Citrus Sinensis ID: 028537

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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-------190-------200-------
Protein Sequence
MKQSKDPFEAALEESPGDSPDELEIETQPQTGTAAGSATAAVTGELEDEFDNLESQAPMSVSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVPKRSVPS
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHccccHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccHEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHcccccccccccHHHHHHHHHHHHHccHHHHHHHHHHHHHcccHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHccccccccccc
Coil and Loop (DISEMBL)
mkqskdpfeaaleespgdspdeleietqpqtgtaagsataavTGELedefdnlesqapmsvsagpaakmtmsknkdeydeeddenvdvelgkfpsssdpaKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITgsqkislpmTIVVCGIAKMFVGELVETARMVMTernesgpirpchIREAYRRLKLegkvpkrsvps
Flexible Loop (DISEMBL)
mkqskdpfeaaleespgdspdelEIETQPQTGTAAGSATAAVTGELEDEFDNLEsqapmsvsagpaakMTMSKNKDEYDEEDDENVDVELGkfpsssdpaKMAKMQAILNQFTEDQMNRYESFRrsalqksnMRRLLVSitgsqkislpMTIVVCGIAKMFVGELVETARMVMternesgpirpchireayrrlklegkvpkrsvps
Low Complexity Region (SEG)
MKQSKDPFEAALEESPGDSPDELEIETQPQtgtaagsataavtgELEDEFDNLESQAPMSVSAGPAAKMTMSknkdeydeeddenvdveLGKFPSSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVPKRSVPS
Disordered region (IsUnstruct)
*************************************************************************************************************************************RRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMT*******IRPCHIREAYR***************
Disordered Region (DISOPRED)
***********************************************************************************************************ILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERN**GPIRPCHIREAYRR**************
Disordered Region (DISEMBL)
***********************EIETQ***********AAVTGELEDEFDNLESQAP****************************DVELGKFPSSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEG*********
Disordered Region (DISPRO)
******PF**ALE**********************************************************************************SSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKQSKDPFEAALEESPGDSPDELEIETQPQTGTAAGSATAAVTGELEDEFDNLESQAPMSVSAGPAAKMTMSKNKDEYDEEDDENVDVELGKFPSSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVPKRSVPS
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	207	2.2.26 [Sep-21-2011]
Q54XM9	450	Transcription initiation	yes	no	0.468	0.215	0.472	2e-23
Q99JX1	211	Transcription initiation	yes	no	0.483	0.473	0.465	5e-21
Q5RA91	211	Transcription initiation	yes	no	0.497	0.488	0.461	5e-21
Q15544	211	Transcription initiation	yes	no	0.497	0.488	0.461	8e-21
Q5U1X0	211	Transcription initiation	yes	no	0.483	0.473	0.465	1e-20
P49906	196	Transcription initiation	yes	no	0.463	0.489	0.474	4e-19
Q9US54	199	Transcription initiation	yes	no	0.613	0.638	0.366	7e-17
A6NLC8	198	Putative TAF11-like prote	no	no	0.497	0.520	0.432	2e-14
Q04226	346	Transcription initiation	yes	no	0.347	0.208	0.287	6e-05

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

 Score =  108 bits (270), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 51/108 (47%), Positives = 75/108 (69%), Gaps = 11/108 (10%)

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 FVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP--KRSVP 206
           FVGE+VE AR +M E  E+GPIRP HIREAYRRLK    +P  K+SVP
Sbjct: 399 FVGEIVELARSIMEEWRETGPIRPRHIREAYRRLKESNSIPYYKKSVP 446

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

 Score =  100 bits (250), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 47/101 (46%), Positives = 75/101 (74%), Gaps = 1/101 (0%)

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

Query: 161 FVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP 201
           FVGE+VE A  V  +  E+ P++P H+REA RRLK +G++P
Sbjct: 161 FVGEVVEEALDVCEKWGETPPLQPKHMREAVRRLKSKGQIP 201

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

 Score =  100 bits (250), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 48/104 (46%), Positives = 75/104 (72%), Gaps = 1/104 (0%)

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

Query: 158 AKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP 201
           +K+FVGE+VE A  V  +  E  P++P H+REA RRLK +G++P
Sbjct: 158 SKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLKSKGQIP 201

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 =  100 bits (248), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 48/104 (46%), Positives = 75/104 (72%), Gaps = 1/104 (0%)

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

Query: 158 AKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP 201
           +K+FVGE+VE A  V  +  E  P++P H+REA RRLK +G++P
Sbjct: 158 SKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLKSKGQIP 201

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 =  100 bits (248), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 47/101 (46%), Positives = 74/101 (73%), Gaps = 1/101 (0%)

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

Query: 161 FVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP 201
           FVGE+VE A  V  +  E  P++P H+REA RRLK +G++P
Sbjct: 161 FVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLKSKGQIP 201

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

 Score = 94.7 bits (234), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 46/97 (47%), Positives = 70/97 (72%), Gaps = 1/97 (1%)

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

Query: 165 LVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP 201
           +VE A  VM  + ESG ++P  IREA RRL+ + ++P
Sbjct: 148 VVEEALDVMEAQGESGALQPKFIREAVRRLRTKDRMP 184

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

 Score = 87.0 bits (214), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 51/139 (36%), Positives = 82/139 (58%), Gaps = 12/139 (8%)

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 EDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVM 173
           E+QM RYE FRR+ L K+N+++L   I  +Q ++  + IV+ G +K+FVGE+VE AR + 
Sbjct: 102 EEQMQRYEVFRRANLNKTNVKKLANQIL-NQSVTPNVAIVISGFSKVFVGEIVELARKIQ 160

Query: 174 TERNESGPIRPCHIREAYR 192
            +  ++GP+ P H+REAYR
Sbjct: 161 DQWGDTGPLSPDHLREAYR 179

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 = 79.3 bits (194), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 45/104 (43%), Positives = 66/104 (63%), Gaps = 1/104 (0%)

Query: 98  DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGI 157
           D  +  +M  +L+  +E+Q++RYE  RRSA  K+ +  L+ SITG + +S  + I + GI
Sbjct: 87  DAEEAQRMTTLLSAMSEEQLSRYEVCRRSAFPKACIAGLMRSITG-RSVSENVAIAMAGI 145

Query: 158 AKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP 201
           AK+FVGE+VE A  V     E  P++P H+REA RRLK +G  P
Sbjct: 146 AKVFVGEVVEEALDVCEMWGEMPPLQPKHLREAVRRLKPKGLFP 189

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 = 47.4 bits (111), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 44/73 (60%), 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 MFVGELVETARMV 172
           ++ GE++E A +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	207
225462089	198	PREDICTED: transcription initiation fact	0.908	0.949	0.666	2e-63
224057892	222	predicted protein [Populus trichocarpa]	0.971	0.905	0.632	2e-61
255583916	205	Transcription initiation factor TFIID su	0.898	0.907	0.688	4e-61
388513279	203	unknown [Medicago truncatula]	0.937	0.955	0.578	5e-59
388491516	203	unknown [Medicago truncatula]	0.937	0.955	0.569	9e-58
217072422	203	unknown [Medicago truncatula]	0.937	0.955	0.574	1e-57
388503812	205	unknown [Lotus japonicus]	0.971	0.980	0.587	8e-57
297804116	211	predicted protein [Arabidopsis lyrata su	0.990	0.971	0.634	7e-56
449460461	220	PREDICTED: uncharacterized protein LOC10	0.961	0.904	0.614	9e-56
351734450	155	uncharacterized protein LOC100305481 [Gl	0.719	0.961	0.578	2e-54

>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 =  247 bits (631), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 140/210 (66%), Positives = 162/210 (77%), Gaps = 22/210 (10%)

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 QMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTE 175
           QM+RYESFRRS  QK+NM++LLVSITGSQKIS PMTIV  GIAKMFVGELVETARMVMTE
Sbjct: 104 QMSRYESFRRSGFQKANMKKLLVSITGSQKISAPMTIVASGIAKMFVGELVETARMVMTE 163

Query: 176 RNESGPIRPCHIREAYRRLKLEGKVPKRSV 205
           R E+GPIRPCHIREAYRRLKLEGKVP+RSV
Sbjct: 164 RKETGPIRPCHIREAYRRLKLEGKVPRRSV 193

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  240 bits (613), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 141/223 (63%), Positives = 160/223 (71%), Gaps = 22/223 (9%)

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 ELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVPKRSVP 206
           ELVETAR+VMTER ESGPIRPCHIREAYRRLKLEGKVPKRSVP
Sbjct: 176 ELVETARIVMTERKESGPIRPCHIREAYRRLKLEGKVPKRSVP 218

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 =  239 bits (611), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 146/212 (68%), Positives = 165/212 (77%), Gaps = 26/212 (12%)

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 DQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMT 174
           +QM RYESFRRSALQK+NMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETAR+VMT
Sbjct: 110 NQMTRYESFRRSALQKANMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARIVMT 169

Query: 175 ERNESGPIRPCHIREAYRRLKLEGKVPKRSVP 206
           ER ESGPIRPCHIREAYRRLKLEGKVPKRSVP
Sbjct: 170 ERKESGPIRPCHIREAYRRLKLEGKVPKRSVP 201

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  232 bits (592), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 121/209 (57%), Positives = 159/209 (76%), Gaps = 15/209 (7%)

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 MNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTER 176
           M+RYESFRR+  QK+NM+RLL SITG+QKIS+P+TI V GIAK+FVGE+VETAR +M ER
Sbjct: 110 MSRYESFRRAGFQKANMKRLLTSITGTQKISIPITIAVSGIAKVFVGEVVETARTIMKER 169

Query: 177 NESGPIRPCHIREAYRRLKLEGKVPKRSV 205
            E+GPIRPCH+REA+RRLKLEGK+ KR+ 
Sbjct: 170 KETGPIRPCHLREAHRRLKLEGKIFKRTT 198

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 =  228 bits (582), Expect = 9e-58,   Method: Compositional matrix adjust.
 Identities = 119/209 (56%), Positives = 158/209 (75%), Gaps = 15/209 (7%)

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 MNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTER 176
           M+RYESFRR+  QK+NM+RLL SITG+QKIS+P+TI +  IAK+FVGE+VETAR +M ER
Sbjct: 110 MSRYESFRRAGFQKANMKRLLTSITGTQKISIPITIAISRIAKVFVGEVVETARTIMKER 169

Query: 177 NESGPIRPCHIREAYRRLKLEGKVPKRSV 205
            E+GPIRPCH+REA+RRLKLEGK+ KR+ 
Sbjct: 170 KETGPIRPCHLREAHRRLKLEGKIFKRTT 198

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 =  228 bits (582), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 120/209 (57%), Positives = 158/209 (75%), Gaps = 15/209 (7%)

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 MNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTER 176
           M+RYESFRR+  QK+NM+RLL SITG+QKIS+P+TI V GIAK+FVGE+VETAR +M ER
Sbjct: 110 MSRYESFRRAGFQKANMKRLLTSITGTQKISIPITIAVSGIAKVFVGEVVETARTIMKER 169

Query: 177 NESGPIRPCHIREAYRRLKLEGKVPKRSV 205
            E+GPIRPCH+REA+RRLKLEGK+ KR+ 
Sbjct: 170 KETGPIRPCHLREAHRRLKLEGKIFKRTT 198

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  225 bits (574), Expect = 8e-57,   Method: Compositional matrix adjust.
 Identities = 121/206 (58%), Positives = 152/206 (73%), Gaps = 5/206 (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  -----SGGGGGGKNKDDEEEEEEDNMDVELTKLQPTGDPQKMAKMQAILSQFTEEQMSRY 115

Query: 121 ESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESG 180
           ESFRR+  QK+NM+RLL SITG+QKI++P+TIVV GIAKMFVGE+VETAR+V+ ER E G
Sbjct: 116 ESFRRAGFQKANMKRLLASITGTQKITIPITIVVSGIAKMFVGEVVETARIVIKERKEFG 175

Query: 181 PIRPCHIREAYRRLKLEGKVPKRSVP 206
           PIRPCH+REAYRRLKLEGKV KRSVP
Sbjct: 176 PIRPCHLREAYRRLKLEGKVFKRSVP 201

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

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 =  222 bits (566), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 132/208 (63%), Positives = 159/208 (76%), Gaps = 3/208 (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 RYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNE 178
           RYESFRRSALQ+  M++LL+ +TGSQKI +PM IVVCGIAKMFVGELVETAR+VM ER E
Sbjct: 120 RYESFRRSALQRPQMKKLLIGVTGSQKIGMPMIIVVCGIAKMFVGELVETARVVMAERKE 179

Query: 179 SGPIRPCHIREAYRRLKLEGKVPKRSVP 206
           SGPIRPCHIRE+YRRLKLEGKVPKRSVP
Sbjct: 180 SGPIRPCHIRESYRRLKLEGKVPKRSVP 207

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 =  222 bits (565), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 137/223 (61%), Positives = 169/223 (75%), Gaps = 24/223 (10%)

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 ELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVPKRSVP 206
           ELVETAR+VMTERN++GPIRPCH+REAYRRLKLEGK+P++SVP
Sbjct: 174 ELVETARVVMTERNDTGPIRPCHLREAYRRLKLEGKIPRKSVP 216

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  217 bits (553), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 118/204 (57%), Positives = 134/204 (65%), Gaps = 55/204 (26%)

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 ESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESG 180
           ESFRR+  QK+NM+RLL SITG+QKIS+PMTIVV GIAKMFVGE+VETAR+VM ER ESG
Sbjct: 66  ESFRRAGFQKANMKRLLASITGTQKISVPMTIVVSGIAKMFVGEVVETARIVMKERKESG 125

Query: 181 PIRPCHIREAYRRLKLEGKVPKRS 204
           PIRPCH+REAYRRLKLEGKV KRS
Sbjct: 126 PIRPCHLREAYRRLKLEGKVFKRS 149

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	207
TAIR|locus:2120422	210	TAF11 "TBP-associated factor 1	0.985	0.971	0.562	7.2e-52
TAIR|locus:2198671	204	TAF11b "TBP-associated factor	0.536	0.544	0.687	4.1e-41
DICTYBASE|DDB_G0278843	450	taf11 "TFIID subunit" [Dictyos	0.492	0.226	0.476	2.8e-21
MGI|MGI:1916026	211	Taf11 "TAF11 RNA polymerase II	0.497	0.488	0.461	2.1e-20
UNIPROTKB|Q3ZBP7	210	TAF11 "TAF11 RNA polymerase II	0.497	0.490	0.461	3.5e-20
UNIPROTKB|E2RFN3	211	TAF11 "Uncharacterized protein	0.497	0.488	0.461	3.5e-20
UNIPROTKB|Q15544	211	TAF11 "Transcription initiatio	0.497	0.488	0.461	3.5e-20
UNIPROTKB|F1RZ14	211	TAF11 "Uncharacterized protein	0.497	0.488	0.461	3.5e-20
RGD|1305626	211	Taf11 "TAF11 RNA polymerase II	0.497	0.488	0.461	3.5e-20
RGD|1562272	207	RGD1562272 "similar to TAF11 R	0.497	0.497	0.461	3.5e-20

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

 Score = 538 (194.4 bits), Expect = 7.2e-52, P = 7.2e-52
 Identities = 117/208 (56%), Positives = 139/208 (66%)

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 RYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNE 178
             RYESFRRSALQ+  M++LL+ +TGSQKI +PM IV CGIAKMFVGELVETAR+VM ER E
Sbjct:   119 RYESFRRSALQRPQMKKLLIGVTGSQKIGMPMIIVACGIAKMFVGELVETARVVMAERKE 178

Query:   179 SGPIRPCHIREAYRRLKLEGKVPKRSVP 206
             SGPIRPCHIRE+YRRLKLEGKVPKRSVP
Sbjct:   179 SGPIRPCHIRESYRRLKLEGKVPKRSVP 206

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 = 381 (139.2 bits), Expect = 4.1e-41, Sum P(2) = 4.1e-41
 Identities = 77/112 (68%), Positives = 92/112 (82%)

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 VCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVPKRSV 205
             V GIAKMFVG+LVETAR+VM ER ESGPIRPCHIRE+YRRLKL+GKVP+RSV
Sbjct:   148 VRGIAKMFVGDLVETARVVMRERKESGPIRPCHIRESYRRLKLQGKVPQRSV 199

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

DICTYBASE|DDB_G0278843 taf11 "TFIID subunit" [Dictyostelium discoideum (taxid:44689)]

 Score = 254 (94.5 bits), Expect = 2.8e-21, P = 2.8e-21
 Identities = 50/105 (47%), Positives = 75/105 (71%)

Query:   104 KMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVG 163
             +M  ++  F+EDQ  R+E ++RS+ Q++N+++++ S+  S  ++    IV+ GIAK+FVG
Sbjct:   343 QMNTLIKHFSEDQQTRFEYYKRSSFQRANIKKVMQSVL-SAPVNQTSAIVMGGIAKVFVG 401

Query:   164 ELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP--KRSVP 206
             E+VE AR +M E  E+GPIRP HIREAYRRLK    +P  K+SVP
Sbjct:   402 EIVELARSIMEEWRETGPIRPRHIREAYRRLKESNSIPYYKKSVP 446

GO:0046982 "protein heterodimerization activity" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

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

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

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

GO:0044351 "macropinocytosis" evidence=RCA

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

 Score = 241 (89.9 bits), Expect = 2.1e-20, P = 2.1e-20
 Identities = 48/104 (46%), Positives = 76/104 (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 AKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP 201
             +K+FVGE+VE A  V  +  E+ P++P H+REA RRLK +G++P
Sbjct:   158 SKVFVGEVVEEALDVCEKWGETPPLQPKHMREAVRRLKSKGQIP 201

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

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

 Score = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 48/104 (46%), Positives = 75/104 (72%)

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

Query:   158 AKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP 201
             +K+FVGE+VE A  V  +  E  P++P H+REA RRLK +G++P
Sbjct:   157 SKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLKSKGQIP 200

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 = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 48/104 (46%), Positives = 75/104 (72%)

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

Query:   158 AKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP 201
             +K+FVGE+VE A  V  +  E  P++P H+REA RRLK +G++P
Sbjct:   158 SKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLKSKGQIP 201

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 = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 48/104 (46%), Positives = 75/104 (72%)

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

Query:   158 AKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP 201
             +K+FVGE+VE A  V  +  E  P++P H+REA RRLK +G++P
Sbjct:   158 SKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLKSKGQIP 201

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 = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 48/104 (46%), Positives = 75/104 (72%)

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

Query:   158 AKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP 201
             +K+FVGE+VE A  V  +  E  P++P H+REA RRLK +G++P
Sbjct:   158 SKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLKSKGQIP 201

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

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

 Score = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 48/104 (46%), Positives = 75/104 (72%)

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

Query:   158 AKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP 201
             +K+FVGE+VE A  V  +  E  P++P H+REA RRLK +G++P
Sbjct:   158 SKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLKSKGQIP 201

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

RGD|1562272 RGD1562272 "similar to TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Rattus norvegicus (taxid:10116)]

 Score = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 48/104 (46%), Positives = 75/104 (72%)

Query:    98 DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGI 157
             D  ++ KMQ +++ F+E+Q+NRYE +RRSA  K+ ++RL+ SITG+  +S  + I + GI
Sbjct:    95 DEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQSITGTS-VSQNVVIAMSGI 153

Query:   158 AKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP 201
             +K+FVGE+VE A  V  +  E  P++P H+REA RRLK +G++P
Sbjct:   154 SKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLKSKGQIP 197

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

Fail to connect to STRING server

---

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	207
pfam04719	89	pfam04719, TAFII28, hTAFII28-like protein conserve	5e-41
cd08048	85	cd08048, TAF11, TATA Binding Protein (TBP) Associa	2e-39
COG5251	199	COG5251, TAF40, Transcription initiation factor TF	1e-21

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

 Score =  134 bits (338), Expect = 5e-41
 Identities = 52/90 (57%), Positives = 71/90 (78%), Gaps = 1/90 (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 LVETARMVMTERNESGPIRPCHIREAYRRL 194
           +VE AR VM E  ESGPI+P HIREAYRRL
Sbjct: 60  IVEEARDVMDEWEESGPIQPDHIREAYRRL 89

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 =  129 bits (327), Expect = 2e-39
 Identities = 49/86 (56%), Positives = 65/86 (75%), Gaps = 3/86 (3%)

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

Query: 172 VMTERNE--SGPIRPCHIREAYRRLK 195
           V  E  E  +GP++P H+REAYRRLK
Sbjct: 60  VQEEWGEANTGPLQPRHLREAYRRLK 85

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 = 87.8 bits (217), Expect = 1e-21
 Identities = 35/95 (36%), Positives = 59/95 (62%), Gaps = 1/95 (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 MFVGELVETARMVMTERNESGPIRPCHIREAYRRL 194
           +FVGE++E A +V  +   SGP+ P H REAYR  
Sbjct: 147 VFVGEIIELAMIVQNKWLTSGPLIPFHKREAYRYK 181

Length = 199

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	207
KOG3219	195	consensus Transcription initiation factor TFIID, s	100.0
PF04719	90	TAFII28: hTAFII28-like protein conserved region; I	100.0
cd08048	85	TAF11 TATA Binding Protein (TBP) Associated Factor	100.0
COG5251	199	TAF40 Transcription initiation factor TFIID, subun	99.97
KOG3902	352	consensus Histone acetyltransferase PCAF/SAGA, sub	99.27
PF00808	65	CBFD_NFYB_HMF: Histone-like transcription factor (	97.89
smart00803	65	TAF TATA box binding protein associated factor. TA	96.49
cd07981	72	TAF12 TATA Binding Protein (TBP) Associated Factor	96.01
cd00074	115	H2A Histone 2A; H2A is a subunit of the nucleosome	95.54
PF00125	75	Histone: Core histone H2A/H2B/H3/H4 histone h2a si	95.24
COG5262	132	HTA1 Histone H2A [Chromatin structure and dynamics	94.4
KOG0871	156	consensus Class 2 transcription repressor NC2, bet	94.26
smart00414	106	H2A Histone 2A.	93.39
COG2036	91	HHT1 Histones H3 and H4 [Chromatin structure and d	93.38
PF02969	66	TAF: TATA box binding protein associated factor (T	93.35
cd00076	85	H4 Histone H4, one of the four histones, along wit	93.05
PTZ00017	134	histone H2A; Provisional	92.1
PTZ00015	102	histone H4; Provisional	91.82
PLN00035	103	histone H4; Provisional	91.38
PLN00154	136	histone H2A; Provisional	90.42
PLN00153	129	histone H2A; Provisional	90.14
PLN00156	139	histone H2AX; Provisional	89.85
PLN00157	132	histone H2A; Provisional	89.82
PTZ00252	134	histone H2A; Provisional	89.04
KOG1659	224	consensus Class 2 transcription repressor NC2, alp	88.54
smart00417	74	H4 Histone H4.	88.12
PF03847	68	TFIID_20kDa: Transcription initiation factor TFIID	87.77
PF09415	72	CENP-X: CENP-S associating Centromere protein X; I	87.19
smart00576	77	BTP Bromodomain transcription factors and PHD doma	86.86
cd08050	343	TAF6 TATA Binding Protein (TBP) Associated Factor	85.23
KOG1756	131	consensus Histone 2A [Chromatin structure and dyna	83.38
PTZ00463	117	histone H2B; Provisional	80.99
COG5208	286	HAP5 CCAAT-binding factor, subunit C [Transcriptio	80.6
PF07524	77	Bromo_TP: Bromodomain associated; InterPro: IPR006	80.38

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

Probab=100.00  E-value=8.4e-44  Score=303.23  Aligned_cols=109  Identities=51%  Similarity=0.845  Sum_probs=102.8

Q ss_pred             CCcHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028537           96 SSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTE  175 (207)
Q Consensus        96 ~~d~e~~~km~~Ll~~fteEQldRYE~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E  175 (207)
                      +.+.++.++|+.||++||+||++|||.||||+|+|+.|||||++|||. +|++|++|+|+||||||||||||+|++||++
T Consensus        81 ~~~~ee~~r~q~L~s~fseEQl~RYEvfRrs~f~Ka~iKkL~~~itg~-~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~  159 (195)
T KOG3219|consen   81 TVDAEEAQRMQTLLSNFSEEQLSRYEVFRRSAFPKAQIKKLMSSITGQ-SVSENVAIAMAGIAKVFVGEVVEEALDVREE  159 (195)
T ss_pred             CcCHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhCC-ccCcceeeeecchhhHhHHHHHHHHHHHHHH
Confidence            345667779999999999999999999999999999999999999986 5999999999999999999999999999999


Q ss_pred             hccCCCCCchHHHHHHHHHHhcCCCC-CCCC
Q 028537          176 RNESGPIRPCHIREAYRRLKLEGKVP-KRSV  205 (207)
Q Consensus       176 ~~e~gPLqP~HIREA~RRL~~~GklP-~rs~  205 (207)
                      |++++||||+|||||||||+.+|++| ++.+
T Consensus       160 ~~e~~PLqP~HIREA~rrL~~qgk~~~~~~~  190 (195)
T KOG3219|consen  160 WGESGPLQPKHIREAYRRLKLQGKLPNSRYK  190 (195)
T ss_pred             hccCCCCCcHHHHHHHHHHHhcCCCCCCccc
Confidence            99999999999999999999999999 5544

>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=2.8e-43  Score=268.98  Aligned_cols=90  Identities=51%  Similarity=0.894  Sum_probs=68.4

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCc
Q 028537          105 MQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRP  184 (207)
Q Consensus       105 m~~Ll~~fteEQldRYE~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP  184 (207)
                      |+.|+++||+||++|||+||||+|+|++|||||++++|+|+||+|++|+|+||||+|||||||+|++||++|++++||+|
T Consensus         1 ~~~L~~~f~~eQ~~Rye~fRRs~~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P   80 (90)
T PF04719_consen    1 MQLLLSNFDEEQLDRYEAFRRSSFNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQP   80 (90)
T ss_dssp             ---------HHHHHHHHHHHH----HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--H
T ss_pred             ChHHHHcCCHHHHHHHHHHHHccCCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCc
Confidence            78999999999999999999999999999999999999899999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHH
Q 028537          185 CHIREAYRRL  194 (207)
Q Consensus       185 ~HIREA~RRL  194 (207)
                      +|||||||||
T Consensus        81 ~hlreA~rrL   90 (90)
T PF04719_consen   81 DHLREAYRRL   90 (90)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHhC
Confidence            9999999998

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.

>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=100.00  E-value=1.8e-38  Score=239.71  Aligned_cols=83  Identities=59%  Similarity=0.965  Sum_probs=80.8

Q ss_pred             CCHHHHHHHHHHHhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhcc--CCCCCchHHHH
Q 028537          112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNE--SGPIRPCHIRE  189 (207)
Q Consensus       112 fteEQldRYE~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e--~gPLqP~HIRE  189 (207)
                      ||+|||+|||.||||+|+|++|||||++++| |+||+||+|+|+||||+|||||||+|++||++|++  ++||+|+||||
T Consensus         1 f~~eQ~~Rye~~Rra~f~k~~iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~Hire   79 (85)
T cd08048           1 FSEEQMNRYEMFRRSSFPKAAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLRE   79 (85)
T ss_pred             CCHHHHHHHHHHHHhhccHHHHHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHH
Confidence            8999999999999999999999999999997 79999999999999999999999999999999999  89999999999


Q ss_pred             HHHHHH
Q 028537          190 AYRRLK  195 (207)
Q Consensus       190 A~RRL~  195 (207)
                      |||||+
T Consensus        80 A~rrl~   85 (85)
T cd08048          80 AYRRLK   85 (85)
T ss_pred             HHHHhC
Confidence            999985

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=99.97  E-value=8.1e-32  Score=227.59  Aligned_cols=94  Identities=36%  Similarity=0.653  Sum_probs=89.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Q 028537          103 AKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPI  182 (207)
Q Consensus       103 ~km~~Ll~~fteEQldRYE~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPL  182 (207)
                      +++..|+.+||+||+.|||.|||++|||..||||+++|++ |+|++|++|+|+||+|||||||||.|+.||.+|.++|||
T Consensus        91 ~r~k~l~~~~deeq~~RyEvFrrt~lnKt~VKKlastV~n-QtVspNi~I~l~g~~KVfvGEiIElA~~Vq~~w~~sgpl  169 (199)
T COG5251          91 ERFKLLVTNLDEEQTNRYEVFRRTSLNKTQVKKLASTVAN-QTVSPNIRIFLQGVGKVFVGEIIELAMIVQNKWLTSGPL  169 (199)
T ss_pred             HHHHHHHhhcCHHHHHHHHHHHhcCCCHHHHHHHHHHHhc-cccCCCeeeeeechhHHHHHHHHHHHHHHHHHhcccCCC
Confidence            5788899999999999999999999999999999999885 799999999999999999999999999999999999999


Q ss_pred             CchHHHHHHHHHHhc
Q 028537          183 RPCHIREAYRRLKLE  197 (207)
Q Consensus       183 qP~HIREA~RRL~~~  197 (207)
                      .|.|+|||||++..+
T Consensus       170 ~p~h~reayr~~~k~  184 (199)
T COG5251         170 IPFHKREAYRYKLKK  184 (199)
T ss_pred             ChHHHHHHHHHHHHh
Confidence            999999999988754

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

Probab=99.27  E-value=2.4e-11  Score=110.77  Aligned_cols=99  Identities=21%  Similarity=0.278  Sum_probs=80.3

Q ss_pred             cHHHHHHHHH---HHhcCCHHHHHHHHHHHhcCCChhHHHHHHHHhcC----CCCCCccHHHHHHHHHHHHHHHHHHHHH
Q 028537           98 DPAKMAKMQA---ILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITG----SQKISLPMTIVVCGIAKMFVGELVETAR  170 (207)
Q Consensus        98 d~e~~~km~~---Ll~~fteEQldRYE~fRRS~F~K~~IKRLi~~vtg----sqsVs~nvvIavaGlAKvFVGELVEeAr  170 (207)
                      |+..+++|..   .-..||.+||..|..||+++|.+.+-||+ ..+++    ..+++.++.-+++.||...|+-||+.|+
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            4444444433   56899999999999999999999999986 44443    2257888999999999999999999999


Q ss_pred             HHHHHh----------------------------------ccCCCCCchHHHHHHHHHHhc
Q 028537          171 MVMTER----------------------------------NESGPIRPCHIREAYRRLKLE  197 (207)
Q Consensus       171 ~Vq~E~----------------------------------~e~gPLqP~HIREA~RRL~~~  197 (207)
                      .|+...                                  ....||+|+||+||||||+-.
T Consensus       270 lvrq~~~~ka~~p~S~~~sa~~s~~~~H~~~e~t~~~G~e~v~~~lqp~hieea~R~~q~~  330 (352)
T KOG3902|consen  270 LVRQRSDNKATEPYSSVTSAGGSSAMMHVCKEVTLFDGMEVVKPPLQPEHIEEARRRLQMS  330 (352)
T ss_pred             HHHhhhhhcccCccccccCCCCchHHhccCcccccccCccccCCCcchHHHHHHHHHHhcc
Confidence            996641                                  136899999999999999954

>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=97.89  E-value=4e-05  Score=53.96  Aligned_cols=65  Identities=15%  Similarity=0.210  Sum_probs=53.7

Q ss_pred             cCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHH
Q 028537          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAY  191 (207)
Q Consensus       126 S~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~  191 (207)
                      +.||.+.|||||...-+...||.+...+|+-.+-+||.+|..+|.++... +.+.=|+|.||..|+
T Consensus         1 ~~lP~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~-~~rkti~~~Dv~~Av   65 (65)
T PF00808_consen    1 ASLPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQR-DKRKTITYEDVAKAV   65 (65)
T ss_dssp             -SS-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTSSEE-HHHHHHHH
T ss_pred             CCCChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCccCHHHHHHHC
Confidence            36999999999998755557999999999999999999999999998774 456789999999885

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

>smart00803 TAF TATA box binding protein associated factor

Probab=96.49  E-value=0.015  Score=41.96  Aligned_cols=64  Identities=19%  Similarity=0.207  Sum_probs=55.1

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR  192 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R  192 (207)
                      .|++..||+|..+ .|-..+|+.+.-.++...+.|+-+|+..|.+++..-+ +.-|.+.+|.-|++
T Consensus         2 ~~p~~~i~ria~~-~Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hak-Rktlt~~DI~~Alk   65 (65)
T smart00803        2 WLPKETIKDVAES-LGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSK-RTTLTTSDIDSALR   65 (65)
T ss_pred             CCCHHHHHHHHHH-CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC-CCeecHHHHHHHhC
Confidence            5899999999876 5656799999999999999999999999999988653 44588999988864

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

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

Probab=96.01  E-value=0.058  Score=39.30  Aligned_cols=67  Identities=21%  Similarity=0.279  Sum_probs=60.3

Q ss_pred             CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537          128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK  195 (207)
Q Consensus       128 F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~  195 (207)
                      ++|.++..|+..+.++..+++++..++.-++=-||-.+++.|..+...++.. -|.++.|.-+++|..
T Consensus         2 ~~k~~l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~-tv~~~Di~l~l~r~~   68 (72)
T cd07981           2 LTKRKLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSD-TLEVKDVQLHLERNW   68 (72)
T ss_pred             CcHHHHHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC-CCCHHHHHHHHHHhc
Confidence            6789999999999988889999999999999999999999999999887544 499999999988753

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

>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome

Probab=95.54  E-value=0.057  Score=43.30  Aligned_cols=66  Identities=15%  Similarity=0.260  Sum_probs=57.0

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR  193 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR  193 (207)
                      .||-+.|.|+|..-.+...|+....+.++++--.++.||.|.|-...... ...-|.|.||..|++-
T Consensus        20 ~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~-k~krItp~hi~lAi~n   85 (115)
T cd00074          20 QFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDN-KKKRITPRHLQLAVRN   85 (115)
T ss_pred             cCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCeEcHHHHHHHHhc
Confidence            47888899999875556789999999999999999999999999887654 4578999999999875

The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.

>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]

Probab=95.24  E-value=0.067  Score=37.96  Aligned_cols=66  Identities=23%  Similarity=0.262  Sum_probs=52.9

Q ss_pred             CCChhHHHHHHHHhcCC----CCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGS----QKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR  193 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgs----qsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR  193 (207)
                      ..++.-++|++..+...    .+++.....+|..+...|+.+|.+.|..+....+ ..=|.|.||.-|.|.
T Consensus         5 ~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~k-R~tI~~~DI~~A~r~   74 (75)
T PF00125_consen    5 LIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAK-RKTITPRDIQLAVRI   74 (75)
T ss_dssp             SSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-BSEEGHHHHHHHHHH
T ss_pred             ccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcC-CcEecHHHHHHHHhc
Confidence            34566677776666543    4789999999999999999999999999987654 445999999999873

Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....

>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]

Probab=94.40  E-value=0.1  Score=42.94  Aligned_cols=66  Identities=18%  Similarity=0.255  Sum_probs=56.4

Q ss_pred             cCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR  192 (207)
Q Consensus       126 S~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R  192 (207)
                      +-|+=..||||+..-...+.|+....+.++++--.++.||.|.|-.+.... ...-|-|+||+.|.|
T Consensus        25 l~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~-kkkri~PrHlqlAIr   90 (132)
T COG5262          25 LIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDN-KKKRIIPRHLQLAIR   90 (132)
T ss_pred             ccccHHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhc-CcceechHHHHHHhc
Confidence            458888999999866667789999999999999999999999999886643 355789999999987

>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]

Probab=94.26  E-value=0.24  Score=42.05  Aligned_cols=69  Identities=13%  Similarity=0.249  Sum_probs=53.4

Q ss_pred             cCCChhHHHHHHHHhcC-CCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537          126 SALQKSNMRRLLVSITG-SQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK  195 (207)
Q Consensus       126 S~F~K~~IKRLi~~vtg-sqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~  195 (207)
                      .+|||++|-|+|..++. .-.|....--++---+=.||--|..+|-+|+.+. ...-|-|.|+-.|+..|-
T Consensus        11 ~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e-~KKTIa~EHV~KALe~Lg   80 (156)
T KOG0871|consen   11 LSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKE-AKKTIAPEHVIKALENLG   80 (156)
T ss_pred             ccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHH-hcccCCHHHHHHHHHHcc
Confidence            47999999999999886 4445555444444445589999999999999876 456799999999998773

>smart00414 H2A Histone 2A

Probab=93.39  E-value=0.29  Score=38.72  Aligned_cols=66  Identities=18%  Similarity=0.293  Sum_probs=54.3

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR  193 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR  193 (207)
                      .|+=..|.|++..-.-...|+....+-++++--.++.||.|.|-...... ...-|.|.||.-|.+-
T Consensus         9 ~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~-k~~rItp~hi~lAi~n   74 (106)
T smart00414        9 QFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDN-KKRRITPRHLQLAIRN   74 (106)
T ss_pred             cCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCccchHHHhhhccC
Confidence            46777799999876556689999999999999999999999998775543 4567999999987653

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

Probab=93.38  E-value=0.44  Score=37.03  Aligned_cols=80  Identities=19%  Similarity=0.274  Sum_probs=68.4

Q ss_pred             HHHHHHHHHHhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHH
Q 028537          115 DQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRL  194 (207)
Q Consensus       115 EQldRYE~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL  194 (207)
                      .+..||..+=...|++..|+|||.++.. ..||....-.+.-....|+=+|.+.|-.+...- .+.-+++..|.-|++++
T Consensus         7 ~~~r~~~~~~~~~Lp~apv~Ri~r~~~~-~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha-~RKTV~~~DI~la~~~~   84 (91)
T COG2036           7 KEIRRYQRSTDLLLPKAPVRRILRKAGA-ERVSSSAIEELQEALEEYLEEIAEDAVELAEHA-KRKTVKAEDIKLALKRL   84 (91)
T ss_pred             HHHHhhhhhhhhhcCchHHHHHHHHHhH-HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCeecHHHHHHHHHHh
Confidence            4567888888889999999999998664 489999999999999999999999999887654 56789999999999887


Q ss_pred             Hh
Q 028537          195 KL  196 (207)
Q Consensus       195 ~~  196 (207)
                      ..
T Consensus        85 ~~   86 (91)
T COG2036          85 GR   86 (91)
T ss_pred             cc
Confidence            54

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

Probab=93.35  E-value=0.46  Score=34.80  Aligned_cols=65  Identities=15%  Similarity=0.194  Sum_probs=47.4

Q ss_pred             cCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR  192 (207)
Q Consensus       126 S~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R  192 (207)
                      +-|++..||-+..+ +|-.+++++++..++-=.-.-+.+||+.|.++|..- .+.-|.+.+|..|+|
T Consensus         2 s~~~~esvk~iAes-~Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hs-kR~~Lt~~Di~~ALr   66 (66)
T PF02969_consen    2 SVFSQESVKDIAES-LGISNLSDEAAKALAEDVEYRLREIIQEALKFMRHS-KRTKLTTDDINSALR   66 (66)
T ss_dssp             ----HHHHHHHHHH-TT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-T-SSB-HHHHHHHH-
T ss_pred             CcCCHHHHHHHHHH-cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCCCHHHHHHHhC
Confidence            35888999987554 665679999999999999999999999999998864 456799999999876

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

>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=93.05  E-value=0.68  Score=35.45  Aligned_cols=66  Identities=18%  Similarity=0.247  Sum_probs=55.4

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRL  194 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL  194 (207)
                      .++|+.|+||+.. .|-..||..+...+..+.+.|+-+|+..|....+.- .+.-+....|.-|++|.
T Consensus        13 gi~k~~I~RLarr-~GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha-~RKTVt~~DV~~alkr~   78 (85)
T cd00076          13 GITKPAIRRLARR-GGVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHA-KRKTVTAMDVVYALKRQ   78 (85)
T ss_pred             cCCHHHHHHHHHH-cCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCcCcHHHHHHHHHHC
Confidence            6999999999876 455689999999999999999999999999887643 44558888898887764

>PTZ00017 histone H2A; Provisional

Probab=92.10  E-value=0.4  Score=39.75  Aligned_cols=65  Identities=17%  Similarity=0.269  Sum_probs=52.8

Q ss_pred             CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537          128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR  193 (207)
Q Consensus       128 F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR  193 (207)
                      |+=..|.|++..-.-...|+....+.++++--.++.||.|.|-...... ...-|.|.||.-|+|-
T Consensus        28 FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~-kk~RItPrHi~lAI~n   92 (134)
T PTZ00017         28 FPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDN-KKKRITPRHIQLAIRN   92 (134)
T ss_pred             cchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhc-CCCeecHHHHHhhccC
Confidence            6667788888764334578888999999999999999999998876644 3568999999988874

>PTZ00015 histone H4; Provisional

Probab=91.82  E-value=1  Score=35.65  Aligned_cols=67  Identities=21%  Similarity=0.275  Sum_probs=56.6

Q ss_pred             cCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHH
Q 028537          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRL  194 (207)
Q Consensus       126 S~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL  194 (207)
                      ..++|+.|+||+.. .|-..||..+...+..+.+.|+-+|+..|..+.+.- .+.-+....|.-|++|.
T Consensus        29 ~gI~k~~IrRLarr-~GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA-~RKTVt~~DV~~AlKr~   95 (102)
T PTZ00015         29 RGITKGAIRRLARR-GGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYA-RRKTVTAMDVVYALKRQ   95 (102)
T ss_pred             cCCCHHHHHHHHHH-cCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCcccHHHHHHHHHhc
Confidence            47999999999876 566689999999999999999999999999886644 45568899998887664

>PLN00035 histone H4; Provisional

Probab=91.38  E-value=1.2  Score=35.39  Aligned_cols=66  Identities=20%  Similarity=0.275  Sum_probs=56.5

Q ss_pred             CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537          128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK  195 (207)
Q Consensus       128 F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~  195 (207)
                      |+++.|+||+.. .|-..||..+...+..+.+.|+-+|+..|....+.. .+.-+....|.-|++|+.
T Consensus        30 ipk~~IrRLARr-~GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA-~RKTV~~~DV~~Alkr~g   95 (103)
T PLN00035         30 ITKPAIRRLARR-GGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHA-RRKTVTAMDVVYALKRQG   95 (103)
T ss_pred             CCHHHHHHHHHH-cCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCcCcHHHHHHHHHHcC
Confidence            999999999876 455689999999999999999999999999887654 455688999999987754

>PLN00154 histone H2A; Provisional

Probab=90.42  E-value=1.1  Score=37.44  Aligned_cols=65  Identities=17%  Similarity=0.253  Sum_probs=51.9

Q ss_pred             CChhHHHHHHHHhc-CCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537          128 LQKSNMRRLLVSIT-GSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR  193 (207)
Q Consensus       128 F~K~~IKRLi~~vt-gsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR  193 (207)
                      |+=.-|.|++..-+ -.+.|+....+.++++--.++.||.|.|-...... ...-|.|.||.-|+|-
T Consensus        39 FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~-kk~RItPrHi~lAIrn  104 (136)
T PLN00154         39 FPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDL-KVKRITPRHLQLAIRG  104 (136)
T ss_pred             CchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhh-CCceecHHHhhhhccC
Confidence            66667888887643 24578999999999999999999999998775544 3466999999988764

>PLN00153 histone H2A; Provisional

Probab=90.14  E-value=0.91  Score=37.46  Aligned_cols=65  Identities=18%  Similarity=0.271  Sum_probs=51.5

Q ss_pred             CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537          128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR  193 (207)
Q Consensus       128 F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR  193 (207)
                      |+=.-|.|++..-.-...|+....+-++++--.++.||.|.|-...... ...-|.|.||.-|+|-
T Consensus        25 FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~-kk~RItPrHi~lAI~n   89 (129)
T PLN00153         25 FPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDN-KKNRIVPRHIQLAIRN   89 (129)
T ss_pred             cchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhc-CCCccChHHHHhhccC
Confidence            5556688887653334578888889999999999999999998876544 4679999999988764

>PLN00156 histone H2AX; Provisional

Probab=89.85  E-value=1  Score=37.66  Aligned_cols=65  Identities=17%  Similarity=0.279  Sum_probs=51.8

Q ss_pred             CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537          128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR  193 (207)
Q Consensus       128 F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR  193 (207)
                      |+=.-|.|++..-.-...|+....+.++++--.++.||.|.|-...... ....|.|.||.-|+|-
T Consensus        30 FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~-kk~RItPrHi~lAIrn   94 (139)
T PLN00156         30 FPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDN-KKNRIVPRHIQLAVRN   94 (139)
T ss_pred             cchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCcCcHHHHHhhccC
Confidence            5666678887654334578888889999999999999999998876554 3579999999988764

>PLN00157 histone H2A; Provisional

Probab=89.82  E-value=0.85  Score=37.74  Aligned_cols=65  Identities=17%  Similarity=0.262  Sum_probs=52.2

Q ss_pred             CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537          128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR  193 (207)
Q Consensus       128 F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR  193 (207)
                      |+=.-|.|++..-.-...|+....+.++++--.++.||.|.|-...... ...-|.|.||.-|+|-
T Consensus        27 FPVgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~-kk~RItPrHi~lAI~n   91 (132)
T PLN00157         27 FPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDN-KKSRIVPRHIQLAVRN   91 (132)
T ss_pred             cchHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhc-CCccccHHHHhhcccC
Confidence            5556688888764434578888889999999999999999998876544 3579999999988764

>PTZ00252 histone H2A; Provisional

Probab=89.04  E-value=1.5  Score=36.56  Aligned_cols=66  Identities=14%  Similarity=0.213  Sum_probs=52.4

Q ss_pred             CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHh-ccCCCCCchHHHHHHHH
Q 028537          128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTER-NESGPIRPCHIREAYRR  193 (207)
Q Consensus       128 F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~-~e~gPLqP~HIREA~RR  193 (207)
                      |+=.-|.|++..-.-...|+....+-++++--.++.||.|.|-...... +...-|.|.||.-|+|-
T Consensus        26 FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrN   92 (134)
T PTZ00252         26 FPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRH   92 (134)
T ss_pred             CchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccC
Confidence            5555677887654434578888889999999999999999999987543 45689999999988764

>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]

Probab=88.54  E-value=1.4  Score=39.41  Aligned_cols=68  Identities=10%  Similarity=0.345  Sum_probs=51.8

Q ss_pred             hcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537          125 RSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR  193 (207)
Q Consensus       125 RS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR  193 (207)
                      -+.|+-+.|||||+.--.-.+|.+.|=++|+=---+|+-.||-+++++-..++ ..-|.|.||+.|+..
T Consensus        11 ~trfp~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~-aKt~s~~hlkq~v~~   78 (224)
T KOG1659|consen   11 KTRFPPARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRG-AKTVSSSHLKQAVES   78 (224)
T ss_pred             hccCCHHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcC-ccccCHHHHHHHHhc
Confidence            46799999999997532222566666566666667999999999999977663 567899999988754

>smart00417 H4 Histone H4

Probab=88.12  E-value=1.7  Score=32.52  Aligned_cols=48  Identities=23%  Similarity=0.259  Sum_probs=42.6

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTE  175 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E  175 (207)
                      .++|+.|+||+.. .|-..||..+...+..+.|.|+-+|+..|....+.
T Consensus        13 gI~k~~IrRLaRr-~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~h   60 (74)
T smart00417       13 GITKPAIRRLARR-GGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEH   60 (74)
T ss_pred             CCCHHHHHHHHHH-cCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            6999999999876 56668999999999999999999999999888653

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

Probab=87.77  E-value=2.2  Score=31.23  Aligned_cols=64  Identities=17%  Similarity=0.273  Sum_probs=47.9

Q ss_pred             ChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537          129 QKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR  193 (207)
Q Consensus       129 ~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR  193 (207)
                      .|.++..||.+|-++..+.+.+.-++.=||=-||-.+|+.|..+.+.|+. .-|.+..|.-.+.|
T Consensus         1 ~K~~l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s-~tle~~Dv~~~Ler   64 (68)
T PF03847_consen    1 SKRKLQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKS-STLEVKDVQLHLER   64 (68)
T ss_dssp             -HHHHHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SEE-HHHHHHHHHH
T ss_pred             ChHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC-CCCCHHHHHHHHHh
Confidence            47889999999988888999999999999999999999999999988753 35666766666655

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

>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex

Probab=87.19  E-value=1.4  Score=32.60  Aligned_cols=65  Identities=20%  Similarity=0.195  Sum_probs=46.0

Q ss_pred             ChhHHHHHHHHhcC--CCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537          129 QKSNMRRLLVSITG--SQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR  193 (207)
Q Consensus       129 ~K~~IKRLi~~vtg--sqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR  193 (207)
                      |+..|.||+.....  ..+|+.+.+.+++-+-++||-|-|-.|.......+..+=|.+.||..-.=.
T Consensus         1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~pq   67 (72)
T PF09415_consen    1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILPQ   67 (72)
T ss_dssp             -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCHC
T ss_pred             ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence            46678888764332  235888899999999999999999999887666555555899999765433

The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.

>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins

Probab=86.86  E-value=6.1  Score=28.80  Aligned_cols=64  Identities=17%  Similarity=0.166  Sum_probs=51.4

Q ss_pred             hhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537          130 KSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK  195 (207)
Q Consensus       130 K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~  195 (207)
                      |..|.+++.. .|..++++...-.+.-+.--|+.+|...++..++--+.+.|. +..|..|+..+.
T Consensus         9 ~~~Vaqil~~-~Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~-~~Dv~~Al~~~g   72 (77)
T smart00576        9 RIAVAQILES-AGFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPN-LGDVVLALENLG   72 (77)
T ss_pred             HHHHHHHHHH-cCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCC-HHHHHHHHHHhC
Confidence            4456666544 677789999999999999999999999999999766666665 899999988764

subdomain of archael histone-like transcription factors

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

Probab=85.23  E-value=4.2  Score=37.45  Aligned_cols=66  Identities=14%  Similarity=0.215  Sum_probs=56.1

Q ss_pred             hhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHhc
Q 028537          130 KSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLE  197 (207)
Q Consensus       130 K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~~  197 (207)
                      +..||-++.+ +|-..+++.++..++-....++.+|+++|.+.|..- .+.=|.+.||..|+|.+.-+
T Consensus         2 ~~~i~~ia~~-~Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hs-kR~~l~~~Di~~Al~~~n~e   67 (343)
T cd08050           2 QESIKLIAES-LGIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHS-KRRKLTTSDVNHALRLRNVE   67 (343)
T ss_pred             hhHHHHHHHH-cCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCcCCHHHHHHHHHHhCCC
Confidence            4667777665 454589999999999999999999999999998865 45789999999999988765

The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as

>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]

Probab=83.38  E-value=4.2  Score=33.81  Aligned_cols=65  Identities=18%  Similarity=0.293  Sum_probs=49.6

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR  192 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R  192 (207)
                      -|+=..|.|++..--.-+.|+..-.+.|+++--.+..||.|.|-....+. ...-|.|+||+-|++
T Consensus        27 ~fPvgri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardn-kk~ri~PrH~~lAI~   91 (131)
T KOG1756|consen   27 QFPVGRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDN-KKTRITPRHLQLAIR   91 (131)
T ss_pred             ccCHHHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhc-CccccChHHHHHHHh
Confidence            35566678887652223467777778888999999999999998876653 356789999999988

>PTZ00463 histone H2B; Provisional

Probab=80.99  E-value=7.7  Score=31.70  Aligned_cols=67  Identities=15%  Similarity=0.168  Sum_probs=45.6

Q ss_pred             HHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHhcCCCC
Q 028537          133 MRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP  201 (207)
Q Consensus       133 IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~~GklP  201 (207)
                      |.|++.+|-....||....-+|.+|..=++-.|..+|-.+..- +...-|.+.+|+.|+| |.+.|.|.
T Consensus        34 I~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~-nkr~TltsrEIQtAvr-LlLpGELa  100 (117)
T PTZ00463         34 IFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKY-TRRDTLSSREIQTAIR-LVLPGELA  100 (117)
T ss_pred             HHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCcCCHHHHHHHHh-hcccHHHH
Confidence            8888888877777777766666654444444444455555432 4677899999999987 55556654

>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]

Probab=80.60  E-value=4.1  Score=36.98  Aligned_cols=75  Identities=17%  Similarity=0.302  Sum_probs=56.0

Q ss_pred             HHHHHHHhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537          118 NRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR  193 (207)
Q Consensus       118 dRYE~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR  193 (207)
                      +|-..+.--+|+-+.|||+|..--+---|+..+-++.+-++-+||.||+-.|--+. +++.+.-||-..|.+|+.+
T Consensus       100 ~~q~~~k~h~LPlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~a-e~NkRRtLQksDia~Av~k  174 (286)
T COG5208         100 ERQILLKDHNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINA-EENKRRTLQKSDIAAAVKK  174 (286)
T ss_pred             hHHHHHHhccCcHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHH-hHhhhhHHHHHHHHHHHHH
Confidence            33366777789999999998643332236666667778889999999999886654 4456677888889988875

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

Probab=80.38  E-value=17  Score=26.18  Aligned_cols=63  Identities=16%  Similarity=0.201  Sum_probs=50.0

Q ss_pred             hHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537          131 SNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK  195 (207)
Q Consensus       131 ~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~  195 (207)
                      ..|.+++.+ .|..++++...-++.-++.-|+.+|...++..++.-+.+.|. +.+|..|+..+-
T Consensus        10 ~~va~il~~-~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~-~~Dv~~al~~~g   72 (77)
T PF07524_consen   10 RSVAQILKH-AGFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPN-LQDVEQALEEMG   72 (77)
T ss_pred             HHHHHHHHH-cCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCC-HHHHHHHHHHhC
Confidence            334444433 676778899999999999999999999999998777777777 888988887653

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	207
1bh8_B	89	Htafii18HTAFII28 HETERODIMER CRYSTAL STRUCTURE Leng		3e-18

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

Iteration: 1
 Score = 88.2 bits (217), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 44/90 (48%), Positives = 66/90 (73%), Gaps = 1/90 (1%)
Query: 112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARM 171
           F+E+Q+NRYE +RRSA  K+ ++RL+ SITG+  +S  + I + GI+K+FVGE+VE A  
Sbjct: 1   FSEEQLNRYEMYRRSAFPKAAIKRLIQSITGTS-VSQNVVIAMSGISKVFVGEVVEEALD 59
Query: 172 VMTERNESGPIRPCHIREAYRRLKLEGKVP 201
           V  +  E  P++P H+REA RRLK +G++P
Sbjct: 60  VCEKWGEMPPLQPKHMREAVRRLKSKGQIP 89
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	207
1bh9_B	89	TAFII28; histone fold, tata binding protein, trans	2e-42
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04

>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 =  137 bits (346), Expect = 2e-42
 Identities = 44/90 (48%), Positives = 65/90 (72%), Gaps = 1/90 (1%)

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

Query: 172 VMTERNESGPIRPCHIREAYRRLKLEGKVP 201
           V  +  E  P++P H+REA RRLK +G++P
Sbjct: 60  VCEKWGEMPPLQPKHMREAVRRLKSKGQIP 89

>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 = 44.1 bits (103), 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

>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 = 40.2 bits (93), Expect = 3e-04
 Identities = 14/111 (12%), Positives = 38/111 (34%), Gaps = 9/111 (8%)

Query: 105 MQAILNQFTED-QMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVC---GIAKM 160
           +    + F ++      +   +S L K  +  +++S             ++     + + 
Sbjct: 22  LSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQK 81

Query: 161 FVGELVETARMVMTERNESGPIRPCHIREAY--RRLKLEG---KVPKRSVP 206
           FV E++      +    ++   +P  +   Y  +R +L        K +V 
Sbjct: 82  FVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVS 132

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	207
1bh9_B	89	TAFII28; histone fold, tata binding protein, trans	100.0
3b0c_W	76	CENP-W, centromere protein W; histone fold, DNA bi	97.99
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	97.79
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	97.67
4g92_C	119	HAPE; transcription factor, nucleosome, minor groo	97.54
1n1j_A	93	NF-YB; histone-like PAIR, DNA binding protein; 1.6	97.32
2yfw_B	103	Histone H4, H4; cell cycle, kinetochore, centromer	96.99
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	96.98
1tzy_D	103	Histone H4-VI; histone-fold, tetramer-dimer-dimer,	96.98
2byk_B	128	Chrac-14; nucleosome sliding, histone fold, DNA-bi	96.87
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	96.85
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	96.74
1jfi_B	179	DR1 protein, transcription regulator NC2 beta chai	96.69
1id3_B	102	Histone H4; nucleosome core particle, chromatin, p	96.26
2hue_C	84	Histone H4; mini beta sheet, elongated beta sandwh	96.2
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	96.13
2nqb_C	123	Histone H2A; nucleosome, NCP, chromatin, structura	95.98
1tzy_A	129	Histone H2A-IV; histone-fold, tetramer-dimer-dimer	95.94
1id3_C	131	Histone H2A.1; nucleosome core particle, chromatin	95.89
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	95.84
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	95.66
2f8n_K	149	Histone H2A type 1; nucleosome, NCP, macroh2A, his	95.6
2f8n_G	120	Core histone macro-H2A.1; nucleosome, NCP, macroh2	95.35
1taf_B	70	TFIID TBP associated factor 62; transcription init	95.15
1f66_C	128	Histone H2A.Z; nucleosome, chromatin, histone vari	94.99
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	94.21
1h3o_B	76	Transcription initiation factor TFIID 20/15 kDa su	94.11
4dra_E	84	Centromere protein X; DNA binding complex, DNA dam	93.7
3b0b_C	81	CENP-X, centromere protein X; histone fold, DNA bi	93.56

>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=100.00  E-value=2.8e-42  Score=261.37  Aligned_cols=89  Identities=49%  Similarity=0.823  Sum_probs=87.2

Q ss_pred             CCHHHHHHHHHHHhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHH
Q 028537          112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAY  191 (207)
Q Consensus       112 fteEQldRYE~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~  191 (207)
                      ||+|||+|||.||||+|+|++|||||+++++ ++||+|++|+|+||||+|||||||+|++||++|++++||+|+||||||
T Consensus         1 ft~eQ~~Rye~~Rrs~f~k~~vKrl~~~~~~-~~v~~~v~i~v~glaKvfVgelVE~A~~V~~~~~~~~Pl~P~HireA~   79 (89)
T 1bh9_B            1 FSEEQLNRYEMYRRSAFPKAAIKRLIQSITG-TSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAV   79 (89)
T ss_dssp             CCHHHHHHHHHHHHCCCCHHHHHHHHHHHHS-SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHcC-CCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHH
Confidence            8999999999999999999999999999996 589999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcCCCC
Q 028537          192 RRLKLEGKVP  201 (207)
Q Consensus       192 RRL~~~GklP  201 (207)
                      |||+.+|++|
T Consensus        80 rrl~~~g~~p   89 (89)
T 1bh9_B           80 RRLKSKGQIP   89 (89)
T ss_dssp             HHHHHTTCCC
T ss_pred             HHHHHcCCCC
Confidence            9999999998

>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=97.99  E-value=3.4e-05  Score=55.57  Aligned_cols=71  Identities=18%  Similarity=0.248  Sum_probs=63.3

Q ss_pred             cCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHhc
Q 028537          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLE  197 (207)
Q Consensus       126 S~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~~  197 (207)
                      ..||++.|+|||.++.++..||.+...+|.-.+-+||-.|..+|.+++... .+.-|.++||..|.+.|..+
T Consensus         3 ~~LP~A~V~rI~K~~~p~~~is~~A~~~i~~~~~~Fi~~la~eA~~~a~~~-~rKTI~~~dI~~A~~~ll~k   73 (76)
T 3b0c_W            3 RTVPRGTLRKIIKKHKPHLRLAANTDLLVHLSFLLFLHRLAEEARTNAFEN-KSKIIKPEHTIAAAKVILKK   73 (76)
T ss_dssp             -CCCHHHHHHHHHHHCTTCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHH-TCSSBCHHHHHHHHHHHHHH
T ss_pred             CcccccHHHHHHHHhCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHH
Confidence            469999999999988887789999999999999999999999999998764 56689999999999988754

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

Probab=97.79  E-value=4.4e-05  Score=57.44  Aligned_cols=75  Identities=17%  Similarity=0.283  Sum_probs=58.1

Q ss_pred             HHHHHhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537          120 YESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK  195 (207)
Q Consensus       120 YE~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~  195 (207)
                      -..|+...||-+.|||||..--....||....++++..+-+||.+|++.|-..... +.+.-|+|.||..|++...
T Consensus        12 ~~~~~~~~lP~arIkrImK~~~~~~~is~eA~~~laka~E~Fi~~l~~~A~~~a~~-~krktI~~~di~~Av~~~e   86 (97)
T 1n1j_B           12 VKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTED-NKRRTLQRNDIAMAITKFD   86 (97)
T ss_dssp             --------CCHHHHHHHHTTSTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTCSEECHHHHHHHHTTCG
T ss_pred             cCCcCCCcCCHHHHHHHHccCccccccChHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCccCCHHHHHHHHhcCc
Confidence            45688999999999999987544357999999999999999999999999988764 4577899999999987653

>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=97.67  E-value=5.8e-05  Score=52.74  Aligned_cols=68  Identities=16%  Similarity=0.225  Sum_probs=60.2

Q ss_pred             cCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK  195 (207)
Q Consensus       126 S~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~  195 (207)
                      +.||++.|+|||..+ +...++.....++.-.+..|+-.|.+.|-.+...- .+.-|.|.||..|.++|+
T Consensus         1 ~~lP~a~v~Ri~k~~-~~~ris~~A~~~l~~a~e~fi~~l~~~A~~~a~~~-kRkTI~~~Di~~A~~~l~   68 (68)
T 1b67_A            1 GELPIAPIGRIIKNA-GAERVSDDARIALAKVLEEMGEEIASEAVKLAKHA-GRKTIKAEDIELARKMFK   68 (68)
T ss_dssp             CCSCHHHHHHHHHHT-TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSEECHHHHHHHGGGGC
T ss_pred             CCCCccHHHHHHhcC-CcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCccCHHHHHHHHHhcC
Confidence            469999999999998 66789999999999999999999999999987653 566799999999998874

>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=97.54  E-value=9.4e-05  Score=57.70  Aligned_cols=72  Identities=14%  Similarity=0.236  Sum_probs=61.6

Q ss_pred             HHHhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHH
Q 028537          122 SFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRL  194 (207)
Q Consensus       122 ~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL  194 (207)
                      .|+-..||-+.|||||..--....|+....++++..+-+||.+|++.|-.++... .+.=|+|.||..|++..
T Consensus        36 d~k~~~lPvaRIkrImK~d~~~~~is~eA~v~la~a~E~Fi~~L~~~A~~~a~~~-krktI~~~di~~Av~~~  107 (119)
T 4g92_C           36 DYKIHQLPLARIKKVMKADPEVKMISAEAPILFAKGCDVFITELTMRAWIHAEDN-KRRTLQRSDIAAALSKS  107 (119)
T ss_dssp             CSSCCSSCHHHHHHHHHTSTTCCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSEECHHHHHHHHTTC
T ss_pred             ccccCCCCHHHHHHHHhhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-ccCccCHHHHHHHHhcC
Confidence            3677789999999999865555579999999999999999999999999987654 45679999999999764

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

Probab=97.32  E-value=0.00068  Score=50.18  Aligned_cols=69  Identities=17%  Similarity=0.106  Sum_probs=59.8

Q ss_pred             cCCChhHHHHHHHHhcC-CCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537          126 SALQKSNMRRLLVSITG-SQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK  195 (207)
Q Consensus       126 S~F~K~~IKRLi~~vtg-sqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~  195 (207)
                      ..||++.|+|||..... ...||.....++.-.+.+||-.|.+.|-.++... .+.-|++.||..|+++|.
T Consensus         7 ~~LP~a~i~ri~K~~~~~~~~is~dA~~~l~~a~e~Fi~~l~~~A~~~a~~~-kRkTI~~~Dv~~Al~~l~   76 (93)
T 1n1j_A            7 IYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQE-KRKTINGEDILFAMSTLG   76 (93)
T ss_dssp             CCCCHHHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSSBCHHHHHHHHHHTT
T ss_pred             ccCChhHHHHHHHHhCCccceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCccCHHHHHHHHHHcC
Confidence            36999999999999854 3479999999999999999999999999997754 566799999999998764

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

Probab=96.99  E-value=0.0023  Score=48.58  Aligned_cols=66  Identities=20%  Similarity=0.226  Sum_probs=58.5

Q ss_pred             CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537          128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK  195 (207)
Q Consensus       128 F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~  195 (207)
                      ||++.|+||+.+. |-..||..+...++.+.+.|+-+|++.|...+..- .+.=|.|.||.-|++++.
T Consensus        30 ip~~~I~Rlar~~-G~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~ha-kRktvt~~DV~~Alr~~g   95 (103)
T 2yfw_B           30 ITKPAIRRLARRG-GVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHA-KRKTVTSLDVVYALKRQG   95 (103)
T ss_dssp             CCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSEECHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCcCcHHHHHHHHHHcC
Confidence            9999999999875 44679999999999999999999999999998754 455699999999999883

>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=96.98  E-value=0.00081  Score=50.70  Aligned_cols=69  Identities=9%  Similarity=0.280  Sum_probs=54.9

Q ss_pred             hcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHH
Q 028537          125 RSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRL  194 (207)
Q Consensus       125 RS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL  194 (207)
                      ...||=+.|||||..--....|+....++++..+-+|+.+|++.|-.+... ..+.-|+|.||..|++.-
T Consensus         9 ~~~fPvaRIkrimK~~~~~~~vs~~A~v~la~a~E~Fi~el~~~A~~~a~~-~krktI~~~di~~av~~~   77 (98)
T 1jfi_A            9 NARFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQS-RNAKTMTTSHLKQCIELE   77 (98)
T ss_dssp             -CCCCHHHHHHHHTTSTTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHT-C---CBCHHHHHTTCC--
T ss_pred             CCCCChHHHHHHHHcCccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCeecHHHHHHHHhcC
Confidence            357999999999987443357999999999999999999999999988664 356789999999988764

>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=96.98  E-value=0.002  Score=48.80  Aligned_cols=66  Identities=20%  Similarity=0.266  Sum_probs=58.4

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRL  194 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL  194 (207)
                      .||++.|+||+.+. |-..||..+...++.+.+.|+-+|++.|...+..- .+.=|.|.||.-|++++
T Consensus        29 gip~~~I~Rlar~~-G~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~ha-kRktIt~~DV~~Alr~~   94 (103)
T 1tzy_D           29 GITKPAIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHA-KRKTVTAMDVVYALKRQ   94 (103)
T ss_dssp             GSCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSEECHHHHHHHHHHT
T ss_pred             cCCHHHHHHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCcCCHHHHHHHHHHc
Confidence            39999999999875 44579999999999999999999999999998754 45569999999999987

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

Probab=96.87  E-value=0.0027  Score=50.15  Aligned_cols=68  Identities=15%  Similarity=0.179  Sum_probs=57.5

Q ss_pred             CCChhHHHHHHHHhcC-CCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITG-SQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK  195 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtg-sqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~  195 (207)
                      .||.+.|+|||..+.. ...||.....+|.=.+-+||-.|..+|.+++... .+.-|++.||-.|+.+|-
T Consensus         9 ~LP~A~I~rImK~~~pd~~~iS~dA~~~l~ka~e~FI~~lt~~A~~~a~~~-kRKTI~~~Dv~~Al~~l~   77 (128)
T 2byk_B            9 NLPNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQ-NHKTITAKDILQTLTELD   77 (128)
T ss_dssp             --CCSHHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSSCCHHHHHHHHHHTT
T ss_pred             cCCHHHHHHHHHHhCcccceECHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCccCHHHHHHHHHHcC
Confidence            6999999999997653 4469999999999999999999999999997653 567899999999988764

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

Probab=96.85  E-value=0.00097  Score=53.65  Aligned_cols=80  Identities=18%  Similarity=0.224  Sum_probs=53.3

Q ss_pred             HhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH----hcCC
Q 028537          124 RRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK----LEGK  199 (207)
Q Consensus       124 RRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~----~~Gk  199 (207)
                      ....||-+.|||||..--....|+....++|+-.+-+||.+|++.|-.++.....+.-|++.||..|++...    +.+-
T Consensus        16 ~~~~LPlaRIKrIMK~dpdv~~Is~eA~vliakA~ElFI~~Lt~~A~~~a~~~~kRKtI~~~Dl~~AV~~~e~~dFL~di   95 (140)
T 2byk_A           16 AETFLPLSRVRTIMKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEFLLQI   95 (140)
T ss_dssp             -------------CCSSSSCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHHTCSTTGGGTTT
T ss_pred             cCCCCCHHHHHHHHhcCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccCHHHHHHHHhcCchhhhHhcc
Confidence            345799999999998654445799999999999999999999999999973344677899999999998532    4466


Q ss_pred             CCCC
Q 028537          200 VPKR  203 (207)
Q Consensus       200 lP~r  203 (207)
                      ||.+
T Consensus        96 vP~k   99 (140)
T 2byk_A           96 VPQK   99 (140)
T ss_dssp             SCSC
T ss_pred             ccch
Confidence            6654

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

Probab=96.74  E-value=0.0036  Score=44.01  Aligned_cols=65  Identities=15%  Similarity=0.209  Sum_probs=56.8

Q ss_pred             cCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR  192 (207)
Q Consensus       126 S~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R  192 (207)
                      +.||++.|+||+... |...+|..+...+..+++.|+-+|.+.|......- .+.-|.|.+|.-|.+
T Consensus         5 ~~lp~a~v~Rl~r~~-g~~ris~~a~~~l~e~~~~~~~~v~~dA~~~a~ha-kRkTI~~~DV~lA~~   69 (70)
T 1ku5_A            5 GELPIAPVDRLIRKA-GAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHA-GRKTVKVEDIKLAIK   69 (70)
T ss_dssp             CCSCHHHHHHHHHHT-TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-TCSEECHHHHHHHHT
T ss_pred             ccCChHHHHHHHHHc-CcceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCcCCHHHHHHHHH
Confidence            579999999999986 66789999999999999999999999999887653 456799999998875

>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=96.69  E-value=0.0067  Score=50.84  Aligned_cols=69  Identities=13%  Similarity=0.263  Sum_probs=61.4

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHh
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKL  196 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~  196 (207)
                      .||++.|.|||.+++.+.+|+.....+|.=.+-+||-.|..+|.+++... .+.-|.+.||-.|+..|--
T Consensus        15 ~LP~A~V~RImK~alp~~rISkDA~~al~ec~~eFI~~LtseA~e~a~~~-~RKTI~~eDVl~Al~~LgF   83 (179)
T 1jfi_B           15 TIPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKS-EKKTISPEHVIQALESLGF   83 (179)
T ss_dssp             CCCHHHHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSSBCHHHHHHHHHHHTT
T ss_pred             hcCHHHHHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCcCCHHHHHHHHHhcCh
Confidence            59999999999998765689999999999999999999999999998754 5678999999999988753

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

Probab=96.26  E-value=0.011  Score=44.96  Aligned_cols=66  Identities=18%  Similarity=0.224  Sum_probs=58.2

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRL  194 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL  194 (207)
                      .||++.|+||+.+. |-..||..+.-.+..+.+.|+-+|+..|...+..- .+.=|.+.+|.-|++++
T Consensus        28 ~ip~~~I~Rlar~~-Gv~rIS~da~~~l~~~le~fi~~I~~dA~~~a~Ha-kRKTVt~~DV~~ALkr~   93 (102)
T 1id3_B           28 GITKPAIRRLARRG-GVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHA-KRKTVTSLDVVYALKRQ   93 (102)
T ss_dssp             GSCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSEECHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHc-CchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCcCcHHHHHHHHHHc
Confidence            49999999999885 55579999999999999999999999999998754 44569999999999987

>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=96.20  E-value=0.0076  Score=44.08  Aligned_cols=67  Identities=19%  Similarity=0.263  Sum_probs=58.2

Q ss_pred             cCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHH
Q 028537          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRL  194 (207)
Q Consensus       126 S~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL  194 (207)
                      ..|+++.|+||+.+. |-..||..+.-.+..+.+.|+-+|+..|...+..- .+.=|.+.+|.-|++++
T Consensus         9 ~~ip~~~I~Riar~~-Gv~rIs~da~~~l~~~l~~~~~~I~~dA~~~a~ha-~RKTvt~~DV~~Alk~~   75 (84)
T 2hue_C            9 QGITKPAIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHA-KRKTVTAMDVVYALKRQ   75 (84)
T ss_dssp             CSSCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSEECHHHHHHHTTTT
T ss_pred             CCCCHHHHHHHHHHc-CchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCcCcHHHHHHHHHHc
Confidence            369999999999875 55579999999999999999999999999998754 34568899999998876

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

Probab=96.13  E-value=0.012  Score=48.12  Aligned_cols=70  Identities=17%  Similarity=0.139  Sum_probs=62.7

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHhcC
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEG  198 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~~G  198 (207)
                      .||++.|+||+... |..+||......+..+.+.|+-+|+.+|-+.+..- .+.-|.|.||..|+++..-+|
T Consensus        82 ~lP~a~V~Ri~k~~-g~~RVS~~A~~~l~~~le~f~~~I~~~A~~~a~ha-~RKTIt~eDV~~Al~~~~~~~  151 (154)
T 1f1e_A           82 LFGRATVRRILKRA-GIERASSDAVDLYNKLICRATEELGEKAAEYADED-GRKTVQGEDVEKAITYSMPKG  151 (154)
T ss_dssp             CCCHHHHHHHHHHT-TCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSEECHHHHHHHHHHHSGGG
T ss_pred             cCCccHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCccCHHHHHHHHHhcCCcc
Confidence            59999999999987 77799999999999999999999999999997654 567899999999999886654

>2nqb_C Histone H2A; nucleosome, NCP, chromatin, structural protein/DNA complex; 2.30A {Drosophila melanogaster} PDB: 2pyo_C*

Probab=95.98  E-value=0.018  Score=45.25  Aligned_cols=65  Identities=17%  Similarity=0.279  Sum_probs=57.2

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR  192 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R  192 (207)
                      .||-+-|.|+|..-.....|+....+.++++--.|+.||.|.|-...... ...-|.|.||+.|++
T Consensus        23 ~fPV~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~-k~krItp~hi~lAI~   87 (123)
T 2nqb_C           23 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDN-KKTRIIPRHLQLAIR   87 (123)
T ss_dssp             SSCHHHHHHHHHHTTSCSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSEECHHHHHHHHH
T ss_pred             eccHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhc-CCccccHHHHHHHHh
Confidence            47888899999987667789999999999999999999999998887653 467899999999988

>1tzy_A Histone H2A-IV; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1eqz_A 1hq3_A 2aro_A 2hio_A 3c9k_A 3azg_C 3a6n_C 3an2_C 3av1_C 3av2_C 3ayw_C 3aze_C 3azf_C 3afa_C 3azh_C 3azi_C 3azj_C 3azk_C 3azl_C 3azm_C ...

Probab=95.94  E-value=0.02  Score=45.49  Aligned_cols=65  Identities=17%  Similarity=0.276  Sum_probs=57.3

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR  192 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R  192 (207)
                      .||-+-|.|+|..-.+...|+....+.++++--.|+.||.|.|-...... ...-|.|.||+.|++
T Consensus        25 qfPV~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~-k~krItp~hi~lAI~   89 (129)
T 1tzy_A           25 QFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDN-KKTRIIPRHLQLAIR   89 (129)
T ss_dssp             SSCHHHHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSEECHHHHHHHHH
T ss_pred             eccHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCeEcHHHHHHHHh
Confidence            57888899999987667789999999999999999999999998887653 467899999999988

>1id3_C Histone H2A.1; nucleosome core particle, chromatin, protein/DNA interaction, nucleoprotein, supercoiled DNA; 3.10A {Saccharomyces cerevisiae} SCOP: a.22.1.1

Probab=95.89  E-value=0.02  Score=45.52  Aligned_cols=65  Identities=20%  Similarity=0.279  Sum_probs=57.0

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR  192 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R  192 (207)
                      .||-+-|+|+|..-.....|+....+.++++--.|+.||.|.|-...... ...-|.|.||+.|++
T Consensus        25 qfPV~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~-k~krItp~hI~lAI~   89 (131)
T 1id3_C           25 TFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDN-KKTRIIPRHLQLAIR   89 (131)
T ss_dssp             SSCHHHHHHHHHTTCSCSEECSSHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSEECHHHHHHHHH
T ss_pred             ecCHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHhhc-CCceEcHHHHHHHHh
Confidence            47888899999987666789999999999999999999999998886653 467899999999988

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

Probab=95.84  E-value=0.02  Score=46.80  Aligned_cols=69  Identities=13%  Similarity=0.194  Sum_probs=61.6

Q ss_pred             cCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK  195 (207)
Q Consensus       126 S~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~  195 (207)
                      +.||++.|+|||...+|..+||......++-..+.|+-.|+..|-+..... .+.-|.+.||..|..+|-
T Consensus         3 ~~LP~a~V~Riik~~lg~~rVS~dA~~~l~~~l~~f~~~i~~~A~~~a~ha-~RKTv~a~DV~~a~~~lg   71 (154)
T 1f1e_A            3 VELPKAAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDAS-GKKTLMEEHLKALADVLM   71 (154)
T ss_dssp             -CCCHHHHHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-TCSEECHHHHHHHHHHHT
T ss_pred             ccCCccHHHHHHHhcCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCcCCHHHHHHHHHhcc
Confidence            469999999999998787889999999999999999999999999997643 577899999999998883

>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=95.66  E-value=0.024  Score=43.66  Aligned_cols=67  Identities=6%  Similarity=0.107  Sum_probs=54.0

Q ss_pred             cCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHH
Q 028537          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRL  194 (207)
Q Consensus       126 S~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL  194 (207)
                      ..|+++.|+||+.... ..+||..+...+..+.+.|+-.|+..|......- .+.-|.+.+|.-|+||.
T Consensus         6 ~~lP~a~I~Ri~r~~g-~~rIS~~a~~~l~e~l~~f~~~v~~da~~~A~HA-~RKTV~~eDV~lalrr~   72 (111)
T 3b0c_T            6 PEIASSLIKQIFSHYV-KTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHA-GRKTVEMADVELLMRRQ   72 (111)
T ss_dssp             ----CHHHHHHHHHHH-CSCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSEECHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHCC-CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCcCCHHHHHHHHHHC
Confidence            4699999999998874 4589999999999999999999999999887654 45568888888888774

>2f8n_K Histone H2A type 1; nucleosome, NCP, macroh2A, histone variant, chromatin, X- RAY structure, crystallography, structural protein/DNA complex; 2.90A {Mus musculus} SCOP: a.22.1.1

Probab=95.60  E-value=0.032  Score=45.52  Aligned_cols=65  Identities=18%  Similarity=0.282  Sum_probs=57.0

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR  192 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R  192 (207)
                      .||=+-|.|+|..-.....|+....+.++++--.|+.||.|.|-...... ...-|.|.||+.|++
T Consensus        44 qFPVgrI~R~LK~~~~a~RVs~~A~VyLAAVLEYL~aEILelAgn~A~~~-krkrItprhI~lAI~  108 (149)
T 2f8n_K           44 QFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDN-KKTRIIPRHLQLAIR  108 (149)
T ss_dssp             SSCHHHHHHHHHHTTSCSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSEECHHHHHHHHH
T ss_pred             eccHHHHHHHHHccccccccCcCcHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCcCcHHHHHHHHh
Confidence            46778899999987677789999999999999999999999998886653 467899999999988

>2f8n_G Core histone macro-H2A.1; nucleosome, NCP, macroh2A, histone variant, chromatin, X- RAY structure, crystallography, structural protein/DNA complex; 2.90A {Homo sapiens} SCOP: a.22.1.1 PDB: 1u35_C

Probab=95.35  E-value=0.046  Score=42.79  Aligned_cols=65  Identities=17%  Similarity=0.251  Sum_probs=55.6

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR  192 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R  192 (207)
                      .||=+.|.|+|....-...|+....+.++++--.|+.||.|.|-...... ...-|.|.||..|++
T Consensus        22 qfPV~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~-k~~rItp~hi~lAI~   86 (120)
T 2f8n_G           22 IFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDN-KKGRVTPRHILLAVA   86 (120)
T ss_dssp             SSCHHHHHHHHHHHSSSCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSEECHHHHHHHHH
T ss_pred             cCChHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHhhc-CCceEcHHHHHHHHh
Confidence            47778899999886545689999999999999999999999998886543 467899999999988

>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=95.15  E-value=0.091  Score=37.83  Aligned_cols=65  Identities=14%  Similarity=0.152  Sum_probs=56.7

Q ss_pred             cCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR  192 (207)
Q Consensus       126 S~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R  192 (207)
                      +.|+...||++..+ +|-..+|+.++..++--.-..+.+|+.+|.+++..- .+.-|...+|..|++
T Consensus         5 s~lp~~~v~~iaes-~Gi~~lsddaa~~LA~dvEyr~~eI~qeA~kfmrHa-kRk~Lt~~DI~~Alk   69 (70)
T 1taf_B            5 SSISAESMKVIAES-IGVGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHA-KRQKLSVRDIDMSLK   69 (70)
T ss_dssp             CCCCHHHHHHHHHH-TTCCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSSBCHHHHHHHHC
T ss_pred             ccCCHHHHHHHHHH-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCeecHHHHHHHHc
Confidence            56999999999877 565689999999999999999999999999998865 456899999998875

>1f66_C Histone H2A.Z; nucleosome, chromatin, histone variant, protein DNA interaction, nucleoprotein, supercoiled DNA, complex (nucleosome core/DNA); 2.60A {Homo sapiens} SCOP: a.22.1.1

Probab=94.99  E-value=0.063  Score=42.49  Aligned_cols=66  Identities=21%  Similarity=0.264  Sum_probs=55.0

Q ss_pred             CCChhHHHHHHHHhcCC-CCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGS-QKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR  193 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgs-qsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR  193 (207)
                      .||-.-|.|+|..-... ..|+....+.++++--.|+.||+|.|-..... ....-|.|.||.-|++.
T Consensus        27 qfPV~ri~R~Lk~~~~a~~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~-~k~krItprhi~lAI~n   93 (128)
T 1f66_C           27 QFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKD-LKVKRITPRHLQLAIRG   93 (128)
T ss_dssp             SSCHHHHHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHT-TTCSEECHHHHHHHHHH
T ss_pred             cCChHHHHHHHHHcccchhhccccHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCeEcHHHHHHHHhc
Confidence            47778899999875422 37999999999999999999999999887654 35678999999999873

>2jss_A Chimera of histone H2B.1 and histone H2A.Z; histone/chaperone complex, intrinsically unfolded protein, chaperone/structural protein complex; NMR {Saccharomyces cerevisiae} SCOP: a.22.1.1 a.22.1.1

Probab=94.21  E-value=0.16  Score=42.12  Aligned_cols=65  Identities=17%  Similarity=0.278  Sum_probs=55.2

Q ss_pred             CCChhHHHHHHHHhcCC-CCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGS-QKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR  192 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgs-qsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R  192 (207)
                      .||=+.|+|+|....+. ..|+....+.++++--.|+.||.|.|-...... ...-|.|.||+.|.+
T Consensus       105 ~fPv~ri~R~lk~~~~a~~Rv~~~A~vyLaavLEyl~~eIlelA~n~a~~~-~~~~I~p~~i~lAi~  170 (192)
T 2jss_A          105 QFPVGRIKRYLKRHATGRTRVGSKAAIYLTAVLEYLTAEVLELAGNAAKDL-KVKRITPRHLQLAIR  170 (192)
T ss_dssp             CSCHHHHHHHHHHTTCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHH-TCSSCCHHHHHHHHH
T ss_pred             cCCHHHHHHHHHhcCccccccccChHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCccCHHHHHHHHh
Confidence            46777899999886443 489999999999999999999999998876553 467899999999987

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

Probab=94.11  E-value=0.25  Score=36.13  Aligned_cols=67  Identities=16%  Similarity=0.263  Sum_probs=58.5

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRL  194 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL  194 (207)
                      -|+|.++..||.+|.++..+.+.+--++.-||=-||-.+++.|..+.+.|+ +..|.++.|.-.+.|.
T Consensus         5 vl~k~~L~~Lv~~idp~~~ld~~vee~ll~lADdFV~~V~~~ac~lAKhR~-s~~le~kDvql~Ler~   71 (76)
T 1h3o_B            5 VLTKKKLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRK-SSTLEVKDVQLHLERQ   71 (76)
T ss_dssp             SSCHHHHHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-CCEECHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCccHHHHHHHHHhh
Confidence            378999999999999998899999999999999999999999999999885 4477787777666653

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

Probab=93.70  E-value=0.32  Score=36.23  Aligned_cols=70  Identities=19%  Similarity=0.151  Sum_probs=57.3

Q ss_pred             cCCChhHHHHHHHHhcC--CCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHh
Q 028537          126 SALQKSNMRRLLVSITG--SQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKL  196 (207)
Q Consensus       126 S~F~K~~IKRLi~~vtg--sqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~  196 (207)
                      .+|++..|.||+.....  ..+|+.+.+.+++-+-++||-|-|..|...... .+.+-|.+.||..-+=.|.+
T Consensus        11 ~~i~~~li~ril~~~F~~~kTkIs~dAl~l~aeyl~iFV~EAv~RA~~~a~~-e~~~~le~e~LEki~pQLlL   82 (84)
T 4dra_E           11 SGFRKELVSRLLHLHFKDDKTKVSGDALQLMVELLKVFVVEAAVRGVRQAQA-EDALRVDVDQLEKVLPQLLL   82 (84)
T ss_dssp             CCCCHHHHHHHHHTTCSSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTCSSBCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhcCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCcccHHHHHHHHHHHhc
Confidence            47999999999986543  346999999999999999999999999886443 46778999999987766643

>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=93.56  E-value=0.32  Score=35.88  Aligned_cols=71  Identities=17%  Similarity=0.236  Sum_probs=57.6

Q ss_pred             hcCCChhHHHHHHHHhcC--CCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHh
Q 028537          125 RSALQKSNMRRLLVSITG--SQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKL  196 (207)
Q Consensus       125 RS~F~K~~IKRLi~~vtg--sqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~  196 (207)
                      ...|++..|.||+.....  ..+|+.+.+.+++-+-++||-|-|..|...... .+.+-|...||..-+=.|.+
T Consensus         6 ~~~~~~~lI~ril~~~f~~~ktrI~~dAl~l~aeyl~iFV~EAv~RA~~~a~~-e~~~~le~~~LEki~pqLlL   78 (81)
T 3b0b_C            6 EGGFRKETVERLLRLHFRDGRTRVNGDALLLMAELLKVFVREAAARAARQAQA-EDLEKVDIEHVEKVLPQLLL   78 (81)
T ss_dssp             -CCCCHHHHHHHHHHHCCSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTCSEECHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHhccCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCeecHHHHHHHHHHHHh
Confidence            678999999999987655  346899999999999999999999998887544 34567999999887766653

---

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	207
d1bh9b_	89	a.22.1.3 (B:) TAF(II)28 {Human (Homo sapiens) [Tax	4e-46

>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 =  145 bits (367), Expect = 4e-46
 Identities = 44/90 (48%), Positives = 65/90 (72%), Gaps = 1/90 (1%)

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

Query: 172 VMTERNESGPIRPCHIREAYRRLKLEGKVP 201
           V  +  E  P++P H+REA RRLK +G++P
Sbjct: 60  VCEKWGEMPPLQPKHMREAVRRLKSKGQIP 89

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	207
d1bh9b_	89	TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]}	100.0
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	98.43
d1jfia_	66	Negative cofactor 2, NC2, alpha chain {Human (Homo	98.15
d1jfib_	135	Negative cofactor 2, NC2, beta chain {Human (Homo	97.72
d1n1jb_	78	Nuclear transcription factor Y subunit gamma (Nf-Y	97.7
d1n1ja_	87	Nuclear transcription factor Y subunit beta (Nf-Yb	97.59
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	97.56
d1ku5a_	66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	97.45
d2bykb1	89	Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax	97.28
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	96.7
d2huec1	82	Histone H4 {African clawed frog (Xenopus laevis) [	95.26
d1q9ca_	172	Histone domain of Son of sevenless protein {Human	94.75
d2byka1	72	Chrac-16 {Fruit fly (Drosophila melanogaster) [Tax	93.47
d1h3ob_	74	TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom	93.37
d1u35c1	106	macro-H2A.1, histone domain {Human (Homo sapiens)	89.83
d1tafb_	70	TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta	89.53
d1f66c_	103	Histone H2A {Human (Homo sapiens), variant H2A.Z [	89.37
d1tzya_	106	Histone H2A {Chicken (Gallus gallus), erythrocytes	88.55

>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=100.00  E-value=2.4e-44  Score=271.81  Aligned_cols=89  Identities=49%  Similarity=0.823  Sum_probs=87.6

Q ss_pred             CCHHHHHHHHHHHhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHH
Q 028537          112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAY  191 (207)
Q Consensus       112 fteEQldRYE~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~  191 (207)
                      ||+|||+|||+||||+|+|++|||||++++| |+||+|++|+|+||||||||||||+|++||++|++++||||+||||||
T Consensus         1 Fs~eQ~~RyE~fRRs~~~K~~vkrl~~~~~g-~sv~~~v~i~v~giaKvFvGEiVE~A~~V~~~~~e~~PL~P~HireA~   79 (89)
T d1bh9b_           1 FSEEQLNRYEMYRRSAFPKAAIKRLIQSITG-TSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAV   79 (89)
T ss_dssp             CCHHHHHHHHHHHHCCCCHHHHHHHHHHHHS-SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhhCCHHHHHHHHHHHcC-CCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCcHHHHHHH
Confidence            8999999999999999999999999999996 699999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcCCCC
Q 028537          192 RRLKLEGKVP  201 (207)
Q Consensus       192 RRL~~~GklP  201 (207)
                      |||+.+|++|
T Consensus        80 rrl~~~g~~p   89 (89)
T d1bh9b_          80 RRLKSKGQIP   89 (89)
T ss_dssp             HHHHHTTCCC
T ss_pred             HHHHHcCCCC
Confidence            9999999998

>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=98.43  E-value=3.7e-07  Score=62.50  Aligned_cols=67  Identities=15%  Similarity=0.213  Sum_probs=60.2

Q ss_pred             cCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHH
Q 028537          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRL  194 (207)
Q Consensus       126 S~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL  194 (207)
                      |.||++.||||+.+. |..+|+.++..+++..+++||.+|+..|.+++... .+.-|+|.||..|++||
T Consensus         2 aeLP~a~I~ri~k~~-~~~ris~ea~~~l~~~~e~fi~~l~~~a~~~a~~~-kRkTi~~~DV~~Alk~~   68 (68)
T d1htaa_           2 GELPIAPIGRIIKNA-GAERVSDDARIALAKVLEEMGEEIASEAVKLAKHA-GRKTIKAEDIELARKMF   68 (68)
T ss_dssp             CCSCHHHHHHHHHHT-TCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSSCCHHHHHHHHHTC
T ss_pred             CcCcHHHHHHHHHHC-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCcCCHHHHHHHHHhC
Confidence            459999999999986 44579999999999999999999999999998854 68899999999999986

>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=98.15  E-value=1.8e-06  Score=58.98  Aligned_cols=65  Identities=11%  Similarity=0.342  Sum_probs=55.3

Q ss_pred             cCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHH
Q 028537          126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAY  191 (207)
Q Consensus       126 S~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~  191 (207)
                      +.||-+.|||||..-.....||.+...+|+..+.+||.+|++.|-.+.... .+.-|+|.||..|+
T Consensus         1 a~fP~srVkkimk~~~~~~~is~~A~~~~~~a~E~Fi~~l~~~A~~~a~~~-krktI~~~dl~~ai   65 (66)
T d1jfia_           1 ARFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSR-NAKTMTTSHLKQCI   65 (66)
T ss_dssp             CCCCHHHHHHHHTTSTTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC----CBCHHHHHTTC
T ss_pred             CCCChHHHHHHHhcCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCcCCHHHHHHHh
Confidence            579999999999976666689999999999999999999999999997754 46689999998764

>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=97.72  E-value=6.5e-05  Score=57.70  Aligned_cols=68  Identities=13%  Similarity=0.257  Sum_probs=62.0

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK  195 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~  195 (207)
                      +||++.|+|||........|+....++|+-.+-+||..|...|-.++... .+.-|+|.||-.|+..|-
T Consensus         4 ~LP~a~I~kI~K~~~~~~~is~dA~~~i~~a~~~Fi~~lt~~A~~~a~~~-~RkTi~~~Dv~~Al~~~~   71 (135)
T d1jfib_           4 TIPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKS-EKKTISPEHVIQALESLG   71 (135)
T ss_dssp             CCCHHHHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSSBCHHHHHHHHHHHT
T ss_pred             cccHHHHHHHHhhCCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCcccHHHHHHHHHHcC
Confidence            69999999999998877789999999999999999999999999997765 466899999999999875

>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=97.70  E-value=3.6e-05  Score=53.52  Aligned_cols=66  Identities=15%  Similarity=0.249  Sum_probs=56.8

Q ss_pred             CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHH
Q 028537          128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRL  194 (207)
Q Consensus       128 F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL  194 (207)
                      ||.+.|||||+.--....++.....+|+-.+-+||..|+++|.+++... .+.=|+|.||-.|++..
T Consensus         1 LP~srVkrImK~~~~~~~is~ea~~~i~~a~E~Fi~~l~~~A~~~a~~~-~rkti~~~dl~~av~~~   66 (78)
T d1n1jb_           1 LPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDN-KRRTLQRNDIAMAITKF   66 (78)
T ss_dssp             CCHHHHHHHHTTSTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSEECHHHHHHHHTTC
T ss_pred             CCHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCcCCHHHHHHHHhcC
Confidence            6889999999865445578999999999999999999999999997754 46689999999998754

>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=97.59  E-value=9.5e-05  Score=52.55  Aligned_cols=67  Identities=18%  Similarity=0.131  Sum_probs=58.4

Q ss_pred             CChhHHHHHHHHhc-CCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537          128 LQKSNMRRLLVSIT-GSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK  195 (207)
Q Consensus       128 F~K~~IKRLi~~vt-gsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~  195 (207)
                      ||++.|+|||.+.. +...||.+...+|+-.+-+||..|..+|-.+.... .+.=|.|.||-.|+..+.
T Consensus         3 LP~a~v~ri~K~~~p~~~~is~ea~~~i~~a~e~Fi~~lt~~A~~~a~~~-~rKTI~~~dv~~Al~~~~   70 (87)
T d1n1ja_           3 LPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQE-KRKTINGEDILFAMSTLG   70 (87)
T ss_dssp             CCHHHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSSBCHHHHHHHHHHTT
T ss_pred             CcHhHHHHHHHHhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCCCHHHHHHHHHHcC
Confidence            89999999998765 44579999999999999999999999999987654 466899999999998764

>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=97.56  E-value=6.9e-05  Score=58.36  Aligned_cols=72  Identities=17%  Similarity=0.132  Sum_probs=63.5

Q ss_pred             hcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHhcC
Q 028537          125 RSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEG  198 (207)
Q Consensus       125 RS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~~G  198 (207)
                      -.-|+++.||||+... |...++.....+|+..+..|+.+|++.|-.++... .+.-|+|.||..|+++..-+|
T Consensus        77 ~~~fp~a~IkRi~k~~-g~~ris~dA~~~l~~~~E~fi~~l~~~A~~~a~~~-kRkTI~~~DI~~Av~~~~~~~  148 (151)
T d1f1ea_          77 GELFGRATVRRILKRA-GIERASSDAVDLYNKLICRATEELGEKAAEYADED-GRKTVQGEDVEKAITYSMPKG  148 (151)
T ss_dssp             SCCCCHHHHHHHHHHT-TCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSEECHHHHHHHHHHHSGGG
T ss_pred             cCccCHHHHHHHHHcC-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCcCCHHHHHHHHHHcCCCc
Confidence            4469999999999874 55579999999999999999999999999998876 466999999999999988664

>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=97.45  E-value=0.00013  Score=49.35  Aligned_cols=64  Identities=14%  Similarity=0.170  Sum_probs=56.5

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR  192 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R  192 (207)
                      -||++.|||||.... .-+|+.+...+|...+++||..|...|-.+.... .+.=|++.||..|++
T Consensus         2 ~LP~a~I~rI~k~~~-~~ris~ea~~~l~~a~e~Fi~~l~~~a~~~a~~~-~RKTI~~~Dv~~Al~   65 (66)
T d1ku5a_           2 ELPIAPVDRLIRKAG-AERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHA-GRKTVKVEDIKLAIK   65 (66)
T ss_dssp             CSCHHHHHHHHHHTT-CSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-TCSEECHHHHHHHHT
T ss_pred             CCCHHHHHHHHHhCc-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCCCCHHHHHHHHh
Confidence            589999999999864 3479999999999999999999999999998765 477899999999874

>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=97.28  E-value=0.00036  Score=49.69  Aligned_cols=66  Identities=14%  Similarity=0.170  Sum_probs=56.4

Q ss_pred             ChhHHHHHHHHhc-CCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537          129 QKSNMRRLLVSIT-GSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK  195 (207)
Q Consensus       129 ~K~~IKRLi~~vt-gsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~  195 (207)
                      |++.|+|||.+.. .+..|+.+...+|+-.+-+||..|.++|..++... .+.=|+|.||..|+..|-
T Consensus         1 P~a~i~ri~K~~~p~~~~iskeA~~~i~~aae~FI~~lt~~A~~~a~~~-~rKtI~~~dv~~Al~~~~   67 (89)
T d2bykb1           1 PNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQ-NHKTITAKDILQTLTELD   67 (89)
T ss_dssp             CCSHHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSSCCHHHHHHHHHHTT
T ss_pred             CccHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCccCHHHHHHHHHHCC
Confidence            5788999998665 34569999999999999999999999999986654 467899999999998764

>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=96.70  E-value=0.0015  Score=50.56  Aligned_cols=67  Identities=13%  Similarity=0.205  Sum_probs=60.9

Q ss_pred             CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537          128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK  195 (207)
Q Consensus       128 F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~  195 (207)
                      ||++.|.|||..+.|...||.+...+|..+.+.|+..|..+|-.++..- .+.=|.|+||..|.+.+.
T Consensus         2 lP~a~I~rilk~~~~~~ris~da~~~l~~~~~~~~~~Ia~eA~~l~~~~-~rKTi~~edi~~a~~~~~   68 (151)
T d1f1ea_           2 LPKAAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDAS-GKKTLMEEHLKALADVLM   68 (151)
T ss_dssp             CCHHHHHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-TCSEECHHHHHHHHHHHT
T ss_pred             CCccHHHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCcCCHHHHHHHHHhcc
Confidence            8999999999988888889999999999999999999999999998865 456799999999998776

>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=95.26  E-value=0.014  Score=41.00  Aligned_cols=66  Identities=20%  Similarity=0.284  Sum_probs=57.2

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRL  194 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL  194 (207)
                      .++|+.||||+.+ .|-..||..+.-.++.+.+.|+-+|+..|...+.. ..+.-|.+..|.-|++|+
T Consensus         9 gI~k~~i~Riar~-~Gv~ris~d~~~~l~~~l~~~l~~i~~~a~~~~~h-akRKTvt~~DV~~Alkr~   74 (82)
T d2huec1           9 GITKPAIRRLARR-GGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEH-AKRKTVTAMDVVYALKRQ   74 (82)
T ss_dssp             SSCHHHHHHHHHH-TTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHH-TTCSEECHHHHHHHTTTT
T ss_pred             CcCHHHHHHHHHH-cCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hCCCcCCHHHHHHHHHhc
Confidence            6899999999887 46557999999999999999999999999999864 456678899999998865

>d1q9ca_ a.22.1.3 (A:) Histone domain of Son of sevenless protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Histone domain of Son of sevenless protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.75  E-value=0.047  Score=43.45  Aligned_cols=64  Identities=14%  Similarity=0.202  Sum_probs=55.4

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR  192 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R  192 (207)
                      .||-+.|.|++.... ...|+....+.++++--.+..||.|.|-.....-+. .-|.|.||..|.|
T Consensus        99 ~fPV~rv~rlLk~~~-a~RVs~~A~vyLaavLEyl~aeILelAgn~a~~~kr-krItp~dI~lAi~  162 (172)
T d1q9ca_          99 SLPVEKIHPLLKEVL-GYKIDHQVSVYIVAVLEYISADILKLAGNYVRNIRH-YEITKQDIKVAMC  162 (172)
T ss_dssp             CCCHHHHHHHHHHHH-SSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC-SBCCHHHHHHHHH
T ss_pred             eecHHHHHHHHHhcc-ccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCC-ceecHHHHHHHHh
Confidence            577788999998874 568999999999999999999999999988766543 4599999999987

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

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

Probab=93.47  E-value=0.056  Score=36.83  Aligned_cols=50  Identities=12%  Similarity=0.157  Sum_probs=42.0

Q ss_pred             CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHH
Q 028537          145 KISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRL  194 (207)
Q Consensus       145 sVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL  194 (207)
                      .||+...++|+--+=+||.+|+++|.....+.+.+.=|++.||.+|+.+-
T Consensus         9 ~is~ea~~lvskAtElFi~~L~~~a~~~a~~~~~~ktl~~~dl~~aV~~~   58 (72)
T d2byka1           9 LITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKN   58 (72)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCccccHHHHHHHHccC
Confidence            47889999999999999999999998766555455679999999998753

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

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

Probab=93.37  E-value=0.19  Score=34.93  Aligned_cols=66  Identities=17%  Similarity=0.275  Sum_probs=58.5

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR  193 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR  193 (207)
                      -|+|.++..|++++.++..+.+.+-.++.-||=-||-.+++.|..+.+.|+ +..|.++.|.--+.|
T Consensus         3 il~K~~L~eLv~~idp~~~ld~~vee~ll~iADdFV~~V~~~ac~lAKhR~-s~~le~kDvql~LeR   68 (74)
T d1h3ob_           3 VLTKKKLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRK-SSTLEVKDVQLHLER   68 (74)
T ss_dssp             SSCHHHHHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-CCEECHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CCCCcHHHHHHHHHh
Confidence            378999999999999988899999999999999999999999999998884 567888887766665

>d1u35c1 a.22.1.1 (C:814-919) macro-H2A.1, histone domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: macro-H2A.1, histone domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.83  E-value=0.52  Score=34.55  Aligned_cols=66  Identities=17%  Similarity=0.249  Sum_probs=54.5

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR  193 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR  193 (207)
                      .|+=+.|.|++..-.-...|+....+-++++--.+..||.|.|-...... ...-|.|+||.-|.|-
T Consensus        11 ~FpV~ri~r~Lk~~~~~~rv~~~apVylaAVLEYL~aEILELAgn~a~~~-k~~rItprhi~lairn   76 (106)
T d1u35c1          11 IFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDN-KKGRVTPRHILLAVAN   76 (106)
T ss_dssp             SSCHHHHHHHHHHHSTTSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSEECHHHHHHHHHH
T ss_pred             ccCHHHHHHHHhCCCCccccCCCCchhHHHHHHHHHHHHHHHHHHHHHHc-CCCeeecchhhhcccC
Confidence            46667788998775555678999999999999999999999998776553 4678999999999864

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

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

Probab=89.53  E-value=0.81  Score=31.46  Aligned_cols=66  Identities=14%  Similarity=0.145  Sum_probs=55.7

Q ss_pred             hcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537          125 RSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR  192 (207)
Q Consensus       125 RS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R  192 (207)
                      .|.|++..||-+..+ .|-..+++.++-.++-=.-.=|.+|+++|.+.|... .+.-|...+|..|+|
T Consensus         4 ~S~~~~esik~iAeS-~Gi~~l~de~a~~LA~DveYRl~eiiQeA~KFMrhs-kR~~Ltt~Did~ALk   69 (70)
T d1tafb_           4 GSSISAESMKVIAES-IGVGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHA-KRQKLSVRDIDMSLK   69 (70)
T ss_dssp             SCCCCHHHHHHHHHH-TTCCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSSBCHHHHHHHHC
T ss_pred             cccCCHHHHHHHHHH-cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-ccCcCcHHHHHHHHc
Confidence            368999999998665 555568999999999888899999999999999865 456899999998875

>d1f66c_ a.22.1.1 (C:) Histone H2A {Human (Homo sapiens), variant H2A.Z [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H2A
species: Human (Homo sapiens), variant H2A.Z [TaxId: 9606]

Probab=89.37  E-value=0.6  Score=33.87  Aligned_cols=66  Identities=21%  Similarity=0.279  Sum_probs=52.5

Q ss_pred             CCChhHHHHHHHHhcCCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQ-KISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR  193 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsq-sVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR  193 (207)
                      .|+=..|.|++....-++ .|+....+-++++--.+..||.|.|-...... ...-|.|+||.-|.+-
T Consensus        11 ~FpVgrv~r~L~~~~~~~~rv~~~A~VyLaAvLEYL~aEILelagn~a~~~-~~~rItpr~l~lai~n   77 (103)
T d1f66c_          11 QFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDL-KVKRITPRHLQLAIRG   77 (103)
T ss_dssp             SSCHHHHHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTT-TCSEECHHHHHHHHHH
T ss_pred             ccChHHHHHHHhccCccceecCCCceeeHHHHHHHHHHHHHHHhhhhhccC-CCCeeechhhhccccC
Confidence            466666888887654444 48999999999999999999999998876543 4567999999998873

>d1tzya_ a.22.1.1 (A:) Histone H2A {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H2A
species: Chicken (Gallus gallus), erythrocytes [TaxId: 9031]

Probab=88.55  E-value=0.65  Score=34.01  Aligned_cols=65  Identities=17%  Similarity=0.276  Sum_probs=52.6

Q ss_pred             CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537          127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR  192 (207)
Q Consensus       127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R  192 (207)
                      .|+=+.|-|++..-.-...|+....+-++++--.+..||.|.|-...... ...-|.|+||.-|.|
T Consensus        12 ~FpV~rv~r~Lk~~~~~~rv~~~apVylaAVLEYLtaEiLELAgn~a~~~-k~~rItPrhi~lAir   76 (106)
T d1tzya_          12 QFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDN-KKTRIIPRHLQLAIR   76 (106)
T ss_dssp             SSCHHHHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCSEECHHHHHHHHH
T ss_pred             cCChHHHHHHHHcCccccccCCCchHHHHHHHHHHHHHHHHHhhHHHHhc-CCceecchhhhhccc
Confidence            35667788998875545678999999999999999999999997776443 466899999998775