPdfyr  197 (197)
T COG5162         142 AKATAQKAKRFAKGGASGIGSSGRRGDRKKPVLTVVDLSKALEEYGINISRPDFYR  197 (197)
T ss_pred             chhhHHHHHHHHhcccccccccccccccCCceeeehHHHHHHHHhccccCCccccC
Confidence            21      10            1123448999999999999999999999999995

>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=99.97  E-value=5.5e-31  Score=175.65  Aligned_cols=51  Identities=55%  Similarity=0.952  Sum_probs=50.2

Q ss_pred             CCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 032126           33 PTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQ   91 (147)
Q Consensus        33 P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~   91 (147)
                      |+|||+||+|||+++||+|+|+||        +|||||||||||+||++|||||||+|+
T Consensus         1 P~IPD~v~~~yL~~~G~~~~D~rv--------~RLvSLaaQKFisdI~~dA~q~~k~r~   51 (51)
T PF03540_consen    1 PTIPDEVTDYYLERSGFQTSDPRV--------KRLVSLAAQKFISDIANDAMQYCKIRT   51 (51)
T ss_pred             CCCCHHHHHHHHHHCCCCCCCHhH--------HHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            999999999999999999999999        999999999999999999999999995

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

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

Probab=97.83  E-value=0.0001  Score=50.76  Aligned_cols=67  Identities=21%  Similarity=0.361  Sum_probs=58.2

Q ss_pred             HHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHH
Q 032126           38 ELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSK  117 (147)
Q Consensus        38 ~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~  117 (147)
                      .++...|+.+||++..+-.        .-.++-.+++||..|+..+.+|+..               .+|..-+..|+..
T Consensus        10 ~~va~il~~~GF~~~~~~a--------l~~Ltdi~~~yl~~l~~~~~~~ae~---------------~gRt~~~~~Dv~~   66 (77)
T PF07524_consen   10 RSVAQILKHAGFDSASPSA--------LDTLTDILQRYLQELGRTAKRYAEH---------------AGRTEPNLQDVEQ   66 (77)
T ss_pred             HHHHHHHHHcCccccCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------cCCCCCCHHHHHH
Confidence            3677899999999999999        9999999999999999999999842               1245567999999


Q ss_pred             HHHHhCcccC
Q 032126          118 ALREYGVNVK  127 (147)
Q Consensus       118 AL~EyGInvk  127 (147)
                      ||.|.||+|.
T Consensus        67 al~~~gi~v~   76 (77)
T PF07524_consen   67 ALEEMGISVN   76 (77)
T ss_pred             HHHHhCCCCC
Confidence            9999999985

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 [, ].

>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins

Probab=97.82  E-value=9.7e-05  Score=51.37  Aligned_cols=67  Identities=19%  Similarity=0.261  Sum_probs=58.3

Q ss_pred             HHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHH
Q 032126           38 ELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSK  117 (147)
Q Consensus        38 ~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~  117 (147)
                      -++..+|+.+||+...|..        .-.+.=..++|+..|+..+.+|+..-               +|...+.+|+..
T Consensus        10 ~~Vaqil~~~Gf~~~~~sa--------le~ltdi~~~yl~~l~~~~~~~a~~a---------------gR~~~~~~Dv~~   66 (77)
T smart00576       10 IAVAQILESAGFDSFQESA--------LETLTDILQSYIQELGRTAHSYAELA---------------GRTEPNLGDVVL   66 (77)
T ss_pred             HHHHHHHHHcCccccCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHc---------------CCCCCCHHHHHH
Confidence            4678899999999999999        99999999999999999999998531               134567999999


Q ss_pred             HHHHhCcccC
Q 032126          118 ALREYGVNVK  127 (147)
Q Consensus       118 AL~EyGInvk  127 (147)
                      ||.+.||++.
T Consensus        67 Al~~~gi~~~   76 (77)
T smart00576       67 ALENLGISVG   76 (77)
T ss_pred             HHHHhCcccC
Confidence            9999999874

subdomain of archael histone-like transcription factors

>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=96.68  E-value=0.014  Score=38.76  Aligned_cols=64  Identities=25%  Similarity=0.356  Sum_probs=44.8

Q ss_pred             CCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHH
Q 032126           34 TIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTME  113 (147)
Q Consensus        34 ~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmE  113 (147)
                      .+|-+-+.-+++..   ..+.+|    ..-=.-+|+.|++.||..++.+|.+.|+-               ++|-+++-+
T Consensus         2 ~lP~a~vkri~k~~---~~~~~v----s~ea~~~i~~a~e~Fi~~l~~~A~~~a~~---------------~~rkti~~~   59 (65)
T PF00808_consen    2 SLPLARVKRIMKSD---PDVMRV----SKEAVEAIAKAAEEFIQYLAKEANEIAQR---------------DKRKTITYE   59 (65)
T ss_dssp             SS-HHHHHHHHHHT---STTSEE-----HHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------TTSSEE-HH
T ss_pred             CCChHHHHHHhccC---CCccch----hHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------cCCCccCHH
Confidence            36778888888876   223333    11114589999999999999999998851               222389999


Q ss_pred             HHHHHH
Q 032126          114 DLSKAL  119 (147)
Q Consensus       114 DLs~AL  119 (147)
                      |+..||
T Consensus        60 Dv~~Av   65 (65)
T PF00808_consen   60 DVAKAV   65 (65)
T ss_dssp             HHHHHH
T ss_pred             HHHHHC
Confidence            999986

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 ....

>smart00803 TAF TATA box binding protein associated factor

Probab=96.68  E-value=0.01  Score=40.79  Aligned_cols=64  Identities=25%  Similarity=0.335  Sum_probs=53.3

Q ss_pred             CCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHH
Q 032126           34 TIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTME  113 (147)
Q Consensus        34 ~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmE  113 (147)
                      .||-+-+.-+.++.|++--..-+        ...++=....|+.+|+.+|..|.+.               -+|-+||.+
T Consensus         2 ~~p~~~i~ria~~~Gi~ris~~a--------~~~l~~~~e~rl~~i~~~A~k~~~h---------------akRktlt~~   58 (65)
T smart00803        2 WLPKETIKDVAESLGIGNLSDEA--------AKLLAEDVEYRIKEIVQEALKFMRH---------------SKRTTLTTS   58 (65)
T ss_pred             CCCHHHHHHHHHHCCCccccHHH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------hCCCeecHH
Confidence            47888899999999999644448        8899999999999999999999742               134579999


Q ss_pred             HHHHHHH
Q 032126          114 DLSKALR  120 (147)
Q Consensus       114 DLs~AL~  120 (147)
                      |+..||+
T Consensus        59 DI~~Alk   65 (65)
T smart00803       59 DIDSALR   65 (65)
T ss_pred             HHHHHhC
Confidence            9999984

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.

>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex

Probab=96.49  E-value=0.012  Score=41.05  Aligned_cols=65  Identities=23%  Similarity=0.280  Sum_probs=47.3

Q ss_pred             CCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeH
Q 032126           33 PTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTM  112 (147)
Q Consensus        33 P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTm  112 (147)
                      +.+|-+-+.-+-+..|+..-+.-+        .+++|--++--|.+|+++|.+|.+.               -+|..||.
T Consensus         2 s~~~~esvk~iAes~Gi~~l~de~--------a~~La~dveyrlreiiq~a~kfm~h---------------skR~~Lt~   58 (66)
T PF02969_consen    2 SVFSQESVKDIAESLGISNLSDEA--------AKALAEDVEYRLREIIQEALKFMRH---------------SKRTKLTT   58 (66)
T ss_dssp             ----HHHHHHHHHHTT---B-HHH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------TT-SSB-H
T ss_pred             CcCCHHHHHHHHHHcCCCCCCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------hCCCCCCH
Confidence            467889999999999998777778        8899999999999999999999642               13567999


Q ss_pred             HHHHHHHH
Q 032126          113 EDLSKALR  120 (147)
Q Consensus       113 EDLs~AL~  120 (147)
                      +|+..||+
T Consensus        59 ~Di~~ALr   66 (66)
T PF02969_consen   59 DDINSALR   66 (66)
T ss_dssp             HHHHHHH-
T ss_pred             HHHHHHhC
Confidence            99999995

TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.

>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=96.20  E-value=0.022  Score=43.03  Aligned_cols=64  Identities=14%  Similarity=0.178  Sum_probs=55.9

Q ss_pred             HHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHH
Q 032126           38 ELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSK  117 (147)
Q Consensus        38 ~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~  117 (147)
                      .++.-+|+..|.+.-++++        +..+.=-+.+++.+|+.||..|++.-               +|-+++.||+..
T Consensus         5 ~~v~~iLk~~Gv~~~~~~v--------~~~Lle~~~ry~~~il~dA~~~a~hA---------------~r~tV~~eDV~l   61 (117)
T cd07979           5 RVIAAILKSMGITEYEPRV--------INQLLEFAYRYTTDVLDDAKVYSEHA---------------GKANIDADDVKL   61 (117)
T ss_pred             HHHHHHHHHCCCCccCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHc---------------CCCCCCHHHHHH
Confidence            4788899999999999999        88888888999999999999998642               236899999999


Q ss_pred             HHHHhCc
Q 032126          118 ALREYGV  124 (147)
Q Consensus       118 AL~EyGI  124 (147)
                      |++.++-
T Consensus        62 Ai~~r~~   68 (117)
T cd07979          62 AIQSRVD   68 (117)
T ss_pred             HHHHHhc
Confidence            9999986

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

>PLN00035 histone H4; Provisional

Probab=95.83  E-value=0.042  Score=41.48  Aligned_cols=75  Identities=17%  Similarity=0.184  Sum_probs=57.9

Q ss_pred             cCCCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccc
Q 032126           28 LMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKR  107 (147)
Q Consensus        28 LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r  107 (147)
                      |-|...-||-.-+.-++.++|..---.-+        .--+.=+...|+.+|+.||..|++-.               +|
T Consensus        23 ~~d~i~~ipk~~IrRLARr~GvkRIS~~a--------y~elr~vle~~l~~I~~dav~ya~HA---------------~R   79 (103)
T PLN00035         23 LRDNIQGITKPAIRRLARRGGVKRISGLI--------YEETRGVLKIFLENVIRDAVTYTEHA---------------RR   79 (103)
T ss_pred             HHhhhccCCHHHHHHHHHHcCcccchHHH--------HHHHHHHHHHHHHHHHHHHHHHHHhc---------------CC
Confidence            34666669999999999999976422224        44555677899999999999998631               23


Q ss_pred             eeeeHHHHHHHHHHhCcc
Q 032126          108 LILTMEDLSKALREYGVN  125 (147)
Q Consensus       108 ~vLTmEDLs~AL~EyGIn  125 (147)
                      -|+|.+|+..||+..|-+
T Consensus        80 KTV~~~DV~~Alkr~g~~   97 (103)
T PLN00035         80 KTVTAMDVVYALKRQGRT   97 (103)
T ss_pred             CcCcHHHHHHHHHHcCCc
Confidence            478999999999999863

>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution

Probab=95.66  E-value=0.06  Score=39.16  Aligned_cols=74  Identities=19%  Similarity=0.212  Sum_probs=55.4

Q ss_pred             cCCCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccc
Q 032126           28 LMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKR  107 (147)
Q Consensus        28 LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r  107 (147)
                      |-|+..-||-.-+.-...++|..-=---+        .--+.=+...|+.+|+.||..|++-.               +|
T Consensus         7 ~~~~~~gi~k~~I~RLarr~GvkRIS~d~--------y~e~~~~l~~~l~~I~~dav~ya~Ha---------------~R   63 (85)
T cd00076           7 LRDNIKGITKPAIRRLARRGGVKRISGGV--------YDEVRNVLKSYLEDVIRDAVTYTEHA---------------KR   63 (85)
T ss_pred             HHHhhccCCHHHHHHHHHHcCcchhhHHH--------HHHHHHHHHHHHHHHHHHHHHHHHhc---------------CC
Confidence            44666779999999999999965311113        33344456899999999999998621               23


Q ss_pred             eeeeHHHHHHHHHHhCc
Q 032126          108 LILTMEDLSKALREYGV  124 (147)
Q Consensus       108 ~vLTmEDLs~AL~EyGI  124 (147)
                      -++|.+|+..||+..|-
T Consensus        64 KTVt~~DV~~alkr~g~   80 (85)
T cd00076          64 KTVTAMDVVYALKRQGR   80 (85)
T ss_pred             CcCcHHHHHHHHHHCCC
Confidence            46899999999999994

>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]

Probab=95.54  E-value=0.065  Score=39.57  Aligned_cols=84  Identities=25%  Similarity=0.362  Sum_probs=64.8

Q ss_pred             HHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchh
Q 032126           20 ALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKR   99 (147)
Q Consensus        20 ~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~   99 (147)
                      -+.|+-.-+......||-.-++-++.++|-+    ||    ..-=+-.+.=+.+-|+.+|+.+|..+|+           
T Consensus         5 ~~~~~r~~~~~~~~~Lp~apv~Ri~r~~~~~----Rv----s~~A~~~l~~~~e~~~~~i~~~A~~~A~-----------   65 (91)
T COG2036           5 GLKEIRRYQRSTDLLLPKAPVRRILRKAGAE----RV----SSSAIEELQEALEEYLEEIAEDAVELAE-----------   65 (91)
T ss_pred             hHHHHHhhhhhhhhhcCchHHHHHHHHHhHH----Hh----hHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------
Confidence            3566666777788999999999999999987    76    0000223444667899999999999985           


Q ss_pred             cccccccceeeeHHHHHHHHHHhCccc
Q 032126          100 DKQQKDKRLILTMEDLSKALREYGVNV  126 (147)
Q Consensus       100 ~~~~kd~r~vLTmEDLs~AL~EyGInv  126 (147)
                          ..+|-|.+-+|+..|+++.|..+
T Consensus        66 ----ha~RKTV~~~DI~la~~~~~~~~   88 (91)
T COG2036          66 ----HAKRKTVKAEDIKLALKRLGRRI   88 (91)
T ss_pred             ----HcCCCeecHHHHHHHHHHhcccc
Confidence                33466999999999999999765

>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=95.50  E-value=0.054  Score=46.96  Aligned_cols=67  Identities=24%  Similarity=0.290  Sum_probs=56.5

Q ss_pred             cHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHH
Q 032126           36 PDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDL  115 (147)
Q Consensus        36 PD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDL  115 (147)
                      |.+.+.-+++.+|.+.-+...        .+.++--.+.++..|+++|..+++.               -+|.+||.||+
T Consensus         1 ~~~~i~~ia~~~Gi~~~~~~a--------~~~La~~~e~~~~~i~~~A~k~~~h---------------skR~~l~~~Di   57 (343)
T cd08050           1 PQESIKLIAESLGIDSLSDEV--------AQLLAEDVEYRLREIIQEAAKFMRH---------------SKRRKLTTSDV   57 (343)
T ss_pred             ChhHHHHHHHHcCCCcCCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------hCCCcCCHHHH
Confidence            456677889999999888888        8999999999999999999999642               12468999999


Q ss_pred             HHHHHHhCcc
Q 032126          116 SKALREYGVN  125 (147)
Q Consensus       116 s~AL~EyGIn  125 (147)
                      ..||+..++.
T Consensus        58 ~~Al~~~n~e   67 (343)
T cd08050          58 NHALRLRNVE   67 (343)
T ss_pred             HHHHHHhCCC
Confidence            9999986554

The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of 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 functions such as serving as

>PTZ00015 histone H4; Provisional

Probab=95.31  E-value=0.11  Score=39.10  Aligned_cols=74  Identities=16%  Similarity=0.173  Sum_probs=59.5

Q ss_pred             CCCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccce
Q 032126           29 MGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRL  108 (147)
Q Consensus        29 ddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~  108 (147)
                      -|..+-||-.-+.-++.++|..---.-+        .--+.-+...|+.+|+.||..|++-.               +|-
T Consensus        25 r~~i~gI~k~~IrRLarr~GvkRIS~d~--------y~e~r~vle~~l~~I~rdav~~aeHA---------------~RK   81 (102)
T PTZ00015         25 RDNIRGITKGAIRRLARRGGVKRISGDI--------YEEVRGVLKAFLENVVRDSTAYTEYA---------------RRK   81 (102)
T ss_pred             hhcccCCCHHHHHHHHHHcCCccchHHH--------HHHHHHHHHHHHHHHHHHHHHHHHhc---------------CCC
Confidence            5788899999999999999997522225        55666678899999999999998531               234


Q ss_pred             eeeHHHHHHHHHHhCcc
Q 032126          109 ILTMEDLSKALREYGVN  125 (147)
Q Consensus       109 vLTmEDLs~AL~EyGIn  125 (147)
                      |.|.+|+..||+..|-+
T Consensus        82 TVt~~DV~~AlKr~g~~   98 (102)
T PTZ00015         82 TVTAMDVVYALKRQGRT   98 (102)
T ss_pred             cccHHHHHHHHHhcCCC
Confidence            78999999999999864

>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=94.82  E-value=0.17  Score=35.18  Aligned_cols=45  Identities=24%  Similarity=0.313  Sum_probs=37.0

Q ss_pred             CcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHHHHH
Q 032126           53 DVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALR  120 (147)
Q Consensus        53 D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~AL~  120 (147)
                      |+-+        ..++.-.|..||.+|++.|.+.||-|.+               -+|...|+.-.|+
T Consensus        19 d~~v--------ee~Ll~laddFv~~v~~~ac~lAKhR~s---------------~tle~~Dv~~~Le   63 (68)
T PF03847_consen   19 DPDV--------EELLLELADDFVDDVVSFACRLAKHRKS---------------STLEVKDVQLHLE   63 (68)
T ss_dssp             -HHH--------HHHHHHHHHHHHHHHHHHHHHHHHHTT----------------SEE-HHHHHHHHH
T ss_pred             CHHH--------HHHHHHHHHHHHHHHHHHHHHHHhccCC---------------CCCCHHHHHHHHH
Confidence            7778        8899999999999999999999998843               2788889888875

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

>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=94.47  E-value=0.18  Score=39.13  Aligned_cols=62  Identities=15%  Similarity=0.223  Sum_probs=45.2

Q ss_pred             HHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHH
Q 032126           38 ELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSK  117 (147)
Q Consensus        38 ~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~  117 (147)
                      .++..+|+..|++--+|||        .-.+-=-+.+++++|..||..|+....               |..++++|+..
T Consensus        16 ~~i~~iL~~~Gv~~yeprV--------v~qLLEfayRYt~~vL~DA~~ya~hA~---------------~~~i~~~DVrL   72 (129)
T PF02291_consen   16 RVIHLILKSMGVTEYEPRV--------VNQLLEFAYRYTSDVLEDAQVYADHAG---------------RSTIDADDVRL   72 (129)
T ss_dssp             HHHHHHHHHTT---B-THH--------HHHHHHHHHHHHHHHHHHHHHHHHHTT----------------SSB-HHHHHH
T ss_pred             HHHHHHHHHcCCcccCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHhcc---------------cccCChHHHHH
Confidence            4778899999999889999        665555569999999999999986431               23667999999


Q ss_pred             HHHHh
Q 032126          118 ALREY  122 (147)
Q Consensus       118 AL~Ey  122 (147)
                      |...+
T Consensus        73 Ai~~r   77 (129)
T PF02291_consen   73 AIQSR   77 (129)
T ss_dssp             HHHHT
T ss_pred             HHHHH
Confidence            98844

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

>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=93.04  E-value=0.57  Score=32.33  Aligned_cols=52  Identities=23%  Similarity=0.337  Sum_probs=42.5

Q ss_pred             CCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHHHHH-HhCc
Q 032126           50 QCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALR-EYGV  124 (147)
Q Consensus        50 ~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~AL~-EyGI  124 (147)
                      ..-|+-+        ..++.=.+..|+.+|+.+|..+||-|.               +-+++.+|+..+|+ +||+
T Consensus        18 ~~~~~da--------~~~l~~~~e~fv~~v~~~a~~lAkHr~---------------~~tv~~~Di~l~l~r~~~~   70 (72)
T cd07981          18 EQLDPDV--------EELLLEIADDFVDDVVEDACRLAKHRK---------------SDTLEVKDVQLHLERNWNI   70 (72)
T ss_pred             CCcCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHcC---------------CCCCCHHHHHHHHHHhcCC
Confidence            4557777        889999999999999999999998763               23599999999986 3444

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

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

Probab=91.44  E-value=0.53  Score=40.75  Aligned_cols=81  Identities=16%  Similarity=0.232  Sum_probs=54.2

Q ss_pred             CCCCchHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 032126           14 RHDDDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAA   93 (147)
Q Consensus        14 ~~~~d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~   93 (147)
                      +-.....|.||+.++|.                  =.--|+-|        ..||.-.|..||++|++-|...||-|.+.
T Consensus       153 ~il~k~kl~dLvqqId~------------------~~~LD~dV--------edlLleiADdFV~sii~~sC~LAKHRKsd  206 (258)
T KOG1142|consen  153 PILSKRKLDDLVQQIDG------------------TTKLDDDV--------EDLLLEIADDFVSSIIHRSCKLAKHRKSD  206 (258)
T ss_pred             ccccccchhHHHHhhcC------------------cccccHHH--------HHHHHHHHHHHHHHHHHHHHHHHHhcccC
Confidence            33445566777776632                  23348899        99999999999999999999999988532


Q ss_pred             hhhchhcccccccceeeeHHHHHHHHHHhCcccCCCCccccCC
Q 032126           94 VVKDKRDKQQKDKRLILTMEDLSKALREYGVNVKHQEYFADNP  136 (147)
Q Consensus        94 ~~~~k~~~~~kd~r~vLTmEDLs~AL~EyGInvkrP~Yy~d~~  136 (147)
                                     +|-.-|+...| |.-.|+.=|.|=+|-.
T Consensus       207 ---------------tlEvrDIqLhL-Er~~Nm~iPgf~sd~~  233 (258)
T KOG1142|consen  207 ---------------TVEVRDIQLHL-ERNFNMEIPGFSSDEK  233 (258)
T ss_pred             ---------------ccchhheeeee-eccccccCCCcccccc
Confidence                           23333443333 4556666676655543

>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=91.35  E-value=0.24  Score=41.19  Aligned_cols=57  Identities=16%  Similarity=0.298  Sum_probs=30.9

Q ss_pred             CCCCCcHHHHHHHHHh----CCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 032126           31 YTPTIPDELVEHYLAK----SGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVV   95 (147)
Q Consensus        31 Y~P~IPD~Vt~yyL~~----aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~   95 (147)
                      -.|.+.-.+...+|++    .|....|+-|        ..|||+|+|-.|.+|+.++...|+.|+....
T Consensus        40 ~~~fL~~~~L~~~i~~i~~~~g~~~~~~d~--------l~llS~A~e~rLr~lie~~~~~s~hR~~~~~  100 (264)
T PF05236_consen   40 EEPFLNPSPLQKRIQKIAKKHGLKSVDEDV--------LELLSLATEERLRNLIEKAIVLSRHRRDSSK  100 (264)
T ss_dssp             ----S-HHHHHHHHHHHHHCTT--EE-TCH--------HHHHHHHHHHHHHHHHHHHH-----------
T ss_pred             cccccCHHHHHHHHHHHHHHcCCcCCCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHhhhcccC
Confidence            3555555555555544    4655578889        9999999999999999999999999987653

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.

>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=89.65  E-value=1  Score=36.47  Aligned_cols=47  Identities=13%  Similarity=0.251  Sum_probs=41.3

Q ss_pred             HHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 032126           40 VEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAV   94 (147)
Q Consensus        40 t~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~   94 (147)
                      +..++.+.|+...|+.+        ..|||+|++-++.+|+.+....|+.|....
T Consensus        54 ~~~i~~~~g~~~~~~d~--------~~lis~a~e~rlr~li~k~~~~s~hR~~~~  100 (212)
T cd08045          54 IRKIAKKHGLKEVDEDV--------LDLISLALEERLRNLLEKLIEVSEHRVDSE  100 (212)
T ss_pred             HHHHHHHcCCCCCCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHhhhhhc
Confidence            44566778888789999        999999999999999999999999998654

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

>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=85.13  E-value=4.1  Score=32.83  Aligned_cols=63  Identities=19%  Similarity=0.198  Sum_probs=49.0

Q ss_pred             HHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHHH
Q 032126           39 LVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKA  118 (147)
Q Consensus        39 Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~A  118 (147)
                      |+.-+|...|.+-=+|||        +--+==-|-.++++|..||.-|++--               +|.+++.||+..|
T Consensus        18 ~i~~iL~s~GI~eyEprV--------i~qlLefa~rYtt~vL~DA~vys~HA---------------~ka~i~~eDVrlA   74 (148)
T KOG3334|consen   18 VIASILKSLGIQEYEPRV--------INQLLEFAYRYTTTVLDDAKVYSSHA---------------KKATIDAEDVRLA   74 (148)
T ss_pred             HHHHHHHHcCccccChHH--------HHHHHHHHHHHHHHHHHHHHHHHHhc---------------cCCCCcHHHHHHH
Confidence            567788999999888888        65555567899999999999998531               1567888888888


Q ss_pred             HHHhCc
Q 032126          119 LREYGV  124 (147)
Q Consensus       119 L~EyGI  124 (147)
                      ..-.+.
T Consensus        75 ~~~~~~   80 (148)
T KOG3334|consen   75 IQMRVD   80 (148)
T ss_pred             HHHHhc
Confidence            776543

>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]

Probab=80.19  E-value=4.3  Score=36.28  Aligned_cols=77  Identities=25%  Similarity=0.404  Sum_probs=58.8

Q ss_pred             CcHHHHHHHHHhCCCCC-CCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHH
Q 032126           35 IPDELVEHYLAKSGFQC-PDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTME  113 (147)
Q Consensus        35 IPD~Vt~yyL~~aGf~~-~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmE  113 (147)
                      |=..|+.-.|...||+. ++.-+        --|+ .+-|+.|..|...+..||..               .+|+.-|.-
T Consensus         6 vl~~VV~~Ll~~~gfd~is~~al--------etlv-ell~~yi~eigrq~~n~cel---------------agRT~pT~~   61 (323)
T KOG4336|consen    6 VLAPVVSNLLKTKGFDSISNAAL--------ETLV-ELLQSYIREIGRQLHNYCEL---------------AGRTIPTQG   61 (323)
T ss_pred             HHHHHHHHHHHHhCchHHHHHHH--------HHHH-HHHHHHHHHHHHHHHHHHHH---------------hcccCCcHH
Confidence            45679999999999997 44444        4444 45689999999999999864               135778899


Q ss_pred             HHHHHHHHhCcccCC-CCccccC
Q 032126          114 DLSKALREYGVNVKH-QEYFADN  135 (147)
Q Consensus       114 DLs~AL~EyGInvkr-P~Yy~d~  135 (147)
                      ||.-.|.+.||+|.- +.||.+.
T Consensus        62 Dv~l~Li~mnI~v~sL~~~~q~~   84 (323)
T KOG4336|consen   62 DVKLTLIEMNIKVSSLYAYFQKQ   84 (323)
T ss_pred             HHHHHHHHhCCChhhhHHHHHhc
Confidence            999999999999864 4455443

---

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	147
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	97.31
2yfw_B	103	Histone H4, H4; cell cycle, kinetochore, centromer	97.31
1id3_B	102	Histone H4; nucleosome core particle, chromatin, p	97.24
1tzy_D	103	Histone H4-VI; histone-fold, tetramer-dimer-dimer,	97.19
2hue_C	84	Histone H4; mini beta sheet, elongated beta sandwh	97.05
1n1j_A	93	NF-YB; histone-like PAIR, DNA binding protein; 1.6	96.85
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	96.58
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	96.48
1taf_B	70	TFIID TBP associated factor 62; transcription init	96.34
1taf_A	68	TFIID TBP associated factor 42; transcription init	95.96
4g92_C	119	HAPE; transcription factor, nucleosome, minor groo	95.94
3b0c_W	76	CENP-W, centromere protein W; histone fold, DNA bi	95.5
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	95.03
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	94.69
1h3o_B	76	Transcription initiation factor TFIID 20/15 kDa su	94.67
2byk_B	128	Chrac-14; nucleosome sliding, histone fold, DNA-bi	94.41
1jfi_B	179	DR1 protein, transcription regulator NC2 beta chai	93.49
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	92.38
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	90.75
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	89.97
3b0b_C	81	CENP-X, centromere protein X; histone fold, DNA bi	88.52
2ly8_A	121	Budding yeast chaperone SCM3; centromere protein,	88.08
4dra_E	84	Centromere protein X; DNA binding complex, DNA dam	85.75
3v9r_B	88	MHF2, uncharacterized protein YDL160C-A; histone f	83.73

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

Probab=97.31  E-value=0.00087  Score=44.75  Aligned_cols=67  Identities=18%  Similarity=0.318  Sum_probs=53.6

Q ss_pred             CCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceee
Q 032126           31 YTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLIL  110 (147)
Q Consensus        31 Y~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vL  110 (147)
                      |-|.||-..+.-.+++.|..-=.+.+        +-.+.=++..|+.+|+.||..|++               ..+|-++
T Consensus         3 ~~~~lp~a~v~Rl~r~~g~~ris~~a--------~~~l~e~~~~~~~~v~~dA~~~a~---------------hakRkTI   59 (70)
T 1ku5_A            3 MMGELPIAPVDRLIRKAGAERVSEQA--------AKVLAEYLEEYAIEIAKKAVEFAR---------------HAGRKTV   59 (70)
T ss_dssp             --CCSCHHHHHHHHHHTTCSEECHHH--------HHHHHHHHHHHHHHHHHHHHHHHH---------------TTTCSEE
T ss_pred             ccccCChHHHHHHHHHcCcceeCHHH--------HHHHHHHHHHHHHHHHHHHHHHHH---------------HcCCCcC
Confidence            57899999999999999865445556        667777899999999999999984               2235589


Q ss_pred             eHHHHHHHHH
Q 032126          111 TMEDLSKALR  120 (147)
Q Consensus       111 TmEDLs~AL~  120 (147)
                      +.+|+..|++
T Consensus        60 ~~~DV~lA~~   69 (70)
T 1ku5_A           60 KVEDIKLAIK   69 (70)
T ss_dssp             CHHHHHHHHT
T ss_pred             CHHHHHHHHH
Confidence            9999999875

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

Probab=97.31  E-value=0.001  Score=47.93  Aligned_cols=71  Identities=20%  Similarity=0.215  Sum_probs=54.7

Q ss_pred             CCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhccccccccee
Q 032126           30 GYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLI  109 (147)
Q Consensus        30 dY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~v  109 (147)
                      +-..-||-+-+.-++++.|+..=-.-+        ..-++=+...|+.+|+.||..|++-               .+|.+
T Consensus        25 ~~~~gip~~~I~Rlar~~G~~rIs~~a--------~~~l~~vle~~~~~V~~dA~~~a~h---------------akRkt   81 (103)
T 2yfw_B           25 DNIQGITKPAIRRLARRGGVKRISGLI--------YEEVRNVLKTFLESVIRDAVTYTEH---------------AKRKT   81 (103)
T ss_dssp             -----CCHHHHHHHHHHTTCCEECTTH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------TTCSE
T ss_pred             hhhccCCHHHHHHHHHHcCccccCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------cCCCc
Confidence            444449999999999999996322335        6677778899999999999999852               23458


Q ss_pred             eeHHHHHHHHHHhC
Q 032126          110 LTMEDLSKALREYG  123 (147)
Q Consensus       110 LTmEDLs~AL~EyG  123 (147)
                      +|.+|+..||+..|
T Consensus        82 vt~~DV~~Alr~~g   95 (103)
T 2yfw_B           82 VTSLDVVYALKRQG   95 (103)
T ss_dssp             ECHHHHHHHHHHHC
T ss_pred             CcHHHHHHHHHHcC
Confidence            99999999999886

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

Probab=97.24  E-value=0.0011  Score=47.91  Aligned_cols=73  Identities=19%  Similarity=0.225  Sum_probs=59.1

Q ss_pred             cCCCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccc
Q 032126           28 LMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKR  107 (147)
Q Consensus        28 LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r  107 (147)
                      |.|...-||-+-+.-++++.|..-=-.-+        +.-+.=+...|+.+|+.||..|++-               .+|
T Consensus        22 ~r~~i~~ip~~~I~Rlar~~Gv~rIS~da--------~~~l~~~le~fi~~I~~dA~~~a~H---------------akR   78 (102)
T 1id3_B           22 LRDNIQGITKPAIRRLARRGGVKRISGLI--------YEEVRAVLKSFLESVIRDSVTYTEH---------------AKR   78 (102)
T ss_dssp             --CCGGGSCHHHHHHHHHHTTCCEECTTH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------TTC
T ss_pred             HHhccCCCCHHHHHHHHHHcCchhccHHH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------cCC
Confidence            45666679999999999999996433346        7788889999999999999999852               234


Q ss_pred             eeeeHHHHHHHHHHhC
Q 032126          108 LILTMEDLSKALREYG  123 (147)
Q Consensus       108 ~vLTmEDLs~AL~EyG  123 (147)
                      -++|.+|+..||+..|
T Consensus        79 KTVt~~DV~~ALkr~g   94 (102)
T 1id3_B           79 KTVTSLDVVYALKRQG   94 (102)
T ss_dssp             SEECHHHHHHHHHHTT
T ss_pred             CcCcHHHHHHHHHHcC
Confidence            5899999999999886

>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=97.19  E-value=0.0015  Score=46.95  Aligned_cols=73  Identities=19%  Similarity=0.201  Sum_probs=57.1

Q ss_pred             cCCCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccc
Q 032126           28 LMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKR  107 (147)
Q Consensus        28 LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r  107 (147)
                      +.+-..-||-+-+.-++.+.|+..--.-+        ..-++=+...|+.+|+.||..|++-               .+|
T Consensus        23 ~r~~~~gip~~~I~Rlar~~G~~rIs~~a--------~~~l~~vle~~~~~V~~dA~~~a~h---------------akR   79 (103)
T 1tzy_D           23 LRDNIQGITKPAIRRLARRGGVKRISGLI--------YEETRGVLKVFLENVIRDAVTYTEH---------------AKR   79 (103)
T ss_dssp             CCCGGGGSCHHHHHHHHHHTTCCEECTTH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------TTC
T ss_pred             hhhhcccCCHHHHHHHHHHcCccccCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------cCC
Confidence            33444449999999999999996322235        5667777899999999999999852               235


Q ss_pred             eeeeHHHHHHHHHHhC
Q 032126          108 LILTMEDLSKALREYG  123 (147)
Q Consensus       108 ~vLTmEDLs~AL~EyG  123 (147)
                      .++|.+|+..||+..|
T Consensus        80 ktIt~~DV~~Alr~~g   95 (103)
T 1tzy_D           80 KTVTAMDVVYALKRQG   95 (103)
T ss_dssp             SEECHHHHHHHHHHTT
T ss_pred             CcCCHHHHHHHHHHcC
Confidence            5899999999999886

>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=97.05  E-value=0.0017  Score=45.11  Aligned_cols=74  Identities=19%  Similarity=0.190  Sum_probs=59.2

Q ss_pred             cCCCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccc
Q 032126           28 LMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKR  107 (147)
Q Consensus        28 LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r  107 (147)
                      |.|...-||-+-+.-++++.|..-=-.-+        +.-+.=....|+.+|+.||..|++-               .+|
T Consensus         4 ~r~~~~~ip~~~I~Riar~~Gv~rIs~da--------~~~l~~~l~~~~~~I~~dA~~~a~h---------------a~R   60 (84)
T 2hue_C            4 LRDNIQGITKPAIRRLARRGGVKRISGLI--------YEETRGVLKVFLENVIRDAVTYTEH---------------AKR   60 (84)
T ss_dssp             GGGGCCSSCHHHHHHHHHHTTCCEECTTH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------TTC
T ss_pred             ccccCCCCCHHHHHHHHHHcCchhccHHH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------cCC
Confidence            44566779999999999999996322336        6778888999999999999999852               224


Q ss_pred             eeeeHHHHHHHHHHhCc
Q 032126          108 LILTMEDLSKALREYGV  124 (147)
Q Consensus       108 ~vLTmEDLs~AL~EyGI  124 (147)
                      -++|.+|+..||+..|.
T Consensus        61 KTvt~~DV~~Alk~~g~   77 (84)
T 2hue_C           61 KTVTAMDVVYALKRQGR   77 (84)
T ss_dssp             SEECHHHHHHHTTTTCE
T ss_pred             CcCcHHHHHHHHHHcCC
Confidence            48999999999998763

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

Probab=96.85  E-value=0.0064  Score=42.48  Aligned_cols=73  Identities=18%  Similarity=0.258  Sum_probs=56.5

Q ss_pred             CCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeee
Q 032126           32 TPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILT  111 (147)
Q Consensus        32 ~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLT  111 (147)
                      -..||-+-+.-+++.+|=+  +.||    ..-=.-+++=|+.-||..|+.+|..+|+               .++|-|++
T Consensus         6 d~~LP~a~i~ri~K~~~~~--~~~i----s~dA~~~l~~a~e~Fi~~l~~~A~~~a~---------------~~kRkTI~   64 (93)
T 1n1j_A            6 DIYLPIANVARIMKNAIPQ--TGKI----AKDAKECVQECVSEFISFITSEASERCH---------------QEKRKTIN   64 (93)
T ss_dssp             -CCCCHHHHHHHHHHTSCT--TCEE----CHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HTTCSSBC
T ss_pred             cccCChhHHHHHHHHhCCc--ccee----CHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HcCCCccC
Confidence            3579999999999999742  3455    1122358888999999999999999984               23355899


Q ss_pred             HHHHHHHHHHhCcc
Q 032126          112 MEDLSKALREYGVN  125 (147)
Q Consensus       112 mEDLs~AL~EyGIn  125 (147)
                      -+|+..||++.|..
T Consensus        65 ~~Dv~~Al~~l~F~   78 (93)
T 1n1j_A           65 GEDILFAMSTLGFD   78 (93)
T ss_dssp             HHHHHHHHHHTTCG
T ss_pred             HHHHHHHHHHcCcH
Confidence            99999999988864

>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=96.58  E-value=0.0045  Score=45.35  Aligned_cols=70  Identities=14%  Similarity=0.264  Sum_probs=52.8

Q ss_pred             CCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeH
Q 032126           33 PTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTM  112 (147)
Q Consensus        33 P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTm  112 (147)
                      |-||-+++.-++.+.|-.---..+        +-.+.=++..|+.+|+.||..||+-               .+|-|+|.
T Consensus         6 ~~lP~a~I~Ri~r~~g~~rIS~~a--------~~~l~e~l~~f~~~v~~da~~~A~H---------------A~RKTV~~   62 (111)
T 3b0c_T            6 PEIASSLIKQIFSHYVKTPVTRDA--------YKIVEKCSERYFKQISSDLEAYSQH---------------AGRKTVEM   62 (111)
T ss_dssp             ----CHHHHHHHHHHHCSCBCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------TTCSEECH
T ss_pred             CCCCHHHHHHHHHHCCCCccCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------cCCCcCCH
Confidence            679999999999999765434445        6677778889999999999999852               12348999


Q ss_pred             HHHHHHHHHhCcc
Q 032126          113 EDLSKALREYGVN  125 (147)
Q Consensus       113 EDLs~AL~EyGIn  125 (147)
                      ||+..||+..|-.
T Consensus        63 eDV~lalrr~g~~   75 (111)
T 3b0c_T           63 ADVELLMRRQGLV   75 (111)
T ss_dssp             HHHHHHHHHTTSS
T ss_pred             HHHHHHHHHCCCc
Confidence            9999999998854

>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=96.48  E-value=0.011  Score=38.78  Aligned_cols=65  Identities=17%  Similarity=0.188  Sum_probs=50.6

Q ss_pred             CCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHH
Q 032126           34 TIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTME  113 (147)
Q Consensus        34 ~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmE  113 (147)
                      .||-.-+.-.+++.    ++.||    ..-=.-+++=|+.-||..|+.||..+|+               ..+|.|++-+
T Consensus         2 ~lP~a~v~Ri~k~~----~~~ri----s~~A~~~l~~a~e~fi~~l~~~A~~~a~---------------~~kRkTI~~~   58 (68)
T 1b67_A            2 ELPIAPIGRIIKNA----GAERV----SDDARIALAKVLEEMGEEIASEAVKLAK---------------HAGRKTIKAE   58 (68)
T ss_dssp             CSCHHHHHHHHHHT----TCSEE----CHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HTTCSEECHH
T ss_pred             CCCccHHHHHHhcC----CcccC----CHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HcCCCccCHH
Confidence            47888899999988    46666    2222346777899999999999999984               3346799999


Q ss_pred             HHHHHHHH
Q 032126          114 DLSKALRE  121 (147)
Q Consensus       114 DLs~AL~E  121 (147)
                      |+..|+++
T Consensus        59 Di~~A~~~   66 (68)
T 1b67_A           59 DIELARKM   66 (68)
T ss_dssp             HHHHHGGG
T ss_pred             HHHHHHHh
Confidence            99999875

>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=96.34  E-value=0.014  Score=40.03  Aligned_cols=67  Identities=18%  Similarity=0.209  Sum_probs=56.9

Q ss_pred             CCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceee
Q 032126           31 YTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLIL  110 (147)
Q Consensus        31 Y~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vL  110 (147)
                      |-..+|-+-+.-+.+..|++.-..-+        .+.++=-..--+.+|+++|..+.+.               -+|.+|
T Consensus         3 ~~s~lp~~~v~~iaes~Gi~~lsdda--------a~~LA~dvEyr~~eI~qeA~kfmrH---------------akRk~L   59 (70)
T 1taf_B            3 YGSSISAESMKVIAESIGVGSLSDDA--------AKELAEDVSIKLKRIVQDAAKFMNH---------------AKRQKL   59 (70)
T ss_dssp             CSCCCCHHHHHHHHHHTTCCCBCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------TTCSSB
T ss_pred             ccccCCHHHHHHHHHHCCCCCCCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------cCCCee
Confidence            55789999999999999998766667        7889999999999999999999642               124589


Q ss_pred             eHHHHHHHHH
Q 032126          111 TMEDLSKALR  120 (147)
Q Consensus       111 TmEDLs~AL~  120 (147)
                      |.+|+..||+
T Consensus        60 t~~DI~~Alk   69 (70)
T 1taf_B           60 SVRDIDMSLK   69 (70)
T ss_dssp             CHHHHHHHHC
T ss_pred             cHHHHHHHHc
Confidence            9999999984

>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=95.96  E-value=0.033  Score=37.96  Aligned_cols=61  Identities=15%  Similarity=0.217  Sum_probs=52.6

Q ss_pred             HHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHH
Q 032126           38 ELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSK  117 (147)
Q Consensus        38 ~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~  117 (147)
                      .++.-+|+..|.+--++++        +-.+.=.+.+++++|+.||..|++-.               +|-+++.||+..
T Consensus         5 ~~i~~iLk~~G~~~~~~~v--------~~~L~e~~~ry~~~il~dA~~~a~HA---------------grktv~~eDVkL   61 (68)
T 1taf_A            5 QVIMSILKELNVQEYEPRV--------VNQLLEFTFRYVTSILDDAKVYANHA---------------RKKTIDLDDVRL   61 (68)
T ss_dssp             HHHHHHHHHTTCCCBCTHH--------HHHHHHHHHHHHHHHHHHHHHHHHHT---------------TCSSBCHHHHHH
T ss_pred             HHHHHHHHHCCCcccCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHc---------------CCCCCCHHHHHH
Confidence            4678899999999999999        88888899999999999999999642               124899999999


Q ss_pred             HHHH
Q 032126          118 ALRE  121 (147)
Q Consensus       118 AL~E  121 (147)
                      |.+.
T Consensus        62 Ai~~   65 (68)
T 1taf_A           62 ATEV   65 (68)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            9864

>4g92_C HAPE; transcription factor, nucleosome, minor groove binding, CCAA complex, histone fold motif, specific binding to the ccaat- nucleus; HET: DNA; 1.80A {Aspergillus nidulans} PDB: 4g91_C*

Probab=95.94  E-value=0.021  Score=41.98  Aligned_cols=97  Identities=20%  Similarity=0.237  Sum_probs=64.3

Q ss_pred             CCCCCcCCCCCCCCCCCchHHHHHHHHc--------CCC-CCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHH
Q 032126            1 MNHNNNFQQSSDGRHDDDAALTEFLSSL--------MGY-TPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVA   71 (147)
Q Consensus         1 ~~~~~~~~~~~~~~~~~d~~L~efl~~L--------ddY-~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLA   71 (147)
                      |+.-.|..++-.+..  ...|.+|+..-        .|+ .+-+|=+-+..+|+. +  ..-.+|    ..-=.=++|-|
T Consensus         1 ~~~~~~~~~~l~~~~--~~~l~~fw~~~~~~~e~~~~d~k~~~lPvaRIkrImK~-d--~~~~~i----s~eA~v~la~a   71 (119)
T 4g92_C            1 MGTWANVNQGLQGTA--RDILTTYWQHVINHLESDNHDYKIHQLPLARIKKVMKA-D--PEVKMI----SAEAPILFAKG   71 (119)
T ss_dssp             -CTTHHHHTTCCTHH--HHHHHHHHHHHHHHHTCSCCCSSCCSSCHHHHHHHHHT-S--TTCCEE----CTHHHHHHHHH
T ss_pred             CchhhhhhhccchHH--HHHHHHHHHHHHHHHHhcccccccCCCCHHHHHHHHhh-C--Cccccc----cHHHHHHHHHH
Confidence            333333344433333  46788887543        134 566999999999974 2  112222    22224489999


Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHHHHHH
Q 032126           72 TQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALRE  121 (147)
Q Consensus        72 aQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~AL~E  121 (147)
                      ++-||++|+..|..+|+.               .+|-+++-+||..|++.
T Consensus        72 ~E~Fi~~L~~~A~~~a~~---------------~krktI~~~di~~Av~~  106 (119)
T 4g92_C           72 CDVFITELTMRAWIHAED---------------NKRRTLQRSDIAAALSK  106 (119)
T ss_dssp             HHHHHHHHHHHHHHHHHH---------------TTCSEECHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHh---------------cccCccCHHHHHHHHhc
Confidence            999999999999998842               22448999999999975

>3b0c_W CENP-W, centromere protein W; histone fold, DNA binding, DNA binding protein; HET: CIT; 2.20A {Gallus gallus} PDB: 3b0d_W* 3vh5_W 3vh6_W

Probab=95.50  E-value=0.064  Score=36.27  Aligned_cols=67  Identities=21%  Similarity=0.217  Sum_probs=50.4

Q ss_pred             CCCcHHHHHHHHHhC-CCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeee
Q 032126           33 PTIPDELVEHYLAKS-GFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILT  111 (147)
Q Consensus        33 P~IPD~Vt~yyL~~a-Gf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLT  111 (147)
                      +.+|-+.+.-+|+++ +    |.+|    .--=.-+|+.++.-||..|+..|.+.|+-               ++|-|++
T Consensus         3 ~~LP~A~V~rI~K~~~p----~~~i----s~~A~~~i~~~~~~Fi~~la~eA~~~a~~---------------~~rKTI~   59 (76)
T 3b0c_W            3 RTVPRGTLRKIIKKHKP----HLRL----AANTDLLVHLSFLLFLHRLAEEARTNAFE---------------NKSKIIK   59 (76)
T ss_dssp             -CCCHHHHHHHHHHHCT----TCEE----CTTHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HTCSSBC
T ss_pred             CcccccHHHHHHHHhCC----CCcc----CHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------cCCCCCC
Confidence            578999999999965 4    3333    11114589999999999999999999852               2345999


Q ss_pred             HHHHHHHHHHh
Q 032126          112 MEDLSKALREY  122 (147)
Q Consensus       112 mEDLs~AL~Ey  122 (147)
                      -||+..||++.
T Consensus        60 ~~dI~~A~~~l   70 (76)
T 3b0c_W           60 PEHTIAAAKVI   70 (76)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999999863

>1f1e_A Histone fold protein; archaeal histone protein, DNA binding protein; HET: MSE; 1.37A {Methanopyrus kandleri} SCOP: a.22.1.2

Probab=95.03  E-value=0.092  Score=40.68  Aligned_cols=70  Identities=17%  Similarity=0.097  Sum_probs=54.9

Q ss_pred             CCCcHHHHHHHHHhC-CCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeee
Q 032126           33 PTIPDELVEHYLAKS-GFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILT  111 (147)
Q Consensus        33 P~IPD~Vt~yyL~~a-Gf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLT  111 (147)
                      +-+|-+.+.-++.++ |-    .||    ..-=+-.++=+.+.|+..|+.+|-.+|+               +.+|-|++
T Consensus         3 ~~LP~a~V~Riik~~lg~----~rV----S~dA~~~l~~~l~~f~~~i~~~A~~~a~---------------ha~RKTv~   59 (154)
T 1f1e_A            3 VELPKAAIERIFRQGIGE----RRL----SQDAKDTIYDFVPTMAEYVANAAKSVLD---------------ASGKKTLM   59 (154)
T ss_dssp             -CCCHHHHHHHHHTTSTT----CEE----CHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------TTTCSEEC
T ss_pred             ccCCccHHHHHHHhcCCc----cch----hHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HcCCCcCC
Confidence            468999999999999 74    666    1111346677888999999999999984               44566999


Q ss_pred             HHHHHHHHHHhCcc
Q 032126          112 MEDLSKALREYGVN  125 (147)
Q Consensus       112 mEDLs~AL~EyGIn  125 (147)
                      -+|+..||...|+.
T Consensus        60 a~DV~~a~~~lg~~   73 (154)
T 1f1e_A           60 EEHLKALADVLMVE   73 (154)
T ss_dssp             HHHHHHHHHHHTCT
T ss_pred             HHHHHHHHHhcccc
Confidence            99999999998864

>1n1j_B NF-YC; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3

Probab=94.69  E-value=0.065  Score=37.88  Aligned_cols=69  Identities=19%  Similarity=0.219  Sum_probs=50.4

Q ss_pred             CCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeee
Q 032126           32 TPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILT  111 (147)
Q Consensus        32 ~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLT  111 (147)
                      .+.+|=+-+..+|+..+--   .||    ..-=.-++|-|++-||.+++..|+.+++.               .+|-+++
T Consensus        17 ~~~lP~arIkrImK~~~~~---~~i----s~eA~~~laka~E~Fi~~l~~~A~~~a~~---------------~krktI~   74 (97)
T 1n1j_B           17 VQELPLARIKKIMKLDEDV---KMI----SAEAPVLFAKAAQIFITELTLRAWIHTED---------------NKRRTLQ   74 (97)
T ss_dssp             ---CCHHHHHHHHTTSTTC---CCB----CTHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------TTCSEEC
T ss_pred             CCcCCHHHHHHHHccCccc---ccc----ChHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------cCCccCC
Confidence            5679999999999988531   222    11113489999999999999999998741               2355999


Q ss_pred             HHHHHHHHHHh
Q 032126          112 MEDLSKALREY  122 (147)
Q Consensus       112 mEDLs~AL~Ey  122 (147)
                      -+||..|+...
T Consensus        75 ~~di~~Av~~~   85 (97)
T 1n1j_B           75 RNDIAMAITKF   85 (97)
T ss_dssp             HHHHHHHHTTC
T ss_pred             HHHHHHHHhcC
Confidence            99999998753

>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=94.67  E-value=0.22  Score=34.64  Aligned_cols=69  Identities=16%  Similarity=0.269  Sum_probs=54.0

Q ss_pred             CchHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 032126           17 DDAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVK   96 (147)
Q Consensus        17 ~d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~   96 (147)
                      .-..|.+|+.+++--                  .+-||-+        .-++.=.|..||.+|+..|.+.||-|.+    
T Consensus         7 ~k~~L~~Lv~~idp~------------------~~ld~~v--------ee~ll~lADdFV~~V~~~ac~lAKhR~s----   56 (76)
T 1h3o_B            7 TKKKLQDLVREVDPN------------------EQLDEDV--------EEMLLQIADDFIESVVTAACQLARHRKS----   56 (76)
T ss_dssp             CHHHHHHHHHHHCSS------------------CCCCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHTTC----
T ss_pred             cHHHHHHHHHhcCCC------------------CCCCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHhcCC----
Confidence            356788888888632                  3458888        8999999999999999999999998843    


Q ss_pred             chhcccccccceeeeHHHHHHHHH-HhCccc
Q 032126           97 DKRDKQQKDKRLILTMEDLSKALR-EYGVNV  126 (147)
Q Consensus        97 ~k~~~~~kd~r~vLTmEDLs~AL~-EyGInv  126 (147)
                                 -+|..-|+.-.|+ +|||.|
T Consensus        57 -----------~~le~kDvql~Ler~wni~i   76 (76)
T 1h3o_B           57 -----------STLEVKDVQLHLERQWNMWI   76 (76)
T ss_dssp             -----------CEECHHHHHHHHHHHTCCCC
T ss_pred             -----------CCccHHHHHHHHHhhcCCcC
Confidence                       3778888888774 566653

>2byk_B Chrac-14; nucleosome sliding, histone fold, DNA-binding protein; 2.4A {Drosophila melanogaster} SCOP: a.22.1.3 PDB: 2bym_B

Probab=94.41  E-value=0.064  Score=40.06  Aligned_cols=71  Identities=14%  Similarity=0.185  Sum_probs=51.6

Q ss_pred             CCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeH
Q 032126           33 PTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTM  112 (147)
Q Consensus        33 P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTm  112 (147)
                      ..+|-+.+.-+++.++=  +..+|    .--=.-+|+-|+.-||..|+..|.++|+               +++|-+++-
T Consensus         8 ~~LP~A~I~rImK~~~p--d~~~i----S~dA~~~l~ka~e~FI~~lt~~A~~~a~---------------~~kRKTI~~   66 (128)
T 2byk_B            8 LNLPNAVIGRLIKEALP--ESASV----SKEARAAIARAASVFAIFVTSSSTALAH---------------KQNHKTITA   66 (128)
T ss_dssp             ---CCSHHHHHHHHHSC--TTCEE----CHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HTTCSSCCH
T ss_pred             ccCCHHHHHHHHHHhCc--ccceE----CHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HcCCCccCH
Confidence            35788889999997652  22333    1111348999999999999999999984               233559999


Q ss_pred             HHHHHHHHHhCc
Q 032126          113 EDLSKALREYGV  124 (147)
Q Consensus       113 EDLs~AL~EyGI  124 (147)
                      +|+..||.+.|.
T Consensus        67 ~Dv~~Al~~l~f   78 (128)
T 2byk_B           67 KDILQTLTELDF   78 (128)
T ss_dssp             HHHHHHHHHTTC
T ss_pred             HHHHHHHHHcCc
Confidence            999999999884

>1jfi_B DR1 protein, transcription regulator NC2 beta chain; histone, H2A/H2B, tata-DNA, transcription initiation, NC2, negative cofactor, structural genomics, PSI; 2.62A {Homo sapiens} SCOP: a.22.1.3

Probab=93.49  E-value=0.26  Score=39.16  Aligned_cols=70  Identities=21%  Similarity=0.367  Sum_probs=54.9

Q ss_pred             CCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHH
Q 032126           34 TIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTME  113 (147)
Q Consensus        34 ~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmE  113 (147)
                      .+|-+.+.-+++.+|=   +.||    .--=+-+|.=++.-||+-|+..|...|+               +++|-|++-|
T Consensus        15 ~LP~A~V~RImK~alp---~~rI----SkDA~~al~ec~~eFI~~LtseA~e~a~---------------~~~RKTI~~e   72 (179)
T 1jfi_B           15 TIPRAAINKMIKETLP---NVRV----ANDARELVVNCCTEFIHLISSEANEICN---------------KSEKKTISPE   72 (179)
T ss_dssp             CCCHHHHHHHHHHHST---TCCB----CHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HTTCSSBCHH
T ss_pred             hcCHHHHHHHHHHhCC---cccc----CHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HcCCCcCCHH
Confidence            6999999999999972   4555    1111347777888999999999999884               2234599999


Q ss_pred             HHHHHHHHhCcc
Q 032126          114 DLSKALREYGVN  125 (147)
Q Consensus       114 DLs~AL~EyGIn  125 (147)
                      |+..||.+-|..
T Consensus        73 DVl~Al~~LgF~   84 (179)
T 1jfi_B           73 HVIQALESLGFG   84 (179)
T ss_dssp             HHHHHHHHHTTG
T ss_pred             HHHHHHHhcChH
Confidence            999999998874

>2byk_A Chrac-16; nucleosome sliding, histone fold, DNA-binding protein; 2.4A {Drosophila melanogaster} SCOP: a.22.1.3 PDB: 2bym_A

Probab=92.38  E-value=0.21  Score=37.95  Aligned_cols=70  Identities=21%  Similarity=0.185  Sum_probs=40.9

Q ss_pred             CCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceee
Q 032126           31 YTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLIL  110 (147)
Q Consensus        31 Y~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vL  110 (147)
                      ..+.+|=+-+..+|+..    +|...   +..-=.-+||-|+.-||..++..|+.+|+ +             +.+|-+|
T Consensus        16 ~~~~LPlaRIKrIMK~d----pdv~~---Is~eA~vliakA~ElFI~~Lt~~A~~~a~-~-------------~~kRKtI   74 (140)
T 2byk_A           16 AETFLPLSRVRTIMKSS----MDTGL---ITNEVLFLMTKCTELFVRHLAGAAYTEEF-G-------------QRPGEAL   74 (140)
T ss_dssp             -------------CCSS----SSCSC---CCHHHHHHHHHHHHHHHHHHHHHHHHHHH-T-------------TCCSCEE
T ss_pred             cCCCCCHHHHHHHHhcC----ccccc---ccHHHHHHHHHHHHHHHHHHHHHHHHHHH-H-------------hcCCccc
Confidence            34567888888888754    23221   12222458999999999999999999983 1             2345599


Q ss_pred             eHHHHHHHHHH
Q 032126          111 TMEDLSKALRE  121 (147)
Q Consensus       111 TmEDLs~AL~E  121 (147)
                      +-+||..|+..
T Consensus        75 ~~~Dl~~AV~~   85 (140)
T 2byk_A           75 KYEHLSQVVNK   85 (140)
T ss_dssp             CHHHHHHHHHT
T ss_pred             CHHHHHHHHhc
Confidence            99999999985

>1jfi_A Transcription regulator NC2 alpha chain; histone, H2A/H2B, tata-DNA, transcription initiation, NC2, negative cofactor, structural genomics, PSI; 2.62A {Homo sapiens} SCOP: a.22.1.3

Probab=90.75  E-value=0.35  Score=34.25  Aligned_cols=67  Identities=13%  Similarity=0.220  Sum_probs=47.7

Q ss_pred             CCCCCCcHHHHHHHHHhCCCC---CCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhccccccc
Q 032126           30 GYTPTIPDELVEHYLAKSGFQ---CPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDK  106 (147)
Q Consensus        30 dY~P~IPD~Vt~yyL~~aGf~---~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~  106 (147)
                      .+.+.+|-+-+..+|+..+--   ..+..          -+++-|++-|+.+|+..|+.+++-               .+
T Consensus         7 k~~~~fPvaRIkrimK~~~~~~~vs~~A~----------v~la~a~E~Fi~el~~~A~~~a~~---------------~k   61 (98)
T 1jfi_A            7 KYNARFPPARIKKIMQTDEEIGKVAAAVP----------VIISRALELFLESLLKKACQVTQS---------------RN   61 (98)
T ss_dssp             ---CCCCHHHHHHHHTTSTTCCCBCTTHH----------HHHHHHHHHHHHHHHHHHHHHHHT---------------C-
T ss_pred             ccCCCCChHHHHHHHHcCccccccchHHH----------HHHHHHHHHHHHHHHHHHHHHHHH---------------cC
Confidence            356788999999999975542   13333          489999999999999999998741               22


Q ss_pred             ceeeeHHHHHHHHHH
Q 032126          107 RLILTMEDLSKALRE  121 (147)
Q Consensus       107 r~vLTmEDLs~AL~E  121 (147)
                      |-+|+-+||..|+..
T Consensus        62 rktI~~~di~~av~~   76 (98)
T 1jfi_A           62 AKTMTTSHLKQCIEL   76 (98)
T ss_dssp             --CBCHHHHHTTCC-
T ss_pred             CCeecHHHHHHHHhc
Confidence            458888999888764

>1f1e_A Histone fold protein; archaeal histone protein, DNA binding protein; HET: MSE; 1.37A {Methanopyrus kandleri} SCOP: a.22.1.2

Probab=89.97  E-value=1  Score=34.74  Aligned_cols=66  Identities=20%  Similarity=0.192  Sum_probs=48.5

Q ss_pred             CCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHH
Q 032126           34 TIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTME  113 (147)
Q Consensus        34 ~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmE  113 (147)
                      .||-+.+.-+|.++|-    .||    ..-=+-.+.=+.+.|++.|+.+|-.+|+               +.+|-++|-|
T Consensus        82 ~lP~a~V~Ri~k~~g~----~RV----S~~A~~~l~~~le~f~~~I~~~A~~~a~---------------ha~RKTIt~e  138 (154)
T 1f1e_A           82 LFGRATVRRILKRAGI----ERA----SSDAVDLYNKLICRATEELGEKAAEYAD---------------EDGRKTVQGE  138 (154)
T ss_dssp             CCCHHHHHHHHHHTTC----CEE----CHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HTTCSEECHH
T ss_pred             cCCccHHHHHHHHcCC----ccc----hHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HcCCCccCHH
Confidence            6899999999999964    465    0001224455667889999999999884               3345589999


Q ss_pred             HHHHHHHHh
Q 032126          114 DLSKALREY  122 (147)
Q Consensus       114 DLs~AL~Ey  122 (147)
                      |+..||+..
T Consensus       139 DV~~Al~~~  147 (154)
T 1f1e_A          139 DVEKAITYS  147 (154)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHhc
Confidence            999999753

>3b0b_C CENP-X, centromere protein X; histone fold, DNA binding, DNA, nucleus, DNA binding protein; 2.15A {Gallus gallus} PDB: 3vh5_D 3vh6_D

Probab=88.52  E-value=3  Score=29.03  Aligned_cols=72  Identities=14%  Similarity=0.112  Sum_probs=44.1

Q ss_pred             CCCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccce
Q 032126           29 MGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRL  108 (147)
Q Consensus        29 ddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~  108 (147)
                      ++..|+||.+++.-+|+. .|+-...||        ..=---+..+++-=.+..|.+-+-.    ..+       -+...
T Consensus         3 ~~~~~~~~~~lI~ril~~-~f~~~ktrI--------~~dAl~l~aeyl~iFV~EAv~RA~~----~a~-------~e~~~   62 (81)
T 3b0b_C            3 EEREGGFRKETVERLLRL-HFRDGRTRV--------NGDALLLMAELLKVFVREAAARAAR----QAQ-------AEDLE   62 (81)
T ss_dssp             ----CCCCHHHHHHHHHH-HCCSTTCEE--------CHHHHHHHHHHHHHHHHHHHHHHHH----HHH-------HTTCS
T ss_pred             CccCCCCCHHHHHHHHHH-HhccCcccc--------cHHHHHHHHHHHHHHHHHHHHHHHH----HHH-------hCCCC
Confidence            567899999999999999 999888888        4333333455555445555442211    111       11224


Q ss_pred             eeeHHHHHHHHH
Q 032126          109 ILTMEDLSKALR  120 (147)
Q Consensus       109 vLTmEDLs~AL~  120 (147)
                      .|+.|||.+.+.
T Consensus        63 ~le~~~LEki~p   74 (81)
T 3b0b_C           63 KVDIEHVEKVLP   74 (81)
T ss_dssp             EECHHHHHHHHH
T ss_pred             eecHHHHHHHHH
Confidence            899999998764

>2ly8_A Budding yeast chaperone SCM3; centromere protein, CENH3 variants, partially unfolded; NMR {Saccharomyces cerevisiae}

Probab=88.08  E-value=1.5  Score=32.75  Aligned_cols=47  Identities=23%  Similarity=0.287  Sum_probs=37.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHHHHHHhCccc
Q 032126           65 IRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREYGVNV  126 (147)
Q Consensus        65 ~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~AL~EyGInv  126 (147)
                      .--+.=+...|+.+|+.||..|++-.               +|-|.|.+|...||+..|.++
T Consensus        70 y~e~r~vl~~~l~~i~rdav~yaehA---------------~RKTVta~DV~~Alkr~G~~l  116 (121)
T 2ly8_A           70 YEEVRAVLKSFLESVIRDSVTYTEHA---------------KRKTVTSLDVVYALKRQGRTL  116 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHT---------------TCCCBCHHHHHHHHHHTTCGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhc---------------CCCcCcHHHHHHHHHhCCCcC
Confidence            55566678899999999999998631               133899999999999999754

>4dra_E Centromere protein X; DNA binding complex, DNA damage repair, histone-fold, DNA BI protein; 2.41A {Homo sapiens} PDB: 4drb_J

Probab=85.75  E-value=6.9  Score=27.53  Aligned_cols=70  Identities=16%  Similarity=0.159  Sum_probs=43.9

Q ss_pred             CCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceee
Q 032126           31 YTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLIL  110 (147)
Q Consensus        31 Y~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vL  110 (147)
                      -.|+||.+++.-+|. ..|+-...||        ..=---+..+++-=.+.+|..-+-....          ..+ .-+|
T Consensus         9 ~~~~i~~~li~ril~-~~F~~~kTkI--------s~dAl~l~aeyl~iFV~EAv~RA~~~a~----------~e~-~~~l   68 (84)
T 4dra_E            9 AGSGFRKELVSRLLH-LHFKDDKTKV--------SGDALQLMVELLKVFVVEAAVRGVRQAQ----------AED-ALRV   68 (84)
T ss_dssp             --CCCCHHHHHHHHH-TTCSSTTCEE--------CHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HTT-CSSB
T ss_pred             CCCCCCHHHHHHHHH-HHhcCCCccc--------cHHHHHHHHHHHHHHHHHHHHHHHHHHH----------hcC-CCcc
Confidence            479999999999999 9999888888        4433334445544444555443211100          011 2369


Q ss_pred             eHHHHHHHHH
Q 032126          111 TMEDLSKALR  120 (147)
Q Consensus       111 TmEDLs~AL~  120 (147)
                      +.|||.+.|-
T Consensus        69 e~e~LEki~p   78 (84)
T 4dra_E           69 DVDQLEKVLP   78 (84)
T ss_dssp             CHHHHHHHHH
T ss_pred             cHHHHHHHHH
Confidence            9999998764

>3v9r_B MHF2, uncharacterized protein YDL160C-A; histone fold, fanconi anemia, DNA repair, DNA BI protein; 2.40A {Saccharomyces cerevisiae}

Probab=83.73  E-value=2.7  Score=30.22  Aligned_cols=72  Identities=15%  Similarity=0.214  Sum_probs=39.2

Q ss_pred             CCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHH
Q 032126           34 TIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTME  113 (147)
Q Consensus        34 ~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmE  113 (147)
                      .||.+++.-+|. -.|.-.+-||        .+=---+.+|+|-=-+.+|.--|.-+..+..+.    ...+...+|++|
T Consensus         1 ~ip~~llaRIL~-~~F~~~kTrI--------t~da~~lv~kY~diFVrEAv~Rs~e~ke~~~~~----~~~~~d~~Leve   67 (88)
T 3v9r_B            1 MLSKEALIKILS-QNEGGNDMKI--------ADEVVPMIQKYLDIFIDEAVLRSLQSHKDINGE----RGDKSPLELSHQ   67 (88)
T ss_dssp             CCCSHHHHHHHT-TTSCSSCCEE--------CTTTHHHHHHHHHHHHHHHHHHHHHHHHCC---------------CCHH
T ss_pred             CCCHHHHHHHHH-HHhCCCCcee--------cHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc----ccCCCCCeeehH
Confidence            389999999999 8999999998        544344444544444444443322222111111    123444789999


Q ss_pred             HHHHH
Q 032126          114 DLSKA  118 (147)
Q Consensus       114 DLs~A  118 (147)
                      ||.+-
T Consensus        68 DLEki   72 (88)
T 3v9r_B           68 DLERI   72 (88)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            99864

---

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	147
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	97.64
d2huec1	82	Histone H4 {African clawed frog (Xenopus laevis) [	97.07
d1ku5a_	66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	96.83
d1tafb_	70	TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta	95.86
d2bykb1	89	Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax	95.85
d1n1ja_	87	Nuclear transcription factor Y subunit beta (Nf-Yb	95.68
d1jfib_	135	Negative cofactor 2, NC2, beta chain {Human (Homo	95.65
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	95.56
d1n1jb_	78	Nuclear transcription factor Y subunit gamma (Nf-Y	95.19
d1jfia_	66	Negative cofactor 2, NC2, alpha chain {Human (Homo	94.32
d2byka1	72	Chrac-16 {Fruit fly (Drosophila melanogaster) [Tax	92.88
d1tafa_	68	TAF(II)42 {Fruit fly (Drosophila melanogaster) [Ta	92.73
d1h3ob_	74	TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom	87.45

>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=97.64  E-value=9.5e-05  Score=47.43  Aligned_cols=66  Identities=18%  Similarity=0.253  Sum_probs=52.9

Q ss_pred             CCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHH
Q 032126           34 TIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTME  113 (147)
Q Consensus        34 ~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmE  113 (147)
                      -||-+.+..++++.|..    ||    ..-=.-+|+=++..||.+|+.+|.++++-               .+|-|+|.+
T Consensus         3 eLP~a~I~ri~k~~~~~----ri----s~ea~~~l~~~~e~fi~~l~~~a~~~a~~---------------~kRkTi~~~   59 (68)
T d1htaa_           3 ELPIAPIGRIIKNAGAE----RV----SDDARIALAKVLEEMGEEIASEAVKLAKH---------------AGRKTIKAE   59 (68)
T ss_dssp             CSCHHHHHHHHHHTTCS----CC----CHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------TTCSSCCHH
T ss_pred             cCcHHHHHHHHHHCCcc----hh----hHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------hCCCcCCHH
Confidence            38999999999998764    33    11226799999999999999999999852               235699999


Q ss_pred             HHHHHHHHh
Q 032126          114 DLSKALREY  122 (147)
Q Consensus       114 DLs~AL~Ey  122 (147)
                      |+..||+-|
T Consensus        60 DV~~Alk~~   68 (68)
T d1htaa_          60 DIELARKMF   68 (68)
T ss_dssp             HHHHHHHTC
T ss_pred             HHHHHHHhC
Confidence            999999854

>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=97.07  E-value=0.00046  Score=46.58  Aligned_cols=67  Identities=19%  Similarity=0.218  Sum_probs=57.0

Q ss_pred             CCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHH
Q 032126           34 TIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTME  113 (147)
Q Consensus        34 ~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmE  113 (147)
                      -||.+-+.-+.+++|..--..-+        ...++-....|+.+|+.||..|++-               .+|-++|.+
T Consensus         9 gI~k~~i~Riar~~Gv~ris~d~--------~~~l~~~l~~~l~~i~~~a~~~~~h---------------akRKTvt~~   65 (82)
T d2huec1           9 GITKPAIRRLARRGGVKRISGLI--------YEETRGVLKVFLENVIRDAVTYTEH---------------AKRKTVTAM   65 (82)
T ss_dssp             SSCHHHHHHHHHHTTCCEECTTH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------TTCSEECHH
T ss_pred             CcCHHHHHHHHHHcCcccchHHH--------HHHHHHHHHHHHHHHHHHHHHHHHH---------------hCCCcCCHH
Confidence            49999999999999998655556        7889999999999999999999842               134588999


Q ss_pred             HHHHHHHHhC
Q 032126          114 DLSKALREYG  123 (147)
Q Consensus       114 DLs~AL~EyG  123 (147)
                      |+..||+-+|
T Consensus        66 DV~~Alkr~g   75 (82)
T d2huec1          66 DVVYALKRQG   75 (82)
T ss_dssp             HHHHHTTTTC
T ss_pred             HHHHHHHhcC
Confidence            9999999766

>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=96.83  E-value=0.0019  Score=41.00  Aligned_cols=63  Identities=21%  Similarity=0.368  Sum_probs=50.9

Q ss_pred             CcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHH
Q 032126           35 IPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMED  114 (147)
Q Consensus        35 IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmED  114 (147)
                      +|-+.+..++++.|    ++||    ..-=.=+++-|+..||.+++.+|..+++               .++|=|++.+|
T Consensus         3 LP~a~I~rI~k~~~----~~ri----s~ea~~~l~~a~e~Fi~~l~~~a~~~a~---------------~~~RKTI~~~D   59 (66)
T d1ku5a_           3 LPIAPVDRLIRKAG----AERV----SEQAAKVLAEYLEEYAIEIAKKAVEFAR---------------HAGRKTVKVED   59 (66)
T ss_dssp             SCHHHHHHHHHHTT----CSEE----CHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------TTTCSEECHHH
T ss_pred             CCHHHHHHHHHhCc----cccc----HHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HcCCCCCCHHH
Confidence            78899999999876    3466    2333568999999999999999999984               23355999999


Q ss_pred             HHHHHH
Q 032126          115 LSKALR  120 (147)
Q Consensus       115 Ls~AL~  120 (147)
                      +..||+
T Consensus        60 v~~Al~   65 (66)
T d1ku5a_          60 IKLAIK   65 (66)
T ss_dssp             HHHHHT
T ss_pred             HHHHHh
Confidence            999985

>d1tafb_ a.22.1.3 (B:) TAF(II)62 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)62
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=95.86  E-value=0.016  Score=38.60  Aligned_cols=67  Identities=18%  Similarity=0.216  Sum_probs=56.0

Q ss_pred             CCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceee
Q 032126           31 YTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLIL  110 (147)
Q Consensus        31 Y~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vL  110 (147)
                      |...+|-+-+.-+-+..|+..-..-+        .+.||-=..==|.+|+++|..|-  |.             -||.+|
T Consensus         3 ~~S~~~~esik~iAeS~Gi~~l~de~--------a~~LA~DveYRl~eiiQeA~KFM--rh-------------skR~~L   59 (70)
T d1tafb_           3 YGSSISAESMKVIAESIGVGSLSDDA--------AKELAEDVSIKLKRIVQDAAKFM--NH-------------AKRQKL   59 (70)
T ss_dssp             CSCCCCHHHHHHHHHHTTCCCBCHHH--------HHHHHHHHHHHHHHHHHHHHHHH--HH-------------TTCSSB
T ss_pred             CcccCCHHHHHHHHHHcCCCCCCHHH--------HHHHHHHHHHHHHHHHHHHHHHH--HH-------------hccCcC
Confidence            77889999999999999998766667        78888777778899999999995  32             235789


Q ss_pred             eHHHHHHHHH
Q 032126          111 TMEDLSKALR  120 (147)
Q Consensus       111 TmEDLs~AL~  120 (147)
                      |.+|+..||+
T Consensus        60 tt~Did~ALk   69 (70)
T d1tafb_          60 SVRDIDMSLK   69 (70)
T ss_dssp             CHHHHHHHHC
T ss_pred             cHHHHHHHHc
Confidence            9999999985

>d2bykb1 a.22.1.3 (B:11-99) Chrac-14 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Chrac-14
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=95.85  E-value=0.0067  Score=40.57  Aligned_cols=44  Identities=18%  Similarity=0.235  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHHHHHHhCc
Q 032126           66 RLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREYGV  124 (147)
Q Consensus        66 RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~AL~EyGI  124 (147)
                      -+|+-||.-||..++..|...|+.               ++|-+++-+|+..||.+.|.
T Consensus        25 ~~i~~aae~FI~~lt~~A~~~a~~---------------~~rKtI~~~dv~~Al~~~~f   68 (89)
T d2bykb1          25 AAIARAASVFAIFVTSSSTALAHK---------------QNHKTITAKDILQTLTELDF   68 (89)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH---------------TTCSSCCHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH---------------hCCCccCHHHHHHHHHHCCc
Confidence            489999999999999999998742               22349999999999999886

>d1n1ja_ a.22.1.3 (A:) Nuclear transcription factor Y subunit beta (Nf-Yb3) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Nuclear transcription factor Y subunit beta (Nf-Yb3)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.68  E-value=0.031  Score=36.90  Aligned_cols=70  Identities=17%  Similarity=0.253  Sum_probs=51.8

Q ss_pred             CCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHH
Q 032126           34 TIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTME  113 (147)
Q Consensus        34 ~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmE  113 (147)
                      .+|-+-+..+++.+-  .++.+|    .--=.-+|+=|+.-||..++..|.+.|+.               ++|-+++-+
T Consensus         2 ~LP~a~v~ri~K~~~--p~~~~i----s~ea~~~i~~a~e~Fi~~lt~~A~~~a~~---------------~~rKTI~~~   60 (87)
T d1n1ja_           2 YLPIANVARIMKNAI--PQTGKI----AKDAKECVQECVSEFISFITSEASERCHQ---------------EKRKTINGE   60 (87)
T ss_dssp             CCCHHHHHHHHHHTS--CTTCEE----CHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------TTCSSBCHH
T ss_pred             CCcHhHHHHHHHHhC--Cccccc----cHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------HCCCCCCHH
Confidence            478888888887651  223333    11113489999999999999999998742               224489999


Q ss_pred             HHHHHHHHhCc
Q 032126          114 DLSKALREYGV  124 (147)
Q Consensus       114 DLs~AL~EyGI  124 (147)
                      |+..||.+.|.
T Consensus        61 dv~~Al~~~~~   71 (87)
T d1n1ja_          61 DILFAMSTLGF   71 (87)
T ss_dssp             HHHHHHHHTTC
T ss_pred             HHHHHHHHcCc
Confidence            99999999884

>d1jfib_ a.22.1.3 (B:) Negative cofactor 2, NC2, beta chain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Negative cofactor 2, NC2, beta chain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.65  E-value=0.02  Score=41.00  Aligned_cols=69  Identities=22%  Similarity=0.408  Sum_probs=53.2

Q ss_pred             CCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHH
Q 032126           34 TIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTME  113 (147)
Q Consensus        34 ~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmE  113 (147)
                      .+|-+.+..+++...   ++.+|    .--=.=+|+-|+.-||..|+..|...|+.               ++|-+++-+
T Consensus         4 ~LP~a~I~kI~K~~~---~~~~i----s~dA~~~i~~a~~~Fi~~lt~~A~~~a~~---------------~~RkTi~~~   61 (135)
T d1jfib_           4 TIPRAAINKMIKETL---PNVRV----ANDARELVVNCCTEFIHLISSEANEICNK---------------SEKKTISPE   61 (135)
T ss_dssp             CCCHHHHHHHHHHHS---TTCCB----CHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------TTCSSBCHH
T ss_pred             cccHHHHHHHHhhCC---ccchh----hHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------hCCCcccHH
Confidence            578899999998864   34444    11113489999999999999999999852               224499999


Q ss_pred             HHHHHHHHhCc
Q 032126          114 DLSKALREYGV  124 (147)
Q Consensus       114 DLs~AL~EyGI  124 (147)
                      |+..||.+.|.
T Consensus        62 Dv~~Al~~~~f   72 (135)
T d1jfib_          62 HVIQALESLGF   72 (135)
T ss_dssp             HHHHHHHHHTT
T ss_pred             HHHHHHHHcCc
Confidence            99999999986

>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=95.56  E-value=0.019  Score=41.74  Aligned_cols=65  Identities=20%  Similarity=0.240  Sum_probs=52.6

Q ss_pred             CCCCcHHHHHHHHHhCCCCC--CCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhccccccccee
Q 032126           32 TPTIPDELVEHYLAKSGFQC--PDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLI  109 (147)
Q Consensus        32 ~P~IPD~Vt~yyL~~aGf~~--~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~v  109 (147)
                      .-.+|-+-+.-++++.|..-  .|.          .-+|+-++.-|+.+|+.+|.++++-               .+|-+
T Consensus        77 ~~~fp~a~IkRi~k~~g~~ris~dA----------~~~l~~~~E~fi~~l~~~A~~~a~~---------------~kRkT  131 (151)
T d1f1ea_          77 GELFGRATVRRILKRAGIERASSDA----------VDLYNKLICRATEELGEKAAEYADE---------------DGRKT  131 (151)
T ss_dssp             SCCCCHHHHHHHHHHTTCCEECHHH----------HHHHHHHHHHHHHHHHHHHHHHHHH---------------TTCSE
T ss_pred             cCccCHHHHHHHHHcCCcchhhHHH----------HHHHHHHHHHHHHHHHHHHHHHHHH---------------hCCCc
Confidence            44689999999999988662  233          4589999999999999999999842               23559


Q ss_pred             eeHHHHHHHHHH
Q 032126          110 LTMEDLSKALRE  121 (147)
Q Consensus       110 LTmEDLs~AL~E  121 (147)
                      ||-+|+..||.-
T Consensus       132 I~~~DI~~Av~~  143 (151)
T d1f1ea_         132 VQGEDVEKAITY  143 (151)
T ss_dssp             ECHHHHHHHHHH
T ss_pred             CCHHHHHHHHHH
Confidence            999999999863

>d1n1jb_ a.22.1.3 (B:) Nuclear transcription factor Y subunit gamma (Nf-Yc2) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Nuclear transcription factor Y subunit gamma (Nf-Yc2)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.19  E-value=0.014  Score=37.77  Aligned_cols=66  Identities=20%  Similarity=0.232  Sum_probs=46.4

Q ss_pred             CcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHH
Q 032126           35 IPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMED  114 (147)
Q Consensus        35 IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmED  114 (147)
                      +|-+-+..+++..   .+..+|    ..-=.-+|+-|++=||..++..|++.++.               ++|-+++.+|
T Consensus         1 LP~srVkrImK~~---~~~~~i----s~ea~~~i~~a~E~Fi~~l~~~A~~~a~~---------------~~rkti~~~d   58 (78)
T d1n1jb_           1 LPLARIKKIMKLD---EDVKMI----SAEAPVLFAKAAQIFITELTLRAWIHTED---------------NKRRTLQRND   58 (78)
T ss_dssp             CCHHHHHHHHTTS---TTCCCB----CTHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------TTCSEECHHH
T ss_pred             CCHHHHHHHHhcC---Cccccc----chHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------cCCCcCCHHH
Confidence            3666677777631   222232    22225689999999999999999998752               1234999999


Q ss_pred             HHHHHHHh
Q 032126          115 LSKALREY  122 (147)
Q Consensus       115 Ls~AL~Ey  122 (147)
                      |..|+.+.
T Consensus        59 l~~av~~~   66 (78)
T d1n1jb_          59 IAMAITKF   66 (78)
T ss_dssp             HHHHHTTC
T ss_pred             HHHHHhcC
Confidence            99999764

>d1jfia_ a.22.1.3 (A:) Negative cofactor 2, NC2, alpha chain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Negative cofactor 2, NC2, alpha chain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.32  E-value=0.031  Score=35.26  Aligned_cols=60  Identities=13%  Similarity=0.213  Sum_probs=42.5

Q ss_pred             CcHHHHHHHHHhCCCC---CCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeee
Q 032126           35 IPDELVEHYLAKSGFQ---CPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILT  111 (147)
Q Consensus        35 IPD~Vt~yyL~~aGf~---~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLT  111 (147)
                      +|-+-+..+|+...--   ..|..          =+++-|++-||.+++..|+++++               .++|-+|+
T Consensus         3 fP~srVkkimk~~~~~~~is~~A~----------~~~~~a~E~Fi~~l~~~A~~~a~---------------~~krktI~   57 (66)
T d1jfia_           3 FPPARIKKIMQTDEEIGKVAAAVP----------VIISRALELFLESLLKKACQVTQ---------------SRNAKTMT   57 (66)
T ss_dssp             CCHHHHHHHHTTSTTCCCBCTTHH----------HHHHHHHHHHHHHHHHHHHHHHH---------------TC---CBC
T ss_pred             CChHHHHHHHhcCCccccccHHHH----------HHHHHHHHHHHHHHHHHHHHHHH---------------HhCCCcCC
Confidence            5778888888853211   12333          48999999999999999999874               22344899


Q ss_pred             HHHHHHHH
Q 032126          112 MEDLSKAL  119 (147)
Q Consensus       112 mEDLs~AL  119 (147)
                      -+||..|+
T Consensus        58 ~~dl~~ai   65 (66)
T d1jfia_          58 TSHLKQCI   65 (66)
T ss_dssp             HHHHHTTC
T ss_pred             HHHHHHHh
Confidence            99998764

>d2byka1 a.22.1.3 (A:29-100) Chrac-16 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Chrac-16
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=92.88  E-value=0.11  Score=33.41  Aligned_cols=43  Identities=23%  Similarity=0.225  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHHHHHHh
Q 032126           66 RLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSKALREY  122 (147)
Q Consensus        66 RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~AL~Ey  122 (147)
                      =|||-|++-||.+++..|+.++..              ..++-+|+-+||+.|....
T Consensus        16 ~lvskAtElFi~~L~~~a~~~a~~--------------~~~~ktl~~~dl~~aV~~~   58 (72)
T d2byka1          16 FLMTKCTELFVRHLAGAAYTEEFG--------------QRPGEALKYEHLSQVVNKN   58 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHT--------------TCCSCEECHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh--------------ccCCccccHHHHHHHHccC
Confidence            489999999999999999886521              1112279999999998754

>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=92.73  E-value=0.26  Score=32.23  Aligned_cols=60  Identities=15%  Similarity=0.231  Sum_probs=47.7

Q ss_pred             HHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhchhcccccccceeeeHHHHHH
Q 032126           38 ELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKDKRDKQQKDKRLILTMEDLSK  117 (147)
Q Consensus        38 ~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~k~~~~~kd~r~vLTmEDLs~  117 (147)
                      .++.-+|+.-|.+-=+|||        .-.+==-+-+++++|..||.-|+.-.               +|..++.||+..
T Consensus         5 ~~i~~iL~~~GV~~yeprV--------~~qlLef~yRYtt~VL~DA~vys~HA---------------~k~~id~dDVkL   61 (68)
T d1tafa_           5 QVIMSILKELNVQEYEPRV--------VNQLLEFTFRYVTSILDDAKVYANHA---------------RKKTIDLDDVRL   61 (68)
T ss_dssp             HHHHHHHHHTTCCCBCTHH--------HHHHHHHHHHHHHHHHHHHHHHHHHT---------------TCSSBCHHHHHH
T ss_pred             HHHHHHHHHcCCccccHHH--------HHHHHHHHHHHHHHHHHHHHHHHhhc---------------CCCCCCHHHHHH
Confidence            4677899999999999999        66555566899999999999997532               123579999988


Q ss_pred             HHH
Q 032126          118 ALR  120 (147)
Q Consensus       118 AL~  120 (147)
                      |..
T Consensus        62 Ai~   64 (68)
T d1tafa_          62 ATE   64 (68)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            865

>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=87.45  E-value=1.6  Score=28.61  Aligned_cols=66  Identities=17%  Similarity=0.283  Sum_probs=49.6

Q ss_pred             chHHHHHHHHcCCCCCCCcHHHHHHHHHhCCCCCCCcccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhc
Q 032126           18 DAALTEFLSSLMGYTPTIPDELVEHYLAKSGFQCPDVRLNCCLCFCRIRLVAVATQKFVAEVATDALQQCKARQAAVVKD   97 (147)
Q Consensus        18 d~~L~efl~~LddY~P~IPD~Vt~yyL~~aGf~~~D~Rv~~~~~~~~~RLvSLAaQKFisDIa~DA~q~~kiR~~~~~~~   97 (147)
                      -..|.||+.+++.=                  ..=|+-+        .-++.=.|..||.+|...|.+.||-|.+     
T Consensus         6 K~~L~eLv~~idp~------------------~~ld~~v--------ee~ll~iADdFV~~V~~~ac~lAKhR~s-----   54 (74)
T d1h3ob_           6 KKKLQDLVREVDPN------------------EQLDEDV--------EEMLLQIADDFIESVVTAACQLARHRKS-----   54 (74)
T ss_dssp             HHHHHHHHHHHCSS------------------CCCCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHHTTC-----
T ss_pred             HHHHHHHHHHhCCC------------------CCCCHHH--------HHHHHHHHHHHHHHHHHHHHHHHHhCCC-----
Confidence            35678888877521                  2247778        8888889999999999999999998843     


Q ss_pred             hhcccccccceeeeHHHHHHHHH-HhCc
Q 032126           98 KRDKQQKDKRLILTMEDLSKALR-EYGV  124 (147)
Q Consensus        98 k~~~~~kd~r~vLTmEDLs~AL~-EyGI  124 (147)
                                -+|...|+.-.|+ +|+|
T Consensus        55 ----------~~le~kDvql~LeR~wNm   72 (74)
T d1h3ob_          55 ----------STLEVKDVQLHLERQWNM   72 (74)
T ss_dssp             ----------CEECHHHHHHHHHHHTCC
T ss_pred             ----------CCCcHHHHHHHHHhhcCc
Confidence                      2677888888774 3444