Citrus Sinensis ID: 030236

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-
Protein Sequence
MKQSKDPFEAALEESPGDSPDELEIETQPQTGTAAGSATAAVTGELEDEFDNLESQAPMSVSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNVTQILFAN
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHcccccHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccccHHHEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHccccccccccHHHHHHHHHHHHHccHHHHHHHHHHHHHcccHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Coil and Loop (DISEMBL)
mkqskdpfeaaleespgdspdeleietqpqtgtaagsataavTGELedefdnlesqapmsvsagpaakmtmsknkdeydeeddenvdvelgkfpsssdpaKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITgsqkislpmTIVVCGIAKMFVGELVETGFCVNVTQILFAN
Flexible Loop (DISEMBL)
mkqskdpfeaaleespgdspdelEIETQPQTGTAAGSATAAVTGELEDEFDNLEsqapmsvsagpaakMTMSKNKDEYDEEDDENVDVELGkfpsssdpaKMAKMQAILNQFTEDQMNRYESFRrsalqksnMRRLLVSitgsqkislpMTIVVCGIAKMFVGELVETGFCVNVTQILFAN
Low Complexity Region (SEG)
MKQSKDPFEAALEESPGDSPDELEIETQPQtgtaagsataavtgELEDEFDNLESQAPMSVSAGPAAKMTMSknkdeydeeddenvdveLGKFPSSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNVTQILFAN
Disordered region (IsUnstruct)
*************************************************************************************************************************************RRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNVTQILF**
Disordered Region (DISOPRED)
************************************************************************************************************LNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNVTQILFAN
Disordered Region (DISEMBL)
***********************EIETQ***********AAVTGELEDEFDNLESQAP****************************DVELGKFPSSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNVTQILFAN
Disordered Region (DISPRO)
************************************************************************************************SDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNVTQILFAN
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKQSKDPFEAALEESPGDSPDELEIETQPQTGTAAGSATAAVTGELEDEFDNLESQAPMSVSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNVTQILFAN
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	181	2.2.26 [Sep-21-2011]
Q5RA91	211	Transcription initiation	yes	no	0.408	0.350	0.453	1e-12
Q15544	211	Transcription initiation	yes	no	0.408	0.350	0.453	1e-12
Q5U1X0	211	Transcription initiation	yes	no	0.392	0.336	0.458	2e-12
Q99JX1	211	Transcription initiation	yes	no	0.392	0.336	0.458	2e-12
P49906	196	Transcription initiation	yes	no	0.370	0.341	0.470	3e-11
Q54XM9	450	Transcription initiation	yes	no	0.348	0.14	0.361	6e-09
Q9US54	199	Transcription initiation	yes	no	0.563	0.512	0.350	1e-08
A6NLC8	198	Putative TAF11-like prote	no	no	0.375	0.343	0.434	1e-07
Q04226	346	Transcription initiation	yes	no	0.397	0.208	0.273	0.0002

>sp|Q5RA91|TAF11_PONAB Transcription initiation factor TFIID subunit 11 OS=Pongo abelii GN=TAF11 PE=2 SV=1

 Score = 72.8 bits (177), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/75 (45%), Positives = 54/75 (72%), Gaps = 1/75 (1%)

Query: 98  DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGI 157
           D  ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+ SITG+  +S  + I + GI
Sbjct: 99  DEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQSITGTS-VSQNVVIAMSGI 157

Query: 158 AKMFVGELVETGFCV 172
           +K+FVGE+VE    V
Sbjct: 158 SKVFVGEVVEEALDV 172

Core TAFII present in both of the previously described TFIID species which either lack or contain TAFII30 (TFIID alpha and TFIID beta respectively).
Pongo abelii (taxid: 9601)

>sp|Q15544|TAF11_HUMAN Transcription initiation factor TFIID subunit 11 OS=Homo sapiens GN=TAF11 PE=1 SV=1

 Score = 72.4 bits (176), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/75 (45%), Positives = 54/75 (72%), Gaps = 1/75 (1%)

Query: 98  DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGI 157
           D  ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+ SITG+  +S  + I + GI
Sbjct: 99  DEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQSITGTS-VSQNVVIAMSGI 157

Query: 158 AKMFVGELVETGFCV 172
           +K+FVGE+VE    V
Sbjct: 158 SKVFVGEVVEEALDV 172

Core TAFII present in both of the previously described TFIID species which either lack or contain TAFII30 (TFIID alpha and TFIID beta respectively).

Homo sapiens (taxid: 9606)

>sp|Q5U1X0|TAF11_RAT Transcription initiation factor TFIID subunit 11 OS=Rattus norvegicus GN=Taf11 PE=2 SV=1

 Score = 72.4 bits (176), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 33/72 (45%), Positives = 53/72 (73%), Gaps = 1/72 (1%)

Query: 101 KMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKM 160
           ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+ SITG+  +S  + I + GI+K+
Sbjct: 102 EIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQSITGTS-VSQNVVIAMSGISKV 160

Query: 161 FVGELVETGFCV 172
           FVGE+VE    V
Sbjct: 161 FVGEVVEEALDV 172

Core TAFII present in both of the previously described TFIID species which either lack or contain TAFII30 (TFIID alpha and TFIID beta respectively).

Rattus norvegicus (taxid: 10116)

>sp|Q99JX1|TAF11_MOUSE Transcription initiation factor TFIID subunit 11 OS=Mus musculus GN=Taf11 PE=2 SV=1

 Score = 72.0 bits (175), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 33/72 (45%), Positives = 53/72 (73%), Gaps = 1/72 (1%)

Query: 101 KMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKM 160
           ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+ SITG+  +S  + I + GI+K+
Sbjct: 102 EIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQSITGTS-VSQNVVIAMSGISKV 160

Query: 161 FVGELVETGFCV 172
           FVGE+VE    V
Sbjct: 161 FVGEVVEEALDV 172

Core TAFII present in both of the previously described TFIID species which either lack or contain TAFII30 (TFIID alpha and TFIID beta respectively).

Mus musculus (taxid: 10090)

>sp|P49906|TAF11_DROME Transcription initiation factor TFIID subunit 11 OS=Drosophila melanogaster GN=Taf11 PE=1 SV=1

 Score = 67.8 bits (164), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 32/68 (47%), Positives = 49/68 (72%), Gaps = 1/68 (1%)

Query: 105 MQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGE 164
           MQ +++ FTE+Q++RYE +RRSA  K+ ++RL+ +ITG   +S  + I + GIAK+FVGE
Sbjct: 89  MQVLVSNFTEEQLDRYEMYRRSAFPKAAVKRLMQTITGC-SVSQNVVIAMSGIAKVFVGE 147

Query: 165 LVETGFCV 172
           +VE    V
Sbjct: 148 VVEEALDV 155

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|Q54XM9|TAF11_DICDI Transcription initiation factor TFIID subunit 11 OS=Dictyostelium discoideum GN=taf11 PE=3 SV=1

 Score = 60.5 bits (145), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 47/72 (65%), Gaps = 9/72 (12%)

Query: 105 MQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMT----IVVCGIAKM 160
           M  ++  F+EDQ  R+E ++RS+ Q++N+++++ S+     +S P+     IV+ GIAK+
Sbjct: 344 MNTLIKHFSEDQQTRFEYYKRSSFQRANIKKVMQSV-----LSAPVNQTSAIVMGGIAKV 398

Query: 161 FVGELVETGFCV 172
           FVGE+VE    +
Sbjct: 399 FVGEIVELARSI 410

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

Dictyostelium discoideum (taxid: 44689)

>sp|Q9US54|TAF11_SCHPO Transcription initiation factor TFIID subunit 11 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=taf11 PE=3 SV=1

 Score = 59.7 bits (143), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 40/114 (35%), Positives = 65/114 (57%), Gaps = 12/114 (10%)

Query: 64  GPAAKMTMSKNKDEYD--EEDDEN------VDVELGKFPSSSDPAKMAKMQA--ILNQFT 113
            P++K   + N+ E +  EEDD +      +    GK P  +D     K++   +L  F 
Sbjct: 43  APSSKEKENWNRQEENDLEEDDRDDFGTAAISKVAGK-PGETDDEANEKLRTKYLLESFD 101

Query: 114 EDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVE 167
           E+QM RYE FRR+ L K+N+++L   I  +Q ++  + IV+ G +K+FVGE+VE
Sbjct: 102 EEQMQRYEVFRRANLNKTNVKKLANQIL-NQSVTPNVAIVISGFSKVFVGEIVE 154

Functions as a component of the DNA-binding general transcription factor complex TFIID. Binding of TFIID to a promoter (with or without TATA element) is the initial step in pre-initiation 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.

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

>sp|A6NLC8|YE016_HUMAN Putative TAF11-like protein ENSP00000332601 OS=Homo sapiens PE=3 SV=2

 Score = 56.2 bits (134), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/69 (43%), Positives = 46/69 (66%), Gaps = 1/69 (1%)

Query: 104 KMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVG 163
           +M  +L+  +E+Q++RYE  RRSA  K+ +  L+ SITG + +S  + I + GIAK+FVG
Sbjct: 93  RMTTLLSAMSEEQLSRYEVCRRSAFPKACIAGLMRSITG-RSVSENVAIAMAGIAKVFVG 151

Query: 164 ELVETGFCV 172
           E+VE    V
Sbjct: 152 EVVEEALDV 160

Homo sapiens (taxid: 9606)

>sp|Q04226|TAF11_YEAST Transcription initiation factor TFIID subunit 11 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TAF11 PE=1 SV=1

 Score = 45.4 bits (106), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/73 (27%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 100 AKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAK 159
           A+  + + ++    +DQ NR+E F R++L K+ +++ L S   +Q IS  + + +  + K
Sbjct: 119 AQDEQFKLLVTNLDKDQTNRFEVFHRTSLNKTQVKK-LASTVANQTISENIRVFLQAVGK 177

Query: 160 MFVGELVETGFCV 172
           ++ GE++E    V
Sbjct: 178 IYAGEIIELAMIV 190

Functions as a component of the DNA-binding general transcription factor complex TFIID. Binding of TFIID to a promoter (with or without TATA element) is the initial step in pre-initiation 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.

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	181
225462089	198	PREDICTED: transcription initiation fact	0.856	0.782	0.604	1e-41
388513279	203	unknown [Medicago truncatula]	0.889	0.793	0.539	2e-41
388491516	203	unknown [Medicago truncatula]	0.889	0.793	0.528	2e-40
217072422	203	unknown [Medicago truncatula]	0.889	0.793	0.534	5e-40
224057892	222	predicted protein [Populus trichocarpa]	0.922	0.752	0.560	2e-38
255583916	205	Transcription initiation factor TFIID su	0.839	0.741	0.623	3e-38
388503812	205	unknown [Lotus japonicus]	0.922	0.814	0.529	4e-37
351734450	155	uncharacterized protein LOC100305481 [Gl	0.646	0.754	0.511	4e-35
297804116	211	predicted protein [Arabidopsis lyrata su	0.944	0.810	0.568	3e-34
449460461	220	PREDICTED: uncharacterized protein LOC10	0.911	0.75	0.566	4e-34

>gi|225462089|ref|XP_002277017.1| PREDICTED: transcription initiation factor TFIID subunit 11 [Vitis vinifera] gi|296086768|emb|CBI32917.3| unnamed protein product [Vitis vinifera]

 Score =  174 bits (441), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 107/177 (60%), Positives = 127/177 (71%), Gaps = 22/177 (12%)

Query: 1   MKQSKDPFEAALEES-PGDSPDELEIETQPQTGTAAGSATAAVTGELEDEFD-NLESQAP 58
           MKQSKDPFE A EES P DSP E EI                V G++EDE D N+     
Sbjct: 1   MKQSKDPFEVAFEESSPPDSPVE-EI----------------VGGQIEDEDDANVNVHPT 43

Query: 59  MSVSAGPAAKMTM---SKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTED 115
            + SA P++  T+   +K+KDE +EE++EN+DVELGK P+S DP KMAKMQAIL+QFTE+
Sbjct: 44  STPSAAPSSGTTVPPTAKSKDEDEEEEEENMDVELGKLPTSGDPHKMAKMQAILSQFTEE 103

Query: 116 QMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCV 172
           QM+RYESFRRS  QK+NM++LLVSITGSQKIS PMTIV  GIAKMFVGELVET   V
Sbjct: 104 QMSRYESFRRSGFQKANMKKLLVSITGSQKISAPMTIVASGIAKMFVGELVETARMV 160

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388513279|gb|AFK44701.1| unknown [Medicago truncatula]

 Score =  173 bits (439), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 95/176 (53%), Positives = 128/176 (72%), Gaps = 15/176 (8%)

Query: 1   MKQSKDPFEAALEESPGDSPDELEIETQPQTGT----AAGSATAAVTGELEDEFDNLESQ 56
           MKQSKDPFEAA EESP +SP  +E E  P   T    +  S+    T   E+E +++++ 
Sbjct: 1   MKQSKDPFEAAFEESPPESP--IETEPDPDASTENPNSTNSSLPQSTLTHEEEHNHIKT- 57

Query: 57  APMSVSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTEDQ 116
                   P +  T++K+KDE D+E+++N+DVEL KFP++ DP KMAKMQAIL+QFTE+Q
Sbjct: 58  --------PNSNNTITKHKDEEDDEEEDNMDVELAKFPTAGDPHKMAKMQAILSQFTEEQ 109

Query: 117 MNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCV 172
           M+RYESFRR+  QK+NM+RLL SITG+QKIS+P+TI V GIAK+FVGE+VET   +
Sbjct: 110 MSRYESFRRAGFQKANMKRLLTSITGTQKISIPITIAVSGIAKVFVGEVVETARTI 165

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388491516|gb|AFK33824.1| unknown [Medicago truncatula]

 Score =  170 bits (430), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 93/176 (52%), Positives = 127/176 (72%), Gaps = 15/176 (8%)

Query: 1   MKQSKDPFEAALEESPGDSPDELEIETQPQTGT----AAGSATAAVTGELEDEFDNLESQ 56
           MKQSKDPFEAA EESP +SP  +E E  P   T    +  S+    T   E+E +++++ 
Sbjct: 1   MKQSKDPFEAAFEESPPESP--IETEPDPDASTENPNSTNSSLPQSTLAHEEEHNHIKT- 57

Query: 57  APMSVSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTEDQ 116
                   P +  T++K+KDE D+E+++N+DVEL KFP++ DP KMAKMQAIL+QFTE+Q
Sbjct: 58  --------PNSNNTITKHKDEEDDEEEDNMDVELAKFPTAGDPHKMAKMQAILSQFTEEQ 109

Query: 117 MNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCV 172
           M+RYESFRR+  QK+NM+RLL SITG+QKIS+P+TI +  IAK+FVGE+VET   +
Sbjct: 110 MSRYESFRRAGFQKANMKRLLTSITGTQKISIPITIAISRIAKVFVGEVVETARTI 165

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217072422|gb|ACJ84571.1| unknown [Medicago truncatula]

 Score =  169 bits (428), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 94/176 (53%), Positives = 127/176 (72%), Gaps = 15/176 (8%)

Query: 1   MKQSKDPFEAALEESPGDSPDELEIETQPQTGT----AAGSATAAVTGELEDEFDNLESQ 56
           MKQSKDPFEAA EES  +SP  +E E  P   T    +  S+    T   E+E +++++ 
Sbjct: 1   MKQSKDPFEAAFEESLPESP--IETEPDPDASTENPNSTNSSLPQSTLTHEEEHNHIKT- 57

Query: 57  APMSVSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTEDQ 116
                   P +  T++K+KDE D+E+++N+DVEL KFP++ DP KMAKMQAIL+QFTE+Q
Sbjct: 58  --------PNSNNTITKHKDEEDDEEEDNMDVELAKFPTAGDPHKMAKMQAILSQFTEEQ 109

Query: 117 MNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCV 172
           M+RYESFRR+  QK+NM+RLL SITG+QKIS+P+TI V GIAK+FVGE+VET   +
Sbjct: 110 MSRYESFRRAGFQKANMKRLLTSITGTQKISIPITIAVSGIAKVFVGEVVETARTI 165

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224057892|ref|XP_002299376.1| predicted protein [Populus trichocarpa] gi|222846634|gb|EEE84181.1| predicted protein [Populus trichocarpa]

 Score =  164 bits (414), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 106/189 (56%), Positives = 124/189 (65%), Gaps = 22/189 (11%)

Query: 1   MKQSKDPFEAAL---EESPGDSP---DELEIETQPQTGTAAGSATAAVTGE--------- 45
           MKQSKDPFEAA    EESP +SP   D+ + +       A  S  A V  +         
Sbjct: 1   MKQSKDPFEAAYVEQEESPPESPVAQDDYDTQASNAAAAADDSQGAVVGQDDDDLGGGGR 60

Query: 46  --LEDEFDNLESQAPMSVSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMA 103
                  D+  +  PM  SA   AK     NKD+ +EE+++N+DVEL K  S++DP KMA
Sbjct: 61  NDFAHSSDHPSASRPMLGSARSKAK-----NKDDDEEEEEDNMDVELSKLASTADPDKMA 115

Query: 104 KMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVG 163
           KMQ IL QFTE QM+RYESFRRSALQK+NM+RLLVSITGSQKISLPMTIVVCGIAKMFVG
Sbjct: 116 KMQTILAQFTEGQMSRYESFRRSALQKTNMKRLLVSITGSQKISLPMTIVVCGIAKMFVG 175

Query: 164 ELVETGFCV 172
           ELVET   V
Sbjct: 176 ELVETARIV 184

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255583916|ref|XP_002532706.1| Transcription initiation factor TFIID subunit, putative [Ricinus communis] gi|223527552|gb|EEF29673.1| Transcription initiation factor TFIID subunit, putative [Ricinus communis]

 Score =  163 bits (412), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 111/178 (62%), Positives = 129/178 (72%), Gaps = 26/178 (14%)

Query: 1   MKQSKDPFEAALEE---SPGDSP---DELEIETQPQTGTAAGSATAAVTGELEDEFDNLE 54
           MKQSKDPFEAA EE   +P +SP   DEL +++Q    T A    AAV  E +D      
Sbjct: 10  MKQSKDPFEAAYEEQEETPPESPLGADEL-LDSQ-TAATTAQDPDAAVLQEDDD------ 61

Query: 55  SQAPMSVSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTE 114
               +  S G         +++E+DEE++ENVDVEL KFPS++DP KMAKMQAIL+QFTE
Sbjct: 62  ----IGSSGG--------GSREEFDEEEEENVDVELAKFPSTADPDKMAKMQAILSQFTE 109

Query: 115 DQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCV 172
           +QM RYESFRRSALQK+NMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVET   V
Sbjct: 110 NQMTRYESFRRSALQKANMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARIV 167

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388503812|gb|AFK39972.1| unknown [Lotus japonicus]

 Score =  159 bits (403), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 91/172 (52%), Positives = 118/172 (68%), Gaps = 5/172 (2%)

Query: 1   MKQSKDPFEAALEESPGDSPDELEIETQPQTGTAAGSATAAVTGELEDEFDNLESQAPMS 60
           MKQSKDPFEAA  ESP +SP E+E E   +    A S+  A   + +++   L      +
Sbjct: 1   MKQSKDPFEAAFVESPPESPVEIEAEPDGEAQNPASSSGVAQVTQAQEDGKKLSKTGTGT 60

Query: 61  VSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTEDQMNRY 120
                       KNKD+ +EE+++N+DVEL K   + DP KMAKMQAIL+QFTE+QM+RY
Sbjct: 61  SGG-----GGGGKNKDDEEEEEEDNMDVELTKLQPTGDPQKMAKMQAILSQFTEEQMSRY 115

Query: 121 ESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCV 172
           ESFRR+  QK+NM+RLL SITG+QKI++P+TIVV GIAKMFVGE+VET   V
Sbjct: 116 ESFRRAGFQKANMKRLLASITGTQKITIPITIVVSGIAKMFVGEVVETARIV 167

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351734450|ref|NP_001236012.1| uncharacterized protein LOC100305481 [Glycine max] gi|255625637|gb|ACU13163.1| unknown [Glycine max]

 Score =  152 bits (385), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 88/172 (51%), Positives = 102/172 (59%), Gaps = 55/172 (31%)

Query: 1   MKQSKDPFEAALEESPGDSPDELEIETQPQTGTAAGSATAAVTGELEDEFDNLESQAPMS 60
           MKQSKDPFEAA EESP            P++ TA                          
Sbjct: 1   MKQSKDPFEAAFEESP------------PESPTAT------------------------- 23

Query: 61  VSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTEDQMNRY 120
                           E +EED  N+DVEL K PS+ DP KMAKMQAIL+QFTE+QM+RY
Sbjct: 24  ----------------ETEEED--NMDVELAKLPSTGDPHKMAKMQAILSQFTEEQMSRY 65

Query: 121 ESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCV 172
           ESFRR+  QK+NM+RLL SITG+QKIS+PMTIVV GIAKMFVGE+VET   V
Sbjct: 66  ESFRRAGFQKANMKRLLASITGTQKISVPMTIVVSGIAKMFVGEVVETARIV 117

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297804116|ref|XP_002869942.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297315778|gb|EFH46201.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  150 bits (378), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 99/174 (56%), Positives = 124/174 (71%), Gaps = 3/174 (1%)

Query: 1   MKQSKDPFEAALEESPGDSPDELEIETQPQTGTAAGSATAAVTGELEDEFDN--LESQAP 58
           MK SKDPFEAA+EE   +SP E  +      G   GS    +  +   E D   ++ + P
Sbjct: 1   MKHSKDPFEAAIEEEQEESPPESPVGGGGGAGGGDGSEEGRIEIDQTQEEDERPVDVRRP 60

Query: 59  MSVSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTEDQMN 118
           M   A  +  +T +KNKDE DEE++EN++VEL K+P+SSDPAKMAKMQ IL+QFTEDQM+
Sbjct: 61  MK-KAKTSVVVTEAKNKDEDDEEEEENMEVELTKYPTSSDPAKMAKMQTILSQFTEDQMS 119

Query: 119 RYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCV 172
           RYESFRRSALQ+  M++LL+ +TGSQKI +PM IVVCGIAKMFVGELVET   V
Sbjct: 120 RYESFRRSALQRPQMKKLLIGVTGSQKIGMPMIIVVCGIAKMFVGELVETARVV 173

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449460461|ref|XP_004147964.1| PREDICTED: uncharacterized protein LOC101207528 [Cucumis sativus] gi|449494264|ref|XP_004159496.1| PREDICTED: uncharacterized protein LOC101229675 [Cucumis sativus]

 Score =  149 bits (377), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 107/189 (56%), Positives = 132/189 (69%), Gaps = 24/189 (12%)

Query: 1   MKQSKDPFEAALEE---SPGDSP---DELEIETQPQTGTAAGSATAAVTGELEDEFDNLE 54
           MKQSKDPFEAA EE   SP +SP   D+LEI T     T A S   A   +L+D  D+ +
Sbjct: 1   MKQSKDPFEAAFEEQEESPPNSPSAADDLEIPT-----TVAPSPADAF--DLQDGDDDPK 53

Query: 55  SQAPMSVSAGPAAKMTM-----------SKNKDEYDEEDDENVDVELGKFPSSSDPAKMA 103
           S +  + S  PA+  +M            K K++ +EE++ENV+VEL KFPSS DP KMA
Sbjct: 54  SASVATHSVAPASTTSMFVSSSSHVSTAPKTKEDDEEEEEENVEVELAKFPSSGDPDKMA 113

Query: 104 KMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVG 163
           KMQAIL+QFTE+QM+RYESFRR+  QK+NM+RLL SI+G+QKIS+PMTIVV GIAKMFVG
Sbjct: 114 KMQAILSQFTEEQMSRYESFRRAGFQKANMKRLLASISGTQKISVPMTIVVSGIAKMFVG 173

Query: 164 ELVETGFCV 172
           ELVET   V
Sbjct: 174 ELVETARVV 182

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	181
TAIR|locus:2120422	210	TAF11 "TBP-associated factor 1	0.917	0.790	0.488	1.1e-32
TAIR|locus:2198671	204	TAF11b "TBP-associated factor	0.408	0.362	0.613	1e-23
ZFIN|ZDB-GENE-040718-283	206	taf11 "TAF11 RNA polymerase II	0.381	0.334	0.485	4.4e-13
UNIPROTKB|E1C6Y5	217	TAF11 "Uncharacterized protein	0.381	0.317	0.471	1.2e-12
UNIPROTKB|Q3ZBP7	210	TAF11 "TAF11 RNA polymerase II	0.381	0.328	0.471	1.2e-12
UNIPROTKB|E2RFN3	211	TAF11 "Uncharacterized protein	0.381	0.327	0.471	1.2e-12
UNIPROTKB|Q15544	211	TAF11 "Transcription initiatio	0.381	0.327	0.471	1.2e-12
UNIPROTKB|F1RZ14	211	TAF11 "Uncharacterized protein	0.381	0.327	0.471	1.2e-12
MGI|MGI:1916026	211	Taf11 "TAF11 RNA polymerase II	0.381	0.327	0.471	1.2e-12
RGD|1305626	211	Taf11 "TAF11 RNA polymerase II	0.381	0.327	0.471	1.2e-12

TAIR|locus:2120422 TAF11 "TBP-associated factor 11" [Arabidopsis thaliana (taxid:3702)]

 Score = 357 (130.7 bits), Expect = 1.1e-32, P = 1.1e-32
 Identities = 83/170 (48%), Positives = 103/170 (60%)

Query:     1 MKQSKDPFEAALEESPGDSPDELEIETQPQXXXXXXXXXXXXXXELEDEFDNLESQAPMS 60
             MK SKDPFEAA+EE   +SP E  +                   + EDE   ++ + PM 
Sbjct:     1 MKHSKDPFEAAIEEEQEESPPESPVGGGGGGDGSEDGRIEIDQTQDEDERP-VDVRRPMK 59

Query:    61 VSAGPAAKMT--MSXXXXXXXXXXXXXXXXXLGKFPSSSDPAKMAKMQAILNQFTEDQMN 118
               A  +  +T   +                 L K+P+SSDPAKMAKMQ IL+QFTEDQM+
Sbjct:    60 -KAKTSVVVTEAKNKDKDEDDEEEEENMDVELTKYPTSSDPAKMAKMQTILSQFTEDQMS 118

Query:   119 RYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVET 168
             RYESFRRSALQ+  M++LL+ +TGSQKI +PM IV CGIAKMFVGELVET
Sbjct:   119 RYESFRRSALQRPQMKKLLIGVTGSQKIGMPMIIVACGIAKMFVGELVET 168

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

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

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

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

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

GO:0009086 "methionine biosynthetic process" evidence=RCA

TAIR|locus:2198671 TAF11b "TBP-associated factor 11B" [Arabidopsis thaliana (taxid:3702)]

 Score = 215 (80.7 bits), Expect = 1.0e-23, Sum P(2) = 1.0e-23
 Identities = 46/75 (61%), Positives = 57/75 (76%)

Query:    95 SSSDPAKMA-KMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIV 153
             + +DP   A KMQ IL+QFTE+QM+RYESFRRS  +KS+M +L+  ITG  K+   M IV
Sbjct:    88 TGADPVTRANKMQKILSQFTEEQMSRYESFRRSGFKKSDMEKLVQRITGGPKMDDTMNIV 147

Query:   154 VCGIAKMFVGELVET 168
             V GIAKMFVG+LVET
Sbjct:   148 VRGIAKMFVGDLVET 162

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

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

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

ZFIN|ZDB-GENE-040718-283 taf11 "TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Danio rerio (taxid:7955)]

 Score = 172 (65.6 bits), Expect = 4.4e-13, P = 4.4e-13
 Identities = 34/70 (48%), Positives = 52/70 (74%)

Query:    98 DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGI 157
             D  ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+ SITGS  +S  + I + GI
Sbjct:    94 DEDEIQKMQVLVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQSITGSS-VSQNVVIAMSGI 152

Query:   158 AKMFVGELVE 167
             AK+F GE+VE
Sbjct:   153 AKVFAGEIVE 162

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

UNIPROTKB|E1C6Y5 TAF11 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 33/70 (47%), Positives = 53/70 (75%)

Query:    98 DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGI 157
             D  ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+ SITG+  +S  + I + GI
Sbjct:   105 DEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQSITGTS-VSQNVVIAMSGI 163

Query:   158 AKMFVGELVE 167
             +K+FVGE+VE
Sbjct:   164 SKVFVGEVVE 173

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

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

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

GO:0042809 "vitamin D receptor binding" evidence=IEA

GO:0043923 "positive regulation by host of viral transcription" evidence=IEA

GO:0046966 "thyroid hormone receptor binding" evidence=IEA

GO:0047485 "protein N-terminus binding" evidence=IEA

UNIPROTKB|Q3ZBP7 TAF11 "TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa" [Bos taurus (taxid:9913)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 33/70 (47%), Positives = 53/70 (75%)

Query:    98 DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGI 157
             D  ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+ SITG+  +S  + I + GI
Sbjct:    98 DEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQSITGTS-VSQNVVIAMSGI 156

Query:   158 AKMFVGELVE 167
             +K+FVGE+VE
Sbjct:   157 SKVFVGEVVE 166

GO:0047485 "protein N-terminus binding" evidence=IEA

GO:0046966 "thyroid hormone receptor binding" evidence=IEA

GO:0043923 "positive regulation by host of viral transcription" evidence=IEA

GO:0042809 "vitamin D receptor binding" evidence=IEA

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

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

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

UNIPROTKB|E2RFN3 TAF11 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 33/70 (47%), Positives = 53/70 (75%)

Query:    98 DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGI 157
             D  ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+ SITG+  +S  + I + GI
Sbjct:    99 DEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQSITGTS-VSQNVVIAMSGI 157

Query:   158 AKMFVGELVE 167
             +K+FVGE+VE
Sbjct:   158 SKVFVGEVVE 167

GO:0047485 "protein N-terminus binding" evidence=IEA

GO:0046966 "thyroid hormone receptor binding" evidence=IEA

GO:0043923 "positive regulation by host of viral transcription" evidence=IEA

GO:0042809 "vitamin D receptor binding" evidence=IEA

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

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

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

UNIPROTKB|Q15544 TAF11 "Transcription initiation factor TFIID subunit 11" [Homo sapiens (taxid:9606)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 33/70 (47%), Positives = 53/70 (75%)

Query:    98 DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGI 157
             D  ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+ SITG+  +S  + I + GI
Sbjct:    99 DEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQSITGTS-VSQNVVIAMSGI 157

Query:   158 AKMFVGELVE 167
             +K+FVGE+VE
Sbjct:   158 SKVFVGEVVE 167

GO:0046982 "protein heterodimerization activity" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

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

GO:0042809 "vitamin D receptor binding" evidence=IPI

GO:0046966 "thyroid hormone receptor binding" evidence=IPI

GO:0043923 "positive regulation by host of viral transcription" evidence=IDA

GO:0003713 "transcription coactivator activity" evidence=IDA

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

GO:0005515 "protein binding" evidence=IPI

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

GO:0047485 "protein N-terminus binding" evidence=IPI

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|F1RZ14 TAF11 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 33/70 (47%), Positives = 53/70 (75%)

Query:    98 DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGI 157
             D  ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+ SITG+  +S  + I + GI
Sbjct:    99 DEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQSITGTS-VSQNVVIAMSGI 157

Query:   158 AKMFVGELVE 167
             +K+FVGE+VE
Sbjct:   158 SKVFVGEVVE 167

GO:0047485 "protein N-terminus binding" evidence=IEA

GO:0046966 "thyroid hormone receptor binding" evidence=IEA

GO:0043923 "positive regulation by host of viral transcription" evidence=IEA

GO:0042809 "vitamin D receptor binding" evidence=IEA

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

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

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

MGI|MGI:1916026 Taf11 "TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Mus musculus (taxid:10090)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 33/70 (47%), Positives = 53/70 (75%)

Query:    98 DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGI 157
             D  ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+ SITG+  +S  + I + GI
Sbjct:    99 DEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQSITGTS-VSQNVVIAMSGI 157

Query:   158 AKMFVGELVE 167
             +K+FVGE+VE
Sbjct:   158 SKVFVGEVVE 167

GO:0003677 "DNA binding" evidence=IDA

GO:0003713 "transcription coactivator activity" evidence=ISO

GO:0005634 "nucleus" evidence=IDA

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

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

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

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

GO:0042809 "vitamin D receptor binding" evidence=ISO

GO:0043923 "positive regulation by host of viral transcription" evidence=ISO

GO:0046966 "thyroid hormone receptor binding" evidence=ISO

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0047485 "protein N-terminus binding" evidence=ISO

RGD|1305626 Taf11 "TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Rattus norvegicus (taxid:10116)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 33/70 (47%), Positives = 53/70 (75%)

Query:    98 DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGI 157
             D  ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+ SITG+  +S  + I + GI
Sbjct:    99 DEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQSITGTS-VSQNVVIAMSGI 157

Query:   158 AKMFVGELVE 167
             +K+FVGE+VE
Sbjct:   158 SKVFVGEVVE 167

GO:0003674 "molecular_function" evidence=ND

GO:0003677 "DNA binding" evidence=IEA;ISO

GO:0003713 "transcription coactivator 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:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

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

GO:0008150 "biological_process" evidence=ND

GO:0042809 "vitamin D receptor binding" evidence=IEA;ISO

GO:0043923 "positive regulation by host of viral transcription" evidence=IEA;ISO

GO:0046966 "thyroid hormone receptor binding" evidence=IEA;ISO

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0047485 "protein N-terminus binding" evidence=IEA;ISO

---

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:
	GSVIVG00000980001	SubName- Full=Chromosome chr19 scaffold_111, whole genome shotgun sequence; (198 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00032691001	SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (676 aa)					•	•	•		0.545
	GSVIVG00024845001	RecName- Full=TATA-box-binding protein; (211 aa)					•	•	•		0.517
	GSVIVG00015071001	SubName- Full=Putative uncharacterized protein (Chromosome chr18 scaffold_1, whole genome shotg [...] (106 aa)				•		•			0.517
	GSVIVG00033123001	SubName- Full=Putative uncharacterized protein (Chromosome chr5 scaffold_64, whole genome shotg [...] (114 aa)				•		•			0.499
	GSVIVG00002744001	SubName- Full=Chromosome chr1 scaffold_135, whole genome shotgun sequence; (78 aa)				•		•	•		0.489
	GSVIVG00014940001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (712 aa)					•	•			0.454
	GSVIVG00002569001	SubName- Full=Chromosome chr2 scaffold_132, whole genome shotgun sequence; (779 aa)				•		•			0.454
	GSVIVG00024229001	SubName- Full=Putative uncharacterized protein (Chromosome chr6 scaffold_3, whole genome shotgu [...] (176 aa)				•		•			0.448
	GSVIVG00034077001	SubName- Full=Chromosome chr9 scaffold_7, whole genome shotgun sequence; (177 aa)					•	•	•		0.435
	GSVIVG00018813001	SubName- Full=Putative uncharacterized protein (Chromosome chr12 scaffold_18, whole genome shot [...] (138 aa)				•		•			0.426

---

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	181
pfam04719	89	pfam04719, TAFII28, hTAFII28-like protein conserve	2e-26
cd08048	85	cd08048, TAF11, TATA Binding Protein (TBP) Associa	4e-24
COG5251	199	COG5251, TAF40, Transcription initiation factor TF	8e-12

>gnl|CDD|218227 pfam04719, TAFII28, hTAFII28-like protein conserved region

 Score = 95.9 bits (239), Expect = 2e-26
 Identities = 32/64 (50%), Positives = 50/64 (78%), Gaps = 1/64 (1%)

Query: 105 MQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGE 164
           MQ +++ FTE+Q+NRYE FRRS+L+K+ +++L+  +TG Q +S  + I + GIAK+FVGE
Sbjct: 1   MQVLVSNFTEEQLNRYEVFRRSSLKKAQVKKLISQVTG-QSVSENVVIAISGIAKVFVGE 59

Query: 165 LVET 168
           +VE 
Sbjct: 60  IVEE 63

The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C-terminal of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3. Length = 89

>gnl|CDD|173967 cd08048, TAF11, TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

 Score = 89.5 bits (223), Expect = 4e-24
 Identities = 33/61 (54%), Positives = 45/61 (73%), Gaps = 1/61 (1%)

Query: 112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFC 171
           F+E+QMNRYE FRRS+  K+ ++RL+ S+TG Q +S  + I V GIAK+FVGE+VE    
Sbjct: 1   FSEEQMNRYEMFRRSSFPKAAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARD 59

Query: 172 V 172
           V
Sbjct: 60  V 60

The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) 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 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 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 proposed for TAFs functions such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. TAF11 interacts with the ligand binding domains of the nuclear receptors for vitamin D3 and thyroid hormone. TAF11 also directly interacts with TFIIA, acting as a bridging factor that stabilizes the TFIIA-TBP-DNA complex. Each TAF, with the help of a specific activator, is required only for the expression of subset of genes and is not universally involved for transcription as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. Several TAFs interact via histone-fold (HFD) motifs; HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and is found in core histones, TAFS and many other transcription factors. TFIID has a histone octamer-like substructure. The TAF11 domain is structurally analogous to histone H3 and interacts with TAF13, making a novel histone-like heterodimer. The dimer may be structurally and functionally similar to the spt3 protein within the SAGA histone acetyltransferase complex. Length = 85

>gnl|CDD|227576 COG5251, TAF40, Transcription initiation factor TFIID, subunit TAF11 [Transcription]

 Score = 60.8 bits (147), Expect = 8e-12
 Identities = 23/68 (33%), Positives = 44/68 (64%), Gaps = 1/68 (1%)

Query: 100 AKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAK 159
           A+  + + ++    E+Q NRYE FRR++L K+ +++L  ++   Q +S  + I + G+ K
Sbjct: 88  AQDERFKLLVTNLDEEQTNRYEVFRRTSLNKTQVKKLASTVAN-QTVSPNIRIFLQGVGK 146

Query: 160 MFVGELVE 167
           +FVGE++E
Sbjct: 147 VFVGEIIE 154

Length = 199

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	181
PF04719	90	TAFII28: hTAFII28-like protein conserved region; I	100.0
KOG3219	195	consensus Transcription initiation factor TFIID, s	99.97
cd08048	85	TAF11 TATA Binding Protein (TBP) Associated Factor	99.95
COG5251	199	TAF40 Transcription initiation factor TFIID, subun	99.94
PF00808	65	CBFD_NFYB_HMF: Histone-like transcription factor (	96.01
smart00803	65	TAF TATA box binding protein associated factor. TA	94.03
smart00417	74	H4 Histone H4.	84.23
KOG3902	352	consensus Histone acetyltransferase PCAF/SAGA, sub	84.2
cd00076	85	H4 Histone H4, one of the four histones, along wit	82.58

>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex

Probab=100.00  E-value=6.3e-35  Score=218.90  Aligned_cols=75  Identities=41%  Similarity=0.658  Sum_probs=55.4

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHHHhhhh
Q 030236          105 MQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNVTQILF  179 (181)
Q Consensus       105 m~~Ll~~fdeEQldRYE~fRRS~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~ewl~~  179 (181)
                      |++|+++||+||++|||+||||+|+|++|||||++++|+|+||+|++|+|+||||||||||||+|++||.+|...
T Consensus         1 ~~~L~~~f~~eQ~~Rye~fRRs~~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~   75 (90)
T PF04719_consen    1 MQLLLSNFDEEQLDRYEAFRRSSFNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGET   75 (90)
T ss_dssp             ---------HHHHHHHHHHHH----HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--
T ss_pred             ChHHHHcCCHHHHHHHHHHHHccCCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            789999999999999999999999999999999999988999999999999999999999999999999999754

The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.

>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]

Probab=99.97  E-value=2.8e-31  Score=222.52  Aligned_cols=82  Identities=41%  Similarity=0.658  Sum_probs=76.8

Q ss_pred             CcHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHHHh
Q 030236           97 SDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNVTQ  176 (181)
Q Consensus        97 ~d~~~~~km~~Ll~~fdeEQldRYE~fRRS~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~ew  176 (181)
                      .++++..||+.||++||+|||+|||+||||+|||+.|||||+++||. +|++|++|||+||||||||||||+|++||.+|
T Consensus        82 ~~~ee~~r~q~L~s~fseEQl~RYEvfRrs~f~Ka~iKkL~~~itg~-~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~  160 (195)
T KOG3219|consen   82 VDAEEAQRMQTLLSNFSEEQLSRYEVFRRSAFPKAQIKKLMSSITGQ-SVSENVAIAMAGIAKVFVGEVVEEALDVREEW  160 (195)
T ss_pred             cCHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhCC-ccCcceeeeecchhhHhHHHHHHHHHHHHHHh
Confidence            35666779999999999999999999999999999999999999986 59999999999999999999999999999999


Q ss_pred             hhh
Q 030236          177 ILF  179 (181)
Q Consensus       177 l~~  179 (181)
                      ...
T Consensus       161 ~e~  163 (195)
T KOG3219|consen  161 GES  163 (195)
T ss_pred             ccC
Confidence            653

>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=99.95  E-value=2.5e-28  Score=180.95  Aligned_cols=66  Identities=50%  Similarity=0.732  Sum_probs=64.1

Q ss_pred             CCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHHHhhh
Q 030236          112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNVTQIL  178 (181)
Q Consensus       112 fdeEQldRYE~fRRS~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~ewl~  178 (181)
                      ||+||++|||.|||++|+|+.|||||++++| |+||+|++|+|+||||+|||||||+|++||.+|..
T Consensus         1 f~~eQ~~Rye~~Rra~f~k~~iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~   66 (85)
T cd08048           1 FSEEQMNRYEMFRRSSFPKAAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGE   66 (85)
T ss_pred             CCHHHHHHHHHHHHhhccHHHHHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            8999999999999999999999999999987 79999999999999999999999999999999976

The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) 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 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 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 hypothes

>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]

Probab=99.94  E-value=2.3e-27  Score=197.67  Aligned_cols=77  Identities=30%  Similarity=0.594  Sum_probs=73.2

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHHHhhhhc
Q 030236          103 AKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNVTQILFA  180 (181)
Q Consensus       103 ~km~~Ll~~fdeEQldRYE~fRRS~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~ewl~~~  180 (181)
                      .++.+|+.+||+||++|||.|||++|||+.||||+++|.+ |+|++|++|+|+||+|||||||||.|+.||.+|+..+
T Consensus        91 ~r~k~l~~~~deeq~~RyEvFrrt~lnKt~VKKlastV~n-QtVspNi~I~l~g~~KVfvGEiIElA~~Vq~~w~~sg  167 (199)
T COG5251          91 ERFKLLVTNLDEEQTNRYEVFRRTSLNKTQVKKLASTVAN-QTVSPNIRIFLQGVGKVFVGEIIELAMIVQNKWLTSG  167 (199)
T ss_pred             HHHHHHHhhcCHHHHHHHHHHHhcCCCHHHHHHHHHHHhc-cccCCCeeeeeechhHHHHHHHHHHHHHHHHHhcccC
Confidence            6888899999999999999999999999999999988875 8999999999999999999999999999999998754

>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=96.01  E-value=0.019  Score=39.42  Aligned_cols=49  Identities=14%  Similarity=0.189  Sum_probs=40.3

Q ss_pred             cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV  174 (181)
Q Consensus       126 S~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~  174 (181)
                      ..||.+.|||||...-+...|+.....+|+=.+-+||.+|...|.++..
T Consensus         1 ~~lP~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~   49 (65)
T PF00808_consen    1 ASLPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQ   49 (65)
T ss_dssp             -SS-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3699999999999885555689999999999999999999999987754

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=94.03  E-value=0.18  Score=35.67  Aligned_cols=48  Identities=17%  Similarity=0.170  Sum_probs=42.4

Q ss_pred             cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV  174 (181)
Q Consensus       126 S~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~  174 (181)
                      +.||++.||+|+.+. |-..++..+.-.++...+.|+-+|+..|..++.
T Consensus         1 ~~~p~~~i~ria~~~-Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~   48 (65)
T smart00803        1 SWLPKETIKDVAESL-GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMR   48 (65)
T ss_pred             CCCCHHHHHHHHHHC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            358999999998775 656799999999999999999999999998875

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.

>smart00417 H4 Histone H4

Probab=84.23  E-value=2.9  Score=30.74  Aligned_cols=46  Identities=22%  Similarity=0.253  Sum_probs=39.8

Q ss_pred             CCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVN  173 (181)
Q Consensus       127 ~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq  173 (181)
                      .++|+.|+||+... |-.-||..+.-.+.++.|.|+-+|+..|....
T Consensus        13 gI~k~~IrRLaRr~-GvkRIS~~~y~elr~vle~~l~~I~rdav~~a   58 (74)
T smart00417       13 GITKPAIRRLARRG-GVKRISGLIYDETRNVLKSFLENVVRDAVTYT   58 (74)
T ss_pred             CCCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            69999999998764 65678989999999999999999999987654

>KOG3902 consensus Histone acetyltransferase PCAF/SAGA, subunit SUPT3H/SPT3 [Transcription]

Probab=84.20  E-value=3.8  Score=37.94  Aligned_cols=75  Identities=15%  Similarity=0.168  Sum_probs=53.1

Q ss_pred             cHHHHHHHHH---HHhcCCHHHHHHHHHHHhcCCChHHHHHHHHHhhcC-c---cCCccHHHHhhhhhHHHHHHHHHHHH
Q 030236           98 DPAKMAKMQA---ILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGS-Q---KISLPMTIVVCGIAKMFVGELVETGF  170 (181)
Q Consensus        98 d~~~~~km~~---Ll~~fdeEQldRYE~fRRS~f~K~~IKKLi~svtgs-Q---sVs~nv~IavaGiAKvFVGEIVE~Ar  170 (181)
                      |+..+++|..   .-..||.+|+--|--.|..+|.+..=||. ...++- +   .++..+.=+++=++==-|.-||+.|+
T Consensus       191 devt~~RLkrADrrTrimt~eqYvefsE~RqaSFt~RkgkrF-Rdwld~s~ld~rp~~~~mdILayLafEtVa~Lvd~AL  269 (352)
T KOG3902|consen  191 DEVTMRRLKRADRRTRIMTGEQYVEFSECRQASFTCRKGKRF-RDWLDLSALDLRPPTDTMDILAYLAFETVAALVDYAL  269 (352)
T ss_pred             HHHHHHHHHHHHHHHhhccHHHHHHHHHHhhhhhhhhcchhH-HhhhCCchhccCCCccHHHHHHHHHHHHHHHHHHHHH
Confidence            4445555543   45789999999999999999988877764 333332 1   23434444567788888999999998


Q ss_pred             HHH
Q 030236          171 CVN  173 (181)
Q Consensus       171 ~Vq  173 (181)
                      -|.
T Consensus       270 lvr  272 (352)
T KOG3902|consen  270 LVR  272 (352)
T ss_pred             HHH
Confidence            874

>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=82.58  E-value=3.6  Score=30.91  Aligned_cols=47  Identities=19%  Similarity=0.268  Sum_probs=39.8

Q ss_pred             cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVN  173 (181)
Q Consensus       126 S~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq  173 (181)
                      ..|+|+.|+||+... |--.||..+.-.+..+.+.|+-+|+..|....
T Consensus        12 ~gi~k~~I~RLarr~-GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya   58 (85)
T cd00076          12 KGITKPAIRRLARRG-GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYT   58 (85)
T ss_pred             ccCCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            359999999998774 55568888889999999999999999887654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	181
1bh8_B	89	Htafii18HTAFII28 HETERODIMER CRYSTAL STRUCTURE Leng		2e-10

>pdb|1BH8|B Chain B, Htafii18HTAFII28 HETERODIMER CRYSTAL STRUCTURE Length = 89

Iteration: 1
 Score = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 30/61 (49%), Positives = 45/61 (73%), Gaps = 1/61 (1%)
Query: 112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFC 171
           F+E+Q+NRYE +RRSA  K+ ++RL+ SITG+  +S  + I + GI+K+FVGE+VE    
Sbjct: 1   FSEEQLNRYEMYRRSAFPKAAIKRLIQSITGTS-VSQNVVIAMSGISKVFVGEVVEEALD 59
Query: 172 V 172
           V
Sbjct: 60  V 60
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	181
1bh9_B	89	TAFII28; histone fold, tata binding protein, trans	1e-22
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-06

>1bh9_B TAFII28; histone fold, tata binding protein, transcription regulation complex; HET: PMB; 2.60A {Homo sapiens} SCOP: a.22.1.3 PDB: 1bh8_B* Length = 89

 Score = 85.6 bits (212), Expect = 1e-22
 Identities = 30/61 (49%), Positives = 44/61 (72%), Gaps = 1/61 (1%)

Query: 112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFC 171
           F+E+Q+NRYE +RRSA  K+ ++RL+ SITG   +S  + I + GI+K+FVGE+VE    
Sbjct: 1   FSEEQLNRYEMYRRSAFPKAAIKRLIQSITG-TSVSQNVVIAMSGISKVFVGEVVEEALD 59

Query: 172 V 172
           V
Sbjct: 60  V 60

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 44.5 bits (104), Expect = 7e-06
 Identities = 22/142 (15%), Positives = 50/142 (35%), Gaps = 17/142 (11%)

Query: 2   KQSKDPFEAALEESPGDSPDELEIETQPQTGTAAGSATAAVTGELEDEFDNLESQAPMSV 61
            + K      L+  P D P E+ + T P+      S  A    +    +DN +      +
Sbjct: 301 DEVKSLLLKYLDCRPQDLPREV-LTTNPR----RLSIIAESIRDGLATWDNWKHVNCDKL 355

Query: 62  SAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSD-PAKMAKM--QAILNQFTEDQMN 118
           +        +  + +  +  +   +   L  FP S+  P  +  +    ++       +N
Sbjct: 356 T------TIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVN 409

Query: 119 RYESFRRSALQKSNMRRLLVSI 140
             +  + S ++K   +   +SI
Sbjct: 410 --KLHKYSLVEKQP-KESTISI 428

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	181
1bh9_B	89	TAFII28; histone fold, tata binding protein, trans	99.95
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	95.69
3b0c_W	76	CENP-W, centromere protein W; histone fold, DNA bi	95.51
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	94.74
4g92_C	119	HAPE; transcription factor, nucleosome, minor groo	94.69
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	94.67
2hue_C	84	Histone H4; mini beta sheet, elongated beta sandwh	93.6
1tzy_D	103	Histone H4-VI; histone-fold, tetramer-dimer-dimer,	93.3
2yfw_B	103	Histone H4, H4; cell cycle, kinetochore, centromer	93.2
1id3_B	102	Histone H4; nucleosome core particle, chromatin, p	92.46
1n1j_A	93	NF-YB; histone-like PAIR, DNA binding protein; 1.6	91.93
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	91.17
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	91.12
1taf_B	70	TFIID TBP associated factor 62; transcription init	90.57
2byk_B	128	Chrac-14; nucleosome sliding, histone fold, DNA-bi	87.9
1jfi_B	179	DR1 protein, transcription regulator NC2 beta chai	86.51
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	85.2
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	84.98
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	84.74
3b0b_C	81	CENP-X, centromere protein X; histone fold, DNA bi	82.73

>1bh9_B TAFII28; histone fold, tata binding protein, transcription regulation complex; HET: PMB; 2.60A {Homo sapiens} SCOP: a.22.1.3 PDB: 1bh8_B*

Probab=99.95  E-value=8e-29  Score=184.00  Aligned_cols=65  Identities=46%  Similarity=0.729  Sum_probs=62.9

Q ss_pred             CCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHHHhh
Q 030236          112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNVTQI  177 (181)
Q Consensus       112 fdeEQldRYE~fRRS~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~ewl  177 (181)
                      ||+||++|||.||||+|+|++|||||++++| |+||+|++|+|+||||+|||||||+|++||.+|.
T Consensus         1 ft~eQ~~Rye~~Rrs~f~k~~vKrl~~~~~~-~~v~~~v~i~v~glaKvfVgelVE~A~~V~~~~~   65 (89)
T 1bh9_B            1 FSEEQLNRYEMYRRSAFPKAAIKRLIQSITG-TSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWG   65 (89)
T ss_dssp             CCHHHHHHHHHHHHCCCCHHHHHHHHHHHHS-SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHcC-CCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            8999999999999999999999999999985 6899999999999999999999999999999995

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

Probab=95.69  E-value=0.018  Score=42.05  Aligned_cols=55  Identities=16%  Similarity=0.279  Sum_probs=40.9

Q ss_pred             HHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236          120 YESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV  174 (181)
Q Consensus       120 YE~fRRS~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~  174 (181)
                      -..|+...||-+.|||||...-....|+....++++-.+-+||-+|++.|.....
T Consensus        12 ~~~~~~~~lP~arIkrImK~~~~~~~is~eA~~~laka~E~Fi~~l~~~A~~~a~   66 (97)
T 1n1j_B           12 VKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTE   66 (97)
T ss_dssp             --------CCHHHHHHHHTTSTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCcCCCcCCHHHHHHHHccCccccccChHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4568999999999999998864435689999999999999999999999977653

>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=95.51  E-value=0.034  Score=38.90  Aligned_cols=49  Identities=10%  Similarity=0.185  Sum_probs=43.8

Q ss_pred             cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV  174 (181)
Q Consensus       126 S~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~  174 (181)
                      ..||++.|+|||.++.+...|+.....+|.-..-.||-.|..+|.++..
T Consensus         3 ~~LP~A~V~rI~K~~~p~~~is~~A~~~i~~~~~~Fi~~la~eA~~~a~   51 (76)
T 3b0c_W            3 RTVPRGTLRKIIKKHKPHLRLAANTDLLVHLSFLLFLHRLAEEARTNAF   51 (76)
T ss_dssp             -CCCHHHHHHHHHHHCTTCEECTTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcccccHHHHHHHHhCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4799999999999887777899999999999999999999999988854

>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=94.74  E-value=0.067  Score=36.13  Aligned_cols=47  Identities=13%  Similarity=0.244  Sum_probs=41.8

Q ss_pred             cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVN  173 (181)
Q Consensus       126 S~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq  173 (181)
                      +.||++.|+|||.++ +...++.....++...+..|+-+|.+.|-.+.
T Consensus         1 ~~lP~a~v~Ri~k~~-~~~ris~~A~~~l~~a~e~fi~~l~~~A~~~a   47 (68)
T 1b67_A            1 GELPIAPIGRIIKNA-GAERVSDDARIALAKVLEEMGEEIASEAVKLA   47 (68)
T ss_dssp             CCSCHHHHHHHHHHT-TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccHHHHHHhcC-CcccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            469999999999998 66678999999999999999999999987664

>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=94.69  E-value=0.042  Score=41.71  Aligned_cols=53  Identities=13%  Similarity=0.226  Sum_probs=44.8

Q ss_pred             HHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236          122 SFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV  174 (181)
Q Consensus       122 ~fRRS~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~  174 (181)
                      .|+-..||-+.|||||...-....|+....++++..+-+||.+|++.|-.+..
T Consensus        36 d~k~~~lPvaRIkrImK~d~~~~~is~eA~v~la~a~E~Fi~~L~~~A~~~a~   88 (119)
T 4g92_C           36 DYKIHQLPLARIKKVMKADPEVKMISAEAPILFAKGCDVFITELTMRAWIHAE   88 (119)
T ss_dssp             CSSCCSSCHHHHHHHHHTSTTCCEECTHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccCCCCHHHHHHHHhhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            37778899999999998654445688889999999999999999999977653

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

Probab=94.67  E-value=0.065  Score=36.65  Aligned_cols=47  Identities=15%  Similarity=0.234  Sum_probs=42.1

Q ss_pred             cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVN  173 (181)
Q Consensus       126 S~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq  173 (181)
                      +.||++.|+||+... |...++..+..++..+.+.|+-+|.+.|....
T Consensus         5 ~~lp~a~v~Rl~r~~-g~~ris~~a~~~l~e~~~~~~~~v~~dA~~~a   51 (70)
T 1ku5_A            5 GELPIAPVDRLIRKA-GAERVSEQAAKVLAEYLEEYAIEIAKKAVEFA   51 (70)
T ss_dssp             CCSCHHHHHHHHHHT-TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCChHHHHHHHHHc-CcceeCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            579999999999986 66789999999999999999999999887654

>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=93.60  E-value=0.16  Score=36.20  Aligned_cols=48  Identities=21%  Similarity=0.300  Sum_probs=42.3

Q ss_pred             cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV  174 (181)
Q Consensus       126 S~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~  174 (181)
                      ..||++.|+||+.+. |-..+|..+.-.++.+.+.|+-+|+..|...+.
T Consensus         9 ~~ip~~~I~Riar~~-Gv~rIs~da~~~l~~~l~~~~~~I~~dA~~~a~   56 (84)
T 2hue_C            9 QGITKPAIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTE   56 (84)
T ss_dssp             CSSCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHc-CchhccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            469999999999886 555699999999999999999999999988764

>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=93.30  E-value=0.17  Score=37.24  Aligned_cols=47  Identities=21%  Similarity=0.305  Sum_probs=41.4

Q ss_pred             CCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV  174 (181)
Q Consensus       127 ~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~  174 (181)
                      .||++.|+||+.+. |-..|+..+...++.+.+.|+-+|++.|...+.
T Consensus        29 gip~~~I~Rlar~~-G~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~   75 (103)
T 1tzy_D           29 GITKPAIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTE   75 (103)
T ss_dssp             GSCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            39999999999886 445799999999999999999999999987753

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

Probab=93.20  E-value=0.18  Score=37.26  Aligned_cols=46  Identities=22%  Similarity=0.267  Sum_probs=41.0

Q ss_pred             CChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236          128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV  174 (181)
Q Consensus       128 f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~  174 (181)
                      ||++.|+||+.+. |-..|+..+...++.+.+.|+-+|++.|...+.
T Consensus        30 ip~~~I~Rlar~~-G~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~   75 (103)
T 2yfw_B           30 ITKPAIRRLARRG-GVKRISGLIYEEVRNVLKTFLESVIRDAVTYTE   75 (103)
T ss_dssp             CCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999886 445799999999999999999999999987653

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

Probab=92.46  E-value=0.25  Score=36.63  Aligned_cols=47  Identities=21%  Similarity=0.259  Sum_probs=41.6

Q ss_pred             CCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV  174 (181)
Q Consensus       127 ~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~  174 (181)
                      .||++.|+||+.+. |-..||..+.-.++.+.+.|+-+|+..|...+.
T Consensus        28 ~ip~~~I~Rlar~~-Gv~rIS~da~~~l~~~le~fi~~I~~dA~~~a~   74 (102)
T 1id3_B           28 GITKPAIRRLARRG-GVKRISGLIYEEVRAVLKSFLESVIRDSVTYTE   74 (102)
T ss_dssp             GSCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHc-CchhccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            49999999999886 555699999999999999999999999988764

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

Probab=91.93  E-value=0.3  Score=35.01  Aligned_cols=49  Identities=14%  Similarity=0.060  Sum_probs=41.5

Q ss_pred             cCCChHHHHHHHHHhhc-CccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236          126 SALQKSNMRRLLVSITG-SQKISLPMTIVVCGIAKMFVGELVETGFCVNV  174 (181)
Q Consensus       126 S~f~K~~IKKLi~svtg-sQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~  174 (181)
                      ..||++.|+|||...+. ...|+.....++.-.+.+||-.|.+.|..+..
T Consensus         7 ~~LP~a~i~ri~K~~~~~~~~is~dA~~~l~~a~e~Fi~~l~~~A~~~a~   56 (93)
T 1n1j_A            7 IYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCH   56 (93)
T ss_dssp             CCCCHHHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCChhHHHHHHHHhCCccceeCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46999999999999853 23588888999999999999999999987653

>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=91.17  E-value=0.44  Score=34.81  Aligned_cols=49  Identities=8%  Similarity=0.304  Sum_probs=41.4

Q ss_pred             hcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236          125 RSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVN  173 (181)
Q Consensus       125 RS~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq  173 (181)
                      ...||=+.|||||..---...|+....+.++...-+|+-+|++.|-.+.
T Consensus         9 ~~~fPvaRIkrimK~~~~~~~vs~~A~v~la~a~E~Fi~el~~~A~~~a   57 (98)
T 1jfi_A            9 NARFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVT   57 (98)
T ss_dssp             -CCCCHHHHHHHHTTSTTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCChHHHHHHHHcCccccccchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4679999999999875433568999999999999999999999997764

>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=91.12  E-value=0.33  Score=36.47  Aligned_cols=49  Identities=6%  Similarity=0.083  Sum_probs=38.1

Q ss_pred             HhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236          124 RRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVN  173 (181)
Q Consensus       124 RRS~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq  173 (181)
                      |-..||++.|+||+... |...|+..+.-++..+.+.|+-.|...|....
T Consensus         4 ~d~~lP~a~I~Ri~r~~-g~~rIS~~a~~~l~e~l~~f~~~v~~da~~~A   52 (111)
T 3b0c_T            4 REPEIASSLIKQIFSHY-VKTPVTRDAYKIVEKCSERYFKQISSDLEAYS   52 (111)
T ss_dssp             ------CHHHHHHHHHH-HCSCBCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34579999999999887 55679999999999999999999998887654

>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=90.57  E-value=0.67  Score=32.65  Aligned_cols=48  Identities=15%  Similarity=0.113  Sum_probs=43.2

Q ss_pred             cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV  174 (181)
Q Consensus       126 S~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~  174 (181)
                      +.||...||+++.++ |-..+|+.++.+++--.-..+.||+..|..+++
T Consensus         5 s~lp~~~v~~iaes~-Gi~~lsddaa~~LA~dvEyr~~eI~qeA~kfmr   52 (70)
T 1taf_B            5 SSISAESMKVIAESI-GVGSLSDDAAKELAEDVSIKLKRIVQDAAKFMN   52 (70)
T ss_dssp             CCCCHHHHHHHHHHT-TCCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            579999999998775 666899999999999999999999999999875

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

Probab=87.90  E-value=0.73  Score=35.40  Aligned_cols=49  Identities=14%  Similarity=0.127  Sum_probs=39.2

Q ss_pred             cCCChHHHHHHHHHhhc-CccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236          126 SALQKSNMRRLLVSITG-SQKISLPMTIVVCGIAKMFVGELVETGFCVNV  174 (181)
Q Consensus       126 S~f~K~~IKKLi~svtg-sQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~  174 (181)
                      ..||++.|+|||..+.. ...|+.....+|+=.+-+||-.|...|.++..
T Consensus         8 ~~LP~A~I~rImK~~~pd~~~iS~dA~~~l~ka~e~FI~~lt~~A~~~a~   57 (128)
T 2byk_B            8 LNLPNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAH   57 (128)
T ss_dssp             ---CCSHHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHhCcccceECHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46999999999997653 34588888999999999999999999987754

>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=86.51  E-value=1.3  Score=36.18  Aligned_cols=48  Identities=4%  Similarity=0.115  Sum_probs=42.3

Q ss_pred             CCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV  174 (181)
Q Consensus       127 ~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~  174 (181)
                      .||+++|+|||.+++.+..|+.-...+|.=.+-+||-.|--.|.++..
T Consensus        15 ~LP~A~V~RImK~alp~~rISkDA~~al~ec~~eFI~~LtseA~e~a~   62 (179)
T 1jfi_B           15 TIPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICN   62 (179)
T ss_dssp             CCCHHHHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            599999999999987555789889999999999999999999988754

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

Probab=85.20  E-value=1.2  Score=35.48  Aligned_cols=48  Identities=13%  Similarity=0.165  Sum_probs=43.2

Q ss_pred             cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVN  173 (181)
Q Consensus       126 S~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq  173 (181)
                      +.||++.|+|||...+|...||.-....++-..+.|+-.|...|.+..
T Consensus         3 ~~LP~a~V~Riik~~lg~~rVS~dA~~~l~~~l~~f~~~i~~~A~~~a   50 (154)
T 1f1e_A            3 VELPKAAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVL   50 (154)
T ss_dssp             -CCCHHHHHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCccHHHHHHHhcCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            479999999999998887789999999999999999999999998765

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

Probab=84.98  E-value=0.47  Score=37.17  Aligned_cols=50  Identities=16%  Similarity=0.254  Sum_probs=30.6

Q ss_pred             HhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236          124 RRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVN  173 (181)
Q Consensus       124 RRS~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq  173 (181)
                      ....||-+.|||||..---...|+....++|+-.+-+||-+|++.|..+.
T Consensus        16 ~~~~LPlaRIKrIMK~dpdv~~Is~eA~vliakA~ElFI~~Lt~~A~~~a   65 (140)
T 2byk_A           16 AETFLPLSRVRTIMKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEE   65 (140)
T ss_dssp             -------------CCSSSSCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHhcCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45679999999999875433458888889999999999999999998775

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

Probab=84.74  E-value=1.5  Score=35.04  Aligned_cols=46  Identities=17%  Similarity=0.122  Sum_probs=42.3

Q ss_pred             CCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVN  173 (181)
Q Consensus       127 ~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq  173 (181)
                      .||++.|+||+... |...||......++.+.+.|+-+|...|.+..
T Consensus        82 ~lP~a~V~Ri~k~~-g~~RVS~~A~~~l~~~le~f~~~I~~~A~~~a  127 (154)
T 1f1e_A           82 LFGRATVRRILKRA-GIERASSDAVDLYNKLICRATEELGEKAAEYA  127 (154)
T ss_dssp             CCCHHHHHHHHHHT-TCCEECHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCccHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            59999999999998 77889999999999999999999999998765

>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=82.73  E-value=2.9  Score=30.11  Aligned_cols=49  Identities=16%  Similarity=0.221  Sum_probs=40.7

Q ss_pred             hcCCChHHHHHHHHHhhcC--ccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236          125 RSALQKSNMRRLLVSITGS--QKISLPMTIVVCGIAKMFVGELVETGFCVN  173 (181)
Q Consensus       125 RS~f~K~~IKKLi~svtgs--QsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq  173 (181)
                      ...|++..|.||+......  .+++...+-+++-+-++||=|-|.+|....
T Consensus         6 ~~~~~~~lI~ril~~~f~~~ktrI~~dAl~l~aeyl~iFV~EAv~RA~~~a   56 (81)
T 3b0b_C            6 EGGFRKETVERLLRLHFRDGRTRVNGDALLLMAELLKVFVREAAARAARQA   56 (81)
T ss_dssp             -CCCCHHHHHHHHHHHCCSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHhccCcccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6789999999999886653  347888899999999999999999887653

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	181
d1bh9b_	89	a.22.1.3 (B:) TAF(II)28 {Human (Homo sapiens) [Tax	1e-24

>d1bh9b_ a.22.1.3 (B:) TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)28
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 89.8 bits (223), Expect = 1e-24
 Identities = 30/61 (49%), Positives = 44/61 (72%), Gaps = 1/61 (1%)

Query: 112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFC 171
           F+E+Q+NRYE +RRSA  K+ ++RL+ SITG   +S  + I + GI+K+FVGE+VE    
Sbjct: 1   FSEEQLNRYEMYRRSAFPKAAIKRLIQSITG-TSVSQNVVIAMSGISKVFVGEVVEEALD 59

Query: 172 V 172
           V
Sbjct: 60  V 60

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	181
d1bh9b_	89	TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]}	99.97
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	97.0
d1jfia_	66	Negative cofactor 2, NC2, alpha chain {Human (Homo	96.97
d1n1jb_	78	Nuclear transcription factor Y subunit gamma (Nf-Y	95.62
d1ku5a_	66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	95.26
d1jfib_	135	Negative cofactor 2, NC2, beta chain {Human (Homo	94.42
d1n1ja_	87	Nuclear transcription factor Y subunit beta (Nf-Yb	93.96
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	93.03
d2bykb1	89	Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax	90.49
d2huec1	82	Histone H4 {African clawed frog (Xenopus laevis) [	89.44
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	87.59

>d1bh9b_ a.22.1.3 (B:) TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)28
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=9.8e-32  Score=198.95  Aligned_cols=66  Identities=45%  Similarity=0.704  Sum_probs=63.9

Q ss_pred             CCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHHHhhh
Q 030236          112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNVTQIL  178 (181)
Q Consensus       112 fdeEQldRYE~fRRS~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~ewl~  178 (181)
                      ||+|||+|||+||||+|+|++|||||++++| |+||+|++|+|+||||||||||||+|++||.+|-.
T Consensus         1 Fs~eQ~~RyE~fRRs~~~K~~vkrl~~~~~g-~sv~~~v~i~v~giaKvFvGEiVE~A~~V~~~~~e   66 (89)
T d1bh9b_           1 FSEEQLNRYEMYRRSAFPKAAIKRLIQSITG-TSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGE   66 (89)
T ss_dssp             CCHHHHHHHHHHHHCCCCHHHHHHHHHHHHS-SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCHHHHHHHHHHHHhhCCHHHHHHHHHHHcC-CCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            8999999999999999999999999999986 79999999999999999999999999999999964

>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=97.00  E-value=0.00081  Score=44.26  Aligned_cols=48  Identities=13%  Similarity=0.227  Sum_probs=42.7

Q ss_pred             cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV  174 (181)
Q Consensus       126 S~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~  174 (181)
                      +.||++.||||+.+. |.-.|+.....+++..+++||.+|...|..++.
T Consensus         2 aeLP~a~I~ri~k~~-~~~ris~ea~~~l~~~~e~fi~~l~~~a~~~a~   49 (68)
T d1htaa_           2 GELPIAPIGRIIKNA-GAERVSDDARIALAKVLEEMGEEIASEAVKLAK   49 (68)
T ss_dssp             CCSCHHHHHHHHHHT-TCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCcHHHHHHHHHHC-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            469999999999886 445699999999999999999999999988875

>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=96.97  E-value=0.00068  Score=44.77  Aligned_cols=49  Identities=8%  Similarity=0.292  Sum_probs=43.2

Q ss_pred             cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV  174 (181)
Q Consensus       126 S~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~  174 (181)
                      +.||-+.|||+|..-.....|+.....+|+..+.+||.+|++.|-.+..
T Consensus         1 a~fP~srVkkimk~~~~~~~is~~A~~~~~~a~E~Fi~~l~~~A~~~a~   49 (66)
T d1jfia_           1 ARFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQ   49 (66)
T ss_dssp             CCCCHHHHHHHHTTSTTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCChHHHHHHHhcCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5799999999999766666789999999999999999999999987653

>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=95.62  E-value=0.01  Score=39.59  Aligned_cols=48  Identities=15%  Similarity=0.246  Sum_probs=40.3

Q ss_pred             CChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHHH
Q 030236          128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNVT  175 (181)
Q Consensus       128 f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~e  175 (181)
                      ||.+.|||||+.--....++.....+|+-.+-+||.+|++.|.++...
T Consensus         1 LP~srVkrImK~~~~~~~is~ea~~~i~~a~E~Fi~~l~~~A~~~a~~   48 (78)
T d1n1jb_           1 LPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTED   48 (78)
T ss_dssp             CCHHHHHHHHTTSTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            789999999986444445788889999999999999999999887654

>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=95.26  E-value=0.016  Score=37.66  Aligned_cols=47  Identities=13%  Similarity=0.162  Sum_probs=41.0

Q ss_pred             CCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV  174 (181)
Q Consensus       127 ~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~  174 (181)
                      .||++.||||+.+.. .-.|+.....++...+++||-.|...|-.+..
T Consensus         2 ~LP~a~I~rI~k~~~-~~ris~ea~~~l~~a~e~Fi~~l~~~a~~~a~   48 (66)
T d1ku5a_           2 ELPIAPVDRLIRKAG-AERVSEQAAKVLAEYLEEYAIEIAKKAVEFAR   48 (66)
T ss_dssp             CSCHHHHHHHHHHTT-CSEECHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHhCc-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            589999999998864 34688899999999999999999999987764

>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=94.42  E-value=0.039  Score=40.72  Aligned_cols=49  Identities=4%  Similarity=0.113  Sum_probs=43.8

Q ss_pred             CCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHHH
Q 030236          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNVT  175 (181)
Q Consensus       127 ~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~e  175 (181)
                      .||++.|+|||........|+....++|+-.+-+||-.|...|-.+...
T Consensus         4 ~LP~a~I~kI~K~~~~~~~is~dA~~~i~~a~~~Fi~~lt~~A~~~a~~   52 (135)
T d1jfib_           4 TIPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNK   52 (135)
T ss_dssp             CCCHHHHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHhhCCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6999999999999887667899999999999999999999999887643

>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=93.96  E-value=0.048  Score=37.10  Aligned_cols=48  Identities=15%  Similarity=0.078  Sum_probs=40.7

Q ss_pred             CCChHHHHHHHHHhh-cCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236          127 ALQKSNMRRLLVSIT-GSQKISLPMTIVVCGIAKMFVGELVETGFCVNV  174 (181)
Q Consensus       127 ~f~K~~IKKLi~svt-gsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~  174 (181)
                      -||++.|||||.+.. ....|+.....+|+-.+-+||..|...|-.+..
T Consensus         2 ~LP~a~v~ri~K~~~p~~~~is~ea~~~i~~a~e~Fi~~lt~~A~~~a~   50 (87)
T d1n1ja_           2 YLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCH   50 (87)
T ss_dssp             CCCHHHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcHhHHHHHHHHhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            389999999997664 345689999999999999999999999987653

>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=93.03  E-value=0.07  Score=39.82  Aligned_cols=51  Identities=16%  Similarity=0.083  Sum_probs=44.2

Q ss_pred             HhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHHH
Q 030236          124 RRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNVT  175 (181)
Q Consensus       124 RRS~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~e  175 (181)
                      .-.-||++.||||+.+. |...++.....+|+.....|+.+|.+.|-.++..
T Consensus        76 ~~~~fp~a~IkRi~k~~-g~~ris~dA~~~l~~~~E~fi~~l~~~A~~~a~~  126 (151)
T d1f1ea_          76 DGELFGRATVRRILKRA-GIERASSDAVDLYNKLICRATEELGEKAAEYADE  126 (151)
T ss_dssp             CSCCCCHHHHHHHHHHT-TCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCccCHHHHHHHHHcC-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35679999999999875 5556899999999999999999999999888754

>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=90.49  E-value=0.19  Score=34.14  Aligned_cols=46  Identities=13%  Similarity=0.130  Sum_probs=38.5

Q ss_pred             ChHHHHHHHHHhh-cCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236          129 QKSNMRRLLVSIT-GSQKISLPMTIVVCGIAKMFVGELVETGFCVNV  174 (181)
Q Consensus       129 ~K~~IKKLi~svt-gsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~  174 (181)
                      |++.|+|||.+.. ..-.++.....+|+=.+-+||..|...|..+..
T Consensus         1 P~a~i~ri~K~~~p~~~~iskeA~~~i~~aae~FI~~lt~~A~~~a~   47 (89)
T d2bykb1           1 PNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAH   47 (89)
T ss_dssp             CCSHHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CccHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6789999998664 334588889999999999999999999987754

>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=89.44  E-value=0.4  Score=32.53  Aligned_cols=47  Identities=21%  Similarity=0.305  Sum_probs=41.8

Q ss_pred             CCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV  174 (181)
Q Consensus       127 ~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~  174 (181)
                      .++|+.||||+.+. |--.|+..+.-.++.+.+.|+=+|+..|...+.
T Consensus         9 gI~k~~i~Riar~~-Gv~ris~d~~~~l~~~l~~~l~~i~~~a~~~~~   55 (82)
T d2huec1           9 GITKPAIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTE   55 (82)
T ss_dssp             SSCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHc-CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            68999999999875 555699999999999999999999999988764

>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=87.59  E-value=0.36  Score=35.77  Aligned_cols=47  Identities=13%  Similarity=0.155  Sum_probs=43.1

Q ss_pred             CChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236          128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV  174 (181)
Q Consensus       128 f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~  174 (181)
                      ||++.|.|||..+.|...|+......|..+.+.|+..|..+|-.++.
T Consensus         2 lP~a~I~rilk~~~~~~ris~da~~~l~~~~~~~~~~Ia~eA~~l~~   48 (151)
T d1f1ea_           2 LPKAAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLD   48 (151)
T ss_dssp             CCHHHHHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCccHHHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999998877877899999999999999999999999988874