Citrus Sinensis ID: 023473

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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-------210-------220-------230-------240-------250-------260-------270-------280-
Protein Sequence
MKSQKTKTKKHQKQNQKPPTEQGEETPSEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSGQGFPGASALNRNCMLDSGVLKEIAGFVRHGCEIPFAKPIPRSKNAHANSVCCKKENDRGSRSLHLHIPKWLPAFPDERSYNKECQGPVCNRSEKLWENSEFPEGERFTFGGYKWEVLGGDLAKEREKVRFKIGVKGNNGVGFGVDLRNGVCRGGKRVRWNVGDVIDDGQNCLFKPKRSLS
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccHHHccccHHHHHccEEEEEccccccccccccccccccccccEEEEcccccccHHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHccccHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccHHHHHHHHHccHHHHHHHcccccccccEEEEEEccccccEEEEEEEcccccccccEEEEEccccccccccccccccccccc
Coil and Loop (DISEMBL)
mksqktktkkhqkqnqkppteqgeetpsefAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYshvahrsesnLVDLTNAlndvssgqgfpgasalnrncmldsgvLKEIAGfvrhgceipfakpiprsknahansvcckkendrgsrslhlhipkwlpafpdersynkecqgpvcnrseklwensefpegerftfggykweVLGGDLAKEREKVRFKIgvkgnngvgfgvdlrngvcrggkrvrwnvgdviddgqnclfkpkrsls
Flexible Loop (DISEMBL)
mksqktktkkhqkqnqkppteqgeetpsEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSGQGFPGASALNRNCMLDSGVLKEIAGFVRHGCEIPfakpiprsknahANSVCCKKENDRGSRSLHLHIPKWLPAFPDERSYNKECQGpvcnrseklwensefpegerftfggyKWEVLGGDLAKEREKVRFkigvkgnngvgfgvdlrngvcRGGKrvrwnvgdviddgqnclfkpkrsls
Low Complexity Region (SEG)
MksqktktkkhqkqnqkPPTEQGEETPSEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSGQGFPGASALNRNCMLDSGVLKEIAGFVRHGCEIPFAKPIPRSKNAHANSVCCKKENDRGSRSLHLHIPKWLPAFPDERSYNKECQGPVCNRSEKLWENSEFPEGERFTFGGYKWEVLGGDLAKEREKVRfkigvkgnngvgfgVDLRNGVCRGGKRVRWNVGDVIDDGQNCLFKPKRSLS
Disordered region (IsUnstruct)
*****************************FAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAH*****LVDLTNALND*****GFPGASALNRNCMLDSGVLKEIAGFVRHGCEIPFAKPIP********SVCC*********SLHLHIPKWLPAFPDERSYNKECQGPVCNRSEKLWENSEFPEGERFTFGGYKWEVLGGDLAKEREKVRFKIGVKGNNGVGFGVDLRNGVCRGGKRVRWNVGDVIDDGQNCLF*******
Disordered Region (DISOPRED)
*******************************FTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSGQGFPGA*******************FVRHGCEIPFAKPI****************************PKWLPAFPDERSYN**************************************************************************RVRWNVGDVIDD*************
Disordered Region (DISEMBL)
****************************EFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLA***********RSESNLVDLTNALNDVSSGQGFPGASALNRNCMLDSGVLKEIAGFVRHGCEIPFAKPIPR**********CKKENDRGSRSLHLHIPKWLPAFPDERSYNKECQGPVCNRSEKLWENSEFPEGERFTFGGYKWEVLGGDLAKEREKVRFKIGVKGNNGVGFGVDLRNGVCRGGKRVRWNVGDVIDDGQNCLFKPKRSLS
Disordered Region (DISPRO)
**************************PSEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSGQGFPGASALNRNCMLDSGVLKEIAGFVRHGCEIPFAKPIPRSKNAHANSVC************HLHIPKWLPAFPDERSY*****************************GGYKWEVLGGDLAKEREKVRFKIGVKGNNGVGFGVDLRNGVCRGGKRVRWNVGD*******C*********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKSQKTKTKKHQKQNQKPPTEQGEETPSEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSGQGFPGASALNRNCMLDSGVLKEIAGFVRHGCEIPFAKPIPRSKNAHANSVCCKKENDRGSRSLHLHIPKWLPAFPDERSYNKECQGPVCNRSEKLWENSEFPEGERFTFGGYKWEVLGGDLAKEREKVRFKIGVKGNNGVGFGVDLRNGVCRGGKRVRWNVGDVIDDGQNCLFKPKRSLS
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	281	2.2.26 [Sep-21-2011]
Q28J24	293	Transcription initiation	yes	no	0.469	0.450	0.240	0.0002
Q7ZYA2	293	Transcription initiation	N/A	no	0.466	0.447	0.257	0.0003
Q5VWG9	929	Transcription initiation	yes	no	0.451	0.136	0.232	0.0005
Q5HZG4	932	Transcription initiation	yes	no	0.451	0.136	0.232	0.0007

>sp|Q28J24|TAF8_XENTR Transcription initiation factor TFIID subunit 8 OS=Xenopus tropicalis GN=taf8 PE=2 SV=1

 Score = 47.0 bits (110), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 38/158 (24%), Positives = 65/158 (41%), Gaps = 26/158 (16%)

Query: 36  KVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNAL 95
           +V VS +    GF++AE +A+E+LT +   YL ++   A SY     R++  L D+   L
Sbjct: 28  QVVVSSLLTEAGFESAEKAAVESLTEMLQSYLSEIGRSAKSYCEHTARTQPTLPDIVVTL 87

Query: 96  NDVSSGQGFPGASALNRNCMLDSGVLKEIAGFVRHGCEIPFAKPIPRSKNAHANSVCCKK 155
            ++    GF                ++ +  + +    +    P P + N          
Sbjct: 88  IEM----GF---------------NVESLPAYAKRSQRMVITAP-PVTNNPVVPKALSAG 127

Query: 156 ENDRGSRSLHLHIPKWLPAFPDERSYNK--ECQGPVCN 191
           +N +       HIP   P FPD  +Y K    + PVC+
Sbjct: 128 QNKQHP----AHIPSHFPEFPDPHTYIKTPTYREPVCD 161

Transcription factor TFIID is one of the general factors required for accurate and regulated initiation by RNA polymerase II. Mediates both basal and activator-dependent transcription.
Xenopus tropicalis (taxid: 8364)

>sp|Q7ZYA2|TAF8_XENLA Transcription initiation factor TFIID subunit 8 OS=Xenopus laevis GN=taf8 PE=2 SV=1

 Score = 45.8 bits (107), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 41/159 (25%), Positives = 64/159 (40%), Gaps = 28/159 (17%)

Query: 36  KVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNAL 95
           +V VS +    GF +AE +A+E+LT +   YL ++   A SY     R++  L D+   L
Sbjct: 28  QVVVSSLLTEAGFDSAEKAAVESLTEMLQSYLSEIGRSAKSYCEHTARTQPTLPDIVVTL 87

Query: 96  NDVSSGQGFPGASALNRNCMLDSGVLKEIAGFVRHGCEIPFAKPIPRSKNAHANSVCCKK 155
            ++    GF           +DS     +  + +    +    P         N+    K
Sbjct: 88  IEM----GF----------NVDS-----LPAYAKRSQRMVITAP------PVTNNPVVPK 122

Query: 156 ENDRGSRSLH-LHIPKWLPAFPDERSYNK--ECQGPVCN 191
               G    H  HIP   P FPD  +Y K    + PVC+
Sbjct: 123 ALSAGDNKPHPAHIPSHFPEFPDPHTYIKTPTYREPVCD 161

Transcription factor TFIID is one of the general factors required for accurate and regulated initiation by RNA polymerase II. Mediates both basal and activator-dependent transcription.

Xenopus laevis (taxid: 8355)

>sp|Q5VWG9|TAF3_HUMAN Transcription initiation factor TFIID subunit 3 OS=Homo sapiens GN=TAF3 PE=1 SV=1

 Score = 45.4 bits (106), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 34/146 (23%), Positives = 65/146 (44%), Gaps = 19/146 (13%)

Query: 30  FAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLV 89
           ++ ++ +V+V+QIC+++G+ + + SA   LT V  +YLQQL      YS +  R++  L 
Sbjct: 5   YSRSLLRVSVAQICQALGWDSVQLSACHLLTDVLQRYLQQLGRGCHRYSELYGRTDPILD 64

Query: 90  DLTNALNDVSSGQGFPGASALNRNCMLDSGVLKEIAGFVRHGCEIPFAKPIPRSKNAHAN 149
           D+         G+ F           L    L E+  ++ +   + F   IP    +  N
Sbjct: 65  DV---------GEAF----------QLMGVSLHELEDYIHNIEPVTFPHQIPSFPVSKNN 105

Query: 150 SVCCKKENDRGSRSLHLHIPKWLPAF 175
            +   +   + +     +IP +LP  
Sbjct: 106 VLQFPQPGSKDAEERKEYIPDYLPPI 131

Transcription factor TFIID is one of the general factors required for accurate and regulated initiation by RNA polymerase II. TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. Required in complex with TBPL2 for the differentiation of myoblasts into myocytes. The complex replaces TFIID at specific promoters at an early stage in the differentiation process.

Homo sapiens (taxid: 9606)

>sp|Q5HZG4|TAF3_MOUSE Transcription initiation factor TFIID subunit 3 OS=Mus musculus GN=Taf3 PE=1 SV=2

 Score = 44.7 bits (104), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 34/146 (23%), Positives = 65/146 (44%), Gaps = 19/146 (13%)

Query: 30  FAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLV 89
           ++ ++ +V+V+QIC+++G+ + + SA   LT V  +YLQQL      YS +  R++  L 
Sbjct: 5   YSRSLLRVSVAQICQALGWDSVQLSACHLLTDVLQRYLQQLGRGCHRYSELYGRTDPILD 64

Query: 90  DLTNALNDVSSGQGFPGASALNRNCMLDSGVLKEIAGFVRHGCEIPFAKPIPRSKNAHAN 149
           D+         G+ F           L    L E+  ++ +   + F   IP    +  N
Sbjct: 65  DV---------GEAF----------QLMGVNLHELEDYIHNIEPVTFPHQIPSFPVSKNN 105

Query: 150 SVCCKKENDRGSRSLHLHIPKWLPAF 175
            +   +   + +     +IP +LP  
Sbjct: 106 VLQFPQPGSKDAEERKDYIPDYLPPI 131

Transcription factor TFIID is one of the general factors required for accurate and regulated initiation by RNA polymerase II. TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. Required in complex with TBPL2 for the differentiation of myoblasts into myocytes. The complex replaces TFIID at specific promoters at an early stage in the differentiation process.

Mus musculus (taxid: 10090)

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	281
357462277	318	hypothetical protein MTR_3g080510 [Medic	0.875	0.773	0.381	2e-44
224134360	267	predicted protein [Populus trichocarpa]	0.725	0.764	0.475	2e-41
224114868	265	predicted protein [Populus trichocarpa]	0.804	0.852	0.470	2e-41
224115430	218	predicted protein [Populus trichocarpa]	0.704	0.908	0.469	1e-37
255578564	257	conserved hypothetical protein [Ricinus	0.868	0.949	0.438	2e-36
297846484	276	hypothetical protein ARALYDRAFT_891076 [	0.879	0.894	0.367	2e-34
15221656	277	Bromodomain transcription factor [Arabid	0.747	0.758	0.375	1e-32
6692136	314	T19E23.2 [Arabidopsis thaliana]	0.747	0.668	0.375	1e-32
356551978	741	PREDICTED: probable polyamine oxidase 4-	0.879	0.333	0.347	2e-32
356499052	721	PREDICTED: probable polyamine oxidase 4-	0.715	0.278	0.352	9e-26

>gi|357462277|ref|XP_003601420.1| hypothetical protein MTR_3g080510 [Medicago truncatula] gi|355490468|gb|AES71671.1| hypothetical protein MTR_3g080510 [Medicago truncatula] gi|388521311|gb|AFK48717.1| unknown [Medicago truncatula]

 Score =  185 bits (469), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 113/296 (38%), Positives = 160/296 (54%), Gaps = 50/296 (16%)

Query: 22  QGEETPSEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVA 81
           Q  ETPSEF+F + K AVSQICRSVG+K ++ +ALE LT V  KY++ +A  AAS+++ +
Sbjct: 34  QVAETPSEFSFAIAKTAVSQICRSVGYKRSKFNALEALTNVTTKYIEAIARSAASFANAS 93

Query: 82  HRSESNLVDLTNALNDVSSGQGFPGASALNRNCMLDSGVLKEIAGFVRHGCEIPFAKPIP 141
           +R+ESN  DL N ++D+ S +GF G S  +++ +L S  LKEI  FV+   ++PF+KPIP
Sbjct: 94  NRTESNFFDLINGIHDLCSVRGFTGGSKTHKSNLLKSAALKEIVDFVKFSNQVPFSKPIP 153

Query: 142 RSKNAHANSVCCKKEN-------------DRGSRSLHLHIPKWLPAFPDERSYNKECQGP 188
            SKN       C  +N                +++  LHIP+WLP FP E  Y K     
Sbjct: 154 -SKNV------CGSQNPEITIESGTPIYCSENTKTQGLHIPRWLPDFPSESLYKKRDLVS 206

Query: 189 VCNRS--EKLWENSEFPEGERFTFGGYKWEVLG---------------GDLAKEREKVRF 231
           V  R   EKLWE+S   E     +  Y    +                 +LAK RE+V+F
Sbjct: 207 VKERKCGEKLWEHSLAMED----YSSYSENSVMLKNNGIAEKEEKDTRMELAKGRERVKF 262

Query: 232 KIGVKGNNGVGFGVDLRNGVCRGGKRVRW---------NVGDVIDDGQNCLFKPKR 278
           KIG +    +G GV++ NGVC+G KRV W         N+ D  +D    L + +R
Sbjct: 263 KIGREEEKQIGLGVNMMNGVCKGRKRVSWSHYKINNCDNMADENEDEMRALKRERR 318

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224134360|ref|XP_002321800.1| predicted protein [Populus trichocarpa] gi|222868796|gb|EEF05927.1| predicted protein [Populus trichocarpa]

 Score =  175 bits (444), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 108/227 (47%), Positives = 139/227 (61%), Gaps = 23/227 (10%)

Query: 25  ETPSEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRS 84
           E PS++AF +TK AVSQIC+SVGFK+ + SALETLT +A  YLQ LA  A SYS+ ++R+
Sbjct: 32  ENPSDYAFKITKTAVSQICQSVGFKSTQLSALETLTHIATLYLQTLAKTAVSYSNASNRT 91

Query: 85  ESNLVDLTNALNDVSSGQGFPGASALNRNC----MLDSGVLKEIAGFVRHGCEIPFAKPI 140
           +SN+ D+ N+L+D+SS QGF G S L+ +     +L SGV K+I  FV    EIPFAKPI
Sbjct: 92  QSNIFDIINSLHDMSSVQGFTGGSTLHCSSGGIGLLRSGVFKDIKSFVEFSDEIPFAKPI 151

Query: 141 PR--SKNAHANSVCCKKE--NDRGSRSLHLHIPKWLPAFPDERSYNKECQGPVCNRSE-- 194
           PR  S +   NS+  + +  + RG     LHIP+WLP FPDE SY K C      R E  
Sbjct: 152 PRGNSISLRRNSIPLEIDELDSRG-----LHIPRWLPRFPDETSY-KNCGDRWEKRREGG 205

Query: 195 -KLWENSEFPEG------ERFTFGGYKWEVLGGDLAKEREKVRFKIG 234
             LWENS+   G      +  +    K     GDL+ ER KV FKIG
Sbjct: 206 LALWENSDLLSGGSGNKSQGISRENEKRSDGDGDLSVERGKVSFKIG 252

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224114868|ref|XP_002332302.1| predicted protein [Populus trichocarpa] gi|222832464|gb|EEE70941.1| predicted protein [Populus trichocarpa]

 Score =  175 bits (444), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 119/253 (47%), Positives = 146/253 (57%), Gaps = 27/253 (10%)

Query: 2   KSQKTKTKKHQKQNQKPPTEQGEETPSEFAFTVTKVAVSQICRSVGFKAAESSALETLTL 61
           K QK     H    QKPP     E PS++ F +TK AVSQIC+SVGFK  + SALETLT 
Sbjct: 4   KPQKKTITTH---FQKPPAPA--ENPSDYVFKITKTAVSQICQSVGFKTTQLSALETLTH 58

Query: 62  VAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSGQGFPGASALNRN----CMLD 117
           VA   LQ LA  A  YS+ ++R++SN+ D+ N+L+D+ S +GF G S L+ N     +L 
Sbjct: 59  VATLCLQTLAKTAVLYSNASNRTQSNIFDIINSLHDMYSVRGFTGGSTLHCNSSGMSLLR 118

Query: 118 SGVLKEIAGFVRHGCEIPFAKPIPR--SKNAHANSVCCKKENDRGSRSLHLHIPKWLPAF 175
           S V K I  FV    EIPFAKPIPR  S +   NS+  +  N  GSR   LHIP+WLP  
Sbjct: 119 SSVFKNIKSFVEFSDEIPFAKPIPRGESISLRRNSIPLEL-NKLGSRG--LHIPRWLPRC 175

Query: 176 PDERSYNKECQGPVCNRSEK----LWENSEFPEGERFT---FGGYKWE----VLGGDLAK 224
           PDE SYNK C G  C +  K    LWE S+   G   +   F G  WE      GGDLA 
Sbjct: 176 PDESSYNK-C-GDRCEKKRKGELVLWEKSDLVGGGIGSGDEFQGISWENERRSGGGDLAV 233

Query: 225 EREKVRFKIGVKG 237
           ER +VRF+IG  G
Sbjct: 234 ERGRVRFRIGEVG 246

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224115430|ref|XP_002332133.1| predicted protein [Populus trichocarpa] gi|222875183|gb|EEF12314.1| predicted protein [Populus trichocarpa]

 Score =  162 bits (410), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 106/226 (46%), Positives = 133/226 (58%), Gaps = 28/226 (12%)

Query: 28  SEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESN 87
           S++ F +TK AVSQIC+SVGFK  + SALETLT VA   LQ LA  A  YS+ ++R++SN
Sbjct: 1   SDYVFKITKTAVSQICQSVGFKTTQLSALETLTHVATLCLQTLAKTAVLYSNASNRTQSN 60

Query: 88  LVDLTNALNDVSSGQGFPGASALNRN----CMLDSGVLKEIAGFVRHGCEIPFAKPIPR- 142
           + D+ N+L+D+ S +GF G S L+ N     +L S V K I  FV    EIPFAKPIPR 
Sbjct: 61  IFDIINSLHDMYSVRGFTGGSTLHCNSSGMSLLRSSVFKNIKSFVEFSDEIPFAKPIPRG 120

Query: 143 -SKNAHANSVCCKKENDRGSRSLHLHIPKWLPAFPDERSYNKECQGPVCNRSEK------ 195
            S +   NS+  +  N  GSR   LHIP+WLP  PDE SYNK       +R EK      
Sbjct: 121 ESISLRRNSIPLEL-NKLGSRG--LHIPRWLPRCPDESSYNK-----CADRCEKKRKGEL 172

Query: 196 -LWENSEFPEGERFT---FGGYKWE----VLGGDLAKEREKVRFKI 233
            LWE S+   G   +   F G  WE      GGDLA ER +VRF+I
Sbjct: 173 VLWEKSDLVGGGIGSGDEFQGISWENERRSGGGDLAVERGRVRFRI 218

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255578564|ref|XP_002530144.1| conserved hypothetical protein [Ricinus communis] gi|223530343|gb|EEF32236.1| conserved hypothetical protein [Ricinus communis]

 Score =  158 bits (400), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 114/260 (43%), Positives = 147/260 (56%), Gaps = 16/260 (6%)

Query: 9   KKHQKQNQKPPTEQGEETPSEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQ 68
           K   KQN           PS+F F +TK++VSQIC+SVGFK+ + SALETLT +A  YL+
Sbjct: 2   KPKSKQNIIETHSPKATDPSDFPFQITKISVSQICQSVGFKSTQLSALETLTHIATLYLK 61

Query: 69  QLASRAASYSHVAHRSESNLVDLTNALNDVSSGQGFPGASALN--RNCMLDSGVLKEIAG 126
            LA  +ASYS  ++R++SN+ D+ NAL+D+SS QGF GAS L+   N +  S V+K+++ 
Sbjct: 62  NLAKASASYSSASNRTQSNVFDIINALHDLSSIQGFTGASTLHYTSNILSSSRVVKDLSV 121

Query: 127 FVRHGCEIPFAKPIPRSKNAHANSVCCKKENDRGSRSLHLHIPKWLPAFPDERSYNK-EC 185
           FV    EIPFAKPIPR      N V  ++     S S+  HIPKWLP FPDE++  K E 
Sbjct: 122 FVNSIVEIPFAKPIPR-----VNPVPPRRSLGLESTSMQ-HIPKWLPRFPDEKACKKWER 175

Query: 186 QGPVCNRSEKLWENSEFPEGERFTFGGYKWEVL------GGDLAKEREKVRFKIG-VKGN 238
                     LWEN+    G        K E         GDL  ER +VRFKIG V+  
Sbjct: 176 DTKRLREDLGLWENNCGGIGNGILLENMKEEEKKKKSHDDGDLVMERGRVRFKIGEVEKG 235

Query: 239 NGVGFGVDLRNGVCRGGKRV 258
             V   V  RN   +GGKRV
Sbjct: 236 GIVDIRVYKRNWASKGGKRV 255

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297846484|ref|XP_002891123.1| hypothetical protein ARALYDRAFT_891076 [Arabidopsis lyrata subsp. lyrata] gi|297336965|gb|EFH67382.1| hypothetical protein ARALYDRAFT_891076 [Arabidopsis lyrata subsp. lyrata]

 Score =  152 bits (384), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 97/264 (36%), Positives = 153/264 (57%), Gaps = 17/264 (6%)

Query: 7   KTKKHQKQNQKPPTEQGEETPSEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKY 66
           + +++ K   +  ++Q   T +EF+F++TK+AVSQICRSVG+ A ++SAL TLTL   K+
Sbjct: 3   RRRRNSKLKLEESSDQSPATTAEFSFSLTKIAVSQICRSVGYIATDTSALNTLTLTTTKF 62

Query: 67  LQQLASRAASYSHVAHRSESNLVDLTNALNDV--SSGQGFPGASA---LNRNCMLDSGVL 121
           LQ LA  A+S+S+ A+R+E NL D+ N L D+  S+   FPG S    +  +C++ S VL
Sbjct: 63  LQSLAELASSFSNTANRTEVNLFDIVNGLQDIALSTSDCFPGGSTVHDIESHCLIKSAVL 122

Query: 122 KEIAGFVRHGCEIPFAKPIPRSKNAHANSVCCKKENDRGSRSLHL-HIPKWLPAFPDERS 180
           + ++ FV +  EIPFAKP+PR +     S+    +    +RS+ +  +P WLP FPD   
Sbjct: 123 RNLSDFVAYAPEIPFAKPLPRRE--RDGSLGGDLDQAPVTRSVEVKSVPAWLPPFPDASL 180

Query: 181 YNKECQGPVCNRSEKLWENSEFPEGERFTFGGYKWEVLGGDLAKEREKVRFKIGVK---- 236
            ++ C   + +R + LWENS+   G        + ++ GG L   RE+VRFK+  +    
Sbjct: 181 CSERC---IKDRPDHLWENSDSVIGREILPESLQSKI-GGRLPVRRERVRFKMDQRDWSN 236

Query: 237 -GNNGVGFGVDLRNGVCRGGKRVR 259
            G+  +    D R+G   GG  V+
Sbjct: 237 SGDTRLERWRDNRDGESDGGVEVK 260

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15221656|ref|NP_174409.1| Bromodomain transcription factor [Arabidopsis thaliana] gi|4512621|gb|AAD21690.1| F28K20.20 [Arabidopsis thaliana] gi|33589802|gb|AAQ22667.1| At1g31240 [Arabidopsis thaliana] gi|110738744|dbj|BAF01296.1| hypothetical protein [Arabidopsis thaliana] gi|332193210|gb|AEE31331.1| Bromodomain transcription factor [Arabidopsis thaliana]

 Score =  146 bits (368), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 92/245 (37%), Positives = 137/245 (55%), Gaps = 35/245 (14%)

Query: 7   KTKKHQKQNQKPPTEQGEETPSEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKY 66
           + +++ K   +  ++Q   + +EF+F++TK+AVSQIC+S+G+KA ++SAL TLTL   K+
Sbjct: 3   RRRRNSKLKFEETSDQSPTSTAEFSFSLTKIAVSQICQSIGYKATDASALNTLTLTTTKF 62

Query: 67  LQQLASRAASYSHVAHRSESNLVDLTNALNDV--SSGQGFPGASA---LNRNCMLDSGVL 121
           LQ LA  A+S+S+ A+R+E NL D+ N L D+  S+   FPG S    +   C++ S VL
Sbjct: 63  LQSLAELASSFSNTANRTEVNLFDIVNGLQDIALSTSDCFPGGSTVHDIESQCLIKSAVL 122

Query: 122 KEIAGFVRHGCEIPFAKPIPR-----SKNAHANSVCCKKENDRGSRSLHLHIPKWLPAFP 176
           + ++ FV +  EIPFAKP+PR     S     + V   +  D  S      +P WLP FP
Sbjct: 123 RNLSDFVTYAPEIPFAKPLPRRERDGSFGGDLDHVAVTRSVDVTS------VPAWLPPFP 176

Query: 177 DERSYNKECQGPVCNRSEKLWENSEFPEGERFTFGGYKWEVL--------GGDLAKEREK 228
           D    +  C     NRS+ LWENS+            + E+L        GG L   R+K
Sbjct: 177 DSSLCSDRCSKD--NRSDHLWENSD---------SVIRREILPESLKSKSGGRLPVMRDK 225

Query: 229 VRFKI 233
           VRFK+
Sbjct: 226 VRFKM 230

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|6692136|gb|AAF24601.1|AC007654_17 T19E23.2 [Arabidopsis thaliana]

 Score =  146 bits (368), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 92/245 (37%), Positives = 137/245 (55%), Gaps = 35/245 (14%)

Query: 7   KTKKHQKQNQKPPTEQGEETPSEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKY 66
           + +++ K   +  ++Q   + +EF+F++TK+AVSQIC+S+G+KA ++SAL TLTL   K+
Sbjct: 40  RRRRNSKLKFEETSDQSPTSTAEFSFSLTKIAVSQICQSIGYKATDASALNTLTLTTTKF 99

Query: 67  LQQLASRAASYSHVAHRSESNLVDLTNALNDV--SSGQGFPGASA---LNRNCMLDSGVL 121
           LQ LA  A+S+S+ A+R+E NL D+ N L D+  S+   FPG S    +   C++ S VL
Sbjct: 100 LQSLAELASSFSNTANRTEVNLFDIVNGLQDIALSTSDCFPGGSTVHDIESQCLIKSAVL 159

Query: 122 KEIAGFVRHGCEIPFAKPIPR-----SKNAHANSVCCKKENDRGSRSLHLHIPKWLPAFP 176
           + ++ FV +  EIPFAKP+PR     S     + V   +  D  S      +P WLP FP
Sbjct: 160 RNLSDFVTYAPEIPFAKPLPRRERDGSFGGDLDHVAVTRSVDVTS------VPAWLPPFP 213

Query: 177 DERSYNKECQGPVCNRSEKLWENSEFPEGERFTFGGYKWEVL--------GGDLAKEREK 228
           D    +  C     NRS+ LWENS+            + E+L        GG L   R+K
Sbjct: 214 DSSLCSDRCSKD--NRSDHLWENSD---------SVIRREILPESLKSKSGGRLPVMRDK 262

Query: 229 VRFKI 233
           VRFK+
Sbjct: 263 VRFKM 267

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356551978|ref|XP_003544349.1| PREDICTED: probable polyamine oxidase 4-like [Glycine max]

 Score =  145 bits (367), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 93/268 (34%), Positives = 145/268 (54%), Gaps = 21/268 (7%)

Query: 3   SQKTKTKKHQKQNQKPPTEQGEETPSEFAFTVTKVAVSQICRSVGFKAAESSALETLTLV 62
           S+  +  K +K+       Q  +  SEF+F + K AV+QIC+SVG+K ++  ALE LT V
Sbjct: 11  SKLPRRAKRKKKGLGVNVAQVADNTSEFSFAIAKTAVAQICQSVGYKISKHHALEALTNV 70

Query: 63  AAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSGQGFPGASALNRNCMLDSGVLK 122
           + +Y++ +   A+S+++ ++R++SNL DL N ++D+ S  GFPG S ++++ +L S  LK
Sbjct: 71  STRYMEAIVRSASSFANASNRTDSNLFDLINGIHDLCSVLGFPGGSMIHKSNLLGSSALK 130

Query: 123 EIAGFVRHGCEIPFAKPIPRSKNAHA-----NSVCCKKENDRGSRSLHLHIPKWLPAFPD 177
           EI  FV    +IPFAKPIP    +        S+C  K+          HIP+WLP FP 
Sbjct: 131 EIMNFVNLSNKIPFAKPIPFRNVSEVTIDSGTSMCLSKQAKT-------HIPRWLPDFPK 183

Query: 178 ERSYNKECQGPVCNRSEKLWENSEFPEGERFTF-----GGYKWEVLGGDLAKEREKVRFK 232
           E       +   C+  EKLWE+    E            G + +    +L K RE+++FK
Sbjct: 184 ENCNRVLVKERKCD--EKLWEHLLAAEENSGLLRSNDINGKEGKNARMELPKGRERMKFK 241

Query: 233 I-GVKGNNGVGFGVDLRNGVCRGGKRVR 259
           I G K  +G G GV++ NG C     ++
Sbjct: 242 IRGEKKKHG-GLGVNMMNGDCTVTSHIK 268

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356499052|ref|XP_003518358.1| PREDICTED: probable polyamine oxidase 4-like [Glycine max]

 Score =  123 bits (308), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 78/221 (35%), Positives = 119/221 (53%), Gaps = 20/221 (9%)

Query: 67  LQQLASRAASYSHVAHRSESNLVDLTNALNDVSSGQGFPGASALNRNCMLDSGVLKEIAG 126
           ++ +   AA++++ ++R++SNL DLTN ++DV S QGFPG S ++++ +L S  LKEI  
Sbjct: 1   MEAIVRSAATFANASNRTDSNLFDLTNGIHDVCSVQGFPGGSIIHKSNLLGSSALKEIMN 60

Query: 127 FVRHGCEIPFAKPIPRSKNAHA-----NSVCCKKENDRGSRSLHLHIPKWLPAFPDERSY 181
           FV    ++PFAKPIP    +        S+C  K+       +  HIP+WLP FP E   
Sbjct: 61  FVNLSNKVPFAKPIPFRNVSEVTIDSGTSMCLSKQ-------VKTHIPRWLPHFPKENCA 113

Query: 182 NKECQGPVCNRSEKLWENSEFPEGERFTF-----GGYKWEVLGGDLAKEREKVRFKIGVK 236
               +   C+  EKLWE+S   E            G + +    +L K RE+++F+I  +
Sbjct: 114 QVLVKERKCD--EKLWEHSLTREENSGLLPSNGIDGKEEKEARMELPKGRERIKFRIRGE 171

Query: 237 GNNGVGFGVDLRNGVCRGGKRVRWNVGDVIDDG-QNCLFKP 276
               V  GV++ NGVC+G KRV WN   + D G   C+  P
Sbjct: 172 KEMHVELGVNMMNGVCKGRKRVSWNHDKINDCGSMTCVKLP 212

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	281
TAIR|locus:2197530	277	AT1G31240 [Arabidopsis thalian	0.733	0.743	0.400	5.1e-35
TAIR|locus:2076567	397	AT3G02160 [Arabidopsis thalian	0.590	0.418	0.352	2.4e-21
TAIR|locus:2116149	353	TAF8 "TBP-associated factor 8"	0.544	0.433	0.348	2.7e-20
TAIR|locus:2180852	381	AT5G15570 "AT5G15570" [Arabido	0.544	0.401	0.358	4.5e-20
UNIPROTKB|C9J7M8	123	TAF8 "Transcription initiation	0.213	0.487	0.316	0.00064

TAIR|locus:2197530 AT1G31240 [Arabidopsis thaliana (taxid:3702)]

 Score = 379 (138.5 bits), Expect = 5.1e-35, P = 5.1e-35
 Identities = 87/217 (40%), Positives = 130/217 (59%)

Query:    20 TEQGEETPSEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSH 79
             ++Q   + +EF+F++TK+AVSQIC+S+G+KA ++SAL TLTL   K+LQ LA  A+S+S+
Sbjct:    16 SDQSPTSTAEFSFSLTKIAVSQICQSIGYKATDASALNTLTLTTTKFLQSLAELASSFSN 75

Query:    80 VAHRSESNLVDLTNALNDV--SSGQGFPGASALN---RNCMLDSGVLKEIAGFVRHGCEI 134
              A+R+E NL D+ N L D+  S+   FPG S ++     C++ S VL+ ++ FV +  EI
Sbjct:    76 TANRTEVNLFDIVNGLQDIALSTSDCFPGGSTVHDIESQCLIKSAVLRNLSDFVTYAPEI 135

Query:   135 PFAKPIPRSKNAHANSVCCKKENDRGSRSLHL-HIPKWLPAFPDERSYNKECQGPVCNRS 193
             PFAKP+PR +     S     ++   +RS+ +  +P WLP FPD    +  C     NRS
Sbjct:   136 PFAKPLPRRERD--GSFGGDLDHVAVTRSVDVTSVPAWLPPFPDSSLCSDRCSKD--NRS 191

Query:   194 EKLWENSEFPEGERFTFGGYKWEVLGGDLAKEREKVR 230
             + LWENS+            K +  GG L   R+KVR
Sbjct:   192 DHLWENSDSVIRREILPESLKSKS-GGRLPVMRDKVR 227

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2076567 AT3G02160 [Arabidopsis thaliana (taxid:3702)]

 Score = 252 (93.8 bits), Expect = 2.4e-21, P = 2.4e-21
 Identities = 68/193 (35%), Positives = 104/193 (53%)

Query:    28 SEFAFTVTKVAVSQICRSV------------G--FKAAESSALETLTLVAAKYLQQLASR 73
             ++FAF++ ++AV+QIC SV            G  F + + SAL+TLT VA +Y+Q +   
Sbjct:    41 NDFAFSIARMAVAQICESVEVNPYQESQTREGVRFSSFQESALDTLTDVAVQYIQSIGKT 100

Query:    74 AASYSHVAHRSESNLVDLTNALNDVSSGQGFPGASALNRNCMLDSGVLKEIAGFVRHGCE 133
             A  Y+++A R + N +D+  AL D+ SG GF G S  + +C+ DSGV+K+I  +     E
Sbjct:   101 AHLYANLAGRVDGNSLDILQALEDLGSGLGFAGVSDTD-HCLADSGVVKDIIRYTGEAEE 159

Query:   134 IPFAKPIPRSKNAHANSVCCKKENDRGSRSLHLHIPKWLPAFPDERSYNKECQGPVCNRS 193
             IPF   +PR   +          ++ G+     HIP WLPAFP+           +C+RS
Sbjct:   160 IPFVYSLPRFPFSKEKKPA-PSFSEVGAEPPDEHIPVWLPAFPETE---------LCDRS 209

Query:   194 EKLWENSEFPEGE 206
             E+   N+   EGE
Sbjct:   210 EET--NAATIEGE 220

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2116149 TAF8 "TBP-associated factor 8" [Arabidopsis thaliana (taxid:3702)]

 Score = 240 (89.5 bits), Expect = 2.7e-20, P = 2.7e-20
 Identities = 55/158 (34%), Positives = 88/158 (55%)

Query:    29 EFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNL 88
             EF+    K AV+Q+C SVG++  +  ALE+L+  A +Y+ QL   A S++++  RS+ N+
Sbjct:    25 EFSHAAAKAAVAQVCESVGYENFKDPALESLSGFALQYILQLGKTATSFANLTGRSQCNV 84

Query:    89 VDLTNALNDVSSGQGFPGASALNRNCMLDSGV-LKEIAGFVRHGCEIPFAKPIPRSKNAH 147
              D+  AL+D++   G  G S+   +C L   + L+EI  FV    E+PF++P+P    A 
Sbjct:    85 FDIILALDDLTDNNGEQGISS--ESCSLGRSIKLREIIDFVNSSEEVPFSQPLPSFPVAI 142

Query:   148 ANSV--CCKKENDRGSRSLHLHIPKWLPAFPDERSYNK 183
             ++          + G      HIP WLPAFPD  +Y +
Sbjct:   143 SDRSRKMIPSFVEIGETPPGKHIPLWLPAFPDPHTYKE 180

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2180852 AT5G15570 "AT5G15570" [Arabidopsis thaliana (taxid:3702)]

 Score = 240 (89.5 bits), Expect = 4.5e-20, P = 4.5e-20
 Identities = 61/170 (35%), Positives = 89/170 (52%)

Query:    28 SEFAFTVTKVAVSQICRSV-------------G--FKAAESSALETLTLVAAKYLQQLAS 72
             ++FA+ + ++A +QIC SV             G  F + + +ALETLT V  +Y+Q +  
Sbjct:    25 NDFAYALARMATAQICESVEINSYQESSQSREGLRFSSFQETALETLTDVVIQYIQNIGK 84

Query:    73 RAASYSHVAHRSESNLVDLTNALNDVSSGQGFPGASALNRNCMLDSGVLKEIAGFVRHGC 132
              A  Y ++A R ESN +D+  AL D+ SG GF GA  +  +C+ DSGV+K+I  +     
Sbjct:    85 TAQFYVNMAGRVESNALDIVQALEDLGSGLGFDGAHDVE-HCLADSGVVKDIIRYTGEAE 143

Query:   133 EIPFAKPIPRSKNAHANSVCCKKENDRGSRSLHLHIPKWLPAFPDERSYN 182
             EIPF   +PR              +D G      HIP WLPAFP+ +  N
Sbjct:   144 EIPFVYSLPRFPFNRGKRPA-PSFSDIGVEPPDEHIPVWLPAFPETKMSN 192

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0009560 "embryo sac egg cell differentiation" evidence=RCA

UNIPROTKB|C9J7M8 TAF8 "Transcription initiation factor TFIID subunit 8" [Homo sapiens (taxid:9606)]

 Score = 91 (37.1 bits), Expect = 0.00064, P = 0.00064
 Identities = 19/60 (31%), Positives = 33/60 (55%)

Query:    36 KVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNAL 95
             +V VS +    GF++AE +++ETLT +   Y+ ++   A SY     R++  L D+   L
Sbjct:    38 QVVVSSLLTEAGFESAEKASVETLTEMLQSYISEIGRSAKSYCEHTARTQPTLSDIVVTL 97


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.316   0.133   0.406    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      281       251   0.00081  114 3  11 22  0.48    33
                                                     32  0.47    36


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  5
  No. of states in DFA:  612 (65 KB)
  Total size of DFA:  210 KB (2117 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  22.00u 0.13s 22.13t   Elapsed:  00:00:01
  Total cpu time:  22.00u 0.13s 22.13t   Elapsed:  00:00:01
  Start:  Fri May 10 04:12:04 2013   End:  Fri May 10 04:12:05 2013

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: eugene3.00150973 hypothetical protein (267 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	281
smart00576	77	smart00576, BTP, Bromodomain transcription factors	1e-22
pfam07524	77	pfam07524, Bromo_TP, Bromodomain associated	2e-20
cd08049	54	cd08049, TAF8, TATA Binding Protein (TBP) Associat	0.002

>gnl|CDD|128846 smart00576, BTP, Bromodomain transcription factors and PHD domain containing proteins

 Score = 88.2 bits (219), Expect = 1e-22
 Identities = 32/76 (42%), Positives = 47/76 (61%)

Query: 29  EFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNL 88
           E AF + ++AV+QI  S GF + + SALETLT +   Y+Q+L   A SY+ +A R+E NL
Sbjct: 2   ELAFALLRIAVAQILESAGFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNL 61

Query: 89  VDLTNALNDVSSGQGF 104
            D+  AL ++    G 
Sbjct: 62  GDVVLALENLGISVGE 77

subdomain of archael histone-like transcription factors. Length = 77

>gnl|CDD|219450 pfam07524, Bromo_TP, Bromodomain associated

 Score = 82.8 bits (205), Expect = 2e-20
 Identities = 30/71 (42%), Positives = 43/71 (60%)

Query: 29 EFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNL 88
          E A  + KV V+QI  + GF +AE SALETLT +A  Y+Q+L  +A  ++  A RSE  L
Sbjct: 2  ELAHDLLKVVVAQILETAGFDSAEESALETLTDIAQSYIQELGRQAKRFAEHAGRSEPTL 61

Query: 89 VDLTNALNDVS 99
           D+   L ++ 
Sbjct: 62 FDVVLTLKEMG 72

This domain is predicted to bind DNA and is often found associated with pfam00439 and in transcription factors. It has a histone-like fold. Length = 77

>gnl|CDD|176263 cd08049, TAF8, TATA Binding Protein (TBP) Associated Factor 8

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 10/15 (66%), Positives = 11/15 (73%)

Query: 167 HIPKWLPAFPDERSY 181
           HIP WLP FPD  +Y
Sbjct: 2   HIPSWLPPFPDPHTY 16

The TATA Binding Protein (TBP) Associated Factor 8 (TAF8) is one of several TAFs that bind TBP, and is 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 the assembly of the preinitiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs' functions, such as serving as activator-binding sites, involvement in the core-promoter recognition, or a role in the essential catalytic activity of the complex. The mouse ortholog of TAF8 is called taube nuss protein (TBN), and is required for early embryonic development. TBN mutant mice exhibit disturbances in the balance between cell death and cell survival in the early embryo. TAF8 plays a role in the differentiation of preadipocyte fibroblasts to adipocytes; it is also required for the integration of TAF10 into the TAF complex. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. TAF8 is also a component of a small TAF complex (SMAT), which contains TAF8, TAF10 and SUPT7L. Several TAFs interact via histone-fold motifs. The histone fold (HFD) is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamer. TAF8 contains an H4 related histone fold motif, and interacts with several subunits of TFIID, including TBP and the histone-fold protein TAF10. Currently, five HF-containing TAF pairs have been described or suggested to exist in TFIID: TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10. Length = 54

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	281
KOG2389	353	consensus Predicted bromodomain transcription fact	100.0
KOG4336	323	consensus TBP-associated transcription factor Prod	99.94
smart00576	77	BTP Bromodomain transcription factors and PHD doma	99.88
PF07524	77	Bromo_TP: Bromodomain associated; InterPro: IPR006	99.87
PF10406	51	TAF8_C: Transcription factor TFIID complex subunit	98.87
cd08049	54	TAF8 TATA Binding Protein (TBP) Associated Factor	98.85
cd07979	117	TAF9 TATA Binding Protein (TBP) Associated Factor	98.83
PF02291	129	TFIID-31kDa: Transcription initiation factor IID,	98.57
cd00076	85	H4 Histone H4, one of the four histones, along wit	98.48
PLN00035	103	histone H4; Provisional	98.46
PTZ00015	102	histone H4; Provisional	98.42
smart00803	65	TAF TATA box binding protein associated factor. TA	98.38
COG2036	91	HHT1 Histones H3 and H4 [Chromatin structure and d	98.3
PF15630	76	CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C	98.1
KOG3334	148	consensus Transcription initiation factor TFIID, s	98.05
smart00417	74	H4 Histone H4.	97.89
PF02969	66	TAF: TATA box binding protein associated factor (T	97.77
cd07981	72	TAF12 TATA Binding Protein (TBP) Associated Factor	97.41
cd08050	343	TAF6 TATA Binding Protein (TBP) Associated Factor	97.38
PF00125	75	Histone: Core histone H2A/H2B/H3/H4 histone h2a si	97.35
COG5094	145	TAF9 Transcription initiation factor TFIID, subuni	97.24
KOG3467	103	consensus Histone H4 [Chromatin structure and dyna	96.87
PF00808	65	CBFD_NFYB_HMF: Histone-like transcription factor (	96.81
cd07978	92	TAF13 The TATA Binding Protein (TBP) Associated Fa	96.34
smart00428	105	H3 Histone H3.	96.08
PF02269	93	TFIID-18kDa: Transcription initiation factor IID,	95.65
PF03540	51	TFIID_30kDa: Transcription initiation factor TFIID	95.23
KOG3423	176	consensus Transcription initiation factor TFIID, s	95.23
PLN00161	135	histone H3; Provisional	94.78
KOG2549	576	consensus Transcription initiation factor TFIID, s	94.7
PF15511	414	CENP-T: Centromere kinetochore component CENP-T; P	94.51
cd00074	115	H2A Histone 2A; H2A is a subunit of the nucleosome	94.41
PLN00160	97	histone H3; Provisional	94.1
PTZ00018	136	histone H3; Provisional	93.29
PLN00121	136	histone H3; Provisional	93.08
KOG0870	172	consensus DNA polymerase epsilon, subunit D [Trans	92.11
COG5095	450	TAF6 Transcription initiation factor TFIID, subuni	89.69
PF03847	68	TFIID_20kDa: Transcription initiation factor TFIID	89.54
KOG0869	168	consensus CCAAT-binding factor, subunit A (HAP3) [	87.32
KOG3901	109	consensus Transcription initiation factor IID subu	84.33
KOG1744	127	consensus Histone H2B [Chromatin structure and dyn	82.11
KOG0871	156	consensus Class 2 transcription repressor NC2, bet	80.99
smart00427	89	H2B Histone H2B.	80.66

>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]

Probab=100.00  E-value=1.7e-35  Score=279.15  Aligned_cols=208  Identities=34%  Similarity=0.482  Sum_probs=175.2

Q ss_pred             CCCCCchHHHHHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC
Q 023473           22 QGEETPSEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSG  101 (281)
Q Consensus        22 ~~~~s~defar~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~  101 (281)
                      +.....++|++++++++|||||+++||++.+.+||++||+++++||++||++||.|++++||++||++|+++||.+|+++
T Consensus        18 ~~~~~~~~ya~sla~~avaQIcqslg~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s   97 (353)
T KOG2389|consen   18 RSESEEAEYAFSLARVAVAQICQSLGYSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSAS   97 (353)
T ss_pred             ccchhHHHHHHHHHHHHHHHHHHhcCCcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhh
Confidence            46778999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCcccccccccchhhHHHHhhhhhcCCCCCCCCCCCCCCCCCCccccccccccCCCCCCCCCCCCCC-CCCCccc
Q 023473          102 QGFPGASALNRNCMLDSGVLKEIAGFVRHGCEIPFAKPIPRSKNAHANSVCCKKENDRGSRSLHLHIPKWLP-AFPDERS  180 (281)
Q Consensus       102 ~gF~g~s~~~~~~ll~S~~l~eL~~yv~~~~~iPf~~plP~fPv~~~~~l~~~~~l~~~~r~~~~HIP~~LP-~FPd~HT  180 (281)
                      .||.|++... +||++|+++++|+.|...+++|||.+++|+||+.+....++++.-+.+.-++..|||.||| +||+.|+
T Consensus        98 ~~~~~~~~~s-~~L~ds~v~rdii~~~g~~eevpF~~~lP~Fp~s~s~~k~~l~~~~~g~~pp~~~Ip~wLP~~fp~~~~  176 (353)
T KOG2389|consen   98 LGASGSSGES-HCLLDSKVLRDIIIFNGKAEEVPFKDDLPRFPVSKSVNKPFLKFGSVGAEPPGESIPIWLPPAFPDLEG  176 (353)
T ss_pred             cccccccchh-HHHhhhhhHHHHHhhccccccCCCCCCCCccccccccccCCCCccccCCCCCCccccccCCCCCCCccc
Confidence            9999999866 9999999999999999999999999999999999754556643334555555699999999 8999999


Q ss_pred             ccccCCCCCCCCccccccCCCCCCCCccccCCCcccccCCCccccccceeeecccc
Q 023473          181 YNKECQGPVCNRSEKLWENSEFPEGERFTFGGYKWEVLGGDLAKEREKVRFKIGVK  236 (281)
Q Consensus       181 Y~~T~~~~~~~r~~~l~e~~~~~~~~~~~~~~~~~~~~~g~~~~~r~~v~f~~~~~  236 (281)
                      |..+|   .+..+...|+......++......++ ...+|.+++.+..  +.+++-
T Consensus       177 ~~~s~---e~~~~~~~~~~~~~~~~s~~~~~~ls-~~~~~r~~v~k~~--~~~~~~  226 (353)
T KOG2389|consen  177 CSKSP---EGNVTVPKPEGRPPEKASLELRASLS-EDSGGRLQVKKDS--EEKEKP  226 (353)
T ss_pred             CCCCc---cccccccCcccCchhhhhhhhhhhhh-hhccccchhhhhh--hhhcCc
Confidence            99997   44444557777766555444433334 3457788888777  444443

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

Probab=99.94  E-value=2.4e-26  Score=214.14  Aligned_cols=142  Identities=22%  Similarity=0.260  Sum_probs=110.3

Q ss_pred             HHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCCCCCCCCcccc
Q 023473           33 TVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSGQGFPGASALNR  112 (281)
Q Consensus        33 ~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~~gF~g~s~~~~  112 (281)
                      .+|..+|+++|...||++++..|+++|+++++.||.+||+.++.||+|+|||+|+..||..+|++|||.           
T Consensus         5 ~vl~~VV~~Ll~~~gfd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~-----------   73 (323)
T KOG4336|consen    5 RVLAPVVSNLLKTKGFDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK-----------   73 (323)
T ss_pred             hHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC-----------
Confidence            399999999999999999999999999999999999999999999999999999999999999999973           


Q ss_pred             cccccchhhHHHHhhhhhcCCCC--CCCCCCCCCCCCCCccccc-ccc-ccCCCCCCCCCCCCCCCCCCcccccccCCCC
Q 023473          113 NCMLDSGVLKEIAGFVRHGCEIP--FAKPIPRSKNAHANSVCCK-KEN-DRGSRSLHLHIPKWLPAFPDERSYNKECQGP  188 (281)
Q Consensus       113 ~~ll~S~~l~eL~~yv~~~~~iP--f~~plP~fPv~~~~~l~~~-~~l-~~~~r~~~~HIP~~LP~FPd~HTY~~T~~~~  188 (281)
                              +.+|..|.+.....-  ....+|.-..+...+.+-. ..+ -..+++++.|||+|||||||+|||++|+...
T Consensus        74 --------v~sL~~~~q~~~~sl~~~~~~aP~~~~q~~ds~~~~~~~l~~gv~~php~yIpshLPpfPdpHTYi~Tpi~~  145 (323)
T KOG4336|consen   74 --------VSSLYAYFQKQEFSLWSVLIAAPENQEQEEDSEQQPELLLTLGVSRPHPKYIPSHLPPFPDPHTYIKTPIYK  145 (323)
T ss_pred             --------hhhhHHHHHhccchhhhccccCCCcCCccccccccchHhhhcCCCCCCCccccccCCCCCCCcccccCCccC
Confidence                    677778876654310  1122222111100111110 111 3345666799999999999999999999887


Q ss_pred             CCCCc
Q 023473          189 VCNRS  193 (281)
Q Consensus       189 ~~~r~  193 (281)
                      +...+
T Consensus       146 ~p~ts  150 (323)
T KOG4336|consen  146 VPDTS  150 (323)
T ss_pred             CCCCC
Confidence            77776

>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins

Probab=99.88  E-value=1.6e-22  Score=155.15  Aligned_cols=74  Identities=42%  Similarity=0.608  Sum_probs=72.3

Q ss_pred             hHHHHHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC
Q 023473           28 SEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSG  101 (281)
Q Consensus        28 defar~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~  101 (281)
                      ++|+|++|+++|+|||+++||++++++|+|+|||++++||.+|++.++.||+|+||++|++.||.+||++||+.
T Consensus         1 ~~~~~~ll~~~Vaqil~~~Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~   74 (77)
T smart00576        1 NELAFALLRIAVAQILESAGFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS   74 (77)
T ss_pred             CHHHHHHHHHHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999974

subdomain of archael histone-like transcription factors

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

Probab=99.87  E-value=6.1e-22  Score=151.20  Aligned_cols=74  Identities=39%  Similarity=0.586  Sum_probs=72.4

Q ss_pred             hHHHHHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC
Q 023473           28 SEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSG  101 (281)
Q Consensus        28 defar~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~  101 (281)
                      ++|++++|+++|+|||+++||++++++|||+|+|++.+||++||+.++.|||++|||+|++.||.+||++||++
T Consensus         1 ~e~~~~~l~~~va~il~~~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~   74 (77)
T PF07524_consen    1 DEFARSLLRRSVAQILKHAGFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS   74 (77)
T ss_pred             CHHHHHHHHHHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999973

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 [, ].

>PF10406 TAF8_C: Transcription factor TFIID complex subunit 8 C-term ; InterPro: IPR019473 This entry represents the C-terminal region of subunit 8 (also known as TAF8) of the transcription factor TFIID []

Probab=98.87  E-value=1.1e-09  Score=78.44  Aligned_cols=28  Identities=32%  Similarity=0.667  Sum_probs=23.4

Q ss_pred             CCCCCCCCCCCCcccccccCCCCCCCCc
Q 023473          166 LHIPKWLPAFPDERSYNKECQGPVCNRS  193 (281)
Q Consensus       166 ~HIP~~LP~FPd~HTY~~T~~~~~~~r~  193 (281)
                      +|||+|||+||++|||++|+.....+.+
T Consensus         1 ~~IP~~lP~fP~~HTY~~Tp~~~~~~~d   28 (51)
T PF10406_consen    1 SHIPDWLPPFPPPHTYKRTPIYNERETD   28 (51)
T ss_pred             CCCcccCCCCCCCcccccCCCCCCCCCC
Confidence            5999999999999999999985544443

The adjacent N-terminal region generally contains a histone fold domain (IPR006565 from INTERPRO). This subunit is one of the key subunits of TFIID, being one of several general cofactors which are typically involved in gene activation to bring about the communication between gene-specific transcription factors and components of the general transcription machinery [].

>cd08049 TAF8 TATA Binding Protein (TBP) Associated Factor 8

Probab=98.85  E-value=1.4e-09  Score=78.63  Aligned_cols=27  Identities=37%  Similarity=0.797  Sum_probs=22.6

Q ss_pred             CCCCCCCCCCCCcccccccCCCCCCCC
Q 023473          166 LHIPKWLPAFPDERSYNKECQGPVCNR  192 (281)
Q Consensus       166 ~HIP~~LP~FPd~HTY~~T~~~~~~~r  192 (281)
                      .|||+|||+||++|||++|+.....+.
T Consensus         1 ~hIP~~LP~FP~~HTY~~Tp~~~~~~~   27 (54)
T cd08049           1 AHIPSWLPPFPDPHTYKRTPTYSERET   27 (54)
T ss_pred             CCCCcCCCCCCCchhhccCCCCCCCcc
Confidence            499999999999999999997544333

The TATA Binding Protein (TBP) Associated Factor 8 (TAF8) is one of several TAFs that bind TBP, and is 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 the assembly of the preinitiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs' functions, such as serving as activator-binding sites, involvement in the core-promo

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

Probab=98.83  E-value=4.3e-08  Score=81.22  Aligned_cols=94  Identities=19%  Similarity=0.259  Sum_probs=79.6

Q ss_pred             HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCCCCCCCCcccccccc
Q 023473           37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSGQGFPGASALNRNCML  116 (281)
Q Consensus        37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~~gF~g~s~~~~~~ll  116 (281)
                      .+|.+||++.|-+..++.|...|.|++.+|..+|+..|..||+||||...+..||.+|+...+- ..|...         
T Consensus         5 ~~v~~iLk~~Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~-~~f~~~---------   74 (117)
T cd07979           5 RVIAAILKSMGITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD-YSFTSP---------   74 (117)
T ss_pred             HHHHHHHHHCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc-cCCCCC---------
Confidence            5789999999999999999999999999999999999999999999999999999999998753 234321         


Q ss_pred             cchhhHHHHhhhhhcCCCCCCCCCCC
Q 023473          117 DSGVLKEIAGFVRHGCEIPFAKPIPR  142 (281)
Q Consensus       117 ~S~~l~eL~~yv~~~~~iPf~~plP~  142 (281)
                        -..+.|.+.+...+.+|+|.+.+.
T Consensus        75 --p~~~~l~~~a~~~N~~pLP~~~~~   98 (117)
T cd07979          75 --PPRDFLLELAREKNSIPLPPIPPS   98 (117)
T ss_pred             --CcHHHHHHHHHHhccCCCCCCCCC
Confidence              136678888888888887755444

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

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

Probab=98.57  E-value=2.1e-07  Score=78.57  Aligned_cols=90  Identities=20%  Similarity=0.245  Sum_probs=53.6

Q ss_pred             HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc-CCCCCCCCCCccccccc
Q 023473           37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV-SSGQGFPGASALNRNCM  115 (281)
Q Consensus        37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm-Gi~~gF~g~s~~~~~~l  115 (281)
                      ++|.+||++.|.+..++.+...|.|.+.+|..+|...|+.||+||||+.++..||.+|..-. +-  -|...        
T Consensus        16 ~~i~~iL~~~Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~--~f~~p--------   85 (129)
T PF02291_consen   16 RVIHLILKSMGVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDH--SFTQP--------   85 (129)
T ss_dssp             HHHHHHHHHTT---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT------------------
T ss_pred             HHHHHHHHHcCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhh--hccCC--------
Confidence            67899999999999999999999999999999999999999999999999999999999843 21  23221        


Q ss_pred             ccchhhHHHHhhhhhcCCCCCCCC
Q 023473          116 LDSGVLKEIAGFVRHGCEIPFAKP  139 (281)
Q Consensus       116 l~S~~l~eL~~yv~~~~~iPf~~p  139 (281)
                         -..+-|.+.++..+.+|+|..
T Consensus        86 ---ppre~llelA~e~N~~PLP~i  106 (129)
T PF02291_consen   86 ---PPREFLLELAREKNSIPLPPI  106 (129)
T ss_dssp             ------------------------
T ss_pred             ---CChHHHHHHHHHhcCCCCCCC
Confidence               124566677777788776643

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

>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=98.48  E-value=8e-07  Score=70.16  Aligned_cols=68  Identities=24%  Similarity=0.368  Sum_probs=64.2

Q ss_pred             HHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473           33 TVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS  100 (281)
Q Consensus        33 ~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi  100 (281)
                      .+-..+|-.+++..|-..++..|.+.+.+++..|+.+|++.+..||+||+|...+..||.+||+.+|-
T Consensus        13 gi~k~~I~RLarr~GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~   80 (85)
T cd00076          13 GITKPAIRRLARRGGVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR   80 (85)
T ss_pred             cCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCC
Confidence            35577888999999999999999999999999999999999999999999999999999999999973

>PLN00035 histone H4; Provisional

Probab=98.46  E-value=1e-06  Score=71.91  Aligned_cols=71  Identities=25%  Similarity=0.352  Sum_probs=65.4

Q ss_pred             HHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC-CCC
Q 023473           34 VTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSG-QGF  104 (281)
Q Consensus        34 lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~-~gF  104 (281)
                      +-..+|-.|++..|-..++..|.+.|.+++..|+.+|++.+..||+||+|...+..||.+||+.+|-. .||
T Consensus        30 ipk~~IrRLARr~GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~lyGf  101 (103)
T PLN00035         30 ITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGF  101 (103)
T ss_pred             CCHHHHHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCcCCCC
Confidence            55677888999999999999999999999999999999999999999999999999999999999843 444

>PTZ00015 histone H4; Provisional

Probab=98.42  E-value=1e-06  Score=71.78  Aligned_cols=69  Identities=22%  Similarity=0.320  Sum_probs=65.0

Q ss_pred             HHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473           32 FTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS  100 (281)
Q Consensus        32 r~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi  100 (281)
                      ..+...+|-.|++..|-..++..|-+.+.+++..|+.+|++.|..||+||+|...+..||.+||...|-
T Consensus        29 ~gI~k~~IrRLarr~GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~   97 (102)
T PTZ00015         29 RGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGR   97 (102)
T ss_pred             cCCCHHHHHHHHHHcCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCC
Confidence            445678899999999999999999999999999999999999999999999999999999999999873

>smart00803 TAF TATA box binding protein associated factor

Probab=98.38  E-value=1.8e-06  Score=64.77  Aligned_cols=60  Identities=15%  Similarity=0.252  Sum_probs=57.1

Q ss_pred             HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Q 023473           37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALN   96 (281)
Q Consensus        37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~   96 (281)
                      .+|-.|.++.|.+.++..|.+.|.+.++.|+.+|++.|..||+|++|...+..||.+||+
T Consensus         6 ~~i~ria~~~Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk   65 (65)
T smart00803        6 ETIKDVAESLGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR   65 (65)
T ss_pred             HHHHHHHHHCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence            467788999999999999999999999999999999999999999999999999999984

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.

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

Probab=98.30  E-value=2.2e-06  Score=68.51  Aligned_cols=65  Identities=29%  Similarity=0.389  Sum_probs=60.3

Q ss_pred             HHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473           36 KVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS  100 (281)
Q Consensus        36 r~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi  100 (281)
                      ...|..|++.+|=+.++.+|.+.|.++++.|+.+|+..|..+|.|+||-.....||.+|+..+|.
T Consensus        22 ~apv~Ri~r~~~~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~   86 (91)
T COG2036          22 KAPVRRILRKAGAERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGR   86 (91)
T ss_pred             chHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhcc
Confidence            34577788888888999999999999999999999999999999999999999999999999974

>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C

Probab=98.10  E-value=1.3e-05  Score=61.98  Aligned_cols=66  Identities=20%  Similarity=0.170  Sum_probs=57.0

Q ss_pred             HHHHHHHHHHHHHHcCcCc---cChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473           32 FTVTKVAVSQICRSVGFKA---AESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND   97 (281)
Q Consensus        32 r~lLr~sVaqIL~~~GFds---a~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d   97 (281)
                      .+-|.-+|++||++.+=+.   +++.++..|++++-+|+..+|.....||.||||+.++..||.+..+.
T Consensus         4 Kaal~~~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rr   72 (76)
T PF15630_consen    4 KAALWYTVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARR   72 (76)
T ss_dssp             HHHHHHHHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhc
Confidence            4678889999999986443   89999999999999999999999999999999999999999987765

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

Probab=98.05  E-value=6.3e-05  Score=64.64  Aligned_cols=95  Identities=16%  Similarity=0.198  Sum_probs=76.5

Q ss_pred             HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCCCCCCCCcccccccc
Q 023473           37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSGQGFPGASALNRNCML  116 (281)
Q Consensus        37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~~gF~g~s~~~~~~ll  116 (281)
                      .+|++||++.|.+..++-...-|-|...+|.+.|...|.-|++||+++.....||.+|..-.. +.-|.+.  ..     
T Consensus        17 ~~i~~iL~s~GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~-~~sf~~p--Pp-----   88 (148)
T KOG3334|consen   17 RVIASILKSLGIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRV-DHSFTPP--PP-----   88 (148)
T ss_pred             HHHHHHHHHcCccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHh-ccccCCC--Cc-----
Confidence            579999999999999999999999999999999999999999999999999999999998764 3344331  11     


Q ss_pred             cchhhHHHHhhhhhcCCCCCCCCCCCC
Q 023473          117 DSGVLKEIAGFVRHGCEIPFAKPIPRS  143 (281)
Q Consensus       117 ~S~~l~eL~~yv~~~~~iPf~~plP~f  143 (281)
                          -+-|.+.+...+..|++++.+.+
T Consensus        89 ----Re~lL~lA~~rN~~pLp~i~~~~  111 (148)
T KOG3334|consen   89 ----REFLLELAAERNSKPLPQIRAGP  111 (148)
T ss_pred             ----hHHHHHHHHhhccCCCCcccCCC
Confidence                23344556666777777665543

>smart00417 H4 Histone H4

Probab=97.89  E-value=2.3e-05  Score=60.42  Aligned_cols=63  Identities=22%  Similarity=0.322  Sum_probs=58.2

Q ss_pred             HHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHH
Q 023473           32 FTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNA   94 (281)
Q Consensus        32 r~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~A   94 (281)
                      ..+...+|-.|++..|-..++..+-+.|.+++..|+.+|++.|-.||+|++|-..+..||..|
T Consensus        12 ~gI~k~~IrRLaRr~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a   74 (74)
T smart00417       12 QGITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA   74 (74)
T ss_pred             cCCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence            345577889999999999999999999999999999999999999999999999999999754

>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=97.77  E-value=0.00017  Score=54.56  Aligned_cols=61  Identities=20%  Similarity=0.283  Sum_probs=51.2

Q ss_pred             HHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Q 023473           36 KVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALN   96 (281)
Q Consensus        36 r~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~   96 (281)
                      ..+|-.+..+.|+...+..+...|++-++.-|.+|.+.|..|+.|+.|+..+..||..||+
T Consensus         6 ~esvk~iAes~Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr   66 (66)
T PF02969_consen    6 QESVKDIAESLGISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR   66 (66)
T ss_dssp             HHHHHHHHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence            3567788899999999999999999999999999999999999999999999999999985

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.

>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=97.41  E-value=0.0014  Score=49.89  Aligned_cols=52  Identities=12%  Similarity=0.136  Sum_probs=49.4

Q ss_pred             CcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           47 GFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        47 GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      +-..+++.|.+.|.+++..|+..++..+..+|.|+||....+.||.++|+..
T Consensus        16 ~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~   67 (72)
T cd07981          16 PREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERN   67 (72)
T ss_pred             CCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            3478999999999999999999999999999999999999999999999875

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

>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=97.38  E-value=0.0011  Score=63.99  Aligned_cols=69  Identities=19%  Similarity=0.262  Sum_probs=64.6

Q ss_pred             HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC--CCCC
Q 023473           37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSG--QGFP  105 (281)
Q Consensus        37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~--~gF~  105 (281)
                      .+|-.|.+++|.+..+..|...|++.++.++.+|++.|..||.|++|...+..||.+||+..++.  .||.
T Consensus         3 ~~i~~ia~~~Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~eplyG~~   73 (343)
T cd08050           3 ESIKLIAESLGIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVEPLYGFS   73 (343)
T ss_pred             hHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCCcccCCC
Confidence            46788999999999999999999999999999999999999999999999999999999999876  6664

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

>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=97.35  E-value=0.00099  Score=49.90  Aligned_cols=60  Identities=22%  Similarity=0.175  Sum_probs=52.7

Q ss_pred             HHHHHHHHHcCcC-ccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Q 023473           37 VAVSQICRSVGFK-AAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALN   96 (281)
Q Consensus        37 ~sVaqIL~~~GFd-sa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~   96 (281)
                      +++-.+....+.+ .++..|++.|..+++.|+.+|...|..+|.+++|...++.|+..|+.
T Consensus        13 r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r   73 (75)
T PF00125_consen   13 RLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVR   73 (75)
T ss_dssp             HHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHH
T ss_pred             eeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHh
Confidence            3444555555665 99999999999999999999999999999999999999999999976

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 ....

>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=97.24  E-value=0.0028  Score=53.60  Aligned_cols=62  Identities=24%  Similarity=0.242  Sum_probs=57.5

Q ss_pred             HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCH---HHHHHHHHhc
Q 023473           37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNL---VDLTNALNDV   98 (281)
Q Consensus        37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl---~DV~~AL~dm   98 (281)
                      +.|..||.+.|.+.+++..-=.|.+...+|-+.+.+.|.-||+|+||++...   .||.+|+.--
T Consensus        18 rlihliL~Slgi~~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~   82 (145)
T COG5094          18 RLIHLILRSLGIEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATK   82 (145)
T ss_pred             hHHHHHHHhcCchhhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHH
Confidence            5688899999999999999999999999999999999999999999997776   9999999764

>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]

Probab=96.87  E-value=0.0053  Score=49.06  Aligned_cols=69  Identities=23%  Similarity=0.301  Sum_probs=63.4

Q ss_pred             HHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC
Q 023473           33 TVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSG  101 (281)
Q Consensus        33 ~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~  101 (281)
                      -+.+.+|-.+.+..|...+.--..+....++..||+++...|.-|++||-|-..+..||..+|..||+-
T Consensus        29 gitKpaIRRlARr~GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~   97 (103)
T KOG3467|consen   29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT   97 (103)
T ss_pred             ccchHHHHHHHHhcCcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence            344666778899999999999999999999999999999999999999999999999999999999964

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

Probab=96.81  E-value=0.006  Score=44.84  Aligned_cols=57  Identities=23%  Similarity=0.317  Sum_probs=49.3

Q ss_pred             HHHHHHHc-CcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHH
Q 023473           39 VSQICRSV-GFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNAL   95 (281)
Q Consensus        39 VaqIL~~~-GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL   95 (281)
                      |-.|++.. +-..++..|.+.|+..++.|+..|+..|...|+..+|-..+..||..|+
T Consensus         8 vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av   65 (65)
T PF00808_consen    8 VKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV   65 (65)
T ss_dssp             HHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred             HHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence            44556666 6777999999999999999999999999999999999999999999886

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 ....

>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=96.34  E-value=0.024  Score=45.37  Aligned_cols=62  Identities=18%  Similarity=0.249  Sum_probs=54.7

Q ss_pred             HHHHHHHHHHcCcC-ccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           36 KVAVSQICRSVGFK-AAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        36 r~sVaqIL~~~GFd-sa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      ..-|.+|+-..|=. .-.+...+.|.+|+..||.+|+..|...|. ++|..+.+.|+..+|+.-
T Consensus         5 ~~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D   67 (92)
T cd07978           5 TKEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKD   67 (92)
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcC
Confidence            45578899988875 457789999999999999999999999999 888888999999999874

The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is 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 TAFs orthologs and paralogs. Several hy

>smart00428 H3 Histone H3

Probab=96.08  E-value=0.03  Score=46.03  Aligned_cols=51  Identities=24%  Similarity=0.108  Sum_probs=47.2

Q ss_pred             CcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           47 GFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        47 GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      +| .++++|++.|.+..+.||..+...+...|.||+|....+.|+.+|..--
T Consensus        51 ~~-R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~rir  101 (105)
T smart00428       51 DL-RFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRIR  101 (105)
T ss_pred             Cc-eeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHHh
Confidence            45 8899999999999999999999999999999999999999999887543

>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18)

Probab=95.65  E-value=0.013  Score=46.68  Aligned_cols=60  Identities=13%  Similarity=0.181  Sum_probs=31.6

Q ss_pred             HHHHHHHcCc-CccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           39 VSQICRSVGF-KAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        39 VaqIL~~~GF-dsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      |.+|+-..|= ....+.+...+.+|+..||.++...|...|...||..+.+.|+..+|+.-
T Consensus         7 I~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D   67 (93)
T PF02269_consen    7 IRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKD   67 (93)
T ss_dssp             CHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC----------------------
T ss_pred             HHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcC
Confidence            6778887775 46678889999999999999999999999999999999999999999985

Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.

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

Probab=95.23  E-value=0.088  Score=38.08  Aligned_cols=44  Identities=18%  Similarity=0.394  Sum_probs=41.1

Q ss_pred             HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 023473           37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHV   80 (281)
Q Consensus        37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAel   80 (281)
                      .++..+|+.+||++..+.....+.-..++||.+|+..|.+||-+
T Consensus         6 ~v~~~yL~~~G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~   49 (51)
T PF03540_consen    6 EVTDYYLERSGFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI   49 (51)
T ss_pred             HHHHHHHHHCCCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            46788999999999999999999999999999999999999864

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

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

Probab=95.23  E-value=0.093  Score=46.49  Aligned_cols=87  Identities=17%  Similarity=0.291  Sum_probs=68.2

Q ss_pred             cCCCCCCCCCCCchHHHHHHH-------HHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-----
Q 023473           15 NQKPPTEQGEETPSEFAFTVT-------KVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAH-----   82 (281)
Q Consensus        15 ~~~p~~~~~~~s~defar~lL-------r~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaG-----   82 (281)
                      ++.+..+.....-++|...+.       ..++...|..+||.+..+.....+.-..+.||..|+..|-+||-..+     
T Consensus        61 ~~~~~~~~~d~~l~efl~qLddYtP~IPDavt~~yL~~aGf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~  140 (176)
T KOG3423|consen   61 NGELNPTTKDTHLEEFLAQLDDYTPTIPDAVTDHYLKKAGFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIG  140 (176)
T ss_pred             cCCcCCCCcchHHHHHHHHHhcCCCCCcHHHHHHHHHhcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccc
Confidence            333344333344445555443       46788999999999999999999999999999999999999998876     


Q ss_pred             ---------CCCCCHHHHHHHHHhcCCC
Q 023473           83 ---------RSESNLVDLTNALNDVSSG  101 (281)
Q Consensus        83 ---------RT~pnl~DV~~AL~dmGi~  101 (281)
                               +..-+..|+.-||.+.||.
T Consensus       141 ~~k~~~kdkK~tLtmeDL~~AL~EyGin  168 (176)
T KOG3423|consen  141 KDKKQAKDKKYTLTMEDLSPALAEYGIN  168 (176)
T ss_pred             cccccccccceeeeHHHHHHHHHHhCcc
Confidence                     2346789999999999974

>PLN00161 histone H3; Provisional

Probab=94.78  E-value=0.18  Score=43.29  Aligned_cols=62  Identities=18%  Similarity=0.059  Sum_probs=51.4

Q ss_pred             HHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473           38 AVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS  100 (281)
Q Consensus        38 sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi  100 (281)
                      -|++-+...+| ..+++||+.|-+..+.||..+-..+...|.||+|....+-|+.+|..--|.
T Consensus        67 EI~~~~~~~~~-Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~rirg~  128 (135)
T PLN00161         67 EISNEMLREPF-RWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRIRGP  128 (135)
T ss_pred             HHHHhcCCCCc-EeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHhccc
Confidence            34443332345 788999999999999999999999999999999999999999999765543

>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=94.70  E-value=0.15  Score=52.48  Aligned_cols=68  Identities=19%  Similarity=0.267  Sum_probs=61.0

Q ss_pred             HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC--CCC
Q 023473           37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSG--QGF  104 (281)
Q Consensus        37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~--~gF  104 (281)
                      .+|--+.++.|.......|+..|++-+..-|.+|.+.+.+|+.|+-|+..++.||..||+-..+.  .||
T Consensus        15 Es~k~vAEslGi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nVep~yg~   84 (576)
T KOG2549|consen   15 ESVKVVAESLGITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNVEPLYGF   84 (576)
T ss_pred             HHHHHHHHHhCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcccccccCc
Confidence            34555667889999999999999999999999999999999999999999999999999998755  455

>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T

Probab=94.51  E-value=0.099  Score=51.89  Aligned_cols=57  Identities=25%  Similarity=0.300  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHHHcCc--CccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHH
Q 023473           34 VTKVAVSQICRSVGF--KAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVD   90 (281)
Q Consensus        34 lLr~sVaqIL~~~GF--dsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~D   90 (281)
                      +.+..+...++..||  ..++..||++|...+..|+++||.....||.||||-.+...|
T Consensus       356 ~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD  414 (414)
T PF15511_consen  356 VVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD  414 (414)
T ss_dssp             HHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred             HHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence            334444444554333  568999999999999999999999999999999998887766

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

Probab=94.41  E-value=0.15  Score=42.55  Aligned_cols=57  Identities=11%  Similarity=0.004  Sum_probs=52.3

Q ss_pred             HHHHH-cCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473           41 QICRS-VGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND   97 (281)
Q Consensus        41 qIL~~-~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d   97 (281)
                      .+|+. .+...++.+|.-.|+.+++.+..+|...|-.+|..++|...++.||.+|...
T Consensus        28 R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n   85 (115)
T cd00074          28 RYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN   85 (115)
T ss_pred             HHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence            34554 6788999999999999999999999999999999999999999999999887

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.

>PLN00160 histone H3; Provisional

Probab=94.10  E-value=0.23  Score=40.36  Aligned_cols=48  Identities=19%  Similarity=0.005  Sum_probs=45.4

Q ss_pred             ccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473           50 AAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND   97 (281)
Q Consensus        50 sa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d   97 (281)
                      ..+++||++|-+..+.||..+-..+...|.||+|....+-|+.+|..-
T Consensus        44 Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~ri   91 (97)
T PLN00160         44 RWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARRI   91 (97)
T ss_pred             EeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHHh
Confidence            789999999999999999999999999999999999999999888743

>PTZ00018 histone H3; Provisional

Probab=93.29  E-value=0.33  Score=41.68  Aligned_cols=51  Identities=24%  Similarity=0.093  Sum_probs=47.2

Q ss_pred             CcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           47 GFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        47 GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      +| ..+++||+.|-+..+.||..+-..+...|.||.|.....-|+.+|..--
T Consensus        82 ~~-rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~rir  132 (136)
T PTZ00018         82 DL-RFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR  132 (136)
T ss_pred             cc-eeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHHhc
Confidence            56 8999999999999999999999999999999999999999998887443

>PLN00121 histone H3; Provisional

Probab=93.08  E-value=0.41  Score=41.10  Aligned_cols=50  Identities=24%  Similarity=0.108  Sum_probs=46.9

Q ss_pred             CcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473           47 GFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND   97 (281)
Q Consensus        47 GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d   97 (281)
                      +| ..+.+||++|-+..+.||..+-..+...|.|+.|.....-|+.++..-
T Consensus        82 ~~-Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ri  131 (136)
T PLN00121         82 DL-RFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI  131 (136)
T ss_pred             cc-eeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHHh
Confidence            56 899999999999999999999999999999999999999999888743

>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]

Probab=92.11  E-value=0.73  Score=40.85  Aligned_cols=72  Identities=13%  Similarity=0.113  Sum_probs=63.1

Q ss_pred             hHHHHHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473           28 SEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS  100 (281)
Q Consensus        28 defar~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi  100 (281)
                      ..|..++..++|--.|.+. =-+++..|+..|..-..=|+..|...+..+|.-..|-..+..||..||.+|+.
T Consensus         9 l~lP~AiI~rlvke~l~E~-~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eief   80 (172)
T KOG0870|consen    9 LNLPNAIITRLVKEVLPES-NVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEF   80 (172)
T ss_pred             hhccHHHHHHHHHHhCccc-cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhch
Confidence            3456677888888888765 56799999999999999999999999999999999999999999999999963

>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=89.69  E-value=1.6  Score=42.64  Aligned_cols=70  Identities=16%  Similarity=0.318  Sum_probs=62.8

Q ss_pred             HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC--CCCCC
Q 023473           37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSG--QGFPG  106 (281)
Q Consensus        37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~--~gF~g  106 (281)
                      ..|-...++.|...+...|+..|+-=++--|.++++.+..|+-|+-||.-+..||..||+-+++.  -||.+
T Consensus         9 et~KdvAeslGi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVePLyGyd~   80 (450)
T COG5095           9 ETLKDVAESLGISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVEPLYGYDP   80 (450)
T ss_pred             HHHHHHHHHcCCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCCcccCCCC
Confidence            34555677889999999999999999999999999999999999999999999999999999876  66655

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

Probab=89.54  E-value=1.2  Score=33.79  Aligned_cols=50  Identities=16%  Similarity=0.163  Sum_probs=41.8

Q ss_pred             cCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473           48 FKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND   97 (281)
Q Consensus        48 Fdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d   97 (281)
                      =....+.+-+.|.+++..|+..+...+...|-|-+-....+.||.+.|+.
T Consensus        15 ~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler   64 (68)
T PF03847_consen   15 NEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLER   64 (68)
T ss_dssp             S----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHh
Confidence            45678899999999999999999999999999999889999999999986

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

>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]

Probab=87.32  E-value=2.5  Score=37.30  Aligned_cols=62  Identities=19%  Similarity=0.198  Sum_probs=52.6

Q ss_pred             HHHHHHHc--CcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473           39 VSQICRSV--GFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS  100 (281)
Q Consensus        39 VaqIL~~~--GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi  100 (281)
                      |+.|++.+  .=-.+...|-|++-+.+-+||.=|...|..-|+.--|-..|-.||..||..+|.
T Consensus        38 V~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGF  101 (168)
T KOG0869|consen   38 VSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGF  101 (168)
T ss_pred             HHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCc
Confidence            44454432  123577889999999999999999999999999999999999999999999974

>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]

Probab=84.33  E-value=3  Score=34.51  Aligned_cols=64  Identities=13%  Similarity=0.190  Sum_probs=45.5

Q ss_pred             HHHHHHHHHHHHHHcCcCc-cChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           32 FTVTKVAVSQICRSVGFKA-AESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        32 r~lLr~sVaqIL~~~GFds-a~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      ..+...=+-.|+-..|=+- --+.+++.|.+++..||.++...|   .+...|-..-+.|+..+|+.=
T Consensus         8 k~lF~Kdl~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a---~~~g~rgk~~veD~~f~lRkD   72 (109)
T KOG3901|consen    8 KHLFSKDLRSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAA---MEIGKRGKVKVEDFKFLLRKD   72 (109)
T ss_pred             HHHHHHHHHHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHH---HHhcccCceeHHHHHHHHHhC
Confidence            3555566666666444222 235678999999999999994444   455567778899999999884

>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]

Probab=82.11  E-value=4.6  Score=34.39  Aligned_cols=69  Identities=22%  Similarity=0.327  Sum_probs=56.3

Q ss_pred             CCCCchHHHHHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           23 GEETPSEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        23 ~~~s~defar~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      .-.+-..|+.++|+.+.    -..|   +...|+..+-..+-..++.|+..+.++|...+|+..+..++..|++-+
T Consensus        35 ~~e~~s~yv~kvlk~Vh----pd~g---is~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl  103 (127)
T KOG1744|consen   35 RKESYSEYVYKVLKQVH----PDLG---ISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL  103 (127)
T ss_pred             ccCceeeehhhhhhccc----CCCC---cCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence            34555566666665544    4445   888888888888888899999999999999999999999999999987

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

Probab=80.99  E-value=5.6  Score=34.81  Aligned_cols=67  Identities=10%  Similarity=0.150  Sum_probs=57.1

Q ss_pred             HHHHHHHHHHHHHH-HcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473           31 AFTVTKVAVSQICR-SVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS  100 (281)
Q Consensus        31 ar~lLr~sVaqIL~-~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi  100 (281)
                      .++.+...|.-||- ..   .+...|-|.|-+....||..|++.|...|+--.+-...+..|..||+.+|.
T Consensus        14 PkAtv~KmIke~lP~d~---rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF   81 (156)
T KOG0871|consen   14 PKATVNKMIKEMLPKDV---RVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGF   81 (156)
T ss_pred             cHHHHHHHHHHhCCccc---ccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcch
Confidence            34666667777765 33   456789999999999999999999999999999999999999999999963

>smart00427 H2B Histone H2B

Probab=80.66  E-value=9  Score=30.75  Aligned_cols=64  Identities=14%  Similarity=0.266  Sum_probs=53.5

Q ss_pred             hHHHHHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           28 SEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        28 defar~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      .-|..++|+    |+....   +++..|+..+..++...++.|+..|...+....|...+..+|..|.+.+
T Consensus         4 ~~Yi~kvLK----qVhpd~---giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~   67 (89)
T smart00427        4 AIYIYKVLK----QVHPDT---GISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI   67 (89)
T ss_pred             HHHHHHHHH----HhCCCc---cccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence            345555555    444444   5788999999999999999999999999999999999999999998887

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	281
1tzy_D	103	Histone H4-VI; histone-fold, tetramer-dimer-dimer,	98.85
2yfw_B	103	Histone H4, H4; cell cycle, kinetochore, centromer	98.83
1taf_A	68	TFIID TBP associated factor 42; transcription init	98.76
1id3_B	102	Histone H4; nucleosome core particle, chromatin, p	98.64
2hue_C	84	Histone H4; mini beta sheet, elongated beta sandwh	98.63
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	98.43
3b0b_B	107	CENP-S, centromere protein S; histone fold, DNA bi	98.41
3v9r_A	90	MHF1, uncharacterized protein YOL086W-A; histone f	98.4
4dra_A	113	Centromere protein S; DNA binding complex, DNA dam	98.38
1taf_B	70	TFIID TBP associated factor 62; transcription init	98.32
3vh5_A	140	CENP-S; histone fold, chromosome segregation, DNA	98.32
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	98.25
2ly8_A	121	Budding yeast chaperone SCM3; centromere protein,	97.9
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	97.88
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	97.66
1n1j_A	93	NF-YB; histone-like PAIR, DNA binding protein; 1.6	97.65
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	97.61
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	97.6
2byk_B	128	Chrac-14; nucleosome sliding, histone fold, DNA-bi	97.37
1jfi_B	179	DR1 protein, transcription regulator NC2 beta chai	97.35
3b0c_W	76	CENP-W, centromere protein W; histone fold, DNA bi	97.21
3nqj_A	82	Histone H3-like centromeric protein A; alpha helix	96.58
2hue_B	77	Histone H3; mini beta sheet, elongated beta sandwh	96.56
3nqu_A	140	Histone H3-like centromeric protein A; alpha helix	96.5
3r45_A	156	Histone H3-like centromeric protein A; histone fol	96.27
2yfv_A	100	Histone H3-like centromeric protein CSE4; cell cyc	96.17
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	95.8
1tzy_C	136	Histone H3; histone-fold, tetramer-dimer-dimer, DN	95.72
2nqb_C	123	Histone H2A; nucleosome, NCP, chromatin, structura	94.81
2nqb_D	123	Histone H2B; nucleosome, NCP, chromatin, structura	94.57
2f8n_G	120	Core histone macro-H2A.1; nucleosome, NCP, macroh2	94.52
1tzy_A	129	Histone H2A-IV; histone-fold, tetramer-dimer-dimer	94.51
1tzy_B	126	Histone H2B; histone-fold, tetramer-dimer-dimer, D	94.44
1f66_C	128	Histone H2A.Z; nucleosome, chromatin, histone vari	94.36
2f8n_K	149	Histone H2A type 1; nucleosome, NCP, macroh2A, his	94.27
1id3_C	131	Histone H2A.1; nucleosome core particle, chromatin	94.01
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	93.57
4g92_C	119	HAPE; transcription factor, nucleosome, minor groo	92.05
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	92.05
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	91.07
1h3o_B	76	Transcription initiation factor TFIID 20/15 kDa su	89.1
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	87.59
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	83.78
4dra_E	84	Centromere protein X; DNA binding complex, DNA dam	80.1

>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=98.85  E-value=6.9e-09  Score=82.84  Aligned_cols=71  Identities=25%  Similarity=0.353  Sum_probs=65.5

Q ss_pred             HHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC-CCC
Q 023473           34 VTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSG-QGF  104 (281)
Q Consensus        34 lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~-~gF  104 (281)
                      +-...|..|++..|+..++..|.+.|+++++.|+.+|++.|..||+|++|+..+..||.+||+.+|.. .||
T Consensus        30 ip~~~I~Rlar~~G~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktIt~~DV~~Alr~~g~~lYGf  101 (103)
T 1tzy_D           30 ITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGF  101 (103)
T ss_dssp             SCHHHHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTTCEEESC
T ss_pred             CCHHHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHcCCCCcCC
Confidence            45568899999999999999999999999999999999999999999999999999999999999753 555

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

Probab=98.83  E-value=7.4e-09  Score=82.71  Aligned_cols=71  Identities=25%  Similarity=0.377  Sum_probs=63.1

Q ss_pred             HHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC-CCC
Q 023473           34 VTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSG-QGF  104 (281)
Q Consensus        34 lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~-~gF  104 (281)
                      +-...|..|++..|+..++..|.+.|+++++.|+.+|++.|..||+|++|+..++.||.+||+.+|.. .||
T Consensus        30 ip~~~I~Rlar~~G~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktvt~~DV~~Alr~~g~~lYGf  101 (103)
T 2yfw_B           30 ITKPAIRRLARRGGVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQGRTLYGF  101 (103)
T ss_dssp             CCHHHHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHC------
T ss_pred             CCHHHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHcCCCCcCC
Confidence            45668889999999999999999999999999999999999999999999999999999999999742 454

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

Probab=98.76  E-value=3.2e-08  Score=73.95  Aligned_cols=61  Identities=16%  Similarity=0.250  Sum_probs=58.9

Q ss_pred             HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473           37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND   97 (281)
Q Consensus        37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d   97 (281)
                      ++|.+||+++|-+..++.+...|.+++.+|..+|++.|..||+||||...+..||.+|...
T Consensus         5 ~~i~~iLk~~G~~~~~~~v~~~L~e~~~ry~~~il~dA~~~a~HAgrktv~~eDVkLAi~~   65 (68)
T 1taf_A            5 QVIMSILKELNVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLATEV   65 (68)
T ss_dssp             HHHHHHHHHTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHh
Confidence            5789999999999999999999999999999999999999999999999999999999875

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

Probab=98.64  E-value=8.4e-08  Score=76.63  Aligned_cols=67  Identities=22%  Similarity=0.349  Sum_probs=62.5

Q ss_pred             HHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473           34 VTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS  100 (281)
Q Consensus        34 lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi  100 (281)
                      +-..+|..|++..|...++..|.+.|.+++..||.+|++.|..||+|++|...+..||.+||+.+|-
T Consensus        29 ip~~~I~Rlar~~Gv~rIS~da~~~l~~~le~fi~~I~~dA~~~a~HakRKTVt~~DV~~ALkr~g~   95 (102)
T 1id3_B           29 ITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGR   95 (102)
T ss_dssp             SCHHHHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTTC
T ss_pred             CCHHHHHHHHHHcCchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHcCC
Confidence            4455788888999999999999999999999999999999999999999999999999999999863

>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=98.63  E-value=5.1e-08  Score=75.08  Aligned_cols=65  Identities=23%  Similarity=0.302  Sum_probs=61.2

Q ss_pred             HHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473           36 KVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS  100 (281)
Q Consensus        36 r~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi  100 (281)
                      ..+|..|++..|-..++..|.+.|.+++..||.++++.|..||+|++|...+..||.+||+.+|.
T Consensus        13 ~~~I~Riar~~Gv~rIs~da~~~l~~~l~~~~~~I~~dA~~~a~ha~RKTvt~~DV~~Alk~~g~   77 (84)
T 2hue_C           13 KPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR   77 (84)
T ss_dssp             HHHHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTTCE
T ss_pred             HHHHHHHHHHcCchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHcCC
Confidence            34678889999999999999999999999999999999999999999999999999999999863

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

Probab=98.43  E-value=6.2e-07  Score=66.45  Aligned_cols=60  Identities=20%  Similarity=0.329  Sum_probs=56.9

Q ss_pred             HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Q 023473           37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALN   96 (281)
Q Consensus        37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~   96 (281)
                      ..|..|+++.|=..+++.|.+.|.+++..|+..|.+.|..||+|+||...+..||.+|++
T Consensus        10 a~v~Rl~r~~g~~ris~~a~~~l~e~~~~~~~~v~~dA~~~a~hakRkTI~~~DV~lA~~   69 (70)
T 1ku5_A           10 APVDRLIRKAGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIK   69 (70)
T ss_dssp             HHHHHHHHHTTCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHT
T ss_pred             HHHHHHHHHcCcceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence            467788888999999999999999999999999999999999999999999999999985

>3b0b_B CENP-S, centromere protein S; histone fold, DNA binding, DNA, nucleus, DNA binding protein; 2.15A {Gallus gallus}

Probab=98.41  E-value=4.3e-07  Score=73.36  Aligned_cols=68  Identities=10%  Similarity=0.133  Sum_probs=63.0

Q ss_pred             HHHHHHHHHHHHHHcCc---CccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcC
Q 023473           32 FTVTKVAVSQICRSVGF---KAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVS   99 (281)
Q Consensus        32 r~lLr~sVaqIL~~~GF---dsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmG   99 (281)
                      .+-|.-+|.+||++.|=   ..+++.++..|++++.+|+..|+..+..||.||||...+..||.+|++...
T Consensus        18 Kaal~~~V~rI~~~~g~~~~~~vs~~~i~aL~E~~~~~~~~ia~Da~~fA~HAgRkTI~~eDV~La~Rrn~   88 (107)
T 3b0b_B           18 RAAVHYTTGCLCQDVAEDKGVLFSKQTVAAISEITFRQCENFARDLEMFARHAKRSTITSEDVKLLARRSN   88 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTCH
T ss_pred             HHHHHHHHHHHHHHHhhhcCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcCcCCHHHHHHHHHhCH
Confidence            45666779999999997   689999999999999999999999999999999999999999999999863

>3v9r_A MHF1, uncharacterized protein YOL086W-A; histone fold, fanconi anemia, DNA repair, DNA BI protein; 2.40A {Saccharomyces cerevisiae}

Probab=98.40  E-value=8.8e-07  Score=69.48  Aligned_cols=68  Identities=18%  Similarity=0.061  Sum_probs=61.0

Q ss_pred             HHHHHHHHHHHHHHHcCc---CccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           31 AFTVTKVAVSQICRSVGF---KAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        31 ar~lLr~sVaqIL~~~GF---dsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      ..+-|.-+|++||++..=   -.+++.++..|++++.+|+.+|+..+..||.||||...+..||.++++..
T Consensus        10 LKaal~~~V~ki~~e~~~~~g~~vs~~~i~aL~e~~~~~~~~ia~Dl~~fA~HAgRkTI~~eDV~L~~Rrn   80 (90)
T 3v9r_A           10 LKARLWIRVEERLQQVLSSEDIKYTPRFINSLLELAYLQLGEMGSDLQAFARHAGRGVVNKSDLMLYLRKQ   80 (90)
T ss_dssp             HHHHHHHHHHHHHHHHSCSSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHHHHHHHHhcCceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhC
Confidence            456788899999998832   13999999999999999999999999999999999999999999998874

>4dra_A Centromere protein S; DNA binding complex, DNA damage repair, histone-fold, DNA BI protein; 2.41A {Homo sapiens} PDB: 4drb_A

Probab=98.38  E-value=5.6e-07  Score=73.29  Aligned_cols=76  Identities=11%  Similarity=0.140  Sum_probs=68.3

Q ss_pred             CCCCchHHHHHHHHHHHHHHHHHcCcCc---cChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           23 GEETPSEFAFTVTKVAVSQICRSVGFKA---AESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        23 ~~~s~defar~lLr~sVaqIL~~~GFds---a~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      -..+..+-..+-|.-+|+.||++.|=+.   +++.++..|++++.+|+.+|+..+..||.||||..++..||.++++..
T Consensus        17 ~~~~~~~rLKaal~y~V~rIvke~gaer~~~vS~~ai~aL~El~~~~~~~ia~Dl~~fAkHAgRkTI~~eDV~La~Rr~   95 (113)
T 4dra_A           17 QRFSYQQRLKAAVHYTVGCLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARRS   95 (113)
T ss_dssp             --CCHHHHHHHHHHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTC
T ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHhC
Confidence            3445556667888999999999999887   999999999999999999999999999999999999999999999886

>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=98.32  E-value=2.1e-06  Score=64.41  Aligned_cols=60  Identities=20%  Similarity=0.285  Sum_probs=57.5

Q ss_pred             HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Q 023473           37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALN   96 (281)
Q Consensus        37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~   96 (281)
                      ..|-.|.+++|.+..+..|...|++-++.++.+|++.|..||.|++|+..+..||.+||+
T Consensus        10 ~~v~~iaes~Gi~~lsddaa~~LA~dvEyr~~eI~qeA~kfmrHakRk~Lt~~DI~~Alk   69 (70)
T 1taf_B           10 ESMKVIAESIGVGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLK   69 (70)
T ss_dssp             HHHHHHHHHTTCCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC
T ss_pred             HHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHc
Confidence            467889999999999999999999999999999999999999999999999999999985

>3vh5_A CENP-S; histone fold, chromosome segregation, DNA binding, nucleus, binding protein; 2.40A {Gallus gallus} PDB: 3vh6_A

Probab=98.32  E-value=1.2e-06  Score=73.65  Aligned_cols=68  Identities=9%  Similarity=0.106  Sum_probs=62.3

Q ss_pred             HHHHHHHHHHHHHHcCcCc---cChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcC
Q 023473           32 FTVTKVAVSQICRSVGFKA---AESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVS   99 (281)
Q Consensus        32 r~lLr~sVaqIL~~~GFds---a~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmG   99 (281)
                      .+-|.-+|++||++.|=+.   +++.++..|++++.+|+.+|+..+..||.||||..++..||.++++...
T Consensus        18 KaAl~y~VgkIvee~~~~~~~~vS~~ai~aL~El~~~~~e~ia~DLe~FAkHAGRKTI~~eDVkLa~Rrn~   88 (140)
T 3vh5_A           18 RAAVHYTTGALAQDVAEDKGVLFSKQTVAAISEITFRQAENFARDLEMFARHAKRSTITSEDVKLLARRSN   88 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTSH
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhCH
Confidence            4667788999999887654   9999999999999999999999999999999999999999999999863

>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=98.25  E-value=2.3e-06  Score=69.27  Aligned_cols=64  Identities=17%  Similarity=0.237  Sum_probs=59.3

Q ss_pred             HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473           37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS  100 (281)
Q Consensus        37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi  100 (281)
                      -+|..|.+..|=..++..|.+.|.+++..|+..+++.+..||+||||...+..||.+||+..|-
T Consensus        11 a~I~Ri~r~~g~~rIS~~a~~~l~e~l~~f~~~v~~da~~~A~HA~RKTV~~eDV~lalrr~g~   74 (111)
T 3b0c_T           11 SLIKQIFSHYVKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAGRKTVEMADVELLMRRQGL   74 (111)
T ss_dssp             HHHHHHHHHHHCSCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHCCC
Confidence            4566677777889999999999999999999999999999999999999999999999999974

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

Probab=97.90  E-value=2.5e-05  Score=64.30  Aligned_cols=78  Identities=17%  Similarity=0.221  Sum_probs=62.9

Q ss_pred             chHHHHHHHHHHHHHHH--HHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC-CC
Q 023473           27 PSEFAFTVTKVAVSQIC--RSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSG-QG  103 (281)
Q Consensus        27 ~defar~lLr~sVaqIL--~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~-~g  103 (281)
                      .++|.-.++..+-.-.+  .-.|-..++..+-+.+.+++..|+++|.+.+-.|++||+|-..+..||.+||+..|.- .|
T Consensus        39 sEayLV~lFEd~nlcaiHA~~gGvkRIS~~iy~e~r~vl~~~l~~i~rdav~yaehA~RKTVta~DV~~Alkr~G~~lyg  118 (121)
T 2ly8_A           39 SEAYLVGLLEHTNLLALHLVPRGSKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYG  118 (121)
T ss_dssp             HHHHHHHHHHHHHHHTTTCCCCCSSCCSSCHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCBCHHHHHHHHHHTTCGGGG
T ss_pred             HHHHHHHHHHHHhHHHHcCCccCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHhCCCcCCC
Confidence            34444455554322222  4568899999999999999999999999999999999999999999999999999853 44


Q ss_pred             C
Q 023473          104 F  104 (281)
Q Consensus       104 F  104 (281)
                      |
T Consensus       119 f  119 (121)
T 2ly8_A          119 F  119 (121)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=97.88  E-value=4.5e-05  Score=55.78  Aligned_cols=60  Identities=20%  Similarity=0.195  Sum_probs=54.4

Q ss_pred             HHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           39 VSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        39 VaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      |..|+++.|=..++..|++.|.+.++.||..|...|..+|.|++|...+..||..|++.+
T Consensus         8 v~Ri~k~~~~~ris~~A~~~l~~a~e~fi~~l~~~A~~~a~~~kRkTI~~~Di~~A~~~l   67 (68)
T 1b67_A            8 IGRIIKNAGAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARKMF   67 (68)
T ss_dssp             HHHHHHHTTCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHGGGG
T ss_pred             HHHHHhcCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhc
Confidence            445555557788999999999999999999999999999999999999999999999876

>2l5a_A Histone H3-like centromeric protein CSE4, protein histone H4; A single chain of CSE4+SCM3+H4, fusion protein; NMR {Saccharomyces cerevisiae}

Probab=97.66  E-value=3.3e-05  Score=69.85  Aligned_cols=69  Identities=17%  Similarity=0.224  Sum_probs=61.2

Q ss_pred             HHHHHHHHHH----HHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcC
Q 023473           31 AFTVTKVAVS----QICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVS   99 (281)
Q Consensus        31 ar~lLr~sVa----qIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmG   99 (281)
                      ...+|+..|-    .|++..|-..++..|-+.+.+++..|+++|++.|-.||+||+|...+..||.+||..+|
T Consensus       155 ~~~vLrD~i~i~~~RlaRrgGVkRIS~~iyeelr~vLe~fle~IirdAv~yaeHA~RKTVta~DV~~ALKr~g  227 (235)
T 2l5a_A          155 YTSVLRDIIDISDEEDGDKGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQG  227 (235)
T ss_dssp             HHHHHHHHHHHTCCTTSCCTTCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHH
T ss_pred             HHHHHHHhhcccHHHHhhcCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHhcC
Confidence            3455554443    55688899999999999999999999999999999999999999999999999999986

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

Probab=97.65  E-value=0.00033  Score=54.35  Aligned_cols=63  Identities=17%  Similarity=0.187  Sum_probs=56.2

Q ss_pred             HHHHHHHHcCc--CccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473           38 AVSQICRSVGF--KAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS  100 (281)
Q Consensus        38 sVaqIL~~~GF--dsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi  100 (281)
                      .|..|+++.|=  ..++..|++.|++.+..||..|+..|..+|.+++|-..+..||..|++.+|.
T Consensus        13 ~i~ri~K~~~~~~~~is~dA~~~l~~a~e~Fi~~l~~~A~~~a~~~kRkTI~~~Dv~~Al~~l~F   77 (93)
T 1n1j_A           13 NVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGF   77 (93)
T ss_dssp             HHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhCCccceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHcCc
Confidence            45566666643  6799999999999999999999999999999999999999999999999863

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

Probab=97.61  E-value=0.00014  Score=62.11  Aligned_cols=62  Identities=21%  Similarity=0.310  Sum_probs=58.5

Q ss_pred             HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      ..|..|++..|=..++..|-+.|.+++..|+..|++.|..||+|++|...+..||.+||+..
T Consensus        86 a~V~Ri~k~~g~~RVS~~A~~~l~~~le~f~~~I~~~A~~~a~ha~RKTIt~eDV~~Al~~~  147 (154)
T 1f1e_A           86 ATVRRILKRAGIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITYS  147 (154)
T ss_dssp             HHHHHHHHHTTCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             cHHHHHHHHcCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhc
Confidence            45777888889999999999999999999999999999999999999999999999999986

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

Probab=97.60  E-value=0.00014  Score=61.94  Aligned_cols=64  Identities=16%  Similarity=0.097  Sum_probs=60.2

Q ss_pred             HHHHHHHHHc-CcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473           37 VAVSQICRSV-GFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS  100 (281)
Q Consensus        37 ~sVaqIL~~~-GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi  100 (281)
                      ..|..|++.. |=..++..|-+.|.+++..|+..|++.|..||+|+||...+..||..||..+|.
T Consensus         8 a~V~Riik~~lg~~rVS~dA~~~l~~~l~~f~~~i~~~A~~~a~ha~RKTv~a~DV~~a~~~lg~   72 (154)
T 1f1e_A            8 AAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADVLMV   72 (154)
T ss_dssp             HHHHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHHHTC
T ss_pred             cHHHHHHHhcCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhccc
Confidence            4577788888 999999999999999999999999999999999999999999999999999964

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

Probab=97.37  E-value=0.0012  Score=54.38  Aligned_cols=63  Identities=10%  Similarity=0.168  Sum_probs=56.5

Q ss_pred             HHHHHHHHcC--cCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473           38 AVSQICRSVG--FKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS  100 (281)
Q Consensus        38 sVaqIL~~~G--Fdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi  100 (281)
                      .|..|++.++  -..++..|...|+..+..||..|+..|..+|.+.+|-..+..||..||..++.
T Consensus        14 ~I~rImK~~~pd~~~iS~dA~~~l~ka~e~FI~~lt~~A~~~a~~~kRKTI~~~Dv~~Al~~l~f   78 (128)
T 2byk_B           14 VIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDF   78 (128)
T ss_dssp             HHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhCcccceECHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHcCc
Confidence            3556666544  57899999999999999999999999999999999999999999999999974

>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=97.35  E-value=0.00095  Score=58.18  Aligned_cols=63  Identities=11%  Similarity=0.168  Sum_probs=55.8

Q ss_pred             HHHHHHHHcC-cCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473           38 AVSQICRSVG-FKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS  100 (281)
Q Consensus        38 sVaqIL~~~G-Fdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi  100 (281)
                      .|..|+++++ =..++..|.+.|++.+..||..|+..|...|.+.+|-..+..||..||.++|.
T Consensus        20 ~V~RImK~alp~~rISkDA~~al~ec~~eFI~~LtseA~e~a~~~~RKTI~~eDVl~Al~~LgF   83 (179)
T 1jfi_B           20 AINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALESLGF   83 (179)
T ss_dssp             HHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhcCh
Confidence            4555555554 26899999999999999999999999999999999999999999999999974

>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=97.21  E-value=0.0014  Score=49.08  Aligned_cols=50  Identities=12%  Similarity=0.016  Sum_probs=48.0

Q ss_pred             CccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           49 KAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        49 dsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      ..++..|.+.|.+.+..|+..|+..|...|.+++|...+..||..|++++
T Consensus        21 ~~is~~A~~~i~~~~~~Fi~~la~eA~~~a~~~~rKTI~~~dI~~A~~~l   70 (76)
T 3b0c_W           21 LRLAANTDLLVHLSFLLFLHRLAEEARTNAFENKSKIIKPEHTIAAAKVI   70 (76)
T ss_dssp             CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSBCHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            46889999999999999999999999999999999999999999999986

>3nqj_A Histone H3-like centromeric protein A; alpha helix, histone fold, centromere, DNA binding protein; 2.10A {Homo sapiens}

Probab=96.58  E-value=0.016  Score=44.47  Aligned_cols=52  Identities=21%  Similarity=0.011  Sum_probs=48.5

Q ss_pred             CccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473           49 KAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS  100 (281)
Q Consensus        49 dsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi  100 (281)
                      ...+++|++.|.+..+.|+..|.+.+...|.||+|....+.|+.+|.+--|.
T Consensus        26 ~R~q~~Al~aLQea~E~ylv~Lfeda~lcAiHAkRvTi~~kDiqLa~rirg~   77 (82)
T 3nqj_A           26 FNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIRGL   77 (82)
T ss_dssp             CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHC-
T ss_pred             ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHHHHHHHHHccc
Confidence            4789999999999999999999999999999999999999999999887664

>2hue_B Histone H3; mini beta sheet, elongated beta sandwhich, DNA binding prote; 1.70A {Xenopus laevis}

Probab=96.56  E-value=0.011  Score=45.01  Aligned_cols=53  Identities=21%  Similarity=0.033  Sum_probs=49.0

Q ss_pred             CcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcC
Q 023473           47 GFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVS   99 (281)
Q Consensus        47 GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmG   99 (281)
                      |=...+.+|++.|.+..+.|+..|.+.+...|.||+|....+.|+.+|.+--|
T Consensus        22 ~~~R~q~~Al~aLQea~Eaylv~lfeda~l~A~HAkRvTi~~kDiqLa~rirg   74 (77)
T 2hue_B           22 TDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRG   74 (77)
T ss_dssp             SSCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTT
T ss_pred             ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHhhHHHHHHHhC
Confidence            44678999999999999999999999999999999999999999999987654

>3nqu_A Histone H3-like centromeric protein A; alpha helix, histone fold, centromere, DNA binding protein; 2.50A {Homo sapiens} PDB: 3an2_A

Probab=96.50  E-value=0.01  Score=49.77  Aligned_cols=53  Identities=21%  Similarity=0.006  Sum_probs=48.7

Q ss_pred             CccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC
Q 023473           49 KAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSG  101 (281)
Q Consensus        49 dsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~  101 (281)
                      ...+.+|++.|.+..+.||..|.+.+...|.||+|....+.|+.+|..--|+.
T Consensus        84 ~Rfq~~Al~ALQEAaEayLv~LFEdanlcAiHAkRVTIm~kDiqLArrirg~~  136 (140)
T 3nqu_A           84 FNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIRGLE  136 (140)
T ss_dssp             CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHC--
T ss_pred             ceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHHHHhcccc
Confidence            47899999999999999999999999999999999999999999999877753

>3r45_A Histone H3-like centromeric protein A; histone fold, centromere, CENP-A, histone chaperone, hjurp; 2.60A {Homo sapiens}

Probab=96.27  E-value=0.011  Score=50.57  Aligned_cols=64  Identities=20%  Similarity=0.054  Sum_probs=53.2

Q ss_pred             HHHHHHHHHHcC---cCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcC
Q 023473           36 KVAVSQICRSVG---FKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVS   99 (281)
Q Consensus        36 r~sVaqIL~~~G---Fdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmG   99 (281)
                      .+.|-.|.+...   =...+.+|++.|.+..+.||..|.+.+...|.||+|....+.|+.+|..--|
T Consensus        84 ~RLVREIa~~~~~~~~lRfqs~Al~ALQEAaEayLV~LFEdanLcAiHAkRVTIm~kDIqLArrIrg  150 (156)
T 3r45_A           84 SRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIRG  150 (156)
T ss_dssp             HHHHHHHHHTTTTTCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSEECHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccCccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHHHHHcc
Confidence            344555554422   2378999999999999999999999999999999999999999999987654

>2yfv_A Histone H3-like centromeric protein CSE4; cell cycle, kinetochore, centromere, histone chaperone, BUDD; 2.32A {Kluyveromyces lactis nrrl y-1140} PDB: 2yfw_A

Probab=96.17  E-value=0.013  Score=46.46  Aligned_cols=48  Identities=21%  Similarity=0.094  Sum_probs=45.3

Q ss_pred             CccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Q 023473           49 KAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALN   96 (281)
Q Consensus        49 dsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~   96 (281)
                      ...+.+|++.|.+..+.||..|...+...|.||+|....+-|+.+|.+
T Consensus        51 ~R~q~~Al~ALQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa~r   98 (100)
T 2yfv_A           51 LRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARR   98 (100)
T ss_dssp             CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             hhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHHH
Confidence            468999999999999999999999999999999999999999999864

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

Probab=95.80  E-value=0.023  Score=44.36  Aligned_cols=62  Identities=16%  Similarity=0.124  Sum_probs=56.6

Q ss_pred             HHHHHHHHcCc-CccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcC
Q 023473           38 AVSQICRSVGF-KAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVS   99 (281)
Q Consensus        38 sVaqIL~~~GF-dsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmG   99 (281)
                      -|..|++..+. ..++..|...|+..++.|+.+|+..|...|...+|...+..||.+|.....
T Consensus        24 rIkrImK~~~~~~~is~eA~~~laka~E~Fi~~l~~~A~~~a~~~krktI~~~di~~Av~~~e   86 (97)
T 1n1j_B           24 RIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFD   86 (97)
T ss_dssp             HHHHHHTTSTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTCG
T ss_pred             HHHHHHccCccccccChHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHHhcCc
Confidence            36778888877 679999999999999999999999999999999999999999999998864

>1tzy_C Histone H3; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1eqz_C 1hq3_C 2aro_C 2f8n_A 2hio_C 3av1_A 3lel_A 3afa_A 3azi_A 3azj_A 3azk_A 3azl_A 3azm_A 3azn_A 2cv5_A* 1u35_A* 2nqb_A 2io5_B 2pyo_A* 3c9k_C ...

Probab=95.72  E-value=0.034  Score=46.39  Aligned_cols=53  Identities=21%  Similarity=0.028  Sum_probs=49.1

Q ss_pred             CcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcC
Q 023473           47 GFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVS   99 (281)
Q Consensus        47 GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmG   99 (281)
                      |=...+.+|++.|.+..+.||..|...+...|.||+|....+-|+.+|..--|
T Consensus        81 ~~~R~q~~Al~aLQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa~rirg  133 (136)
T 1tzy_C           81 TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG  133 (136)
T ss_dssp             TTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHT
T ss_pred             hhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHhHHHHHHHhC
Confidence            44688999999999999999999999999999999999999999999987654

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

Probab=94.81  E-value=0.081  Score=43.24  Aligned_cols=58  Identities=12%  Similarity=0.025  Sum_probs=53.1

Q ss_pred             HHHHHHc-CcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473           40 SQICRSV-GFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND   97 (281)
Q Consensus        40 aqIL~~~-GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d   97 (281)
                      -.+|+.. +...+...|-..|+.+++.+..+|...|-.+|.+++|...++.||.+|..+
T Consensus        30 ~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hi~lAI~n   88 (123)
T 2nqb_C           30 HRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN   88 (123)
T ss_dssp             HHHHHHTTSCSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT
T ss_pred             HHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHHHHHhc
Confidence            3446664 888999999999999999999999999999999999999999999999886

>2nqb_D Histone H2B; nucleosome, NCP, chromatin, structural protein/DNA complex; 2.30A {Drosophila melanogaster} PDB: 2pyo_D*

Probab=94.57  E-value=0.13  Score=42.29  Aligned_cols=67  Identities=19%  Similarity=0.284  Sum_probs=56.8

Q ss_pred             CCCchHHHHHHHHHHHHHHHHHcCcC-ccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           24 EETPSEFAFTVTKVAVSQICRSVGFK-AAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        24 ~~s~defar~lLr~sVaqIL~~~GFd-sa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      ..+-.-|+.++|+        +++-+ +++..|++.|..++...++.|+..|...|.+++|...+..||..|.+.+
T Consensus        32 ~esy~~YIyKVLK--------QVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtAvrLl   99 (123)
T 2nqb_D           32 KESYAIYIYTVLK--------QVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLL   99 (123)
T ss_dssp             CCCSHHHHHHHHH--------HHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHH--------HhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHHHh
Confidence            3455555555554        44555 7899999999999999999999999999999999999999999999887

>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=94.52  E-value=0.1  Score=42.50  Aligned_cols=58  Identities=7%  Similarity=-0.055  Sum_probs=52.9

Q ss_pred             HHHHHHcC-cCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473           40 SQICRSVG-FKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND   97 (281)
Q Consensus        40 aqIL~~~G-Fdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d   97 (281)
                      ..+|+..+ ...+...|-..|+.+++.+..+|...|-.+|.+++|+..++.||.+|..+
T Consensus        29 ~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~~rItp~hi~lAI~n   87 (120)
T 2f8n_G           29 LRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILLAVAN   87 (120)
T ss_dssp             HHHHHHHSSSCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT
T ss_pred             HHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHHHHhc
Confidence            34577777 57899999999999999999999999999999999999999999999885

>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=94.51  E-value=0.1  Score=42.97  Aligned_cols=67  Identities=12%  Similarity=0.025  Sum_probs=56.9

Q ss_pred             HHHHHHHHH---HHHHHH-cCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473           31 AFTVTKVAV---SQICRS-VGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND   97 (281)
Q Consensus        31 ar~lLr~sV---aqIL~~-~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d   97 (281)
                      .++-|+--|   -.+|+. .+...+...|-..|+.+++.+..+|...|-.+|.+++|...++.||.+|..+
T Consensus        20 ~ragLqfPV~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hi~lAI~n   90 (129)
T 1tzy_A           20 SRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRN   90 (129)
T ss_dssp             HHHTCSSCHHHHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT
T ss_pred             ccCceeccHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEcHHHHHHHHhc
Confidence            444444333   344666 4888999999999999999999999999999999999999999999999886

>1tzy_B Histone H2B; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1eqz_B 1hq3_B 2aro_B 2hio_B 3c9k_B 3azg_D 3a6n_D 3an2_D 3av1_D 3av2_D 3ayw_D 3aze_D 3azf_D 3afa_D 3azh_D 3azi_D 3azj_D 3azk_D 3azl_D 3azm_D ...

Probab=94.44  E-value=0.14  Score=42.24  Aligned_cols=67  Identities=18%  Similarity=0.271  Sum_probs=56.6

Q ss_pred             CCCchHHHHHHHHHHHHHHHHHcCcC-ccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           24 EETPSEFAFTVTKVAVSQICRSVGFK-AAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        24 ~~s~defar~lLr~sVaqIL~~~GFd-sa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      ..+-.-|+.++|        ++++-| +++..|++.|..++...++.|+..|...|..+.|...+..||..|.+.+
T Consensus        35 ~esy~~YIyKVL--------KQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtAvrLl  102 (126)
T 1tzy_B           35 KESYSIYVYKVL--------KQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLL  102 (126)
T ss_dssp             CCCCHHHHHHHH--------HHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             cccHHHHHHHHH--------HHhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            344455555544        455555 7999999999999999999999999999999999999999999999887

>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=94.36  E-value=0.11  Score=42.74  Aligned_cols=68  Identities=10%  Similarity=-0.063  Sum_probs=58.2

Q ss_pred             HHHHHHHHHH---HHHHHHcCc--CccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473           30 FAFTVTKVAV---SQICRSVGF--KAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND   97 (281)
Q Consensus        30 far~lLr~sV---aqIL~~~GF--dsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d   97 (281)
                      -.++-|+--|   ..+|+..++  ..+...|--.|+.+++.+..+|...|-.+|..++|+..++.||.+|..+
T Consensus        21 S~ragLqfPV~ri~R~Lk~~~~a~~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItprhi~lAI~n   93 (128)
T 1f66_C           21 SQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG   93 (128)
T ss_dssp             HHHHTCSSCHHHHHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHH
T ss_pred             cccCCccCChHHHHHHHHHcccchhhccccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEcHHHHHHHHhc
Confidence            3455554444   456888885  3899999999999999999999999999999999999999999999987

>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=94.27  E-value=0.12  Score=43.77  Aligned_cols=68  Identities=12%  Similarity=0.004  Sum_probs=57.7

Q ss_pred             HHHHHHHHH---HHHHHHHc-CcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473           30 FAFTVTKVA---VSQICRSV-GFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND   97 (281)
Q Consensus        30 far~lLr~s---VaqIL~~~-GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d   97 (281)
                      -.++-|+--   |..+|+.. +...+...|-..|+.+++.+..+|...|-.+|..++|...++.||.+|...
T Consensus        38 S~ragLqFPVgrI~R~LK~~~~a~RVs~~A~VyLAAVLEYL~aEILelAgn~A~~~krkrItprhI~lAI~n  109 (149)
T 2f8n_K           38 SSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRN  109 (149)
T ss_dssp             HHHHTCSSCHHHHHHHHHHTTSCSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             cccCCeeccHHHHHHHHHccccccccCcCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHhc
Confidence            344445433   34456664 888999999999999999999999999999999999999999999999986

>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=94.01  E-value=0.12  Score=42.79  Aligned_cols=58  Identities=16%  Similarity=0.046  Sum_probs=52.8

Q ss_pred             HHHHHH-cCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473           40 SQICRS-VGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND   97 (281)
Q Consensus        40 aqIL~~-~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d   97 (281)
                      ..+|+. .+...+...|-..|+.+++.+..+|...|-.+|.+++|+..++.||.+|..+
T Consensus        32 ~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hI~lAI~n   90 (131)
T 1id3_C           32 HRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRHLQLAIRN   90 (131)
T ss_dssp             HHHHHTTCSCSEECSSHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT
T ss_pred             HHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHHHHhc
Confidence            445555 4788999999999999999999999999999999999999999999999986

>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=93.57  E-value=0.088  Score=41.15  Aligned_cols=60  Identities=8%  Similarity=0.107  Sum_probs=50.4

Q ss_pred             HHHHHHHcCc-CccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           39 VSQICRSVGF-KAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        39 VaqIL~~~GF-dsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      |-.|++..+. ..++..|.-.|+..++-|+.+|...|..+|...+|...+..||.+|.+..
T Consensus        17 IkrimK~~~~~~~vs~~A~v~la~a~E~Fi~el~~~A~~~a~~~krktI~~~di~~av~~~   77 (98)
T 1jfi_A           17 IKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQCIELE   77 (98)
T ss_dssp             HHHHHTTSTTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC---CBCHHHHHTTCC--
T ss_pred             HHHHHHcCccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHhcC
Confidence            5677777766 78999999999999999999999999999999999999999999888764

>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=92.05  E-value=0.35  Score=38.97  Aligned_cols=53  Identities=17%  Similarity=0.116  Sum_probs=49.6

Q ss_pred             cCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           46 VGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        46 ~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      -....++..|...++..++-||..|...|...|...+|...+..||..|+...
T Consensus        55 ~~~~~is~eA~v~la~a~E~Fi~~L~~~A~~~a~~~krktI~~~di~~Av~~~  107 (119)
T 4g92_C           55 PEVKMISAEAPILFAKGCDVFITELTMRAWIHAEDNKRRTLQRSDIAAALSKS  107 (119)
T ss_dssp             TTCCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTC
T ss_pred             CccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccCHHHHHHHHhcC
Confidence            44668999999999999999999999999999999999999999999999875

>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=92.05  E-value=0.76  Score=39.85  Aligned_cols=59  Identities=8%  Similarity=0.174  Sum_probs=51.4

Q ss_pred             HHHHHHcCc-CccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           40 SQICRSVGF-KAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        40 aqIL~~~GF-dsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      -.+|++++- .+++..|++.|..++.+.+..|+..|...+..+.|...+..||..|.+-+
T Consensus        10 ~kvLkqv~p~~~iS~~Am~~m~s~v~di~~rIa~eA~~L~~~~~r~Tit~~eIq~Avrl~   69 (192)
T 2jss_A           10 YKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLI   69 (192)
T ss_dssp             HHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCSCCHHHHHHHHHHH
T ss_pred             HHHHcccCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHh
Confidence            334444443 55999999999999999999999999999999999999999999999876

>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=91.07  E-value=0.66  Score=40.25  Aligned_cols=58  Identities=14%  Similarity=-0.025  Sum_probs=51.6

Q ss_pred             HHHHHHc-Cc-CccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473           40 SQICRSV-GF-KAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND   97 (281)
Q Consensus        40 aqIL~~~-GF-dsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d   97 (281)
                      ..+|+.. +. ..+...|-..|+.+++.+..+|...|-.+|.+++|...++.|+.+|...
T Consensus       112 ~R~lk~~~~a~~Rv~~~A~vyLaavLEyl~~eIlelA~n~a~~~~~~~I~p~~i~lAi~n  171 (192)
T 2jss_A          112 KRYLKRHATGRTRVGSKAAIYLTAVLEYLTAEVLELAGNAAKDLKVKRITPRHLQLAIRG  171 (192)
T ss_dssp             HHHHHHTTCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCHHHHHHHHHT
T ss_pred             HHHHHhcCccccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhc
Confidence            3456665 44 4899999999999999999999999999999999999999999999885

>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=89.10  E-value=1.4  Score=33.10  Aligned_cols=64  Identities=13%  Similarity=0.125  Sum_probs=54.7

Q ss_pred             HHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           32 FTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        32 r~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      ..-|+..|-||.   +=....+.+-|.|.+|+..|+..+...+.+.|-|-+-....+-||.+.|+..
T Consensus         8 k~~L~~Lv~~id---p~~~ld~~vee~ll~lADdFV~~V~~~ac~lAKhR~s~~le~kDvql~Ler~   71 (76)
T 1h3o_B            8 KKKLQDLVREVD---PNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLERQ   71 (76)
T ss_dssp             HHHHHHHHHHHC---SSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC---CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHhh
Confidence            455666666664   4477889999999999999999999999999999888778999999999874

>2l5a_A Histone H3-like centromeric protein CSE4, protein histone H4; A single chain of CSE4+SCM3+H4, fusion protein; NMR {Saccharomyces cerevisiae}

Probab=87.59  E-value=1.2  Score=40.13  Aligned_cols=50  Identities=20%  Similarity=0.069  Sum_probs=46.9

Q ss_pred             ccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcC
Q 023473           50 AAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVS   99 (281)
Q Consensus        50 sa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmG   99 (281)
                      ..+++|+.+|-+..+.||..|-..+...|.||.|....+-|+.+|.+--|
T Consensus        36 Rfqs~Al~ALQEAaEayLV~LFEd~nLcaiHAkRVTim~kDiqLarrirg   85 (235)
T 2l5a_A           36 RWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMKKDMQLARRIRG   85 (235)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTSGGGTTHHHHHHTSSC
T ss_pred             eecHHHHHHHHHHHHHHHHHHHhhhHHHHhcccccccchhhHHHHHHHhh
Confidence            57899999999999999999999999999999999999999999986655

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

Probab=83.78  E-value=1.9  Score=35.82  Aligned_cols=51  Identities=14%  Similarity=0.104  Sum_probs=47.9

Q ss_pred             CccChHHHHHHHHHHHHHHHHHHHHHHHHH-HhcCCCCCCHHHHHHHHHhcC
Q 023473           49 KAAESSALETLTLVAAKYLQQLASRAASYS-HVAHRSESNLVDLTNALNDVS   99 (281)
Q Consensus        49 dsa~~sALetLTdil~~YL~~Lg~sa~~yA-elaGRT~pnl~DV~~AL~dmG   99 (281)
                      ..++..|.-.++..++-||..|...|..+| ...+|...+..||..|+....
T Consensus        36 ~~Is~eA~vliakA~ElFI~~Lt~~A~~~a~~~~kRKtI~~~Dl~~AV~~~e   87 (140)
T 2byk_A           36 GLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNK   87 (140)
T ss_dssp             SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHHTCS
T ss_pred             ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccCHHHHHHHHhcCc
Confidence            579999999999999999999999999999 999999999999999999763

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

Probab=80.10  E-value=11  Score=28.69  Aligned_cols=62  Identities=18%  Similarity=0.263  Sum_probs=52.4

Q ss_pred             HHHHHHHHHHcCcC----ccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           36 KVAVSQICRSVGFK----AAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        36 r~sVaqIL~~~GFd----sa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      ...|+.||+ ..|.    .++..|+..+++.+.-|+.+-...|...|+.-|.......|++..+-++
T Consensus        15 ~~li~ril~-~~F~~~kTkIs~dAl~l~aeyl~iFV~EAv~RA~~~a~~e~~~~le~e~LEki~pQL   80 (84)
T 4dra_E           15 KELVSRLLH-LHFKDDKTKVSGDALQLMVELLKVFVVEAAVRGVRQAQAEDALRVDVDQLEKVLPQL   80 (84)
T ss_dssp             HHHHHHHHH-TTCSSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             HHHHHHHHH-HHhcCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHH
Confidence            345777777 6785    7899999999999999999999999989998888889999998877655

---

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	281
d2huec1	82	a.22.1.1 (C:20-101) Histone H4 {African clawed fro	9e-05

>d2huec1 a.22.1.1 (C:20-101) Histone H4 {African clawed frog (Xenopus laevis) [TaxId: 8355]} Length = 82

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]

 Score = 38.2 bits (89), Expect = 9e-05
 Identities = 16/62 (25%), Positives = 27/62 (43%)

Query: 34 VTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTN 93
          +TK A+ ++ R  G K       E    V   +L+ +   A +Y+  A R     +D+  
Sbjct: 10 ITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVY 69

Query: 94 AL 95
          AL
Sbjct: 70 AL 71

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	281
d2huec1	82	Histone H4 {African clawed frog (Xenopus laevis) [	98.46
d1tafa_	68	TAF(II)42 {Fruit fly (Drosophila melanogaster) [Ta	98.39
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	98.2
d1ku5a_	66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	97.76
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	97.44
d1tafb_	70	TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta	97.4
d2bykb1	89	Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax	97.24
d1n1ja_	87	Nuclear transcription factor Y subunit beta (Nf-Yb	97.2
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	96.66
d1jfib_	135	Negative cofactor 2, NC2, beta chain {Human (Homo	96.6
d1tzyc_	95	Histone H3 {Chicken (Gallus gallus), erythrocytes	95.25
d1q9ca_	172	Histone domain of Son of sevenless protein {Human	94.83
d1n1jb_	78	Nuclear transcription factor Y subunit gamma (Nf-Y	94.4
d1jfia_	66	Negative cofactor 2, NC2, alpha chain {Human (Homo	93.83
d1tzyb_	92	Histone H2B {Chicken (Gallus gallus), erythrocytes	86.32
d1h3ob_	74	TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom	85.14
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	81.29
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	81.01

>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=98.46  E-value=1.6e-07  Score=70.42  Aligned_cols=66  Identities=24%  Similarity=0.327  Sum_probs=62.1

Q ss_pred             HHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcC
Q 023473           34 VTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVS   99 (281)
Q Consensus        34 lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmG   99 (281)
                      +-+.+|-.|++++|...++..+.+.|.+++..||.+|.+.+..||+|++|...+..||..||..+|
T Consensus        10 I~k~~i~Riar~~Gv~ris~d~~~~l~~~l~~~l~~i~~~a~~~~~hakRKTvt~~DV~~Alkr~g   75 (82)
T d2huec1          10 ITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQG   75 (82)
T ss_dssp             SCHHHHHHHHHHTTCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTTC
T ss_pred             cCHHHHHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHhcC
Confidence            335678889999999999999999999999999999999999999999999999999999999875

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

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

Probab=98.39  E-value=7e-07  Score=64.94  Aligned_cols=61  Identities=16%  Similarity=0.250  Sum_probs=58.6

Q ss_pred             HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473           37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND   97 (281)
Q Consensus        37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d   97 (281)
                      ++|.+||++.|-+..++.....|.|.+-+|...+...|+-|++||||.+.+..||.+|..-
T Consensus         5 ~~i~~iL~~~GV~~yeprV~~qlLef~yRYtt~VL~DA~vys~HA~k~~id~dDVkLAi~~   65 (68)
T d1tafa_           5 QVIMSILKELNVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLATEV   65 (68)
T ss_dssp             HHHHHHHHHTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHh
Confidence            5789999999999999999999999999999999999999999999999999999999763

>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=98.20  E-value=4.3e-06  Score=59.63  Aligned_cols=61  Identities=20%  Similarity=0.194  Sum_probs=56.6

Q ss_pred             HHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           38 AVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        38 sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      .|-.|.++.|-..++..|.+.|+..+..||..|+..+..||++++|...+..||..||+.+
T Consensus         8 ~I~ri~k~~~~~ris~ea~~~l~~~~e~fi~~l~~~a~~~a~~~kRkTi~~~DV~~Alk~~   68 (68)
T d1htaa_           8 PIGRIIKNAGAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARKMF   68 (68)
T ss_dssp             HHHHHHHHTTCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHTC
T ss_pred             HHHHHHHHCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHhC
Confidence            4556777889999999999999999999999999999999999999999999999999863

>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=97.76  E-value=4.3e-05  Score=54.03  Aligned_cols=59  Identities=20%  Similarity=0.334  Sum_probs=54.4

Q ss_pred             HHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Q 023473           38 AVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALN   96 (281)
Q Consensus        38 sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~   96 (281)
                      .|-.|++..|=..++..|.+.|+..++.||..|+..+..||++++|-..+..||..||+
T Consensus         7 ~I~rI~k~~~~~ris~ea~~~l~~a~e~Fi~~l~~~a~~~a~~~~RKTI~~~Dv~~Al~   65 (66)
T d1ku5a_           7 PVDRLIRKAGAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIK   65 (66)
T ss_dssp             HHHHHHHHTTCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHT
T ss_pred             HHHHHHHhCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHh
Confidence            45566777788899999999999999999999999999999999999999999999986

>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=97.44  E-value=0.00018  Score=58.62  Aligned_cols=61  Identities=21%  Similarity=0.315  Sum_probs=56.3

Q ss_pred             HHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           38 AVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        38 sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      .|-.|+++.|...++..|++.|+..++.|+.+|...|..||.+++|...+..||.+|+...
T Consensus        84 ~IkRi~k~~g~~ris~dA~~~l~~~~E~fi~~l~~~A~~~a~~~kRkTI~~~DI~~Av~~~  144 (151)
T d1f1ea_          84 TVRRILKRAGIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITYS  144 (151)
T ss_dssp             HHHHHHHHTTCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             HHHHHHHcCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHc
Confidence            3445566789999999999999999999999999999999999999999999999999885

>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=97.40  E-value=0.00038  Score=50.38  Aligned_cols=61  Identities=20%  Similarity=0.278  Sum_probs=57.6

Q ss_pred             HHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Q 023473           36 KVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALN   96 (281)
Q Consensus        36 r~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~   96 (281)
                      ..+|-.|..++|+......+...|++=+.--|.+|.+.|.+|+.|+.|+.-+..||..||+
T Consensus         9 ~esik~iAeS~Gi~~l~de~a~~LA~DveYRl~eiiQeA~KFMrhskR~~Ltt~Did~ALk   69 (70)
T d1tafb_           9 AESMKVIAESIGVGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLK   69 (70)
T ss_dssp             HHHHHHHHHHTTCCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC
T ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcCcHHHHHHHHc
Confidence            3467788999999999999999999999999999999999999999999999999999985

>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=97.24  E-value=0.0013  Score=48.85  Aligned_cols=62  Identities=10%  Similarity=0.190  Sum_probs=55.5

Q ss_pred             HHHHHHHc--CcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473           39 VSQICRSV--GFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS  100 (281)
Q Consensus        39 VaqIL~~~--GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi  100 (281)
                      |-.|+++.  .-..++..|+..++.....||..|+..|...|...+|...+..||..||.++|.
T Consensus         5 i~ri~K~~~p~~~~iskeA~~~i~~aae~FI~~lt~~A~~~a~~~~rKtI~~~dv~~Al~~~~f   68 (89)
T d2bykb1           5 IGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDF   68 (89)
T ss_dssp             HHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTC
T ss_pred             HHHHHHHhCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHCCc
Confidence            45556543  567899999999999999999999999999999999999999999999999974

>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=97.20  E-value=0.0013  Score=48.58  Aligned_cols=63  Identities=17%  Similarity=0.213  Sum_probs=56.9

Q ss_pred             HHHHHHHHc--CcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473           38 AVSQICRSV--GFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS  100 (281)
Q Consensus        38 sVaqIL~~~--GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi  100 (281)
                      .|..|+++.  +-..++..|+..++..++.||..|+..|...|...+|...+..||..|+.+++.
T Consensus         7 ~v~ri~K~~~p~~~~is~ea~~~i~~a~e~Fi~~lt~~A~~~a~~~~rKTI~~~dv~~Al~~~~~   71 (87)
T d1n1ja_           7 NVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGF   71 (87)
T ss_dssp             HHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHcCc
Confidence            456677654  567799999999999999999999999999999999999999999999999964

>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=96.66  E-value=0.0025  Score=51.61  Aligned_cols=64  Identities=16%  Similarity=0.130  Sum_probs=59.3

Q ss_pred             HHHHHHHHH-cCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473           37 VAVSQICRS-VGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS  100 (281)
Q Consensus        37 ~sVaqIL~~-~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi  100 (281)
                      ..|..++++ .|=..++..|.+.|.+++..|+..|+..|...|++++|......||..|+..+|.
T Consensus         5 a~I~rilk~~~~~~ris~da~~~l~~~~~~~~~~Ia~eA~~l~~~~~rKTi~~edi~~a~~~~~~   69 (151)
T d1f1ea_           5 AAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADVLMV   69 (151)
T ss_dssp             HHHHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHHHTC
T ss_pred             cHHHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhccc
Confidence            457778875 5889999999999999999999999999999999999999999999999999875

>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=96.60  E-value=0.0061  Score=48.44  Aligned_cols=52  Identities=12%  Similarity=0.172  Sum_probs=50.1

Q ss_pred             CccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473           49 KAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS  100 (281)
Q Consensus        49 dsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi  100 (281)
                      ..++..|...|+..+..||..|+..|...|...+|...+..||..||.++|.
T Consensus        21 ~~is~dA~~~i~~a~~~Fi~~lt~~A~~~a~~~~RkTi~~~Dv~~Al~~~~f   72 (135)
T d1jfib_          21 VRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALESLGF   72 (135)
T ss_dssp             CCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHTT
T ss_pred             chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHcCc
Confidence            5799999999999999999999999999999999999999999999999974

>d1tzyc_ a.22.1.1 (C:) Histone H3 {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H3
species: Chicken (Gallus gallus), erythrocytes [TaxId: 9031]

Probab=95.25  E-value=0.039  Score=41.52  Aligned_cols=52  Identities=21%  Similarity=0.091  Sum_probs=48.3

Q ss_pred             CcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcC
Q 023473           47 GFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVS   99 (281)
Q Consensus        47 GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmG   99 (281)
                      ++ ..+++|++.|-+..+.||.++-..+...|.|++|....+.|+.+|..--|
T Consensus        41 ~~-r~~~~Al~aLQea~E~yLv~lfeda~~~a~HakRvTl~~kD~~LarrirG   92 (95)
T d1tzyc_          41 DL-RFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG   92 (95)
T ss_dssp             TC-EECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHT
T ss_pred             CC-EeeHHHHHHHHHHHHHHHHHHHHHhHHHHHhcCCCcCCHHHHHHHHHHhc
Confidence            55 79999999999999999999999999999999999999999999987554

>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=94.83  E-value=0.036  Score=45.85  Aligned_cols=56  Identities=13%  Similarity=0.035  Sum_probs=51.2

Q ss_pred             HHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473           42 ICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND   97 (281)
Q Consensus        42 IL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d   97 (281)
                      +|+..+-..++.+|--.|+.+++.+..+|...|..||.+++|...++.||..|+..
T Consensus       108 lLk~~~a~RVs~~A~vyLaavLEyl~aeILelAgn~a~~~krkrItp~dI~lAi~n  163 (172)
T d1q9ca_         108 LLKEVLGYKIDHQVSVYIVAVLEYISADILKLAGNYVRNIRHYEITKQDIKVAMCA  163 (172)
T ss_dssp             HHHHHHSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSBCCHHHHHHHHHT
T ss_pred             HHHhccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCceecHHHHHHHHhC
Confidence            34455566899999999999999999999999999999999999999999999987

>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=94.40  E-value=0.052  Score=38.50  Aligned_cols=60  Identities=17%  Similarity=0.164  Sum_probs=52.3

Q ss_pred             HHHHH-HcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcC
Q 023473           40 SQICR-SVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVS   99 (281)
Q Consensus        40 aqIL~-~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmG   99 (281)
                      -.|++ .-....++..|+..++..++.|++.|+..|...|...+|...+..||..|+++..
T Consensus         7 krImK~~~~~~~is~ea~~~i~~a~E~Fi~~l~~~A~~~a~~~~rkti~~~dl~~av~~~~   67 (78)
T d1n1jb_           7 KKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFD   67 (78)
T ss_dssp             HHHHTTSTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTCG
T ss_pred             HHHHhcCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHhcCC
Confidence            33444 2345788999999999999999999999999999999999999999999998863

>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=93.83  E-value=0.038  Score=38.26  Aligned_cols=57  Identities=9%  Similarity=0.170  Sum_probs=46.5

Q ss_pred             HHHHHH-HcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHH
Q 023473           39 VSQICR-SVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNAL   95 (281)
Q Consensus        39 VaqIL~-~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL   95 (281)
                      |-.|++ +-....++..|+..|+..++-|+.+|...|..+|...+|...+..||..|.
T Consensus         8 Vkkimk~~~~~~~is~~A~~~~~~a~E~Fi~~l~~~A~~~a~~~krktI~~~dl~~ai   65 (66)
T d1jfia_           8 IKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQCI   65 (66)
T ss_dssp             HHHHHTTSTTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC---CBCHHHHHTTC
T ss_pred             HHHHHhcCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHh
Confidence            344555 445678999999999999999999999999999999999999999997763

>d1tzyb_ a.22.1.1 (B:) Histone H2B {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H2B
species: Chicken (Gallus gallus), erythrocytes [TaxId: 9031]

Probab=86.32  E-value=0.74  Score=34.05  Aligned_cols=66  Identities=17%  Similarity=0.219  Sum_probs=55.1

Q ss_pred             CchHHHHHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           26 TPSEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        26 s~defar~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      +-+-|..++|+.+    --   -.+++..|+..+..++...++.|+..|...|....|...+..||..|.+-+
T Consensus         4 sy~~Yi~kVLKqV----hp---~~giS~kam~imnsfvndiferIa~EA~~La~~~kr~TitsreIqtAvrL~   69 (92)
T d1tzyb_           4 SYSIYVYKVLKQV----HP---DTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLL   69 (92)
T ss_dssp             CCHHHHHHHHHHH----CT---TCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHhh----CC---CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHH
Confidence            3445566666533    22   347889999999999999999999999999999999999999999999877

>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=85.14  E-value=2.9  Score=29.48  Aligned_cols=63  Identities=13%  Similarity=0.146  Sum_probs=52.6

Q ss_pred             HHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           33 TVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        33 ~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      +-|+..|-+|   .+=....+.+-|.|.+++..|+..+...|.+.|-|-+=....+-||.+.|+..
T Consensus         7 ~~L~eLv~~i---dp~~~ld~~vee~ll~iADdFV~~V~~~ac~lAKhR~s~~le~kDvql~LeR~   69 (74)
T d1h3ob_           7 KKLQDLVREV---DPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLERQ   69 (74)
T ss_dssp             HHHHHHHHHH---CSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHh---CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCcHHHHHHHHHhh
Confidence            3455555555   34556789999999999999999999999999999888788999999999874

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=81.29  E-value=3.1  Score=32.83  Aligned_cols=48  Identities=17%  Similarity=0.066  Sum_probs=41.0

Q ss_pred             ccChHHHHHHHHHH---------HHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473           50 AAESSALETLTLVA---------AKYLQQLASRAASYSHVAHRSESNLVDLTNALND   97 (281)
Q Consensus        50 sa~~sALetLTdil---------~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d   97 (281)
                      ..++.|++.++++.         .|-..++.+.|...|+.-|+...+..||..|+.+
T Consensus       230 ~~~~~al~~ia~~~~~~~~~~gd~R~ai~~l~~a~~~A~~~~~~~It~~~V~~A~~e  286 (287)
T d1w5sa2         230 VWEPRHLELISDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSE  286 (287)
T ss_dssp             SCCHHHHHHHHHHHCGGGTSCCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhccccCCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhc
Confidence            46789999999887         3455678889999999999999999999999875

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=81.01  E-value=6  Score=30.82  Aligned_cols=52  Identities=13%  Similarity=0.133  Sum_probs=44.4

Q ss_pred             CcCccChHHHHHHHHHH------------HHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473           47 GFKAAESSALETLTLVA------------AKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV   98 (281)
Q Consensus        47 GFdsa~~sALetLTdil------------~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm   98 (281)
                      ........+++.+.+..            .+.+.++.+.|...|..-|+...+..||..|++++
T Consensus       210 ~~~~~~~~~l~~ia~~~~~~~~~~~~~G~~R~a~~ll~~a~~~A~~~~~~~I~~edv~~A~~~~  273 (276)
T d1fnna2         210 AEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPEDVRKSSKEV  273 (276)
T ss_dssp             CTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHH
T ss_pred             ccccccHHHHHHHHHHhhhhhhhhhcCCCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence            34557889999998876            46677888899999999999999999999999986