Psyllid ID: psy3828

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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-------290-------300-------310-------320-------330-------340-------350-------360-----
Protein Sequence
MVIRGELFCKRNDSSITQSRSFSIPGAVPIPQIYTMSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAGAALTFERVDDVHGGDGLSLGVLGVGDGVADHVLEEHLENATGLLVDEPGDTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTAAGKSSGKAVKKAGKAQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Secondary Structure (PSIPRED)
ccEEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHccHHHHccccccccccHHHHHccHHHHHHHHcccEEccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccHHHHEHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHcccHHHHHHHcccccccccccccc
Secondary Structure Prediction (SSPRO)
cEEEEEEEEEccccccccccccccccccccccEEEEcccccccccccccccHHHHHcccccHHHHHHHHHHcccccEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEcHHHHHHHHHHcHHHHHHcccEEEccccccccccHHHcccccccccccccccccccccccccccccHHHHHHHHHHHcccEcccccccccccccccccccccccccEEEEcccccccccccccccccccccccccHHHHHHHHHHHccccccccccccccccccHHHHHHHHHHHccccEEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEcHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
mvirgelfckrndssitqsrsfsipgavpipqiytmsgrgkggkakaksktrssraglqfpvgrIHRLLRkgnyaervgagAPVYLAAVMEYLAAEVLELAGnaardnkktriiPRHLQLAIRNDEELNKLLSgvtiaqggvlpniqagaaltfervddvhggdglslgvlgvgdgVADHVLEEHLENatgllvdepgdtldststrqttdgglgdsldvvteyfpvplgasfsesLSSLTTAAGKSSGKAVKKAGKAQKNIaksdkkkkhrrkESYAIYIYKVLKQvhpdtgvsSKAMSIMNSFVNDIFERIAAESSRLahynkrstiTSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Flexible Loop (DISEMBL)
mvirgelfckrndssitqsrsfsipgavpipqiytmsgrgkggkakaksktrssraglqfpvgrihrllrkgnyaerVGAGAPVYLAAVMEYLAAEVLELAGnaardnkktriiPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAGAALTFERVDDVHGGDGLSLGVLGVGDGVADHVLEEHLENAtgllvdepgdtLDSTStrqttdgglgdsLDVVTEYFPVPLGASFSESLSSLTTAagkssgkavkkagkaqkniaksdkkkkhrrkeSYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLahynkrstitsreIQTAVRLLLPGelakhavsegtkavtkytssk
Low Complexity Region (SEG)
MVIRGELFCKRNDSSITQSRSFSIPGAVPIPQIYTMsgrgkggkakaksktrssragLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAGAALTFERvddvhggdglslgvlgvgdgvadhvlEEHLENATGLLVDEPGDTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTaagkssgkavkkagkaQKNIAksdkkkkhrrkESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Disordered region (IsUnstruct)
*********************************************************LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAGAALTFERVDDVHGGDGLSLGVLGVGDGVADHVLEEHLENATGLLV**********************SLDVVTEYFPVPLG**********************************************YAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELA******************
Disordered Region (DISOPRED)
*******FCKR****I****SFSI**********************************QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA**********************************************DEPGDTLDSTSTRQTTD*******************************************************************IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKY****
Disordered Region (DISEMBL)
MVIRGELFCKRNDSSITQSRSFSIPGAVPIPQIYTMS*******************GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAGAALTFERVDDVHGGDGLSLGVLGVGDGVADHVLEEHLENATGLLVDEPGDTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSS**********************************KESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHA***************
Disordered Region (DISPRO)
MVIRGELFCKRNDSSITQSRSFSIPGAVPIPQIYTM********************GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAGAALTFE*****************VGDGVADHVLEEHLENATGLLVDEPGDTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGAS******************************************ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAV*K*T***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVIRGELFCKRNDSSITQSRSFSIPGAVPIPQIYTMSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAGAALTFERVDDVHGGDGLSLGVLGVGDGVADHVLEEHLENATGLLVDEPGDTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTAAGKSSGKAVKKAGKAQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
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	365	2.2.26 [Sep-21-2011]
P19178	124	Histone H2A OS=Platynerei	N/A	N/A	0.309	0.911	0.991	1e-58
P02269	125	Histone H2A OS=Asterias r	N/A	N/A	0.309	0.904	0.938	2e-56
P02264	128	Histone H2A OS=Oncorhynch	N/A	N/A	0.309	0.882	0.921	5e-55
Q96QV6	131	Histone H2A type 1-A OS=H	yes	N/A	0.309	0.862	0.921	8e-55
Q7ZUY3	142	Histone H2A.x OS=Danio re	no	N/A	0.309	0.795	0.921	9e-55
P16886	126	Late histone H2A.L3 OS=St	yes	N/A	0.309	0.896	0.903	1e-54
P06897	130	Histone H2A type 1 OS=Xen	N/A	N/A	0.309	0.869	0.903	2e-54
Q8IUE6	130	Histone H2A type 2-B OS=H	yes	N/A	0.309	0.869	0.912	2e-54
P16104	143	Histone H2A.x OS=Homo sap	no	N/A	0.309	0.790	0.912	3e-54
P27661	143	Histone H2A.x OS=Mus musc	yes	N/A	0.309	0.790	0.912	3e-54

>sp|P19178|H2A_PLADU Histone H2A OS=Platynereis dumerilii PE=3 SV=2

 Score =  227 bits (578), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 112/113 (99%), Positives = 112/113 (99%)

Query: 36  MSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 95
           MSGRGKGGKAK KSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA
Sbjct: 1   MSGRGKGGKAKGKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 60

Query: 96  EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA
Sbjct: 61  EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 113

Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.
Platynereis dumerilii (taxid: 6359)

>sp|P02269|H2A_ASTRU Histone H2A OS=Asterias rubens PE=1 SV=2

 Score =  219 bits (558), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 106/113 (93%), Positives = 111/113 (98%)

Query: 36  MSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 95
           MSGRGKGGKA+AK+K+RSSRAGLQFPVGR+HR LRKGNYAERVGAGAPVYLAAVMEYLAA
Sbjct: 1   MSGRGKGGKARAKAKSRSSRAGLQFPVGRVHRFLRKGNYAERVGAGAPVYLAAVMEYLAA 60

Query: 96  EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           E+LELAGNAARDNKKTRI PRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA
Sbjct: 61  EILELAGNAARDNKKTRINPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 113

Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.

Asterias rubens (taxid: 7604)

>sp|P02264|H2A_ONCMY Histone H2A OS=Oncorhynchus mykiss PE=1 SV=2

 Score =  215 bits (547), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 105/114 (92%), Positives = 111/114 (97%), Gaps = 1/114 (0%)

Query: 36  MSGRGK-GGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLA 94
           MSGRGK GGKA+AK+KTRSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL 
Sbjct: 1   MSGRGKTGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT 60

Query: 95  AEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           AE+LELAGNAARDNKKTRIIPRHLQLA+RNDEELNKLL GVTIAQGGVLPNIQA
Sbjct: 61  AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQA 114

The secreted form has antibacterial activity against Gram-positive bacteria and antifungal activity against S.cerevisiae.

Oncorhynchus mykiss (taxid: 8022)

>sp|Q96QV6|H2A1A_HUMAN Histone H2A type 1-A OS=Homo sapiens GN=HIST1H2AA PE=1 SV=3

 Score =  214 bits (545), Expect = 8e-55,   Method: Compositional matrix adjust.
 Identities = 105/114 (92%), Positives = 111/114 (97%), Gaps = 1/114 (0%)

Query: 36  MSGRGK-GGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLA 94
           MSGRGK GGKA+AKSK+RSSRAGLQFPVGRIHRLLRKGNYAER+GAGAPVYLAAV+EYL 
Sbjct: 1   MSGRGKQGGKARAKSKSRSSRAGLQFPVGRIHRLLRKGNYAERIGAGAPVYLAAVLEYLT 60

Query: 95  AEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           AE+LELAGNA+RDNKKTRIIPRHLQLAIRNDEELNKLL GVTIAQGGVLPNIQA
Sbjct: 61  AEILELAGNASRDNKKTRIIPRHLQLAIRNDEELNKLLGGVTIAQGGVLPNIQA 114

Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.

Homo sapiens (taxid: 9606)

>sp|Q7ZUY3|H2AX_DANRE Histone H2A.x OS=Danio rerio GN=h2afx PE=2 SV=3

 Score =  214 bits (545), Expect = 9e-55,   Method: Compositional matrix adjust.
 Identities = 105/114 (92%), Positives = 111/114 (97%), Gaps = 1/114 (0%)

Query: 36  MSGRGK-GGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLA 94
           MSGRGK GGKA+AK+KTRSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL 
Sbjct: 1   MSGRGKTGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT 60

Query: 95  AEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           AE+LELAGNAARDNKKTRIIPRHLQLA+RNDEELNKLL GVTIAQGGVLPNIQA
Sbjct: 61  AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQA 114

Variant histone H2A which replaces conventional H2A in a subset of nucleosomes. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. Required for checkpoint-mediated arrest of cell cycle progression in response to low doses of ionizing radiation and for efficient repair of DNA double strand breaks (DSBs) specifically when modified by C-terminal phosphorylation.

Danio rerio (taxid: 7955)

>sp|P16886|H2AL_STRPU Late histone H2A.L3 OS=Strongylocentrotus purpuratus PE=1 SV=2

 Score =  214 bits (544), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 103/114 (90%), Positives = 112/114 (98%), Gaps = 1/114 (0%)

Query: 36  MSGRGKG-GKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLA 94
           MSGRGKG GKA+AK+K+RS+RAGLQFPVGR+HR LRKGNYA+RVGAGAPVYLAAV+EYLA
Sbjct: 1   MSGRGKGAGKARAKAKSRSARAGLQFPVGRVHRFLRKGNYAQRVGAGAPVYLAAVLEYLA 60

Query: 95  AEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           AE+LELAGNAARDNKKTRIIPRHLQLA+RNDEELNKLLSGVTIAQGGVLPNIQA
Sbjct: 61  AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLSGVTIAQGGVLPNIQA 114

Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.

Strongylocentrotus purpuratus (taxid: 7668)

>sp|P06897|H2A1_XENLA Histone H2A type 1 OS=Xenopus laevis PE=1 SV=2

 Score =  213 bits (542), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 103/114 (90%), Positives = 110/114 (96%), Gaps = 1/114 (0%)

Query: 36  MSGRGK-GGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLA 94
           MSGRGK GGK +AK+KTRSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL 
Sbjct: 1   MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT 60

Query: 95  AEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           AE+LELAGNAARDNKKTRIIPRHLQLA+RNDEELNKLL GVTIAQGGVLPNIQ+
Sbjct: 61  AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQS 114

Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.

Xenopus laevis (taxid: 8355)

>sp|Q8IUE6|H2A2B_HUMAN Histone H2A type 2-B OS=Homo sapiens GN=HIST2H2AB PE=1 SV=3

 Score =  213 bits (541), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 104/114 (91%), Positives = 111/114 (97%), Gaps = 1/114 (0%)

Query: 36  MSGRGK-GGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLA 94
           MSGRGK GGKA+AK+K+RSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL 
Sbjct: 1   MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT 60

Query: 95  AEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           AE+LELAGNAARDNKKTRIIPRHLQLA+RNDEELNKLL GVTIAQGGVLPNIQA
Sbjct: 61  AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQA 114

Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.

Homo sapiens (taxid: 9606)

>sp|P16104|H2AX_HUMAN Histone H2A.x OS=Homo sapiens GN=H2AFX PE=1 SV=2

 Score =  213 bits (541), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 104/114 (91%), Positives = 111/114 (97%), Gaps = 1/114 (0%)

Query: 36  MSGRGK-GGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLA 94
           MSGRGK GGKA+AK+K+RSSRAGLQFPVGR+HRLLRKG+YAERVGAGAPVYLAAV+EYL 
Sbjct: 1   MSGRGKTGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGHYAERVGAGAPVYLAAVLEYLT 60

Query: 95  AEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           AE+LELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLL GVTIAQGGVLPNIQA
Sbjct: 61  AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGGVTIAQGGVLPNIQA 114

Variant histone H2A which replaces conventional H2A in a subset of nucleosomes. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. Required for checkpoint-mediated arrest of cell cycle progression in response to low doses of ionizing radiation and for efficient repair of DNA double strand breaks (DSBs) specifically when modified by C-terminal phosphorylation.

Homo sapiens (taxid: 9606)

>sp|P27661|H2AX_MOUSE Histone H2A.x OS=Mus musculus GN=H2afx PE=1 SV=2

 Score =  212 bits (540), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 104/114 (91%), Positives = 111/114 (97%), Gaps = 1/114 (0%)

Query: 36  MSGRGK-GGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLA 94
           MSGRGK GGKA+AK+K+RSSRAGLQFPVGR+HRLLRKG+YAERVGAGAPVYLAAV+EYL 
Sbjct: 1   MSGRGKTGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGHYAERVGAGAPVYLAAVLEYLT 60

Query: 95  AEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           AE+LELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLL GVTIAQGGVLPNIQA
Sbjct: 61  AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGGVTIAQGGVLPNIQA 114

Variant histone H2A which replaces conventional H2A in a subset of nucleosomes. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. Required for checkpoint-mediated arrest of cell cycle progression in response to low doses of ionizing radiation and for efficient repair of DNA double strand breaks (DSBs) specifically when modified by C-terminal phosphorylation.

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	365
397609826	324	hypothetical protein THAOC_19092 [Thalas	0.498	0.561	0.568	3e-62
156544915	136	PREDICTED: histone H2A type 1 [Nasonia v	0.309	0.830	0.991	2e-57
122008	124	RecName: Full=Histone H2A gi|9820|emb|CA	0.309	0.911	0.991	8e-57
328699742	126	PREDICTED: histone H2B.3-like [Acyrthosi	0.331	0.960	0.934	2e-56
340712625	135	PREDICTED: histone H2A-like [Bombus terr	0.309	0.837	0.982	2e-56
66506394	135	PREDICTED: histone H2A-like isoform 6 [A	0.309	0.837	0.982	2e-56
346470069	124	hypothetical protein [Amblyomma maculatu	0.309	0.911	0.982	3e-56
225710358	125	Histone H2B [Caligus rogercresseyi]	0.328	0.96	0.942	7e-56
193582492	126	PREDICTED: histone H2B.3-like [Acyrthosi	0.331	0.960	0.926	7e-56
157137737	124	histone h2a [Aedes aegypti] gi|108880814	0.309	0.911	0.964	1e-55

>gi|397609826|gb|EJK60529.1| hypothetical protein THAOC_19092 [Thalassiosira oceanica]

 Score =  245 bits (625), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 132/232 (56%), Positives = 151/232 (65%), Gaps = 50/232 (21%)

Query: 49  SKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDN 108
           S T S++AGLQFPVGRI R LR+G YA R+GAGAPVYLAAV+EYL AE+LELAGNAARDN
Sbjct: 14  STTSSAKAGLQFPVGRIGRYLRQGKYATRMGAGAPVYLAAVLEYLCAEILELAGNAARDN 73

Query: 109 KKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA-------------------- 148
           KK RIIPRH+ LA++NDEELNKLL GVTIA GGVLPNI A                    
Sbjct: 74  KKARIIPRHITLAVKNDEELNKLLGGVTIASGGVLPNIHAVLLPKKSGKARAQRSQAPGD 133

Query: 149 ------------------------------GAALTFERVDDVHGGDGLSLGVLGVGDGVA 178
                                         G +L+ + VDDVHG D L+ GVLGVGDGV 
Sbjct: 134 DGKQKFIFDRWVDFRKSGFVLKRLSAEAVEGLSLSLQGVDDVHGRDSLTAGVLGVGDGVT 193

Query: 179 DHVLEEHLENATGLLVDEPGDTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLG 230
           D VLEE LE+A GLLVDE GDTLD+ +T +T DGGLGD+LDVV +   V LG
Sbjct: 194 DDVLEEDLEDAAGLLVDETGDTLDTATTGETADGGLGDALDVVAKDLAVALG 245

Source: Thalassiosira oceanica

Species: Thalassiosira oceanica

Genus: Thalassiosira

Family: Thalassiosiraceae

Class: Coscinodiscophyceae

Phylum: Bacillariophyta

Superkingdom: Eukaryota

>gi|156544915|ref|XP_001600014.1| PREDICTED: histone H2A type 1 [Nasonia vitripennis]

 Score =  229 bits (584), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 112/113 (99%), Positives = 113/113 (100%)

Query: 36  MSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 95
           MSGRGKGGKAKAKSKTRS+RAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA
Sbjct: 1   MSGRGKGGKAKAKSKTRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 60

Query: 96  EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA
Sbjct: 61  EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 113

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|122008|sp|P19178.2|H2A_PLADU RecName: Full=Histone H2A gi|9820|emb|CAA37416.1| unnamed protein product [Platynereis dumerilii]

 Score =  227 bits (578), Expect = 8e-57,   Method: Compositional matrix adjust.
 Identities = 112/113 (99%), Positives = 112/113 (99%)

Query: 36  MSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 95
           MSGRGKGGKAK KSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA
Sbjct: 1   MSGRGKGGKAKGKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 60

Query: 96  EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA
Sbjct: 61  EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 113

Source: Platynereis dumerilii

Species: Platynereis dumerilii

Genus: Platynereis

Family: Nereididae

Order: Phyllodocida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|328699742|ref|XP_003241030.1| PREDICTED: histone H2B.3-like [Acyrthosiphon pisum] gi|328699758|ref|XP_003241035.1| PREDICTED: histone H2B.3-like [Acyrthosiphon pisum] gi|328713529|ref|XP_003245104.1| PREDICTED: histone H2B.3-like [Acyrthosiphon pisum] gi|328726557|ref|XP_003248948.1| PREDICTED: histone H2B.3-like [Acyrthosiphon pisum]

 Score =  225 bits (574), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 114/122 (93%), Positives = 120/122 (98%), Gaps = 1/122 (0%)

Query: 245 GKSSGKAVKKA-GKAQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMN 303
           GKS+GKA+KK+ GKAQKNIAKSDKK+K +RKESYAIYIYKVLKQVHPDTGVSSKAMSIMN
Sbjct: 5   GKSAGKAMKKSSGKAQKNIAKSDKKRKPKRKESYAIYIYKVLKQVHPDTGVSSKAMSIMN 64

Query: 304 SFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 363
           SFVND+FERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
Sbjct: 65  SFVNDLFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 124

Query: 364 SK 365
           SK
Sbjct: 125 SK 126

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340712625|ref|XP_003394856.1| PREDICTED: histone H2A-like [Bombus terrestris] gi|350399678|ref|XP_003485606.1| PREDICTED: histone H2A-like [Bombus impatiens]

 Score =  225 bits (574), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 111/113 (98%), Positives = 112/113 (99%)

Query: 36  MSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 95
           MSGRGKGGKAK K+KTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA
Sbjct: 1   MSGRGKGGKAKGKAKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 60

Query: 96  EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA
Sbjct: 61  EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 113

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66506394|ref|XP_624700.1| PREDICTED: histone H2A-like isoform 6 [Apis mellifera] gi|328790010|ref|XP_003251357.1| PREDICTED: histone H2A-like isoform 1 [Apis mellifera] gi|328790012|ref|XP_003251358.1| PREDICTED: histone H2A-like isoform 2 [Apis mellifera] gi|328790014|ref|XP_003251359.1| PREDICTED: histone H2A-like isoform 3 [Apis mellifera] gi|328790016|ref|XP_003251360.1| PREDICTED: histone H2A-like isoform 4 [Apis mellifera] gi|328790018|ref|XP_003251361.1| PREDICTED: histone H2A-like isoform 5 [Apis mellifera] gi|380011741|ref|XP_003689955.1| PREDICTED: histone H2A-like [Apis florea]

 Score =  225 bits (574), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 111/113 (98%), Positives = 112/113 (99%)

Query: 36  MSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 95
           MSGRGKGGKAK K+KTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA
Sbjct: 1   MSGRGKGGKAKGKAKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 60

Query: 96  EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA
Sbjct: 61  EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 113

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|346470069|gb|AEO34879.1| hypothetical protein [Amblyomma maculatum]

 Score =  225 bits (573), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 111/113 (98%), Positives = 112/113 (99%)

Query: 36  MSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 95
           MSGRGKGGKAK KSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAV+EYLAA
Sbjct: 1   MSGRGKGGKAKGKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLAA 60

Query: 96  EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA
Sbjct: 61  EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 113

Source: Amblyomma maculatum

Species: Amblyomma maculatum

Genus: Amblyomma

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|225710358|gb|ACO11025.1| Histone H2B [Caligus rogercresseyi]

 Score =  224 bits (570), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 115/122 (94%), Positives = 116/122 (95%), Gaps = 2/122 (1%)

Query: 246 KSSGKAVKKAGKAQKNIAKSD--KKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMN 303
           KS GKAVKKAGKAQKNI KSD  KKK H+RKESYAIYIYKVLKQVHPDTGVSSKAMSIMN
Sbjct: 4   KSVGKAVKKAGKAQKNITKSDGVKKKSHKRKESYAIYIYKVLKQVHPDTGVSSKAMSIMN 63

Query: 304 SFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 363
           S VNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
Sbjct: 64  SLVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 123

Query: 364 SK 365
           SK
Sbjct: 124 SK 125

Source: Caligus rogercresseyi

Species: Caligus rogercresseyi

Genus: Caligus

Family: Caligidae

Order: Siphonostomatoida

Class: Maxillopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193582492|ref|XP_001947771.1| PREDICTED: histone H2B.3-like [Acyrthosiphon pisum] gi|193603782|ref|XP_001950698.1| PREDICTED: histone H2B.3-like [Acyrthosiphon pisum]

 Score =  224 bits (570), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 113/122 (92%), Positives = 120/122 (98%), Gaps = 1/122 (0%)

Query: 245 GKSSG-KAVKKAGKAQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMN 303
           GKS+G KA+KK+GKAQKNIAKSDKK+K +RKESYAIYIYKVLKQVHPDTGVSSKAMSIMN
Sbjct: 5   GKSAGGKAMKKSGKAQKNIAKSDKKRKPKRKESYAIYIYKVLKQVHPDTGVSSKAMSIMN 64

Query: 304 SFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 363
           SFVND+FERIA+ESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
Sbjct: 65  SFVNDLFERIASESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 124

Query: 364 SK 365
           SK
Sbjct: 125 SK 126

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157137737|ref|XP_001657157.1| histone h2a [Aedes aegypti] gi|108880814|gb|EAT45039.1| AAEL003669-PA [Aedes aegypti]

 Score =  223 bits (567), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 109/113 (96%), Positives = 111/113 (98%)

Query: 36  MSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 95
           MSGRGKGGK +AK+KTRSSRAGLQFPVGR HRLLRKGNYAERVGAGAPVYLAAVMEYLAA
Sbjct: 1   MSGRGKGGKVRAKAKTRSSRAGLQFPVGRTHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 60

Query: 96  EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA
Sbjct: 61  EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 113

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

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	365
FB|FBgn0061209	123	His2B:CG17949 "His2B:CG17949"	0.293	0.869	0.869	7.3e-43
FB|FBgn0053868	123	His2B:CG33868 "His2B:CG33868"	0.293	0.869	0.869	7.3e-43
FB|FBgn0053870	123	His2B:CG33870 "His2B:CG33870"	0.293	0.869	0.869	7.3e-43
FB|FBgn0053872	123	His2B:CG33872 "His2B:CG33872"	0.293	0.869	0.869	7.3e-43
FB|FBgn0053874	123	His2B:CG33874 "His2B:CG33874"	0.293	0.869	0.869	7.3e-43
FB|FBgn0053876	123	His2B:CG33876 "His2B:CG33876"	0.293	0.869	0.869	7.3e-43
FB|FBgn0053878	123	His2B:CG33878 "His2B:CG33878"	0.293	0.869	0.869	7.3e-43
FB|FBgn0053880	123	His2B:CG33880 "His2B:CG33880"	0.293	0.869	0.869	7.3e-43
FB|FBgn0053882	123	His2B:CG33882 "His2B:CG33882"	0.293	0.869	0.869	7.3e-43
FB|FBgn0053884	123	His2B:CG33884 "His2B:CG33884"	0.293	0.869	0.869	7.3e-43

FB|FBgn0061209 His2B:CG17949 "His2B:CG17949" [Drosophila melanogaster (taxid:7227)]

 Score = 453 (164.5 bits), Expect = 7.3e-43, P = 7.3e-43
 Identities = 93/107 (86%), Positives = 95/107 (88%)

Query:   259 QKNIAXXXXXXXXXXXESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESS 318
             QKNI            ESYAIYIYKVLKQVHPDTG+SSKAMSIMNSFVNDIFERIAAE+S
Sbjct:    17 QKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEAS 76

Query:   319 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
             RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Sbjct:    77 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 123

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000786 "nucleosome" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005811 "lipid particle" evidence=IDA

FB|FBgn0053868 His2B:CG33868 "His2B:CG33868" [Drosophila melanogaster (taxid:7227)]

 Score = 453 (164.5 bits), Expect = 7.3e-43, P = 7.3e-43
 Identities = 93/107 (86%), Positives = 95/107 (88%)

Query:   259 QKNIAXXXXXXXXXXXESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESS 318
             QKNI            ESYAIYIYKVLKQVHPDTG+SSKAMSIMNSFVNDIFERIAAE+S
Sbjct:    17 QKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEAS 76

Query:   319 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
             RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Sbjct:    77 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 123

GO:0005634 "nucleus" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0003677 "DNA binding" evidence=ISS

GO:0000786 "nucleosome" evidence=ISS

GO:0006333 "chromatin assembly or disassembly" evidence=ISS

FB|FBgn0053870 His2B:CG33870 "His2B:CG33870" [Drosophila melanogaster (taxid:7227)]

 Score = 453 (164.5 bits), Expect = 7.3e-43, P = 7.3e-43
 Identities = 93/107 (86%), Positives = 95/107 (88%)

Query:   259 QKNIAXXXXXXXXXXXESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESS 318
             QKNI            ESYAIYIYKVLKQVHPDTG+SSKAMSIMNSFVNDIFERIAAE+S
Sbjct:    17 QKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEAS 76

Query:   319 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
             RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Sbjct:    77 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 123

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=ISS

GO:0006333 "chromatin assembly or disassembly" evidence=ISS

GO:0000786 "nucleosome" evidence=ISS

FB|FBgn0053872 His2B:CG33872 "His2B:CG33872" [Drosophila melanogaster (taxid:7227)]

 Score = 453 (164.5 bits), Expect = 7.3e-43, P = 7.3e-43
 Identities = 93/107 (86%), Positives = 95/107 (88%)

Query:   259 QKNIAXXXXXXXXXXXESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESS 318
             QKNI            ESYAIYIYKVLKQVHPDTG+SSKAMSIMNSFVNDIFERIAAE+S
Sbjct:    17 QKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEAS 76

Query:   319 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
             RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Sbjct:    77 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 123

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0006333 "chromatin assembly or disassembly" evidence=ISS

GO:0000786 "nucleosome" evidence=ISS

GO:0003677 "DNA binding" evidence=ISS

FB|FBgn0053874 His2B:CG33874 "His2B:CG33874" [Drosophila melanogaster (taxid:7227)]

 Score = 453 (164.5 bits), Expect = 7.3e-43, P = 7.3e-43
 Identities = 93/107 (86%), Positives = 95/107 (88%)

Query:   259 QKNIAXXXXXXXXXXXESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESS 318
             QKNI            ESYAIYIYKVLKQVHPDTG+SSKAMSIMNSFVNDIFERIAAE+S
Sbjct:    17 QKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEAS 76

Query:   319 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
             RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Sbjct:    77 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 123

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006333 "chromatin assembly or disassembly" evidence=ISS

GO:0003677 "DNA binding" evidence=ISS

GO:0000786 "nucleosome" evidence=ISS

FB|FBgn0053876 His2B:CG33876 "His2B:CG33876" [Drosophila melanogaster (taxid:7227)]

 Score = 453 (164.5 bits), Expect = 7.3e-43, P = 7.3e-43
 Identities = 93/107 (86%), Positives = 95/107 (88%)

Query:   259 QKNIAXXXXXXXXXXXESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESS 318
             QKNI            ESYAIYIYKVLKQVHPDTG+SSKAMSIMNSFVNDIFERIAAE+S
Sbjct:    17 QKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEAS 76

Query:   319 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
             RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Sbjct:    77 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 123

GO:0005634 "nucleus" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0000786 "nucleosome" evidence=ISS

GO:0006333 "chromatin assembly or disassembly" evidence=ISS

GO:0003677 "DNA binding" evidence=ISS

FB|FBgn0053878 His2B:CG33878 "His2B:CG33878" [Drosophila melanogaster (taxid:7227)]

 Score = 453 (164.5 bits), Expect = 7.3e-43, P = 7.3e-43
 Identities = 93/107 (86%), Positives = 95/107 (88%)

Query:   259 QKNIAXXXXXXXXXXXESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESS 318
             QKNI            ESYAIYIYKVLKQVHPDTG+SSKAMSIMNSFVNDIFERIAAE+S
Sbjct:    17 QKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEAS 76

Query:   319 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
             RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Sbjct:    77 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 123

GO:0005634 "nucleus" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0000786 "nucleosome" evidence=ISS

GO:0006333 "chromatin assembly or disassembly" evidence=ISS

GO:0003677 "DNA binding" evidence=ISS

FB|FBgn0053880 His2B:CG33880 "His2B:CG33880" [Drosophila melanogaster (taxid:7227)]

 Score = 453 (164.5 bits), Expect = 7.3e-43, P = 7.3e-43
 Identities = 93/107 (86%), Positives = 95/107 (88%)

Query:   259 QKNIAXXXXXXXXXXXESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESS 318
             QKNI            ESYAIYIYKVLKQVHPDTG+SSKAMSIMNSFVNDIFERIAAE+S
Sbjct:    17 QKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEAS 76

Query:   319 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
             RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Sbjct:    77 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 123

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0000786 "nucleosome" evidence=ISS

GO:0006333 "chromatin assembly or disassembly" evidence=ISS

GO:0003677 "DNA binding" evidence=ISS

FB|FBgn0053882 His2B:CG33882 "His2B:CG33882" [Drosophila melanogaster (taxid:7227)]

 Score = 453 (164.5 bits), Expect = 7.3e-43, P = 7.3e-43
 Identities = 93/107 (86%), Positives = 95/107 (88%)

Query:   259 QKNIAXXXXXXXXXXXESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESS 318
             QKNI            ESYAIYIYKVLKQVHPDTG+SSKAMSIMNSFVNDIFERIAAE+S
Sbjct:    17 QKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEAS 76

Query:   319 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
             RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Sbjct:    77 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 123

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0003677 "DNA binding" evidence=ISS

GO:0000786 "nucleosome" evidence=ISS

GO:0006333 "chromatin assembly or disassembly" evidence=ISS

FB|FBgn0053884 His2B:CG33884 "His2B:CG33884" [Drosophila melanogaster (taxid:7227)]

 Score = 453 (164.5 bits), Expect = 7.3e-43, P = 7.3e-43
 Identities = 93/107 (86%), Positives = 95/107 (88%)

Query:   259 QKNIAXXXXXXXXXXXESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESS 318
             QKNI            ESYAIYIYKVLKQVHPDTG+SSKAMSIMNSFVNDIFERIAAE+S
Sbjct:    17 QKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEAS 76

Query:   319 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
             RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Sbjct:    77 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 123

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000786 "nucleosome" evidence=ISS

GO:0006333 "chromatin assembly or disassembly" evidence=ISS

GO:0003677 "DNA binding" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q96KK5	H2A1H_HUMAN	No assigned EC number	0.9210	0.3095	0.8828	yes	N/A
Q93077	H2A1C_HUMAN	No assigned EC number	0.9122	0.3095	0.8692	no	N/A
P35069	H2B3_TIGCA	No assigned EC number	0.9252	0.2931	0.8699	N/A	N/A
Q3ZBX9	H2AJ_BOVIN	No assigned EC number	0.9035	0.3095	0.8759	yes	N/A
Q4R3X5	H2AJ_MACFA	No assigned EC number	0.9035	0.3095	0.8759	N/A	N/A
Q64522	H2A2B_MOUSE	No assigned EC number	0.9035	0.3095	0.8692	no	N/A
Q64523	H2A2C_MOUSE	No assigned EC number	0.9035	0.3095	0.8759	no	N/A
P20671	H2A1D_HUMAN	No assigned EC number	0.9122	0.3095	0.8692	no	N/A
P16886	H2AL_STRPU	No assigned EC number	0.9035	0.3095	0.8968	yes	N/A
P35062	H2A3_CHICK	No assigned EC number	0.9035	0.3095	0.8759	yes	N/A
P70082	H2AJ_CHICK	No assigned EC number	0.8947	0.3095	0.8759	yes	N/A
P22752	H2A1_MOUSE	No assigned EC number	0.9122	0.3095	0.8692	no	N/A
P0C169	H2A1C_RAT	No assigned EC number	0.9122	0.3095	0.8692	no	N/A
Q8CGP7	H2A1K_MOUSE	No assigned EC number	0.9122	0.3095	0.8692	no	N/A
Q8CGP6	H2A1H_MOUSE	No assigned EC number	0.9122	0.3095	0.8828	no	N/A
P13912	H2A_CAIMO	No assigned EC number	0.9122	0.3095	0.8759	N/A	N/A
Q8R1M2	H2AJ_MOUSE	No assigned EC number	0.9035	0.3095	0.8759	no	N/A
A1A4R1	H2A2C_BOVIN	No assigned EC number	0.9035	0.3095	0.8759	yes	N/A
P0CC09	H2A2A_RAT	No assigned EC number	0.9035	0.3095	0.8692	no	N/A
Q8IUE6	H2A2B_HUMAN	No assigned EC number	0.9122	0.3095	0.8692	yes	N/A
Q96QV6	H2A1A_HUMAN	No assigned EC number	0.9210	0.3095	0.8625	yes	N/A
P27661	H2AX_MOUSE	No assigned EC number	0.9122	0.3095	0.7902	yes	N/A
P19178	H2A_PLADU	No assigned EC number	0.9911	0.3095	0.9112	N/A	N/A
Q64598	H2A1F_RAT	No assigned EC number	0.9035	0.3095	0.8692	no	N/A
Q16777	H2A2C_HUMAN	No assigned EC number	0.9035	0.3095	0.8759	no	N/A
Q7L7L0	H2A3_HUMAN	No assigned EC number	0.9035	0.3095	0.8692	no	N/A
Q99878	H2A1J_HUMAN	No assigned EC number	0.9210	0.3095	0.8828	yes	N/A
Q9BTM1	H2AJ_HUMAN	No assigned EC number	0.9035	0.3095	0.8759	no	N/A
P06897	H2A1_XENLA	No assigned EC number	0.9035	0.3095	0.8692	N/A	N/A
P0C0S8	H2A1_HUMAN	No assigned EC number	0.9210	0.3095	0.8692	no	N/A
P0C0S9	H2A1_BOVIN	No assigned EC number	0.9210	0.3095	0.8692	no	N/A
A9UMV8	H2AJ_RAT	No assigned EC number	0.9035	0.3095	0.8759	yes	N/A
P16104	H2AX_HUMAN	No assigned EC number	0.9122	0.3095	0.7902	no	N/A
Q6FI13	H2A2A_HUMAN	No assigned EC number	0.9035	0.3095	0.8692	no	N/A
Q7ZUY3	H2AX_DANRE	No assigned EC number	0.9210	0.3095	0.7957	no	N/A
P04908	H2A1B_HUMAN	No assigned EC number	0.9122	0.3095	0.8692	no	N/A
Q6GSS7	H2A2A_MOUSE	No assigned EC number	0.9035	0.3095	0.8692	no	N/A
Q8BFU2	H2A3_MOUSE	No assigned EC number	0.9035	0.3095	0.8692	no	N/A
P0C170	H2A1E_RAT	No assigned EC number	0.9210	0.3095	0.8692	no	N/A
P02269	H2A_ASTRU	No assigned EC number	0.9380	0.3095	0.904	N/A	N/A
Q4FZT6	H2A3_RAT	No assigned EC number	0.9035	0.3095	0.8692	no	N/A
P02262	H2A1_RAT	No assigned EC number	0.9122	0.3095	0.8692	no	N/A
P02263	H2A4_CHICK	No assigned EC number	0.9122	0.3095	0.8759	yes	N/A
P02264	H2A_ONCMY	No assigned EC number	0.9210	0.3095	0.8828	N/A	N/A
Q8CGP5	H2A1F_MOUSE	No assigned EC number	0.9122	0.3095	0.8692	no	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	365
PTZ00017	134	PTZ00017, PTZ00017, histone H2A; Provisional	3e-65
cd00074	115	cd00074, H2A, Histone 2A; H2A is a subunit of the	6e-64
PLN00157	132	PLN00157, PLN00157, histone H2A; Provisional	6e-62
smart00414	106	smart00414, H2A, Histone 2A	9e-61
smart00427	97	smart00427, H2B, Histone H2B	3e-56
PLN00156	139	PLN00156, PLN00156, histone H2AX; Provisional	2e-53
COG5262	132	COG5262, HTA1, Histone H2A [Chromatin structure an	2e-51
PLN00158	116	PLN00158, PLN00158, histone H2B; Provisional	4e-51
PLN00153	129	PLN00153, PLN00153, histone H2A; Provisional	1e-49
PTZ00463	117	PTZ00463, PTZ00463, histone H2B; Provisional	3e-41
PLN00154	136	PLN00154, PLN00154, histone H2A; Provisional	1e-37
PTZ00252	134	PTZ00252, PTZ00252, histone H2A; Provisional	2e-27
pfam00125	75	pfam00125, Histone, Core histone H2A/H2B/H3/H4	2e-23
pfam00125	75	pfam00125, Histone, Core histone H2A/H2B/H3/H4	9e-23
PLN00155	58	PLN00155, PLN00155, histone H2A; Provisional	5e-19
COG5247	113	COG5247, BUR6, Class 2 transcription repressor NC2	4e-05
pfam00808	65	pfam00808, CBFD_NFYB_HMF, Histone-like transcripti	0.003

>gnl|CDD|185399 PTZ00017, PTZ00017, histone H2A; Provisional

 Score =  203 bits (517), Expect = 3e-65
 Identities = 87/116 (75%), Positives = 98/116 (84%), Gaps = 3/116 (2%)

Query: 36  MSGRGKGGKAKAKSK---TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEY 92
             G+GK G  KA  K   +RS++AGLQFPVGR+HR L+KG YA+RVGAGAPVYLAAV+EY
Sbjct: 1   KGGKGKTGGGKAGKKKPVSRSAKAGLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEY 60

Query: 93  LAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           L AEVLELAGNAA+DNKK RI PRH+QLAIRNDEELNKLL+GVTIA GGVLPNI  
Sbjct: 61  LTAEVLELAGNAAKDNKKKRITPRHIQLAIRNDEELNKLLAGVTIASGGVLPNIHK 116

Length = 134

>gnl|CDD|238029 cd00074, H2A, Histone 2A; H2A is a subunit of the nucleosome

 Score =  198 bits (506), Expect = 6e-64
 Identities = 89/106 (83%), Positives = 96/106 (90%)

Query: 42  GGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELA 101
           GGK K+K ++RS+RAGLQFPVGRIHR L+KG YAERVGAGAPVYLAAV+EYL AEVLELA
Sbjct: 3   GGKKKSKKRSRSARAGLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELA 62

Query: 102 GNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQ 147
           GNAARDNKK RI PRHLQLA+RNDEELNKLL GVTIA GGVLPNI 
Sbjct: 63  GNAARDNKKKRITPRHLQLAVRNDEELNKLLKGVTIASGGVLPNIH 108

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. Length = 115

>gnl|CDD|177758 PLN00157, PLN00157, histone H2A; Provisional

 Score =  194 bits (494), Expect = 6e-62
 Identities = 88/115 (76%), Positives = 100/115 (86%), Gaps = 2/115 (1%)

Query: 36  MSGRGK--GGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYL 93
           MSGRGK  GG    K+ +RS++AGLQFPVGRI R L+ G YA RVGAGAPVYLAAV+EYL
Sbjct: 1   MSGRGKRKGGGGGKKATSRSAKAGLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYL 60

Query: 94  AAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           AAEVLELAGNAARDNKK+RI+PRH+QLA+RNDEEL+KLL GVTIA GGVLPNI +
Sbjct: 61  AAEVLELAGNAARDNKKSRIVPRHIQLAVRNDEELSKLLGGVTIAAGGVLPNIHS 115

Length = 132

>gnl|CDD|197711 smart00414, H2A, Histone 2A

 Score =  190 bits (484), Expect = 9e-61
 Identities = 87/98 (88%), Positives = 91/98 (92%)

Query: 51  TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKK 110
           +RS+RAGLQFPVGRIHRLLRKG YA+RVGAGAPVYLAAV+EYL AEVLELAGNAARDNKK
Sbjct: 1   SRSARAGLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKK 60

Query: 111 TRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
            RI PRHLQLAIRNDEELNKLL GVTIAQGGVLPNI  
Sbjct: 61  RRITPRHLQLAIRNDEELNKLLKGVTIAQGGVLPNIHK 98

Length = 106

>gnl|CDD|197718 smart00427, H2B, Histone H2B

 Score =  178 bits (453), Expect = 3e-56
 Identities = 81/97 (83%), Positives = 93/97 (95%)

Query: 267 KKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR 326
           KK+  +RKE+YAIYIYKVLKQVHPDTG+SS+AMSIMNSFVNDIFERIAAE+S+LA YNK+
Sbjct: 1   KKRVKKRKETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKK 60

Query: 327 STITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 363
           ST++SREIQTAVRL+LPGELAKHAVSEGTKAVTK +S
Sbjct: 61  STLSSREIQTAVRLILPGELAKHAVSEGTKAVTKASS 97

Length = 97

>gnl|CDD|215080 PLN00156, PLN00156, histone H2AX; Provisional

 Score =  172 bits (438), Expect = 2e-53
 Identities = 86/114 (75%), Positives = 98/114 (85%), Gaps = 1/114 (0%)

Query: 35  TMSGRGKGGKAKA-KSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYL 93
           + + +G  GK KA KS +RSS+AGLQFPVGRI R L+ G YAERVGAGAPVYL+AV+EYL
Sbjct: 4   SGTTKGGRGKPKATKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYL 63

Query: 94  AAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQ 147
           AAEVLELAGNAARDNKK RI+PRH+QLA+RNDEEL+KLL  VTIA GGVLPNI 
Sbjct: 64  AAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGSVTIAAGGVLPNIH 117

Length = 139

>gnl|CDD|227587 COG5262, HTA1, Histone H2A [Chromatin structure and dynamics]

 Score =  167 bits (424), Expect = 2e-51
 Identities = 89/114 (78%), Positives = 98/114 (85%), Gaps = 2/114 (1%)

Query: 38  GRGKGGKAKA--KSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 95
             GKGGKA     S++RS++AGL FPVGR+ RLL+KGNY  R+GAGAPVYLAAV+EYLAA
Sbjct: 3   SGGKGGKAADARVSQSRSAKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAA 62

Query: 96  EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAG 149
           E+LELAGNAARDNKK RIIPRHLQLAIRNDEELNKLL  VTIAQGGVLPNI  G
Sbjct: 63  EILELAGNAARDNKKKRIIPRHLQLAIRNDEELNKLLGDVTIAQGGVLPNINPG 116

Length = 132

>gnl|CDD|215081 PLN00158, PLN00158, histone H2B; Provisional

 Score =  166 bits (420), Expect = 4e-51
 Identities = 84/121 (69%), Positives = 96/121 (79%), Gaps = 6/121 (4%)

Query: 244 AGKSSGKAVKKAGKAQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMN 303
           A   S K  KKA K  K      KK    + E+Y IYIYKVLKQVHPDTG+SSKAMSIMN
Sbjct: 2   AKTPSKKPAKKAAKGAK------KKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMN 55

Query: 304 SFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 363
           SF+NDIFE+IA E+ +LA YNK+ T+TSREIQTAVRL+LPGELAKHAVSEGTKAVTK+TS
Sbjct: 56  SFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLILPGELAKHAVSEGTKAVTKFTS 115

Query: 364 S 364
           +
Sbjct: 116 A 116

Length = 116

>gnl|CDD|165721 PLN00153, PLN00153, histone H2A; Provisional

 Score =  162 bits (411), Expect = 1e-49
 Identities = 87/113 (76%), Positives = 98/113 (86%)

Query: 36  MSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 95
           M+GRGKG  +  K+ +RS++AGLQFPVGRI R L+KG YAER+GAGAPVYLAAV+EYL A
Sbjct: 1   MAGRGKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTA 60

Query: 96  EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           EVLELAGNAARDNKK RI+PRH+QLAIRNDEEL KLL  VTIA GGVLPNI A
Sbjct: 61  EVLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLLGEVTIASGGVLPNIHA 113

Length = 129

>gnl|CDD|185642 PTZ00463, PTZ00463, histone H2B; Provisional

 Score =  140 bits (353), Expect = 3e-41
 Identities = 75/113 (66%), Positives = 92/113 (81%), Gaps = 2/113 (1%)

Query: 253 KKAGKAQKNIAKSD--KKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIF 310
           KK  KA+K     D  KK+K  R +SY +YI+KVLKQVHPDTG+S K+M+IMNSF+ D F
Sbjct: 4   KKPAKAKKAATGPDGKKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTF 63

Query: 311 ERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 363
           E+IA E+SRL  Y +R T++SREIQTA+RL+LPGELAKHAVSEGTKAVTK+TS
Sbjct: 64  EKIATEASRLCKYTRRDTLSSREIQTAIRLVLPGELAKHAVSEGTKAVTKFTS 116

Length = 117

>gnl|CDD|177756 PLN00154, PLN00154, histone H2A; Provisional

 Score =  131 bits (331), Expect = 1e-37
 Identities = 72/114 (63%), Positives = 84/114 (73%), Gaps = 2/114 (1%)

Query: 35  TMSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVMEYL 93
           T +   K  K K K  +RSSRAGLQFPVGRIHR L++   A  RVGA A VY AA++EYL
Sbjct: 14  TTAAAAKKDKDKKKPTSRSSRAGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYL 73

Query: 94  AAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQ 147
            AEVLELAGNA++D K  RI PRHLQLAIR DEEL+ L+ G TIA GGV+P+I 
Sbjct: 74  TAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIKG-TIAGGGVIPHIH 126

Length = 136

>gnl|CDD|240330 PTZ00252, PTZ00252, histone H2A; Provisional

 Score =  104 bits (261), Expect = 2e-27
 Identities = 54/110 (49%), Positives = 75/110 (68%), Gaps = 2/110 (1%)

Query: 44  KAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGN 103
           KA      RS++AGL FPVGR+  LLR+G YA R+GA   VY+AAV+EYL AE+LEL+  
Sbjct: 10  KASKSGSGRSAKAGLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVK 69

Query: 104 AARDN--KKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAGAA 151
           AA     K  R+ PR + LA+R+D++L  LL  VT+++GGV+P++    A
Sbjct: 70  AAAQQAKKPKRLTPRTVTLAVRHDDDLGSLLKNVTLSRGGVMPSLNKALA 119

Length = 134

>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4

 Score = 92.2 bits (230), Expect = 2e-23
 Identities = 33/75 (44%), Positives = 44/75 (58%), Gaps = 1/75 (1%)

Query: 52  RSSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKK 110
            S    L+ P  R+ R L++G YAE R+ + APV L   +E L  E+LE AG  AR  K+
Sbjct: 1   SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKR 60

Query: 111 TRIIPRHLQLAIRND 125
             I PR +QLA+R D
Sbjct: 61  KTITPRDIQLAVRLD 75

Length = 75

>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4

 Score = 90.3 bits (225), Expect = 9e-23
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 4/75 (5%)

Query: 271 HRRKESYAIYIYKVLKQVHPD----TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR 326
             R     +   +V++++         +SSKA   +   + D+ E I  ++  LA + KR
Sbjct: 1   SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKR 60

Query: 327 STITSREIQTAVRLL 341
            TIT R+IQ AVRL 
Sbjct: 61  KTITPRDIQLAVRLD 75

Length = 75

>gnl|CDD|165723 PLN00155, PLN00155, histone H2A; Provisional

 Score = 79.4 bits (195), Expect = 5e-19
 Identities = 41/58 (70%), Positives = 50/58 (86%)

Query: 36 MSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYL 93
          M+GRGKG  +  K+ +RS++AGLQFPVGRI R L+KG YAER+GAGAPVYLAAV+EYL
Sbjct: 1  MAGRGKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYL 58

Length = 58

>gnl|CDD|227572 COG5247, BUR6, Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]

 Score = 42.3 bits (99), Expect = 4e-05
 Identities = 18/82 (21%), Positives = 37/82 (45%)

Query: 59  QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHL 118
           +FP+ R+ ++++      +VG   PV  +  +E    E++ L+   AR     R+    L
Sbjct: 23  RFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFL 82

Query: 119 QLAIRNDEELNKLLSGVTIAQG 140
           + A  +DE+ + L +       
Sbjct: 83  KRATESDEKFDFLKNMEQFKNR 104

Length = 113

>gnl|CDD|201453 pfam00808, CBFD_NFYB_HMF, Histone-like transcription factor (CBF/NF-Y) and archaeal histone

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 14/63 (22%), Positives = 28/63 (44%)

Query: 60  FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQ 119
            P+ R+ R+++    A R+   A   +A  +E     +   A    +  K+  I   H++
Sbjct: 3   LPIARVKRIMKSDPDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAEHIK 62

Query: 120 LAI 122
           LA+
Sbjct: 63  LAV 65

This family includes archaebacterial histones and histone like transcription factors from eukaryotes. Length = 65

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	365
PLN00158	116	histone H2B; Provisional	100.0
PTZ00463	117	histone H2B; Provisional	100.0
smart00427	89	H2B Histone H2B.	100.0
PLN00153	129	histone H2A; Provisional	100.0
PLN00157	132	histone H2A; Provisional	100.0
PTZ00017	134	histone H2A; Provisional	100.0
PLN00156	139	histone H2AX; Provisional	100.0
KOG1744|consensus	127		100.0
PTZ00252	134	histone H2A; Provisional	100.0
KOG1756|consensus	131		100.0
PLN00154	136	histone H2A; Provisional	100.0
smart00414	106	H2A Histone 2A.	100.0
cd00074	115	H2A Histone 2A; H2A is a subunit of the nucleosome	100.0
COG5262	132	HTA1 Histone H2A [Chromatin structure and dynamics	100.0
KOG1757|consensus	131		100.0
PLN00155	58	histone H2A; Provisional	99.85
PF00125	75	Histone: Core histone H2A/H2B/H3/H4 histone h2a si	99.38
PF00125	75	Histone: Core histone H2A/H2B/H3/H4 histone h2a si	99.26
COG5247	113	BUR6 Class 2 transcription repressor NC2, alpha su	99.06
KOG1659|consensus	224		98.66
PF00808	65	CBFD_NFYB_HMF: Histone-like transcription factor (	98.33
PLN00035	103	histone H4; Provisional	98.2
cd07981	72	TAF12 TATA Binding Protein (TBP) Associated Factor	97.76
PF00808	65	CBFD_NFYB_HMF: Histone-like transcription factor (	97.64
PTZ00015	102	histone H4; Provisional	97.59
COG2036	91	HHT1 Histones H3 and H4 [Chromatin structure and d	97.38
smart00803	65	TAF TATA box binding protein associated factor. TA	97.33
COG2036	91	HHT1 Histones H3 and H4 [Chromatin structure and d	96.93
COG5208	286	HAP5 CCAAT-binding factor, subunit C [Transcriptio	96.74
KOG1657|consensus	236		96.66
PF03847	68	TFIID_20kDa: Transcription initiation factor TFIID	96.65
cd00074	115	H2A Histone 2A; H2A is a subunit of the nucleosome	96.52
cd00076	85	H4 Histone H4, one of the four histones, along wit	96.46
smart00803	65	TAF TATA box binding protein associated factor. TA	96.4
PLN00035	103	histone H4; Provisional	96.27
cd00076	85	H4 Histone H4, one of the four histones, along wit	96.06
PTZ00015	102	histone H4; Provisional	96.01
smart00428	105	H3 Histone H3.	95.9
smart00417	74	H4 Histone H4.	95.9
cd07981	72	TAF12 TATA Binding Protein (TBP) Associated Factor	95.75
cd08048	85	TAF11 TATA Binding Protein (TBP) Associated Factor	95.27
cd07979	117	TAF9 TATA Binding Protein (TBP) Associated Factor	94.88
smart00417	74	H4 Histone H4.	94.53
KOG0869|consensus	168		94.52
PLN00156	139	histone H2AX; Provisional	93.65
KOG0871|consensus	156		93.63
KOG1142|consensus	258		92.95
PLN00153	129	histone H2A; Provisional	92.82
PF02969	66	TAF: TATA box binding protein associated factor (T	92.73
KOG3219|consensus	195		92.5
cd07979	117	TAF9 TATA Binding Protein (TBP) Associated Factor	92.26
smart00414	106	H2A Histone 2A.	92.17
PF04719	90	TAFII28: hTAFII28-like protein conserved region; I	92.05
PTZ00017	134	histone H2A; Provisional	91.74
smart00427	89	H2B Histone H2B.	91.68
PLN00157	132	histone H2A; Provisional	91.47
PLN00158	116	histone H2B; Provisional	91.25
PTZ00252	134	histone H2A; Provisional	91.14
PLN00154	136	histone H2A; Provisional	91.03
PF02969	66	TAF: TATA box binding protein associated factor (T	90.5
cd08050	343	TAF6 TATA Binding Protein (TBP) Associated Factor	90.47
cd08050	343	TAF6 TATA Binding Protein (TBP) Associated Factor	90.17
PF15510	102	CENP-W: Centromere kinetochore component W	89.94
COG5262	132	HTA1 Histone H2A [Chromatin structure and dynamics	89.73
PTZ00463	117	histone H2B; Provisional	89.22
smart00576	77	BTP Bromodomain transcription factors and PHD doma	87.84
KOG0870|consensus	172		86.97
smart00428	105	H3 Histone H3.	86.49
PLN00121	136	histone H3; Provisional	85.96
PF15630	76	CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C	84.89
PTZ00018	136	histone H3; Provisional	84.53
PF09415	72	CENP-X: CENP-S associating Centromere protein X; I	84.44
KOG1756|consensus	131		84.43
smart00576	77	BTP Bromodomain transcription factors and PHD doma	81.96

>PLN00158 histone H2B; Provisional

Probab=100.00  E-value=6.5e-51  Score=345.66  Aligned_cols=114  Identities=72%  Similarity=1.016  Sum_probs=103.8

Q ss_pred             CCCChhhHHhhcccccccccccccccccCccchhhhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcC
Q psy3828         245 GKSSGKAVKKAGKAQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYN  324 (365)
Q Consensus       245 ~~~~~k~~~~~~~~~~~~~~~~~k~~~kr~esy~~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~n  324 (365)
                      ..|++|++++..+.+      ++|++++|+|+|++||||||||||||+|||++||+||||||||||||||.||++|++||
T Consensus         3 ~~~~~k~~~~~~~~~------~kk~~~kr~esy~~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~n   76 (116)
T PLN00158          3 KTPSKKPAKKAAKGA------KKKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYN   76 (116)
T ss_pred             CCcchhhhhhccccc------cccccccccccHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            345677666655543      34567778999999999999999999999999999999999999999999999999999


Q ss_pred             CCcccChhHHHHHHHHhCcHHHHhhHHhhhhhhhhccccC
Q psy3828         325 KRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS  364 (365)
Q Consensus       325 kr~TitsreIqtAvrllLPgeLakhAvseGtkAV~ky~~~  364 (365)
                      +|+|||+||||+||||+|||||+||||+||||||++|+++
T Consensus        77 kr~TltsrEIqtAvrLvLpgELaKhAvsEGtkAv~k~~~~  116 (116)
T PLN00158         77 KKPTVTSREIQTAVRLILPGELAKHAVSEGTKAVTKFTSA  116 (116)
T ss_pred             CCCcCCHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhhcC
Confidence            9999999999999999999999999999999999999985

>PTZ00463 histone H2B; Provisional

Probab=100.00  E-value=9.8e-50  Score=338.36  Aligned_cols=98  Identities=70%  Similarity=1.067  Sum_probs=94.8

Q ss_pred             cccccccCccchhhhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHhCcHH
Q psy3828         266 DKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGE  345 (365)
Q Consensus       266 ~~k~~~kr~esy~~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrllLPge  345 (365)
                      +++++++|+|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+++|||+|||||||||+||||
T Consensus        19 ~kk~~~kr~esy~~YI~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLlLpGE   98 (117)
T PTZ00463         19 KKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLVLPGE   98 (117)
T ss_pred             cccccccccchHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhcccHH
Confidence            45677778999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhHHhhhhhhhhcccc
Q psy3828         346 LAKHAVSEGTKAVTKYTS  363 (365)
Q Consensus       346 LakhAvseGtkAV~ky~~  363 (365)
                      |+||||+||||||+||++
T Consensus        99 LaKhAvsEGtkAv~k~~~  116 (117)
T PTZ00463         99 LAKHAVSEGTKAVTKFTS  116 (117)
T ss_pred             HHHhhhhHHHHHHHHhhc
Confidence            999999999999999986

>smart00427 H2B Histone H2B

Probab=100.00  E-value=1.3e-47  Score=313.26  Aligned_cols=89  Identities=89%  Similarity=1.240  Sum_probs=87.8

Q ss_pred             cchhhhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHhCcHHHHhhHHhhh
Q psy3828         275 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEG  354 (365)
Q Consensus       275 esy~~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrllLPgeLakhAvseG  354 (365)
                      |+|++||||||||||||+|||++||+||||||||||||||.||++|++||+|+|||+||||+||||+|||||+||||+||
T Consensus         1 esy~~Yi~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~LpgeLakhAvsEg   80 (89)
T smart00427        1 ETYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVSEG   80 (89)
T ss_pred             CcHHHHHHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHHccHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhcccc
Q psy3828         355 TKAVTKYTS  363 (365)
Q Consensus       355 tkAV~ky~~  363 (365)
                      ||||+||++
T Consensus        81 tkAv~k~~~   89 (89)
T smart00427       81 TKAVTKYSS   89 (89)
T ss_pred             HHHHHhhcC
Confidence            999999985

>PLN00153 histone H2A; Provisional

Probab=100.00  E-value=2.2e-45  Score=317.84  Aligned_cols=116  Identities=75%  Similarity=1.127  Sum_probs=112.4

Q ss_pred             cCCCCCCCCCCCCCCCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccc
Q psy3828          36 MSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIP  115 (365)
Q Consensus        36 mSg~gkggk~~~k~~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP  115 (365)
                      |||+|||++.+++..|||+|||||||||||+|||++++|+.||+++||||||||||||++||||||+|+|++++++||+|
T Consensus         1 m~g~~~~~~~~~k~~srS~ragL~FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItP   80 (129)
T PLN00153          1 MAGRGKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVP   80 (129)
T ss_pred             CCCCCCCCccccCccCcccccCcccchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCh
Confidence            89999876666788999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhcCcHHHHhhhcCCeecCCcccCCcccccc
Q psy3828         116 RHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAGAA  151 (365)
Q Consensus       116 ~hI~lAI~nDeEL~~Lf~~vtIa~GGV~P~i~~gl~  151 (365)
                      +||++||+||+|||+||+++||++|||+|+||+.+.
T Consensus        81 rHi~lAI~nDeEL~~Ll~~vTIa~GGV~P~i~~~l~  116 (129)
T PLN00153         81 RHIQLAIRNDEELGKLLGEVTIASGGVLPNIHAVLL  116 (129)
T ss_pred             HHHHhhccCcHHHHHHHCCCccCCCccCCCcchhhc
Confidence            999999999999999999999999999999999986

>PLN00157 histone H2A; Provisional

Probab=100.00  E-value=1.1e-44  Score=314.72  Aligned_cols=116  Identities=76%  Similarity=1.156  Sum_probs=112.0

Q ss_pred             cCCCCC--CCCCCCCCCCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccc
Q psy3828          36 MSGRGK--GGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRI  113 (365)
Q Consensus        36 mSg~gk--ggk~~~k~~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrI  113 (365)
                      |||+|+  +++++++..|+|+|||||||||||+|||++++|+.||+++||||||||||||++||||||+|+|++++++||
T Consensus         1 ms~~g~~~~~~~~~k~~srS~ragL~FPVgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RI   80 (132)
T PLN00157          1 MSGRGKRKGGGGGKKATSRSAKAGLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRI   80 (132)
T ss_pred             CCCCCCCCCCccCcCCcCcccccCcccchHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccc
Confidence            899987  556677889999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cchhhhhhhcCcHHHHhhhcCCeecCCcccCCcccccc
Q psy3828         114 IPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAGAA  151 (365)
Q Consensus       114 tP~hI~lAI~nDeEL~~Lf~~vtIa~GGV~P~i~~gl~  151 (365)
                      +|+||++||+||+||++||+++||++|||+|+||+.+.
T Consensus        81 tPrHi~lAI~nDeEL~~Ll~~vtIa~GGV~P~i~~~ll  118 (132)
T PLN00157         81 VPRHIQLAVRNDEELSKLLGGVTIAAGGVLPNIHSVLL  118 (132)
T ss_pred             cHHHHhhcccCcHHHHHHHcCceecCCccCCCcchhhc
Confidence            99999999999999999999999999999999999986

>PTZ00017 histone H2A; Provisional

Probab=100.00  E-value=5e-43  Score=305.08  Aligned_cols=116  Identities=74%  Similarity=1.123  Sum_probs=107.8

Q ss_pred             cCCCCCC-CCC--CCCCCCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCcc
Q psy3828          36 MSGRGKG-GKA--KAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTR  112 (365)
Q Consensus        36 mSg~gkg-gk~--~~k~~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkr  112 (365)
                      |||+|+. +++  +++..|+|+||||||||+||+|||++++|+.||+++|||||+||||||++||||||+|+|++++++|
T Consensus         1 ~~~~~~~~~~~~~~~k~~srS~ragL~FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~R   80 (134)
T PTZ00017          1 KGGKGKTGGGKAGKKKPVSRSAKAGLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKR   80 (134)
T ss_pred             CCCCCcCCCCcccCcCcccccccCCcccchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCe
Confidence            4566542 222  5567899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccchhhhhhhcCcHHHHhhhcCCeecCCcccCCcccccc
Q psy3828         113 IIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAGAA  151 (365)
Q Consensus       113 ItP~hI~lAI~nDeEL~~Lf~~vtIa~GGV~P~i~~gl~  151 (365)
                      |+|+||++||+||+|||+||+++||++|||+|+||+.+.
T Consensus        81 ItPrHi~lAI~nDeEL~~Ll~~vtIa~GGV~P~i~~~l~  119 (134)
T PTZ00017         81 ITPRHIQLAIRNDEELNKLLAGVTIASGGVLPNIHKVLL  119 (134)
T ss_pred             ecHHHHHhhccCcHHHHHHHcCCcccCCccCCCccHhhc
Confidence            999999999999999999999999999999999999986

>PLN00156 histone H2AX; Provisional

Probab=100.00  E-value=3.7e-43  Score=306.98  Aligned_cols=112  Identities=74%  Similarity=1.119  Sum_probs=107.3

Q ss_pred             CCCCCCCCCCCCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhh
Q psy3828          40 GKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQ  119 (365)
Q Consensus        40 gkggk~~~k~~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~  119 (365)
                      |+|++++++..|||+||||||||+||+|||++++|+.||+++|||||+||||||++||||||+|+|++++++||+|+||+
T Consensus        10 ~~g~~~~~k~~srS~rAgL~FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~   89 (139)
T PLN00156         10 GRGKPKATKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQ   89 (139)
T ss_pred             CCCcccccCCcCcccccCcccchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHH
Confidence            34456677889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhcCcHHHHhhhcCCeecCCcccCCcccccc
Q psy3828         120 LAIRNDEELNKLLSGVTIAQGGVLPNIQAGAA  151 (365)
Q Consensus       120 lAI~nDeEL~~Lf~~vtIa~GGV~P~i~~gl~  151 (365)
                      +||+||+|||+||+++||++|||+|+||+.+.
T Consensus        90 lAIrnDeEL~~Ll~~vTIa~GGV~P~i~~~l~  121 (139)
T PLN00156         90 LAVRNDEELSKLLGSVTIAAGGVLPNIHQTLL  121 (139)
T ss_pred             hhccCcHHHHHHHCCCccCCCccCCCccHhhc
Confidence            99999999999999999999999999999986

>KOG1744|consensus

Probab=100.00  E-value=8.2e-43  Score=300.25  Aligned_cols=99  Identities=86%  Similarity=1.188  Sum_probs=96.6

Q ss_pred             ccccccCccchhhhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHhCcHHH
Q psy3828         267 KKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGEL  346 (365)
Q Consensus       267 ~k~~~kr~esy~~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrllLPgeL  346 (365)
                      |++..++.|+|+.||||||||||||+|||++||+||||||||||||||.||++|++||+|+||++||||+||||+|||||
T Consensus        29 k~~~~~~~e~~s~yv~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLllPgel  108 (127)
T KOG1744|consen   29 KKRSTRRKESYSEYVYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLLLPGEL  108 (127)
T ss_pred             ccCcccccCceeeehhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHhCchHH
Confidence            56778899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhHHhhhhhhhhccccCC
Q psy3828         347 AKHAVSEGTKAVTKYTSSK  365 (365)
Q Consensus       347 akhAvseGtkAV~ky~~~k  365 (365)
                      +|||++||||||++|+++|
T Consensus       109 ~khA~seGtkav~ky~~sk  127 (127)
T KOG1744|consen  109 AKHAVSEGTKAVTKYTSSK  127 (127)
T ss_pred             hhhhhcccchhheeeccCC
Confidence            9999999999999999986

>PTZ00252 histone H2A; Provisional

Probab=100.00  E-value=4.7e-42  Score=298.11  Aligned_cols=104  Identities=52%  Similarity=0.899  Sum_probs=99.7

Q ss_pred             CCCC-cccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhh--cCCccccchhhhhhhcC
Q psy3828          48 KSKT-RSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARD--NKKTRIIPRHLQLAIRN  124 (365)
Q Consensus        48 k~~S-rSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~--~kkkrItP~hI~lAI~n  124 (365)
                      +..+ ||+|||||||||||+|||++++|+.||+++||||||||||||++||||||||+|++  ++++||+|+||++||+|
T Consensus        13 ~~~~~rS~rAGL~FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrN   92 (134)
T PTZ00252         13 KSGSGRSAKAGLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRH   92 (134)
T ss_pred             ccccccccccCccCchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccC
Confidence            3455 99999999999999999999999999999999999999999999999999999976  78899999999999999


Q ss_pred             cHHHHhhhcCCeecCCcccCCcccccc
Q psy3828         125 DEELNKLLSGVTIAQGGVLPNIQAGAA  151 (365)
Q Consensus       125 DeEL~~Lf~~vtIa~GGV~P~i~~gl~  151 (365)
                      |+|||+||+++||++|||+|+||+.+.
T Consensus        93 DeEL~~Ll~~vTIa~GGVlP~i~~~l~  119 (134)
T PTZ00252         93 DDDLGSLLKNVTLSRGGVMPSLNKALA  119 (134)
T ss_pred             hHHHHHHHcCCccCCCccCCCccHhhc
Confidence            999999999999999999999999986

>KOG1756|consensus

Probab=100.00  E-value=6.8e-42  Score=293.92  Aligned_cols=116  Identities=86%  Similarity=1.224  Sum_probs=110.2

Q ss_pred             cCCCCCCCCCC---CCCCCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCcc
Q psy3828          36 MSGRGKGGKAK---AKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTR  112 (365)
Q Consensus        36 mSg~gkggk~~---~k~~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkr  112 (365)
                      |||+|++||.+   +++.++|.|+|||||||||+|+|++++|++||+.+|||||+||||||++||||+|+|+|+++++.|
T Consensus         1 ~s~~~k~gk~~~~~~~~~srs~~agl~fPvgri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~r   80 (131)
T KOG1756|consen    1 MSGRGKGGKAKPRAKAKSSRSSRAGLQFPVGRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTR   80 (131)
T ss_pred             CCccCCCCcccchhhhhcchhhhcccccCHHHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccc
Confidence            68888877653   446788999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccchhhhhhhcCcHHHHhhhcCCeecCCcccCCcccccc
Q psy3828         113 IIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAGAA  151 (365)
Q Consensus       113 ItP~hI~lAI~nDeEL~~Lf~~vtIa~GGV~P~i~~gl~  151 (365)
                      |+|+||++||+||+||++|+++|||++|||+|+||+.+.
T Consensus        81 i~PrH~~lAI~NDeEL~~lL~~vtIa~GGvlPnI~~~lL  119 (131)
T KOG1756|consen   81 ITPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAILL  119 (131)
T ss_pred             cChHHHHHHHhCcHHHHHHhccceeccCCcccccchhhc
Confidence            999999999999999999999999999999999999986

>PLN00154 histone H2A; Provisional

Probab=100.00  E-value=7.4e-41  Score=291.44  Aligned_cols=106  Identities=63%  Similarity=0.909  Sum_probs=101.3

Q ss_pred             CCCCCCCcccccccccchhhhhhhhhcCC-cccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          45 AKAKSKTRSSRAGLQFPVGRIHRLLRKGN-YAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        45 ~~~k~~SrSsRAgLqFPVsRI~RlLke~~-ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      .+++..|||+||||||||+||||+|++++ |.+||+++|||||+||||||++||||||||+|++++++||+|+||++||+
T Consensus        24 ~~~k~~srS~rAgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr  103 (136)
T PLN00154         24 DKKKPTSRSSRAGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR  103 (136)
T ss_pred             CCcCCcCcccccCccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence            34578999999999999999999999997 57899999999999999999999999999999999999999999999999


Q ss_pred             CcHHHHhhhcCCeecCCcccCCcccccc
Q psy3828         124 NDEELNKLLSGVTIAQGGVLPNIQAGAA  151 (365)
Q Consensus       124 nDeEL~~Lf~~vtIa~GGV~P~i~~gl~  151 (365)
                      ||+||++||+ +||++|||+|+||+.+.
T Consensus       104 nDeEL~~Ll~-~TIa~GGVlP~i~~~l~  130 (136)
T PLN00154        104 GDEELDTLIK-GTIAGGGVIPHIHKSLI  130 (136)
T ss_pred             CcHHHHHHhc-CCccCCccCCCcchhhc
Confidence            9999999998 69999999999999986

>smart00414 H2A Histone 2A

Probab=100.00  E-value=9.8e-41  Score=281.19  Aligned_cols=101  Identities=86%  Similarity=1.245  Sum_probs=99.2

Q ss_pred             CcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHHHh
Q psy3828          51 TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNK  130 (365)
Q Consensus        51 SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL~~  130 (365)
                      |||+|||||||||||+|||++++|++||+++|+|||+||||||++||||||+|+|++++++||+|+||++||+||+|||+
T Consensus         1 srS~ragL~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~nD~EL~~   80 (106)
T smart00414        1 SRSARAGLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRNDEELNK   80 (106)
T ss_pred             CccccCCccCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccCCHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCCeecCCcccCCcccccc
Q psy3828         131 LLSGVTIAQGGVLPNIQAGAA  151 (365)
Q Consensus       131 Lf~~vtIa~GGV~P~i~~gl~  151 (365)
                      ||+++||++|||+|+||+.+.
T Consensus        81 L~~~vti~~ggv~p~i~~~l~  101 (106)
T smart00414       81 LLKGVTIAQGGVLPNIHKVLL  101 (106)
T ss_pred             HHcCcccCCCccCCCcchhhc
Confidence            999999999999999999875

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

Probab=100.00  E-value=2.1e-40  Score=282.77  Aligned_cols=109  Identities=81%  Similarity=1.193  Sum_probs=105.7

Q ss_pred             CCCCCCCCCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhh
Q psy3828          43 GKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAI  122 (365)
Q Consensus        43 gk~~~k~~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI  122 (365)
                      ||++++.+|+|+||||||||+||+|||++++|+.||+++|+|||+||||||++||||+|+|.|+++++++|+|+||++||
T Consensus         4 ~k~~~~~~s~s~ragL~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi   83 (115)
T cd00074           4 GKKKSKKRSRSARAGLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAV   83 (115)
T ss_pred             CccCcCccccccccCccCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHH
Confidence            46777889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCcHHHHhhhcCCeecCCcccCCcccccc
Q psy3828         123 RNDEELNKLLSGVTIAQGGVLPNIQAGAA  151 (365)
Q Consensus       123 ~nDeEL~~Lf~~vtIa~GGV~P~i~~gl~  151 (365)
                      +||+|||+||+++||++|||+|+||+.+.
T Consensus        84 ~nD~EL~~L~~~vtI~~ggv~p~i~~~l~  112 (115)
T cd00074          84 RNDEELNKLLKGVTIASGGVLPNIHKVLL  112 (115)
T ss_pred             hccHHHHHHHcCCcccCCccCCCcchhhc
Confidence            99999999999999999999999999875

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.

>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]

Probab=100.00  E-value=2.1e-40  Score=281.56  Aligned_cols=114  Identities=79%  Similarity=1.182  Sum_probs=107.3

Q ss_pred             CCCCCC-CCCC-CCCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccch
Q psy3828          39 RGKGGK-AKAK-SKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPR  116 (365)
Q Consensus        39 ~gkggk-~~~k-~~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~  116 (365)
                      .||||| ...+ ..++|.++||+||||||+|+|++++|.+||++.|+||++||||||++||||+|+|+|++++++||+|+
T Consensus         4 ~GKGgK~a~~r~~~s~sa~agl~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~Pr   83 (132)
T COG5262           4 GGKGGKAADARVSQSRSAKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPR   83 (132)
T ss_pred             CCcCcccccchhccchhhhcCccccHHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechH
Confidence            377787 3333 47999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhcCcHHHHhhhcCCeecCCcccCCccccccc
Q psy3828         117 HLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAGAAL  152 (365)
Q Consensus       117 hI~lAI~nDeEL~~Lf~~vtIa~GGV~P~i~~gl~l  152 (365)
                      ||++||+||+||++|+++|||++|||+|||++++.+
T Consensus        84 HlqlAIrnD~EL~~l~~~~tIa~GGvlp~I~~~ll~  119 (132)
T COG5262          84 HLQLAIRNDEELNKLLGDVTIAQGGVLPNINPGLLP  119 (132)
T ss_pred             HHHHHhcCcHHHHHHhhhheeecCCcccccChhhhh
Confidence            999999999999999999999999999999999864

>KOG1757|consensus

Probab=100.00  E-value=2.6e-34  Score=242.94  Aligned_cols=105  Identities=63%  Similarity=0.913  Sum_probs=99.1

Q ss_pred             CCCCCcccccccccchhhhhhhhhcCCc-ccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCc
Q psy3828          47 AKSKTRSSRAGLQFPVGRIHRLLRKGNY-AERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND  125 (365)
Q Consensus        47 ~k~~SrSsRAgLqFPVsRI~RlLke~~y-a~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nD  125 (365)
                      .+.+++|.|+||||||+||||+|+.... ..||++.+.||.+|+||||++|+||||||++++.+.+||||+|+|+||+.|
T Consensus        18 ~k~vs~s~raGlqFpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiRGD   97 (131)
T KOG1757|consen   18 AKAVSRSARAGLQFPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGD   97 (131)
T ss_pred             hhhhhHHHhcccccchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheeeecCc
Confidence            5678999999999999999999998654 589999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhcCCeecCCcccCCccccccc
Q psy3828         126 EELNKLLSGVTIAQGGVLPNIQAGAAL  152 (365)
Q Consensus       126 eEL~~Lf~~vtIa~GGV~P~i~~gl~l  152 (365)
                      |||+.|++ .||+.|||+||||+.+..
T Consensus        98 eELDtLIk-~TiagGgViPhihk~l~~  123 (131)
T KOG1757|consen   98 EELDTLIK-ATIAGGGVIPHIHKSLIN  123 (131)
T ss_pred             HHHHHHHH-HhhccCccccchHHHHhc
Confidence            99999997 589999999999999864

>PLN00155 histone H2A; Provisional

Probab=99.85  E-value=6.6e-22  Score=150.26  Aligned_cols=58  Identities=71%  Similarity=1.180  Sum_probs=54.5

Q ss_pred             cCCCCCCCCCCCCCCCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHH
Q psy3828          36 MSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYL   93 (365)
Q Consensus        36 mSg~gkggk~~~k~~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYL   93 (365)
                      |||+|||++..++.+++|+||||||||+||+|+|++++|+.||+++||||||||||||
T Consensus         1 msg~g~g~~~~~k~~srS~rAgL~FPVgri~r~Lr~g~~a~Rvga~apVYlAAVLEYL   58 (58)
T PLN00155          1 MAGRGKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYL   58 (58)
T ss_pred             CCCCCCCCccccCccCcccccccccchHHHHHHHhcCChhhcccCCcHHHHHHHHHhC
Confidence            8999887666667899999999999999999999999999999999999999999997

>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=99.38  E-value=3.7e-13  Score=104.97  Aligned_cols=69  Identities=30%  Similarity=0.423  Sum_probs=65.9

Q ss_pred             cCccchhhhhhhhhhhcCCC----CCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         272 RRKESYAIYIYKVLKQVHPD----TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       272 kr~esy~~YIykVLKQVhpd----~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      ++...++.||+|++|+++++    ..||++||.+|+++++|++++|.++|..++.++||.||+++|||.|+|+
T Consensus         2 ~~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~   74 (75)
T PF00125_consen    2 TRRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRI   74 (75)
T ss_dssp             HSHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHH
T ss_pred             cccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhc
Confidence            35678999999999999999    8999999999999999999999999999999999999999999999986

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 ....

>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=99.26  E-value=3e-12  Score=99.82  Aligned_cols=73  Identities=41%  Similarity=0.607  Sum_probs=68.5

Q ss_pred             ccccccccchhhhhhhhhcCCccc-ccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCc
Q psy3828          53 SSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND  125 (365)
Q Consensus        53 SsRAgLqFPVsRI~RlLke~~ya~-RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nD  125 (365)
                      +.+..+.||+.|+.+-+.++.+.. ||+..|.+||.+++||++.+|+|.|++.|..+++++|+|+||+.|+++|
T Consensus         2 ~~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~~   75 (75)
T PF00125_consen    2 TRRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRID   75 (75)
T ss_dssp             HSHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHHT
T ss_pred             cccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhcC
Confidence            456789999999999999987774 9999999999999999999999999999999999999999999999876

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 ....

>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]

Probab=99.06  E-value=1.8e-10  Score=96.91  Aligned_cols=79  Identities=23%  Similarity=0.456  Sum_probs=75.3

Q ss_pred             ccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHHHhhhc
Q psy3828          55 RAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLS  133 (365)
Q Consensus        55 RAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL~~Lf~  133 (365)
                      +-.-.||++|++++||-++...+|++.+||...-.||+++.+|+.+++.+|+..+.+|||.+||..|+.+|+.+++|-.
T Consensus        19 ~~ktrFP~ar~KkIMQ~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~   97 (113)
T COG5247          19 KKKTRFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKN   97 (113)
T ss_pred             hhhhcCCHHHHHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHH
Confidence            4566899999999999999999999999999999999999999999999999999999999999999999999999854

>KOG1659|consensus

Probab=98.66  E-value=2.3e-08  Score=93.67  Aligned_cols=78  Identities=19%  Similarity=0.383  Sum_probs=73.9

Q ss_pred             ccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHHHhhh
Q psy3828          55 RAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLL  132 (365)
Q Consensus        55 RAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL~~Lf  132 (365)
                      +-.-.||++||+++||-+....+|...+||.+.-.||.|+.+|+..++.+++..+.+++++.||..||.||+.|++|-
T Consensus         9 ~~~trfp~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk   86 (224)
T KOG1659|consen    9 KYKTRFPPARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLK   86 (224)
T ss_pred             hhhccCCHHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHH
Confidence            334579999999999999999999999999999999999999999999999999999999999999999999999883

>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=98.33  E-value=7.2e-07  Score=68.35  Aligned_cols=64  Identities=20%  Similarity=0.288  Sum_probs=57.8

Q ss_pred             ccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhh
Q psy3828          59 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAI  122 (365)
Q Consensus        59 qFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI  122 (365)
                      .||+++|+|+|+......+|+..|...++-+.|.++.+|...|...|...+++.|+++||..||
T Consensus         2 ~lP~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av   65 (65)
T PF00808_consen    2 SLPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV   65 (65)
T ss_dssp             SS-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred             CCChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence            5999999999999867789999999999999999999999999999999999999999999875

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 ....

>PLN00035 histone H4; Provisional

Probab=98.20  E-value=1.2e-06  Score=74.32  Aligned_cols=85  Identities=27%  Similarity=0.393  Sum_probs=70.4

Q ss_pred             cCCCCCCCCC----CCCC---CCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhc
Q psy3828          36 MSGRGKGGKA----KAKS---KTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDN  108 (365)
Q Consensus        36 mSg~gkggk~----~~k~---~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~  108 (365)
                      |||+|||||.    ..++   ..+.+-+|  +|..-|.|+.+.+. +.||+.++-..|..+||.+..+|+.-|...|...
T Consensus         1 m~~~~k~~~g~g~~g~kr~~k~~~d~i~~--ipk~~IrRLARr~G-vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA   77 (103)
T PLN00035          1 MSGRGKGGKGLGKGGAKRHRKVLRDNIQG--ITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHA   77 (103)
T ss_pred             CCCCCCCCCCCCCCcchHHHHHHHhhhcc--CCHHHHHHHHHHcC-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            8899886543    2222   23334455  77778999999974 8999999999999999999999999999999999


Q ss_pred             CCccccchhhhhhhc
Q psy3828         109 KKTRIIPRHLQLAIR  123 (365)
Q Consensus       109 kkkrItP~hI~lAI~  123 (365)
                      +++.|+.+||.+|+.
T Consensus        78 ~RKTV~~~DV~~Alk   92 (103)
T PLN00035         78 RRKTVTAMDVVYALK   92 (103)
T ss_pred             CCCcCcHHHHHHHHH
Confidence            999999999999875

>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=97.76  E-value=9.6e-05  Score=58.41  Aligned_cols=60  Identities=17%  Similarity=0.402  Sum_probs=57.2

Q ss_pred             hhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         281 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       281 IykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      +...+|++.|...++..|...|-.+..|+.+.++.+|.+||.+.++.||..+|||-+++-
T Consensus         7 l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r   66 (72)
T cd07981           7 LQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLER   66 (72)
T ss_pred             HHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence            667899999999999999999999999999999999999999999999999999999864

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

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

Probab=97.64  E-value=0.00015  Score=55.49  Aligned_cols=57  Identities=28%  Similarity=0.480  Sum_probs=51.9

Q ss_pred             hhhhhhhcCCCC-CcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHH
Q psy3828         281 IYKVLKQVHPDT-GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAV  338 (365)
Q Consensus       281 IykVLKQVhpd~-gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAv  338 (365)
                      |.|++|+. |+. .||.+|...|+.....+.+.|+.+|...+..++|+||+.+||..||
T Consensus         8 vkri~k~~-~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av   65 (65)
T PF00808_consen    8 VKRIMKSD-PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV   65 (65)
T ss_dssp             HHHHHHHT-STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred             HHHHhccC-CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence            78999998 775 5999999999999999999999999999999999999999999986

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 ....

>PTZ00015 histone H4; Provisional

Probab=97.59  E-value=0.00012  Score=62.05  Aligned_cols=69  Identities=17%  Similarity=0.289  Sum_probs=60.0

Q ss_pred             cccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          52 RSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        52 rSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      +.+-.|  +|..-|.|+.+.+ =+.||+.++-..+..+||.++.+|+.-|...|...+++.|+.+||.+|+.
T Consensus        25 r~~i~g--I~k~~IrRLarr~-GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlK   93 (102)
T PTZ00015         25 RDNIRG--ITKGAIRRLARRG-GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALK   93 (102)
T ss_pred             hhcccC--CCHHHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHH
Confidence            344445  4555699999986 67899999999999999999999999999999999999999999999874

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

Probab=97.38  E-value=0.00033  Score=58.37  Aligned_cols=63  Identities=25%  Similarity=0.407  Sum_probs=59.1

Q ss_pred             hhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHhCcH
Q psy3828         281 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPG  344 (365)
Q Consensus       281 IykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrllLPg  344 (365)
                      |-|++|++-++ .+|..|...|+..+..+++-|+.+|..+|.+.+|+||+..||+.|.+.+.+.
T Consensus        25 v~Ri~r~~~~~-Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~   87 (91)
T COG2036          25 VRRILRKAGAE-RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRR   87 (91)
T ss_pred             HHHHHHHHhHH-HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhccc
Confidence            77888888888 9999999999999999999999999999999999999999999999987654

>smart00803 TAF TATA box binding protein associated factor

Probab=97.33  E-value=0.0004  Score=54.22  Aligned_cols=64  Identities=22%  Similarity=0.267  Sum_probs=58.4

Q ss_pred             ccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          59 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        59 qFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      .+|..-|.|+.+... ..||+..+...|+-.+||.+.||++-|.+.++..+++.++++||..|++
T Consensus         2 ~~p~~~i~ria~~~G-i~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk   65 (65)
T smart00803        2 WLPKETIKDVAESLG-IGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR   65 (65)
T ss_pred             CCCHHHHHHHHHHCC-CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence            478888999999864 4599999999999999999999999999999999999999999998863

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=96.93  E-value=0.0009  Score=55.79  Aligned_cols=67  Identities=30%  Similarity=0.393  Sum_probs=59.9

Q ss_pred             cccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          56 AGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        56 AgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      ..+-+|+.=|.|+|++. -..||+.+|-..|.-++|-++.+|.|.|...|...|++.|++++|++|+.
T Consensus        16 ~~~~Lp~apv~Ri~r~~-~~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~   82 (91)
T COG2036          16 TDLLLPKAPVRRILRKA-GAERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALK   82 (91)
T ss_pred             hhhhcCchHHHHHHHHH-hHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHH
Confidence            34567777799999984 44599999999999999999999999999999999999999999999975

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

Probab=96.74  E-value=0.0023  Score=61.10  Aligned_cols=77  Identities=22%  Similarity=0.383  Sum_probs=71.6

Q ss_pred             ccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHHHhhhc
Q psy3828          57 GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLS  133 (365)
Q Consensus        57 gLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL~~Lf~  133 (365)
                      -+.+|..||+++|+.+....-|++.|||.++.+-|-+++|+--.|.-.|..|++..+.-.+|..|+...+-+++|+-
T Consensus       107 ~h~LPlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLid  183 (286)
T COG5208         107 DHNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLID  183 (286)
T ss_pred             hccCcHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHhh
Confidence            34599999999999998889999999999999999999999999998899999988999999999999999999974

>KOG1657|consensus

Probab=96.66  E-value=0.0013  Score=63.12  Aligned_cols=83  Identities=18%  Similarity=0.260  Sum_probs=74.8

Q ss_pred             cccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHHHhh
Q psy3828          52 RSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKL  131 (365)
Q Consensus        52 rSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL~~L  131 (365)
                      ...-....||.+||+++||......-|+..|||.++-++|+++.|+-..++..+..++++.+.-.||..++.+.+-+++|
T Consensus        67 ~~d~~~~~lPlaRiKkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL  146 (236)
T KOG1657|consen   67 QLDFKNHILPLARIKKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFL  146 (236)
T ss_pred             ccchhhccCcHhhccccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccce
Confidence            33344678999999999999999999999999999999999999999999999999999888889999999999999999


Q ss_pred             hcC
Q psy3828         132 LSG  134 (365)
Q Consensus       132 f~~  134 (365)
                      ...
T Consensus       147 ~Di  149 (236)
T KOG1657|consen  147 RDI  149 (236)
T ss_pred             ecc
Confidence            753

>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=96.65  E-value=0.0055  Score=48.41  Aligned_cols=59  Identities=19%  Similarity=0.412  Sum_probs=48.5

Q ss_pred             hhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         281 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       281 IykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      +-..++||-|...+...+..+|-.+.+|+.+.+..-|++||++.+..||..+|||....
T Consensus         5 l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Le   63 (68)
T PF03847_consen    5 LQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLE   63 (68)
T ss_dssp             HHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHH
T ss_pred             HHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHH
Confidence            56789999999999999999999999999999999999999999999999999997654

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

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

Probab=96.52  E-value=0.0093  Score=51.66  Aligned_cols=60  Identities=25%  Similarity=0.257  Sum_probs=55.3

Q ss_pred             hhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         280 YIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       280 YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      =|+|.||+-.--.-||..|.--|-..+.++...|.+.|.+.++.+++++||+|+|+.|++
T Consensus        25 ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~   84 (115)
T cd00074          25 RIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVR   84 (115)
T ss_pred             HHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHh
Confidence            389999986556889999999999999999999999999999999999999999999998

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.

>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=96.46  E-value=0.0046  Score=50.96  Aligned_cols=70  Identities=20%  Similarity=0.318  Sum_probs=61.3

Q ss_pred             cccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcC
Q psy3828          52 RSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN  124 (365)
Q Consensus        52 rSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~n  124 (365)
                      +.+-+|  +|..-|.|+.+.+. ..|||.++-.-+..+||.+..+|+..|...+...+++.|++++|.+|+..
T Consensus         8 ~~~~~g--i~k~~I~RLarr~G-vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr   77 (85)
T cd00076           8 RDNIKG--ITKPAIRRLARRGG-VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKR   77 (85)
T ss_pred             HHhhcc--CCHHHHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence            344456  56667999999975 89999999999999999999999999999999999999999999998763

>smart00803 TAF TATA box binding protein associated factor

Probab=96.40  E-value=0.009  Score=46.65  Aligned_cols=59  Identities=24%  Similarity=0.327  Sum_probs=51.5

Q ss_pred             hhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         280 YIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       280 YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      .|.++.+..-= ..||..+..-|-..+.+..+.|+.||..++++.+|+|+|..||-.|.|
T Consensus         7 ~i~ria~~~Gi-~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk   65 (65)
T smart00803        7 TIKDVAESLGI-GNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR   65 (65)
T ss_pred             HHHHHHHHCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence            36777777643 368999999999999999999999999999999999999999988864

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.

>PLN00035 histone H4; Provisional

Probab=96.27  E-value=0.014  Score=49.83  Aligned_cols=59  Identities=12%  Similarity=0.183  Sum_probs=53.4

Q ss_pred             hhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         281 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       281 IykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      |.|+++.-- --.||..+..-+...+.+++|.|+.+|..++.+.+|+|++..||-.|++.
T Consensus        35 IrRLARr~G-vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr   93 (103)
T PLN00035         35 IRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR   93 (103)
T ss_pred             HHHHHHHcC-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence            778887754 46799999999999999999999999999999999999999999999874

>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=96.06  E-value=0.015  Score=48.01  Aligned_cols=60  Identities=13%  Similarity=0.209  Sum_probs=52.4

Q ss_pred             hhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         280 YIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       280 YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      -|.|+.+.-- -..||..++.-+...+...+|.|+.+|..++.+.+|+|++..||-.|++.
T Consensus        18 ~I~RLarr~G-vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr   77 (85)
T cd00076          18 AIRRLARRGG-VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKR   77 (85)
T ss_pred             HHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence            3677777643 45689999999999999999999999999999999999999999988863

>PTZ00015 histone H4; Provisional

Probab=96.01  E-value=0.015  Score=49.59  Aligned_cols=61  Identities=15%  Similarity=0.262  Sum_probs=53.1

Q ss_pred             hhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         279 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       279 ~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      .-|.|+++.- ---.||..+..-+...++++++.|+.+|..++.+.+|+|+|..||--|++.
T Consensus        34 ~~IrRLarr~-GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr   94 (102)
T PTZ00015         34 GAIRRLARRG-GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKR   94 (102)
T ss_pred             HHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHh
Confidence            3477777764 335699999999999999999999999999999999999999999988764

>smart00428 H3 Histone H3

Probab=95.90  E-value=0.029  Score=48.04  Aligned_cols=68  Identities=22%  Similarity=0.312  Sum_probs=62.4

Q ss_pred             CccchhhhhhhhhhhcCC--CCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         273 RKESYAIYIYKVLKQVHP--DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       273 r~esy~~YIykVLKQVhp--d~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      ++-.|+..+..+..+..+  +.-+++.|+..|.....+....+.++|..++.+.||.||..+|||-|.|+
T Consensus        31 ~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~ri  100 (105)
T smart00428       31 RKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRI  100 (105)
T ss_pred             ccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHH
Confidence            456788888888888888  88999999999999999999999999999999999999999999999886

>smart00417 H4 Histone H4

Probab=95.90  E-value=0.013  Score=47.24  Aligned_cols=67  Identities=18%  Similarity=0.201  Sum_probs=57.3

Q ss_pred             cccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhh
Q psy3828          52 RSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLA  121 (365)
Q Consensus        52 rSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lA  121 (365)
                      +.+-.|  +|..-|.|+++.+ =+.|||..+-..+..+||.+..+|+..|...|...+++.|+.+++..|
T Consensus         8 ~d~i~g--I~k~~IrRLaRr~-GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a   74 (74)
T smart00417        8 RDNIQG--ITKPAIRRLARRG-GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA   74 (74)
T ss_pred             HhhhcC--CCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence            334456  4555699999996 578999999999999999999999999999999999999999998654

>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=95.75  E-value=0.019  Score=45.41  Aligned_cols=65  Identities=17%  Similarity=0.274  Sum_probs=58.2

Q ss_pred             chhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCc
Q psy3828          61 PVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND  125 (365)
Q Consensus        61 PVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nD  125 (365)
                      +-..+..++++..-..|++.+|...|..+.|-++.+|++.|...|+..+++.|.+++|++++..+
T Consensus         3 ~k~~l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~   67 (72)
T cd07981           3 TKRKLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERN   67 (72)
T ss_pred             cHHHHHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            34567778888666689999999999999999999999999999999999999999999998765

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

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

Probab=95.27  E-value=0.042  Score=45.22  Aligned_cols=63  Identities=25%  Similarity=0.419  Sum_probs=54.3

Q ss_pred             cchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcC---Cccccchhhhhhhc
Q psy3828          60 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNK---KTRIIPRHLQLAIR  123 (365)
Q Consensus        60 FPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~k---kkrItP~hI~lAI~  123 (365)
                      ||-..++|++.. ...+.++....+.++++---++.||+|.|...-...+   ...|.|+||+.|.+
T Consensus        17 f~k~~iKr~~~~-~~~~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~r   82 (85)
T cd08048          17 FPKAAIKRLIQS-VTGQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYR   82 (85)
T ss_pred             ccHHHHHHHHHH-HcCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHH
Confidence            777779999987 3558999999999999999999999999998765544   47899999998865

The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes

>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=94.88  E-value=0.096  Score=45.27  Aligned_cols=64  Identities=11%  Similarity=0.171  Sum_probs=56.8

Q ss_pred             hhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHhCc
Q psy3828         279 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLP  343 (365)
Q Consensus       279 ~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrllLP  343 (365)
                      ..|.++||.- -....+.++...|--|+....+.|+.+|..++++.+|+||+..||..|+...+.
T Consensus         5 ~~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~   68 (117)
T cd07979           5 RVIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD   68 (117)
T ss_pred             HHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc
Confidence            4678888875 234679999999999999999999999999999999999999999999988774

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

>smart00417 H4 Histone H4

Probab=94.53  E-value=0.062  Score=43.32  Aligned_cols=54  Identities=11%  Similarity=0.218  Sum_probs=46.8

Q ss_pred             hhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHH
Q psy3828         281 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQ  335 (365)
Q Consensus       281 IykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIq  335 (365)
                      |.|+++.- ---.||..+..-+..+++++++.|+.+|..++.+.+|+|++..||-
T Consensus        19 IrRLaRr~-GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~   72 (74)
T smart00417       19 IRRLARRG-GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVV   72 (74)
T ss_pred             HHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhe
Confidence            67777753 2345899999999999999999999999999999999999999985

>KOG0869|consensus

Probab=94.52  E-value=0.089  Score=48.09  Aligned_cols=78  Identities=23%  Similarity=0.316  Sum_probs=63.9

Q ss_pred             hhhhhhhcCCC-CCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHh--------CcHHHHhhHH
Q psy3828         281 IYKVLKQVHPD-TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL--------LPGELAKHAV  351 (365)
Q Consensus       281 IykVLKQVhpd-~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrll--------LPgeLakhAv  351 (365)
                      |-|+.|+.-|. ..||..|-..|.-.|..+.-=|+.||+.-++..||+||+..||..|+--|        |---|.|+=.
T Consensus        38 V~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGFe~Y~eplkiyL~kYRe  117 (168)
T KOG0869|consen   38 VSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGFENYAEPLKIYLQKYRE  117 (168)
T ss_pred             HHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCcHhHHHHHHHHHHHHHH
Confidence            77889988776 56999999999999999999999999999999999999999999998643        2334555555


Q ss_pred             hhhhhhh
Q psy3828         352 SEGTKAV  358 (365)
Q Consensus       352 seGtkAV  358 (365)
                      .||-+..
T Consensus       118 ~e~e~~~  124 (168)
T KOG0869|consen  118 LEGERGR  124 (168)
T ss_pred             Hhhhccc
Confidence            5555443

>PLN00156 histone H2AX; Provisional

Probab=93.65  E-value=0.19  Score=45.15  Aligned_cols=64  Identities=23%  Similarity=0.287  Sum_probs=55.0

Q ss_pred             chhh-hhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         276 SYAI-YIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       276 sy~~-YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      .|.. -|+|.||.-+-..-|+.-|.--|-..+.++...|-+-|..-++.+++.-|++|.||.|+|
T Consensus        29 ~FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr   93 (139)
T PLN00156         29 QFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
T ss_pred             ccchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence            4543 489999998777789999988888888888888888888889999999999999999998

>KOG0871|consensus

Probab=93.63  E-value=0.18  Score=45.71  Aligned_cols=66  Identities=21%  Similarity=0.349  Sum_probs=59.2

Q ss_pred             hhhhhhhhcCC-CCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHhCcHH
Q psy3828         280 YIYKVLKQVHP-DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGE  345 (365)
Q Consensus       280 YIykVLKQVhp-d~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrllLPge  345 (365)
                      -|.|++|.+-| |..+..+|-.+++..-..+..-|+.||.+.+....|+||....|+.|..-|==||
T Consensus        17 tv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~e   83 (156)
T KOG0871|consen   17 TVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGE   83 (156)
T ss_pred             HHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHH
Confidence            38899999999 9999999999988888888899999999999999999999999999987554343

>KOG1142|consensus

Probab=92.95  E-value=0.11  Score=50.84  Aligned_cols=62  Identities=19%  Similarity=0.300  Sum_probs=57.1

Q ss_pred             hhhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         278 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       278 ~~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      +.-+...++||.+++.|-.+.-++|--+..|+.|-|..-|++||++.|..||-.||||..+.
T Consensus       157 k~kl~dLvqqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLE  218 (258)
T KOG1142|consen  157 KRKLDDLVQQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLE  218 (258)
T ss_pred             ccchhHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeee
Confidence            33478899999999999999999999999999999999999999999999999999998764

>PLN00153 histone H2A; Provisional

Probab=92.82  E-value=0.27  Score=43.63  Aligned_cols=66  Identities=20%  Similarity=0.253  Sum_probs=55.0

Q ss_pred             ccchhh-hhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         274 KESYAI-YIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       274 ~esy~~-YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      .-.|.. =|.|.||+-+.-.-|+.-|.--|-..+..+...|-+-|..-++.+++.-|++|.||.|++
T Consensus        22 gL~FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~   88 (129)
T PLN00153         22 GLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR   88 (129)
T ss_pred             CcccchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc
Confidence            344543 489999987777789998988888888888888888888889999999999999999998

>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=92.73  E-value=0.22  Score=39.33  Aligned_cols=64  Identities=20%  Similarity=0.273  Sum_probs=46.1

Q ss_pred             ccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          59 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        59 qFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      .||..-|+.+-..-.. .-++..+.-.|+-=+||-+.||++-|.+.++..+++++|+.||+.|++
T Consensus         3 ~~~~esvk~iAes~Gi-~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr   66 (66)
T PF02969_consen    3 VFSQESVKDIAESLGI-SNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR   66 (66)
T ss_dssp             ---HHHHHHHHHHTT----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred             cCCHHHHHHHHHHcCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence            3555555554444222 357888999999999999999999999999999999999999999874

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.

>KOG3219|consensus

Probab=92.50  E-value=0.11  Score=48.85  Aligned_cols=66  Identities=21%  Similarity=0.347  Sum_probs=55.0

Q ss_pred             ccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcC-Cccccchhhhhhhc
Q psy3828          57 GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNK-KTRIIPRHLQLAIR  123 (365)
Q Consensus        57 gLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~k-kkrItP~hI~lAI~  123 (365)
                      ..-||=+.|+++|..- ..+-|+..+.|+++++=.-|+.||+|.|.......+ ...+.|.||..|.+
T Consensus       110 rs~f~Ka~iKkL~~~i-tg~~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~r  176 (195)
T KOG3219|consen  110 RSAFPKAQIKKLMSSI-TGQSVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYR  176 (195)
T ss_pred             HhcCCHHHHHHHHHHH-hCCccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHH
Confidence            3459999999999984 334499999999999999999999999998755443 56799999998865

>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=92.26  E-value=0.24  Score=42.78  Aligned_cols=61  Identities=18%  Similarity=0.105  Sum_probs=54.2

Q ss_pred             hhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCc
Q psy3828          64 RIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND  125 (365)
Q Consensus        64 RI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nD  125 (365)
                      -|+++|++. -..+++..++..|.-.++-.+.+|+.-|...|+..+++.|+.++|++||..=
T Consensus         6 ~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r   66 (117)
T cd07979           6 VIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSR   66 (117)
T ss_pred             HHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            478888884 4468899999999999999999999999999999999999999999999753

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

>smart00414 H2A Histone 2A

Probab=92.17  E-value=0.27  Score=42.06  Aligned_cols=61  Identities=21%  Similarity=0.234  Sum_probs=47.7

Q ss_pred             hhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         279 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       279 ~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      ..|+|.||.-..-..|++-|.--|-..+..+...|-+-|..-++.+++..||+|+||.|++
T Consensus        13 gRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~   73 (106)
T smart00414       13 GRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIR   73 (106)
T ss_pred             HHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhcc
Confidence            3588999887666688888876666666666666666677777888999999999999998

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

Probab=92.05  E-value=0.17  Score=42.29  Aligned_cols=63  Identities=21%  Similarity=0.355  Sum_probs=45.9

Q ss_pred             cchhhhhhhhhcCCcc-cccCCChhHHHHHHHHHHHHHHHHHHhHHHhhc-CCccccchhhhhhhc
Q psy3828          60 FPVGRIHRLLRKGNYA-ERVGAGAPVYLAAVMEYLAAEVLELAGNAARDN-KKTRIIPRHLQLAIR  123 (365)
Q Consensus        60 FPVsRI~RlLke~~ya-~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~-kkkrItP~hI~lAI~  123 (365)
                      ||=+-|++++..- .. +-|+....+.++++--.++.||+|.|....... ....|.|.||..|.+
T Consensus        24 ~~k~~ikkli~~~-~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~r   88 (90)
T PF04719_consen   24 FNKAAIKKLINQV-LGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYR   88 (90)
T ss_dssp             --HHHHHHHHHHH-HS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHH
T ss_pred             CCHHHHHHHHHHH-cCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHH
Confidence            7777899999983 44 799999999999999999999999999875544 345899999998754

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

>PTZ00017 histone H2A; Provisional

Probab=91.74  E-value=0.44  Score=42.54  Aligned_cols=60  Identities=23%  Similarity=0.258  Sum_probs=49.5

Q ss_pred             hhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         280 YIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       280 YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      =|.|.||+-+.-.-|+.-|.--|-..+..+...|-+-|..-++.+++.-||+|.||.|++
T Consensus        32 Ri~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~   91 (134)
T PTZ00017         32 RVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR   91 (134)
T ss_pred             HHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence            388999987666688888877677777777777777778888999999999999999998

>smart00427 H2B Histone H2B

Probab=91.68  E-value=0.31  Score=40.76  Aligned_cols=60  Identities=22%  Similarity=0.282  Sum_probs=51.9

Q ss_pred             hhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          64 RIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        64 RI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      .|+|.|++-....-|+..|.-.+...+..++..|-..|...++-+++..|++++|+.|++
T Consensus         6 Yi~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvr   65 (89)
T smart00427        6 YIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVR   65 (89)
T ss_pred             HHHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHH
Confidence            588999987666678888887788888888888888888889999999999999999987

>PLN00157 histone H2A; Provisional

Probab=91.47  E-value=0.4  Score=42.72  Aligned_cols=66  Identities=26%  Similarity=0.266  Sum_probs=55.3

Q ss_pred             ccchhh-hhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         274 KESYAI-YIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       274 ~esy~~-YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      .-.|.. -|+|.||+-+...-|++.|.--|-..+.++...|-+-|..-++.+++.-|++|.||.|++
T Consensus        24 gL~FPVgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~   90 (132)
T PLN00157         24 GLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR   90 (132)
T ss_pred             CcccchHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence            334543 499999998777789999988888888888888888888888999999999999999998

>PLN00158 histone H2B; Provisional

Probab=91.25  E-value=0.37  Score=42.09  Aligned_cols=61  Identities=23%  Similarity=0.295  Sum_probs=52.7

Q ss_pred             hhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          63 GRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        63 sRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      ..|+|.|++-....-|+..|.-.+...+..++..|...|...++-+++..|++++|+.|++
T Consensus        31 ~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvr   91 (116)
T PLN00158         31 IYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVR   91 (116)
T ss_pred             HHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHH
Confidence            3699999997666778888887888888888888888888889999999999999999987

>PTZ00252 histone H2A; Provisional

Probab=91.14  E-value=0.67  Score=41.43  Aligned_cols=66  Identities=15%  Similarity=0.198  Sum_probs=50.1

Q ss_pred             ccchhh-hhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhh--cCCCcccChhHHHHHHH
Q psy3828         274 KESYAI-YIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAH--YNKRSTITSREIQTAVR  339 (365)
Q Consensus       274 ~esy~~-YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~--~nkr~TitsreIqtAvr  339 (365)
                      .-.|.. -|+|.|++-+-.--|++-|.--|-..+.++...|-+-|..-++  .|++.-|++|.||.|||
T Consensus        23 GL~FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr   91 (134)
T PTZ00252         23 GLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR   91 (134)
T ss_pred             CccCchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence            445553 4889999888778898888876666666666666666666663  48889999999999998

>PLN00154 histone H2A; Provisional

Probab=91.03  E-value=0.67  Score=41.53  Aligned_cols=60  Identities=22%  Similarity=0.201  Sum_probs=45.3

Q ss_pred             hhhhhhhhcC-CCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         280 YIYKVLKQVH-PDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       280 YIykVLKQVh-pd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      -|.|.||+-. -..-|++.|.--|-..+.++--.|-+-|.+-++.+++.-||+|.||.|+|
T Consensus        43 Ri~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr  103 (136)
T PLN00154         43 RIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR  103 (136)
T ss_pred             HHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence            4889999974 34578887776555555555555555566777889999999999999998

>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=90.50  E-value=0.76  Score=36.28  Aligned_cols=47  Identities=23%  Similarity=0.355  Sum_probs=37.5

Q ss_pred             CcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         293 GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       293 gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      .++.++-..+-.=|..-...|..||.++++..||.+||..||..|.|
T Consensus        20 ~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr   66 (66)
T PF02969_consen   20 NLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR   66 (66)
T ss_dssp             -B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence            45677777777778888889999999999999999999999999976

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.

>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=90.47  E-value=0.33  Score=48.78  Aligned_cols=58  Identities=22%  Similarity=0.313  Sum_probs=51.2

Q ss_pred             cccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc--CcHHHHhh
Q psy3828          74 YAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR--NDEELNKL  131 (365)
Q Consensus        74 ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~--nDeEL~~L  131 (365)
                      -..|++..|...|+..+||...+|++.|.+.++..++++++++||+.|++  |.+.|.+.
T Consensus        13 Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~eplyG~   72 (343)
T cd08050          13 GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVEPLYGF   72 (343)
T ss_pred             CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCCcccCC
Confidence            45699999999999999999999999999999999999999999999987  45544443

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

>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=90.17  E-value=0.58  Score=47.01  Aligned_cols=49  Identities=20%  Similarity=0.355  Sum_probs=46.0

Q ss_pred             CcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHh
Q psy3828         293 GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  341 (365)
Q Consensus       293 gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrll  341 (365)
                      .+|.+|...+..-+.+....|+.||.++++..||+||+..||..|+|..
T Consensus        16 ~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~   64 (343)
T cd08050          16 SLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLR   64 (343)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHh
Confidence            5789999999999999999999999999999999999999999999863

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

>PF15510 CENP-W: Centromere kinetochore component W

Probab=89.94  E-value=0.33  Score=40.91  Aligned_cols=64  Identities=22%  Similarity=0.362  Sum_probs=51.7

Q ss_pred             hhhhhhhhhhcCCCCCcc--hhHH--------------HHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHh
Q psy3828         278 AIYIYKVLKQVHPDTGVS--SKAM--------------SIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  341 (365)
Q Consensus       278 ~~YIykVLKQVhpd~gIS--skam--------------~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrll  341 (365)
                      ..++.||+|+--|.+.+-  ...|              -=+|.++  +..|+|+||---|.-||..||....|+.|.+.+
T Consensus        19 rgfLkrv~Kr~KphlRl~~~~Dllv~~~~f~~~~~~~~vhLncLL--FvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaKvi   96 (102)
T PF15510_consen   19 RGFLKRVFKRQKPHLRLETSGDLLVRFCPFSGWQWGGEVHLNCLL--FVHRLAEEARTNACENKCGTIKKEHVLAAAKVI   96 (102)
T ss_pred             hHHHHHHHHhcCCceeecccccHHHhhcccccccccceeehhHHH--HHHHHHHHHHHHHHHHhhccccHHHHHHHHHHH
Confidence            356888999888887663  3334              4456665  678999999999999999999999999999988


Q ss_pred             Cc
Q psy3828         342 LP  343 (365)
Q Consensus       342 LP  343 (365)
                      |.
T Consensus        97 LK   98 (102)
T PF15510_consen   97 LK   98 (102)
T ss_pred             HH
Confidence            75

>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]

Probab=89.73  E-value=0.6  Score=41.07  Aligned_cols=60  Identities=20%  Similarity=0.253  Sum_probs=52.7

Q ss_pred             hhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         280 YIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       280 YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      -|.|.||.-.-.+.|+++|.--+...+..+--.|-+-|.+-|+-++++-|++|.||-|+|
T Consensus        31 rvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr   90 (132)
T COG5262          31 RVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR   90 (132)
T ss_pred             HHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence            388999977777889999988778888777788888888889999999999999999998

>PTZ00463 histone H2B; Provisional

Probab=89.22  E-value=0.69  Score=40.46  Aligned_cols=60  Identities=13%  Similarity=0.191  Sum_probs=50.1

Q ss_pred             hhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          64 RIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        64 RI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      .|++.|++-....-|+..|.-.|...+.=++..|-..|...|+-+++..|++++||.|++
T Consensus        33 YI~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvr   92 (117)
T PTZ00463         33 YIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIR   92 (117)
T ss_pred             HHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHh
Confidence            699999997666677777777777777777777777788888889999999999999987

>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins

Probab=87.84  E-value=1.7  Score=34.56  Aligned_cols=48  Identities=8%  Similarity=0.184  Sum_probs=42.9

Q ss_pred             CcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         293 GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       293 gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      .++..|++.|-.++.+.++.|+.++.+++...+|.+.+..||..|..-
T Consensus        23 ~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~   70 (77)
T smart00576       23 SFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALEN   70 (77)
T ss_pred             ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence            467888888888888999999999999999999999999999988763

subdomain of archael histone-like transcription factors

>KOG0870|consensus

Probab=86.97  E-value=2  Score=39.70  Aligned_cols=62  Identities=21%  Similarity=0.306  Sum_probs=48.3

Q ss_pred             hhhhhhhhcCCC--CCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHh
Q psy3828         280 YIYKVLKQVHPD--TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  341 (365)
Q Consensus       280 YIykVLKQVhpd--~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrll  341 (365)
                      -|-|+.|.+-|+  .+||.+|...|-.-..=+.--+..=|..+|+.++|+||+..||-.|.+-+
T Consensus        15 iI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Ei   78 (172)
T KOG0870|consen   15 IITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEI   78 (172)
T ss_pred             HHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHh
Confidence            477788888776  58999998777654433334566677789999999999999999999865

>smart00428 H3 Histone H3

Probab=86.49  E-value=1  Score=38.66  Aligned_cols=67  Identities=25%  Similarity=0.310  Sum_probs=56.2

Q ss_pred             ccccchhhhhhhhhcC--Cc----ccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          57 GLQFPVGRIHRLLRKG--NY----AERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        57 gLqFPVsRI~RlLke~--~y----a~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      +|-+|-.-|.|+.++-  .+    ..|+..+|-..|-.+.|..+.++.|-|..-|...++..|+|+++++|.+
T Consensus        27 ~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~r   99 (105)
T smart00428       27 DLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARR   99 (105)
T ss_pred             ccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHH
Confidence            5667777777777661  12    3599999999999999999999999999889999999999999998853

>PLN00121 histone H3; Provisional

Probab=85.96  E-value=2.2  Score=38.29  Aligned_cols=67  Identities=19%  Similarity=0.245  Sum_probs=53.4

Q ss_pred             ccchhhhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         274 KESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       274 ~esy~~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      +-.|...+..+.....++.-+.+.|+.-|.--..+..-.+-+++...+.+.||-||..+|||-|.||
T Consensus        65 k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ri  131 (136)
T PLN00121         65 KLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI  131 (136)
T ss_pred             cccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHHh
Confidence            3467777777777777888999999888766555555555558888899999999999999999875

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

Probab=84.89  E-value=2.1  Score=34.67  Aligned_cols=59  Identities=20%  Similarity=0.315  Sum_probs=47.5

Q ss_pred             hhhhhhhc--CCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         281 IYKVLKQV--HPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       281 IykVLKQV--hpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      +-|+..++  ..+..+|++.+.-|--++.+..+.+|.+---.|++.+|+||+..|+.-.+|
T Consensus        11 v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~R   71 (76)
T PF15630_consen   11 VGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLAR   71 (76)
T ss_dssp             HHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTT
T ss_pred             HHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhh
Confidence            44555555  466779999999999999999999999999999999999999999875544

>PTZ00018 histone H3; Provisional

Probab=84.53  E-value=2.8  Score=37.62  Aligned_cols=67  Identities=19%  Similarity=0.245  Sum_probs=53.0

Q ss_pred             ccchhhhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         274 KESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       274 ~esy~~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      +-.|...+..+..+..++.-+.+.|+.-|.--..+..-.+-+++...+.+.||-||..+|||-|.||
T Consensus        65 k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ri  131 (136)
T PTZ00018         65 KLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI  131 (136)
T ss_pred             cccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHHh
Confidence            3467777777777777888999999888866555555555557888889999999999999999875

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

Probab=84.44  E-value=2.8  Score=33.57  Aligned_cols=61  Identities=20%  Similarity=0.229  Sum_probs=47.2

Q ss_pred             chhhhhhhhhcC--CcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCcc-ccchhhhhh
Q psy3828          61 PVGRIHRLLRKG--NYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTR-IIPRHLQLA  121 (365)
Q Consensus        61 PVsRI~RlLke~--~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkr-ItP~hI~lA  121 (365)
                      |..-|.|+|+..  .-.-||+..|---++..|+-|+.|-+-.|...|++.+... |..+||+..
T Consensus         1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki   64 (72)
T PF09415_consen    1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKI   64 (72)
T ss_dssp             -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHH
T ss_pred             ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHH
Confidence            344567777752  3457999999999999999999999999999999999888 999999863

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

>KOG1756|consensus

Probab=84.43  E-value=2.5  Score=37.59  Aligned_cols=60  Identities=23%  Similarity=0.282  Sum_probs=45.5

Q ss_pred             hhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         280 YIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       280 YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      -|.|.||.-..-..|+.-|---|--.+..+--.|-+-|..-++-|++.-|++|.||-|++
T Consensus        32 ri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~   91 (131)
T KOG1756|consen   32 RIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR   91 (131)
T ss_pred             HHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence            488999997777888888876555544444444444556667889999999999999998

>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins

Probab=81.96  E-value=2.9  Score=33.22  Aligned_cols=58  Identities=17%  Similarity=0.104  Sum_probs=49.1

Q ss_pred             hhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcC
Q psy3828          66 HRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN  124 (365)
Q Consensus        66 ~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~n  124 (365)
                      -++|+.. =..+++.+|.-.|+-++|-.+.+|.+.+-+.|...|++..++.+|.+|+.+
T Consensus        13 aqil~~~-Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~   70 (77)
T smart00576       13 AQILESA-GFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALEN   70 (77)
T ss_pred             HHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence            3455552 346899999999999999999999999999999999999999999988754

subdomain of archael histone-like transcription factors

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	365
2nqb_C	123	Drosophila Nucleosome Structure Length = 123		5e-48
2pyo_C	120	Drosophila Nucleosome Core Length = 120		8e-48
2pyo_D	122	Drosophila Nucleosome Core Length = 122		1e-47
2nqb_D	123	Drosophila Nucleosome Structure Length = 123		5e-47
3c9k_B	125	Model Of Histone Octamer Tubular Crystals Length =		8e-46
1s32_D	122	Molecular Recognition Of The Nucleosomal 'supergroo		8e-46
2f8n_H	123	2.9 Angstrom X-Ray Structure Of Hybrid Macroh2a Nuc		8e-46
3c1b_D	125	The Effect Of H3 K79 Dimethylation And H4 K20 Trime		9e-46
1zla_D	125	X-Ray Structure Of A Kaposi's Sarcoma Herpesvirus L		9e-46
1kx3_D	125	X-Ray Structure Of The Nucleosome Core Particle, Nc		1e-45
1f66_D	126	2.6 A Crystal Structure Of A Nucleosome Core Partic		1e-45
1p34_D	125	Crystallographic Studies Of Nucleosome Core Particl		1e-45
1aoi_D	99	Complex Between Nucleosome Core Particle (H3,H4,H2a		2e-45
3kwq_D	93	Structural Characterization Of H3k56q Nucleosomes A		2e-45
1eqz_A	129	X-Ray Structure Of The Nucleosome Core Particle At		2e-45
2hio_A	128	Histone Octamer (Chicken), Chromosomal Protein Leng		2e-45
1eqz_B	126	X-Ray Structure Of The Nucleosome Core Particle At		4e-45
2hio_B	125	Histone Octamer (Chicken), Chromosomal Protein Leng		4e-45
3c1b_C	129	The Effect Of H3 K79 Dimethylation And H4 K20 Trime		5e-45
1u35_D	126	Crystal Structure Of The Nucleosome Core Particle C		5e-45
1zbb_C	129	Structure Of The 4_601_167 Tetranucleosome Length =		6e-45
1m18_C	129	Ligand Binding Alters The Structure And Dynamics Of		6e-45
2cv5_C	130	Crystal Structure Of Human Nucleosome Core Particle		7e-45
3a6n_C	133	The Nucleosome Containing A Testis-Specific Histone		7e-45
3a6n_D	129	The Nucleosome Containing A Testis-Specific Histone		8e-45
2f8n_K	149	2.9 Angstrom X-Ray Structure Of Hybrid Macroh2a Nuc		9e-45
2cv5_D	126	Crystal Structure Of Human Nucleosome Core Particle		1e-44
1s32_C	119	Molecular Recognition Of The Nucleosomal 'supergroo		2e-44
1aoi_C	116	Complex Between Nucleosome Core Particle (H3,H4,H2a		2e-44
2xql_B	90	Fitting Of The H2a-H2b Histones In The Electron Mic		2e-44
3kwq_C	107	Structural Characterization Of H3k56q Nucleosomes A		2e-44
1kx3_C	128	X-Ray Structure Of The Nucleosome Core Particle, Nc		3e-44
1zla_C	129	X-Ray Structure Of A Kaposi's Sarcoma Herpesvirus L		9e-44
3an2_D	129	The Structure Of The Centromeric Nucleosome Contain		4e-43
1hio_A	95	Histone Octamer (Chicken), Chromosomal Protein, Alp		2e-42
1hio_B	90	Histone Octamer (Chicken), Chromosomal Protein, Alp		6e-42
1id3_C	131	Crystal Structure Of The Yeast Nucleosome Core Part		7e-42
2xql_A	91	Fitting Of The H2a-H2b Histones In The Electron Mic		5e-40
1id3_D	130	Crystal Structure Of The Yeast Nucleosome Core Part		6e-39
2jss_A	192	Nmr Structure Of Chaperone Chz1 Complexed With Hist		4e-37
1u35_C	120	Crystal Structure Of The Nucleosome Core Particle C		7e-31
1f66_C	128	2.6 A Crystal Structure Of A Nucleosome Core Partic		2e-25
1q9c_A	191	Crystal Structure Of The Histone Domain Of Son Of S		8e-05
3ksy_A	1049	Crystal Structure Of The Histone Domain, Dh-Ph Unit		1e-04

>pdb|2NQB|C Chain C, Drosophila Nucleosome Structure Length = 123

Iteration: 1
 Score =  187 bits (476), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 91/91 (100%), Positives = 91/91 (100%)
Query: 58  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 117
           LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH
Sbjct: 22  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 81
Query: 118 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           LQLAIRNDEELNKLLSGVTIAQGGVLPNIQA
Sbjct: 82  LQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 112

>pdb|2PYO|C Chain C, Drosophila Nucleosome Core Length = 120

Iteration: 1
 Score =  187 bits (475), Expect = 8e-48,   Method: Compositional matrix adjust.
 Identities = 91/91 (100%), Positives = 91/91 (100%)
Query: 58  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 117
           LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH
Sbjct: 22  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 81
Query: 118 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           LQLAIRNDEELNKLLSGVTIAQGGVLPNIQA
Sbjct: 82  LQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 112

>pdb|2PYO|D Chain D, Drosophila Nucleosome Core Length = 122

Iteration: 1
 Score =  187 bits (474), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 93/107 (86%), Positives = 95/107 (88%)
Query: 259 QKNIAXXXXXXXXXXXESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESS 318
           QKNI            ESYAIYIYKVLKQVHPDTG+SSKAMSIMNSFVNDIFERIAAE+S
Sbjct: 16  QKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEAS 75
Query: 319 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
           RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Sbjct: 76  RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 122

>pdb|2NQB|D Chain D, Drosophila Nucleosome Structure Length = 123

Iteration: 1
 Score =  184 bits (468), Expect = 5e-47,   Method: Compositional matrix adjust.
 Identities = 92/107 (85%), Positives = 94/107 (87%)
Query: 259 QKNIAXXXXXXXXXXXESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESS 318
           QKNI            ESYAIYIY VLKQVHPDTG+SSKAMSIMNSFVNDIFERIAAE+S
Sbjct: 17  QKNITKTDKKKKRKRKESYAIYIYTVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEAS 76
Query: 319 RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
           RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Sbjct: 77  RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 123

>pdb|3C9K|B Chain B, Model Of Histone Octamer Tubular Crystals Length = 125

Iteration: 1
 Score =  181 bits (458), Expect = 8e-46,   Method: Compositional matrix adjust.
 Identities = 86/91 (94%), Positives = 90/91 (98%)
Query: 275 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 334
           ESY+IY+YKVLKQVHPDTG+SSKAMSIMNSFVNDIFERIA E+SRLAHYNKRSTITSREI
Sbjct: 35  ESYSIYVYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAGEASRLAHYNKRSTITSREI 94
Query: 335 QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
           QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Sbjct: 95  QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 125

>pdb|1S32|D Chain D, Molecular Recognition Of The Nucleosomal 'supergroove' Length = 122

Iteration: 1
 Score =  181 bits (458), Expect = 8e-46,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 90/91 (98%)
Query: 275 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 334
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTITSREI
Sbjct: 32  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 91
Query: 335 QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
           QTAVRLLLPGELAKHAVSEGTKAVTKYTS+K
Sbjct: 92  QTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 122

>pdb|2F8N|H Chain H, 2.9 Angstrom X-Ray Structure Of Hybrid Macroh2a Nucleosomes Length = 123

Iteration: 1
 Score =  181 bits (458), Expect = 8e-46,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 90/91 (98%)
Query: 275 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 334
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTITSREI
Sbjct: 33  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 92
Query: 335 QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
           QTAVRLLLPGELAKHAVSEGTKAVTKYTS+K
Sbjct: 93  QTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 123

>pdb|3C1B|D Chain D, The Effect Of H3 K79 Dimethylation And H4 K20 Trimethylation On Nucleosome And Chromatin Structure Length = 125

Iteration: 1
 Score =  180 bits (457), Expect = 9e-46,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 90/91 (98%)
Query: 275 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 334
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTITSREI
Sbjct: 35  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 94
Query: 335 QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
           QTAVRLLLPGELAKHAVSEGTKAVTKYTS+K
Sbjct: 95  QTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 125

>pdb|1ZLA|D Chain D, X-Ray Structure Of A Kaposi's Sarcoma Herpesvirus Lana Peptide Bound To The Nucleosomal Core Length = 125

Iteration: 1
 Score =  180 bits (457), Expect = 9e-46,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 90/91 (98%)
Query: 275 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 334
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTITSREI
Sbjct: 35  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 94
Query: 335 QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
           QTAVRLLLPGELAKHAVSEGTKAVTKYTS+K
Sbjct: 95  QTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 125

>pdb|1KX3|D Chain D, X-Ray Structure Of The Nucleosome Core Particle, Ncp146, At 2.0 A Resolution Length = 125

Iteration: 1
 Score =  180 bits (457), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 90/91 (98%)
Query: 275 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 334
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTITSREI
Sbjct: 35  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 94
Query: 335 QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
           QTAVRLLLPGELAKHAVSEGTKAVTKYTS+K
Sbjct: 95  QTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 125

>pdb|1F66|D Chain D, 2.6 A Crystal Structure Of A Nucleosome Core Particle Containing The Variant Histone H2a.Z Length = 126

Iteration: 1
 Score =  180 bits (457), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 90/91 (98%)
Query: 275 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 334
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTITSREI
Sbjct: 36  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 95
Query: 335 QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
           QTAVRLLLPGELAKHAVSEGTKAVTKYTS+K
Sbjct: 96  QTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 126

>pdb|1P34|D Chain D, Crystallographic Studies Of Nucleosome Core Particles Containing Histone 'sin' Mutants Length = 125

Iteration: 1
 Score =  180 bits (456), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 90/91 (98%)
Query: 275 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 334
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTITSREI
Sbjct: 35  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 94
Query: 335 QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
           QTAVRLLLPGELAKHAVSEGTKAVTKYTS+K
Sbjct: 95  QTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 125

>pdb|1AOI|D Chain D, Complex Between Nucleosome Core Particle (H3,H4,H2a,H2b) And 146 Bp Long Dna Fragment Length = 99

Iteration: 1
 Score =  179 bits (455), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 90/91 (98%)
Query: 275 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 334
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTITSREI
Sbjct: 9   ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 68
Query: 335 QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
           QTAVRLLLPGELAKHAVSEGTKAVTKYTS+K
Sbjct: 69  QTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 99

>pdb|3KWQ|D Chain D, Structural Characterization Of H3k56q Nucleosomes And Nucleo Arrays Length = 93

Iteration: 1
 Score =  179 bits (454), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 90/91 (98%)
Query: 275 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 334
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTITSREI
Sbjct: 3   ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 62
Query: 335 QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
           QTAVRLLLPGELAKHAVSEGTKAVTKYTS+K
Sbjct: 63  QTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 93

>pdb|1EQZ|A Chain A, X-Ray Structure Of The Nucleosome Core Particle At 2.5 A Resolution Length = 129

Iteration: 1
 Score =  179 bits (454), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 88/91 (96%)
Query: 58  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 117
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 24  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 83
Query: 118 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           LQLAIRNDEELNKLL  VTIAQGGVLPNIQA
Sbjct: 84  LQLAIRNDEELNKLLGKVTIAQGGVLPNIQA 114

>pdb|2HIO|A Chain A, Histone Octamer (Chicken), Chromosomal Protein Length = 128

Iteration: 1
 Score =  179 bits (454), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 88/91 (96%)
Query: 58  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 117
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 23  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 82
Query: 118 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           LQLAIRNDEELNKLL  VTIAQGGVLPNIQA
Sbjct: 83  LQLAIRNDEELNKLLGKVTIAQGGVLPNIQA 113

>pdb|1EQZ|B Chain B, X-Ray Structure Of The Nucleosome Core Particle At 2.5 A Resolution Length = 126

Iteration: 1
 Score =  178 bits (451), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 89/91 (97%)
Query: 275 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 334
           ESY+IY+YKVLKQVHPDTG+SSKAM IMNSFVNDIFERIA E+SRLAHYNKRSTITSREI
Sbjct: 36  ESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREI 95
Query: 335 QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
           QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Sbjct: 96  QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 126

>pdb|2HIO|B Chain B, Histone Octamer (Chicken), Chromosomal Protein Length = 125

Iteration: 1
 Score =  178 bits (451), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 89/91 (97%)
Query: 275 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 334
           ESY+IY+YKVLKQVHPDTG+SSKAM IMNSFVNDIFERIA E+SRLAHYNKRSTITSREI
Sbjct: 35  ESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREI 94
Query: 335 QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
           QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Sbjct: 95  QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 125

>pdb|3C1B|C Chain C, The Effect Of H3 K79 Dimethylation And H4 K20 Trimethylation On Nucleosome And Chromatin Structure Length = 129

Iteration: 1
 Score =  178 bits (451), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 83/91 (91%), Positives = 88/91 (96%)
Query: 58  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 117
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 23  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 82
Query: 118 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           LQLA+RNDEELNKLL  VTIAQGGVLPNIQ+
Sbjct: 83  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQS 113

>pdb|1U35|D Chain D, Crystal Structure Of The Nucleosome Core Particle Containing The Histone Domain Of Macroh2a Length = 126

Iteration: 1
 Score =  178 bits (451), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 84/91 (92%), Positives = 90/91 (98%)
Query: 275 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 334
           ESY+IY+YKVLKQVHPDTG+SSKAM IMNSFVNDIFERIA+E+SRLAHYNKRSTITSRE+
Sbjct: 36  ESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIASEASRLAHYNKRSTITSREV 95
Query: 335 QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
           QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Sbjct: 96  QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 126

>pdb|1ZBB|C Chain C, Structure Of The 4_601_167 Tetranucleosome Length = 129

Iteration: 1
 Score =  177 bits (450), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 83/91 (91%), Positives = 88/91 (96%)
Query: 58  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 117
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 23  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 82
Query: 118 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           LQLA+RNDEELNKLL  VTIAQGGVLPNIQ+
Sbjct: 83  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQS 113

>pdb|1M18|C Chain C, Ligand Binding Alters The Structure And Dynamics Of Nucleosomal Dna Length = 129

Iteration: 1
 Score =  177 bits (450), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 83/91 (91%), Positives = 88/91 (96%)
Query: 58  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 117
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 23  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 82
Query: 118 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           LQLA+RNDEELNKLL  VTIAQGGVLPNIQ+
Sbjct: 83  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQS 113

>pdb|2CV5|C Chain C, Crystal Structure Of Human Nucleosome Core Particle Length = 130

Iteration: 1
 Score =  177 bits (449), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 84/91 (92%), Positives = 88/91 (96%)
Query: 58  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 117
           LQFPVGR+HRLLRKGNY+ERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 24  LQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 83
Query: 118 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           LQLAIRNDEELNKLL  VTIAQGGVLPNIQA
Sbjct: 84  LQLAIRNDEELNKLLGRVTIAQGGVLPNIQA 114

>pdb|3A6N|C Chain C, The Nucleosome Containing A Testis-Specific Histone Variant, Human H3t Length = 133

Iteration: 1
 Score =  177 bits (449), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 84/91 (92%), Positives = 88/91 (96%)
Query: 58  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 117
           LQFPVGR+HRLLRKGNY+ERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 27  LQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 86
Query: 118 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           LQLAIRNDEELNKLL  VTIAQGGVLPNIQA
Sbjct: 87  LQLAIRNDEELNKLLGRVTIAQGGVLPNIQA 117

>pdb|3A6N|D Chain D, The Nucleosome Containing A Testis-Specific Histone Variant, Human H3t Length = 129

Iteration: 1
 Score =  177 bits (449), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 84/91 (92%), Positives = 89/91 (97%)
Query: 275 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 334
           ESY+IY+YKVLKQVHPDTG+SSKAM IMNSFVNDIFERIA E+SRLAHYNKRSTITSREI
Sbjct: 39  ESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREI 98
Query: 335 QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
           QTAVRLLLPGELAKHAVSEGTKAVTKYTS+K
Sbjct: 99  QTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 129

>pdb|2F8N|K Chain K, 2.9 Angstrom X-Ray Structure Of Hybrid Macroh2a Nucleosomes Length = 149

Iteration: 1
 Score =  177 bits (449), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 84/91 (92%), Positives = 88/91 (96%)
Query: 58  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 117
           LQFPVGR+HRLLRKGNY+ERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 43  LQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 102
Query: 118 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           LQLAIRNDEELNKLL  VTIAQGGVLPNIQA
Sbjct: 103 LQLAIRNDEELNKLLGRVTIAQGGVLPNIQA 133

>pdb|2CV5|D Chain D, Crystal Structure Of Human Nucleosome Core Particle Length = 126

Iteration: 1
 Score =  177 bits (448), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 83/91 (91%), Positives = 89/91 (97%)
Query: 275 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 334
           ESY++Y+YKVLKQVHPDTG+SSKAM IMNSFVNDIFERIA E+SRLAHYNKRSTITSREI
Sbjct: 36  ESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREI 95
Query: 335 QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
           QTAVRLLLPGELAKHAVSEGTKAVTKYTS+K
Sbjct: 96  QTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 126

>pdb|1S32|C Chain C, Molecular Recognition Of The Nucleosomal 'supergroove' Length = 119

Iteration: 1
 Score =  176 bits (446), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 83/91 (91%), Positives = 88/91 (96%)
Query: 58  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 117
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 23  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 82
Query: 118 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           LQLA+RNDEELNKLL  VTIAQGGVLPNIQ+
Sbjct: 83  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQS 113

>pdb|1AOI|C Chain C, Complex Between Nucleosome Core Particle (H3,H4,H2a,H2b) And 146 Bp Long Dna Fragment Length = 116

Iteration: 1
 Score =  176 bits (445), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 83/91 (91%), Positives = 88/91 (96%)
Query: 58  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 117
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 20  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 79
Query: 118 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           LQLA+RNDEELNKLL  VTIAQGGVLPNIQ+
Sbjct: 80  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQS 110

>pdb|2XQL|B Chain B, Fitting Of The H2a-H2b Histones In The Electron Microscopy Map Of The Complex Nucleoplasmin:h2a-H2b Histones (1:5). Length = 90

Iteration: 1
 Score =  176 bits (445), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 84/90 (93%), Positives = 88/90 (97%)
Query: 276 SYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQ 335
           SY+IY+YKVLKQVHPDTG+SSKAM IMNSFVNDIFERIA E+SRLAHYNKRSTITSREIQ
Sbjct: 1   SYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQ 60
Query: 336 TAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
           TAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Sbjct: 61  TAVRLLLPGELAKHAVSEGTKAVTKYTSSK 90

>pdb|3KWQ|C Chain C, Structural Characterization Of H3k56q Nucleosomes And Nucleo Arrays Length = 107

Iteration: 1
 Score =  176 bits (445), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 83/91 (91%), Positives = 88/91 (96%)
Query: 58  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 117
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 10  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 69
Query: 118 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           LQLA+RNDEELNKLL  VTIAQGGVLPNIQ+
Sbjct: 70  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQS 100

>pdb|1KX3|C Chain C, X-Ray Structure Of The Nucleosome Core Particle, Ncp146, At 2.0 A Resolution Length = 128

Iteration: 1
 Score =  176 bits (445), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 83/91 (91%), Positives = 88/91 (96%)
Query: 58  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 117
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 23  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 82
Query: 118 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           LQLA+RNDEELNKLL  VTIAQGGVLPNIQ+
Sbjct: 83  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQS 113

>pdb|1ZLA|C Chain C, X-Ray Structure Of A Kaposi's Sarcoma Herpesvirus Lana Peptide Bound To The Nucleosomal Core Length = 129

Iteration: 1
 Score =  174 bits (440), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 81/91 (89%), Positives = 86/91 (94%)
Query: 58  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 117
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGN  RDNKKTRIIPRH
Sbjct: 23  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNWERDNKKTRIIPRH 82
Query: 118 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           LQLA+RNDEELNKLL  VTIAQGGVLPNIQ+
Sbjct: 83  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQS 113

>pdb|3AN2|D Chain D, The Structure Of The Centromeric Nucleosome Containing Cenp-A Length = 129

Iteration: 1
 Score =  172 bits (435), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 82/91 (90%), Positives = 87/91 (95%)
Query: 275 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 334
           ESY+IY+YKVLKQVHPDTG+SSKA  I NSFVNDIFERIA E+SRLAHYNKRSTITSREI
Sbjct: 39  ESYSIYVYKVLKQVHPDTGISSKAXGIXNSFVNDIFERIAGEASRLAHYNKRSTITSREI 98
Query: 335 QTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
           QTAVRLLLPGELAKHAVSEGTKAVTKYTS+K
Sbjct: 99  QTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 129

>pdb|1HIO|A Chain A, Histone Octamer (Chicken), Chromosomal Protein, Alpha Carbons Only Length = 95

Iteration: 1
 Score =  169 bits (429), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 81/87 (93%), Positives = 84/87 (96%)
Query: 58  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 117
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 9   LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 68
Query: 118 LQLAIRNDEELNKLLSGVTIAQGGVLP 144
           LQLAIRNDEELNKLL  VTIAQGGVLP
Sbjct: 69  LQLAIRNDEELNKLLGKVTIAQGGVLP 95

>pdb|1HIO|B Chain B, Histone Octamer (Chicken), Chromosomal Protein, Alpha Carbons Only Length = 90

Iteration: 1
 Score =  167 bits (424), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 81/90 (90%), Positives = 86/90 (95%)
Query: 276 SYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQ 335
           SY+IY+YKVLKQVHPDTG+SSKAM  MNSFVNDIFERIA  +SRLAHYNKRSTITSREIQ
Sbjct: 1   SYSIYVYKVLKQVHPDTGISSKAMGSMNSFVNDIFERIAGLASRLAHYNKRSTITSREIQ 60
Query: 336 TAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
           TAVRLLLPGELAKHAVSEGTKAVTK+TSSK
Sbjct: 61  TAVRLLLPGELAKHAVSEGTKAVTKHTSSK 90

>pdb|1ID3|C Chain C, Crystal Structure Of The Yeast Nucleosome Core Particle Reveals Fundamental Differences In Inter-Nucleosome Interactions Length = 131

Iteration: 1
 Score =  167 bits (424), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 77/90 (85%), Positives = 85/90 (94%)
Query: 58  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 117
           L FPVGR+HRLLR+GNYA+R+G+GAPVYL AV+EYLAAE+LELAGNAARDNKKTRIIPRH
Sbjct: 24  LTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRH 83
Query: 118 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQ 147
           LQLAIRND+ELNKLL  VTIAQGGVLPNI 
Sbjct: 84  LQLAIRNDDELNKLLGNVTIAQGGVLPNIH 113

>pdb|2XQL|A Chain A, Fitting Of The H2a-H2b Histones In The Electron Microscopy Map Of The Complex Nucleoplasmin:h2a-H2b Histones (1:5). Length = 91

Iteration: 1
 Score =  161 bits (408), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 77/83 (92%), Positives = 80/83 (96%)
Query: 58  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 117
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 9   LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 68
Query: 118 LQLAIRNDEELNKLLSGVTIAQG 140
           LQLAIRNDEELNKLL  VTIAQG
Sbjct: 69  LQLAIRNDEELNKLLGKVTIAQG 91

>pdb|1ID3|D Chain D, Crystal Structure Of The Yeast Nucleosome Core Particle Reveals Fundamental Differences In Inter-Nucleosome Interactions Length = 130

Iteration: 1
 Score =  158 bits (399), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 72/90 (80%), Positives = 85/90 (94%)
Query: 275 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 334
           E+Y+ YIYKVLKQ HPDTG+S K+MSI+NSFVNDIFERIA E+S+LA YNK+STI++REI
Sbjct: 38  ETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREI 97
Query: 335 QTAVRLLLPGELAKHAVSEGTKAVTKYTSS 364
           QTAVRL+LPGELAKHAVSEGT+AVTKY+SS
Sbjct: 98  QTAVRLILPGELAKHAVSEGTRAVTKYSSS 127

>pdb|2JSS|A Chain A, Nmr Structure Of Chaperone Chz1 Complexed With Histone H2a.Z-H2b Length = 192

Iteration: 1
 Score =  152 bits (383), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 70/87 (80%), Positives = 82/87 (94%)
Query: 275 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 334
           E+Y+ YIYKVLKQ HPDTG+S K+MSI+NSFVNDIFERIA E+S+LA YNK+STI++REI
Sbjct: 3   ETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREI 62
Query: 335 QTAVRLLLPGELAKHAVSEGTKAVTKY 361
           QTAVRL+LPGELAKHAVSEGT+AVTKY
Sbjct: 63  QTAVRLILPGELAKHAVSEGTRAVTKY 89

>pdb|1U35|C Chain C, Crystal Structure Of The Nucleosome Core Particle Containing The Histone Domain Of Macroh2a Length = 120

Iteration: 1
 Score =  131 bits (329), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 61/88 (69%), Positives = 73/88 (82%)
Query: 60  FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQ 119
           FPVGR+ R ++KG+   R+G GAPVY+AAV+EYL AE+LELA NAARDNKK R+ PRH+ 
Sbjct: 23  FPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHIL 82
Query: 120 LAIRNDEELNKLLSGVTIAQGGVLPNIQ 147
           LA+ NDEELN+LL GVTIA GGVLPNI 
Sbjct: 83  LAVANDEELNQLLKGVTIASGGVLPNIH 110

>pdb|1F66|C Chain C, 2.6 A Crystal Structure Of A Nucleosome Core Particle Containing The Variant Histone H2a.Z Length = 128

Iteration: 1
 Score =  113 bits (282), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 59/91 (64%), Positives = 69/91 (75%), Gaps = 2/91 (2%)
Query: 58  LQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPR 116
           LQFPVGRIHR L+    +  RVGA A VY AA++EYL AEVLELAGNA++D K  RI PR
Sbjct: 26  LQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPR 85
Query: 117 HLQLAIRNDEELNKLLSGVTIAQGGVLPNIQ 147
           HLQLAIR DEEL+ L+   TIA GGV+P+I 
Sbjct: 86  HLQLAIRGDEELDSLIK-ATIAGGGVIPHIH 115

>pdb|1Q9C|A Chain A, Crystal Structure Of The Histone Domain Of Son Of Sevenless Length = 191

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 43/71 (60%), Gaps = 1/71 (1%)
Query: 58  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 117
           L  PV +IH LL++     ++     VY+ AV+EY++A++L+LAGN  R+ +   I  + 
Sbjct: 103 LSLPVEKIHPLLKEV-LGYKIDHQVSVYIVAVLEYISADILKLAGNYVRNIRHYEITKQD 161
Query: 118 LQLAIRNDEEL 128
           +++A   D+ L
Sbjct: 162 IKVAXCADKVL 172

>pdb|3KSY|A Chain A, Crystal Structure Of The Histone Domain, Dh-Ph Unit, And Catalytic Unit Of The Ras Activator Son Of Sevenless (Sos) Length = 1049

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 58  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 117
           L  PV +IH LL K     ++     VY+ AV+EY++A++L+L GN  R+ +   I  + 
Sbjct: 103 LSLPVEKIHPLL-KEVLGYKIDHQVSVYIVAVLEYISADILKLVGNYVRNIRHYEITKQD 161
Query: 118 LQLAIRNDEELNKLL 132
           +++A+  D+ L  + 
Sbjct: 162 IKVAMCADKVLMDMF 176

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	365
2nqb_D	123	Histone H2B; nucleosome, NCP, chromatin, structura	1e-55
1tzy_B	126	Histone H2B; histone-fold, tetramer-dimer-dimer, D	1e-49
2f8n_K	149	Histone H2A type 1; nucleosome, NCP, macroh2A, his	2e-48
1tzy_A	129	Histone H2A-IV; histone-fold, tetramer-dimer-dimer	3e-48
2nqb_C	123	Histone H2A; nucleosome, NCP, chromatin, structura	3e-47
2f8n_G	120	Core histone macro-H2A.1; nucleosome, NCP, macroh2	9e-45
1id3_C	131	Histone H2A.1; nucleosome core particle, chromatin	9e-42
1f66_C	128	Histone H2A.Z; nucleosome, chromatin, histone vari	1e-37
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	2e-31
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	7e-27
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	6e-21
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-11
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	3e-09
3ksy_A	1049	SOS-1, SON of sevenless homolog 1; RAS, RAS activa	2e-08
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	3e-05
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	1e-04

>2nqb_D Histone H2B; nucleosome, NCP, chromatin, structural protein/DNA complex; 2.30A {Drosophila melanogaster} PDB: 2pyo_D* Length = 123

 Score =  177 bits (450), Expect = 1e-55
 Identities = 111/120 (92%), Positives = 116/120 (96%)

Query: 246 KSSGKAVKKAGKAQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSF 305
           K+SGKA KKAGKAQKNI K+DKKKK +RKESYAIYIY VLKQVHPDTG+SSKAMSIMNSF
Sbjct: 4   KTSGKAAKKAGKAQKNITKTDKKKKRKRKESYAIYIYTVLKQVHPDTGISSKAMSIMNSF 63

Query: 306 VNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 365
           VNDIFERIAAE+SRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Sbjct: 64  VNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 123

>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 ... Length = 126

 Score =  162 bits (410), Expect = 1e-49
 Identities = 98/122 (80%), Positives = 103/122 (84%), Gaps = 2/122 (1%)

Query: 246 KSSGKAVKKAGK--AQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMN 303
             S  A KK  K    K   K DKK+K  RKESY+IY+YKVLKQVHPDTG+SSKAM IMN
Sbjct: 5   AKSAPAPKKGSKKAVTKTQKKGDKKRKKSRKESYSIYVYKVLKQVHPDTGISSKAMGIMN 64

Query: 304 SFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 363
           SFVNDIFERIA E+SRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
Sbjct: 65  SFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 124

Query: 364 SK 365
           SK
Sbjct: 125 SK 126

>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 Length = 149

 Score =  159 bits (403), Expect = 2e-48
 Identities = 104/123 (84%), Positives = 113/123 (91%), Gaps = 1/123 (0%)

Query: 27  AVPIPQIYTMSGRGK-GGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVY 85
           +  +    +MSGRGK GGKA+AK+KTRSSRAGLQFPVGR+HRLLRKGNY+ERVGAGAPVY
Sbjct: 11  SSGLVPRGSMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVY 70

Query: 86  LAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPN 145
           LAAV+EYL AE+LELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLL  VTIAQGGVLPN
Sbjct: 71  LAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPN 130

Query: 146 IQA 148
           IQA
Sbjct: 131 IQA 133

>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 ... Length = 129

 Score =  158 bits (400), Expect = 3e-48
 Identities = 104/114 (91%), Positives = 110/114 (96%), Gaps = 1/114 (0%)

Query: 36  MSGRGK-GGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLA 94
           MSGRGK GGKA+AK+K+RSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL 
Sbjct: 1   MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT 60

Query: 95  AEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           AE+LELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLL  VTIAQGGVLPNIQA
Sbjct: 61  AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQA 114

>2nqb_C Histone H2A; nucleosome, NCP, chromatin, structural protein/DNA complex; 2.30A {Drosophila melanogaster} PDB: 2pyo_C* Length = 123

 Score =  155 bits (393), Expect = 3e-47
 Identities = 107/112 (95%), Positives = 110/112 (98%)

Query: 37  SGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE 96
           SGRGKGGK K K+K+RS+RAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE
Sbjct: 1   SGRGKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE 60

Query: 97  VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA
Sbjct: 61  VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 112

>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 Length = 120

 Score =  149 bits (376), Expect = 9e-45
 Identities = 72/113 (63%), Positives = 89/113 (78%), Gaps = 2/113 (1%)

Query: 36  MSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 95
           MS RG  GK K+   +RS++AG+ FPVGR+ R ++KG+   R+G GAPVY+AAV+EYL A
Sbjct: 1   MSSRG--GKKKSTKTSRSAKAGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTA 58

Query: 96  EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           E+LELA NAARDNKK R+ PRH+ LA+ NDEELN+LL GVTIA GGVLPNI  
Sbjct: 59  EILELAVNAARDNKKGRVTPRHILLAVANDEELNQLLKGVTIASGGVLPNIHP 111

>1id3_C Histone H2A.1; nucleosome core particle, chromatin, protein/DNA interaction, nucleoprotein, supercoiled DNA; 3.10A {Saccharomyces cerevisiae} SCOP: a.22.1.1 Length = 131

 Score =  141 bits (357), Expect = 9e-42
 Identities = 87/113 (76%), Positives = 100/113 (88%), Gaps = 1/113 (0%)

Query: 37  SGRG-KGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 95
            G+G K G A   S++RS++AGL FPVGR+HRLLR+GNYA+R+G+GAPVYL AV+EYLAA
Sbjct: 2   GGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAA 61

Query: 96  EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           E+LELAGNAARDNKKTRIIPRHLQLAIRND+ELNKLL  VTIAQGGVLPNI  
Sbjct: 62  EILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQ 114

>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 Length = 128

 Score =  130 bits (328), Expect = 1e-37
 Identities = 71/117 (60%), Positives = 84/117 (71%), Gaps = 5/117 (4%)

Query: 36  MSGRGKG---GKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAER-VGAGAPVYLAAVME 91
           M+G   G   GKAK K+ +RS RAGLQFPVGRIHR L+    +   VGA A VY AA++E
Sbjct: 1   MAGGKAGKDSGKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILE 60

Query: 92  YLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           YL AEVLELAGNA++D K  RI PRHLQLAIR DEEL+ L+   TIA GGV+P+I  
Sbjct: 61  YLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLI-KATIAGGGVIPHIHK 116

>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 Length = 192

 Score =  116 bits (291), Expect = 2e-31
 Identities = 72/90 (80%), Positives = 85/90 (94%)

Query: 273 RKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSR 332
           RKE+Y+ YIYKVLKQ HPDTG+S K+MSI+NSFVNDIFERIA E+S+LA YNK+STI++R
Sbjct: 1   RKETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAR 60

Query: 333 EIQTAVRLLLPGELAKHAVSEGTKAVTKYT 362
           EIQTAVRL+LPGELAKHAVSEGT+AVTKY+
Sbjct: 61  EIQTAVRLILPGELAKHAVSEGTRAVTKYS 90

>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 Length = 192

 Score =  104 bits (259), Expect = 7e-27
 Identities = 61/116 (52%), Positives = 79/116 (68%), Gaps = 2/116 (1%)

Query: 32  QIYTMSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAER-VGAGAPVYLAAVM 90
            +   +       +  ++++ S+RAGLQFPVGRI R L++       VG+ A +YL AV+
Sbjct: 78  AVSEGTRAVTKYSSSTQAQSSSARAGLQFPVGRIKRYLKRHATGRTRVGSKAAIYLTAVL 137

Query: 91  EYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNI 146
           EYL AEVLELAGNAA+D K  RI PRHLQLAIR D+EL+ L+   TIA GGVLP+I
Sbjct: 138 EYLTAEVLELAGNAAKDLKVKRITPRHLQLAIRGDDELDSLI-RATIASGGVLPHI 192

>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 Length = 98

 Score = 85.7 bits (212), Expect = 6e-21
 Identities = 14/77 (18%), Positives = 33/77 (42%)

Query: 51  TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKK 110
           ++  +   +FP  RI ++++      +V A  PV ++  +E     +L+ A    +    
Sbjct: 3   SKKKKYNARFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNA 62

Query: 111 TRIIPRHLQLAIRNDEE 127
             +   HL+  I  + +
Sbjct: 63  KTMTTSHLKQCIELEGD 79

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

 Score = 64.1 bits (155), Expect = 3e-11
 Identities = 57/368 (15%), Positives = 101/368 (27%), Gaps = 109/368 (29%)

Query: 61  PVGRIHRLLRKGNYAERV------GAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRII 114
           P  ++ + L +   A+ V      G+G           +A +V           K    +
Sbjct: 136 PYLKLRQALLELRPAKNVLIDGVLGSGKTW--------VALDVC-------LSYKVQCKM 180

Query: 115 PRH---LQLAIRNDEE-----LNKLLSGVTIAQGGVLPNIQAGAALTFERVDDVHGGDGL 166
                 L L   N  E     L KLL  +        PN  + +               +
Sbjct: 181 DFKIFWLNLKNCNSPETVLEMLQKLLYQID-------PNWTSRS----------DHSSNI 223

Query: 167 SLGVLGVGDGVADHVLEEHLENATGLLVDEPGDTLDSTSTRQ-------------TT-DG 212
            L +  +   +   +  +  EN   LLV      L +    +             TT   
Sbjct: 224 KLRIHSIQAELRRLLKSKPYENC--LLV------LLNVQNAKAWNAFNLSCKILLTTRFK 275

Query: 213 GLGDSLDV--VTEYFPVPLGASFS--ESLSSLTTAAGKSSGK----AVKKAGKAQKNIAK 264
            + D L     T         + +  E  S L               +    +    IA+
Sbjct: 276 QVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAE 335

Query: 265 SDKKK-------KHRRKESYAIYIYKVLKQVHP---------------DTGVSSKAMSIM 302
           S +         KH   +     I   L  + P                  + +  +S++
Sbjct: 336 SIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLI 395

Query: 303 --NSFVNDIFERIAAE---SSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKA 357
             +   +D+   +  +    S +    K STI+   I   +++ L  E A H        
Sbjct: 396 WFDVIKSDV-MVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHR-----SI 449

Query: 358 VTKYTSSK 365
           V  Y   K
Sbjct: 450 VDHYNIPK 457

>1n1j_B NF-YC; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3 Length = 97

 Score = 52.6 bits (126), Expect = 3e-09
 Identities = 15/70 (21%), Positives = 31/70 (44%)

Query: 59  QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHL 118
           + P+ RI ++++     + + A APV  A   +    E+   A     DNK+  +    +
Sbjct: 19  ELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDI 78

Query: 119 QLAIRNDEEL 128
            +AI   ++ 
Sbjct: 79  AMAITKFDQF 88

>3ksy_A SOS-1, SON of sevenless homolog 1; RAS, RAS activator, disease mutation, guanine-nucleotide releasing factor, signaling protein; 3.18A {Homo sapiens} PDB: 1xd4_A 1xdv_A 1q9c_A Length = 1049

 Score = 55.2 bits (132), Expect = 2e-08
 Identities = 26/84 (30%), Positives = 49/84 (58%), Gaps = 1/84 (1%)

Query: 45  AKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNA 104
           A++  + R  R  L  PV +IH LL++     ++     VY+ AV+EY++A++L+L GN 
Sbjct: 90  AQSAIEKRKRRNPLSLPVEKIHPLLKEVL-GYKIDHQVSVYIVAVLEYISADILKLVGNY 148

Query: 105 ARDNKKTRIIPRHLQLAIRNDEEL 128
            R+ +   I  + +++A+  D+ L
Sbjct: 149 VRNIRHYEITKQDIKVAMCADKVL 172

>2l5a_A Histone H3-like centromeric protein CSE4, protein histone H4; A single chain of CSE4+SCM3+H4, fusion protein; NMR {Saccharomyces cerevisiae} Length = 235

 Score = 44.2 bits (103), Expect = 3e-05
 Identities = 19/109 (17%), Positives = 39/109 (35%), Gaps = 4/109 (3%)

Query: 235 ESLSSLTTAAGKSSGKAVKKAGKAQKNIAKSDKKKKHRRKESYAIYIYKV----LKQVHP 290
           ES+          +G+ V+  G  +   A +  K K  +  S    I  +          
Sbjct: 116 ESIEEQGDLVDLKTGEIVEDNGHIKTLTANNSTKDKRTKYTSVLRDIIDISDEEDGDKGG 175

Query: 291 DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR 339
              +S      + + +    E +  +S     + KR T+TS ++  A++
Sbjct: 176 VKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALK 224

>2byk_A Chrac-16; nucleosome sliding, histone fold, DNA-binding protein; 2.4A {Drosophila melanogaster} SCOP: a.22.1.3 PDB: 2bym_A Length = 140

 Score = 40.5 bits (94), Expect = 1e-04
 Identities = 10/88 (11%), Positives = 23/88 (26%), Gaps = 1/88 (1%)

Query: 42  GGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELA 101
           G         R   A    P+ R+  +++       +       +    E     +   A
Sbjct: 2   GEPRSQPPVERPPTAETFLPLSRVRTIMKSSMDTGLITNEVLFLMTKCTELFVRHLAGAA 61

Query: 102 GNAARDNKKTRII-PRHLQLAIRNDEEL 128
                  +    +   HL   +  ++ L
Sbjct: 62  YTEEFGQRPGEALKYEHLSQVVNKNKNL 89

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	365
2nqb_D	123	Histone H2B; nucleosome, NCP, chromatin, structura	100.0
1tzy_B	126	Histone H2B; histone-fold, tetramer-dimer-dimer, D	100.0
2nqb_C	123	Histone H2A; nucleosome, NCP, chromatin, structura	100.0
2f8n_G	120	Core histone macro-H2A.1; nucleosome, NCP, macroh2	100.0
1tzy_A	129	Histone H2A-IV; histone-fold, tetramer-dimer-dimer	100.0
2f8n_K	149	Histone H2A type 1; nucleosome, NCP, macroh2A, his	100.0
1id3_C	131	Histone H2A.1; nucleosome core particle, chromatin	100.0
1f66_C	128	Histone H2A.Z; nucleosome, chromatin, histone vari	100.0
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	100.0
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	100.0
3ksy_A	1049	SOS-1, SON of sevenless homolog 1; RAS, RAS activa	99.86
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	99.8
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	99.6
4g92_C	119	HAPE; transcription factor, nucleosome, minor groo	99.58
1tzy_D	103	Histone H4-VI; histone-fold, tetramer-dimer-dimer,	99.5
2yfw_B	103	Histone H4, H4; cell cycle, kinetochore, centromer	99.49
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	99.47
3b0c_W	76	CENP-W, centromere protein W; histone fold, DNA bi	99.46
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	99.3
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	98.87
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	98.63
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	98.44
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	98.3
1id3_B	102	Histone H4; nucleosome core particle, chromatin, p	98.08
1tzy_D	103	Histone H4-VI; histone-fold, tetramer-dimer-dimer,	97.92
2yfw_B	103	Histone H4, H4; cell cycle, kinetochore, centromer	97.9
1n1j_A	93	NF-YB; histone-like PAIR, DNA binding protein; 1.6	97.86
3b0c_W	76	CENP-W, centromere protein W; histone fold, DNA bi	97.77
2byk_B	128	Chrac-14; nucleosome sliding, histone fold, DNA-bi	97.69
1id3_B	102	Histone H4; nucleosome core particle, chromatin, p	97.53
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	97.51
2hue_C	84	Histone H4; mini beta sheet, elongated beta sandwh	97.36
1n1j_A	93	NF-YB; histone-like PAIR, DNA binding protein; 1.6	97.24
1taf_B	70	TFIID TBP associated factor 62; transcription init	97.04
2hue_C	84	Histone H4; mini beta sheet, elongated beta sandwh	97.04
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	97.01
1jfi_B	179	DR1 protein, transcription regulator NC2 beta chai	96.99
1id3_C	131	Histone H2A.1; nucleosome core particle, chromatin	96.98
2f8n_K	149	Histone H2A type 1; nucleosome, NCP, macroh2A, his	96.85
1f66_C	128	Histone H2A.Z; nucleosome, chromatin, histone vari	96.82
2nqb_C	123	Histone H2A; nucleosome, NCP, chromatin, structura	96.79
2f8n_G	120	Core histone macro-H2A.1; nucleosome, NCP, macroh2	96.76
2byk_B	128	Chrac-14; nucleosome sliding, histone fold, DNA-bi	96.69
1tzy_A	129	Histone H2A-IV; histone-fold, tetramer-dimer-dimer	96.68
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	96.6
4g92_C	119	HAPE; transcription factor, nucleosome, minor groo	96.55
1jfi_B	179	DR1 protein, transcription regulator NC2 beta chai	96.51
1h3o_B	76	Transcription initiation factor TFIID 20/15 kDa su	96.37
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	96.34
1taf_B	70	TFIID TBP associated factor 62; transcription init	96.29
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	95.89
2hue_B	77	Histone H3; mini beta sheet, elongated beta sandwh	95.83
3v9r_A	90	MHF1, uncharacterized protein YOL086W-A; histone f	95.72
1taf_A	68	TFIID TBP associated factor 42; transcription init	95.71
3v9r_A	90	MHF1, uncharacterized protein YOL086W-A; histone f	95.69
1tzy_B	126	Histone H2B; histone-fold, tetramer-dimer-dimer, D	95.67
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	95.47
3b0b_B	107	CENP-S, centromere protein S; histone fold, DNA bi	95.42
4dra_A	113	Centromere protein S; DNA binding complex, DNA dam	95.39
3nqj_A	82	Histone H3-like centromeric protein A; alpha helix	95.29
2nqb_D	123	Histone H2B; nucleosome, NCP, chromatin, structura	95.29
1taf_A	68	TFIID TBP associated factor 42; transcription init	95.22
3vh5_A	140	CENP-S; histone fold, chromosome segregation, DNA	94.86
3b0b_B	107	CENP-S, centromere protein S; histone fold, DNA bi	94.66
4dra_A	113	Centromere protein S; DNA binding complex, DNA dam	94.64
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	94.59
2yfv_A	100	Histone H3-like centromeric protein CSE4; cell cyc	94.5
3ksy_A	1049	SOS-1, SON of sevenless homolog 1; RAS, RAS activa	94.5
1tzy_C	136	Histone H3; histone-fold, tetramer-dimer-dimer, DN	94.43
2ly8_A	121	Budding yeast chaperone SCM3; centromere protein,	94.35
3nqu_A	140	Histone H3-like centromeric protein A; alpha helix	93.84
3r45_A	156	Histone H3-like centromeric protein A; histone fol	93.69
3vh5_A	140	CENP-S; histone fold, chromosome segregation, DNA	93.35
1bh9_B	89	TAFII28; histone fold, tata binding protein, trans	92.64
2hue_B	77	Histone H3; mini beta sheet, elongated beta sandwh	92.44
3nqj_A	82	Histone H3-like centromeric protein A; alpha helix	92.24
3nqu_A	140	Histone H3-like centromeric protein A; alpha helix	91.13
3r45_A	156	Histone H3-like centromeric protein A; histone fol	91.1
3b0b_C	81	CENP-X, centromere protein X; histone fold, DNA bi	90.18
2yfv_A	100	Histone H3-like centromeric protein CSE4; cell cyc	89.94
1tzy_C	136	Histone H3; histone-fold, tetramer-dimer-dimer, DN	89.93
2ly8_A	121	Budding yeast chaperone SCM3; centromere protein,	89.62
4dra_E	84	Centromere protein X; DNA binding complex, DNA dam	88.94
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	88.21

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

Probab=100.00  E-value=3.2e-51  Score=350.09  Aligned_cols=103  Identities=93%  Similarity=1.236  Sum_probs=93.8

Q ss_pred             ccccccccccCccchhhhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHhC
Q psy3828         263 AKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLL  342 (365)
Q Consensus       263 ~~~~~k~~~kr~esy~~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrllL  342 (365)
                      +++++|++++|+|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+|+|||+||||+||||+|
T Consensus        21 ~~~~~k~~~~~~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtAvrLlL  100 (123)
T 2nqb_D           21 TKTDKKKKRKRKESYAIYIYTVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLL  100 (123)
T ss_dssp             --------CCCCCCSHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHHHS
T ss_pred             CCCCCCCCccccchHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHHHhC
Confidence            34456677889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cHHHHhhHHhhhhhhhhccccCC
Q psy3828         343 PGELAKHAVSEGTKAVTKYTSSK  365 (365)
Q Consensus       343 PgeLakhAvseGtkAV~ky~~~k  365 (365)
                      ||||+||||+||||||++|++++
T Consensus       101 pGELaKhAvseGtkAV~ky~ss~  123 (123)
T 2nqb_D          101 PGELAKHAVSEGTKAVTKYTSSK  123 (123)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             cHHHHHHHHHHHHHHHhcccCCC
Confidence            99999999999999999999986

>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=100.00  E-value=9.9e-51  Score=348.32  Aligned_cols=102  Identities=90%  Similarity=1.222  Sum_probs=91.5

Q ss_pred             cccccccccCccchhhhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHhCc
Q psy3828         264 KSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLP  343 (365)
Q Consensus       264 ~~~~k~~~kr~esy~~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrllLP  343 (365)
                      ++++||+++|+|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+|+|||+||||+|||||||
T Consensus        25 ~~~~k~~~~~~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtAvrLlLp  104 (126)
T 1tzy_B           25 KGDKKRKKSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLP  104 (126)
T ss_dssp             ---------CCCCCHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHSC
T ss_pred             CCCCCccccccccHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Confidence            34466778899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhHHhhhhhhhhccccCC
Q psy3828         344 GELAKHAVSEGTKAVTKYTSSK  365 (365)
Q Consensus       344 geLakhAvseGtkAV~ky~~~k  365 (365)
                      |||+||||+||||||++|++++
T Consensus       105 GELaKhAvseGtkAV~ky~ssk  126 (126)
T 1tzy_B          105 GELAKHAVSEGTKAVTKYTSSK  126 (126)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHhcccCCC
Confidence            9999999999999999999985

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

Probab=100.00  E-value=3.2e-42  Score=295.63  Aligned_cols=115  Identities=93%  Similarity=1.307  Sum_probs=101.9

Q ss_pred             CCCCCCCCCCCCCCCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccch
Q psy3828          37 SGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPR  116 (365)
Q Consensus        37 Sg~gkggk~~~k~~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~  116 (365)
                      ||+|||||.+++++|+|+||||||||+||+|||++++|++||+++|||||+||||||++||||+|+|+|+++++++|+|+
T Consensus         1 ~~~~~~~~~~~~~~s~s~ragL~fPV~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~   80 (123)
T 2nqb_C            1 SGRGKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPR   80 (123)
T ss_dssp             ------------CCCHHHHHTCSSCHHHHHHHHHHTTSCSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHH
T ss_pred             CCCCCCCCCCCCCCCccccCCeeccHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccHH
Confidence            57888888888999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhcCcHHHHhhhcCCeecCCcccCCcccccc
Q psy3828         117 HLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAGAA  151 (365)
Q Consensus       117 hI~lAI~nDeEL~~Lf~~vtIa~GGV~P~i~~gl~  151 (365)
                      ||++||+||+|||+||+++||++|||+||||+.+.
T Consensus        81 hi~lAI~nDeEL~~Ll~~vtia~ggvlp~i~~~l~  115 (123)
T 2nqb_C           81 HLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLL  115 (123)
T ss_dssp             HHHHHHHTSHHHHHHTTTEEETTCCCCCCCCGGGS
T ss_pred             HHHHHHhccHHHHHHhcCceeCCCCcCCCccHHHc
Confidence            99999999999999999999999999999999986

>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=100.00  E-value=4.2e-42  Score=293.77  Aligned_cols=114  Identities=63%  Similarity=0.991  Sum_probs=103.3

Q ss_pred             cCCCCCCCCCCCCCCCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccc
Q psy3828          36 MSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIP  115 (365)
Q Consensus        36 mSg~gkggk~~~k~~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP  115 (365)
                      |||+|  ||++++++|+|+||||||||+||+|||++++|++||+++|||||+||||||++||||+|+|+|+++++++|+|
T Consensus         1 m~~~~--~~~~~~~~srs~ragLqfPV~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~~rItp   78 (120)
T 2f8n_G            1 MSSRG--GKKKSTKTSRSAKAGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTP   78 (120)
T ss_dssp             -----------CCCCCHHHHHTCSSCHHHHHHHHHHHSSSCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECH
T ss_pred             CCCCC--CCCCcCCcCcccccCccCChHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcH
Confidence            78876  6677788999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhcCcHHHHhhhcCCeecCCcccCCcccccc
Q psy3828         116 RHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAGAA  151 (365)
Q Consensus       116 ~hI~lAI~nDeEL~~Lf~~vtIa~GGV~P~i~~gl~  151 (365)
                      +||++||+||+|||+||+++||++|||+||||+.+.
T Consensus        79 ~hi~lAI~nDeEL~~Ll~~vtia~ggv~p~i~~~l~  114 (120)
T 2f8n_G           79 RHILLAVANDEELNQLLKGVTIASGGVLPNIHPELL  114 (120)
T ss_dssp             HHHHHHHHTSHHHHHHTTTEEETTCCCCCCCCGGGS
T ss_pred             HHHHHHHhcCHHHHHHhCCceECCCCcCCCcCHHHc
Confidence            999999999999999999999999999999999985

>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=100.00  E-value=4.7e-42  Score=296.77  Aligned_cols=116  Identities=90%  Similarity=1.282  Sum_probs=102.7

Q ss_pred             cCCCCC-CCCCCCCCCCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCcccc
Q psy3828          36 MSGRGK-GGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRII  114 (365)
Q Consensus        36 mSg~gk-ggk~~~k~~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrIt  114 (365)
                      |||+|+ |||.+++.+|+|+||||||||+||+|||++++|++||+++|||||+||||||++||||+|+|+|+++++++|+
T Consensus         1 m~~~~~~~~~~~~~~~srS~ragLqfPV~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krIt   80 (129)
T 1tzy_A            1 MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRII   80 (129)
T ss_dssp             -------------CCCCHHHHHTCSSCHHHHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEEC
T ss_pred             CCCCCCCCCCCCCCCCCccccCceeccHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEc
Confidence            889887 7787888999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chhhhhhhcCcHHHHhhhcCCeecCCcccCCcccccc
Q psy3828         115 PRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAGAA  151 (365)
Q Consensus       115 P~hI~lAI~nDeEL~~Lf~~vtIa~GGV~P~i~~gl~  151 (365)
                      |+||++||+||+|||+||+++||++|||+||||+.+.
T Consensus        81 p~hi~lAI~nDeEL~~L~~~vtIa~ggvlP~i~~~l~  117 (129)
T 1tzy_A           81 PRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLL  117 (129)
T ss_dssp             HHHHHHHHHTSHHHHHHTTTEEETTCCCCCCCCGGGS
T ss_pred             HHHHHHHHhccHHHHHHhCCCeecCCCcCCCCCHHHc
Confidence            9999999999999999999999999999999999986

>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=100.00  E-value=2.7e-41  Score=298.11  Aligned_cols=117  Identities=88%  Similarity=1.253  Sum_probs=101.8

Q ss_pred             ccCCCCCC-CCCCCCCCCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccc
Q psy3828          35 TMSGRGKG-GKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRI  113 (365)
Q Consensus        35 ~mSg~gkg-gk~~~k~~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrI  113 (365)
                      +|||+|++ ||.+++.+|+|+||||||||+||+|||++++|++||+++|||||+||||||++||||+|+|+|+++++++|
T Consensus        19 ~~~~~~~~~~~~~~k~~srS~ragLqFPVgrI~R~LK~~~~a~RVs~~A~VyLAAVLEYL~aEILelAgn~A~~~krkrI   98 (149)
T 2f8n_K           19 SMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRI   98 (149)
T ss_dssp             ---------------CCCHHHHHTCSSCHHHHHHHHHHTTSCSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEE
T ss_pred             ccccCCCCCCCCCCCCCCccccCCeeccHHHHHHHHHccccccccCcCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcC
Confidence            69999885 77788899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cchhhhhhhcCcHHHHhhhcCCeecCCcccCCcccccc
Q psy3828         114 IPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAGAA  151 (365)
Q Consensus       114 tP~hI~lAI~nDeEL~~Lf~~vtIa~GGV~P~i~~gl~  151 (365)
                      +|+||++||+||+|||+||+++||++|||+|+||+.+.
T Consensus        99 tprhI~lAI~nDeEL~~Ll~~vtIa~gGVlP~i~~~l~  136 (149)
T 2f8n_K           99 IPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLL  136 (149)
T ss_dssp             CHHHHHHHHHHSHHHHHHTTTEEETTCCCCCCCCGGGS
T ss_pred             cHHHHHHHHhccHHHHHHhcCceEcCCCCCCCccHHHc
Confidence            99999999999999999999999999999999999986

>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=100.00  E-value=2.7e-40  Score=286.40  Aligned_cols=112  Identities=77%  Similarity=1.189  Sum_probs=100.9

Q ss_pred             CCCCCCCCCCCCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhh
Q psy3828          40 GKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQ  119 (365)
Q Consensus        40 gkggk~~~k~~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~  119 (365)
                      |+++|.+++.+|+|+||||||||+||+|||++++|++||+++|||||+||||||++||||+|+|+|+++++++|+|+||+
T Consensus         6 ~~~~~~~~~~~srS~ragLqfPV~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hI~   85 (131)
T 1id3_C            6 GKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRHLQ   85 (131)
T ss_dssp             ----------CCTTGGGTCSSCHHHHHHHHHTTCSCSEECSSHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHH
T ss_pred             CCCCCCCCCCCCccccCCeecCHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHH
Confidence            34566677889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhcCcHHHHhhhcCCeecCCcccCCcccccc
Q psy3828         120 LAIRNDEELNKLLSGVTIAQGGVLPNIQAGAA  151 (365)
Q Consensus       120 lAI~nDeEL~~Lf~~vtIa~GGV~P~i~~gl~  151 (365)
                      +||+||+|||+||+++||++|||+||||+.+.
T Consensus        86 lAI~nDeEL~~Ll~~vtIa~ggvlP~i~~~l~  117 (131)
T 1id3_C           86 LAIRNDDELNKLLGNVTIAQGGVLPNIHQNLL  117 (131)
T ss_dssp             HHHHTCHHHHHHTTTEEETTCCCCCCCCGGGS
T ss_pred             HHHhccHHHHHHhcCceecCCccCCCccHHHc
Confidence            99999999999999999999999999999986

>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=100.00  E-value=7.8e-40  Score=282.57  Aligned_cols=108  Identities=64%  Similarity=0.942  Sum_probs=99.1

Q ss_pred             CCCCCCCCCcccccccccchhhhhhhhhcCCcc-cccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhh
Q psy3828          43 GKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYA-ERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLA  121 (365)
Q Consensus        43 gk~~~k~~SrSsRAgLqFPVsRI~RlLke~~ya-~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lA  121 (365)
                      ++.+++.+|+|+||||||||+||+|||++++|+ +||+++|||||+||||||++||||+|+|+|+++++++|+|+||++|
T Consensus        11 ~~~~~~~~srS~ragLqfPV~ri~R~Lk~~~~a~~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItprhi~lA   90 (128)
T 1f66_C           11 GKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLA   90 (128)
T ss_dssp             ------CCCHHHHHTCSSCHHHHHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHH
T ss_pred             CCcCCCCcCccccCCccCChHHHHHHHHHcccchhhccccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEcHHHHHHH
Confidence            445667899999999999999999999999987 5999999999999999999999999999999999999999999999


Q ss_pred             hcCcHHHHhhhcCCeecCCcccCCcccccc
Q psy3828         122 IRNDEELNKLLSGVTIAQGGVLPNIQAGAA  151 (365)
Q Consensus       122 I~nDeEL~~Lf~~vtIa~GGV~P~i~~gl~  151 (365)
                      |+||+|||+||+ +||++|||+||||+.+.
T Consensus        91 I~nDeEL~~Ll~-~tia~ggv~P~i~~~l~  119 (128)
T 1f66_C           91 IRGDEELDSLIK-ATIAGGGVIPHIHKSLI  119 (128)
T ss_dssp             HHHSHHHHHHCC-SEETTCCCCCCCCGGGC
T ss_pred             HhccHHHhhhhc-ceecCCccCCCCCHHhc
Confidence            999999999996 59999999999999986

>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=100.00  E-value=9.5e-36  Score=271.79  Aligned_cols=124  Identities=52%  Similarity=0.753  Sum_probs=116.0

Q ss_pred             cCCCcccccccccCCCCCcccccccCCCCCCCCCCCCCCCcccccccccchhhhhhhhhcCCcc-cccCCChhHHHHHHH
Q psy3828          12 NDSSITQSRSFSIPGAVPIPQIYTMSGRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYA-ERVGAGAPVYLAAVM   90 (365)
Q Consensus        12 ~~~s~~~a~~c~~~~a~~a~~~~~mSg~gkggk~~~k~~SrSsRAgLqFPVsRI~RlLke~~ya-~RVs~~ApVYLaAVL   90 (365)
                      -+.+|.|+..|. ..+.+|.+.|++++         +.+++|+|+||||||+||+|||++++++ .||+++|||||+|||
T Consensus        68 l~lpgeLak~Av-~eG~kAv~k~~~sk---------~~~s~s~ragl~fPv~ri~R~lk~~~~a~~Rv~~~A~vyLaavL  137 (192)
T 2jss_A           68 LILPGELAKHAV-SEGTRAVTKYSSST---------QAQSSSARAGLQFPVGRIKRYLKRHATGRTRVGSKAAIYLTAVL  137 (192)
T ss_dssp             HHSCSHHHHHHH-HHHHHHHHHHHHHC---------SSSCHHHHSSCCSCHHHHHHHHHHTTCSSCCCCTTTHHHHHHHH
T ss_pred             HhcCHHHHHHHH-HHHHHHHHhhcccc---------ccccccccCCCcCCHHHHHHHHHhcCccccccccChHHHHHHHH
Confidence            356799999998 57999999999975         2469999999999999999999999887 799999999999999


Q ss_pred             HHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHHHhhhcCCeecCCcccCCc
Q psy3828          91 EYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNI  146 (365)
Q Consensus        91 EYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL~~Lf~~vtIa~GGV~P~i  146 (365)
                      |||++||||+|+|+|+++++++|+|+||++||+||+|||+||+ +||++|||+|||
T Consensus       138 Eyl~~eIlelA~n~a~~~~~~~I~p~~i~lAi~nD~eL~~L~~-~ti~~ggv~p~i  192 (192)
T 2jss_A          138 EYLTAEVLELAGNAAKDLKVKRITPRHLQLAIRGDDELDSLIR-ATIASGGVLPHI  192 (192)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCSSCCHHHHHHHHHTSHHHHHHHC-SCCTTTCCSSCC
T ss_pred             HHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhccHHHHHHHh-hhhcCCCcCCCC
Confidence            9999999999999999999999999999999999999999996 699999999997

>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=100.00  E-value=5.4e-35  Score=266.82  Aligned_cols=92  Identities=80%  Similarity=1.168  Sum_probs=89.5

Q ss_pred             CccchhhhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHhCcHHHHhhHHh
Q psy3828         273 RKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVS  352 (365)
Q Consensus       273 r~esy~~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrllLPgeLakhAvs  352 (365)
                      |+|+|++||||||||||||++||++||++||+|++|+|||||.||++|++||+|+|||+||||+||||+|||||+|||++
T Consensus         1 ~~~~~~~yi~kvLkqv~p~~~iS~~Am~~m~s~v~di~~rIa~eA~~L~~~~~r~Tit~~eIq~Avrl~lpgeLak~Av~   80 (192)
T 2jss_A            1 RKETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVS   80 (192)
T ss_dssp             CCSTTHHHHHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCSCCHHHHHHHHHHHSCSHHHHHHHH
T ss_pred             CcchHHHHHHHHHcccCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcCHHHHHHHHH
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhccccC
Q psy3828         353 EGTKAVTKYTSS  364 (365)
Q Consensus       353 eGtkAV~ky~~~  364 (365)
                      ||+|||++|+++
T Consensus        81 eG~kAv~k~~~s   92 (192)
T 2jss_A           81 EGTRAVTKYSSS   92 (192)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHhhccc
Confidence            999999999653

>3ksy_A SOS-1, SON of sevenless homolog 1; RAS, RAS activator, disease mutation, guanine-nucleotide releasing factor, signaling protein; 3.18A {Homo sapiens} PDB: 1xd4_A 1xdv_A 1q9c_A

Probab=99.86  E-value=4.9e-23  Score=225.57  Aligned_cols=98  Identities=28%  Similarity=0.478  Sum_probs=82.2

Q ss_pred             CCCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHH
Q psy3828          49 SKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEEL  128 (365)
Q Consensus        49 ~~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL  128 (365)
                      ..++|+|||||||||||||+| +|+|++||+++||||||||||||++||||||||+|+++++.+|+|+||++||+||+||
T Consensus        94 ~~~~~~~~~l~~pv~~~~~~l-~~~~~~r~~~~~~~y~~avleyl~~~~l~la~~~~~~~~~~~i~p~~~~~ai~~d~eL  172 (1049)
T 3ksy_A           94 IEKRKRRNPLSLPVEKIHPLL-KEVLGYKIDHQVSVYIVAVLEYISADILKLVGNYVRNIRHYEITKQDIKVAMCADKVL  172 (1049)
T ss_dssp             HTTCCCSSSCSSCHHHHHHHH-HHHHCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCBCCHHHHHHHHHHCSSH
T ss_pred             hhcccccCCccccHHHHHHHh-hcccccccCCCCcchhHHHHHHHHHHHHHHHHHHHHHcCCceecCccccccccCCHHH
Confidence            469999999999999999999 9999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhcCCeecCCcccCCccc
Q psy3828         129 NKLLSGVTIAQGGVLPNIQA  148 (365)
Q Consensus       129 ~~Lf~~vtIa~GGV~P~i~~  148 (365)
                      ..||++. ...+|++|....
T Consensus       173 ~~l~~~d-ee~~~~lp~~~~  191 (1049)
T 3ksy_A          173 MDMFHQD-VEDINILSLTDE  191 (1049)
T ss_dssp             HHHCC---------------
T ss_pred             HHHHhhc-cccccCCCCccc
Confidence            9999765 456677786543

>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=99.80  E-value=3.4e-20  Score=152.92  Aligned_cols=82  Identities=17%  Similarity=0.346  Sum_probs=62.6

Q ss_pred             CcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHHHh
Q psy3828          51 TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNK  130 (365)
Q Consensus        51 SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL~~  130 (365)
                      +++.+++++|||+||+|+||.+.+..||++.|++|+++++|||+.||+++|++.|+++++++|+|+||..||++|++|++
T Consensus         3 ~~~kk~~~~fPvaRIkrimK~~~~~~~vs~~A~v~la~a~E~Fi~el~~~A~~~a~~~krktI~~~di~~av~~~e~l~F   82 (98)
T 1jfi_A            3 SKKKKYNARFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQCIELEGDPAA   82 (98)
T ss_dssp             -------CCCCHHHHHHHHTTSTTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC---CBCHHHHHTTCC-------
T ss_pred             CcccccCCCCChHHHHHHHHcCccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHhcCchhhH
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hh
Q psy3828         131 LL  132 (365)
Q Consensus       131 Lf  132 (365)
                      |+
T Consensus        83 L~   84 (98)
T 1jfi_A           83 NK   84 (98)
T ss_dssp             --
T ss_pred             HH
Confidence            97

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

Probab=99.60  E-value=5.9e-16  Score=127.15  Aligned_cols=78  Identities=21%  Similarity=0.323  Sum_probs=71.8

Q ss_pred             ccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHHHhhh
Q psy3828          55 RAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLL  132 (365)
Q Consensus        55 RAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL~~Lf  132 (365)
                      -.+++||++||+|+||.+.+..||++.|++|+++++|||+.+|++.|++.|+.+++++|+|+||..||++|++|++|.
T Consensus        15 ~~~~~lP~arIkrImK~~~~~~~is~eA~~~laka~E~Fi~~l~~~A~~~a~~~krktI~~~di~~Av~~~e~~~FL~   92 (97)
T 1n1j_B           15 FRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLI   92 (97)
T ss_dssp             -----CCHHHHHHHHTTSTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTCGGGGGGT
T ss_pred             cCCCcCCHHHHHHHHccCccccccChHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHHhcCcHHHHHH
Confidence            347899999999999999999999999999999999999999999999999999999999999999999999999996

>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=99.58  E-value=1.3e-15  Score=129.62  Aligned_cols=76  Identities=21%  Similarity=0.319  Sum_probs=73.0

Q ss_pred             ccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHHHhhh
Q psy3828          57 GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLL  132 (365)
Q Consensus        57 gLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL~~Lf  132 (365)
                      -.+||++||+|+||.+.+..+|+..|++|+++++|||+.+|++.|++.|+++++++|+|+||..||++|++|++|.
T Consensus        39 ~~~lPvaRIkrImK~d~~~~~is~eA~v~la~a~E~Fi~~L~~~A~~~a~~~krktI~~~di~~Av~~~e~~dFL~  114 (119)
T 4g92_C           39 IHQLPLARIKKVMKADPEVKMISAEAPILFAKGCDVFITELTMRAWIHAEDNKRRTLQRSDIAAALSKSDMFDFLI  114 (119)
T ss_dssp             CCSSCHHHHHHHHHTSTTCCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTCGGGGGGT
T ss_pred             cCCCCHHHHHHHHhhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccCHHHHHHHHhcCchhhHHH
Confidence            3479999999999999999999999999999999999999999999999999999999999999999999999874

>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=99.50  E-value=2e-14  Score=119.33  Aligned_cols=87  Identities=25%  Similarity=0.386  Sum_probs=70.1

Q ss_pred             cCCCCCCCCC-------CCCCCCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhc
Q psy3828          36 MSGRGKGGKA-------KAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDN  108 (365)
Q Consensus        36 mSg~gkggk~-------~~k~~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~  108 (365)
                      |||+|||||.       +.++.++++.+|  ||+..|+|+++.+.+ .||+..+..+|+.+|||++.||++.|.+.|+..
T Consensus         1 m~g~gk~~kg~~~~~~kr~~k~~r~~~~g--ip~~~I~Rlar~~G~-~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~ha   77 (103)
T 1tzy_D            1 MSGRGKGGKGLGKGGAKRHRKVLRDNIQG--ITKPAIRRLARRGGV-KRISGLIYEETRGVLKVFLENVIRDAVTYTEHA   77 (103)
T ss_dssp             --------------------CCCCCGGGG--SCHHHHHHHHHHTTC-CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCCCCCccccccchhhhccc--CCHHHHHHHHHHcCc-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            7888775553       334568999999  999999999999877 899999999999999999999999999999999


Q ss_pred             CCccccchhhhhhhcCc
Q psy3828         109 KKTRIIPRHLQLAIRND  125 (365)
Q Consensus       109 kkkrItP~hI~lAI~nD  125 (365)
                      +++.|+|+||.+|+++.
T Consensus        78 kRktIt~~DV~~Alr~~   94 (103)
T 1tzy_D           78 KRKTVTAMDVVYALKRQ   94 (103)
T ss_dssp             TCSEECHHHHHHHHHHT
T ss_pred             CCCcCCHHHHHHHHHHc
Confidence            99999999999999865

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

Probab=99.49  E-value=2e-14  Score=119.38  Aligned_cols=88  Identities=25%  Similarity=0.378  Sum_probs=63.1

Q ss_pred             cCCCCCCCCC-------CCCCCCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhc
Q psy3828          36 MSGRGKGGKA-------KAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDN  108 (365)
Q Consensus        36 mSg~gkggk~-------~~k~~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~  108 (365)
                      |||+|||||.       +.+++++++.+|  ||+..|+|+++.+.+ .||+..+..+|+.+|||++.||++.|.+.|+..
T Consensus         1 m~~~gk~gkg~~~~~~kr~~~~~r~~~~g--ip~~~I~Rlar~~G~-~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~ha   77 (103)
T 2yfw_B            1 MSGRGKGGKGLGKGGAKRHRKILRDNIQG--ITKPAIRRLARRGGV-KRISGLIYEEVRNVLKTFLESVIRDAVTYTEHA   77 (103)
T ss_dssp             -------------------------------CCHHHHHHHHHHTTC-CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCCCCCccchhhhhhhhhcc--CCHHHHHHHHHHcCc-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            7888876664       334556899999  999999999999877 899999999999999999999999999999999


Q ss_pred             CCccccchhhhhhhcCcH
Q psy3828         109 KKTRIIPRHLQLAIRNDE  126 (365)
Q Consensus       109 kkkrItP~hI~lAI~nDe  126 (365)
                      +++.|+|+||.+|+++..
T Consensus        78 kRktvt~~DV~~Alr~~g   95 (103)
T 2yfw_B           78 KRKTVTSLDVVYALKRQG   95 (103)
T ss_dssp             TCSEECHHHHHHHHHHHC
T ss_pred             CCCcCcHHHHHHHHHHcC
Confidence            999999999999999654

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

Probab=99.47  E-value=1.9e-14  Score=125.87  Aligned_cols=85  Identities=13%  Similarity=0.195  Sum_probs=62.5

Q ss_pred             CCCCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHH-hhcCCccccchhhhhhhcCcH
Q psy3828          48 KSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAA-RDNKKTRIIPRHLQLAIRNDE  126 (365)
Q Consensus        48 k~~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A-~~~kkkrItP~hI~lAI~nDe  126 (365)
                      +..+++.+.+++||++||+|+||.+....+|+..|+++++.++|||+.+|++.|++.| ...++++|+++||..||.+++
T Consensus         8 k~~s~~~~~~~~LPlaRIKrIMK~dpdv~~Is~eA~vliakA~ElFI~~Lt~~A~~~a~~~~kRKtI~~~Dl~~AV~~~e   87 (140)
T 2byk_A            8 PPVERPPTAETFLPLSRVRTIMKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNK   87 (140)
T ss_dssp             ---------------------CCSSSSCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHHTCS
T ss_pred             CCCCCCcccCCCCCHHHHHHHHhcCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccCHHHHHHHHhcCc
Confidence            3478888999999999999999999999999999999999999999999999999999 999999999999999999999


Q ss_pred             HHHhhh
Q psy3828         127 ELNKLL  132 (365)
Q Consensus       127 EL~~Lf  132 (365)
                      +|.+|.
T Consensus        88 ~~dFL~   93 (140)
T 2byk_A           88 NLEFLL   93 (140)
T ss_dssp             TTGGGT
T ss_pred             hhhhHh
Confidence            999996

>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=99.46  E-value=4e-14  Score=111.42  Aligned_cols=65  Identities=18%  Similarity=0.227  Sum_probs=62.7

Q ss_pred             hhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHhCc
Q psy3828         279 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLP  343 (365)
Q Consensus       279 ~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrllLP  343 (365)
                      .+|+|++||+||+..||.+|+.+|+.++.+++++|+.||..++++++|+||+++||+.|++.+|-
T Consensus         8 A~V~rI~K~~~p~~~is~~A~~~i~~~~~~Fi~~la~eA~~~a~~~~rKTI~~~dI~~A~~~ll~   72 (76)
T 3b0c_W            8 GTLRKIIKKHKPHLRLAANTDLLVHLSFLLFLHRLAEEARTNAFENKSKIIKPEHTIAAAKVILK   72 (76)
T ss_dssp             HHHHHHHHHHCTTCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSBCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHhCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHH
Confidence            57999999999999999999999999999999999999999999999999999999999998863

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

Probab=99.30  E-value=1.6e-11  Score=108.92  Aligned_cols=147  Identities=19%  Similarity=0.261  Sum_probs=123.0

Q ss_pred             ccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHHHhhhcCCeec
Q psy3828          59 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIA  138 (365)
Q Consensus        59 qFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL~~Lf~~vtIa  138 (365)
                      .+|..-|.|+||++--..|||..|...|+.++|.+..+|...|.+.|...+++.|+++||..|+      ..        
T Consensus         4 ~LP~a~V~Riik~~lg~~rVS~dA~~~l~~~l~~f~~~i~~~A~~~a~ha~RKTv~a~DV~~a~------~~--------   69 (154)
T 1f1e_A            4 ELPKAAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALA------DV--------   69 (154)
T ss_dssp             CCCHHHHHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHH------HH--------
T ss_pred             cCCccHHHHHHHhcCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHH------Hh--------
Confidence            4788889999999845599999999999999999999999999999999999999999999887      11        


Q ss_pred             CCcccCCccccccccccccccccCCCCCccceeccCCCcCcchhhhhhcccccccccCCCCccccCCccccCCCCCcccc
Q psy3828         139 QGGVLPNIQAGAALTFERVDDVHGGDGLSLGVLGVGDGVADHVLEEHLENATGLLVDEPGDTLDSTSTRQTTDGGLGDSL  218 (365)
Q Consensus       139 ~GGV~P~i~~gl~l~lekv~~vhgg~gl~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l  218 (365)
                                                      |++++-+    -++++                                
T Consensus        70 --------------------------------lg~~~v~----d~~~l--------------------------------   81 (154)
T 1f1e_A           70 --------------------------------LMVEGVE----DYDGE--------------------------------   81 (154)
T ss_dssp             --------------------------------HTCTTST----TCCSC--------------------------------
T ss_pred             --------------------------------cccccCC----ccccc--------------------------------
Confidence                                            1111111    11110                                


Q ss_pred             ccccccccccCCcccccccccccccCCCCChhhHHhhcccccccccccccccccCccchhhhhhhhhhhcCCCCCcchhH
Q psy3828         219 DVVTEYFPVPLGASFSESLSSLTTAAGKSSGKAVKKAGKAQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKA  298 (365)
Q Consensus       219 ~~~~~~~~v~~~~~~~~~~~s~~t~~~~~~~k~~~~~~~~~~~~~~~~~k~~~kr~esy~~YIykVLKQVhpd~gISska  298 (365)
                           +||+                                                   .=|.|++|+. ....||+.|
T Consensus        82 -----~lP~---------------------------------------------------a~V~Ri~k~~-g~~RVS~~A  104 (154)
T 1f1e_A           82 -----LFGR---------------------------------------------------ATVRRILKRA-GIERASSDA  104 (154)
T ss_dssp             -----CCCH---------------------------------------------------HHHHHHHHHT-TCCEECHHH
T ss_pred             -----cCCc---------------------------------------------------cHHHHHHHHc-CCccchHHH
Confidence                 0111                                                   1188888888 678999999


Q ss_pred             HHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHhCcH
Q psy3828         299 MSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPG  344 (365)
Q Consensus       299 m~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrllLPg  344 (365)
                      ...|..++.++.+.|+.+|..++++.+|+||+.+||+.|++..||.
T Consensus       105 ~~~l~~~le~f~~~I~~~A~~~a~ha~RKTIt~eDV~~Al~~~~~~  150 (154)
T 1f1e_A          105 VDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITYSMPK  150 (154)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHSGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhcCCc
Confidence            9999999999999999999999999999999999999999999993

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

Probab=98.87  E-value=1.2e-09  Score=96.90  Aligned_cols=72  Identities=18%  Similarity=0.217  Sum_probs=68.5

Q ss_pred             ccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCc
Q psy3828          53 SSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND  125 (365)
Q Consensus        53 SsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nD  125 (365)
                      -.+.+|.||++.|.|+|+++ ...|||..|.++|..+|||++.+|.+.|.+.|+..+++.|+|+||.+|+.++
T Consensus        76 ~d~~~l~lP~a~V~Ri~k~~-g~~RVS~~A~~~l~~~le~f~~~I~~~A~~~a~ha~RKTIt~eDV~~Al~~~  147 (154)
T 1f1e_A           76 EDYDGELFGRATVRRILKRA-GIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITYS  147 (154)
T ss_dssp             TTCCSCCCCHHHHHHHHHHT-TCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             CccccccCCccHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhc
Confidence            34789999999999999998 8899999999999999999999999999999999999999999999999875

>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=98.63  E-value=3.6e-08  Score=75.25  Aligned_cols=60  Identities=27%  Similarity=0.384  Sum_probs=57.8

Q ss_pred             hhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHh
Q psy3828         281 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  341 (365)
Q Consensus       281 IykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrll  341 (365)
                      |.|++|++ ++..||+.|+..|...+.++++.|++||...+.+++|+||+.+|||.|++.|
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 IGRIIKNA-GAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARKMF   67 (68)
T ss_dssp             HHHHHHHT-TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHGGGG
T ss_pred             HHHHHhcC-CcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhc
Confidence            78999999 8899999999999999999999999999999999999999999999999865

>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=98.44  E-value=1.8e-07  Score=71.32  Aligned_cols=65  Identities=28%  Similarity=0.413  Sum_probs=61.5

Q ss_pred             ccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcC
Q psy3828          59 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN  124 (365)
Q Consensus        59 qFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~n  124 (365)
                      .||.++|.|+|++. ...||+..|...|.-++|+++.+|.+.|...|...+++.|+|+||++|++.
T Consensus         2 ~lP~a~v~Ri~k~~-~~~ris~~A~~~l~~a~e~fi~~l~~~A~~~a~~~kRkTI~~~Di~~A~~~   66 (68)
T 1b67_A            2 ELPIAPIGRIIKNA-GAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARKM   66 (68)
T ss_dssp             CSCHHHHHHHHHHT-TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHGGG
T ss_pred             CCCccHHHHHHhcC-CcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHh
Confidence            48999999999998 778999999999999999999999999999999999999999999999863

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

Probab=98.30  E-value=6.2e-07  Score=68.97  Aligned_cols=65  Identities=32%  Similarity=0.446  Sum_probs=61.6

Q ss_pred             ccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcC
Q psy3828          59 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN  124 (365)
Q Consensus        59 qFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~n  124 (365)
                      .||.+.|+|+++++ -..|++..+...|..++|+++.+|++-|...|...|++.|+++||++|+++
T Consensus         6 ~lp~a~v~Rl~r~~-g~~ris~~a~~~l~e~~~~~~~~v~~dA~~~a~hakRkTI~~~DV~lA~~~   70 (70)
T 1ku5_A            6 ELPIAPVDRLIRKA-GAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIKS   70 (70)
T ss_dssp             CSCHHHHHHHHHHT-TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHTC
T ss_pred             cCChHHHHHHHHHc-CcceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHC
Confidence            68999999999996 578999999999999999999999999999999999999999999999875

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

Probab=98.08  E-value=4.8e-06  Score=69.01  Aligned_cols=77  Identities=17%  Similarity=0.254  Sum_probs=63.5

Q ss_pred             CCCCCCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCc
Q psy3828          46 KAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND  125 (365)
Q Consensus        46 ~~k~~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nD  125 (365)
                      +-+++.+.+..+  +|..-|.|+++.+. ..||+..+..-|.-+|||++.+|++-|...++..+++.|+++||.+|+...
T Consensus        17 r~~k~~r~~i~~--ip~~~I~Rlar~~G-v~rIS~da~~~l~~~le~fi~~I~~dA~~~a~HakRKTVt~~DV~~ALkr~   93 (102)
T 1id3_B           17 RHRKILRDNIQG--ITKPAIRRLARRGG-VKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQ   93 (102)
T ss_dssp             -------CCGGG--SCHHHHHHHHHHTT-CCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHT
T ss_pred             hHHHHHHhccCC--CCHHHHHHHHHHcC-chhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHc
Confidence            334456666666  78888999999964 589999999999999999999999999999999999999999999998843

>1tzy_D Histone H4-VI; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1f66_B 1eqz_D 1hq3_D 1u35_B 2aro_D 2cv5_B* 2f8n_B 3nqu_B 3r45_B 3azg_B 3a6n_B 3an2_B 3av1_B 3av2_B 3ayw_B 3aze_B 3azf_B 3afa_B 3azh_B 3azk_B ...

Probab=97.92  E-value=1.8e-05  Score=65.33  Aligned_cols=62  Identities=13%  Similarity=0.154  Sum_probs=57.7

Q ss_pred             hhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHh
Q psy3828         279 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  341 (365)
Q Consensus       279 ~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrll  341 (365)
                      -.|.|+++..-. ..||..+..-|...+.+.++.|+.+|..++++++|+|||.+||+.|++-+
T Consensus        33 ~~I~Rlar~~G~-~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktIt~~DV~~Alr~~   94 (103)
T 1tzy_D           33 PAIRRLARRGGV-KRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ   94 (103)
T ss_dssp             HHHHHHHHHTTC-CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCc-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHc
Confidence            458899999876 68999999999999999999999999999999999999999999999854

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

Probab=97.90  E-value=1.7e-05  Score=65.54  Aligned_cols=62  Identities=15%  Similarity=0.184  Sum_probs=57.8

Q ss_pred             hhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHh
Q psy3828         279 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  341 (365)
Q Consensus       279 ~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrll  341 (365)
                      -.|.|+++..-. ..||..+..-|..++.+.++.|+.+|..++++++|+|||.+||+.|++-+
T Consensus        33 ~~I~Rlar~~G~-~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktvt~~DV~~Alr~~   94 (103)
T 2yfw_B           33 PAIRRLARRGGV-KRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQ   94 (103)
T ss_dssp             HHHHHHHHHTTC-CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCc-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHc
Confidence            458899999876 68999999999999999999999999999999999999999999999965

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

Probab=97.86  E-value=1.4e-05  Score=64.50  Aligned_cols=68  Identities=10%  Similarity=0.257  Sum_probs=62.5

Q ss_pred             cccccchhhhhhhhhcC-CcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          56 AGLQFPVGRIHRLLRKG-NYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        56 AgLqFPVsRI~RlLke~-~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      ..+.||.++|.|+||+. ....||+..|...|+-+.|.++.+|.+.|...|...+++.|+++||..|+.
T Consensus         5 ~d~~LP~a~i~ri~K~~~~~~~~is~dA~~~l~~a~e~Fi~~l~~~A~~~a~~~kRkTI~~~Dv~~Al~   73 (93)
T 1n1j_A            5 QDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMS   73 (93)
T ss_dssp             --CCCCHHHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHH
T ss_pred             ccccCChhHHHHHHHHhCCccceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHH
Confidence            36789999999999997 446899999999999999999999999999999999999999999999997

>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=97.77  E-value=3.1e-05  Score=60.53  Aligned_cols=65  Identities=22%  Similarity=0.296  Sum_probs=60.1

Q ss_pred             ccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          59 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        59 qFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      .+|.+.|.|+|++..-..+|+..|...+.-+.|-++.+|-..|...|+..+++.|+++||..|+.
T Consensus         4 ~LP~A~V~rI~K~~~p~~~is~~A~~~i~~~~~~Fi~~la~eA~~~a~~~~rKTI~~~dI~~A~~   68 (76)
T 3b0c_W            4 TVPRGTLRKIIKKHKPHLRLAANTDLLVHLSFLLFLHRLAEEARTNAFENKSKIIKPEHTIAAAK   68 (76)
T ss_dssp             CCCHHHHHHHHHHHCTTCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSBCHHHHHHHHH
T ss_pred             cccccHHHHHHHHhCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence            58999999999975446899999999999999999999999999999999999999999999985

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

Probab=97.69  E-value=1.9e-05  Score=67.85  Aligned_cols=72  Identities=17%  Similarity=0.155  Sum_probs=62.5

Q ss_pred             ccccchhhhhhhhhc-CCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHH
Q psy3828          57 GLQFPVGRIHRLLRK-GNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEEL  128 (365)
Q Consensus        57 gLqFPVsRI~RlLke-~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL  128 (365)
                      .+.||+++|.|+|++ .....+|+..|...|+-+.|.|+.+|-..|...|...+++.|+++||..|+...+-+
T Consensus         7 d~~LP~A~I~rImK~~~pd~~~iS~dA~~~l~ka~e~FI~~lt~~A~~~a~~~kRKTI~~~Dv~~Al~~l~f~   79 (128)
T 2byk_B            7 DLNLPNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFE   79 (128)
T ss_dssp             ----CCSHHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCT
T ss_pred             cccCCHHHHHHHHHHhCcccceECHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHcCcH
Confidence            578999999999996 556789999999999999999999999999999999999999999999999876533

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

Probab=97.53  E-value=0.00015  Score=59.96  Aligned_cols=62  Identities=16%  Similarity=0.194  Sum_probs=56.7

Q ss_pred             hhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHh
Q psy3828         279 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  341 (365)
Q Consensus       279 ~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrll  341 (365)
                      -.|.|+.+..-. ..||..+...+..++.+.++.|+.||..++++.+|+|||..||..|++-+
T Consensus        32 ~~I~Rlar~~Gv-~rIS~da~~~l~~~le~fi~~I~~dA~~~a~HakRKTVt~~DV~~ALkr~   93 (102)
T 1id3_B           32 PAIRRLARRGGV-KRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQ   93 (102)
T ss_dssp             HHHHHHHHHTTC-CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCc-hhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHc
Confidence            348899998754 67999999999999999999999999999999999999999999999854

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

Probab=97.51  E-value=0.00014  Score=55.66  Aligned_cols=59  Identities=17%  Similarity=0.340  Sum_probs=54.9

Q ss_pred             hhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         280 YIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       280 YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      -|.|++|+. ....||+.+..-+..++...++.|+.+|...+++.+|+||+.+||+.|++
T Consensus        11 ~v~Rl~r~~-g~~ris~~a~~~l~e~~~~~~~~v~~dA~~~a~hakRkTI~~~DV~lA~~   69 (70)
T 1ku5_A           11 PVDRLIRKA-GAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIK   69 (70)
T ss_dssp             HHHHHHHHT-TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHT
T ss_pred             HHHHHHHHc-CcceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence            478899986 46789999999999999999999999999999999999999999999975

>2hue_C Histone H4; mini beta sheet, elongated beta sandwhich, DNA binding prote; 1.70A {Xenopus laevis} SCOP: a.22.1.1 PDB: 3nqj_B 1aoi_B 3kwq_B* 1hio_D 2yfv_B

Probab=97.36  E-value=0.00031  Score=55.96  Aligned_cols=71  Identities=18%  Similarity=0.261  Sum_probs=63.5

Q ss_pred             cccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCc
Q psy3828          52 RSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND  125 (365)
Q Consensus        52 rSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nD  125 (365)
                      |.+..|  +|..-|+|+++.+. ..||+..+..-|..++||++.+|++-|...++..+++.|+++||.+|+...
T Consensus         5 r~~~~~--ip~~~I~Riar~~G-v~rIs~da~~~l~~~l~~~~~~I~~dA~~~a~ha~RKTvt~~DV~~Alk~~   75 (84)
T 2hue_C            5 RDNIQG--ITKPAIRRLARRGG-VKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ   75 (84)
T ss_dssp             GGGCCS--SCHHHHHHHHHHTT-CCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTT
T ss_pred             cccCCC--CCHHHHHHHHHHcC-chhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHc
Confidence            445556  67778999999974 489999999999999999999999999999999999999999999999854

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

Probab=97.24  E-value=0.00061  Score=54.85  Aligned_cols=60  Identities=23%  Similarity=0.378  Sum_probs=56.4

Q ss_pred             hhhhhhhhcCCC-CCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         280 YIYKVLKQVHPD-TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       280 YIykVLKQVhpd-~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      =|.|+.|..-|+ ..||+.|...|.-....+...|+.+|...+...+|+||+..||+.|++
T Consensus        13 ~i~ri~K~~~~~~~~is~dA~~~l~~a~e~Fi~~l~~~A~~~a~~~kRkTI~~~Dv~~Al~   73 (93)
T 1n1j_A           13 NVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMS   73 (93)
T ss_dssp             HHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHH
T ss_pred             HHHHHHHHhCCccceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHH
Confidence            388999999775 679999999999999999999999999999999999999999999997

>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=97.04  E-value=0.00081  Score=52.38  Aligned_cols=66  Identities=11%  Similarity=0.177  Sum_probs=60.5

Q ss_pred             ccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          57 GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        57 gLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      .-.||+.-|.++.+.-. ..+|+..+...|+--+||-..||++-|.+.++..|+++++.+||+.|++
T Consensus         4 ~s~lp~~~v~~iaes~G-i~~lsddaa~~LA~dvEyr~~eI~qeA~kfmrHakRk~Lt~~DI~~Alk   69 (70)
T 1taf_B            4 GSSISAESMKVIAESIG-VGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLK   69 (70)
T ss_dssp             SCCCCHHHHHHHHHHTT-CCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC
T ss_pred             cccCCHHHHHHHHHHCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHc
Confidence            34689999999999843 4799999999999999999999999999999999999999999999875

>2hue_C Histone H4; mini beta sheet, elongated beta sandwhich, DNA binding prote; 1.70A {Xenopus laevis} SCOP: a.22.1.1 PDB: 3nqj_B 1aoi_B 3kwq_B* 1hio_D 2yfv_B

Probab=97.04  E-value=0.00066  Score=54.01  Aligned_cols=62  Identities=13%  Similarity=0.154  Sum_probs=56.3

Q ss_pred             hhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHh
Q psy3828         279 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  341 (365)
Q Consensus       279 ~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrll  341 (365)
                      -.|.|+.+..-. ..||..+...+...+...++.|+.||..++++.+|+|||..||..|.+-+
T Consensus        14 ~~I~Riar~~Gv-~rIs~da~~~l~~~l~~~~~~I~~dA~~~a~ha~RKTvt~~DV~~Alk~~   75 (84)
T 2hue_C           14 PAIRRLARRGGV-KRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ   75 (84)
T ss_dssp             HHHHHHHHHTTC-CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTT
T ss_pred             HHHHHHHHHcCc-hhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHc
Confidence            358899998754 67999999999999999999999999999999999999999999998743

>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=97.01  E-value=0.00097  Score=55.90  Aligned_cols=61  Identities=16%  Similarity=0.280  Sum_probs=56.2

Q ss_pred             hhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         279 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       279 ~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      ..|.|+.|.- ....||..+...|..++.++++.|+.+|..++++.+|+||+..||..|++-
T Consensus        11 a~I~Ri~r~~-g~~rIS~~a~~~l~e~l~~f~~~v~~da~~~A~HA~RKTV~~eDV~lalrr   71 (111)
T 3b0c_T           11 SLIKQIFSHY-VKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAGRKTVEMADVELLMRR   71 (111)
T ss_dssp             HHHHHHHHHH-HCSCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             HHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHH
Confidence            4578877776 678999999999999999999999999999999999999999999999884

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

Probab=96.99  E-value=0.0015  Score=59.25  Aligned_cols=61  Identities=18%  Similarity=0.355  Sum_probs=58.1

Q ss_pred             hhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         280 YIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       280 YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      =|.|++|++-|+..||..|...|...+..+..-|+.||..++...+|+||+..||-.|+.-
T Consensus        20 ~V~RImK~alp~~rISkDA~~al~ec~~eFI~~LtseA~e~a~~~~RKTI~~eDVl~Al~~   80 (179)
T 1jfi_B           20 AINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALES   80 (179)
T ss_dssp             HHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             HHHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHh
Confidence            3899999999999999999999999999999999999999999999999999999999874

>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=96.98  E-value=0.0013  Score=56.70  Aligned_cols=64  Identities=19%  Similarity=0.267  Sum_probs=57.3

Q ss_pred             chh-hhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         276 SYA-IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       276 sy~-~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      .|. ..|+|.||+-.---.|+..|.-.|-..+.++...|.+.|...++.+++.+|++|+||.|++
T Consensus        25 qfPV~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hI~lAI~   89 (131)
T 1id3_C           25 TFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRHLQLAIR   89 (131)
T ss_dssp             SSCHHHHHHHHHTTCSCSEECSSHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             ecCHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHHHHh
Confidence            444 4699999996444589999999999999999999999999999999999999999999999

>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=96.85  E-value=0.0011  Score=58.37  Aligned_cols=64  Identities=19%  Similarity=0.256  Sum_probs=57.7

Q ss_pred             chh-hhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         276 SYA-IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       276 sy~-~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      .|. ..|+|.||+-.---.|+..|.-.|-..+.++...|.+.|...++.+++.+|++|+||.|++
T Consensus        44 qFPVgrI~R~LK~~~~a~RVs~~A~VyLAAVLEYL~aEILelAgn~A~~~krkrItprhI~lAI~  108 (149)
T 2f8n_K           44 QFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIR  108 (149)
T ss_dssp             SSCHHHHHHHHHHTTSCSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             eccHHHHHHHHHccccccccCcCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHh
Confidence            444 4699999997555589999999999999999999999999999999999999999999999

>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=96.82  E-value=0.0014  Score=56.41  Aligned_cols=65  Identities=18%  Similarity=0.166  Sum_probs=57.1

Q ss_pred             cchh-hhhhhhhhhcCC-CCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         275 ESYA-IYIYKVLKQVHP-DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       275 esy~-~YIykVLKQVhp-d~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      -.|- ..|+|.||.-.. ...|++.|--.|-..+..+...|.+.|...++.+++++|++|+||-||+
T Consensus        26 LqfPV~ri~R~Lk~~~~a~~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItprhi~lAI~   92 (128)
T 1f66_C           26 LQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR   92 (128)
T ss_dssp             CSSCHHHHHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHH
T ss_pred             ccCChHHHHHHHHHcccchhhccccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEcHHHHHHHHh
Confidence            3454 369999998764 3479999999999999999999999999999999999999999999998

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

Probab=96.79  E-value=0.0021  Score=54.90  Aligned_cols=64  Identities=19%  Similarity=0.251  Sum_probs=57.8

Q ss_pred             chh-hhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         276 SYA-IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       276 sy~-~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      .|. ..|+|.||+-.---.||..|.-.|-..+..+...|.+.|...++.+++.+|++|+||.|++
T Consensus        23 ~fPV~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hi~lAI~   87 (123)
T 2nqb_C           23 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR   87 (123)
T ss_dssp             SSCHHHHHHHHHHTTSCSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             eccHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHHHHHh
Confidence            454 4799999997544589999999999999999999999999999999999999999999999

>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=96.76  E-value=0.0022  Score=54.58  Aligned_cols=64  Identities=22%  Similarity=0.258  Sum_probs=57.9

Q ss_pred             chh-hhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         276 SYA-IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       276 sy~-~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      .|. ..|+|.||...----|+..|--.|-..+..+...|.+.|...++.+++++|++|+||.|++
T Consensus        22 qfPV~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~~rItp~hi~lAI~   86 (120)
T 2f8n_G           22 IFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILLAVA   86 (120)
T ss_dssp             SSCHHHHHHHHHHHSSSCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             cCChHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHHHHh
Confidence            444 4699999998756689999999999999999999999999999999999999999999999

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

Probab=96.69  E-value=0.0032  Score=53.95  Aligned_cols=61  Identities=25%  Similarity=0.341  Sum_probs=56.8

Q ss_pred             hhhhhhhcCCC-CCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHh
Q psy3828         281 IYKVLKQVHPD-TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  341 (365)
Q Consensus       281 IykVLKQVhpd-~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrll  341 (365)
                      |.|+.|++-|+ ..||..|...|.-...-+...|+.+|..++...+|+||+..||..|+.-+
T Consensus        15 I~rImK~~~pd~~~iS~dA~~~l~ka~e~FI~~lt~~A~~~a~~~kRKTI~~~Dv~~Al~~l   76 (128)
T 2byk_B           15 IGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTEL   76 (128)
T ss_dssp             HHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHT
T ss_pred             HHHHHHHhCcccceECHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHc
Confidence            89999988875 67999999999999999999999999999999999999999999999854

>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=96.68  E-value=0.0027  Score=54.68  Aligned_cols=64  Identities=19%  Similarity=0.252  Sum_probs=57.5

Q ss_pred             chh-hhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         276 SYA-IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       276 sy~-~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      .|- ..|+|.||+-.---.||..|--.|-..+..+...|.+.|...++.+++.+|++|+||.|++
T Consensus        25 qfPV~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hi~lAI~   89 (129)
T 1tzy_A           25 QFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIR   89 (129)
T ss_dssp             SSCHHHHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             eccHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEcHHHHHHHHh
Confidence            444 4699999997444589999999999999999999999999999999999999999999999

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

Probab=96.60  E-value=0.0038  Score=50.76  Aligned_cols=58  Identities=21%  Similarity=0.236  Sum_probs=53.1

Q ss_pred             hhhhhhhcCCC-CCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         281 IYKVLKQVHPD-TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       281 IykVLKQVhpd-~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      |.|++|.- |+ ..||..|--.|.-....+.+.|+.+|...++.++|+||+.++|+.||+
T Consensus        25 IkrImK~~-~~~~~is~eA~~~laka~E~Fi~~l~~~A~~~a~~~krktI~~~di~~Av~   83 (97)
T 1n1j_B           25 IKKIMKLD-EDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAIT   83 (97)
T ss_dssp             HHHHHTTS-TTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHT
T ss_pred             HHHHHccC-ccccccChHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHHh
Confidence            88999986 77 459999999998888888899999999999999999999999999986

>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=96.55  E-value=0.0032  Score=53.14  Aligned_cols=58  Identities=24%  Similarity=0.282  Sum_probs=52.5

Q ss_pred             hhhhhhhcCCC-CCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         281 IYKVLKQVHPD-TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       281 IykVLKQVhpd-~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      |.|++|.. |+ ..||..|.-.|.--.--+...|+.+|...++.++|+||+.++|+.||+
T Consensus        47 IkrImK~d-~~~~~is~eA~v~la~a~E~Fi~~L~~~A~~~a~~~krktI~~~di~~Av~  105 (119)
T 4g92_C           47 IKKVMKAD-PEVKMISAEAPILFAKGCDVFITELTMRAWIHAEDNKRRTLQRSDIAAALS  105 (119)
T ss_dssp             HHHHHHTS-TTCCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHT
T ss_pred             HHHHHhhC-CccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccCHHHHHHHHh
Confidence            89999976 55 568999988888888888899999999999999999999999999996

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

Probab=96.51  E-value=0.0021  Score=58.18  Aligned_cols=76  Identities=16%  Similarity=0.216  Sum_probs=65.1

Q ss_pred             ccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHHHhh
Q psy3828          55 RAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKL  131 (365)
Q Consensus        55 RAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL~~L  131 (365)
                      --.+.||.+.|.|+|++.--..||+..|...|+-+.+-++.+|--.|...|...+++.|+++||..|+. +-++..+
T Consensus        11 ~eD~~LP~A~V~RImK~alp~~rISkDA~~al~ec~~eFI~~LtseA~e~a~~~~RKTI~~eDVl~Al~-~LgF~~f   86 (179)
T 1jfi_B           11 DDDLTIPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALE-SLGFGSY   86 (179)
T ss_dssp             -CCCCCCHHHHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHH-HHTTGGG
T ss_pred             hhhhhcCHHHHHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH-hcChHHH
Confidence            346789999999999995336899999999999999999999999999999999999999999999998 3344433

>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=96.37  E-value=0.0083  Score=47.39  Aligned_cols=59  Identities=17%  Similarity=0.406  Sum_probs=55.1

Q ss_pred             hhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         281 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       281 IykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      +-..++||-|...+...+...|-.+.+|+.+.+.+.|.+||++.+..||..+|||....
T Consensus        11 L~~Lv~~idp~~~ld~~vee~ll~lADdFV~~V~~~ac~lAKhR~s~~le~kDvql~Le   69 (76)
T 1h3o_B           11 LQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLE   69 (76)
T ss_dssp             HHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHH
T ss_pred             HHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHHH
Confidence            66789999999999999999999999999999999999999999999999999997654

>3b0c_T CENP-T, centromere protein T; histone fold, DNA binding, DNA binding protein; HET: CIT; 2.20A {Gallus gallus} PDB: 3b0d_T* 3vh5_T 3vh6_T

Probab=96.34  E-value=0.0046  Score=51.74  Aligned_cols=71  Identities=8%  Similarity=0.045  Sum_probs=60.4

Q ss_pred             ccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHH
Q psy3828          57 GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEEL  128 (365)
Q Consensus        57 gLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL  128 (365)
                      .+.+|-+-|.|+++++ -..||+..+...|.-+++.++.+|..-|...|+..+++.|+++||.+|++.+..+
T Consensus         5 d~~lP~a~I~Ri~r~~-g~~rIS~~a~~~l~e~l~~f~~~v~~da~~~A~HA~RKTV~~eDV~lalrr~g~~   75 (111)
T 3b0c_T            5 EPEIASSLIKQIFSHY-VKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAGRKTVEMADVELLMRRQGLV   75 (111)
T ss_dssp             -----CHHHHHHHHHH-HCSCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTTSS
T ss_pred             CCCCCHHHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHCCCc
Confidence            3568999999999997 5689999999999999999999999999999999999999999999999865433

>1taf_B TFIID TBP associated factor 62; transcription initiation, histone fold, complex (TWO transcr factors); 2.00A {Drosophila melanogaster} SCOP: a.22.1.3

Probab=96.29  E-value=0.0087  Score=46.54  Aligned_cols=60  Identities=15%  Similarity=0.279  Sum_probs=52.5

Q ss_pred             hhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         280 YIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       280 YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      .|.++.+++-= ..+|.++-..|-.-|.+....|+.||.+++++.+|+|||..||..|.++
T Consensus        11 ~v~~iaes~Gi-~~lsddaa~~LA~dvEyr~~eI~qeA~kfmrHakRk~Lt~~DI~~Alk~   70 (70)
T 1taf_B           11 SMKVIAESIGV-GSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLKV   70 (70)
T ss_dssp             HHHHHHHHTTC-CCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC-
T ss_pred             HHHHHHHHCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHcC
Confidence            36677777643 4789999999999999999999999999999999999999999999864

>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=95.89  E-value=0.0068  Score=49.47  Aligned_cols=59  Identities=12%  Similarity=0.272  Sum_probs=50.0

Q ss_pred             hhhhhhhhcCCC-CCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         280 YIYKVLKQVHPD-TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       280 YIykVLKQVhpd-~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      =|.|++|. .|+ ..||..|--.|.-..-.+.+.|+.+|...++.++|+||+.++|+.||+
T Consensus        16 RIkrimK~-~~~~~~vs~~A~v~la~a~E~Fi~el~~~A~~~a~~~krktI~~~di~~av~   75 (98)
T 1jfi_A           16 RIKKIMQT-DEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQCIE   75 (98)
T ss_dssp             HHHHHHTT-STTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC---CBCHHHHHTTCC
T ss_pred             HHHHHHHc-CccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHh
Confidence            38899997 566 569999999888888888899999999999999999999999999986

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

Probab=95.83  E-value=0.018  Score=45.55  Aligned_cols=65  Identities=18%  Similarity=0.251  Sum_probs=54.8

Q ss_pred             chhhhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         276 SYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       276 sy~~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      .|..-+..+..+..++..+++.|+..|.--..+....+.++|..++.+.||.||.++|||-|.|+
T Consensus         8 PF~RLVRei~~~~~~~~R~q~~Al~aLQea~Eaylv~lfeda~l~A~HAkRvTi~~kDiqLa~ri   72 (77)
T 2hue_B            8 PFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRI   72 (77)
T ss_dssp             HHHHHHHHHHHTTCSSCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHcCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHhhHHHHHHH
Confidence            35555555555556788999999999988888888888889999999999999999999999986

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

Probab=95.72  E-value=0.014  Score=47.47  Aligned_cols=78  Identities=14%  Similarity=0.052  Sum_probs=56.6

Q ss_pred             ccccccchhhhhhhh-hcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHHHhhhc
Q psy3828          55 RAGLQFPVGRIHRLL-RKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLS  133 (365)
Q Consensus        55 RAgLqFPVsRI~RlL-ke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL~~Lf~  133 (365)
                      |+.|.|-|++|=.-. +++  ...++..+...|+-.++..+.+|.+-+...|+..|++.|++.++.++++.++.|..+++
T Consensus        11 Kaal~~~V~ki~~e~~~~~--g~~vs~~~i~aL~e~~~~~~~~ia~Dl~~fA~HAgRkTI~~eDV~L~~Rrn~~L~~~l~   88 (90)
T 3v9r_A           11 KARLWIRVEERLQQVLSSE--DIKYTPRFINSLLELAYLQLGEMGSDLQAFARHAGRGVVNKSDLMLYLRKQPDLQERVT   88 (90)
T ss_dssp             HHHHHHHHHHHHHHHSCSS--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHhc--CceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhChHHHHHhh
Confidence            456778888765433 222  13466666666666666666666666667789999999999999999999999999876


Q ss_pred             C
Q psy3828         134 G  134 (365)
Q Consensus       134 ~  134 (365)
                      +
T Consensus        89 ~   89 (90)
T 3v9r_A           89 Q   89 (90)
T ss_dssp             C
T ss_pred             c
Confidence            4

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

Probab=95.71  E-value=0.035  Score=42.86  Aligned_cols=63  Identities=16%  Similarity=0.252  Sum_probs=55.1

Q ss_pred             hhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHhC
Q psy3828         279 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLL  342 (365)
Q Consensus       279 ~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrllL  342 (365)
                      .-|.++||.--- ...|..+...|--|+...-+.|+.+|..++.+.+|+||+..||+.|++..+
T Consensus         5 ~~i~~iLk~~G~-~~~~~~v~~~L~e~~~ry~~~il~dA~~~a~HAgrktv~~eDVkLAi~~~~   67 (68)
T 1taf_A            5 QVIMSILKELNV-QEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLATEVTL   67 (68)
T ss_dssp             HHHHHHHHHTTC-CCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTC
T ss_pred             HHHHHHHHHCCC-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcc
Confidence            357888887432 467999999999999999999999999999999999999999999998643

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

Probab=95.69  E-value=0.017  Score=46.87  Aligned_cols=60  Identities=12%  Similarity=0.177  Sum_probs=52.3

Q ss_pred             hhhhhhhcCC--CCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         281 IYKVLKQVHP--DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       281 IykVLKQVhp--d~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      +-|+..++-+  +..+|.+++.-|--++.+.++.||.++..+|++.+|+||+..||..++|-
T Consensus        18 V~ki~~e~~~~~g~~vs~~~i~aL~e~~~~~~~~ia~Dl~~fA~HAgRkTI~~eDV~L~~Rr   79 (90)
T 3v9r_A           18 VEERLQQVLSSEDIKYTPRFINSLLELAYLQLGEMGSDLQAFARHAGRGVVNKSDLMLYLRK   79 (90)
T ss_dssp             HHHHHHHHSCSSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTT
T ss_pred             HHHHHHHHHHhcCceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHh
Confidence            4455556644  36699999999999999999999999999999999999999999998873

>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=95.67  E-value=0.0096  Score=51.22  Aligned_cols=71  Identities=18%  Similarity=0.244  Sum_probs=61.4

Q ss_pred             ccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc--CcHHH
Q psy3828          57 GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR--NDEEL  128 (365)
Q Consensus        57 gLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~--nDeEL  128 (365)
                      .-.|.+ .|+|.|++-.-...|++.|.-.|...++.++..|...|...++-+++..|++++||.|++  -..||
T Consensus        35 ~esy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtAvrLlLpGEL  107 (126)
T 1tzy_B           35 KESYSI-YVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGEL  107 (126)
T ss_dssp             CCCCHH-HHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHSCHHH
T ss_pred             cccHHH-HHHHHHHHhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcHHH
Confidence            345766 899999996556689999999999999999999999999999999999999999999986  33444

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

Probab=95.47  E-value=0.28  Score=46.14  Aligned_cols=207  Identities=17%  Similarity=0.180  Sum_probs=117.8

Q ss_pred             cccchhhhhhhhhcC--Cc-----ccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHHHh
Q psy3828          58 LQFPVGRIHRLLRKG--NY-----AERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNK  130 (365)
Q Consensus        58 LqFPVsRI~RlLke~--~y-----a~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL~~  130 (365)
                      |-+|=--|.|+.++-  .+     ..|..++|-..|--+-|..+-.++|-+.--|...++..|.|+++++|-+       
T Consensus        10 ~lI~KlPFqRLVREIaq~~~~~~~~lRfqs~Al~ALQEAaEayLV~LFEd~nLcaiHAkRVTim~kDiqLarr-------   82 (235)
T 2l5a_A           10 LLISKIPFARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMKKDMQLARR-------   82 (235)
T ss_dssp             -CCSCCHHHHHHHHHHHTSCGGGTTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTSGGGTTHHHHHHT-------
T ss_pred             ccccCccHHHHHHHHHHHhccCCccceecHHHHHHHHHHHHHHHHHHHhhhHHHHhcccccccchhhHHHHHH-------
Confidence            444444455655541  12     3588888888887777877778889887777778888999999999854       


Q ss_pred             hhcCCeecCCcccCCccccccccccccccccCCCCCccceeccCCCcCcchhhhhhcccccccccCCCCccccCCccc-c
Q psy3828         131 LLSGVTIAQGGVLPNIQAGAALTFERVDDVHGGDGLSLGVLGVGDGVADHVLEEHLENATGLLVDEPGDTLDSTSTRQ-T  209 (365)
Q Consensus       131 Lf~~vtIa~GGV~P~i~~gl~l~lekv~~vhgg~gl~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~-~  209 (365)
                      +-+...++.+ | ..-+.-   +-|+--+                 +-++|.    +.= |= +|+-+|..|-.|-.- +
T Consensus        83 irg~~~~p~e-v-me~~~~---~~~~~k~-----------------~~~~i~----~ky-~~-~~~~gd~idl~tG~iv~  134 (235)
T 2l5a_A           83 IRGQFLVPRG-S-MERHKL---ADENMRK-----------------VWSNII----SKY-ES-IEEQGDLVDLKTGEIVE  134 (235)
T ss_dssp             SSCSCCCCSS-S-CHHHHH---HHHHHHH-----------------HHHHHH----HHH-TT-CCCCSCCCSSSSCCCCC
T ss_pred             HhhccCCchh-H-HHHHHH---HHHHHHH-----------------HHHHHH----HHH-hc-ccCCCCcccCCCCceee
Confidence            2111111110 0 000000   1111000                 001111    111 12 666777777666433 3


Q ss_pred             CCCCCcccccc--ccccccccCCcccccccccccccCCCCChhhHHhhcccccccccccccccccCccchhhhhhhhhhh
Q psy3828         210 TDGGLGDSLDV--VTEYFPVPLGASFSESLSSLTTAAGKSSGKAVKKAGKAQKNIAKSDKKKKHRRKESYAIYIYKVLKQ  287 (365)
Q Consensus       210 ~~~~~~~~l~~--~~~~~~v~~~~~~~~~~~s~~t~~~~~~~k~~~~~~~~~~~~~~~~~k~~~kr~esy~~YIykVLKQ  287 (365)
                      -||-+ +.|..  .+.+.++..+..|                                        ++...+-|-|+++.
T Consensus       135 dnGh~-~~l~~~~~~~~~~~r~~~vL----------------------------------------rD~i~i~~~RlaRr  173 (235)
T 2l5a_A          135 DNGHI-KTLTANNSTKDKRTKYTSVL----------------------------------------RDIIDISDEEDGDK  173 (235)
T ss_dssp             CCCCC-CSCCCCCGGGCCSSTHHHHH----------------------------------------HHHHHHTCCTTSCC
T ss_pred             eCcHH-HHhhcCCCCCccchhHHHHH----------------------------------------HHhhcccHHHHhhc
Confidence            44444 33331  0000000000000                                        01111112344443


Q ss_pred             cCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHh
Q psy3828         288 VHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  341 (365)
Q Consensus       288 Vhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrll  341 (365)
                      --- -.||..+..-+...+.+..|.|+.+|..++.+.+|+|+|+.||--|++..
T Consensus       174 gGV-kRIS~~iyeelr~vLe~fle~IirdAv~yaeHA~RKTVta~DV~~ALKr~  226 (235)
T 2l5a_A          174 GGV-KRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQ  226 (235)
T ss_dssp             TTC-CTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHH
T ss_pred             CCc-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHhc
Confidence            221 35899999999999999999999999999999999999999999998854

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

Probab=95.42  E-value=0.012  Score=49.28  Aligned_cols=61  Identities=21%  Similarity=0.185  Sum_probs=54.1

Q ss_pred             hhhhhhhhcCC--CCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         280 YIYKVLKQVHP--DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       280 YIykVLKQVhp--d~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      .|-|+++.+-.  +..+|.+++..|.-|+.+.++.|+.+|..++++.+|+||+..||..|+|-
T Consensus        24 ~V~rI~~~~g~~~~~~vs~~~i~aL~E~~~~~~~~ia~Da~~fA~HAgRkTI~~eDV~La~Rr   86 (107)
T 3b0b_B           24 TTGCLCQDVAEDKGVLFSKQTVAAISEITFRQCENFARDLEMFARHAKRSTITSEDVKLLARR   86 (107)
T ss_dssp             HHHHHHHHHHHHHTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTT
T ss_pred             HHHHHHHHHhhhcCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcCcCCHHHHHHHHHh
Confidence            36677776633  56799999999999999999999999999999999999999999999884

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

Probab=95.39  E-value=0.018  Score=48.73  Aligned_cols=61  Identities=16%  Similarity=0.220  Sum_probs=54.6

Q ss_pred             hhhhhhhhcCC--CCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         280 YIYKVLKQVHP--DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       280 YIykVLKQVhp--d~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      -|.|+++++-.  +..+|.+++.-|.-++.+.++.||.++..+|+..+|+||+..||..++|-
T Consensus        32 ~V~rIvke~gaer~~~vS~~ai~aL~El~~~~~~~ia~Dl~~fAkHAgRkTI~~eDV~La~Rr   94 (113)
T 4dra_A           32 TVGCLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARR   94 (113)
T ss_dssp             HHHHHHHHHHHHHTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHcCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHh
Confidence            36777777643  56799999999999999999999999999999999999999999999873

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

Probab=95.29  E-value=0.036  Score=44.36  Aligned_cols=66  Identities=12%  Similarity=0.171  Sum_probs=53.1

Q ss_pred             chhhhhhhhhhhcC--CCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHh
Q psy3828         276 SYAIYIYKVLKQVH--PDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  341 (365)
Q Consensus       276 sy~~YIykVLKQVh--pd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrll  341 (365)
                      .|...+..+-.+..  .+..+++.|+..+---..+..-.+.++|...+.+.||.||.++|||-|.|+-
T Consensus         8 PF~RLVREI~~~~~~~~~~R~q~~Al~aLQea~E~ylv~Lfeda~lcAiHAkRvTi~~kDiqLa~rir   75 (82)
T 3nqj_A            8 PFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIR   75 (82)
T ss_dssp             HHHHHHHHHHHHHHSSCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHHHHHHHHHc
Confidence            34444444444444  3678999999999888888888888899999999999999999999999973

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

Probab=95.29  E-value=0.015  Score=49.86  Aligned_cols=69  Identities=20%  Similarity=0.238  Sum_probs=59.6

Q ss_pred             ccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc--CcHHH
Q psy3828          59 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR--NDEEL  128 (365)
Q Consensus        59 qFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~--nDeEL  128 (365)
                      .|. ..|+|.|++-.-...|++.|.-.|...++.++..|...|...++-+++..|++++||.|++  -..||
T Consensus        34 sy~-~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtAvrLlLpGEL  104 (123)
T 2nqb_D           34 SYA-IYIYTVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGEL  104 (123)
T ss_dssp             CSH-HHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHHHSCHHH
T ss_pred             hHH-HHHHHHHHHhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHHHhCcHHH
Confidence            455 4789999996556789999999999999999999999999999999999999999999986  33444

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

Probab=95.22  E-value=0.031  Score=43.16  Aligned_cols=60  Identities=17%  Similarity=0.077  Sum_probs=54.6

Q ss_pred             hhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcC
Q psy3828          64 RIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN  124 (365)
Q Consensus        64 RI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~n  124 (365)
                      -|+++|++. =..|++..++..|.-.+|-.+.+|+.-|...|...|++.|+.++|++||..
T Consensus         6 ~i~~iLk~~-G~~~~~~~v~~~L~e~~~ry~~~il~dA~~~a~HAgrktv~~eDVkLAi~~   65 (68)
T 1taf_A            6 VIMSILKEL-NVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLATEV   65 (68)
T ss_dssp             HHHHHHHHT-TCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             HHHHHHHHC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHh
Confidence            478889985 347999999999999999999999999999999999999999999999964

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

Probab=94.86  E-value=0.029  Score=49.02  Aligned_cols=60  Identities=22%  Similarity=0.205  Sum_probs=52.7

Q ss_pred             hhhhhhhcC--CCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         281 IYKVLKQVH--PDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       281 IykVLKQVh--pd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      |-|+.+++-  .++.+|..++..|--++.+.++.|+.++..+|++.+|+||+..||..++|-
T Consensus        25 VgkIvee~~~~~~~~vS~~ai~aL~El~~~~~e~ia~DLe~FAkHAGRKTI~~eDVkLa~Rr   86 (140)
T 3vh5_A           25 TGALAQDVAEDKGVLFSKQTVAAISEITFRQAENFARDLEMFARHAKRSTITSEDVKLLARR   86 (140)
T ss_dssp             HHHHHHHHHHHHTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTT
T ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHh
Confidence            445555552  357799999999999999999999999999999999999999999999884

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

Probab=94.66  E-value=0.022  Score=47.59  Aligned_cols=78  Identities=14%  Similarity=0.184  Sum_probs=63.0

Q ss_pred             ccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHHHhhhc
Q psy3828          55 RAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLS  133 (365)
Q Consensus        55 RAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL~~Lf~  133 (365)
                      |+.|.|-|+||-+---. ....|++..+...|+-+++..+.+|..-+...|+..|++.|++.+|.++++.++.|...++
T Consensus        18 Kaal~~~V~rI~~~~g~-~~~~~vs~~~i~aL~E~~~~~~~~ia~Da~~fA~HAgRkTI~~eDV~La~Rrn~~l~~~l~   95 (107)
T 3b0b_B           18 RAAVHYTTGCLCQDVAE-DKGVLFSKQTVAAISEITFRQCENFARDLEMFARHAKRSTITSEDVKLLARRSNSLLKYIT   95 (107)
T ss_dssp             HHHHHHHHHHHHHHHHH-HHTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhh-hcCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcCcCCHHHHHHHHHhCHHHHHHHH
Confidence            56788888887653322 1235888888888888888888888888888899999999999999999999999877765

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

Probab=94.64  E-value=0.024  Score=47.93  Aligned_cols=79  Identities=15%  Similarity=0.158  Sum_probs=61.4

Q ss_pred             cccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHHHhhhc
Q psy3828          54 SRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLS  133 (365)
Q Consensus        54 sRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL~~Lf~  133 (365)
                      =++.|.|.|+||=+-.-.. ....++..+...|+-+++..+.+|..-+...|+..|++.|++.+|.++++.++.|..+++
T Consensus        25 LKaal~y~V~rIvke~gae-r~~~vS~~ai~aL~El~~~~~~~ia~Dl~~fAkHAgRkTI~~eDV~La~Rr~~~L~~~l~  103 (113)
T 4dra_A           25 LKAAVHYTVGCLCEEVALD-KEMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARRSNSLLKYIT  103 (113)
T ss_dssp             HHHHHHHHHHHHHHHHHHH-HTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHH-cCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHhCHHHHHHHH
Confidence            3678889998876533221 122477777777777777777777777778899999999999999999999999988875

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

Probab=94.59  E-value=0.06  Score=46.79  Aligned_cols=58  Identities=10%  Similarity=0.173  Sum_probs=48.0

Q ss_pred             hhhhhhhcCCCC-CcchhHHHHHHhHHHHHHHHHHHHHhhhh-hcCCCcccChhHHHHHHH
Q psy3828         281 IYKVLKQVHPDT-GVSSKAMSIMNSFVNDIFERIAAESSRLA-HYNKRSTITSREIQTAVR  339 (365)
Q Consensus       281 IykVLKQVhpd~-gISskam~ImnSfvnDiferIa~EAs~La-~~nkr~TitsreIqtAvr  339 (365)
                      |.|++|.- |+. .||..|.-+|.-..--+...|+.+|...+ +.++|+||+.++|..||+
T Consensus        25 IKrIMK~d-pdv~~Is~eA~vliakA~ElFI~~Lt~~A~~~a~~~~kRKtI~~~Dl~~AV~   84 (140)
T 2byk_A           25 VRTIMKSS-MDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVN   84 (140)
T ss_dssp             ----CCSS-SSCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHH
T ss_pred             HHHHHhcC-cccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccCHHHHHHHHh
Confidence            88888885 775 48999988888877777788999999999 999999999999999997

>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=94.50  E-value=0.058  Score=44.59  Aligned_cols=66  Identities=21%  Similarity=0.212  Sum_probs=52.7

Q ss_pred             cchhhhhhhhhhhcCC---CCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         275 ESYAIYIYKVLKQVHP---DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       275 esy~~YIykVLKQVhp---d~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      -.|...+..+..+..+   +.-+++.|+..|.--..+..-.+.++|..++.+.+|.||..+|||-|.|+
T Consensus        31 ~PF~RLVREI~~~~~~~~~~~R~q~~Al~ALQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa~ri   99 (100)
T 2yfv_A           31 MPFARLVKEVTDQFTTESEPLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARRI   99 (100)
T ss_dssp             HHHHHHHHHHHHTTC-----CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHC
T ss_pred             ccHHHHHHHHHHHhccccchhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHHHh
Confidence            3455555555555555   78899999998888888888888889999999999999999999999885

>3ksy_A SOS-1, SON of sevenless homolog 1; RAS, RAS activator, disease mutation, guanine-nucleotide releasing factor, signaling protein; 3.18A {Homo sapiens} PDB: 1xd4_A 1xdv_A 1q9c_A

Probab=94.50  E-value=0.07  Score=58.94  Aligned_cols=75  Identities=16%  Similarity=0.317  Sum_probs=65.2

Q ss_pred             ccchhhhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHhCcHHHHhhHHhh
Q psy3828         274 KESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSE  353 (365)
Q Consensus       274 ~esy~~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrllLPgeLakhAvse  353 (365)
                      +.-|-.-|+||+.||||+..|.-.|+.-+++++--+.-.|+.          ...-|..|++..|.-.+|..+.++|+.+
T Consensus        20 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~   89 (1049)
T 3ksy_A           20 RGLLVPALKKVQGQVHPTLESNDDALQYVEELILQLLNMLCQ----------AQPRSASDVEERVQKSFPHPIDKWAIAD   89 (1049)
T ss_dssp             SSSSHHHHHHHHHHHCTTSBCCHHHHHHHHHHHHHHHHHHHH----------TCCCSHHHHHHHHHHHSCTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCCCccHhHHHHHHHHHHHHHHHHhc----------CCCccHHHHHHHHHHhCCCchHHHHHHH
Confidence            456778899999999999999999999999999877776664          4467889999999999999999999999


Q ss_pred             hhhhh
Q psy3828         354 GTKAV  358 (365)
Q Consensus       354 GtkAV  358 (365)
                      +-.|.
T Consensus        90 ~~~~~   94 (1049)
T 3ksy_A           90 AQSAI   94 (1049)
T ss_dssp             HHHHH
T ss_pred             HHHhh
Confidence            86663

>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=94.43  E-value=0.065  Score=46.54  Aligned_cols=64  Identities=19%  Similarity=0.251  Sum_probs=53.6

Q ss_pred             hhhhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         277 YAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       277 y~~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      |...|..+..+..+|.-+++.|+..|.-...+....+.+++..++.+.+|.||..+|||-|.|+
T Consensus        68 F~RLVREI~~~~~~~~R~q~~Al~aLQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa~ri  131 (136)
T 1tzy_C           68 FQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI  131 (136)
T ss_dssp             HHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHhHHHHHHH
Confidence            4444444444446789999999999988888888888889999999999999999999999986

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

Probab=94.35  E-value=0.056  Score=46.13  Aligned_cols=48  Identities=19%  Similarity=0.271  Sum_probs=45.0

Q ss_pred             CcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         293 GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       293 gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      .||..+..-+...+.+.+|.|+.+|..++.+.+|+|+|..||--|++.
T Consensus        64 RIS~~iy~e~r~vl~~~l~~i~rdav~yaehA~RKTVta~DV~~Alkr  111 (121)
T 2ly8_A           64 RISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKR  111 (121)
T ss_dssp             CCSSCHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCBCHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHh
Confidence            389999999999999999999999999999999999999999998874

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

Probab=93.84  E-value=0.094  Score=45.81  Aligned_cols=61  Identities=13%  Similarity=0.210  Sum_probs=49.9

Q ss_pred             hhhhhhhcC------CCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHh
Q psy3828         281 IYKVLKQVH------PDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  341 (365)
Q Consensus       281 IykVLKQVh------pd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrll  341 (365)
                      |-|+++++-      -+.-+++.|+..|--...+..-.+.++|..++.+.+|.||..+|||-|.|+-
T Consensus        67 F~RLVREI~~~~~~~~~~Rfq~~Al~ALQEAaEayLv~LFEdanlcAiHAkRVTIm~kDiqLArrir  133 (140)
T 3nqu_A           67 FSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIR  133 (140)
T ss_dssp             HHHHHHHHHHHHHTTCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcccccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHHHHhc
Confidence            344555543      3678999999988887777777787899999999999999999999999973

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

Probab=93.69  E-value=0.084  Score=46.87  Aligned_cols=60  Identities=13%  Similarity=0.226  Sum_probs=49.2

Q ss_pred             hhhhhhhcC------CCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         281 IYKVLKQVH------PDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       281 IykVLKQVh------pd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      |-|+++++-      -+.-+++.|+..|--...+..-.|.++|..+|.+.+|.||..+|||-|.|+
T Consensus        83 F~RLVREIa~~~~~~~~lRfqs~Al~ALQEAaEayLV~LFEdanLcAiHAkRVTIm~kDIqLArrI  148 (156)
T 3r45_A           83 FSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRI  148 (156)
T ss_dssp             HHHHHHHHHHTTTTTCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSEECHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHHHHH
Confidence            345555553      356789999998887777777777789999999999999999999999997

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

Probab=93.35  E-value=0.053  Score=47.36  Aligned_cols=79  Identities=15%  Similarity=0.185  Sum_probs=62.0

Q ss_pred             ccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHHHhhhcC
Q psy3828          55 RAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSG  134 (365)
Q Consensus        55 RAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL~~Lf~~  134 (365)
                      ++.|.|-|++|=.-.-.. ....|+..+...|+-+++..+.+|..-+-..|+..|++.|++.+|.++++.++.|..+++.
T Consensus        18 KaAl~y~VgkIvee~~~~-~~~~vS~~ai~aL~El~~~~~e~ia~DLe~FAkHAGRKTI~~eDVkLa~Rrn~~L~~~L~~   96 (140)
T 3vh5_A           18 RAAVHYTTGALAQDVAED-KGVLFSKQTVAAISEITFRQAENFARDLEMFARHAKRSTITSEDVKLLARRSNSLLKYITQ   96 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHH-HTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHh-cCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhCHHHHHHHHH
Confidence            567888888876533221 2345777787778888877777777777788999999999999999999999999988863

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

Probab=92.64  E-value=0.11  Score=42.07  Aligned_cols=64  Identities=22%  Similarity=0.375  Sum_probs=52.3

Q ss_pred             ccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhc-CCccccchhhhhhhc
Q psy3828          59 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDN-KKTRIIPRHLQLAIR  123 (365)
Q Consensus        59 qFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~-kkkrItP~hI~lAI~  123 (365)
                      .||=..|+|+++.- ....++....+.|+++--.++.||+|.|....... ....|.|.||+.|.+
T Consensus        16 ~f~k~~vKrl~~~~-~~~~v~~~v~i~v~glaKvfVgelVE~A~~V~~~~~~~~Pl~P~HireA~r   80 (89)
T 1bh9_B           16 AFPKAAIKRLIQSI-TGTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVR   80 (89)
T ss_dssp             CCCHHHHHHHHHHH-HSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHH-cCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHH
Confidence            35556688888763 56789999999999999999999999999876554 456899999998864

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

Probab=92.44  E-value=0.14  Score=40.52  Aligned_cols=65  Identities=25%  Similarity=0.251  Sum_probs=53.7

Q ss_pred             ccchhhhhhhhhcC----CcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          59 QFPVGRIHRLLRKG----NYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        59 qFPVsRI~RlLke~----~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      -+|.--|.|++++-    .-..|++++|...|--..|....++.|-+..-|...|+..|.|+||++|.+
T Consensus         3 li~k~PF~RLVRei~~~~~~~~R~q~~Al~aLQea~Eaylv~lfeda~l~A~HAkRvTi~~kDiqLa~r   71 (77)
T 2hue_B            3 LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARR   71 (77)
T ss_dssp             CSCHHHHHHHHHHHHHTTCSSCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             ccccchHHHHHHHHHHHcCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHhhHHHHHH
Confidence            45555566666652    135799999999999999999999999998889999999999999999865

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

Probab=92.24  E-value=0.13  Score=41.18  Aligned_cols=64  Identities=22%  Similarity=0.130  Sum_probs=53.4

Q ss_pred             cchhhhhhhhhcCC------cccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          60 FPVGRIHRLLRKGN------YAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        60 FPVsRI~RlLke~~------ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      +|---|.|++++-.      ...|++++|...|--+.|....++.|-+..-|...++..|.|++|++|.+
T Consensus         4 I~klPF~RLVREI~~~~~~~~~~R~q~~Al~aLQea~E~ylv~Lfeda~lcAiHAkRvTi~~kDiqLa~r   73 (82)
T 3nqj_A            4 IRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARR   73 (82)
T ss_dssp             SCHHHHHHHHHHHHHHHHSSCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHH
T ss_pred             cccccHHHHHHHHHHHhccCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHHHHHHHH
Confidence            44455666666522      35799999999999999999999999998889889999999999999865

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

Probab=91.13  E-value=0.18  Score=44.10  Aligned_cols=68  Identities=22%  Similarity=0.131  Sum_probs=59.1

Q ss_pred             cccccchhhhhhhhhcCC------cccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          56 AGLQFPVGRIHRLLRKGN------YAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        56 AgLqFPVsRI~RlLke~~------ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      .+|-+|.--|.|++++-.      ...|+.++|...|--+.|..+.++.|-+..-|...++..|+|+||++|.+
T Consensus        58 t~LLIpKlPF~RLVREI~~~~~~~~~~Rfq~~Al~ALQEAaEayLv~LFEdanlcAiHAkRVTIm~kDiqLArr  131 (140)
T 3nqu_A           58 THLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARR  131 (140)
T ss_dssp             -CCCSCTTHHHHHHHHHHHHHHTTCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             cccccccccHHHHHHHHHHHhcccccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHHHH
Confidence            467888888888888732      35799999999999999999999999998888888999999999999865

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

Probab=91.10  E-value=0.14  Score=45.50  Aligned_cols=69  Identities=22%  Similarity=0.115  Sum_probs=59.5

Q ss_pred             cccccchhhhhhhhhcCC------cccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcC
Q psy3828          56 AGLQFPVGRIHRLLRKGN------YAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN  124 (365)
Q Consensus        56 AgLqFPVsRI~RlLke~~------ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~n  124 (365)
                      .+|-+|.--|.|++++-.      ...|+.++|...|--+.|..+.+++|-+..-|...++..|+|+||++|.+=
T Consensus        74 teLLIpKlPF~RLVREIa~~~~~~~~lRfqs~Al~ALQEAaEayLV~LFEdanLcAiHAkRVTIm~kDIqLArrI  148 (156)
T 3r45_A           74 THLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRI  148 (156)
T ss_dssp             -CCCSCHHHHHHHHHHHHHTTTTTCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSEECHHHHHHHHHH
T ss_pred             cccccccccHHHHHHHHHHHhccCccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHHHHH
Confidence            467888888889888732      247999999999999999999999999988888889999999999999763

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

Probab=90.18  E-value=0.39  Score=38.18  Aligned_cols=64  Identities=20%  Similarity=0.251  Sum_probs=55.9

Q ss_pred             ccccchhhhhhhhhcC--CcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhh
Q psy3828          57 GLQFPVGRIHRLLRKG--NYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQL  120 (365)
Q Consensus        57 gLqFPVsRI~RlLke~--~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~l  120 (365)
                      +-.||..-|+|+|+..  +..-||+.+|-.-++..|+-|+.|.+.+|...|+..+...|..+||+.
T Consensus         6 ~~~~~~~lI~ril~~~f~~~ktrI~~dAl~l~aeyl~iFV~EAv~RA~~~a~~e~~~~le~~~LEk   71 (81)
T 3b0b_C            6 EGGFRKETVERLLRLHFRDGRTRVNGDALLLMAELLKVFVREAAARAARQAQAEDLEKVDIEHVEK   71 (81)
T ss_dssp             -CCCCHHHHHHHHHHHCCSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHhccCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeecHHHHHH
Confidence            4479999999999883  235799999999999999999999999999999888888899999986

>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=89.94  E-value=0.24  Score=40.88  Aligned_cols=68  Identities=24%  Similarity=0.222  Sum_probs=55.7

Q ss_pred             cccccchhhhhhhhhcCC--c-----ccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          56 AGLQFPVGRIHRLLRKGN--Y-----AERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        56 AgLqFPVsRI~RlLke~~--y-----a~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      .+|-+|..-|.|++++-.  +     ..|+.++|-..|--+.|..+.++.|-+..-|...++..|.|+||++|.+
T Consensus        24 t~llIpk~PF~RLVREI~~~~~~~~~~~R~q~~Al~ALQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa~r   98 (100)
T 2yfv_A           24 TDLLISRMPFARLVKEVTDQFTTESEPLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARR   98 (100)
T ss_dssp             ----CCHHHHHHHHHHHHHTTC-----CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             chhhhccccHHHHHHHHHHHhccccchhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHHH
Confidence            477888888888888732  2     5799999999999999999999999998889999999999999999864

>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=89.93  E-value=0.3  Score=42.36  Aligned_cols=68  Identities=25%  Similarity=0.255  Sum_probs=58.9

Q ss_pred             cccccchhhhhhhhhcC----CcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          56 AGLQFPVGRIHRLLRKG----NYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        56 AgLqFPVsRI~RlLke~----~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      .+|-+|.--|.|++++-    .-..|+.++|...|.-..|..+.++.|-+..-|...++..|.|+||++|.+
T Consensus        59 t~lLIpk~PF~RLVREI~~~~~~~~R~q~~Al~aLQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa~r  130 (136)
T 1tzy_C           59 TELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR  130 (136)
T ss_dssp             CSCCSCHHHHHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             hhhhhccchHHHHHHHHHHHhhhhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHhHHHHHH
Confidence            36778888888888773    124799999999999999999999999999889999999999999999864

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

Probab=89.62  E-value=0.48  Score=40.39  Aligned_cols=49  Identities=12%  Similarity=0.159  Sum_probs=46.5

Q ss_pred             ccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          75 AERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        75 a~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      ..|||..+-.-+..+||.+..+|+.-|...+...++|.|+..||.+|++
T Consensus        62 vkRIS~~iy~e~r~vl~~~l~~i~rdav~yaehA~RKTVta~DV~~Alk  110 (121)
T 2ly8_A           62 SKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALK  110 (121)
T ss_dssp             SSCCSSCHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCBCHHHHHHHHH
T ss_pred             ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHH
Confidence            4799999999999999999999999999999999999999999999876

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

Probab=88.94  E-value=0.63  Score=37.31  Aligned_cols=66  Identities=18%  Similarity=0.178  Sum_probs=56.0

Q ss_pred             cccccchhhhhhhhhcCC--cccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhh
Q psy3828          56 AGLQFPVGRIHRLLRKGN--YAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLA  121 (365)
Q Consensus        56 AgLqFPVsRI~RlLke~~--ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lA  121 (365)
                      ++..||..-|.|+|+..-  ..-||+..|-..++..|+-|+.|.+-.|...|...+...|..+||+..
T Consensus         9 ~~~~i~~~li~ril~~~F~~~kTkIs~dAl~l~aeyl~iFV~EAv~RA~~~a~~e~~~~le~e~LEki   76 (84)
T 4dra_E            9 AGSGFRKELVSRLLHLHFKDDKTKVSGDALQLMVELLKVFVVEAAVRGVRQAQAEDALRVDVDQLEKV   76 (84)
T ss_dssp             --CCCCHHHHHHHHHTTCSSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHH
Confidence            466899999999999632  347999999999999999999999999999888877778999999863

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

Probab=88.21  E-value=0.4  Score=45.05  Aligned_cols=59  Identities=14%  Similarity=0.095  Sum_probs=52.9

Q ss_pred             hhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcC
Q psy3828          65 IHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN  124 (365)
Q Consensus        65 I~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~n  124 (365)
                      +.|+.+.+ =+.|||..+-.-+..+||.+..+|+.-|...|...+++.|++.+|.+|+..
T Consensus       167 ~~RlaRrg-GVkRIS~~iyeelr~vLe~fle~IirdAv~yaeHA~RKTVta~DV~~ALKr  225 (235)
T 2l5a_A          167 DEEDGDKG-GVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKR  225 (235)
T ss_dssp             CCTTSCCT-TCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHH
T ss_pred             HHHHhhcC-CchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHh
Confidence            44677775 348999999999999999999999999999999999999999999999874

---

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	365
d1tzyb_	92	a.22.1.1 (B:) Histone H2B {Chicken (Gallus gallus)	2e-58
d1tzya_	106	a.22.1.1 (A:) Histone H2A {Chicken (Gallus gallus)	3e-58
d1u35c1	106	a.22.1.1 (C:814-919) macro-H2A.1, histone domain {	8e-56
d1f66c_	103	a.22.1.1 (C:) Histone H2A {Human (Homo sapiens), v	8e-49
d1q9ca_	172	a.22.1.3 (A:) Histone domain of Son of sevenless p	2e-44
d1q9ca_	172	a.22.1.3 (A:) Histone domain of Son of sevenless p	3e-22
d1jfia_	66	a.22.1.3 (A:) Negative cofactor 2, NC2, alpha chai	9e-23
d1jfia_	66	a.22.1.3 (A:) Negative cofactor 2, NC2, alpha chai	5e-04
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	6e-21
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	2e-13
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	2e-10
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	6e-05
d1n1jb_	78	a.22.1.3 (B:) Nuclear transcription factor Y subun	8e-20

>d1tzyb_ a.22.1.1 (B:) Histone H2B {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]} Length = 92

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

 Score =  182 bits (463), Expect = 2e-58
 Identities = 86/92 (93%), Positives = 90/92 (97%)

Query: 273 RKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSR 332
           RKESY+IY+YKVLKQVHPDTG+SSKAM IMNSFVNDIFERIA E+SRLAHYNKRSTITSR
Sbjct: 1   RKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSR 60

Query: 333 EIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS 364
           EIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS
Sbjct: 61  EIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS 92

>d1tzya_ a.22.1.1 (A:) Histone H2A {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]} Length = 106

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

 Score =  181 bits (462), Expect = 3e-58
 Identities = 93/101 (92%), Positives = 98/101 (97%)

Query: 48  KSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARD 107
           K+K+RSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARD
Sbjct: 1   KAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARD 60

Query: 108 NKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           NKKTRIIPRHLQLAIRNDEELNKLL  VTIAQGGVLPNIQA
Sbjct: 61  NKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQA 101

>d1u35c1 a.22.1.1 (C:814-919) macro-H2A.1, histone domain {Human (Homo sapiens) [TaxId: 9606]} Length = 106

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

 Score =  176 bits (447), Expect = 8e-56
 Identities = 65/99 (65%), Positives = 81/99 (81%)

Query: 50  KTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNK 109
            +RS++AG+ FPVGR+ R ++KG+   R+G GAPVY+AAV+EYL AE+LELA NAARDNK
Sbjct: 2   TSRSAKAGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNK 61

Query: 110 KTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
           K R+ PRH+ LA+ NDEELN+LL GVTIA GGVLPNI  
Sbjct: 62  KGRVTPRHILLAVANDEELNQLLKGVTIASGGVLPNIHP 100

>d1f66c_ a.22.1.1 (C:) Histone H2A {Human (Homo sapiens), variant H2A.Z [TaxId: 9606]} Length = 103

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

 Score =  157 bits (399), Expect = 8e-49
 Identities = 64/101 (63%), Positives = 76/101 (75%), Gaps = 2/101 (1%)

Query: 49  SKTRSSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVMEYLAAEVLELAGNAARD 107
           + +RS RAGLQFPVGRIHR L+    +  RVGA A VY AA++EYL AEVLELAGNA++D
Sbjct: 1   AVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKD 60

Query: 108 NKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 148
            K  RI PRHLQLAIR DEEL+ L+   TIA GGV+P+I  
Sbjct: 61  LKVKRITPRHLQLAIRGDEELDSLI-KATIAGGGVIPHIHK 100

>d1q9ca_ a.22.1.3 (A:) Histone domain of Son of sevenless protein {Human (Homo sapiens) [TaxId: 9606]} Length = 172

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]

 Score =  148 bits (376), Expect = 2e-44
 Identities = 27/95 (28%), Positives = 52/95 (54%), Gaps = 1/95 (1%)

Query: 38  GRGKGGKAKAKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEV 97
            +     A++  + R  R  L  PV +IH LL++     ++     VY+ AV+EY++A++
Sbjct: 78  DKWAIADAQSAIEKRKRRNPLSLPVEKIHPLLKEV-LGYKIDHQVSVYIVAVLEYISADI 136

Query: 98  LELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLL 132
           L+LAGN  R+ +   I  + +++A+  D+ L  + 
Sbjct: 137 LKLAGNYVRNIRHYEITKQDIKVAMCADKVLMDMF 171

>d1q9ca_ a.22.1.3 (A:) Histone domain of Son of sevenless protein {Human (Homo sapiens) [TaxId: 9606]} Length = 172

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]

 Score = 90.2 bits (224), Expect = 3e-22
 Identities = 14/97 (14%), Positives = 36/97 (37%), Gaps = 10/97 (10%)

Query: 267 KKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR 326
           ++   + +      + KV  QVHP    +  A+  +   +  +   +     R       
Sbjct: 8   EENAPKWRGLLVPALKKVQGQVHPTLESNDDALQYVEELILQLLNMLCQAQPR------- 60

Query: 327 STITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 363
              ++ +++  V+   P  + K A+++   A+ K   
Sbjct: 61  ---SASDVEERVQKSFPHPIDKWAIADAQSAIEKRKR 94

>d1jfia_ a.22.1.3 (A:) Negative cofactor 2, NC2, alpha chain {Human (Homo sapiens) [TaxId: 9606]} Length = 66

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]

 Score = 88.3 bits (219), Expect = 9e-23
 Identities = 14/64 (21%), Positives = 28/64 (43%)

Query: 59  QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHL 118
           +FP  RI ++++      +V A  PV ++  +E     +L+ A    +      +   HL
Sbjct: 2   RFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHL 61

Query: 119 QLAI 122
           +  I
Sbjct: 62  KQCI 65

>d1jfia_ a.22.1.3 (A:) Negative cofactor 2, NC2, alpha chain {Human (Homo sapiens) [TaxId: 9606]} Length = 66

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]

 Score = 35.9 bits (83), Expect = 5e-04
 Identities = 7/58 (12%), Positives = 25/58 (43%)

Query: 281 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAV 338
           I K+++       V++    I++  +    E +  ++ ++       T+T+  ++  +
Sbjct: 8   IKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQCI 65

>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} Length = 151

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon Methanopyrus kandleri [TaxId: 2320]

 Score = 86.0 bits (213), Expect = 6e-21
 Identities = 11/80 (13%), Positives = 32/80 (40%)

Query: 281 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL 340
           I ++ +Q   +  +S  A   +  FV  + E +A  +  +   + + T+    ++    +
Sbjct: 7   IERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADV 66

Query: 341 LLPGELAKHAVSEGTKAVTK 360
           L+   +  +      +A  +
Sbjct: 67  LMVEGVEDYDGELFGRATVR 86

>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} Length = 151

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon Methanopyrus kandleri [TaxId: 2320]

 Score = 64.8 bits (158), Expect = 2e-13
 Identities = 13/76 (17%), Positives = 28/76 (36%), Gaps = 1/76 (1%)

Query: 49  SKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDN 108
            +      G  F    + R+L++    ER  + A      ++     E+ E A   A ++
Sbjct: 69  VEGVEDYDGELFGRATVRRILKRAG-IERASSDAVDLYNKLICRATEELGEKAAEYADED 127

Query: 109 KKTRIIPRHLQLAIRN 124
            +  +    ++ AI  
Sbjct: 128 GRKTVQGEDVEKAITY 143

>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} Length = 151

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon Methanopyrus kandleri [TaxId: 2320]

 Score = 56.3 bits (136), Expect = 2e-10
 Identities = 13/65 (20%), Positives = 25/65 (38%)

Query: 59  QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHL 118
           + P   I R+ R+G    R+   A   +   +  +A  V   A +    + K  ++  HL
Sbjct: 1   ELPKAAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHL 60

Query: 119 QLAIR 123
           +    
Sbjct: 61  KALAD 65

>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} Length = 151

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon Methanopyrus kandleri [TaxId: 2320]

 Score = 40.5 bits (95), Expect = 6e-05
 Identities = 21/122 (17%), Positives = 50/122 (40%), Gaps = 9/122 (7%)

Query: 229 LGASFSESLSSLTTAAGKSSGKA--VKKAGKAQKNIAKSDKKKKHRRKESYAIYIYKVLK 286
           +    + +  S+  A+GK +     +K            D   +   + +    + ++LK
Sbjct: 35  MAEYVANAAKSVLDASGKKTLMEEHLKALADVLMVEGVEDYDGELFGRAT----VRRILK 90

Query: 287 QVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLP--G 344
           +   +   SS A+ + N  +    E +  +++  A  + R T+   +++ A+   +P  G
Sbjct: 91  RAGIER-ASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITYSMPKGG 149

Query: 345 EL 346
           EL
Sbjct: 150 EL 151

>d1n1jb_ a.22.1.3 (B:) Nuclear transcription factor Y subunit gamma (Nf-Yc2) {Human (Homo sapiens) [TaxId: 9606]} Length = 78

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]

 Score = 80.7 bits (199), Expect = 8e-20
 Identities = 17/75 (22%), Positives = 34/75 (45%)

Query: 61  PVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQL 120
           P+ RI ++++     + + A APV  A   +    E+   A     DNK+  +    + +
Sbjct: 2   PLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAM 61

Query: 121 AIRNDEELNKLLSGV 135
           AI   ++ + L+  V
Sbjct: 62  AITKFDQFDFLIDIV 76

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	365
d1tzyb_	92	Histone H2B {Chicken (Gallus gallus), erythrocytes	100.0
d1tzya_	106	Histone H2A {Chicken (Gallus gallus), erythrocytes	100.0
d1u35c1	106	macro-H2A.1, histone domain {Human (Homo sapiens)	100.0
d1f66c_	103	Histone H2A {Human (Homo sapiens), variant H2A.Z [	100.0
d1q9ca_	172	Histone domain of Son of sevenless protein {Human	99.92
d1q9ca_	172	Histone domain of Son of sevenless protein {Human	99.61
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	99.55
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	99.49
d1jfia_	66	Negative cofactor 2, NC2, alpha chain {Human (Homo	99.41
d1n1jb_	78	Nuclear transcription factor Y subunit gamma (Nf-Y	99.14
d1ku5a_	66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	98.31
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	98.29
d1n1ja_	87	Nuclear transcription factor Y subunit beta (Nf-Yb	98.2
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	97.78
d1jfib_	135	Negative cofactor 2, NC2, beta chain {Human (Homo	97.77
d2byka1	72	Chrac-16 {Fruit fly (Drosophila melanogaster) [Tax	97.57
d1ku5a_	66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	97.53
d2bykb1	89	Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax	97.33
d1n1ja_	87	Nuclear transcription factor Y subunit beta (Nf-Yb	97.14
d1jfia_	66	Negative cofactor 2, NC2, alpha chain {Human (Homo	96.91
d2bykb1	89	Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax	96.85
d1jfib_	135	Negative cofactor 2, NC2, beta chain {Human (Homo	96.79
d2huec1	82	Histone H4 {African clawed frog (Xenopus laevis) [	96.59
d1n1jb_	78	Nuclear transcription factor Y subunit gamma (Nf-Y	96.43
d2huec1	82	Histone H4 {African clawed frog (Xenopus laevis) [	95.98
d1h3ob_	74	TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom	95.77
d1tzyc_	95	Histone H3 {Chicken (Gallus gallus), erythrocytes	95.3
d1u35c1	106	macro-H2A.1, histone domain {Human (Homo sapiens)	94.12
d1tzyb_	92	Histone H2B {Chicken (Gallus gallus), erythrocytes	93.85
d1tzya_	106	Histone H2A {Chicken (Gallus gallus), erythrocytes	93.75
d1f66c_	103	Histone H2A {Human (Homo sapiens), variant H2A.Z [	92.77
d1bh9b_	89	TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]}	92.72
d1tafb_	70	TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta	90.1
d2byka1	72	Chrac-16 {Fruit fly (Drosophila melanogaster) [Tax	86.99
d1tafb_	70	TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta	82.07
d1k6ka_	142	N-terminal, ClpS-binding domain of ClpA, an Hsp100	80.93
d1tzyc_	95	Histone H3 {Chicken (Gallus gallus), erythrocytes	80.24

>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=100.00  E-value=4.5e-49  Score=320.96  Aligned_cols=92  Identities=93%  Similarity=1.267  Sum_probs=90.6

Q ss_pred             CccchhhhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHhCcHHHHhhHHh
Q psy3828         273 RKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVS  352 (365)
Q Consensus       273 r~esy~~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrllLPgeLakhAvs  352 (365)
                      |+|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+|+|||+||||+||||+|||||+||||+
T Consensus         1 R~esy~~Yi~kVLKqVhp~~giS~kam~imnsfvndiferIa~EA~~La~~~kr~TitsreIqtAvrL~LPgeLaKhAvs   80 (92)
T d1tzyb_           1 RKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVS   80 (92)
T ss_dssp             CCCCCHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHSCHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHHCcHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhccccC
Q psy3828         353 EGTKAVTKYTSS  364 (365)
Q Consensus       353 eGtkAV~ky~~~  364 (365)
                      ||||||+||++|
T Consensus        81 eGtkAv~ky~ss   92 (92)
T d1tzyb_          81 EGTKAVTKYTSS   92 (92)
T ss_dssp             HHHHHHHHHHHC
T ss_pred             HHHHHHHHhccC
Confidence            999999999986

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

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

Probab=100.00  E-value=2.1e-42  Score=287.97  Aligned_cols=104  Identities=89%  Similarity=1.265  Sum_probs=101.5

Q ss_pred             CCCCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHH
Q psy3828          48 KSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEE  127 (365)
Q Consensus        48 k~~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeE  127 (365)
                      |.+|||+|||||||||||+|+|++++|++||+++|||||+||||||++||||||||+|++++++||||+||++||+||+|
T Consensus         1 k~~Srs~rAgL~FpV~rv~r~Lk~~~~~~rv~~~apVylaAVLEYLtaEiLELAgn~a~~~k~~rItPrhi~lAirnDee   80 (106)
T d1tzya_           1 KAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEE   80 (106)
T ss_dssp             CCCCHHHHHTCSSCHHHHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHTSHH
T ss_pred             CCccccccCCccCChHHHHHHHHcCccccccCCCchHHHHHHHHHHHHHHHHHhhHHHHhcCCceecchhhhhcccCHHH
Confidence            35799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhcCCeecCCcccCCcccccc
Q psy3828         128 LNKLLSGVTIAQGGVLPNIQAGAA  151 (365)
Q Consensus       128 L~~Lf~~vtIa~GGV~P~i~~gl~  151 (365)
                      |++||+++||++|||+|+||+.+.
T Consensus        81 L~~L~~~vtI~~GGv~P~Ih~~Ll  104 (106)
T d1tzya_          81 LNKLLGKVTIAQGGVLPNIQAVLL  104 (106)
T ss_dssp             HHHHTTTEEETTCCCCCCCCGGGS
T ss_pred             HHHHHcCCeecCCCccCccCHhhc
Confidence            999999999999999999999875

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

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

Probab=100.00  E-value=6.3e-42  Score=285.12  Aligned_cols=102  Identities=64%  Similarity=1.003  Sum_probs=100.4

Q ss_pred             CCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHHH
Q psy3828          50 KTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELN  129 (365)
Q Consensus        50 ~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL~  129 (365)
                      .|||+|||||||||||+|+|++++|++||+++|||||+||||||++||||||||+|++++++||+|+||++||+||+||+
T Consensus         2 ~srs~ragL~FpV~ri~r~Lk~~~~~~rv~~~apVylaAVLEYL~aEILELAgn~a~~~k~~rItprhi~lairnD~EL~   81 (106)
T d1u35c1           2 TSRSAKAGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILLAVANDEELN   81 (106)
T ss_dssp             CCHHHHHTCSSCHHHHHHHHHHHSTTSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHSHHHH
T ss_pred             CCccccCCcccCHHHHHHHHhCCCCccccCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCeeecchhhhcccCHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhcCCeecCCcccCCcccccc
Q psy3828         130 KLLSGVTIAQGGVLPNIQAGAA  151 (365)
Q Consensus       130 ~Lf~~vtIa~GGV~P~i~~gl~  151 (365)
                      +||+++||++|||+|+||+.+.
T Consensus        82 ~L~~~vtI~~GGv~p~Ih~~Ll  103 (106)
T d1u35c1          82 QLLKGVTIASGGVLPNIHPELL  103 (106)
T ss_dssp             HHTTTEEETTCCCCCCCCGGGS
T ss_pred             HHHcCCeEeCCcccCCcCHHhc
Confidence            9999999999999999999975

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

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

Probab=100.00  E-value=5.5e-41  Score=278.26  Aligned_cols=100  Identities=64%  Similarity=0.956  Sum_probs=97.1

Q ss_pred             CCcccccccccchhhhhhhhhcCCccc-ccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHH
Q psy3828          50 KTRSSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEEL  128 (365)
Q Consensus        50 ~SrSsRAgLqFPVsRI~RlLke~~ya~-RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL  128 (365)
                      +|||+|||||||||||+|||++++|++ ||+++|||||+||||||++||||+|+|+|+++++++|||+||++||+||+||
T Consensus         2 ~Srs~rAgL~FpVgrv~r~L~~~~~~~~rv~~~A~VyLaAvLEYL~aEILelagn~a~~~~~~rItpr~l~lai~nD~EL   81 (103)
T d1f66c_           2 VSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEEL   81 (103)
T ss_dssp             CCHHHHHTCSSCHHHHHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHHSHHH
T ss_pred             CCccccCCcccChHHHHHHHhccCccceecCCCceeeHHHHHHHHHHHHHHHhhhhhccCCCCeeechhhhccccCcHHH
Confidence            699999999999999999999999985 6999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhcCCeecCCcccCCccccc
Q psy3828         129 NKLLSGVTIAQGGVLPNIQAGA  150 (365)
Q Consensus       129 ~~Lf~~vtIa~GGV~P~i~~gl  150 (365)
                      |+||+ +||++|||+|+||+.+
T Consensus        82 ~~L~~-vti~~GGv~p~I~~~L  102 (103)
T d1f66c_          82 DSLIK-ATIAGGGVIPHIHKSL  102 (103)
T ss_dssp             HHHCC-SEETTCCCCCCCCGGG
T ss_pred             HHHhC-eEeeCCeecccccHhh
Confidence            99995 9999999999999986

>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=99.92  E-value=2e-26  Score=205.51  Aligned_cols=85  Identities=31%  Similarity=0.557  Sum_probs=74.2

Q ss_pred             CCCCcccccccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHH
Q psy3828          48 KSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEE  127 (365)
Q Consensus        48 k~~SrSsRAgLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeE  127 (365)
                      ...|+|+|+||+|||+||+|+||++ +++||+++|+|||+||||||++||||+|||+|+++++++|+|+||++||+||+|
T Consensus        88 ~~~srs~ragL~fPV~rv~rlLk~~-~a~RVs~~A~vyLaavLEyl~aeILelAgn~a~~~krkrItp~dI~lAi~nD~e  166 (172)
T d1q9ca_          88 AIEKRKRRNPLSLPVEKIHPLLKEV-LGYKIDHQVSVYIVAVLEYISADILKLAGNYVRNIRHYEITKQDIKVAMCADKV  166 (172)
T ss_dssp             HHC--------CCCHHHHHHHHHHH-HSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSBCCHHHHHHHHHTCHH
T ss_pred             HHhccccccCceecHHHHHHHHHhc-cccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCceecHHHHHHHHhCCHH
Confidence            3478999999999999999999997 999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhc
Q psy3828         128 LNKLLS  133 (365)
Q Consensus       128 L~~Lf~  133 (365)
                      |+.||.
T Consensus       167 L~~Lf~  172 (172)
T d1q9ca_         167 LMDMFH  172 (172)
T ss_dssp             HHHHCC
T ss_pred             HHHhhC
Confidence            999984

>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=99.61  E-value=2.9e-16  Score=139.34  Aligned_cols=79  Identities=16%  Similarity=0.307  Sum_probs=72.3

Q ss_pred             CccchhhhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHhCcHHHHhhHHh
Q psy3828         273 RKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVS  352 (365)
Q Consensus       273 r~esy~~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrllLPgeLakhAvs  352 (365)
                      -+..|..||+||||||||+++|+.+||.+||+|++++|++|+          ...+.|.+|||.+|+++|||+|++||++
T Consensus        14 w~g~f~~~i~KVl~qvhP~l~i~~~Al~~i~~~i~~ll~~L~----------~~~p~sv~dVe~~v~~~fp~~i~~~ai~   83 (172)
T d1q9ca_          14 WRGLLVPALKKVQGQVHPTLESNDDALQYVEELILQLLNMLC----------QAQPRSASDVEERVQKSFPHPIDKWAIA   83 (172)
T ss_dssp             HTTSSHHHHHHHHHHHCSSSBCCHHHHHHHHHHHHHHHHHHH----------TTCCCSTTHHHHHHHHSSCTTHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHHHHHHHHH----------ccCCccHHHHHHHHHHhCCchHHHHHHH
Confidence            356899999999999999999999999999999999999996          3668899999999999999999999999


Q ss_pred             hhhhhhhcc
Q psy3828         353 EGTKAVTKY  361 (365)
Q Consensus       353 eGtkAV~ky  361 (365)
                      |+.+++.+.
T Consensus        84 ~a~~~~~sr   92 (172)
T d1q9ca_          84 DAQSAIEKR   92 (172)
T ss_dssp             HHHHHHC--
T ss_pred             HHHHHHhcc
Confidence            999988653

>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=99.55  E-value=1.2e-15  Score=132.17  Aligned_cols=70  Identities=14%  Similarity=0.237  Sum_probs=68.7

Q ss_pred             hhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHhCcHHHHhhH
Q psy3828         281 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHA  350 (365)
Q Consensus       281 IykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrllLPgeLakhA  350 (365)
                      |+|||||+||+.+||.+||.+||+|++|+|++||.||..|+.+++|+||+++|||.|++++++|++.+|+
T Consensus         7 I~rilk~~~~~~ris~da~~~l~~~~~~~~~~Ia~eA~~l~~~~~rKTi~~edi~~a~~~~~~~~~~~~~   76 (151)
T d1f1ea_           7 IERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADVLMVEGVEDYD   76 (151)
T ss_dssp             HHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHHHTCTTSTTCC
T ss_pred             HHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhcccccccccc
Confidence            8999999999999999999999999999999999999999999999999999999999999999999885

>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=99.49  E-value=6.4e-14  Score=121.15  Aligned_cols=149  Identities=23%  Similarity=0.330  Sum_probs=124.6

Q ss_pred             ccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHHHhhhcCCeec
Q psy3828          59 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIA  138 (365)
Q Consensus        59 qFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL~~Lf~~vtIa  138 (365)
                      .+|++.|+|+|++.....||+..|...|..+++++..+|-..|.+.+...+++.|+|+||+.|++       ++      
T Consensus         1 ~lP~a~I~rilk~~~~~~ris~da~~~l~~~~~~~~~~Ia~eA~~l~~~~~rKTi~~edi~~a~~-------~~------   67 (151)
T d1f1ea_           1 ELPKAAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALAD-------VL------   67 (151)
T ss_dssp             CCCHHHHHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHH-------HH------
T ss_pred             CCCccHHHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH-------hc------
Confidence            48999999999997778899999999999999999999999999999999999999999999884       00      


Q ss_pred             CCcccCCccccccccccccccccCCCCCccceeccCCCcCcchhhhhhcccccccccCCCCccccCCccccCCCCCcccc
Q psy3828         139 QGGVLPNIQAGAALTFERVDDVHGGDGLSLGVLGVGDGVADHVLEEHLENATGLLVDEPGDTLDSTSTRQTTDGGLGDSL  218 (365)
Q Consensus       139 ~GGV~P~i~~gl~l~lekv~~vhgg~gl~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l  218 (365)
                                                       ++| +..||         +|+                          
T Consensus        68 ---------------------------------~~~-~~~~~---------~~~--------------------------   78 (151)
T d1f1ea_          68 ---------------------------------MVE-GVEDY---------DGE--------------------------   78 (151)
T ss_dssp             ---------------------------------TCT-TSTTC---------CSC--------------------------
T ss_pred             ---------------------------------ccc-ccccc---------ccC--------------------------
Confidence                                             011 00011         000                          


Q ss_pred             ccccccccccCCcccccccccccccCCCCChhhHHhhcccccccccccccccccCccchhhhhhhhhhhcCCCCCcchhH
Q psy3828         219 DVVTEYFPVPLGASFSESLSSLTTAAGKSSGKAVKKAGKAQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKA  298 (365)
Q Consensus       219 ~~~~~~~~v~~~~~~~~~~~s~~t~~~~~~~k~~~~~~~~~~~~~~~~~k~~~kr~esy~~YIykVLKQVhpd~gISska  298 (365)
                                                                              .--..+|.|++|... ...||++|
T Consensus        79 --------------------------------------------------------~fp~a~IkRi~k~~g-~~ris~dA  101 (151)
T d1f1ea_          79 --------------------------------------------------------LFGRATVRRILKRAG-IERASSDA  101 (151)
T ss_dssp             --------------------------------------------------------CCCHHHHHHHHHHTT-CCEECHHH
T ss_pred             --------------------------------------------------------ccCHHHHHHHHHcCC-cchhhHHH
Confidence                                                                    011346888888542 45699999


Q ss_pred             HHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHhCc--HHH
Q psy3828         299 MSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLP--GEL  346 (365)
Q Consensus       299 m~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrllLP--geL  346 (365)
                      ...|+..+.++++.|+.+|...+.++||+||+.+||+.||+..+|  |||
T Consensus       102 ~~~l~~~~E~fi~~l~~~A~~~a~~~kRkTI~~~DI~~Av~~~~~~~~~~  151 (151)
T d1f1ea_         102 VDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITYSMPKGGEL  151 (151)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHSGGGGCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHcCCCcCCC
Confidence            999999999999999999999999999999999999999999999  886

>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=99.41  E-value=1.2e-13  Score=104.04  Aligned_cols=65  Identities=22%  Similarity=0.449  Sum_probs=60.1

Q ss_pred             ccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          59 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        59 qFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      +||++||+|+||.+....+|+..|+++++.++|||+.|+++.|++.|..+++++|+|+||..||.
T Consensus         2 ~fP~srVkkimk~~~~~~~is~~A~~~~~~a~E~Fi~~l~~~A~~~a~~~krktI~~~dl~~ai~   66 (66)
T d1jfia_           2 RFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQCIE   66 (66)
T ss_dssp             CCCHHHHHHHHTTSTTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC---CBCHHHHHTTCC
T ss_pred             CCChHHHHHHHhcCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHhC
Confidence            79999999999999999999999999999999999999999999999999999999999999874

>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=99.14  E-value=2.4e-11  Score=93.61  Aligned_cols=73  Identities=22%  Similarity=0.377  Sum_probs=70.1

Q ss_pred             cchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHHHhhh
Q psy3828          60 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLL  132 (365)
Q Consensus        60 FPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL~~Lf  132 (365)
                      +|++||+|+||......+|+..|+++++.++|+|+.++.+.|++.|...+++.|+++||..||++++++++|.
T Consensus         1 LP~srVkrImK~~~~~~~is~ea~~~i~~a~E~Fi~~l~~~A~~~a~~~~rkti~~~dl~~av~~~~~~~FL~   73 (78)
T d1n1jb_           1 LPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLI   73 (78)
T ss_dssp             CCHHHHHHHHTTSTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTCGGGGGGT
T ss_pred             CCHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHhcCChhHHHH
Confidence            5999999999988888999999999999999999999999999999999999999999999999999998874

>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=98.31  E-value=2.8e-07  Score=68.35  Aligned_cols=65  Identities=32%  Similarity=0.468  Sum_probs=61.2

Q ss_pred             ccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcC
Q psy3828          59 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN  124 (365)
Q Consensus        59 qFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~n  124 (365)
                      ++|.++|.|+|+.+. ..||+..|...+.-++|.|+.++.+.|...|...+++.|+++||..|+.+
T Consensus         2 ~LP~a~I~rI~k~~~-~~ris~ea~~~l~~a~e~Fi~~l~~~a~~~a~~~~RKTI~~~Dv~~Al~s   66 (66)
T d1ku5a_           2 ELPIAPVDRLIRKAG-AERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIKS   66 (66)
T ss_dssp             CSCHHHHHHHHHHTT-CSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHhCc-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhC
Confidence            689999999999974 46999999999999999999999999999999999999999999999875

>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=98.29  E-value=3.3e-07  Score=68.13  Aligned_cols=64  Identities=28%  Similarity=0.431  Sum_probs=60.0

Q ss_pred             ccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          59 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        59 qFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      .+|.++|.|+++.+ ...||+..|...++-++|+++.+|.+.|...+...+++.|+|+||..|++
T Consensus         3 eLP~a~I~ri~k~~-~~~ris~ea~~~l~~~~e~fi~~l~~~a~~~a~~~kRkTi~~~DV~~Alk   66 (68)
T d1htaa_           3 ELPIAPIGRIIKNA-GAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARK   66 (68)
T ss_dssp             CSCHHHHHHHHHHT-TCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHH
T ss_pred             cCcHHHHHHHHHHC-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHH
Confidence            37999999999996 45799999999999999999999999999999999999999999999975

>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=98.20  E-value=4.3e-07  Score=70.82  Aligned_cols=73  Identities=10%  Similarity=0.179  Sum_probs=66.2

Q ss_pred             cccchhhhhhhhhcC-CcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHHHh
Q psy3828          58 LQFPVGRIHRLLRKG-NYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNK  130 (365)
Q Consensus        58 LqFPVsRI~RlLke~-~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL~~  130 (365)
                      |-+|.++|.|+|++. ....+|+..|+..++.+.|.++.++.+.|.+.|...+++.|+|+||..|+.+.+-++.
T Consensus         1 l~LP~a~v~ri~K~~~p~~~~is~ea~~~i~~a~e~Fi~~lt~~A~~~a~~~~rKTI~~~dv~~Al~~~~~~~f   74 (87)
T d1n1ja_           1 IYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSY   74 (87)
T ss_dssp             CCCCHHHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTTCGGG
T ss_pred             CCCcHhHHHHHHHHhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHcCcHhH
Confidence            568999999999974 4678999999999999999999999999999999999999999999999998764443

>d1htaa_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanothermus fervidus, histone A [TaxId: 2180]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon Methanothermus fervidus, histone A [TaxId: 2180]

Probab=97.78  E-value=2.6e-05  Score=57.51  Aligned_cols=61  Identities=26%  Similarity=0.350  Sum_probs=56.2

Q ss_pred             hhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         279 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       279 ~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      ..|.|+.|...+ ..||.+|...+......+++.|+.+|...+.+.+|+||+.+||..|++.
T Consensus         7 a~I~ri~k~~~~-~ris~ea~~~l~~~~e~fi~~l~~~a~~~a~~~kRkTi~~~DV~~Alk~   67 (68)
T d1htaa_           7 APIGRIIKNAGA-ERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARKM   67 (68)
T ss_dssp             HHHHHHHHHTTC-SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHT
T ss_pred             HHHHHHHHHCCc-chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHh
Confidence            348889999855 5799999999999999999999999999999999999999999999985

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

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

Probab=97.77  E-value=6.7e-06  Score=68.91  Aligned_cols=70  Identities=17%  Similarity=0.221  Sum_probs=65.2

Q ss_pred             ccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCcH
Q psy3828          57 GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDE  126 (365)
Q Consensus        57 gLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nDe  126 (365)
                      .|.||.++|.|+|+..-...+|+..|+..++-+.|.|+.+|...|...|...+++.|+|.||..|+.+-+
T Consensus         2 dl~LP~a~I~kI~K~~~~~~~is~dA~~~i~~a~~~Fi~~lt~~A~~~a~~~~RkTi~~~Dv~~Al~~~~   71 (135)
T d1jfib_           2 DLTIPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALESLG   71 (135)
T ss_dssp             CCCCCHHHHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHT
T ss_pred             cccccHHHHHHHHhhCCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHcC
Confidence            3789999999999997667899999999999999999999999999999999999999999999998643

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

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

Probab=97.57  E-value=2e-05  Score=59.43  Aligned_cols=64  Identities=11%  Similarity=0.123  Sum_probs=56.2

Q ss_pred             hhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHh-hcCCccccchhhhhhhcCcHHHHhhh
Q psy3828          69 LRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAAR-DNKKTRIIPRHLQLAIRNDEELNKLL  132 (365)
Q Consensus        69 Lke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~-~~kkkrItP~hI~lAI~nDeEL~~Lf  132 (365)
                      ||-+.....|++.|++.++-.+|.++.++.+.|.+.+. .++++.|++.||..||.+++.|++|-
T Consensus         1 Mk~d~dv~~is~ea~~lvskAtElFi~~L~~~a~~~a~~~~~~ktl~~~dl~~aV~~~~~f~FL~   65 (72)
T d2byka1           1 MKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEFLL   65 (72)
T ss_dssp             CCSSSSCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHHTCSTTGGGT
T ss_pred             CCCCHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCccccHHHHHHHHccCchhhHHH
Confidence            45566778999999999999999999999999988775 45567899999999999999999884

>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=97.53  E-value=6.4e-05  Score=55.20  Aligned_cols=60  Identities=17%  Similarity=0.335  Sum_probs=55.5

Q ss_pred             hhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         279 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       279 ~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      ..|.|+.|...| ..||.+|...|.-....+++.|+.+|...+.+.+|+||+..||..|++
T Consensus         6 a~I~rI~k~~~~-~ris~ea~~~l~~a~e~Fi~~l~~~a~~~a~~~~RKTI~~~Dv~~Al~   65 (66)
T d1ku5a_           6 APVDRLIRKAGA-ERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIK   65 (66)
T ss_dssp             HHHHHHHHHTTC-SEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHT
T ss_pred             HHHHHHHHhCcc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHh
Confidence            358899998865 589999999999999999999999999999999999999999999975

>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=97.33  E-value=8.1e-05  Score=57.82  Aligned_cols=65  Identities=17%  Similarity=0.182  Sum_probs=59.9

Q ss_pred             chhhhhhhhhcC-CcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCc
Q psy3828          61 PVGRIHRLLRKG-NYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND  125 (365)
Q Consensus        61 PVsRI~RlLke~-~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nD  125 (365)
                      |.++|.|+|++. ....+|+..|...++-+.|.++.++.+.|...|..++++.|+++||..|+.+-
T Consensus         1 P~a~i~ri~K~~~p~~~~iskeA~~~i~~aae~FI~~lt~~A~~~a~~~~rKtI~~~dv~~Al~~~   66 (89)
T d2bykb1           1 PNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTEL   66 (89)
T ss_dssp             CCSHHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHT
T ss_pred             CccHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHC
Confidence            789999999963 46689999999999999999999999999999999999999999999999753

>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=97.14  E-value=0.00046  Score=53.09  Aligned_cols=61  Identities=25%  Similarity=0.394  Sum_probs=56.6

Q ss_pred             hhhhhhhcCCC-CCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHh
Q psy3828         281 IYKVLKQVHPD-TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  341 (365)
Q Consensus       281 IykVLKQVhpd-~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrll  341 (365)
                      |.|+.|+.-|+ ..||++|...|......+...|+.||...+..++|+||+..||..|+.-+
T Consensus         8 v~ri~K~~~p~~~~is~ea~~~i~~a~e~Fi~~lt~~A~~~a~~~~rKTI~~~dv~~Al~~~   69 (87)
T d1n1ja_           8 VARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTL   69 (87)
T ss_dssp             HHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHT
T ss_pred             HHHHHHHhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHc
Confidence            78999998776 66999999999999999999999999999999999999999999999865

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

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

Probab=96.91  E-value=0.0005  Score=50.38  Aligned_cols=58  Identities=12%  Similarity=0.231  Sum_probs=49.5

Q ss_pred             hhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHH
Q psy3828         281 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAV  338 (365)
Q Consensus       281 IykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAv  338 (365)
                      |.|++|.......||+.|...|.-....+...|+.+|...++.++|+||+.+||..||
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            7889998744467999999999999999999999999999999999999999998875

>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=96.85  E-value=0.0011  Score=51.13  Aligned_cols=61  Identities=25%  Similarity=0.341  Sum_probs=55.7

Q ss_pred             hhhhhhhcCCC-CCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHh
Q psy3828         281 IYKVLKQVHPD-TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  341 (365)
Q Consensus       281 IykVLKQVhpd-~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrll  341 (365)
                      |.|+.|+.-|+ ..||++|...|.....-+...|+.+|...+..++|+||+..||..|+.-+
T Consensus         5 i~ri~K~~~p~~~~iskeA~~~i~~aae~FI~~lt~~A~~~a~~~~rKtI~~~dv~~Al~~~   66 (89)
T d2bykb1           5 IGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTEL   66 (89)
T ss_dssp             HHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHT
T ss_pred             HHHHHHHhCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHC
Confidence            78899988665 77999999999999999999999999999999999999999999999854

>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=96.79  E-value=0.0014  Score=54.38  Aligned_cols=61  Identities=20%  Similarity=0.389  Sum_probs=57.8

Q ss_pred             hhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHh
Q psy3828         281 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  341 (365)
Q Consensus       281 IykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrll  341 (365)
                      |.|+.|..-|+..||..|...|.-...-+...|+.+|...+...+|+||+..||..|+.-+
T Consensus        10 I~kI~K~~~~~~~is~dA~~~i~~a~~~Fi~~lt~~A~~~a~~~~RkTi~~~Dv~~Al~~~   70 (135)
T d1jfib_          10 INKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALESL   70 (135)
T ss_dssp             HHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             HHHHHhhCCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHc
Confidence            7899999999999999999999999999999999999999999999999999999999864

>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=96.59  E-value=0.00082  Score=51.61  Aligned_cols=58  Identities=14%  Similarity=0.206  Sum_probs=50.9

Q ss_pred             hhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         281 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       281 IykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      |.|+.+.. --..||..+...+...+.+.++.|+.||..++.+.+|+|||..||..|.+
T Consensus        15 i~Riar~~-Gv~ris~d~~~~l~~~l~~~l~~i~~~a~~~~~hakRKTvt~~DV~~Alk   72 (82)
T d2huec1          15 IRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALK   72 (82)
T ss_dssp             HHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTT
T ss_pred             HHHHHHHc-CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHH
Confidence            55666654 22458999999999999999999999999999999999999999999886

>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=96.43  E-value=0.003  Score=47.21  Aligned_cols=59  Identities=20%  Similarity=0.238  Sum_probs=53.0

Q ss_pred             hhhhhhhcCCC-CCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         281 IYKVLKQVHPD-TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       281 IykVLKQVhpd-~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      |.|++|. .|| ..||++|.-+|.--..-+.+.++.+|...++.++|+||+.+||..||+-
T Consensus         6 VkrImK~-~~~~~~is~ea~~~i~~a~E~Fi~~l~~~A~~~a~~~~rkti~~~dl~~av~~   65 (78)
T d1n1jb_           6 IKKIMKL-DEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITK   65 (78)
T ss_dssp             HHHHHTT-STTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTT
T ss_pred             HHHHHhc-CCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHhc
Confidence            6788886 566 5689999999999999999999999999999999999999999999874

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

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H4
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=95.98  E-value=0.0061  Score=46.54  Aligned_cols=65  Identities=17%  Similarity=0.211  Sum_probs=57.8

Q ss_pred             cchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhcCc
Q psy3828          60 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND  125 (365)
Q Consensus        60 FPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~nD  125 (365)
                      +|=.-|.|+++.+ =..||+.++..-|..++||++.||+.-|...+...+++.|++++|.+|++..
T Consensus        10 I~k~~i~Riar~~-Gv~ris~d~~~~l~~~l~~~l~~i~~~a~~~~~hakRKTvt~~DV~~Alkr~   74 (82)
T d2huec1          10 ITKPAIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ   74 (82)
T ss_dssp             SCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTT
T ss_pred             cCHHHHHHHHHHc-CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHhc
Confidence            3444688999886 4469999999999999999999999999999999999999999999999854

>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=95.77  E-value=0.012  Score=44.55  Aligned_cols=59  Identities=17%  Similarity=0.406  Sum_probs=53.7

Q ss_pred             hhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         281 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       281 IykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      +-..++||-|+..+...+-.++-.+..|+.+.+..-|.+||++.+-.||..+|||.-..
T Consensus         9 L~eLv~~idp~~~ld~~vee~ll~iADdFV~~V~~~ac~lAKhR~s~~le~kDvql~Le   67 (74)
T d1h3ob_           9 LQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLE   67 (74)
T ss_dssp             HHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHH
T ss_pred             HHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCcHHHHHHHHH
Confidence            66789999999999999999988888888999999999999999999999999997543

>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=95.30  E-value=0.015  Score=45.74  Aligned_cols=69  Identities=20%  Similarity=0.249  Sum_probs=61.3

Q ss_pred             CccchhhhhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHHh
Q psy3828         273 RKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  341 (365)
Q Consensus       273 r~esy~~YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrll  341 (365)
                      ++-.|...|..+.....+|..+++.|+..|-..+.+..-.+=++|...+.+.||.||+++|||-|.|+-
T Consensus        23 pk~pF~RLVRei~~~~~~~~r~~~~Al~aLQea~E~yLv~lfeda~~~a~HakRvTl~~kD~~Larrir   91 (95)
T d1tzyc_          23 RKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR   91 (95)
T ss_dssp             CHHHHHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             ccccHHHHHHHHHHhcCCCCEeeHHHHHHHHHHHHHHHHHHHHHhHHHHHhcCCCcCCHHHHHHHHHHh
Confidence            466899999999999999999999999999887777777777789999999999999999999999863

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

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

Probab=94.12  E-value=0.039  Score=44.11  Aligned_cols=59  Identities=24%  Similarity=0.295  Sum_probs=51.7

Q ss_pred             hhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         281 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       281 IykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      |.|.||+-+....|++.|---|-..+.++...|-+-|.+-++.+++.-||+|+||-|+|
T Consensus        17 i~r~Lk~~~~~~rv~~~apVylaAVLEYL~aEILELAgn~a~~~k~~rItprhi~lair   75 (106)
T d1u35c1          17 MLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILLAVA   75 (106)
T ss_dssp             HHHHHHHHSTTSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             HHHHHhCCCCccccCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCeeecchhhhccc
Confidence            88999987777789999988777777777777888888888999999999999999997

>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=93.85  E-value=0.026  Score=44.13  Aligned_cols=60  Identities=18%  Similarity=0.244  Sum_probs=56.0

Q ss_pred             hhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          64 RIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        64 RI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      .|+|.|++-.....|++.|.--+-..+..+...|...|...|+-+++..|+.++||.|++
T Consensus         8 Yi~kVLKqVhp~~giS~kam~imnsfvndiferIa~EA~~La~~~kr~TitsreIqtAvr   67 (92)
T d1tzyb_           8 YVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVR   67 (92)
T ss_dssp             HHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             HHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHH
Confidence            588999997777899999999999999999999999999999999999999999999987

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

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

Probab=93.75  E-value=0.055  Score=43.22  Aligned_cols=60  Identities=20%  Similarity=0.263  Sum_probs=46.7

Q ss_pred             hhhhhhhhcCCCCCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         280 YIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       280 YIykVLKQVhpd~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      .|+|.||+-+-...|++.|---|-..+..+-..|-+-|.+-++-++++-||+|+||-|||
T Consensus        17 rv~r~Lk~~~~~~rv~~~apVylaAVLEYLtaEiLELAgn~a~~~k~~rItPrhi~lAir   76 (106)
T d1tzya_          17 RVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIR   76 (106)
T ss_dssp             HHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             HHHHHHHcCccccccCCCchHHHHHHHHHHHHHHHHHhhHHHHhcCCceecchhhhhccc
Confidence            489999996656688888876555555555555555566677889999999999999997

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

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

Probab=92.77  E-value=0.11  Score=41.00  Aligned_cols=59  Identities=20%  Similarity=0.202  Sum_probs=48.1

Q ss_pred             hhhhhhhcCCC-CCcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHH
Q psy3828         281 IYKVLKQVHPD-TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR  339 (365)
Q Consensus       281 IykVLKQVhpd-~gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvr  339 (365)
                      |.|.||..+.- .-|++.|---|...+.++...|-+-|.+-++.+++..||+|+||-|++
T Consensus        17 v~r~L~~~~~~~~rv~~~A~VyLaAvLEYL~aEILelagn~a~~~~~~rItpr~l~lai~   76 (103)
T d1f66c_          17 IHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR   76 (103)
T ss_dssp             HHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHH
T ss_pred             HHHHHhccCccceecCCCceeeHHHHHHHHHHHHHHHhhhhhccCCCCeeechhhhcccc
Confidence            77888877544 348888877777777777777777777788999999999999999998

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

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

Probab=92.72  E-value=0.048  Score=42.36  Aligned_cols=63  Identities=22%  Similarity=0.370  Sum_probs=54.4

Q ss_pred             cchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcC-Cccccchhhhhhhc
Q psy3828          60 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNK-KTRIIPRHLQLAIR  123 (365)
Q Consensus        60 FPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~k-kkrItP~hI~lAI~  123 (365)
                      ||=..|+|+++.- ..+.|+....+.++++---++.||+|.|.......+ ...|.|.||..|.+
T Consensus        17 ~~K~~vkrl~~~~-~g~sv~~~v~i~v~giaKvFvGEiVE~A~~V~~~~~e~~PL~P~HireA~r   80 (89)
T d1bh9b_          17 FPKAAIKRLIQSI-TGTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVR   80 (89)
T ss_dssp             CCHHHHHHHHHHH-HSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH-cCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCcHHHHHHHH
Confidence            8888899999984 568899999999999999999999999998765443 45799999998875

>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=90.10  E-value=0.32  Score=36.03  Aligned_cols=48  Identities=19%  Similarity=0.356  Sum_probs=38.6

Q ss_pred             CcchhHHHHHHhHHHHHHHHHHHHHhhhhhcCCCcccChhHHHHHHHH
Q psy3828         293 GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       293 gISskam~ImnSfvnDiferIa~EAs~La~~nkr~TitsreIqtAvrl  340 (365)
                      .++.++-..+-.=|..=...|..||.+.++..||.+||..||..|.|+
T Consensus        23 ~l~de~a~~LA~DveYRl~eiiQeA~KFMrhskR~~Ltt~Did~ALkv   70 (70)
T d1tafb_          23 SLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLKV   70 (70)
T ss_dssp             CBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC-
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcCcHHHHHHHHcC
Confidence            355666666655566667788999999999999999999999999874

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

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

Probab=86.99  E-value=0.78  Score=33.38  Aligned_cols=53  Identities=11%  Similarity=0.176  Sum_probs=39.6

Q ss_pred             cCCCCC-cchhHHHHHHhHHHHHHHHHHHHHhhhh-hcCCCcccChhHHHHHHHH
Q psy3828         288 VHPDTG-VSSKAMSIMNSFVNDIFERIAAESSRLA-HYNKRSTITSREIQTAVRL  340 (365)
Q Consensus       288 Vhpd~g-ISskam~ImnSfvnDiferIa~EAs~La-~~nkr~TitsreIqtAvrl  340 (365)
                      -.||.+ ||++|.-++.--.--+.+.++.+|...+ ..++++||+..||-.||.-
T Consensus         3 ~d~dv~~is~ea~~lvskAtElFi~~L~~~a~~~a~~~~~~ktl~~~dl~~aV~~   57 (72)
T d2byka1           3 SSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNK   57 (72)
T ss_dssp             SSSSCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHHT
T ss_pred             CCHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCccccHHHHHHHHcc
Confidence            357766 5777776666555555678888997776 4667789999999999863

>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=82.07  E-value=1.2  Score=32.73  Aligned_cols=66  Identities=11%  Similarity=0.164  Sum_probs=55.1

Q ss_pred             ccccchhhhhhhhhcCCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          57 GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        57 gLqFPVsRI~RlLke~~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      +-+||..-|+-+-.. .-...++..+.-.||-=+||=+.||++-|.+..+..+++++|++||..|.+
T Consensus         4 ~S~~~~esik~iAeS-~Gi~~l~de~a~~LA~DveYRl~eiiQeA~KFMrhskR~~Ltt~Did~ALk   69 (70)
T d1tafb_           4 GSSISAESMKVIAES-IGVGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLK   69 (70)
T ss_dssp             SCCCCHHHHHHHHHH-TTCCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC
T ss_pred             cccCCHHHHHHHHHH-cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcCcHHHHHHHHc
Confidence            446777777765544 223468889999999999999999999999999999999999999998864

>d1k6ka_ a.174.1.1 (A:) N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone
species: Escherichia coli [TaxId: 562]

Probab=80.93  E-value=0.58  Score=36.42  Aligned_cols=39  Identities=23%  Similarity=0.273  Sum_probs=34.0

Q ss_pred             HHHHHHHHhHHHhhcCCccccchhhhhhhcCcHHHHhhh
Q psy3828          94 AAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLL  132 (365)
Q Consensus        94 taEILELAgn~A~~~kkkrItP~hI~lAI~nDeEL~~Lf  132 (365)
                      +.++|..|-+.|...+...|+|+||-+|+-+|++...++
T Consensus         6 l~~~l~~A~~~A~~~~h~~i~~EHLL~aLl~~~~~~~~l   44 (142)
T d1k6ka_           6 LELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREAL   44 (142)
T ss_dssp             HHHHHHHHHHHHHHHTBSEECHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCcccHHHHHHHHHhchhHHHHH
Confidence            356889999999999999999999999999998865554

>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=80.24  E-value=0.97  Score=34.93  Aligned_cols=68  Identities=25%  Similarity=0.255  Sum_probs=57.2

Q ss_pred             cccccchhhhhhhhhcC----CcccccCCChhHHHHHHHHHHHHHHHHHHhHHHhhcCCccccchhhhhhhc
Q psy3828          56 AGLQFPVGRIHRLLRKG----NYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  123 (365)
Q Consensus        56 AgLqFPVsRI~RlLke~----~ya~RVs~~ApVYLaAVLEYLtaEILELAgn~A~~~kkkrItP~hI~lAI~  123 (365)
                      .+|-+|-.-|.|++++-    ....|+..+|-..|=-+.|..+.+++|-|...|...++..|+|+|+++|.+
T Consensus        18 t~lLIpk~pF~RLVRei~~~~~~~~r~~~~Al~aLQea~E~yLv~lfeda~~~a~HakRvTl~~kD~~Larr   89 (95)
T d1tzyc_          18 TELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR   89 (95)
T ss_dssp             CSCCSCHHHHHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             cccccccccHHHHHHHHHHhcCCCCEeeHHHHHHHHHHHHHHHHHHHHHhHHHHHhcCCCcCCHHHHHHHHH
Confidence            46777888888887762    234689999999999999999999999999999999999999999998753