Citrus Sinensis ID: 031136

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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-----
Protein Sequence
MKQSKDPFEAALEESPGDSPDELEIETQPQTGTAAGSATAAVTGELEDEFDNLESQAPMSVSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHcccccHHHHHHHHHHHccccccccHHHHHHHccEEEcccc
Secondary Structure Prediction (SSPRO)
ccccccccHHEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccHcccccccccccccccHHHHHHHHHHHHHccHHHHHHHHHHHHHcccHHHHHHHHHHHcccccccHcHEEEEEHHHHEEEccc
Coil and Loop (DISEMBL)
mkqskdpfeaaleespgdspdeleietqpqtgtaagsataavTGELedefdnlesqapmsvsagpaakmtmsknkdeydeeddenvdvelgkfpsssdpaKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITgsqkislpmTIVVCGIAKMFLEWL
Flexible Loop (DISEMBL)
mkqskdpfeaaleespgdspdelEIETQPQTGTAAGSATAAVTGELEDEFDNLEsqapmsvsagpaakMTMSKNKDEYDEEDDENVDVELGkfpsssdpaKMAKMQAILNQFTEDQMNRYESFRrsalqksnMRRLLVSitgsqkislpmtIVVCGIAKMFLEWL
Low Complexity Region (SEG)
MKQSKDPFEAALEESPGDSPDELEIETQPQtgtaagsataavtgELEDEFDNLESQAPMSVSAGPAAKMTMSknkdeydeeddenvdveLGKFPSSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL
Disordered region (IsUnstruct)
*************************************************************************************************************************************RRLLVSITGSQKISLPMTIVVCGIAKMFLEW*
Disordered Region (DISOPRED)
***********************************************************************************************************ILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL
Disordered Region (DISEMBL)
***********************EIETQ***********AAVTGELEDEFDNLESQAP****************************DVELGKFPSSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL
Disordered Region (DISPRO)
**********************************************************************************************SSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKQSKDPFEAALEESPGDSPDELEIETQPQTGTAAGSATAAVTGELEDEFDNLESQAPMSVSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL
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	165	2.2.26 [Sep-21-2011]
Q5RA91	211	Transcription initiation	yes	no	0.387	0.303	0.430	7e-10
Q5U1X0	211	Transcription initiation	yes	no	0.369	0.289	0.435	9e-10
Q15544	211	Transcription initiation	yes	no	0.387	0.303	0.430	1e-09
Q99JX1	211	Transcription initiation	yes	no	0.363	0.284	0.442	1e-09
P49906	196	Transcription initiation	yes	no	0.345	0.290	0.448	2e-08
Q54XM9	450	Transcription initiation	yes	no	0.321	0.117	0.338	6e-06
Q9US54	199	Transcription initiation	yes	no	0.351	0.291	0.372	8e-06
A6NLC8	198	Putative TAF11-like prote	no	no	0.351	0.292	0.406	4e-05

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

 Score = 63.2 bits (152), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 28/65 (43%), Positives = 48/65 (73%), Gaps = 1/65 (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 AKMFL 162
           +K+F+
Sbjct: 158 SKVFV 162

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

 Score = 62.8 bits (151), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 27/62 (43%), Positives = 47/62 (75%), Gaps = 1/62 (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 FL 162
           F+
Sbjct: 161 FV 162

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

 Score = 62.8 bits (151), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/65 (43%), Positives = 48/65 (73%), Gaps = 1/65 (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 AKMFL 162
           +K+F+
Sbjct: 158 SKVFV 162

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

 Score = 62.4 bits (150), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 27/61 (44%), Positives = 46/61 (75%), Gaps = 1/61 (1%)

Query: 102 MAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMF 161
           + KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+ SITG+  +S  + I + GI+K+F
Sbjct: 103 IQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQSITGTS-VSQNVVIAMSGISKVF 161

Query: 162 L 162
           +
Sbjct: 162 V 162

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 = 58.5 bits (140), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 26/58 (44%), Positives = 43/58 (74%), Gaps = 1/58 (1%)

Query: 105 MQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFL 162
           MQ +++ FTE+Q++RYE +RRSA  K+ ++RL+ +ITG   +S  + I + GIAK+F+
Sbjct: 89  MQVLVSNFTEEQLDRYEMYRRSAFPKAAVKRLMQTITGC-SVSQNVVIAMSGIAKVFV 145

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 = 50.1 bits (118), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 41/62 (66%), Gaps = 9/62 (14%)

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 FL 162
           F+
Sbjct: 399 FV 400

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 = 49.7 bits (117), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 39/59 (66%), Gaps = 1/59 (1%)

Query: 104 KMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFL 162
           + + +L  F E+QM RYE FRR+ L K+N+++L   I  +Q ++  + IV+ G +K+F+
Sbjct: 92  RTKYLLESFDEEQMQRYEVFRRANLNKTNVKKLANQIL-NQSVTPNVAIVISGFSKVFV 149

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 = 47.8 bits (112), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 40/59 (67%), Gaps = 1/59 (1%)

Query: 104 KMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFL 162
           +M  +L+  +E+Q++RYE  RRSA  K+ +  L+ SITG + +S  + I + GIAK+F+
Sbjct: 93  RMTTLLSAMSEEQLSRYEVCRRSAFPKACIAGLMRSITG-RSVSENVAIAMAGIAKVFV 150

Homo sapiens (taxid: 9606)

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	165
388513279	203	unknown [Medicago truncatula]	0.915	0.743	0.536	8e-38
225462089	198	PREDICTED: transcription initiation fact	0.896	0.747	0.588	9e-38
388491516	203	unknown [Medicago truncatula]	0.915	0.743	0.524	1e-36
217072422	203	unknown [Medicago truncatula]	0.915	0.743	0.530	2e-36
224057892	222	predicted protein [Populus trichocarpa]	0.969	0.720	0.543	2e-34
255583916	205	Transcription initiation factor TFIID su	0.878	0.707	0.608	3e-34
388503812	205	unknown [Lotus japonicus]	0.951	0.765	0.518	1e-33
351734450	155	uncharacterized protein LOC100305481 [Gl	0.648	0.690	0.5	1e-31
297804116	211	predicted protein [Arabidopsis lyrata su	0.975	0.763	0.554	2e-30
449460461	220	PREDICTED: uncharacterized protein LOC10	0.957	0.718	0.549	7e-30

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

 Score =  161 bits (408), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 89/166 (53%), Positives = 121/166 (72%), Gaps = 15/166 (9%)

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 MNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFL 162
           M+RYESFRR+  QK+NM+RLL SITG+QKIS+P+TI V GIAK+F+
Sbjct: 110 MSRYESFRRAGFQKANMKRLLTSITGTQKISIPITIAVSGIAKVFV 155

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>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 =  161 bits (407), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 100/170 (58%), Positives = 121/170 (71%), Gaps = 22/170 (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 QMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL 165
           QM+RYESFRRS  QK+NM++LLVSITGSQKIS PMTIV  GIAKMF+  L
Sbjct: 104 QMSRYESFRRSGFQKANMKKLLVSITGSQKISAPMTIVASGIAKMFVGEL 153

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  157 bits (398), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 87/166 (52%), Positives = 120/166 (72%), Gaps = 15/166 (9%)

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 MNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFL 162
           M+RYESFRR+  QK+NM+RLL SITG+QKIS+P+TI +  IAK+F+
Sbjct: 110 MSRYESFRRAGFQKANMKRLLTSITGTQKISIPITIAISRIAKVFV 155

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 =  157 bits (396), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 88/166 (53%), Positives = 120/166 (72%), Gaps = 15/166 (9%)

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 MNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFL 162
           M+RYESFRR+  QK+NM+RLL SITG+QKIS+P+TI V GIAK+F+
Sbjct: 110 MSRYESFRRAGFQKANMKRLLTSITGTQKISIPITIAVSGIAKVFV 155

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 =  150 bits (378), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 99/182 (54%), Positives = 118/182 (64%), Gaps = 22/182 (12%)

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 KMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLE 163
           KMQ IL QFTE QM+RYESFRRSALQK+NM+RLLVSITGSQKISLPMTIVVCGIAKMF+ 
Sbjct: 116 KMQTILAQFTEGQMSRYESFRRSALQKTNMKRLLVSITGSQKISLPMTIVVCGIAKMFVG 175

Query: 164 WL 165
            L
Sbjct: 176 EL 177

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 =  149 bits (377), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 104/171 (60%), Positives = 123/171 (71%), Gaps = 26/171 (15%)

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 DQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL 165
           +QM RYESFRRSALQK+NMRRLLVSITGSQKISLPMTIVVCGIAKMF+  L
Sbjct: 110 NQMTRYESFRRSALQKANMRRLLVSITGSQKISLPMTIVVCGIAKMFVGEL 160

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 =  147 bits (372), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 84/162 (51%), Positives = 112/162 (69%), Gaps = 5/162 (3%)

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  -----SGGGGGGKNKDDEEEEEEDNMDVELTKLQPTGDPQKMAKMQAILSQFTEEQMSRY 115

Query: 121 ESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFL 162
           ESFRR+  QK+NM+RLL SITG+QKI++P+TIVV GIAKMF+
Sbjct: 116 ESFRRAGFQKANMKRLLASITGTQKITIPITIVVSGIAKMFV 157

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 =  140 bits (354), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 81/162 (50%), Positives = 95/162 (58%), Gaps = 55/162 (33%)

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 ESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFL 162
           ESFRR+  QK+NM+RLL SITG+QKIS+PMTIVV GIAKMF+
Sbjct: 66  ESFRRAGFQKANMKRLLASITGTQKISVPMTIVVSGIAKMFV 107

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 =  137 bits (344), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 91/164 (55%), Positives = 117/164 (71%), Gaps = 3/164 (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 RYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFL 162
           RYESFRRSALQ+  M++LL+ +TGSQKI +PM IVVCGIAKMF+
Sbjct: 120 RYESFRRSALQRPQMKKLLIGVTGSQKIGMPMIIVVCGIAKMFV 163

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 =  135 bits (339), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 100/182 (54%), Positives = 126/182 (69%), Gaps = 24/182 (13%)

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 KMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLE 163
           KMQAIL+QFTE+QM+RYESFRR+  QK+NM+RLL SI+G+QKIS+PMTIVV GIAKMF+ 
Sbjct: 114 KMQAILSQFTEEQMSRYESFRRAGFQKANMKRLLASISGTQKISVPMTIVVSGIAKMFVG 173

Query: 164 WL 165
            L
Sbjct: 174 EL 175

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	165
TAIR|locus:2120422	210	TAF11 "TBP-associated factor 1	0.969	0.761	0.463	2.7e-29
TAIR|locus:2198671	204	TAF11b "TBP-associated factor	0.412	0.333	0.579	1.1e-20
ZFIN|ZDB-GENE-040718-283	206	taf11 "TAF11 RNA polymerase II	0.381	0.305	0.468	9.4e-11
UNIPROTKB|E1C6Y5	217	TAF11 "Uncharacterized protein	0.387	0.294	0.430	4.1e-10
UNIPROTKB|Q3ZBP7	210	TAF11 "TAF11 RNA polymerase II	0.387	0.304	0.430	4.1e-10
UNIPROTKB|E2RFN3	211	TAF11 "Uncharacterized protein	0.387	0.303	0.430	4.1e-10
UNIPROTKB|Q15544	211	TAF11 "Transcription initiatio	0.387	0.303	0.430	4.1e-10
UNIPROTKB|F1RZ14	211	TAF11 "Uncharacterized protein	0.387	0.303	0.430	4.1e-10
MGI|MGI:1916026	211	Taf11 "TAF11 RNA polymerase II	0.387	0.303	0.430	4.1e-10
RGD|1305626	211	Taf11 "TAF11 RNA polymerase II	0.387	0.303	0.430	4.1e-10

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

 Score = 325 (119.5 bits), Expect = 2.7e-29, P = 2.7e-29
 Identities = 76/164 (46%), Positives = 97/164 (59%)

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 RYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFL 162
             RYESFRRSALQ+  M++LL+ +TGSQKI +PM IV CGIAKMF+
Sbjct:   119 RYESFRRSALQRPQMKKLLIGVTGSQKIGMPMIIVACGIAKMFV 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

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 = 186 (70.5 bits), Expect = 1.1e-20, Sum P(2) = 1.1e-20
 Identities = 40/69 (57%), Positives = 51/69 (73%)

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 VCGIAKMFL 162
             V GIAKMF+
Sbjct:   148 VRGIAKMFV 156

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 = 150 (57.9 bits), Expect = 9.4e-11, P = 9.4e-11
 Identities = 30/64 (46%), Positives = 47/64 (73%)

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

Query:   158 AKMF 161
             AK+F
Sbjct:   153 AKVF 156

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 = 144 (55.7 bits), Expect = 4.1e-10, P = 4.1e-10
 Identities = 28/65 (43%), Positives = 48/65 (73%)

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

Query:   158 AKMFL 162
             +K+F+
Sbjct:   164 SKVFV 168

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 = 144 (55.7 bits), Expect = 4.1e-10, P = 4.1e-10
 Identities = 28/65 (43%), Positives = 48/65 (73%)

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

Query:   158 AKMFL 162
             +K+F+
Sbjct:   157 SKVFV 161

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 = 144 (55.7 bits), Expect = 4.1e-10, P = 4.1e-10
 Identities = 28/65 (43%), Positives = 48/65 (73%)

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

Query:   158 AKMFL 162
             +K+F+
Sbjct:   158 SKVFV 162

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 = 144 (55.7 bits), Expect = 4.1e-10, P = 4.1e-10
 Identities = 28/65 (43%), Positives = 48/65 (73%)

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

Query:   158 AKMFL 162
             +K+F+
Sbjct:   158 SKVFV 162

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 = 144 (55.7 bits), Expect = 4.1e-10, P = 4.1e-10
 Identities = 28/65 (43%), Positives = 48/65 (73%)

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

Query:   158 AKMFL 162
             +K+F+
Sbjct:   158 SKVFV 162

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 = 144 (55.7 bits), Expect = 4.1e-10, P = 4.1e-10
 Identities = 28/65 (43%), Positives = 48/65 (73%)

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

Query:   158 AKMFL 162
             +K+F+
Sbjct:   158 SKVFV 162

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 = 144 (55.7 bits), Expect = 4.1e-10, P = 4.1e-10
 Identities = 28/65 (43%), Positives = 48/65 (73%)

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

Query:   158 AKMFL 162
             +K+F+
Sbjct:   158 SKVFV 162

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	165
pfam04719	89	pfam04719, TAFII28, hTAFII28-like protein conserve	1e-21
cd08048	85	cd08048, TAF11, TATA Binding Protein (TBP) Associa	8e-19
COG5251	199	COG5251, TAF40, Transcription initiation factor TF	4e-08

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

 Score = 83.2 bits (206), Expect = 1e-21
 Identities = 27/57 (47%), Positives = 44/57 (77%), Gaps = 1/57 (1%)

Query: 105 MQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMF 161
           MQ +++ FTE+Q+NRYE FRRS+L+K+ +++L+  +TG Q +S  + I + GIAK+F
Sbjct: 1   MQVLVSNFTEEQLNRYEVFRRSSLKKAQVKKLISQVTG-QSVSENVVIAISGIAKVF 56

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 = 75.7 bits (187), Expect = 8e-19
 Identities = 27/51 (52%), Positives = 39/51 (76%), Gaps = 1/51 (1%)

Query: 112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFL 162
           F+E+QMNRYE FRRS+  K+ ++RL+ S+TG Q +S  + I V GIAK+F+
Sbjct: 1   FSEEQMNRYEMFRRSSFPKAAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFV 50

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 = 50.0 bits (119), Expect = 4e-08
 Identities = 19/62 (30%), Positives = 38/62 (61%), Gaps = 1/62 (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 MF 161
           +F
Sbjct: 147 VF 148

Length = 199

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	165
PF04719	90	TAFII28: hTAFII28-like protein conserved region; I	99.95
KOG3219	195	consensus Transcription initiation factor TFIID, s	99.94
cd08048	85	TAF11 TATA Binding Protein (TBP) Associated Factor	99.87
COG5251	199	TAF40 Transcription initiation factor TFIID, subun	99.86
PF00808	65	CBFD_NFYB_HMF: Histone-like transcription factor (	91.4

>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=99.95  E-value=3.2e-29  Score=185.65  Aligned_cols=61  Identities=41%  Similarity=0.767  Sum_probs=43.3

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhcccC
Q 031136          105 MQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL  165 (165)
Q Consensus       105 m~~Ll~~fdeEQl~RYE~fRRS~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGEI  165 (165)
                      |++|+++||+||++|||+||||+|+|++|||||++++|+|+||+|++|+|+||||||||||
T Consensus         1 ~~~L~~~f~~eQ~~Rye~fRRs~~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEi   61 (90)
T PF04719_consen    1 MQLLLSNFDEEQLDRYEAFRRSSFNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEI   61 (90)
T ss_dssp             ---------HHHHHHHHHHHH----HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHcCCHHHHHHHHHHHHccCCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHH
Confidence            7899999999999999999999999999999999999889999999999999999999996

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=99.94  E-value=3.5e-27  Score=195.42  Aligned_cols=67  Identities=43%  Similarity=0.762  Sum_probs=63.4

Q ss_pred             cHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhcccC
Q 031136           98 DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL  165 (165)
Q Consensus        98 de~k~~km~~Ll~~fdeEQl~RYE~fRRS~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGEI  165 (165)
                      ++++..||+.|+++||+||++|||+||||+|||+.|||||++++| ++|++||+|||+||||||||||
T Consensus        83 ~~ee~~r~q~L~s~fseEQl~RYEvfRrs~f~Ka~iKkL~~~itg-~~v~~nv~Ia~~GiaKvFVGEv  149 (195)
T KOG3219|consen   83 DAEEAQRMQTLLSNFSEEQLSRYEVFRRSAFPKAQIKKLMSSITG-QSVSENVAIAMAGIAKVFVGEV  149 (195)
T ss_pred             CHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhC-CccCcceeeeecchhhHhHHHH
Confidence            466667999999999999999999999999999999999999998 5699999999999999999996

>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=99.87  E-value=4.9e-23  Score=150.70  Aligned_cols=53  Identities=51%  Similarity=0.848  Sum_probs=51.7

Q ss_pred             CCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhcccC
Q 031136          112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL  165 (165)
Q Consensus       112 fdeEQl~RYE~fRRS~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGEI  165 (165)
                      ||+||++|||.|||++|+|+.|||||++++| |+|++||+|+|+||||+|||||
T Consensus         1 f~~eQ~~Rye~~Rra~f~k~~iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGei   53 (85)
T cd08048           1 FSEEQMNRYEMFRRSSFPKAAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEI   53 (85)
T ss_pred             CCHHHHHHHHHHHHhhccHHHHHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHH
Confidence            8999999999999999999999999999997 7999999999999999999996

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=99.86  E-value=2.3e-22  Score=165.90  Aligned_cols=63  Identities=29%  Similarity=0.595  Sum_probs=60.5

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhcccC
Q 031136          102 MAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL  165 (165)
Q Consensus       102 ~~km~~Ll~~fdeEQl~RYE~fRRS~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGEI  165 (165)
                      ..|+.+|+.+||+||++|||.|||++|||+.||||+++|++ |+|++|++|+|+||+|||||||
T Consensus        90 ~~r~k~l~~~~deeq~~RyEvFrrt~lnKt~VKKlastV~n-QtVspNi~I~l~g~~KVfvGEi  152 (199)
T COG5251          90 DERFKLLVTNLDEEQTNRYEVFRRTSLNKTQVKKLASTVAN-QTVSPNIRIFLQGVGKVFVGEI  152 (199)
T ss_pred             HHHHHHHHhhcCHHHHHHHHHHHhcCCCHHHHHHHHHHHhc-cccCCCeeeeeechhHHHHHHH
Confidence            47788899999999999999999999999999999999996 8999999999999999999996

>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=91.40  E-value=0.12  Score=34.96  Aligned_cols=40  Identities=18%  Similarity=0.333  Sum_probs=31.4

Q ss_pred             cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhcccC
Q 031136          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL  165 (165)
Q Consensus       126 S~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGEI  165 (165)
                      ..||.+.|||||...-+...|+.....+|+=.+-+||.+|
T Consensus         1 ~~lP~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l   40 (65)
T PF00808_consen    1 ASLPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYL   40 (65)
T ss_dssp             -SS-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHH
T ss_pred             CCCChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHH
Confidence            3699999999999985555689999999998899998653

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 ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	165
1bh8_B	89	Htafii18HTAFII28 HETERODIMER CRYSTAL STRUCTURE Leng		9e-08

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 24/51 (47%), Positives = 39/51 (76%), Gaps = 1/51 (1%)
Query: 112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFL 162
           F+E+Q+NRYE +RRSA  K+ ++RL+ SITG+  +S  + I + GI+K+F+
Sbjct: 1   FSEEQLNRYEMYRRSAFPKAAIKRLIQSITGTS-VSQNVVIAMSGISKVFV 50
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	165
1bh9_B	89	TAFII28; histone fold, tata binding protein, trans	3e-17
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05

>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 = 71.3 bits (175), Expect = 3e-17
 Identities = 24/51 (47%), Positives = 38/51 (74%), Gaps = 1/51 (1%)

Query: 112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFL 162
           F+E+Q+NRYE +RRSA  K+ ++RL+ SITG   +S  + I + GI+K+F+
Sbjct: 1   FSEEQLNRYEMYRRSAFPKAAIKRLIQSITG-TSVSQNVVIAMSGISKVFV 50

>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 = 43.3 bits (101), Expect = 2e-05
 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	165
1bh9_B	89	TAFII28; histone fold, tata binding protein, trans	99.88
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	87.81
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	87.63
3b0c_W	76	CENP-W, centromere protein W; histone fold, DNA bi	87.37
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	86.69
4g92_C	119	HAPE; transcription factor, nucleosome, minor groo	80.83

>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=99.88  E-value=1.4e-23  Score=153.78  Aligned_cols=53  Identities=45%  Similarity=0.795  Sum_probs=51.4

Q ss_pred             CCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhcccC
Q 031136          112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL  165 (165)
Q Consensus       112 fdeEQl~RYE~fRRS~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGEI  165 (165)
                      ||+||++|||.||||+|+|++|||||++++| |+||+||+|+|+||||+|||||
T Consensus         1 ft~eQ~~Rye~~Rrs~f~k~~vKrl~~~~~~-~~v~~~v~i~v~glaKvfVgel   53 (89)
T 1bh9_B            1 FSEEQLNRYEMYRRSAFPKAAIKRLIQSITG-TSVSQNVVIAMSGISKVFVGEV   53 (89)
T ss_dssp             CCHHHHHHHHHHHHCCCCHHHHHHHHHHHHS-SCCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHcC-CCCCccHHHHHHHHHHHHHHHH
Confidence            8999999999999999999999999999996 7999999999999999999986

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

Probab=87.81  E-value=0.21  Score=35.88  Aligned_cols=46  Identities=17%  Similarity=0.305  Sum_probs=32.1

Q ss_pred             HHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhcccC
Q 031136          120 YESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL  165 (165)
Q Consensus       120 YE~fRRS~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGEI  165 (165)
                      -..|+...||-+.|||||+.--....|+....++++-.+-+||-+|
T Consensus        12 ~~~~~~~~lP~arIkrImK~~~~~~~is~eA~~~laka~E~Fi~~l   57 (97)
T 1n1j_B           12 VKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITEL   57 (97)
T ss_dssp             --------CCHHHHHHHHTTSTTCCCBCTHHHHHHHHHHHHHHHHH
T ss_pred             cCCcCCCcCCHHHHHHHHccCccccccChHHHHHHHHHHHHHHHHH
Confidence            4668999999999999999864434689999999999999998653

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

Probab=87.63  E-value=0.25  Score=33.15  Aligned_cols=38  Identities=16%  Similarity=0.210  Sum_probs=33.6

Q ss_pred             cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhccc
Q 031136          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEW  164 (165)
Q Consensus       126 S~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGE  164 (165)
                      +.||++.|+||+... |...++..+..++..+++.|+-+
T Consensus         5 ~~lp~a~v~Rl~r~~-g~~ris~~a~~~l~e~~~~~~~~   42 (70)
T 1ku5_A            5 GELPIAPVDRLIRKA-GAERVSEQAAKVLAEYLEEYAIE   42 (70)
T ss_dssp             CCSCHHHHHHHHHHT-TCSEECHHHHHHHHHHHHHHHHH
T ss_pred             ccCChHHHHHHHHHc-CcceeCHHHHHHHHHHHHHHHHH
Confidence            579999999999986 66789999999999999998754

>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=87.37  E-value=0.47  Score=32.49  Aligned_cols=38  Identities=11%  Similarity=0.252  Sum_probs=31.8

Q ss_pred             cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhcc
Q 031136          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLE  163 (165)
Q Consensus       126 S~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVG  163 (165)
                      ..||++.|+|||.++++...|+.....+|.-..-.||-
T Consensus         3 ~~LP~A~V~rI~K~~~p~~~is~~A~~~i~~~~~~Fi~   40 (76)
T 3b0c_W            3 RTVPRGTLRKIIKKHKPHLRLAANTDLLVHLSFLLFLH   40 (76)
T ss_dssp             -CCCHHHHHHHHHHHCTTCEECTTHHHHHHHHHHHHHH
T ss_pred             CcccccHHHHHHHHhCCCCccCHHHHHHHHHHHHHHHH
Confidence            47999999999998887778899888888887777764

>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=86.69  E-value=0.31  Score=32.30  Aligned_cols=38  Identities=16%  Similarity=0.240  Sum_probs=32.4

Q ss_pred             cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhccc
Q 031136          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEW  164 (165)
Q Consensus       126 S~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGE  164 (165)
                      +.||++.|+|||..+ +...++.....++...+..|+-+
T Consensus         1 ~~lP~a~v~Ri~k~~-~~~ris~~A~~~l~~a~e~fi~~   38 (68)
T 1b67_A            1 GELPIAPIGRIIKNA-GAERVSDDARIALAKVLEEMGEE   38 (68)
T ss_dssp             CCSCHHHHHHHHHHT-TCSEECHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccHHHHHHhcC-CcccCCHHHHHHHHHHHHHHHHH
Confidence            469999999999998 66788988889999888888743

>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=80.83  E-value=0.51  Score=35.13  Aligned_cols=44  Identities=14%  Similarity=0.243  Sum_probs=36.0

Q ss_pred             HHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhcccC
Q 031136          122 SFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL  165 (165)
Q Consensus       122 ~fRRS~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGEI  165 (165)
                      .|+-..||-+.|||||...-....|+....++++..+-+||.+|
T Consensus        36 d~k~~~lPvaRIkrImK~d~~~~~is~eA~v~la~a~E~Fi~~L   79 (119)
T 4g92_C           36 DYKIHQLPLARIKKVMKADPEVKMISAEAPILFAKGCDVFITEL   79 (119)
T ss_dssp             CSSCCSSCHHHHHHHHHTSTTCCEECTHHHHHHHHHHHHHHHHH
T ss_pred             ccccCCCCHHHHHHHHhhCCccccccHHHHHHHHHHHHHHHHHH
Confidence            37778899999999998755445788888899999899998653

---

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	165
d1bh9b_	89	a.22.1.3 (B:) TAF(II)28 {Human (Homo sapiens) [Tax	1e-19

>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 = 76.3 bits (188), Expect = 1e-19
 Identities = 24/51 (47%), Positives = 38/51 (74%), Gaps = 1/51 (1%)

Query: 112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFL 162
           F+E+Q+NRYE +RRSA  K+ ++RL+ SITG   +S  + I + GI+K+F+
Sbjct: 1   FSEEQLNRYEMYRRSAFPKAAIKRLIQSITG-TSVSQNVVIAMSGISKVFV 50

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	165
d1bh9b_	89	TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]}	99.92
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	94.44
d1jfia_	66	Negative cofactor 2, NC2, alpha chain {Human (Homo	94.04
d1ku5a_	66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	88.33
d1n1ja_	87	Nuclear transcription factor Y subunit beta (Nf-Yb	83.99
d1n1jb_	78	Nuclear transcription factor Y subunit gamma (Nf-Y	83.49

>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=99.92  E-value=2.6e-26  Score=167.50  Aligned_cols=53  Identities=45%  Similarity=0.795  Sum_probs=51.7

Q ss_pred             CCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhcccC
Q 031136          112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL  165 (165)
Q Consensus       112 fdeEQl~RYE~fRRS~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGEI  165 (165)
                      ||+|||+|||+||||+|+|++|||||++++| |+||+|++|+|+||||||||||
T Consensus         1 Fs~eQ~~RyE~fRRs~~~K~~vkrl~~~~~g-~sv~~~v~i~v~giaKvFvGEi   53 (89)
T d1bh9b_           1 FSEEQLNRYEMYRRSAFPKAAIKRLIQSITG-TSVSQNVVIAMSGISKVFVGEV   53 (89)
T ss_dssp             CCHHHHHHHHHHHHCCCCHHHHHHHHHHHHS-SCCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhhCCHHHHHHHHHHHcC-CCCChhHHHHHHHHHHHHHHHH
Confidence            8999999999999999999999999999997 7999999999999999999996

>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=94.44  E-value=0.0097  Score=38.24  Aligned_cols=39  Identities=13%  Similarity=0.187  Sum_probs=33.9

Q ss_pred             cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhcccC
Q 031136          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL  165 (165)
Q Consensus       126 S~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGEI  165 (165)
                      +.||++.||||+.+... -.|+..+..+++..+++||.+|
T Consensus         2 aeLP~a~I~ri~k~~~~-~ris~ea~~~l~~~~e~fi~~l   40 (68)
T d1htaa_           2 GELPIAPIGRIIKNAGA-ERVSDDARIALAKVLEEMGEEI   40 (68)
T ss_dssp             CCSCHHHHHHHHHHTTC-SCCCHHHHHHHHHHHHHHHHHH
T ss_pred             CcCcHHHHHHHHHHCCc-chhhHHHHHHHHHHHHHHHHHH
Confidence            46999999999999754 4799999999999999999764

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

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

Probab=94.04  E-value=0.011  Score=38.15  Aligned_cols=40  Identities=13%  Similarity=0.360  Sum_probs=35.2

Q ss_pred             cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhcccC
Q 031136          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL  165 (165)
Q Consensus       126 S~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGEI  165 (165)
                      +.||-+.|||||..-.....|+.....+|+..+.+||.+|
T Consensus         1 a~fP~srVkkimk~~~~~~~is~~A~~~~~~a~E~Fi~~l   40 (66)
T d1jfia_           1 ARFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESL   40 (66)
T ss_dssp             CCCCHHHHHHHHTTSTTCCCBCTTHHHHHHHHHHHHHHHH
T ss_pred             CCCChHHHHHHHhcCCccccccHHHHHHHHHHHHHHHHHH
Confidence            5799999999999776666899999999999999999764

>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=88.33  E-value=0.1  Score=33.15  Aligned_cols=37  Identities=14%  Similarity=0.137  Sum_probs=32.2

Q ss_pred             CCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhccc
Q 031136          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEW  164 (165)
Q Consensus       127 ~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGE  164 (165)
                      -||++.||||+..... -.|+.....++...+++||-.
T Consensus         2 ~LP~a~I~rI~k~~~~-~ris~ea~~~l~~a~e~Fi~~   38 (66)
T d1ku5a_           2 ELPIAPVDRLIRKAGA-ERVSEQAAKVLAEYLEEYAIE   38 (66)
T ss_dssp             CSCHHHHHHHHHHTTC-SEECHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHhCcc-cccHHHHHHHHHHHHHHHHHH
Confidence            5899999999998754 478899999999999999864

>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=83.99  E-value=0.21  Score=33.29  Aligned_cols=38  Identities=18%  Similarity=0.231  Sum_probs=31.6

Q ss_pred             CCChHHHHHHHHHhh-cCccCCccHHHHhhhhhhhhccc
Q 031136          127 ALQKSNMRRLLVSIT-GSQKISLPMTIVVCGIAKMFLEW  164 (165)
Q Consensus       127 ~f~K~~IKKLinsvt-gsQsVs~nvvIaVaGiAKvFVGE  164 (165)
                      -||++.|+|||.+.+ +...|+.....+|+-.+-+||..
T Consensus         2 ~LP~a~v~ri~K~~~p~~~~is~ea~~~i~~a~e~Fi~~   40 (87)
T d1n1ja_           2 YLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISF   40 (87)
T ss_dssp             CCCHHHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHH
T ss_pred             CCcHhHHHHHHHHhCCccccccHHHHHHHHHHHHHHHHH
Confidence            389999999998775 34578999999999999999854

>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=83.49  E-value=0.22  Score=32.31  Aligned_cols=37  Identities=14%  Similarity=0.249  Sum_probs=30.0

Q ss_pred             CChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhccc
Q 031136          128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEW  164 (165)
Q Consensus       128 f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGE  164 (165)
                      ||.+.|||||+.--....++.....+|+-.+-+||..
T Consensus         1 LP~srVkrImK~~~~~~~is~ea~~~i~~a~E~Fi~~   37 (78)
T d1n1jb_           1 LPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITE   37 (78)
T ss_dssp             CCHHHHHHHHTTSTTCCCBCTHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHH
Confidence            7899999999864444567888888999888899865