Psyllid ID: psy17765

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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-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-----
Protein Sequence
MAAGKSSGKAVKKAGKAQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTHQVGLASLLQGHHGRALEAQRVDDVHGGDGLSLGVLGVGDGVADHVLEEHLENATGLLVDESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAAGKSSGKAVKKAGKAQKNITKSDKKKKPRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDLCPSVCLYSYTLYERTCVTLWACTHLFFSV
Secondary Structure (PSIPRED)
ccccccccHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHccccHHHHHHHcccEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHccHHcccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHEEEEEHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHccccHHHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHccccEEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEcHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHcccccHHHHHHHHHHcccccEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEcHHHHHHHHHHcHHHHHHcccEEEccccccccccHHHccccccccccccccccccccccHcccccccccccccEEEEEccccccHHHHHHHHHHHHHccEEccccccccccccccccccccccHHHHHHHHccccccccccccccccccHHHHHHccccccccHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHccccEEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEcHHHcHHEEEEHHHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
maagkssgKAVKKAGKAQKNIaksdkkkkhrrkESYAIYIYKVLKQvhpdtgvsSKAMSIMNSFVNDIFERIAAESSRLahynkrstiTSREIQTAVRLLLPGELAKHAVSEGTKAVTKYtsskgkggkaktksktrssraglqfpvgrIHRLLRkgnyaervgagAPVYLAAVMEYLAAEVLELAGnaardnkktriiPRHLQLAIRNDEELNKLLSgvtiaqggvlpnIQAVRVLEQTHQVGLASLLqghhgraleaqrvddvhggdglslgvlgvgdgVADHVLEEHLENATgllvdesgntldststrqttdgglgdsldvvteyfpvplgasfseslsslTTADLLSITMAAGKSSGKAVKKAGKaqknitksdkkkkprrkeSYAIYIYKVLKQvhpdtgvsSKAMSIMNSFVNDIFERIAAESSRLahynkrstitkdlcpsvclysytlyerTCVTLWActhlffsv
Flexible Loop (DISEMBL)
maagkssgkavkkagkaqkniaksdkkkkhrrkeSYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLahynkrstitsreIQTAVRLLLPGELAkhavsegtkavtkytsskgkggkaktksktrssraglqfpvgrihrllrkgnyaerVGAGAPVYLAAVMEYLAAEVLELAGnaardnkktriiPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTHQVGLASLLQGHHGRALEAQRVDDVHGGDGLSLGVLGVGDGVADHVLEEHLENATGLLVDESGNTLDSTstrqttdgglgdSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAagkssgkavkkagkaqknitksdkkkkprrkeSYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAhynkrstitkdlcpSVCLYSYTLYERTCVTLWACTHLFFSV
Low Complexity Region (SEG)
MaagkssgkavkkagkaQKNIAksdkkkkhrrkESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVtkytsskgkggkaktksktrssragLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTHQVGLASLLQGHHGRALEAQRvddvhggdglslgvlgvgdgvadhvlEEHLENATGLLVDESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFseslsslttadllsitMaagkssgkavkkagkaQKNITksdkkkkprrkESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDLCPSVCLYSYTLYERTCVTLWACTHLFFSV
Disordered region (IsUnstruct)
***********************************YAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAK***********************************LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTHQVGLASLLQGHHGRALEAQRVDDVHGGDGLSLGVLGVGDGVADHVLEEHLENATGLLV*********************DSLDVVTEYFPVPLGASFS*****LTTADLLS*************************************YAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDLCPSVCLYSYTLYERTCVTLWACTHLFF**
Disordered Region (DISOPRED)
*************************************IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGEL***************************************FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQ**********************************************************LENATGLLVDESGNTLDSTSTRQTTDGGLGDSLDVVTEYF************************************************************AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDLCPSVCLYSYTLYERTCVTLWACTHLFFSV
Disordered Region (DISEMBL)
********************************KESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHA*******************************AGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTHQVGLASLLQGHHGRALEAQRVDDVHGGDGLSLGVLGVGDGVADHVLEEHLENATGLLVDESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAA*****************************KESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDLCPSVCLYSYTLYERTCVTLWACTHLFFSV
Disordered Region (DISPRO)
*********************************ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEG****************************GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQ*****************************DGLSLGVLGVGDGVADHVLEEHLENATGLLVDESGNTL**********GGLGDSLDVVTEYFPVPLGASF***L*SLTTADLLSITMA*******************************ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDLCPSVCLYSYTLYERTCVTLWACTHLFFSV
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAAGKSSGKAVKKAGKAQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTHQVGLASLLQGHHGRALEAQRVDDVHGGDGLSLGVLGVGDGVADHVLEEHLENATGLLVDESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAAGKSSGKAVKKAGKAQKNITKSDKKKKPRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDLCPSVCLYSYTLYERTCVTLWACTHLFFSV
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	475	2.2.26 [Sep-21-2011]
P02269	125	Histone H2A OS=Asterias r	N/A	N/A	0.250	0.952	0.873	3e-55
Q7ZUY3	142	Histone H2A.x OS=Danio re	no	N/A	0.254	0.852	0.852	4e-54
P02264	128	Histone H2A OS=Oncorhynch	N/A	N/A	0.254	0.945	0.844	5e-54
Q96QV6	131	Histone H2A type 1-A OS=H	yes	N/A	0.250	0.908	0.858	1e-53
P16886	126	Late histone H2A.L3 OS=St	yes	N/A	0.250	0.944	0.841	2e-53
Q8IUE6	130	Histone H2A type 2-B OS=H	yes	N/A	0.250	0.915	0.85	3e-53
P06897	130	Histone H2A type 1 OS=Xen	N/A	N/A	0.252	0.923	0.834	3e-53
Q64522	130	Histone H2A type 2-B OS=M	yes	N/A	0.250	0.915	0.841	4e-53
P16104	143	Histone H2A.x OS=Homo sap	no	N/A	0.250	0.832	0.85	5e-53
P69141	124	Histone H2A, embryonic OS	no	N/A	0.250	0.959	0.823	5e-53

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

 Score =  216 bits (550), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 104/119 (87%), Positives = 113/119 (94%)

Query: 122 SSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE 181
           S +GKGGKA+ K+K+RSSRAGLQFPVGR+HR LRKGNYAERVGAGAPVYLAAVMEYLAAE
Sbjct: 2   SGRGKGGKARAKAKSRSSRAGLQFPVGRVHRFLRKGNYAERVGAGAPVYLAAVMEYLAAE 61

Query: 182 VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240
           +LELAGNAARDNKKTRI PRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV + ++T
Sbjct: 62  ILELAGNAARDNKKTRINPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKT 120

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

 Score =  212 bits (540), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 104/122 (85%), Positives = 114/122 (93%), Gaps = 1/122 (0%)

Query: 122 SSKGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 180
           S +GK GGKA+ K+KTRSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL A
Sbjct: 2   SGRGKTGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA 61

Query: 181 EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240
           E+LELAGNAARDNKKTRIIPRHLQLA+RNDEELNKLL GVTIAQGGVLPNIQAV + ++T
Sbjct: 62  EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKT 121

Query: 241 HQ 242
            Q
Sbjct: 122 GQ 123

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

 Score =  212 bits (539), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 103/122 (84%), Positives = 114/122 (93%), Gaps = 1/122 (0%)

Query: 122 SSKGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 180
           S +GK GGKA+ K+KTRSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL A
Sbjct: 2   SGRGKTGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA 61

Query: 181 EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240
           E+LELAGNAARDNKKTRIIPRHLQLA+RNDEELNKLL GVTIAQGGVLPNIQAV + ++T
Sbjct: 62  EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKT 121

Query: 241 HQ 242
            +
Sbjct: 122 EK 123

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 =  211 bits (536), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 103/120 (85%), Positives = 113/120 (94%), Gaps = 1/120 (0%)

Query: 122 SSKGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 180
           S +GK GGKA+ KSK+RSSRAGLQFPVGRIHRLLRKGNYAER+GAGAPVYLAAV+EYL A
Sbjct: 2   SGRGKQGGKARAKSKSRSSRAGLQFPVGRIHRLLRKGNYAERIGAGAPVYLAAVLEYLTA 61

Query: 181 EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240
           E+LELAGNA+RDNKKTRIIPRHLQLAIRNDEELNKLL GVTIAQGGVLPNIQAV + ++T
Sbjct: 62  EILELAGNASRDNKKTRIIPRHLQLAIRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKT 121

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

 Score =  210 bits (535), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 101/120 (84%), Positives = 114/120 (95%), Gaps = 1/120 (0%)

Query: 122 SSKGKG-GKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 180
           S +GKG GKA+ K+K+RS+RAGLQFPVGR+HR LRKGNYA+RVGAGAPVYLAAV+EYLAA
Sbjct: 2   SGRGKGAGKARAKAKSRSARAGLQFPVGRVHRFLRKGNYAQRVGAGAPVYLAAVLEYLAA 61

Query: 181 EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240
           E+LELAGNAARDNKKTRIIPRHLQLA+RNDEELNKLLSGVTIAQGGVLPNIQAV + ++T
Sbjct: 62  EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKT 121

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

 Score =  209 bits (533), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 102/120 (85%), Positives = 113/120 (94%), Gaps = 1/120 (0%)

Query: 122 SSKGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 180
           S +GK GGKA+ K+K+RSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL A
Sbjct: 2   SGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA 61

Query: 181 EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240
           E+LELAGNAARDNKKTRIIPRHLQLA+RNDEELNKLL GVTIAQGGVLPNIQAV + ++T
Sbjct: 62  EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKT 121

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

 Score =  209 bits (532), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 101/121 (83%), Positives = 112/121 (92%), Gaps = 1/121 (0%)

Query: 122 SSKGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 180
           S +GK GGK + K+KTRSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL A
Sbjct: 2   SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA 61

Query: 181 EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240
           E+LELAGNAARDNKKTRIIPRHLQLA+RNDEELNKLL GVTIAQGGVLPNIQ+V + ++T
Sbjct: 62  EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQSVLLPKKT 121

Query: 241 H 241
            
Sbjct: 122 E 122

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|Q64522|H2A2B_MOUSE Histone H2A type 2-B OS=Mus musculus GN=Hist2h2ab PE=1 SV=3

 Score =  209 bits (531), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 101/120 (84%), Positives = 113/120 (94%), Gaps = 1/120 (0%)

Query: 122 SSKGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 180
           S +GK GGKA+ K+K+RSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVY+AAV+EYL A
Sbjct: 2   SGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLTA 61

Query: 181 EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240
           E+LELAGNAARDNKKTRIIPRHLQLA+RNDEELNKLL GVTIAQGGVLPNIQAV + ++T
Sbjct: 62  EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKT 121

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.

Mus musculus (taxid: 10090)

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

 Score =  209 bits (531), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 102/120 (85%), Positives = 113/120 (94%), Gaps = 1/120 (0%)

Query: 122 SSKGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 180
           S +GK GGKA+ K+K+RSSRAGLQFPVGR+HRLLRKG+YAERVGAGAPVYLAAV+EYL A
Sbjct: 2   SGRGKTGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGHYAERVGAGAPVYLAAVLEYLTA 61

Query: 181 EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240
           E+LELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLL GVTIAQGGVLPNIQAV + ++T
Sbjct: 62  EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKT 121

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|P69141|H2A_STRPU Histone H2A, embryonic OS=Strongylocentrotus purpuratus PE=1 SV=2

 Score =  209 bits (531), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 98/119 (82%), Positives = 111/119 (93%)

Query: 122 SSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE 181
           S +GK GKA+TK+KTRSSRAGLQFPVGR+HR LRKGNYA+RVG GAPVY+AAV+EYL AE
Sbjct: 2   SGRGKSGKARTKAKTRSSRAGLQFPVGRVHRFLRKGNYAKRVGGGAPVYMAAVLEYLTAE 61

Query: 182 VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240
           +LELAGNAARDNKK+RIIPRHLQLA+RNDEELNKLL GVTIAQGGVLPNIQAV + ++T
Sbjct: 62  ILELAGNAARDNKKSRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKT 120

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)

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	475
188595808	192	Chain A, Nmr Structure Of Chaperone Chz1	0.402	0.994	0.686	2e-66
397609826	324	hypothetical protein THAOC_19092 [Thalas	0.425	0.623	0.577	2e-63
328699742	126	PREDICTED: histone H2B.3-like [Acyrthosi	0.254	0.960	0.934	2e-56
193582492	126	PREDICTED: histone H2B.3-like [Acyrthosi	0.261	0.984	0.904	7e-56
225710358	125	Histone H2B [Caligus rogercresseyi]	0.252	0.96	0.942	9e-56
405975240	133	Histone H2A [Crassostrea gigas]	0.258	0.924	0.886	1e-55
162319741	123	histone H2A [Penaeus monodon]	0.254	0.983	0.892	2e-54
157137737	124	histone h2a [Aedes aegypti] gi|108880814	0.254	0.975	0.884	2e-54
225717540	124	Histone H2B [Caligus clemensi]	0.252	0.967	0.925	6e-54
256070862	125	histone H2A [Schistosoma mansoni] gi|360	0.256	0.976	0.860	6e-54

>gi|188595808|pdb|2JSS|A Chain A, Nmr Structure Of Chaperone Chz1 Complexed With Histone H2a.Z-H2b

 Score =  259 bits (661), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 138/201 (68%), Positives = 164/201 (81%), Gaps = 10/201 (4%)

Query: 32  RKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSR 91
           RKE+Y+ YIYKVLKQ HPDTG+S K+MSI+NSFVNDIFERIA E+S+LA YNK+STI++R
Sbjct: 1   RKETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAR 60

Query: 92  EIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSKGKGGKAKTKSKTRSSRAGLQFPVGRIH 151
           EIQTAVRL+LPGELAKHAVSEGT+AVTKY+SS        T++++ S+RAGLQFPVGRI 
Sbjct: 61  EIQTAVRLILPGELAKHAVSEGTRAVTKYSSS--------TQAQSSSARAGLQFPVGRIK 112

Query: 152 RLL-RKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND 210
           R L R      RVG+ A +YL AV+EYL AEVLELAGNAA+D K  RI PRHLQLAIR D
Sbjct: 113 RYLKRHATGRTRVGSKAAIYLTAVLEYLTAEVLELAGNAAKDLKVKRITPRHLQLAIRGD 172

Query: 211 EELNKLLSGVTIAQGGVLPNI 231
           +EL+ L+   TIA GGVLP+I
Sbjct: 173 DELDSLIRA-TIASGGVLPHI 192

Source: Saccharomyces cerevisiae

Species: Saccharomyces cerevisiae

Genus: Saccharomyces

Family: Saccharomycetaceae

Order: Saccharomycetales

Class: Saccharomycetes

Phylum: Ascomycota

Superkingdom: Eukaryota

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

 Score =  249 bits (636), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 134/232 (57%), Positives = 160/232 (68%), Gaps = 30/232 (12%)

Query: 134 SKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDN 193
           S T S++AGLQFPVGRI R LR+G YA R+GAGAPVYLAAV+EYL AE+LELAGNAARDN
Sbjct: 14  STTSSAKAGLQFPVGRIGRYLRQGKYATRMGAGAPVYLAAVLEYLCAEILELAGNAARDN 73

Query: 194 KKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTHQV---------- 243
           KK RIIPRH+ LA++NDEELNKLL GVTIA GGVLPNI AV + +++ +           
Sbjct: 74  KKARIIPRHITLAVKNDEELNKLLGGVTIASGGVLPNIHAVLLPKKSGKARAQRSQAPGD 133

Query: 244 -GLASLL-------------------QGHHGRALEAQRVDDVHGGDGLSLGVLGVGDGVA 283
            G    +                   +   G +L  Q VDDVHG D L+ GVLGVGDGV 
Sbjct: 134 DGKQKFIFDRWVDFRKSGFVLKRLSAEAVEGLSLSLQGVDDVHGRDSLTAGVLGVGDGVT 193

Query: 284 DHVLEEHLENATGLLVDESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLG 335
           D VLEE LE+A GLLVDE+G+TLD+ +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|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 =  226 bits (575), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 114/122 (93%), Positives = 120/122 (98%), Gaps = 1/122 (0%)

Query: 4   GKSSGKAVKKA-GKAQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMN 62
           GKS+GKA+KK+ GKAQKNIAKSDKK+K +RKESYAIYIYKVLKQVHPDTGVSSKAMSIMN
Sbjct: 5   GKSAGKAMKKSSGKAQKNIAKSDKKRKPKRKESYAIYIYKVLKQVHPDTGVSSKAMSIMN 64

Query: 63  SFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 122
           SFVND+FERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
Sbjct: 65  SFVNDLFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 124

Query: 123 SK 124
           SK
Sbjct: 125 SK 126

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

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 (571), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 114/126 (90%), Positives = 120/126 (95%), Gaps = 2/126 (1%)

Query: 1   MAAGKSS--GKAVKKAGKAQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAM 58
           MA G  S  GKA+KK+GKAQKNIAKSDKK+K +RKESYAIYIYKVLKQVHPDTGVSSKAM
Sbjct: 1   MAPGGKSAGGKAMKKSGKAQKNIAKSDKKRKPKRKESYAIYIYKVLKQVHPDTGVSSKAM 60

Query: 59  SIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT 118
           SIMNSFVND+FERIA+ESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
Sbjct: 61  SIMNSFVNDLFERIASESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT 120

Query: 119 KYTSSK 124
           KYTSSK
Sbjct: 121 KYTSSK 126

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  224 bits (570), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 115/122 (94%), Positives = 116/122 (95%), Gaps = 2/122 (1%)

Query: 5   KSSGKAVKKAGKAQKNIAKSD--KKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMN 62
           KS GKAVKKAGKAQKNI KSD  KKK H+RKESYAIYIYKVLKQVHPDTGVSSKAMSIMN
Sbjct: 4   KSVGKAVKKAGKAQKNITKSDGVKKKSHKRKESYAIYIYKVLKQVHPDTGVSSKAMSIMN 63

Query: 63  SFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 122
           S VNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
Sbjct: 64  SLVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 123

Query: 123 SK 124
           SK
Sbjct: 124 SK 125

Source: Caligus rogercresseyi

Species: Caligus rogercresseyi

Genus: Caligus

Family: Caligidae

Order: Siphonostomatoida

Class: Maxillopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|405975240|gb|EKC39821.1| Histone H2A [Crassostrea gigas]

 Score =  224 bits (570), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 109/123 (88%), Positives = 117/123 (95%)

Query: 122 SSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE 181
           S +GKGGK K+K+K+RSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAV+EYLAAE
Sbjct: 2   SGRGKGGKTKSKAKSRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLAAE 61

Query: 182 VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTH 241
           VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV + ++T 
Sbjct: 62  VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTG 121

Query: 242 QVG 244
            VG
Sbjct: 122 SVG 124

Source: Crassostrea gigas

Species: Crassostrea gigas

Genus: Crassostrea

Family: Ostreidae

Order: Ostreoida

Class: Bivalvia

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|162319741|gb|ABX84387.1| histone H2A [Penaeus monodon]

 Score =  219 bits (559), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 108/121 (89%), Positives = 114/121 (94%)

Query: 122 SSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE 181
           S +G GGK K KSK+RSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE
Sbjct: 2   SGRGNGGKVKGKSKSRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE 61

Query: 182 VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTH 241
           VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV + ++T 
Sbjct: 62  VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTE 121

Query: 242 Q 242
           +
Sbjct: 122 K 122

Source: Penaeus monodon

Species: Penaeus monodon

Genus: Penaeus

Family: Penaeidae

Order: Decapoda

Class: Malacostraca

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  219 bits (559), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 107/121 (88%), Positives = 114/121 (94%)

Query: 122 SSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE 181
           S +GKGGK + K+KTRSSRAGLQFPVGR HRLLRKGNYAERVGAGAPVYLAAVMEYLAAE
Sbjct: 2   SGRGKGGKVRAKAKTRSSRAGLQFPVGRTHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE 61

Query: 182 VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTH 241
           VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV + ++T 
Sbjct: 62  VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTE 121

Query: 242 Q 242
           +
Sbjct: 122 K 122

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|225717540|gb|ACO14616.1| Histone H2B [Caligus clemensi]

 Score =  218 bits (555), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 112/121 (92%), Positives = 113/121 (93%), Gaps = 1/121 (0%)

Query: 5   KSSGKAVKKAGKAQKNIAKSD-KKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNS 63
           KS GKA KKAGK QK I KSD KKK H+RKESYAIYIYKVLKQVHPDTGVSSKAMSIMNS
Sbjct: 4   KSVGKAAKKAGKTQKKITKSDGKKKSHKRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNS 63

Query: 64  FVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS 123
           FVNDIFERIAAESSR AHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS
Sbjct: 64  FVNDIFERIAAESSRPAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS 123

Query: 124 K 124
           K
Sbjct: 124 K 124

Source: Caligus clemensi

Species: Caligus clemensi

Genus: Caligus

Family: Caligidae

Order: Siphonostomatoida

Class: Maxillopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|256070862|ref|XP_002571761.1| histone H2A [Schistosoma mansoni] gi|360043244|emb|CCD78657.1| putative histone H2A [Schistosoma mansoni]

 Score =  218 bits (555), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 105/122 (86%), Positives = 116/122 (95%)

Query: 122 SSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE 181
           S +GKGGK ++K+KTRS+RAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYLAAE
Sbjct: 2   SGRGKGGKVRSKAKTRSARAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLAAE 61

Query: 182 VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTH 241
           VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLL GVTIAQGGVLPNIQAV + ++T 
Sbjct: 62  VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKTD 121

Query: 242 QV 243
           +V
Sbjct: 122 KV 123

Source: Schistosoma mansoni

Species: Schistosoma mansoni

Genus: Schistosoma

Family: Schistosomatidae

Order: Strigeidida

Class: Trematoda

Phylum: Platyhelminthes

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	475
FB|FBgn0051618	124	His2A:CG31618 "His2A:CG31618"	0.210	0.806	0.93	1.3e-43
FB|FBgn0053808	124	His2A:CG33808 "His2A:CG33808"	0.210	0.806	0.93	1.3e-43
FB|FBgn0053814	124	His2A:CG33814 "His2A:CG33814"	0.210	0.806	0.93	1.3e-43
FB|FBgn0053817	124	His2A:CG33817 "His2A:CG33817"	0.210	0.806	0.93	1.3e-43
FB|FBgn0053820	124	His2A:CG33820 "His2A:CG33820"	0.210	0.806	0.93	1.3e-43
FB|FBgn0053823	124	His2A:CG33823 "His2A:CG33823"	0.210	0.806	0.93	1.3e-43
FB|FBgn0053826	124	His2A:CG33826 "His2A:CG33826"	0.210	0.806	0.93	1.3e-43
FB|FBgn0053829	124	His2A:CG33829 "His2A:CG33829"	0.210	0.806	0.93	1.3e-43
FB|FBgn0053832	124	His2A:CG33832 "His2A:CG33832"	0.210	0.806	0.93	1.3e-43
FB|FBgn0053835	124	His2A:CG33835 "His2A:CG33835"	0.210	0.806	0.93	1.3e-43

FB|FBgn0051618 His2A:CG31618 "His2A:CG31618" [Drosophila melanogaster (taxid:7227)]

 Score = 460 (167.0 bits), Expect = 1.3e-43, P = 1.3e-43
 Identities = 93/100 (93%), Positives = 97/100 (97%)

Query:   143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
             LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH
Sbjct:    23 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 82

Query:   203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTHQ 242
             LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV + ++T +
Sbjct:    83 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTEK 122

GO:0000786 "nucleosome" evidence=ISS

GO:0006334 "nucleosome assembly" evidence=ISS

GO:0003677 "DNA binding" evidence=ISS

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

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005811 "lipid particle" evidence=IDA

GO:0051298 "centrosome duplication" evidence=IMP

FB|FBgn0053808 His2A:CG33808 "His2A:CG33808" [Drosophila melanogaster (taxid:7227)]

 Score = 460 (167.0 bits), Expect = 1.3e-43, P = 1.3e-43
 Identities = 93/100 (93%), Positives = 97/100 (97%)

Query:   143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
             LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH
Sbjct:    23 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 82

Query:   203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTHQ 242
             LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV + ++T +
Sbjct:    83 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTEK 122

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0046982 "protein heterodimerization activity" 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|FBgn0053814 His2A:CG33814 "His2A:CG33814" [Drosophila melanogaster (taxid:7227)]

 Score = 460 (167.0 bits), Expect = 1.3e-43, P = 1.3e-43
 Identities = 93/100 (93%), Positives = 97/100 (97%)

Query:   143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
             LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH
Sbjct:    23 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 82

Query:   203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTHQ 242
             LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV + ++T +
Sbjct:    83 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTEK 122

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|FBgn0053817 His2A:CG33817 "His2A:CG33817" [Drosophila melanogaster (taxid:7227)]

 Score = 460 (167.0 bits), Expect = 1.3e-43, P = 1.3e-43
 Identities = 93/100 (93%), Positives = 97/100 (97%)

Query:   143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
             LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH
Sbjct:    23 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 82

Query:   203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTHQ 242
             LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV + ++T +
Sbjct:    83 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTEK 122

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000786 "nucleosome" evidence=ISS

GO:0003677 "DNA binding" evidence=ISS

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

FB|FBgn0053820 His2A:CG33820 "His2A:CG33820" [Drosophila melanogaster (taxid:7227)]

 Score = 460 (167.0 bits), Expect = 1.3e-43, P = 1.3e-43
 Identities = 93/100 (93%), Positives = 97/100 (97%)

Query:   143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
             LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH
Sbjct:    23 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 82

Query:   203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTHQ 242
             LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV + ++T +
Sbjct:    83 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTEK 122

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|FBgn0053823 His2A:CG33823 "His2A:CG33823" [Drosophila melanogaster (taxid:7227)]

 Score = 460 (167.0 bits), Expect = 1.3e-43, P = 1.3e-43
 Identities = 93/100 (93%), Positives = 97/100 (97%)

Query:   143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
             LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH
Sbjct:    23 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 82

Query:   203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTHQ 242
             LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV + ++T +
Sbjct:    83 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTEK 122

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|FBgn0053826 His2A:CG33826 "His2A:CG33826" [Drosophila melanogaster (taxid:7227)]

 Score = 460 (167.0 bits), Expect = 1.3e-43, P = 1.3e-43
 Identities = 93/100 (93%), Positives = 97/100 (97%)

Query:   143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
             LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH
Sbjct:    23 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 82

Query:   203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTHQ 242
             LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV + ++T +
Sbjct:    83 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTEK 122

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:0000786 "nucleosome" evidence=ISS

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

FB|FBgn0053829 His2A:CG33829 "His2A:CG33829" [Drosophila melanogaster (taxid:7227)]

 Score = 460 (167.0 bits), Expect = 1.3e-43, P = 1.3e-43
 Identities = 93/100 (93%), Positives = 97/100 (97%)

Query:   143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
             LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH
Sbjct:    23 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 82

Query:   203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTHQ 242
             LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV + ++T +
Sbjct:    83 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTEK 122

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=ISS

GO:0000786 "nucleosome" evidence=ISS

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

FB|FBgn0053832 His2A:CG33832 "His2A:CG33832" [Drosophila melanogaster (taxid:7227)]

 Score = 460 (167.0 bits), Expect = 1.3e-43, P = 1.3e-43
 Identities = 93/100 (93%), Positives = 97/100 (97%)

Query:   143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
             LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH
Sbjct:    23 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 82

Query:   203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTHQ 242
             LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV + ++T +
Sbjct:    83 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTEK 122

GO:0005634 "nucleus" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0000786 "nucleosome" evidence=ISS

GO:0003677 "DNA binding" evidence=ISS

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

FB|FBgn0053835 His2A:CG33835 "His2A:CG33835" [Drosophila melanogaster (taxid:7227)]

 Score = 460 (167.0 bits), Expect = 1.3e-43, P = 1.3e-43
 Identities = 93/100 (93%), Positives = 97/100 (97%)

Query:   143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
             LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH
Sbjct:    23 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 82

Query:   203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTHQ 242
             LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV + ++T +
Sbjct:    83 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTEK 122

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

---

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	0.8583	0.2505	0.9296	yes	N/A
P35069	H2B3_TIGCA	No assigned EC number	0.9252	0.2252	0.8699	N/A	N/A
Q3ZBX9	H2AJ_BOVIN	No assigned EC number	0.8347	0.2526	0.9302	yes	N/A
Q64522	H2A2B_MOUSE	No assigned EC number	0.8416	0.2505	0.9153	yes	N/A
Q64523	H2A2C_MOUSE	No assigned EC number	0.8416	0.2505	0.9224	yes	N/A
P35068	H2B1_TIGCA	No assigned EC number	0.9252	0.2252	0.8699	N/A	N/A
A9UMV8	H2AJ_RAT	No assigned EC number	0.8347	0.2526	0.9302	yes	N/A
P16886	H2AL_STRPU	No assigned EC number	0.8416	0.2505	0.9444	yes	N/A
P35062	H2A3_CHICK	No assigned EC number	0.8416	0.2505	0.9224	yes	N/A
P70082	H2AJ_CHICK	No assigned EC number	0.8333	0.2505	0.9224	yes	N/A
Q8R1M2	H2AJ_MOUSE	No assigned EC number	0.8347	0.2526	0.9302	yes	N/A
A1A4R1	H2A2C_BOVIN	No assigned EC number	0.8416	0.2505	0.9224	yes	N/A
Q8IUE6	H2A2B_HUMAN	No assigned EC number	0.85	0.2505	0.9153	yes	N/A
Q96QV6	H2A1A_HUMAN	No assigned EC number	0.8583	0.2505	0.9083	yes	N/A
P19178	H2A_PLADU	No assigned EC number	0.9523	0.2210	0.8467	N/A	N/A
Q99878	H2A1J_HUMAN	No assigned EC number	0.8583	0.2505	0.9296	yes	N/A
Q6GSS7	H2A2A_MOUSE	No assigned EC number	0.8416	0.2505	0.9153	yes	N/A
P02263	H2A4_CHICK	No assigned EC number	0.85	0.2505	0.9224	yes	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	475
PTZ00017	134	PTZ00017, PTZ00017, histone H2A; Provisional	1e-64
cd00074	115	cd00074, H2A, Histone 2A; H2A is a subunit of the	3e-63
PLN00157	132	PLN00157, PLN00157, histone H2A; Provisional	5e-61
smart00414	106	smart00414, H2A, Histone 2A	1e-60
smart00427	97	smart00427, H2B, Histone H2B	5e-54
PLN00156	139	PLN00156, PLN00156, histone H2AX; Provisional	9e-54
COG5262	132	COG5262, HTA1, Histone H2A [Chromatin structure an	8e-50
PLN00158	116	PLN00158, PLN00158, histone H2B; Provisional	5e-49
PLN00153	129	PLN00153, PLN00153, histone H2A; Provisional	2e-48
PTZ00463	117	PTZ00463, PTZ00463, histone H2B; Provisional	2e-39
PLN00154	136	PLN00154, PLN00154, histone H2A; Provisional	4e-37
smart00427	97	smart00427, H2B, Histone H2B	4e-30
PLN00158	116	PLN00158, PLN00158, histone H2B; Provisional	1e-26
PTZ00252	134	PTZ00252, PTZ00252, histone H2A; Provisional	1e-26
pfam00125	75	pfam00125, Histone, Core histone H2A/H2B/H3/H4	8e-23
pfam00125	75	pfam00125, Histone, Core histone H2A/H2B/H3/H4	5e-22
PTZ00463	117	PTZ00463, PTZ00463, histone H2B; Provisional	2e-20
PLN00155	58	PLN00155, PLN00155, histone H2A; Provisional	3e-17
pfam00125	75	pfam00125, Histone, Core histone H2A/H2B/H3/H4	7e-17
COG5247	113	COG5247, BUR6, Class 2 transcription repressor NC2	3e-05

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

 Score =  204 bits (521), Expect = 1e-64
 Identities = 87/117 (74%), Positives = 97/117 (82%), Gaps = 3/117 (2%)

Query: 121 TSSKGKGGKAKTKSK---TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEY 177
              KGK G  K   K   +RS++AGLQFPVGR+HR L+KG YA+RVGAGAPVYLAAV+EY
Sbjct: 1   KGGKGKTGGGKAGKKKPVSRSAKAGLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEY 60

Query: 178 LAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV 234
           L AEVLELAGNAA+DNKK RI PRH+QLAIRNDEELNKLL+GVTIA GGVLPNI  V
Sbjct: 61  LTAEVLELAGNAAKDNKKKRITPRHIQLAIRNDEELNKLLAGVTIASGGVLPNIHKV 117

Length = 134

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

 Score =  200 bits (510), Expect = 3e-63
 Identities = 90/109 (82%), Positives = 97/109 (88%)

Query: 127 GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELA 186
           GGK K+K ++RS+RAGLQFPVGRIHR L+KG YAERVGAGAPVYLAAV+EYL AEVLELA
Sbjct: 3   GGKKKSKKRSRSARAGLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELA 62

Query: 187 GNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVR 235
           GNAARDNKK RI PRHLQLA+RNDEELNKLL GVTIA GGVLPNI  V 
Sbjct: 63  GNAARDNKKKRITPRHLQLAVRNDEELNKLLKGVTIASGGVLPNIHKVL 111

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 =  195 bits (497), Expect = 5e-61
 Identities = 85/111 (76%), Positives = 97/111 (87%)

Query: 124 KGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVL 183
           K KGG    K+ +RS++AGLQFPVGRI R L+ G YA RVGAGAPVYLAAV+EYLAAEVL
Sbjct: 6   KRKGGGGGKKATSRSAKAGLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVL 65

Query: 184 ELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV 234
           ELAGNAARDNKK+RI+PRH+QLA+RNDEEL+KLL GVTIA GGVLPNI +V
Sbjct: 66  ELAGNAARDNKKSRIVPRHIQLAVRNDEELSKLLGGVTIAAGGVLPNIHSV 116

Length = 132

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

 Score =  192 bits (491), Expect = 1e-60
 Identities = 88/99 (88%), Positives = 92/99 (92%)

Query: 136 TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKK 195
           +RS+RAGLQFPVGRIHRLLRKG YA+RVGAGAPVYLAAV+EYL AEVLELAGNAARDNKK
Sbjct: 1   SRSARAGLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKK 60

Query: 196 TRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV 234
            RI PRHLQLAIRNDEELNKLL GVTIAQGGVLPNI  V
Sbjct: 61  RRITPRHLQLAIRNDEELNKLLKGVTIAQGGVLPNIHKV 99

Length = 106

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

 Score =  175 bits (446), Expect = 5e-54
 Identities = 81/97 (83%), Positives = 93/97 (95%)

Query: 26  KKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR 85
           KK+  +RKE+YAIYIYKVLKQVHPDTG+SS+AMSIMNSFVNDIFERIAAE+S+LA YNK+
Sbjct: 1   KKRVKKRKETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKK 60

Query: 86  STITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 122
           ST++SREIQTAVRL+LPGELAKHAVSEGTKAVTK +S
Sbjct: 61  STLSSREIQTAVRLILPGELAKHAVSEGTKAVTKASS 97

Length = 97

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

 Score =  176 bits (448), Expect = 9e-54
 Identities = 87/119 (73%), Positives = 97/119 (81%), Gaps = 3/119 (2%)

Query: 119 KYTSSKGKGGKAK---TKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVM 175
              S   KGG+ K   TKS +RSS+AGLQFPVGRI R L+ G YAERVGAGAPVYL+AV+
Sbjct: 1   GAGSGTTKGGRGKPKATKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVL 60

Query: 176 EYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV 234
           EYLAAEVLELAGNAARDNKK RI+PRH+QLA+RNDEEL+KLL  VTIA GGVLPNI   
Sbjct: 61  EYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGSVTIAAGGVLPNIHQT 119

Length = 139

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

 Score =  166 bits (421), Expect = 8e-50
 Identities = 89/113 (78%), Positives = 98/113 (86%), Gaps = 2/113 (1%)

Query: 123 SKGKGGKA--KTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 180
           S GKGGKA     S++RS++AGL FPVGR+ RLL+KGNY  R+GAGAPVYLAAV+EYLAA
Sbjct: 3   SGGKGGKAADARVSQSRSAKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAA 62

Query: 181 EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQA 233
           E+LELAGNAARDNKK RIIPRHLQLAIRNDEELNKLL  VTIAQGGVLPNI  
Sbjct: 63  EILELAGNAARDNKKKRIIPRHLQLAIRNDEELNKLLGDVTIAQGGVLPNINP 115

Length = 132

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

 Score =  163 bits (413), Expect = 5e-49
 Identities = 78/107 (72%), Positives = 92/107 (85%)

Query: 17  AQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAES 76
           A+K    + KK    + E+Y IYIYKVLKQVHPDTG+SSKAMSIMNSF+NDIFE+IA E+
Sbjct: 10  AKKAAKGAKKKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEA 69

Query: 77  SRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS 123
            +LA YNK+ T+TSREIQTAVRL+LPGELAKHAVSEGTKAVTK+TS+
Sbjct: 70  GKLARYNKKPTVTSREIQTAVRLILPGELAKHAVSEGTKAVTKFTSA 116

Length = 116

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

 Score =  162 bits (410), Expect = 2e-48
 Identities = 86/119 (72%), Positives = 101/119 (84%)

Query: 122 SSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE 181
           + +GKG  +  K+ +RS++AGLQFPVGRI R L+KG YAER+GAGAPVYLAAV+EYL AE
Sbjct: 2   AGRGKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAE 61

Query: 182 VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240
           VLELAGNAARDNKK RI+PRH+QLAIRNDEEL KLL  VTIA GGVLPNI AV + ++T
Sbjct: 62  VLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLLGEVTIASGGVLPNIHAVLLPKKT 120

Length = 129

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

 Score =  137 bits (347), Expect = 2e-39
 Identities = 75/113 (66%), Positives = 92/113 (81%), Gaps = 2/113 (1%)

Query: 12  KKAGKAQKNIAKSD--KKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIF 69
           KK  KA+K     D  KK+K  R +SY +YI+KVLKQVHPDTG+S K+M+IMNSF+ D F
Sbjct: 4   KKPAKAKKAATGPDGKKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTF 63

Query: 70  ERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 122
           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 =  132 bits (334), Expect = 4e-37
 Identities = 73/116 (62%), Positives = 86/116 (74%), Gaps = 2/116 (1%)

Query: 118 TKYTSSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVME 176
            K T++  K  K K K  +RSSRAGLQFPVGRIHR L++   A  RVGA A VY AA++E
Sbjct: 12  AKTTAAAAKKDKDKKKPTSRSSRAGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILE 71

Query: 177 YLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQ 232
           YL AEVLELAGNA++D K  RI PRHLQLAIR DEEL+ L+ G TIA GGV+P+I 
Sbjct: 72  YLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIKG-TIAGGGVIPHIH 126

Length = 136

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

 Score =  112 bits (282), Expect = 4e-30
 Identities = 51/64 (79%), Positives = 61/64 (95%)

Query: 380 KKKKPRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR 439
           KK+  +RKE+YAIYIYKVLKQVHPDTG+SS+AMSIMNSFVNDIFERIAAE+S+LA YNK+
Sbjct: 1   KKRVKKRKETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKK 60

Query: 440 STIT 443
           ST++
Sbjct: 61  STLS 64

Length = 97

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

 Score =  103 bits (258), Expect = 1e-26
 Identities = 47/73 (64%), Positives = 58/73 (79%)

Query: 371 AQKNITKSDKKKKPRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAES 430
           A+K    + KK    + E+Y IYIYKVLKQVHPDTG+SSKAMSIMNSF+NDIFE+IA E+
Sbjct: 10  AKKAAKGAKKKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEA 69

Query: 431 SRLAHYNKRSTIT 443
            +LA YNK+ T+T
Sbjct: 70  GKLARYNKKPTVT 82

Length = 116

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

 Score =  104 bits (260), Expect = 1e-26
 Identities = 53/105 (50%), Positives = 74/105 (70%), Gaps = 2/105 (1%)

Query: 129 KAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGN 188
           KA      RS++AGL FPVGR+  LLR+G YA R+GA   VY+AAV+EYL AE+LEL+  
Sbjct: 10  KASKSGSGRSAKAGLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVK 69

Query: 189 AARDN--KKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNI 231
           AA     K  R+ PR + LA+R+D++L  LL  VT+++GGV+P++
Sbjct: 70  AAAQQAKKPKRLTPRTVTLAVRHDDDLGSLLKNVTLSRGGVMPSL 114

Length = 134

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

 Score = 91.5 bits (228), Expect = 8e-23
 Identities = 33/75 (44%), Positives = 44/75 (58%), Gaps = 1/75 (1%)

Query: 137 RSSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKK 195
            S    L+ P  R+ R L++G YAE R+ + APV L   +E L  E+LE AG  AR  K+
Sbjct: 1   SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKR 60

Query: 196 TRIIPRHLQLAIRND 210
             I PR +QLA+R D
Sbjct: 61  KTITPRDIQLAVRLD 75

Length = 75

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

 Score = 89.2 bits (222), Expect = 5e-22
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 4/75 (5%)

Query: 30  HRRKESYAIYIYKVLKQVHPD----TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR 85
             R     +   +V++++         +SSKA   +   + D+ E I  ++  LA + KR
Sbjct: 1   SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKR 60

Query: 86  STITSREIQTAVRLL 100
            TIT R+IQ AVRL 
Sbjct: 61  KTITPRDIQLAVRLD 75

Length = 75

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

 Score = 86.4 bits (213), Expect = 2e-20
 Identities = 46/80 (57%), Positives = 60/80 (75%), Gaps = 2/80 (2%)

Query: 366 KKAGKAQKNITKSD--KKKKPRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIF 423
           KK  KA+K  T  D  KK+K  R +SY +YI+KVLKQVHPDTG+S K+M+IMNSF+ D F
Sbjct: 4   KKPAKAKKAATGPDGKKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTF 63

Query: 424 ERIAAESSRLAHYNKRSTIT 443
           E+IA E+SRL  Y +R T++
Sbjct: 64  EKIATEASRLCKYTRRDTLS 83

Length = 117

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

 Score = 75.1 bits (184), Expect = 3e-17
 Identities = 38/57 (66%), Positives = 48/57 (84%)

Query: 122 SSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYL 178
           + +GKG  +  K+ +RS++AGLQFPVGRI R L+KG YAER+GAGAPVYLAAV+EYL
Sbjct: 2   AGRGKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYL 58

Length = 58

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

 Score = 74.5 bits (184), Expect = 7e-17
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 5/72 (6%)

Query: 386 RKESYAIYIYKVLKQVHPD----TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRST 441
           R     +   +V++++         +SSKA   +   + D+ E I  ++  LA + KR T
Sbjct: 3   RLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKRKT 62

Query: 442 IT-KDLCPSVCL 452
           IT +D+  +V L
Sbjct: 63  ITPRDIQLAVRL 74

Length = 75

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

 Score = 42.6 bits (100), Expect = 3e-05
 Identities = 22/95 (23%), Positives = 41/95 (43%), Gaps = 7/95 (7%)

Query: 131 KTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAA 190
           + K KTR       FP+ R+ ++++      +VG   PV  +  +E    E++ L+   A
Sbjct: 17  QKKKKTR-------FPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEA 69

Query: 191 RDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQG 225
           R     R+    L+ A  +DE+ + L +       
Sbjct: 70  RKKSSKRMTSEFLKRATESDEKFDFLKNMEQFKNR 104

Length = 113

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	475
PLN00153	129	histone H2A; Provisional	100.0
PLN00156	139	histone H2AX; Provisional	100.0
PLN00157	132	histone H2A; Provisional	100.0
PTZ00017	134	histone H2A; Provisional	100.0
PTZ00252	134	histone H2A; Provisional	100.0
smart00414	106	H2A Histone 2A.	100.0
PLN00154	136	histone H2A; Provisional	100.0
cd00074	115	H2A Histone 2A; H2A is a subunit of the nucleosome	100.0
KOG1756|consensus	131		100.0
PLN00158	116	histone H2B; Provisional	100.0
PTZ00463	117	histone H2B; Provisional	100.0
COG5262	132	HTA1 Histone H2A [Chromatin structure and dynamics	100.0
smart00427	89	H2B Histone H2B.	100.0
PLN00158	116	histone H2B; Provisional	100.0
PTZ00463	117	histone H2B; Provisional	100.0
KOG1757|consensus	131		99.97
smart00427	89	H2B Histone H2B.	99.97
KOG1744|consensus	127		99.96
KOG1744|consensus	127		99.95
PLN00155	58	histone H2A; Provisional	99.73
PF00125	75	Histone: Core histone H2A/H2B/H3/H4 histone h2a si	99.26
PF00125	75	Histone: Core histone H2A/H2B/H3/H4 histone h2a si	98.95
COG5247	113	BUR6 Class 2 transcription repressor NC2, alpha su	98.74
KOG1659|consensus	224		98.25
PF00808	65	CBFD_NFYB_HMF: Histone-like transcription factor (	97.94
cd07981	72	TAF12 TATA Binding Protein (TBP) Associated Factor	97.44
PF00808	65	CBFD_NFYB_HMF: Histone-like transcription factor (	97.21
smart00803	65	TAF TATA box binding protein associated factor. TA	97.14
COG2036	91	HHT1 Histones H3 and H4 [Chromatin structure and d	96.95
COG2036	91	HHT1 Histones H3 and H4 [Chromatin structure and d	96.89
PLN00035	103	histone H4; Provisional	96.85
PLN00035	103	histone H4; Provisional	96.79
cd00076	85	H4 Histone H4, one of the four histones, along wit	96.44
cd00074	115	H2A Histone 2A; H2A is a subunit of the nucleosome	96.35
smart00803	65	TAF TATA box binding protein associated factor. TA	96.23
PF03847	68	TFIID_20kDa: Transcription initiation factor TFIID	96.06
cd07981	72	TAF12 TATA Binding Protein (TBP) Associated Factor	95.93
cd00076	85	H4 Histone H4, one of the four histones, along wit	95.9
PTZ00015	102	histone H4; Provisional	95.8
smart00417	74	H4 Histone H4.	95.69
PTZ00015	102	histone H4; Provisional	95.62
smart00428	105	H3 Histone H3.	95.46
KOG0871|consensus	156		94.58
cd07979	117	TAF9 TATA Binding Protein (TBP) Associated Factor	94.27
PLN00156	139	histone H2AX; Provisional	94.24
KOG0869|consensus	168		94.21
KOG1657|consensus	236		94.02
smart00417	74	H4 Histone H4.	93.47
cd07979	117	TAF9 TATA Binding Protein (TBP) Associated Factor	93.44
COG5208	286	HAP5 CCAAT-binding factor, subunit C [Transcriptio	93.32
cd08048	85	TAF11 TATA Binding Protein (TBP) Associated Factor	93.24
PTZ00017	134	histone H2A; Provisional	93.16
PLN00153	129	histone H2A; Provisional	93.09
PF02969	66	TAF: TATA box binding protein associated factor (T	92.53
PLN00154	136	histone H2A; Provisional	92.17
KOG1142|consensus	258		92.1
KOG1756|consensus	131		92.01
PF02969	66	TAF: TATA box binding protein associated factor (T	92.01
PLN00157	132	histone H2A; Provisional	91.92
PTZ00252	134	histone H2A; Provisional	91.43
smart00414	106	H2A Histone 2A.	91.39
smart00576	77	BTP Bromodomain transcription factors and PHD doma	90.48
COG5262	132	HTA1 Histone H2A [Chromatin structure and dynamics	90.46
KOG0869|consensus	168		90.25
PF03847	68	TFIID_20kDa: Transcription initiation factor TFIID	89.79
cd08050	343	TAF6 TATA Binding Protein (TBP) Associated Factor	88.86
KOG0870|consensus	172		88.47
smart00428	105	H3 Histone H3.	88.43
PF15630	76	CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C	88.09
PF04719	90	TAFII28: hTAFII28-like protein conserved region; I	87.95
KOG3219|consensus	195		86.92
cd08050	343	TAF6 TATA Binding Protein (TBP) Associated Factor	86.83
PLN00121	136	histone H3; Provisional	86.52
PTZ00018	136	histone H3; Provisional	86.25
smart00325	180	RhoGEF Guanine nucleotide exchange factor for Rho/	86.22
smart00576	77	BTP Bromodomain transcription factors and PHD doma	84.03
cd00160	181	RhoGEF Guanine nucleotide exchange factor for Rho/	82.86
PF15510	102	CENP-W: Centromere kinetochore component W	81.99
PF07524	77	Bromo_TP: Bromodomain associated; InterPro: IPR006	80.09

>PLN00153 histone H2A; Provisional

Probab=100.00  E-value=2.2e-42  Score=308.18  Aligned_cols=116  Identities=74%  Similarity=1.114  Sum_probs=110.2

Q ss_pred             CCCCCCCCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHH
Q psy17765        125 GKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQ  204 (475)
Q Consensus       125 g~~~k~~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~  204 (475)
                      |++++.+++..|||+||||||||+||||||++++|+.||+++||||||||||||++||||||||.|++++++||+|+||+
T Consensus         5 ~~~~~~~~k~~srS~ragL~FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~   84 (129)
T PLN00153          5 GKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQ   84 (129)
T ss_pred             CCCCccccCccCcccccCcccchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHH
Confidence            44444445778999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhccHHHHhhhcCceecCCcccCCcccccccccc
Q psy17765        205 LAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT  240 (475)
Q Consensus       205 lAI~nD~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~  240 (475)
                      +||+||+||++||+++||++|||+|+||++|+|+++
T Consensus        85 lAI~nDeEL~~Ll~~vTIa~GGV~P~i~~~l~~kk~  120 (129)
T PLN00153         85 LAIRNDEELGKLLGEVTIASGGVLPNIHAVLLPKKT  120 (129)
T ss_pred             hhccCcHHHHHHHCCCccCCCccCCCcchhhcCccc
Confidence            999999999999999999999999999999999987

>PLN00156 histone H2AX; Provisional

Probab=100.00  E-value=3.7e-42  Score=309.52  Aligned_cols=116  Identities=72%  Similarity=1.096  Sum_probs=112.0

Q ss_pred             CCCCCCCCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHH
Q psy17765        125 GKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQ  204 (475)
Q Consensus       125 g~~~k~~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~  204 (475)
                      |+|++++++..|||+||||||||+||||||++++|+.||+++||||||||||||++||||||||.|++++++||+|+||+
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            45666667889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhccHHHHhhhcCceecCCcccCCcccccccccc
Q psy17765        205 LAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT  240 (475)
Q Consensus       205 lAI~nD~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~  240 (475)
                      +||+||+||+.||+++||++|||+|+||++|+|+++
T Consensus        90 lAIrnDeEL~~Ll~~vTIa~GGV~P~i~~~l~~kk~  125 (139)
T PLN00156         90 LAVRNDEELSKLLGSVTIAAGGVLPNIHQTLLPKKV  125 (139)
T ss_pred             hhccCcHHHHHHHCCCccCCCccCCCccHhhccccc
Confidence            999999999999999999999999999999999998

>PLN00157 histone H2A; Provisional

Probab=100.00  E-value=6.2e-42  Score=306.26  Aligned_cols=113  Identities=73%  Similarity=1.118  Sum_probs=109.2

Q ss_pred             CCCCCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHH
Q psy17765        128 GKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAI  207 (475)
Q Consensus       128 ~k~~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI  207 (475)
                      ++.+++..|+|+||||||||+||||+|++++|++||+++|+||||||||||++||||||||.|++++++||+|+||++||
T Consensus        10 ~~~~~k~~srS~ragL~FPVgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI   89 (132)
T PLN00157         10 GGGGKKATSRSAKAGLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAV   89 (132)
T ss_pred             CccCcCCcCcccccCcccchHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcc
Confidence            34456789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccHHHHhhhcCceecCCcccCCcccccccccc
Q psy17765        208 RNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT  240 (475)
Q Consensus       208 ~nD~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~  240 (475)
                      +||+||++||+++||++|||+|+||++|+|+++
T Consensus        90 ~nDeEL~~Ll~~vtIa~GGV~P~i~~~ll~kk~  122 (132)
T PLN00157         90 RNDEELSKLLGGVTIAAGGVLPNIHSVLLPKKS  122 (132)
T ss_pred             cCcHHHHHHHcCceecCCccCCCcchhhcCCCC
Confidence            999999999999999999999999999999988

>PTZ00017 histone H2A; Provisional

Probab=100.00  E-value=2.9e-41  Score=302.89  Aligned_cols=110  Identities=75%  Similarity=1.151  Sum_probs=107.4

Q ss_pred             CCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhcc
Q psy17765        131 KTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND  210 (475)
Q Consensus       131 ~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD  210 (475)
                      +++..|||+||||||||+||||||++++|++||+++|||||+||||||++||||||||+|++++++||+|+||++||+||
T Consensus        14 ~~k~~srS~ragL~FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~nD   93 (134)
T PTZ00017         14 KKKPVSRSAKAGLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRND   93 (134)
T ss_pred             CcCcccccccCCcccchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccCc
Confidence            44678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhcCceecCCcccCCcccccccccc
Q psy17765        211 EELNKLLSGVTIAQGGVLPNIQAVRVLEQT  240 (475)
Q Consensus       211 ~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~  240 (475)
                      +||+.||+++||++|||+|+||++|+|+++
T Consensus        94 eEL~~Ll~~vtIa~GGV~P~i~~~l~~k~~  123 (134)
T PTZ00017         94 EELNKLLAGVTIASGGVLPNIHKVLLPKKS  123 (134)
T ss_pred             HHHHHHHcCCcccCCccCCCccHhhccCCC
Confidence            999999999999999999999999999988

>PTZ00252 histone H2A; Provisional

Probab=100.00  E-value=4.9e-41  Score=300.13  Aligned_cols=107  Identities=50%  Similarity=0.863  Sum_probs=102.4

Q ss_pred             CccC-cCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHh--cCCcccchhHHHHHHhc
Q psy17765        133 KSKT-RSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARD--NKKTRIIPRHLQLAIRN  209 (475)
Q Consensus       133 ~~~s-rSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~--~k~~rItP~hI~lAI~n  209 (475)
                      +..+ ||+|||||||||||||||++++|+.||+++||||||||||||++||||||||.|++  ++++||+|+||++||+|
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            3445 99999999999999999999999999999999999999999999999999999976  78899999999999999


Q ss_pred             cHHHHhhhcCceecCCcccCCccccccccc
Q psy17765        210 DEELNKLLSGVTIAQGGVLPNIQAVRVLEQ  239 (475)
Q Consensus       210 D~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~  239 (475)
                      |+||++||+++||++|||+|+||++|+|++
T Consensus        93 DeEL~~Ll~~vTIa~GGVlP~i~~~l~~k~  122 (134)
T PTZ00252         93 DDDLGSLLKNVTLSRGGVMPSLNKALAKKH  122 (134)
T ss_pred             hHHHHHHHcCCccCCCccCCCccHhhcccc
Confidence            999999999999999999999999999983

>smart00414 H2A Histone 2A

Probab=100.00  E-value=1.2e-40  Score=289.59  Aligned_cols=105  Identities=85%  Similarity=1.235  Sum_probs=103.3

Q ss_pred             CcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHHHh
Q psy17765        136 TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNK  215 (475)
Q Consensus       136 srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL~~  215 (475)
                      |||+|||||||||||||||++++|++||+++|+|||+||||||++||||||||+|++++++||+|+||++||+||+|||+
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            57999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCceecCCcccCCcccccccccc
Q psy17765        216 LLSGVTIAQGGVLPNIQAVRVLEQT  240 (475)
Q Consensus       216 Lf~~~tIa~gGV~p~i~~~ll~~~~  240 (475)
                      ||+++||++|||+|+||+.|+|+++
T Consensus        81 L~~~vti~~ggv~p~i~~~l~~~~~  105 (106)
T smart00414       81 LLKGVTIAQGGVLPNIHKVLLPKKT  105 (106)
T ss_pred             HHcCcccCCCccCCCcchhhcccCC
Confidence            9999999999999999999999986

>PLN00154 histone H2A; Provisional

Probab=100.00  E-value=4.6e-40  Score=294.83  Aligned_cols=109  Identities=62%  Similarity=0.893  Sum_probs=104.8

Q ss_pred             CCCccCcCCCCCcccchhHHHHHHhhcC-cccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhc
Q psy17765        131 KTKSKTRSSRAGLQFPVGRIHRLLRKGN-YAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN  209 (475)
Q Consensus       131 ~~~~~srSsRagL~FPVsRi~r~Lke~~-~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~n  209 (475)
                      +++..|||+||||||||+||||+||+++ |++||+++|||||+||||||++||||||||+|++++++||+|+||++||+|
T Consensus        25 ~~k~~srS~rAgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn  104 (136)
T PLN00154         25 KKKPTSRSSRAGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG  104 (136)
T ss_pred             CcCCcCcccccCccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence            4567899999999999999999999997 578999999999999999999999999999999999999999999999999


Q ss_pred             cHHHHhhhcCceecCCcccCCcccccccccc
Q psy17765        210 DEELNKLLSGVTIAQGGVLPNIQAVRVLEQT  240 (475)
Q Consensus       210 D~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~  240 (475)
                      |+||++||+ +||++|||+|+||++|+|+++
T Consensus       105 DeEL~~Ll~-~TIa~GGVlP~i~~~l~~k~~  134 (136)
T PLN00154        105 DEELDTLIK-GTIAGGGVIPHIHKSLINKST  134 (136)
T ss_pred             cHHHHHHhc-CCccCCccCCCcchhhccccc
Confidence            999999998 699999999999999999986

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

Probab=100.00  E-value=1.6e-39  Score=286.28  Aligned_cols=112  Identities=79%  Similarity=1.190  Sum_probs=108.1

Q ss_pred             CCCCCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHH
Q psy17765        128 GKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAI  207 (475)
Q Consensus       128 ~k~~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI  207 (475)
                      ||.+++.+|+|+||||+|||+||||||++++|++||+++|+|||+||||||++||||+|+|.|+++++++|+|+||++||
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            36667788999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccHHHHhhhcCceecCCcccCCccccccccc
Q psy17765        208 RNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQ  239 (475)
Q Consensus       208 ~nD~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~  239 (475)
                      +||+|||+||+++||++|||+|+||+.|+|++
T Consensus        84 ~nD~EL~~L~~~vtI~~ggv~p~i~~~l~~~~  115 (115)
T cd00074          84 RNDEELNKLLKGVTIASGGVLPNIHKVLLPKK  115 (115)
T ss_pred             hccHHHHHHHcCCcccCCccCCCcchhhcCCC
Confidence            99999999999999999999999999999874

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.

>KOG1756|consensus

Probab=100.00  E-value=4.9e-39  Score=283.69  Aligned_cols=109  Identities=83%  Similarity=1.191  Sum_probs=106.3

Q ss_pred             CCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccH
Q psy17765        132 TKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDE  211 (475)
Q Consensus       132 ~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~  211 (475)
                      +...|+|.|+|||||||||+|+|++++|.+||+.+|||||+||||||++||||+|||+|+++++.||+|+||++||+||+
T Consensus        15 ~~~~srs~~agl~fPvgri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~NDe   94 (131)
T KOG1756|consen   15 KAKSSRSSRAGLQFPVGRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIRNDE   94 (131)
T ss_pred             hhhcchhhhcccccCHHHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHhCcH
Confidence            45668899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhcCceecCCcccCCcccccccccc
Q psy17765        212 ELNKLLSGVTIAQGGVLPNIQAVRVLEQT  240 (475)
Q Consensus       212 EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~  240 (475)
                      ||+.|++++||++|||+|+||+.+||+++
T Consensus        95 EL~~lL~~vtIa~GGvlPnI~~~lLpKk~  123 (131)
T KOG1756|consen   95 ELNKLLGKVTIAQGGVLPNIQAILLPKKT  123 (131)
T ss_pred             HHHHHhccceeccCCcccccchhhccccc
Confidence            99999999999999999999999999987

>PLN00158 histone H2B; Provisional

Probab=100.00  E-value=2.1e-38  Score=276.89  Aligned_cols=112  Identities=73%  Similarity=1.037  Sum_probs=102.5

Q ss_pred             CCcchhhhhhccccccccccccccccCchhHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCC
Q psy17765          6 SSGKAVKKAGKAQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR   85 (475)
Q Consensus         6 ~k~~~~~k~gka~~~~~~~~kk~~~k~~~sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr   85 (475)
                      |.+++++|+++++      ++|++++++++|++||||||||||||++||++||.+||||++||||||+.||++|+++|++
T Consensus         5 ~~~k~~~~~~~~~------~kk~~~kr~esy~~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr   78 (116)
T PLN00158          5 PSKKPAKKAAKGA------KKKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKK   78 (116)
T ss_pred             cchhhhhhccccc------cccccccccccHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence            4566666665554      4566777899999999999999999999999999999999999999999999999999999


Q ss_pred             CCCChHHHHHHHHHhCcHHHHHHHHHHhhhhhhhcccc
Q psy17765         86 STITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS  123 (475)
Q Consensus        86 ~TlT~rdIqtAVrllLPgeLaKhAvseG~kAV~ky~sS  123 (475)
                      +|||+||||+|||++|||||+|||++||++||++|.++
T Consensus        79 ~TltsrEIqtAvrLvLpgELaKhAvsEGtkAv~k~~~~  116 (116)
T PLN00158         79 PTVTSREIQTAVRLILPGELAKHAVSEGTKAVTKFTSA  116 (116)
T ss_pred             CcCCHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhhcC
Confidence            99999999999999999999999999999999999764

>PTZ00463 histone H2B; Provisional

Probab=100.00  E-value=6.7e-38  Score=273.54  Aligned_cols=111  Identities=67%  Similarity=0.995  Sum_probs=99.8

Q ss_pred             hhhhcccccc--ccccccccccCchhHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCC
Q psy17765         12 KKAGKAQKNI--AKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT   89 (475)
Q Consensus        12 ~k~gka~~~~--~~~~kk~~~k~~~sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT   89 (475)
                      +|+|++++..  .+++++++++++++|+.||||||||||||++||++||.+||||++|||||||.||++|+++++++|||
T Consensus         4 ~~~~~~~~~~~~~~~~kk~~~kr~esy~~YI~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~Tlt   83 (117)
T PTZ00463          4 KKPAKAKKAATGPDGKKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLS   83 (117)
T ss_pred             ccccccccCCCCCCccccccccccchHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCC
Confidence            3455555432  33345667778999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHhCcHHHHHHHHHHhhhhhhhccc
Q psy17765         90 SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS  122 (475)
Q Consensus        90 ~rdIqtAVrllLPgeLaKhAvseG~kAV~ky~s  122 (475)
                      +||||+||||+|||||+|||++||++||++|.+
T Consensus        84 srEIQtAvrLlLpGELaKhAvsEGtkAv~k~~~  116 (117)
T PTZ00463         84 SREIQTAIRLVLPGELAKHAVSEGTKAVTKFTS  116 (117)
T ss_pred             HHHHHHHHhhcccHHHHHhhhhHHHHHHHHhhc
Confidence            999999999999999999999999999999964

>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]

Probab=100.00  E-value=7.5e-37  Score=266.28  Aligned_cols=118  Identities=75%  Similarity=1.114  Sum_probs=109.5

Q ss_pred             cCCCCCCC-C-CCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccch
Q psy17765        123 SKGKGGKA-K-TKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIP  200 (475)
Q Consensus       123 Skg~~~k~-~-~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP  200 (475)
                      +.|||||+ . +...|+|.++||+|||+||+|+|++++|..||++.|+||++||||||++||||+|||+|++++++||+|
T Consensus         3 ~~GKGgK~a~~r~~~s~sa~agl~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~P   82 (132)
T COG5262           3 SGGKGGKAADARVSQSRSAKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIP   82 (132)
T ss_pred             cCCcCcccccchhccchhhhcCccccHHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceech
Confidence            34666662 2 345689999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHhccHHHHhhhcCceecCCcccCCcccccccccc
Q psy17765        201 RHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT  240 (475)
Q Consensus       201 ~hI~lAI~nD~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~  240 (475)
                      +|||+|||||+||+.|++++||++|||+|+||+.+||+..
T Consensus        83 rHlqlAIrnD~EL~~l~~~~tIa~GGvlp~I~~~ll~k~s  122 (132)
T COG5262          83 RHLQLAIRNDEELNKLLGDVTIAQGGVLPNINPGLLPKSS  122 (132)
T ss_pred             HHHHHHhcCcHHHHHHhhhheeecCCcccccChhhhhhhh
Confidence            9999999999999999999999999999999999998754

>smart00427 H2B Histone H2B

Probab=100.00  E-value=6.2e-35  Score=245.59  Aligned_cols=89  Identities=89%  Similarity=1.240  Sum_probs=87.2

Q ss_pred             hhHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHHHHHHHh
Q psy17765         34 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEG  113 (475)
Q Consensus        34 ~sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaKhAvseG  113 (475)
                      ++|++||||||||||||++||++||.+||||++|+|||||.||++|+++++|+|||+||||+|||++|||||+|||++||
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             hhhhhhccc
Q psy17765        114 TKAVTKYTS  122 (475)
Q Consensus       114 ~kAV~ky~s  122 (475)
                      ++||++|.+
T Consensus        81 tkAv~k~~~   89 (89)
T smart00427       81 TKAVTKYSS   89 (89)
T ss_pred             HHHHHhhcC
Confidence            999999963

>PLN00158 histone H2B; Provisional

Probab=100.00  E-value=3.2e-35  Score=256.97  Aligned_cols=88  Identities=60%  Similarity=0.860  Sum_probs=77.3

Q ss_pred             cCccchhccccccccccccCCccCcCCCccceeehhhhhccccCCCCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCC
Q psy17765        360 SSGKAVKKAGKAQKNITKSDKKKKPRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR  439 (475)
Q Consensus       360 ~~~k~~~~~~~~~~~~~~~~~k~~~~~~esy~~Yi~kvLkqvhp~~giS~kam~imnsfv~Diferia~Eas~L~~~~kr  439 (475)
                      +++|+.+++++.+      ++|++++|+|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+|
T Consensus         5 ~~~k~~~~~~~~~------~kk~~~kr~esy~~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr   78 (116)
T PLN00158          5 PSKKPAKKAAKGA------KKKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKK   78 (116)
T ss_pred             cchhhhhhccccc------cccccccccccHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence            4566665554432      4556777899999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCc-hhheehc
Q psy17765        440 STITKDL-CPSVCLY  453 (475)
Q Consensus       440 ~Tltsr~-~~~~~~~  453 (475)
                      +|||+|| |+||+|+
T Consensus        79 ~TltsrEIqtAvrLv   93 (116)
T PLN00158         79 PTVTSREIQTAVRLI   93 (116)
T ss_pred             CcCCHHHHHHHHHHh
Confidence            9999987 7899984

>PTZ00463 histone H2B; Provisional

Probab=100.00  E-value=5.3e-35  Score=255.38  Aligned_cols=75  Identities=53%  Similarity=0.862  Sum_probs=70.6

Q ss_pred             CCccCcCCCccceeehhhhhccccCCCCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCCcCCCCCc-hhheehc
Q psy17765        379 DKKKKPRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDL-CPSVCLY  453 (475)
Q Consensus       379 ~~k~~~~~~esy~~Yi~kvLkqvhp~~giS~kam~imnsfv~Diferia~Eas~L~~~~kr~Tltsr~-~~~~~~~  453 (475)
                      ++|++++|+|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+|+|||+|| |+||+|+
T Consensus        19 ~kk~~~kr~esy~~YI~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl   94 (117)
T PTZ00463         19 KKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV   94 (117)
T ss_pred             cccccccccchHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence            45567778999999999999999999999999999999999999999999999999999999999986 9999984

>KOG1757|consensus

Probab=99.97  E-value=1.9e-32  Score=237.18  Aligned_cols=108  Identities=60%  Similarity=0.891  Sum_probs=101.8

Q ss_pred             CCccCcCCCCCcccchhHHHHHHhhcCc-ccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhcc
Q psy17765        132 TKSKTRSSRAGLQFPVGRIHRLLRKGNY-AERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND  210 (475)
Q Consensus       132 ~~~~srSsRagL~FPVsRi~r~Lke~~~-~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD  210 (475)
                      .+..|+|+|+||||||+||||.|+.... ..||++.++||.+|+||||++|+||||||.+++.+.+||||+|+|+||+.|
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 579999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhcCceecCCcccCCcccccccccc
Q psy17765        211 EELNKLLSGVTIAQGGVLPNIQAVRVLEQT  240 (475)
Q Consensus       211 ~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~  240 (475)
                      +||+.|++ .||++|||+||||..|+-+++
T Consensus        98 eELDtLIk-~TiagGgViPhihk~l~~k~~  126 (131)
T KOG1757|consen   98 EELDTLIK-ATIAGGGVIPHIHKSLINKKG  126 (131)
T ss_pred             HHHHHHHH-HhhccCccccchHHHHhcccc
Confidence            99999997 589999999999999987766

>smart00427 H2B Histone H2B

Probab=99.97  E-value=8.6e-32  Score=226.61  Aligned_cols=66  Identities=76%  Similarity=1.062  Sum_probs=63.8

Q ss_pred             ccceeehhhhhccccCCCCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCCcCCCCCc-hhheehc
Q psy17765        388 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDL-CPSVCLY  453 (475)
Q Consensus       388 esy~~Yi~kvLkqvhp~~giS~kam~imnsfv~Diferia~Eas~L~~~~kr~Tltsr~-~~~~~~~  453 (475)
                      |+|++||||||||||||+|||++||+||||||||||||||.||++|++||||+|||+|| |+||+|+
T Consensus         1 esy~~Yi~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~   67 (89)
T smart00427        1 ETYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI   67 (89)
T ss_pred             CcHHHHHHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence            78999999999999999999999999999999999999999999999999999999987 7899884

>KOG1744|consensus

Probab=99.96  E-value=1.5e-30  Score=230.87  Aligned_cols=99  Identities=85%  Similarity=1.178  Sum_probs=95.5

Q ss_pred             cccccccCchhHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHH
Q psy17765         25 DKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGE  104 (475)
Q Consensus        25 ~kk~~~k~~~sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPge  104 (475)
                      +|++..++.++|+.|++|||||||||++|+.+||.+||+|+||||++||.||++|+++++++|||++|||+||+|+|||+
T Consensus        28 gk~~~~~~~e~~s~yv~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLllPge  107 (127)
T KOG1744|consen   28 GKKRSTRRKESYSEYVYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLLLPGE  107 (127)
T ss_pred             cccCcccccCceeeehhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHhCchH
Confidence            36677888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhhhhhcccc
Q psy17765        105 LAKHAVSEGTKAVTKYTSS  123 (475)
Q Consensus       105 LaKhAvseG~kAV~ky~sS  123 (475)
                      |++||++||++||.+|.++
T Consensus       108 l~khA~seGtkav~ky~~s  126 (127)
T KOG1744|consen  108 LAKHAVSEGTKAVTKYTSS  126 (127)
T ss_pred             HhhhhhcccchhheeeccC
Confidence            9999999999999999876

>KOG1744|consensus

Probab=99.95  E-value=5.8e-29  Score=220.71  Aligned_cols=76  Identities=68%  Similarity=0.995  Sum_probs=70.9

Q ss_pred             cCCccCcCCCccceeehhhhhccccCCCCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCCcCCCCCc-hhheehc
Q psy17765        378 SDKKKKPRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDL-CPSVCLY  453 (475)
Q Consensus       378 ~~~k~~~~~~esy~~Yi~kvLkqvhp~~giS~kam~imnsfv~Diferia~Eas~L~~~~kr~Tltsr~-~~~~~~~  453 (475)
                      .+|++..++.|+|+.||||||||||||+|||++||+||||||||||||||+||++|++||+|+|||||| |++++|+
T Consensus        27 ~gk~~~~~~~e~~s~yv~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl  103 (127)
T KOG1744|consen   27 AGKKRSTRRKESYSEYVYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL  103 (127)
T ss_pred             ccccCcccccCceeeehhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence            346677889999999999999999999999999999999999999999999999999999999999987 8888873

>PLN00155 histone H2A; Provisional

Probab=99.73  E-value=2e-18  Score=134.80  Aligned_cols=54  Identities=70%  Similarity=1.167  Sum_probs=48.2

Q ss_pred             CCCCCCCCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHH
Q psy17765        125 GKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYL  178 (475)
Q Consensus       125 g~~~k~~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYL  178 (475)
                      |++++.+++..|+|+||||||||+||||+|++++|+.||+++||||||||||||
T Consensus         5 g~g~~~~~k~~srS~rAgL~FPVgri~r~Lr~g~~a~Rvga~apVYlAAVLEYL   58 (58)
T PLN00155          5 GKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYL   58 (58)
T ss_pred             CCCCccccCccCcccccccccchHHHHHHHhcCChhhcccCCcHHHHHHHHHhC
Confidence            333444456789999999999999999999999999999999999999999997

>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=6.7e-12  Score=101.61  Aligned_cols=73  Identities=41%  Similarity=0.607  Sum_probs=68.4

Q ss_pred             CCCCCcccchhHHHHHHhhcCccc-ccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhcc
Q psy17765        138 SSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND  210 (475)
Q Consensus       138 SsRagL~FPVsRi~r~Lke~~~~~-RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD  210 (475)
                      +.+..+.||+.|+.+-+.++.+.+ ||++.|.+||.+++||++.+|++.|++.|.+.++.+|+|+||++|+++|
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            346789999999999999988774 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 ....

>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=98.95  E-value=6.3e-10  Score=90.08  Aligned_cols=69  Identities=30%  Similarity=0.423  Sum_probs=65.1

Q ss_pred             cCchhHHHHHHHHhhccCCC----CCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         31 RRKESYAIYIYKVLKQVHPD----TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        31 k~~~sf~~yI~KVLKQVhPd----~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      ++...+..+|+|++++++++    ..||.+|+.+|++++.+++.+|..+|..++.+++|.||+++|||.|+++
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            34567899999999999998    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 ....

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

Probab=98.74  E-value=2.1e-08  Score=86.65  Aligned_cols=78  Identities=23%  Similarity=0.437  Sum_probs=73.6

Q ss_pred             CcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHHHhhhcC
Q psy17765        142 GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSG  219 (475)
Q Consensus       142 gL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL~~Lf~~  219 (475)
                      .-.||++|+.++||-+....+|+..+||...-.||.+.++|+.+++..|+....+|||.+||..|+.+|+.++.|=..
T Consensus        21 ktrFP~ar~KkIMQ~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~   98 (113)
T COG5247          21 KTRFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNM   98 (113)
T ss_pred             hhcCCHHHHHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHH
Confidence            457999999999999999999999999999999999999999999999999999999999999999999999877543

>KOG1659|consensus

Probab=98.25  E-value=1.8e-06  Score=83.51  Aligned_cols=75  Identities=20%  Similarity=0.401  Sum_probs=71.7

Q ss_pred             cccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHHHhhh
Q psy17765        143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLL  217 (475)
Q Consensus       143 L~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL~~Lf  217 (475)
                      -.||++||+++||-+....||...+||.+.-.||.++.+||..++..++..+-++++++||..||.||+.++.|=
T Consensus        12 trfp~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk   86 (224)
T KOG1659|consen   12 TRFPPARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLK   86 (224)
T ss_pred             ccCCHHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHH
Confidence            469999999999999999999999999999999999999999999999999999999999999999999988763

>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=97.94  E-value=2.7e-05  Score=61.85  Aligned_cols=64  Identities=20%  Similarity=0.288  Sum_probs=57.4

Q ss_pred             ccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHH
Q psy17765        144 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAI  207 (475)
Q Consensus       144 ~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI  207 (475)
                      .||.++|.|+||......+|+..|...++-..|.++.+|..-|...|.+.+++.|+++||..||
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            5999999999999866679999999999999999999999999999999999999999999886

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 ....

>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=97.44  E-value=0.00057  Score=55.90  Aligned_cols=63  Identities=16%  Similarity=0.353  Sum_probs=59.1

Q ss_pred             HHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhC
Q psy17765         39 YIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLL  101 (475)
Q Consensus        39 yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllL  101 (475)
                      -|...++++.|+..++.+|...|..+..++.+.++..|.+|+.+.+++|+..+|||-+++..+
T Consensus         6 ~l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~~   68 (72)
T cd07981           6 KLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERNW   68 (72)
T ss_pred             HHHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhc
Confidence            377889999999999999999999999999999999999999999999999999999988753

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=97.21  E-value=0.001  Score=52.83  Aligned_cols=59  Identities=27%  Similarity=0.449  Sum_probs=52.8

Q ss_pred             HHHHHHhhccCCCC-CcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHH
Q psy17765         38 IYIYKVLKQVHPDT-GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAV   97 (475)
Q Consensus        38 ~yI~KVLKQVhPd~-~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAV   97 (475)
                      .-|.|+.|+. |+. .+|.+|...|......+++.|+.+|...+..++|+|++.+||..||
T Consensus         6 a~vkri~k~~-~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av   65 (65)
T PF00808_consen    6 ARVKRIMKSD-PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV   65 (65)
T ss_dssp             HHHHHHHHHT-STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred             HHHHHHhccC-CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence            4589999998 664 6999999999999999999999999999999999999999999886

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

>smart00803 TAF TATA box binding protein associated factor

Probab=97.14  E-value=0.0014  Score=52.88  Aligned_cols=64  Identities=22%  Similarity=0.267  Sum_probs=58.5

Q ss_pred             ccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765        144 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  208 (475)
Q Consensus       144 ~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~  208 (475)
                      .+|..-|.|+.+... ..||+..+.-.|+-.+||...+|+.-|.+++++.+++.++++||..|+.
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            478889999998755 4599999999999999999999999999999999999999999999863

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=96.95  E-value=0.0017  Score=55.86  Aligned_cols=67  Identities=30%  Similarity=0.415  Sum_probs=60.9

Q ss_pred             CCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765        141 AGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  208 (475)
Q Consensus       141 agL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~  208 (475)
                      ..+.+|+-=|.|+|++.. ..||+.+|...|..++|-+..+|.+-|...|.+.+++.|+++||++|+.
T Consensus        16 ~~~~Lp~apv~Ri~r~~~-~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~   82 (91)
T COG2036          16 TDLLLPKAPVRRILRKAG-AERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALK   82 (91)
T ss_pred             hhhhcCchHHHHHHHHHh-HHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHH
Confidence            347889999999998743 4599999999999999999999999999999999999999999999975

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

Probab=96.89  E-value=0.0018  Score=55.65  Aligned_cols=65  Identities=25%  Similarity=0.378  Sum_probs=58.9

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCc
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLP  102 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLP  102 (475)
                      ..-|.|++|++-++ .+|.+|...|+..+..+++-|+.+|..++...+|+|++..||+-|.+.+-.
T Consensus        22 ~apv~Ri~r~~~~~-Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~   86 (91)
T COG2036          22 KAPVRRILRKAGAE-RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGR   86 (91)
T ss_pred             chHHHHHHHHHhHH-HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhcc
Confidence            34577888888777 899999999999999999999999999999999999999999999998754

>PLN00035 histone H4; Provisional

Probab=96.85  E-value=0.0035  Score=55.08  Aligned_cols=63  Identities=11%  Similarity=0.136  Sum_probs=56.1

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  100 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll  100 (475)
                      ...|.|+++..- --.||.++.+-+...+..+++.|+.+|..++.+.+|+|+|..||..|++..
T Consensus        32 k~~IrRLARr~G-vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~   94 (103)
T PLN00035         32 KPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ   94 (103)
T ss_pred             HHHHHHHHHHcC-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHc
Confidence            467888888764 346999999999999999999999999999999999999999999988763

>PLN00035 histone H4; Provisional

Probab=96.79  E-value=0.0022  Score=56.34  Aligned_cols=64  Identities=16%  Similarity=0.232  Sum_probs=60.3

Q ss_pred             cchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhc
Q psy17765        145 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN  209 (475)
Q Consensus       145 FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~n  209 (475)
                      +|..-|.|+.+.+. ..||+..+..-|..+||.+..+|+.-|..++...+++.|+.+||.+|+..
T Consensus        30 ipk~~IrRLARr~G-vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr   93 (103)
T PLN00035         30 ITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR   93 (103)
T ss_pred             CCHHHHHHHHHHcC-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence            89999999999876 78999999999999999999999999999999999999999999999864

>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=96.44  E-value=0.0092  Score=50.78  Aligned_cols=64  Identities=19%  Similarity=0.296  Sum_probs=59.8

Q ss_pred             cchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhc
Q psy17765        145 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN  209 (475)
Q Consensus       145 FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~n  209 (475)
                      +|..-|.|+.+.+. ..||+..+-.-+..+||.+..+|+.-|..++.+.+++.|+.+||.+|+..
T Consensus        14 i~k~~I~RLarr~G-vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr   77 (85)
T cd00076          14 ITKPAIRRLARRGG-VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKR   77 (85)
T ss_pred             CCHHHHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence            78889999999876 78999999999999999999999999999999999999999999999864

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

Probab=96.35  E-value=0.011  Score=53.02  Aligned_cols=68  Identities=25%  Similarity=0.219  Sum_probs=60.1

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHH
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELA  106 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLa  106 (475)
                      ...|+|.|++-.-...|+..|..+|...+..+...|.+.|...+..+++++||+++|+.|++-  ..||.
T Consensus        23 V~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n--D~EL~   90 (115)
T cd00074          23 VGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN--DEELN   90 (115)
T ss_pred             HHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc--cHHHH
Confidence            578999999866667899999999999999999999999999999999999999999999987  44443

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.

>smart00803 TAF TATA box binding protein associated factor

Probab=96.23  E-value=0.015  Score=46.95  Aligned_cols=60  Identities=23%  Similarity=0.314  Sum_probs=52.6

Q ss_pred             HHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHH
Q psy17765         38 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR   98 (475)
Q Consensus        38 ~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVr   98 (475)
                      ..|+++.++.-=+ .||.++..-|...+...+..|+++|..++...+|+|+|..||..|++
T Consensus         6 ~~i~ria~~~Gi~-ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk   65 (65)
T smart00803        6 ETIKDVAESLGIG-NLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR   65 (65)
T ss_pred             HHHHHHHHHCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence            4578888876332 59999999999999999999999999999999999999999988764

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.

>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=96.06  E-value=0.026  Score=46.09  Aligned_cols=62  Identities=18%  Similarity=0.353  Sum_probs=50.7

Q ss_pred             HHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765         39 YIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  100 (475)
Q Consensus        39 yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll  100 (475)
                      -|...++||-|+..+..++.+.|-.+..++.+.++..+++||.+.+..|+..+|||.....-
T Consensus         4 ~l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler~   65 (68)
T PF03847_consen    4 KLQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLERN   65 (68)
T ss_dssp             HHHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHhh
Confidence            37788999999999999999999999999999999999999999999999999999887653

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

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

Probab=95.93  E-value=0.028  Score=46.05  Aligned_cols=66  Identities=17%  Similarity=0.280  Sum_probs=59.0

Q ss_pred             cchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhcc
Q psy17765        145 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND  210 (475)
Q Consensus       145 FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD  210 (475)
                      ++-..+..++++..-..|++..|...|..+.|-+..+|++.|...|++.++..|.++||++++..+
T Consensus         2 ~~k~~l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~   67 (72)
T cd07981           2 LTKRKLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERN   67 (72)
T ss_pred             CcHHHHHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            345667788887666789999999999999999999999999999999999999999999998765

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

>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=95.90  E-value=0.033  Score=47.40  Aligned_cols=62  Identities=13%  Similarity=0.186  Sum_probs=54.9

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      ...|.|+.+..- --.||.++.+-+...+..+++.|+.+|..++.+.+|+|+|..||..|++.
T Consensus        16 k~~I~RLarr~G-vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr   77 (85)
T cd00076          16 KPAIRRLARRGG-VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKR   77 (85)
T ss_pred             HHHHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence            467888888753 34699999999999999999999999999999999999999999988875

>PTZ00015 histone H4; Provisional

Probab=95.80  E-value=0.029  Score=49.36  Aligned_cols=64  Identities=16%  Similarity=0.255  Sum_probs=58.6

Q ss_pred             ccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765        144 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  208 (475)
Q Consensus       144 ~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~  208 (475)
                      -+|..-|.|+.+.+ =..||+..+-.-+..+||.+..+|+.-|..++...+++.|+.+||.+|+.
T Consensus        30 gI~k~~IrRLarr~-GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlK   93 (102)
T PTZ00015         30 GITKGAIRRLARRG-GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALK   93 (102)
T ss_pred             CCCHHHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHH
Confidence            47778999999875 36899999999999999999999999999999999999999999999975

>smart00417 H4 Histone H4

Probab=95.69  E-value=0.019  Score=47.78  Aligned_cols=60  Identities=15%  Similarity=0.180  Sum_probs=54.9

Q ss_pred             cchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHH
Q psy17765        145 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQL  205 (475)
Q Consensus       145 FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~l  205 (475)
                      +|..-|.|+++.+. ..||+..+-..+..+||.+..+|+..|..++...+++.|+.+||..
T Consensus        14 I~k~~IrRLaRr~G-vkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~   73 (74)
T smart00417       14 ITKPAIRRLARRGG-VKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY   73 (74)
T ss_pred             CCHHHHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence            67889999999764 6899999999999999999999999999999999999999999864

>PTZ00015 histone H4; Provisional

Probab=95.62  E-value=0.048  Score=47.98  Aligned_cols=63  Identities=14%  Similarity=0.242  Sum_probs=55.5

Q ss_pred             HHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         36 YAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        36 f~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      =...|.|+++..- --.||.++.+.+...+..+++.|+.+|..++.+.+|+|+|..||..|++.
T Consensus        32 ~k~~IrRLarr~G-vkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr   94 (102)
T PTZ00015         32 TKGAIRRLARRGG-VKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKR   94 (102)
T ss_pred             CHHHHHHHHHHcC-CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHh
Confidence            3578888888752 24699999999999999999999999999999999999999999988875

>smart00428 H3 Histone H3

Probab=95.46  E-value=0.057  Score=47.74  Aligned_cols=68  Identities=22%  Similarity=0.312  Sum_probs=62.6

Q ss_pred             CchhHHHHHHHHhhccCC--CCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         32 RKESYAIYIYKVLKQVHP--DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        32 ~~~sf~~yI~KVLKQVhP--d~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      ++-.|+-.++.+..+..+  ++.++.+|+.-|.......+..+..+|..++.+.+|.|++++||+-|.++
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            345699999999999888  88999999999999999999999999999999999999999999998876

>KOG0871|consensus

Probab=94.58  E-value=0.09  Score=48.99  Aligned_cols=79  Identities=16%  Similarity=0.312  Sum_probs=66.3

Q ss_pred             HHHHHHhhccCC-CCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh-CcHHHHHHHHHHhhh
Q psy17765         38 IYIYKVLKQVHP-DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL-LPGELAKHAVSEGTK  115 (475)
Q Consensus        38 ~yI~KVLKQVhP-d~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll-LPgeLaKhAvseG~k  115 (475)
                      .-|.|+.+.+-| |+.+..+|-+++...+..++..|+.||.+.|....|+||....|+.|..-+ |-..     +.++.+
T Consensus        16 Atv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eY-----iee~~~   90 (156)
T KOG0871|consen   16 ATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEY-----IEEAEE   90 (156)
T ss_pred             HHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHH-----HHHHHH
Confidence            348889999999 999999999999999999999999999999999999999999999999987 4422     334444


Q ss_pred             hhhhcc
Q psy17765        116 AVTKYT  121 (475)
Q Consensus       116 AV~ky~  121 (475)
                      ++..|.
T Consensus        91 vl~~~K   96 (156)
T KOG0871|consen   91 VLENCK   96 (156)
T ss_pred             HHHHHH
Confidence            454443

>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=94.27  E-value=0.17  Score=45.28  Aligned_cols=65  Identities=12%  Similarity=0.182  Sum_probs=57.0

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCc
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLP  102 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLP  102 (475)
                      ...|+++|+.-. ....+.++...|-.|+.+....|+.+|..++.+.+|+|++..||..|++....
T Consensus         4 ~~~v~~iLk~~G-v~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~   68 (117)
T cd07979           4 ARVIAAILKSMG-ITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD   68 (117)
T ss_pred             HHHHHHHHHHCC-CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc
Confidence            356888888752 24679999999999999999999999999999999999999999999988653

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

>PLN00156 histone H2AX; Provisional

Probab=94.24  E-value=0.11  Score=47.97  Aligned_cols=68  Identities=25%  Similarity=0.227  Sum_probs=58.2

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHH
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELA  106 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLa  106 (475)
                      ...|+|.|+.-+-...|+..|.-+|...+..+...|.+.|..-++.+++..||++.||.||+-  ..||.
T Consensus        32 VgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIrn--DeEL~   99 (139)
T PLN00156         32 VGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN--DEELS   99 (139)
T ss_pred             hHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhccC--cHHHH
Confidence            467999999987777899999999988888888888888888889999999999999999987  44444

>KOG0869|consensus

Probab=94.21  E-value=0.14  Score=48.19  Aligned_cols=67  Identities=19%  Similarity=0.323  Sum_probs=59.1

Q ss_pred             HHHHHHHhhccCCCC-CcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh-CcH
Q psy17765         37 AIYIYKVLKQVHPDT-GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL-LPG  103 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~-~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll-LPg  103 (475)
                      ..-|-|+.|+.-|.. .||.+|-+.|...|..+..-|..||+.-|..-+|+|||-.||..|+--+ |+.
T Consensus        35 IANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGFe~  103 (168)
T KOG0869|consen   35 IANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGFEN  103 (168)
T ss_pred             HHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCcHh
Confidence            344678888887764 6999999999999999999999999999999999999999999999877 554

>KOG1657|consensus

Probab=94.02  E-value=0.053  Score=54.11  Aligned_cols=78  Identities=19%  Similarity=0.293  Sum_probs=72.5

Q ss_pred             CcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHHHhhhcC
Q psy17765        142 GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSG  219 (475)
Q Consensus       142 gL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL~~Lf~~  219 (475)
                      ...||.+||.+.||-+.....|...|||.++-..|++..|+=..+...+..+++..+.-.||.-++.+..-++.|...
T Consensus        72 ~~~lPlaRiKkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL~Di  149 (236)
T KOG1657|consen   72 NHILPLARIKKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFLRDI  149 (236)
T ss_pred             hccCcHhhccccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccceecc
Confidence            479999999999999988899999999999999999999999889999999999999999999999999999888863

>smart00417 H4 Histone H4

Probab=93.47  E-value=0.23  Score=41.30  Aligned_cols=57  Identities=11%  Similarity=0.178  Sum_probs=49.7

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHH
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQ   94 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIq   94 (475)
                      ...|.|+++..- --.||..+.+-+..++..+++.|+.+|..++.+.+++|+|..||.
T Consensus        16 k~~IrRLaRr~G-vkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~   72 (74)
T smart00417       16 KPAIRRLARRGG-VKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVV   72 (74)
T ss_pred             HHHHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhe
Confidence            567888888652 235999999999999999999999999999999999999999984

>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=93.44  E-value=0.22  Score=44.58  Aligned_cols=63  Identities=17%  Similarity=0.086  Sum_probs=55.8

Q ss_pred             hHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccH
Q psy17765        148 GRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDE  211 (475)
Q Consensus       148 sRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~  211 (475)
                      --|+++|++. -..+++..++..|.-.++-.+.+|+.-|..+|++.+++.|+.+||++||..--
T Consensus         5 ~~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~   67 (117)
T cd07979           5 RVIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRV   67 (117)
T ss_pred             HHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHh
Confidence            3578899873 34689999999999999999999999999999999999999999999998643

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

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

Probab=93.32  E-value=0.19  Score=49.67  Aligned_cols=76  Identities=22%  Similarity=0.388  Sum_probs=69.3

Q ss_pred             cccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHHHhhhc
Q psy17765        143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLS  218 (475)
Q Consensus       143 L~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL~~Lf~  218 (475)
                      +.+|..||.++||-+....-|++.|||.++-+-|-+.+|+--.|--.|..+++..+--.||..|+...+-++.|+.
T Consensus       108 h~LPlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLid  183 (286)
T COG5208         108 HNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLID  183 (286)
T ss_pred             ccCcHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHhh
Confidence            6799999999999888888999999999999999999998888877788888888899999999999999888885

>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=93.24  E-value=0.35  Score=41.15  Aligned_cols=63  Identities=25%  Similarity=0.419  Sum_probs=55.1

Q ss_pred             cchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcC---CcccchhHHHHHHh
Q psy17765        145 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNK---KTRIIPRHLQLAIR  208 (475)
Q Consensus       145 FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k---~~rItP~hI~lAI~  208 (475)
                      ||-..+.|++.. ...+.++....+.++++---++.||.|.|.......+   ...|.|.||+.|.+
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            888889999874 5678999999999999999999999999988866544   47899999998875

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

>PTZ00017 histone H2A; Provisional

Probab=93.16  E-value=0.2  Score=46.06  Aligned_cols=68  Identities=24%  Similarity=0.220  Sum_probs=57.4

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHH
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELA  106 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLa  106 (475)
                      ...|+|.|+..+....|+..|.-+|-..+..+...|.+.|..-++.+++..||+++||.||+-  ..||.
T Consensus        30 VgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~n--DeEL~   97 (134)
T PTZ00017         30 VGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRN--DEELN   97 (134)
T ss_pred             hHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccC--cHHHH
Confidence            578999999886667888889888888888888888888888888999999999999999986  44554

>PLN00153 histone H2A; Provisional

Probab=93.09  E-value=0.21  Score=45.66  Aligned_cols=68  Identities=22%  Similarity=0.218  Sum_probs=58.5

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHH
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELA  106 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLa  106 (475)
                      ...|+|.|++-+....|+..|.-+|-..+..+...|.+.|..-++.+++..||++.||.||+-  ..||.
T Consensus        27 VgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n--DeEL~   94 (129)
T PLN00153         27 VGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRN--DEELG   94 (129)
T ss_pred             hHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccC--cHHHH
Confidence            468999999987777899999999988888888888888888889999999999999999986  44444

>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=92.53  E-value=0.45  Score=38.77  Aligned_cols=64  Identities=20%  Similarity=0.272  Sum_probs=46.8

Q ss_pred             ccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765        144 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  208 (475)
Q Consensus       144 ~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~  208 (475)
                      .||.+-|..+-..-. ...++..+.-.|+-=+||-..||+.-|.+..++.+++++|++||..|++
T Consensus         3 ~~~~esvk~iAes~G-i~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr   66 (66)
T PF02969_consen    3 VFSQESVKDIAESLG-ISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR   66 (66)
T ss_dssp             ---HHHHHHHHHHTT----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred             cCCHHHHHHHHHHcC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence            456666665553322 2468999999999999999999999999999999999999999999874

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.

>PLN00154 histone H2A; Provisional

Probab=92.17  E-value=0.44  Score=44.00  Aligned_cols=70  Identities=21%  Similarity=0.151  Sum_probs=55.4

Q ss_pred             HHHHHHHhhccCC-CCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHHH
Q psy17765         37 AIYIYKVLKQVHP-DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKH  108 (475)
Q Consensus        37 ~~yI~KVLKQVhP-d~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaKh  108 (475)
                      ...|+|.||.... ...|+..|.-+|-..+..+...|.+.|..-++.++++.||+++||.||+-  ..||.+-
T Consensus        41 VgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn--DeEL~~L  111 (136)
T PLN00154         41 VGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG--DEELDTL  111 (136)
T ss_pred             hHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC--cHHHHHH
Confidence            5789999999753 45778888888777777777777777777778899999999999999987  5555543

>KOG1142|consensus

Probab=92.10  E-value=0.15  Score=51.41  Aligned_cols=65  Identities=18%  Similarity=0.250  Sum_probs=60.0

Q ss_pred             HHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765         36 YAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  100 (475)
Q Consensus        36 f~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll  100 (475)
                      +..-|...++||-++..|..++-++|-.+..|+.+.|..-++.||.+.+..||-++||+..++..
T Consensus       156 ~k~kl~dLvqqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~  220 (258)
T KOG1142|consen  156 SKRKLDDLVQQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERN  220 (258)
T ss_pred             cccchhHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeecc
Confidence            44558899999999999999999999999999999999999999999999999999999888775

>KOG1756|consensus

Probab=92.01  E-value=0.38  Score=43.92  Aligned_cols=69  Identities=25%  Similarity=0.253  Sum_probs=54.5

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHH
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAK  107 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaK  107 (475)
                      ...|.|.|+.-+....|+..|--+|.--+..+...|.+.|..-++.|++..+|++.|+-||+-  ..||.+
T Consensus        30 vgri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~N--DeEL~~   98 (131)
T KOG1756|consen   30 VGRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIRN--DEELNK   98 (131)
T ss_pred             HHHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHhC--cHHHHH
Confidence            348999999988788899999888877666666666666666778899999999999999985  444443

>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=92.01  E-value=0.43  Score=38.89  Aligned_cols=47  Identities=23%  Similarity=0.355  Sum_probs=39.9

Q ss_pred             CcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHH
Q psy17765         52 GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR   98 (475)
Q Consensus        52 ~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVr   98 (475)
                      .++.++...|..-+..-+..|.++|.++++..+|.++|+.||..|.|
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            47899999999999999999999999999999999999999999875

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.

>PLN00157 histone H2A; Provisional

Probab=91.92  E-value=0.34  Score=44.52  Aligned_cols=68  Identities=28%  Similarity=0.234  Sum_probs=58.3

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHH
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELA  106 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLa  106 (475)
                      ...|+|.|++.+-...|+..|.-+|...+..+...|.+.|..-++.+++..||+++||.||+-  ..||.
T Consensus        29 VgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n--DeEL~   96 (132)
T PLN00157         29 VGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRN--DEELS   96 (132)
T ss_pred             hHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccC--cHHHH
Confidence            478999999987777899999999888888888888888888888999999999999999987  44544

>PTZ00252 histone H2A; Provisional

Probab=91.43  E-value=0.64  Score=42.83  Aligned_cols=70  Identities=16%  Similarity=0.191  Sum_probs=54.3

Q ss_pred             hH-HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhh--cCCCCCCChHHHHHHHHHhCcHHHH
Q psy17765         35 SY-AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAH--YNKRSTITSREIQTAVRLLLPGELA  106 (475)
Q Consensus        35 sf-~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~--~~kr~TlT~rdIqtAVrllLPgeLa  106 (475)
                      .| ...|+|.|++-+-...|+..|.-+|-..+..+...|.+.|..-++  .+++..||+++||.||+-  ..||.
T Consensus        25 ~FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrN--DeEL~   97 (134)
T PTZ00252         25 IFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRH--DDDLG   97 (134)
T ss_pred             cCchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccC--hHHHH
Confidence            34 468999999988777899999888888777777777666666663  378889999999999986  44444

>smart00414 H2A Histone 2A

Probab=91.39  E-value=0.42  Score=42.30  Aligned_cols=68  Identities=22%  Similarity=0.225  Sum_probs=56.0

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHH
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELA  106 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLa  106 (475)
                      ...|+|.|+..+....|+..|.-+|-..+..+...|.+.|..-+..+++..||+++|+.|++-  ..||.
T Consensus        12 VgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n--D~EL~   79 (106)
T smart00414       12 VGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN--DEELN   79 (106)
T ss_pred             hHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC--CHHHH
Confidence            457999999887666889889888888887777777777888888889999999999999987  44554

>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins

Probab=90.48  E-value=1  Score=37.11  Aligned_cols=61  Identities=10%  Similarity=0.183  Sum_probs=49.7

Q ss_pred             HHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         38 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        38 ~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      ..+-++|+..- =-.++..|++.|-.++.+.+..|+.++..++...+|.+.+..||..|+.-
T Consensus        10 ~~Vaqil~~~G-f~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~   70 (77)
T smart00576       10 IAVAQILESAG-FDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALEN   70 (77)
T ss_pred             HHHHHHHHHcC-ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence            34445555431 12478999999999999999999999999999999999999999988764

subdomain of archael histone-like transcription factors

>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]

Probab=90.46  E-value=0.51  Score=42.60  Aligned_cols=69  Identities=22%  Similarity=0.228  Sum_probs=59.4

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHH
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAK  107 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaK  107 (475)
                      ...|+|.||.-.-.+.|+.+|.-++...+..+...|.+.|..-++.++++.|+++.+|-|+|-  ..||.+
T Consensus        29 vgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIrn--D~EL~~   97 (132)
T COG5262          29 VGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIRN--DEELNK   97 (132)
T ss_pred             HHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhcC--cHHHHH
Confidence            457999999777778899999999888888888888888888889999999999999999986  556554

>KOG0869|consensus

Probab=90.25  E-value=0.25  Score=46.54  Aligned_cols=53  Identities=23%  Similarity=0.369  Sum_probs=48.7

Q ss_pred             hhhhhccccCC-CCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCCcCCCCCc
Q psy17765        394 IYKVLKQVHPD-TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDL  446 (475)
Q Consensus       394 i~kvLkqvhp~-~giS~kam~imnsfv~Diferia~Eas~L~~~~kr~Tltsr~  446 (475)
                      |-|+.|+.-|. .-||+.|-.+|.-.|...--=|+.||+--|+-.||.||+..+
T Consensus        38 V~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdD   91 (168)
T KOG0869|consen   38 VSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDD   91 (168)
T ss_pred             HHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHH
Confidence            67888988877 669999999999999999999999999999999999999976

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

Probab=89.79  E-value=0.23  Score=40.62  Aligned_cols=55  Identities=18%  Similarity=0.347  Sum_probs=43.7

Q ss_pred             hhhhhccccCCCCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCCcCCCCCchh
Q psy17765        394 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDLCP  448 (475)
Q Consensus       394 i~kvLkqvhp~~giS~kam~imnsfv~Diferia~Eas~L~~~~kr~Tltsr~~~  448 (475)
                      +-..++||-|+..+...+..++-.+.+|--+.+..-|++||++.+..||..++++
T Consensus         5 l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~   59 (68)
T PF03847_consen    5 LQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQ   59 (68)
T ss_dssp             HHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHH
T ss_pred             HHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHH
Confidence            4567899999999999999999999999999999999999999999999998865

; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_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=88.86  E-value=0.77  Score=47.94  Aligned_cols=58  Identities=22%  Similarity=0.284  Sum_probs=50.9

Q ss_pred             CcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh--ccHHHHh
Q psy17765        158 NYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR--NDEELNK  215 (475)
Q Consensus       158 ~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~--nD~EL~~  215 (475)
                      .-..|++..|...|+..+||...+|++.|.+.+++.++++++++||..|++  |.+.|.+
T Consensus        12 ~Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~eplyG   71 (343)
T cd08050          12 LGIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVEPLYG   71 (343)
T ss_pred             cCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCCcccC
Confidence            335699999999999999999999999999999999999999999999987  4444433

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

>KOG0870|consensus

Probab=88.47  E-value=3.5  Score=39.35  Aligned_cols=63  Identities=21%  Similarity=0.297  Sum_probs=48.8

Q ss_pred             HHHHHHhhccCCC--CCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765         38 IYIYKVLKQVHPD--TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  100 (475)
Q Consensus        38 ~yI~KVLKQVhPd--~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll  100 (475)
                      .-|.|+.|.+-|+  ..||.+|...|.---.=+...+..-+..+|..++|+||+..||-.|+.-+
T Consensus        14 AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Ei   78 (172)
T KOG0870|consen   14 AIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEI   78 (172)
T ss_pred             HHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHh
Confidence            3466677777665  58999998887654444455566667779999999999999999999877

>smart00428 H3 Histone H3

Probab=88.43  E-value=1.5  Score=38.92  Aligned_cols=67  Identities=25%  Similarity=0.310  Sum_probs=56.7

Q ss_pred             CcccchhHHHHHHhhc--Cc----ccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765        142 GLQFPVGRIHRLLRKG--NY----AERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  208 (475)
Q Consensus       142 gL~FPVsRi~r~Lke~--~~----~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~  208 (475)
                      +|.+|-.-|.|+.++=  .+    ..|+.++|-.-|-...|....++.|-|...|...++..|+|+|+++|.+
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            4777777777777652  11    3599999999999999999999999999999999999999999999854

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

Probab=88.09  E-value=1.2  Score=37.16  Aligned_cols=62  Identities=19%  Similarity=0.274  Sum_probs=49.5

Q ss_pred             HHHHHHhhcc--CCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         38 IYIYKVLKQV--HPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        38 ~yI~KVLKQV--hPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      ..+-|+.++.  ..+..+|.+.+.-|..++.+.++.++.+.-.+++..+|+||+..||.-..|.
T Consensus         9 ~~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rr   72 (76)
T PF15630_consen    9 YTVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARR   72 (76)
T ss_dssp             HHHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT
T ss_pred             HHHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhc
Confidence            3455566655  4667899999999999999999999999999999999999999999765553

>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=87.95  E-value=1.2  Score=38.36  Aligned_cols=63  Identities=21%  Similarity=0.348  Sum_probs=47.1

Q ss_pred             cchhHHHHHHhhcCcc-cccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcC-CcccchhHHHHHHh
Q psy17765        145 FPVGRIHRLLRKGNYA-ERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNK-KTRIIPRHLQLAIR  208 (475)
Q Consensus       145 FPVsRi~r~Lke~~~~-~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k-~~rItP~hI~lAI~  208 (475)
                      ||=+-|.++++. ..+ +-|+....+.++++--.+..||+|.|.......+ ...|.|.||.-|.+
T Consensus        24 ~~k~~ikkli~~-~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~r   88 (90)
T PF04719_consen   24 FNKAAIKKLINQ-VLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYR   88 (90)
T ss_dssp             --HHHHHHHHHH-HHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHH
T ss_pred             CCHHHHHHHHHH-HcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHH
Confidence            788889999986 455 8999999999999999999999999988765543 45899999998864

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

>KOG3219|consensus

Probab=86.92  E-value=0.95  Score=44.10  Aligned_cols=66  Identities=21%  Similarity=0.374  Sum_probs=55.5

Q ss_pred             cccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhc-CCcccchhHHHHHHhc
Q psy17765        143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDN-KKTRIIPRHLQLAIRN  209 (475)
Q Consensus       143 L~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~-k~~rItP~hI~lAI~n  209 (475)
                      -.||-+.|.+++.. ..++-|+..+.|.++++-.-++.||+|.|....... ....+-|.||..|.+-
T Consensus       111 s~f~Ka~iKkL~~~-itg~~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rr  177 (195)
T KOG3219|consen  111 SAFPKAQIKKLMSS-ITGQSVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRR  177 (195)
T ss_pred             hcCCHHHHHHHHHH-HhCCccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHH
Confidence            36999999999986 445559999999999999999999999998875543 3568999999988753

>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=86.83  E-value=1.3  Score=46.20  Aligned_cols=49  Identities=20%  Similarity=0.355  Sum_probs=46.8

Q ss_pred             CcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765         52 GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  100 (475)
Q Consensus        52 ~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll  100 (475)
                      .++.+|...+..-+......|+.||..+++..+|+|+|..||..|++..
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            6899999999999999999999999999999999999999999999875

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

>PLN00121 histone H3; Provisional

Probab=86.52  E-value=2  Score=39.81  Aligned_cols=65  Identities=18%  Similarity=0.251  Sum_probs=57.4

Q ss_pred             hHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         35 SYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        35 sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      .|+-.++.+.....+++.++.+|+.-|..-....+..+-+++...+.+.+|-||.++|||-+.++
T Consensus        67 pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ri  131 (136)
T PLN00121         67 PFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI  131 (136)
T ss_pred             cHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHHh
Confidence            38888888888888889999999999988888888888888888888999999999999988765

>PTZ00018 histone H3; Provisional

Probab=86.25  E-value=2.1  Score=39.61  Aligned_cols=65  Identities=18%  Similarity=0.251  Sum_probs=57.3

Q ss_pred             hHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         35 SYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        35 sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      .|+-.++.+..+..+++.++.+|+.-|..-..+.+..+-+++...+.+.+|-||..+|||-+.++
T Consensus        67 pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ri  131 (136)
T PTZ00018         67 PFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI  131 (136)
T ss_pred             cHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHHh
Confidence            38888888888888889999999999998888888888888888888999999999999988765

>smart00325 RhoGEF Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases

Probab=86.22  E-value=0.16  Score=46.33  Aligned_cols=68  Identities=13%  Similarity=-0.033  Sum_probs=54.9

Q ss_pred             hhHHHHHHhcccccc-----ccccccccccccccccCCcchhhhhccccCCCCcccchhhhccccccchhhhhhhcc
Q psy17765        286 VLEEHLENATGLLVD-----ESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAA  357 (475)
Q Consensus       286 Vfre~l~~~~~l~~~-----~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~~~~~~~~~~~m~~  357 (475)
                      +|.++|.....++.+     +|+|+.+|+.+...++..|++.++-..  ...+.+|.||..+  ..-+++|..|...
T Consensus        22 ~y~~~l~~~~~~~~~~~~~~iF~~i~~i~~~h~~~l~~l~~~~~~~~--~~~~~i~~~f~~~--~~~~~~Y~~Y~~~   94 (180)
T smart00325       22 VFLKPLKKELKLLSPNELETLFGNIEEIYEFHRDFLDELEERIEEWD--DSPERIGDVFLKL--EEFFKIYSEYCSN   94 (180)
T ss_pred             HHHHHHHHhhCCCCHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhccc--ccccHHHHHHHHh--hHHHHHHHHHHHh
Confidence            677778776544443     999999999999999999998876532  3579999999999  5568999999775

Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains. Improved coverage.

>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins

Probab=84.03  E-value=3.8  Score=33.73  Aligned_cols=58  Identities=17%  Similarity=0.104  Sum_probs=49.9

Q ss_pred             HHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhc
Q psy17765        151 HRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN  209 (475)
Q Consensus       151 ~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~n  209 (475)
                      -++|+.. -+.++..+|.-.|+-++|-...+|.+.+-+++...+++..++.||..|+.+
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            3455542 347999999999999999999999999999999999999999999999864

subdomain of archael histone-like transcription factors

>cd00160 RhoGEF Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain

Probab=82.86  E-value=0.28  Score=44.78  Aligned_cols=69  Identities=13%  Similarity=-0.046  Sum_probs=55.1

Q ss_pred             hhHHHHHHhcc-ccc----cccccccccccccccccCCcchhhhhccccCCCCcccchhhhccccccchhhhhhhccC
Q psy17765        286 VLEEHLENATG-LLV----DESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAAG  358 (475)
Q Consensus       286 Vfre~l~~~~~-l~~----~~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~~~~~~~~~~~m~~~  358 (475)
                      +|.++|..... +..    .+|+|+-+|+.+...++..|++.++-..  .+.+.+|.||.....  -+++|..|....
T Consensus        25 ~y~~~l~~~~~~~~~~~~~~iF~~i~~i~~~h~~~l~~l~~~~~~~~--~~~~~i~~~f~~~~~--~~~~Y~~Y~~~~   98 (181)
T cd00160          25 VFLKPLDKELLPLSPEEVELLFGNIEEIYEFHRIFLKSLEERVEEWD--KSGPRIGDVFLKLAP--FFKIYSEYCSNH   98 (181)
T ss_pred             HHHHHHHhccCCCCHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhccC--cccchHHHHHHHhhh--HHHHHHHHHhCh
Confidence            57777776554 222    2999999999999999999998887644  257899999999988  789999997763

It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.

>PF15510 CENP-W: Centromere kinetochore component W

Probab=81.99  E-value=1.6  Score=37.91  Aligned_cols=63  Identities=24%  Similarity=0.372  Sum_probs=50.9

Q ss_pred             HHHHHHhhccCCCCC--cChHHH--------------HHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhC
Q psy17765         38 IYIYKVLKQVHPDTG--VSSKAM--------------SIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLL  101 (475)
Q Consensus        38 ~yI~KVLKQVhPd~~--IS~~Am--------------~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllL  101 (475)
                      .+++||+|+--|.+.  -+.+.|              -.+|.++  ++.|+|+|+-.-+..|+..+|..+.|..|.+.+|
T Consensus        20 gfLkrv~Kr~KphlRl~~~~Dllv~~~~f~~~~~~~~vhLncLL--FvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaKviL   97 (102)
T PF15510_consen   20 GFLKRVFKRQKPHLRLETSGDLLVRFCPFSGWQWGGEVHLNCLL--FVHRLAEEARTNACENKCGTIKKEHVLAAAKVIL   97 (102)
T ss_pred             HHHHHHHHhcCCceeecccccHHHhhcccccccccceeehhHHH--HHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHH
Confidence            468999998888865  445555              4455555  6789999999999999999999999999998877


Q ss_pred             c
Q psy17765        102 P  102 (475)
Q Consensus       102 P  102 (475)
                      -
T Consensus        98 K   98 (102)
T PF15510_consen   98 K   98 (102)
T ss_pred             H
Confidence            4

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

Probab=80.09  E-value=7.3  Score=31.80  Aligned_cols=48  Identities=13%  Similarity=0.273  Sum_probs=43.8

Q ss_pred             CcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         52 GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        52 ~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      +++..|++.+..++.+.+..|+..+...+...+|...+..||..|..-
T Consensus        23 ~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~   70 (77)
T PF07524_consen   23 SASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEE   70 (77)
T ss_pred             ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence            589999999999999999999999999999999988999999877654

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	475
2jss_A	192	Nmr Structure Of Chaperone Chz1 Complexed With Hist		4e-63
2jss_A	192	Nmr Structure Of Chaperone Chz1 Complexed With Hist		5e-20
2nqb_C	123	Drosophila Nucleosome Structure Length = 123		1e-48
2pyo_C	120	Drosophila Nucleosome Core Length = 120		2e-48
1eqz_A	129	X-Ray Structure Of The Nucleosome Core Particle At		4e-46
2hio_A	128	Histone Octamer (Chicken), Chromosomal Protein Leng		5e-46
3c1b_C	129	The Effect Of H3 K79 Dimethylation And H4 K20 Trime		9e-46
1zbb_C	129	Structure Of The 4_601_167 Tetranucleosome Length =		1e-45
1m18_C	129	Ligand Binding Alters The Structure And Dynamics Of		1e-45
3a6n_C	133	The Nucleosome Containing A Testis-Specific Histone		2e-45
2cv5_C	130	Crystal Structure Of Human Nucleosome Core Particle		2e-45
2f8n_K	149	2.9 Angstrom X-Ray Structure Of Hybrid Macroh2a Nuc		2e-45
1s32_C	119	Molecular Recognition Of The Nucleosomal 'supergroo		5e-45
3kwq_C	107	Structural Characterization Of H3k56q Nucleosomes A		6e-45
1aoi_C	116	Complex Between Nucleosome Core Particle (H3,H4,H2a		7e-45
1kx3_C	128	X-Ray Structure Of The Nucleosome Core Particle, Nc		8e-45
1zla_C	129	X-Ray Structure Of A Kaposi's Sarcoma Herpesvirus L		3e-44
2pyo_D	122	Drosophila Nucleosome Core Length = 122		1e-43
2pyo_D	122	Drosophila Nucleosome Core Length = 122		3e-27
2nqb_D	123	Drosophila Nucleosome Structure Length = 123		6e-43
2nqb_D	123	Drosophila Nucleosome Structure Length = 123		1e-26
1hio_A	95	Histone Octamer (Chicken), Chromosomal Protein, Alp		2e-42
2f8n_H	123	2.9 Angstrom X-Ray Structure Of Hybrid Macroh2a Nuc		3e-42
2f8n_H	123	2.9 Angstrom X-Ray Structure Of Hybrid Macroh2a Nuc		7e-26
1s32_D	122	Molecular Recognition Of The Nucleosomal 'supergroo		3e-42
1s32_D	122	Molecular Recognition Of The Nucleosomal 'supergroo		7e-26
3c1b_D	125	The Effect Of H3 K79 Dimethylation And H4 K20 Trime		4e-42
3c1b_D	125	The Effect Of H3 K79 Dimethylation And H4 K20 Trime		8e-26
1zla_D	125	X-Ray Structure Of A Kaposi's Sarcoma Herpesvirus L		4e-42
1zla_D	125	X-Ray Structure Of A Kaposi's Sarcoma Herpesvirus L		8e-26
1kx3_D	125	X-Ray Structure Of The Nucleosome Core Particle, Nc		4e-42
1kx3_D	125	X-Ray Structure Of The Nucleosome Core Particle, Nc		7e-26
1p34_D	125	Crystallographic Studies Of Nucleosome Core Particl		4e-42
1p34_D	125	Crystallographic Studies Of Nucleosome Core Particl		8e-26
1f66_D	126	2.6 A Crystal Structure Of A Nucleosome Core Partic		4e-42
1f66_D	126	2.6 A Crystal Structure Of A Nucleosome Core Partic		8e-26
3c9k_B	125	Model Of Histone Octamer Tubular Crystals Length =		6e-42
3c9k_B	125	Model Of Histone Octamer Tubular Crystals Length =		1e-25
1aoi_D	99	Complex Between Nucleosome Core Particle (H3,H4,H2a		8e-42
1aoi_D	99	Complex Between Nucleosome Core Particle (H3,H4,H2a		2e-25
1id3_C	131	Crystal Structure Of The Yeast Nucleosome Core Part		9e-42
3kwq_D	93	Structural Characterization Of H3k56q Nucleosomes A		1e-41
3kwq_D	93	Structural Characterization Of H3k56q Nucleosomes A		2e-25
3a6n_D	129	The Nucleosome Containing A Testis-Specific Histone		3e-41
3a6n_D	129	The Nucleosome Containing A Testis-Specific Histone		4e-25
2hio_B	125	Histone Octamer (Chicken), Chromosomal Protein Leng		3e-41
2hio_B	125	Histone Octamer (Chicken), Chromosomal Protein Leng		6e-25
2cv5_D	126	Crystal Structure Of Human Nucleosome Core Particle		3e-41
2cv5_D	126	Crystal Structure Of Human Nucleosome Core Particle		6e-25
1eqz_B	126	X-Ray Structure Of The Nucleosome Core Particle At		3e-41
1eqz_B	126	X-Ray Structure Of The Nucleosome Core Particle At		6e-25
1u35_D	126	Crystal Structure Of The Nucleosome Core Particle C		4e-41
1u35_D	126	Crystal Structure Of The Nucleosome Core Particle C		5e-25
2xql_B	90	Fitting Of The H2a-H2b Histones In The Electron Mic		3e-40
2xql_B	90	Fitting Of The H2a-H2b Histones In The Electron Mic		5e-24
2xql_A	91	Fitting Of The H2a-H2b Histones In The Electron Mic		6e-40
3an2_D	129	The Structure Of The Centromeric Nucleosome Contain		1e-39
3an2_D	129	The Structure Of The Centromeric Nucleosome Contain		2e-23
1hio_B	90	Histone Octamer (Chicken), Chromosomal Protein, Alp		2e-38
1hio_B	90	Histone Octamer (Chicken), Chromosomal Protein, Alp		3e-22
1id3_D	130	Crystal Structure Of The Yeast Nucleosome Core Part		4e-36
1id3_D	130	Crystal Structure Of The Yeast Nucleosome Core Part		1e-20
1u35_C	120	Crystal Structure Of The Nucleosome Core Particle C		1e-30
1f66_C	128	2.6 A Crystal Structure Of A Nucleosome Core Partic		4e-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|2JSS|A Chain A, Nmr Structure Of Chaperone Chz1 Complexed With Histone H2a.Z-H2b Length = 192

Iteration: 1
 Score =  238 bits (608), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 126/199 (63%), Positives = 146/199 (73%), Gaps = 10/199 (5%)
Query: 34  ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 93
           E+Y+ YIYKVLKQ HPDTG+S K+MSI+NSFVNDIFERIA E+S+LA YNK+STI++REI
Sbjct: 3   ETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREI 62
Query: 94  QTAVRLLLPGELAKHAVSEGTKAVXXXXXXXXXXXXXXXXXXXXXXXXXLQFPVGRIHRL 153
           QTAVRL+LPGELAKHAVSEGT+AV                         LQFPVGRI R 
Sbjct: 63  QTAVRLILPGELAKHAVSEGTRAV--------TKYSSSTQAQSSSARAGLQFPVGRIKRY 114
Query: 154 L-RKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEE 212
           L R      RVG+ A +YL AV+EYL AEVLELAGNAA+D K  RI PRHLQLAIR D+E
Sbjct: 115 LKRHATGRTRVGSKAAIYLTAVLEYLTAEVLELAGNAAKDLKVKRITPRHLQLAIRGDDE 174
Query: 213 LNKLLSGVTIAQGGVLPNI 231
           L+ L+   TIA GGVLP+I
Sbjct: 175 LDSLIRA-TIASGGVLPHI 192

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

Iteration: 1
 Score = 95.9 bits (237), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 42/56 (75%), Positives = 51/56 (91%)
Query: 388 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT 443
           E+Y+ YIYKVLKQ HPDTG+S K+MSI+NSFVNDIFERIA E+S+LA YNK+STI+
Sbjct: 3   ETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTIS 58

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

Iteration: 1
 Score =  191 bits (484), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 93/100 (93%), Positives = 97/100 (97%)
Query: 143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
           LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH
Sbjct: 22  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 81
Query: 203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTHQ 242
           LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV + ++T +
Sbjct: 82  LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTEK 121

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

Iteration: 1
 Score =  189 bits (481), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 93/99 (93%), Positives = 96/99 (96%)
Query: 143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
           LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH
Sbjct: 22  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 81
Query: 203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTH 241
           LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV + ++T 
Sbjct: 82  LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTE 120

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

Iteration: 1
 Score =  182 bits (462), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 87/98 (88%), Positives = 93/98 (94%)
Query: 143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 24  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 83
Query: 203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240
           LQLAIRNDEELNKLL  VTIAQGGVLPNIQAV + ++T
Sbjct: 84  LQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKT 121

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

Iteration: 1
 Score =  182 bits (461), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 87/98 (88%), Positives = 93/98 (94%)
Query: 143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 23  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 82
Query: 203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240
           LQLAIRNDEELNKLL  VTIAQGGVLPNIQAV + ++T
Sbjct: 83  LQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKT 120

>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 =  181 bits (458), Expect = 9e-46,   Method: Compositional matrix adjust.
 Identities = 85/99 (85%), Positives = 93/99 (93%)
Query: 143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 23  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 82
Query: 203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTH 241
           LQLA+RNDEELNKLL  VTIAQGGVLPNIQ+V + ++T 
Sbjct: 83  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTE 121

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

Iteration: 1
 Score =  181 bits (458), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 85/99 (85%), Positives = 93/99 (93%)
Query: 143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 23  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 82
Query: 203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTH 241
           LQLA+RNDEELNKLL  VTIAQGGVLPNIQ+V + ++T 
Sbjct: 83  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTE 121

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

Iteration: 1
 Score =  181 bits (458), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 85/99 (85%), Positives = 93/99 (93%)
Query: 143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 23  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 82
Query: 203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTH 241
           LQLA+RNDEELNKLL  VTIAQGGVLPNIQ+V + ++T 
Sbjct: 83  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTE 121

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

Iteration: 1
 Score =  180 bits (456), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 86/98 (87%), Positives = 93/98 (94%)
Query: 143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
           LQFPVGR+HRLLRKGNY+ERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 27  LQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 86
Query: 203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240
           LQLAIRNDEELNKLL  VTIAQGGVLPNIQAV + ++T
Sbjct: 87  LQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKT 124

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

Iteration: 1
 Score =  180 bits (456), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 86/98 (87%), Positives = 93/98 (94%)
Query: 143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
           LQFPVGR+HRLLRKGNY+ERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 24  LQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 83
Query: 203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240
           LQLAIRNDEELNKLL  VTIAQGGVLPNIQAV + ++T
Sbjct: 84  LQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKT 121

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

Iteration: 1
 Score =  180 bits (456), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 86/98 (87%), Positives = 93/98 (94%)
Query: 143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
           LQFPVGR+HRLLRKGNY+ERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 43  LQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 102
Query: 203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240
           LQLAIRNDEELNKLL  VTIAQGGVLPNIQAV + ++T
Sbjct: 103 LQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKT 140

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

Iteration: 1
 Score =  178 bits (452), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 84/92 (91%), Positives = 89/92 (96%)
Query: 143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 23  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 82
Query: 203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV 234
           LQLA+RNDEELNKLL  VTIAQGGVLPNIQ+V
Sbjct: 83  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQSV 114

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

Iteration: 1
 Score =  178 bits (451), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 85/98 (86%), Positives = 93/98 (94%)
Query: 143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 10  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 69
Query: 203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240
           LQLA+RNDEELNKLL  VTIAQGGVLPNIQ+V + ++T
Sbjct: 70  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT 107

>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 =  178 bits (451), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 84/92 (91%), Positives = 89/92 (96%)
Query: 143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 20  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 79
Query: 203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV 234
           LQLA+RNDEELNKLL  VTIAQGGVLPNIQ+V
Sbjct: 80  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQSV 111

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

Iteration: 1
 Score =  178 bits (451), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 84/92 (91%), Positives = 89/92 (96%)
Query: 143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 23  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 82
Query: 203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV 234
           LQLA+RNDEELNKLL  VTIAQGGVLPNIQ+V
Sbjct: 83  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQSV 114

>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 =  176 bits (446), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 83/99 (83%), Positives = 91/99 (91%)
Query: 143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGN  RDNKKTRIIPRH
Sbjct: 23  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNWERDNKKTRIIPRH 82
Query: 203 LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTH 241
           LQLA+RNDEELNKLL  VTIAQGGVLPNIQ+V + ++T 
Sbjct: 83  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTE 121

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

Iteration: 1
 Score =  174 bits (440), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 86/100 (86%), Positives = 88/100 (88%)
Query: 18  QKNIAXXXXXXXXXXXESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESS 77
           QKNI            ESYAIYIYKVLKQVHPDTG+SSKAMSIMNSFVNDIFERIAAE+S
Sbjct: 16  QKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEAS 75
Query: 78  RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAV 117
           RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAV
Sbjct: 76  RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAV 115

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

Iteration: 1
 Score =  119 bits (299), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 59/72 (81%), Positives = 61/72 (84%)
Query: 372 QKNITXXXXXXXXXXXESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESS 431
           QKNIT           ESYAIYIYKVLKQVHPDTG+SSKAMSIMNSFVNDIFERIAAE+S
Sbjct: 16  QKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEAS 75
Query: 432 RLAHYNKRSTIT 443
           RLAHYNKRSTIT
Sbjct: 76  RLAHYNKRSTIT 87

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

Iteration: 1
 Score =  171 bits (434), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 85/100 (85%), Positives = 87/100 (87%)
Query: 18  QKNIAXXXXXXXXXXXESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESS 77
           QKNI            ESYAIYIY VLKQVHPDTG+SSKAMSIMNSFVNDIFERIAAE+S
Sbjct: 17  QKNITKTDKKKKRKRKESYAIYIYTVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEAS 76
Query: 78  RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAV 117
           RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAV
Sbjct: 77  RLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAV 116

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

Iteration: 1
 Score =  117 bits (293), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 58/72 (80%), Positives = 60/72 (83%)
Query: 372 QKNITXXXXXXXXXXXESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESS 431
           QKNIT           ESYAIYIY VLKQVHPDTG+SSKAMSIMNSFVNDIFERIAAE+S
Sbjct: 17  QKNITKTDKKKKRKRKESYAIYIYTVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEAS 76
Query: 432 RLAHYNKRSTIT 443
           RLAHYNKRSTIT
Sbjct: 77  RLAHYNKRSTIT 88

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

Iteration: 1
 Score =  170 bits (430), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 81/87 (93%), Positives = 84/87 (96%)
Query: 143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 9   LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 68
Query: 203 LQLAIRNDEELNKLLSGVTIAQGGVLP 229
           LQLAIRNDEELNKLL  VTIAQGGVLP
Sbjct: 69  LQLAIRNDEELNKLLGKVTIAQGGVLP 95

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

Iteration: 1
 Score =  169 bits (428), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 79/84 (94%), Positives = 83/84 (98%)
Query: 34  ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 93
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTITSREI
Sbjct: 33  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 92
Query: 94  QTAVRLLLPGELAKHAVSEGTKAV 117
           QTAVRLLLPGELAKHAVSEGTKAV
Sbjct: 93  QTAVRLLLPGELAKHAVSEGTKAV 116

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

Iteration: 1
 Score =  115 bits (287), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 51/56 (91%), Positives = 55/56 (98%)
Query: 388 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT 443
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTIT
Sbjct: 33  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTIT 88

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

Iteration: 1
 Score =  169 bits (428), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 79/84 (94%), Positives = 83/84 (98%)
Query: 34  ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 93
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTITSREI
Sbjct: 32  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 91
Query: 94  QTAVRLLLPGELAKHAVSEGTKAV 117
           QTAVRLLLPGELAKHAVSEGTKAV
Sbjct: 92  QTAVRLLLPGELAKHAVSEGTKAV 115

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

Iteration: 1
 Score =  115 bits (287), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 51/56 (91%), Positives = 55/56 (98%)
Query: 388 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT 443
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTIT
Sbjct: 32  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTIT 87

>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 =  169 bits (427), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 79/84 (94%), Positives = 83/84 (98%)
Query: 34  ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 93
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTITSREI
Sbjct: 35  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 94
Query: 94  QTAVRLLLPGELAKHAVSEGTKAV 117
           QTAVRLLLPGELAKHAVSEGTKAV
Sbjct: 95  QTAVRLLLPGELAKHAVSEGTKAV 118

>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 =  115 bits (287), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 51/56 (91%), Positives = 55/56 (98%)
Query: 388 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT 443
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTIT
Sbjct: 35  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTIT 90

>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 =  169 bits (427), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 79/84 (94%), Positives = 83/84 (98%)
Query: 34  ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 93
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTITSREI
Sbjct: 35  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 94
Query: 94  QTAVRLLLPGELAKHAVSEGTKAV 117
           QTAVRLLLPGELAKHAVSEGTKAV
Sbjct: 95  QTAVRLLLPGELAKHAVSEGTKAV 118

>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 =  115 bits (287), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 51/56 (91%), Positives = 55/56 (98%)
Query: 388 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT 443
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTIT
Sbjct: 35  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTIT 90

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

Iteration: 1
 Score =  169 bits (427), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 79/84 (94%), Positives = 83/84 (98%)
Query: 34  ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 93
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTITSREI
Sbjct: 35  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 94
Query: 94  QTAVRLLLPGELAKHAVSEGTKAV 117
           QTAVRLLLPGELAKHAVSEGTKAV
Sbjct: 95  QTAVRLLLPGELAKHAVSEGTKAV 118

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

Iteration: 1
 Score =  115 bits (287), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 51/56 (91%), Positives = 55/56 (98%)
Query: 388 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT 443
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTIT
Sbjct: 35  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTIT 90

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

Iteration: 1
 Score =  169 bits (427), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 79/84 (94%), Positives = 83/84 (98%)
Query: 34  ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 93
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTITSREI
Sbjct: 35  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 94
Query: 94  QTAVRLLLPGELAKHAVSEGTKAV 117
           QTAVRLLLPGELAKHAVSEGTKAV
Sbjct: 95  QTAVRLLLPGELAKHAVSEGTKAV 118

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

Iteration: 1
 Score =  115 bits (287), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 51/56 (91%), Positives = 55/56 (98%)
Query: 388 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT 443
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTIT
Sbjct: 35  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTIT 90

>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 =  169 bits (427), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 79/84 (94%), Positives = 83/84 (98%)
Query: 34  ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 93
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTITSREI
Sbjct: 36  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 95
Query: 94  QTAVRLLLPGELAKHAVSEGTKAV 117
           QTAVRLLLPGELAKHAVSEGTKAV
Sbjct: 96  QTAVRLLLPGELAKHAVSEGTKAV 119

>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 =  114 bits (286), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 51/56 (91%), Positives = 55/56 (98%)
Query: 388 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT 443
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTIT
Sbjct: 36  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTIT 91

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

Iteration: 1
 Score =  168 bits (426), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 79/84 (94%), Positives = 83/84 (98%)
Query: 34  ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 93
           ESY+IY+YKVLKQVHPDTG+SSKAMSIMNSFVNDIFERIA E+SRLAHYNKRSTITSREI
Sbjct: 35  ESYSIYVYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAGEASRLAHYNKRSTITSREI 94
Query: 94  QTAVRLLLPGELAKHAVSEGTKAV 117
           QTAVRLLLPGELAKHAVSEGTKAV
Sbjct: 95  QTAVRLLLPGELAKHAVSEGTKAV 118

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

Iteration: 1
 Score =  114 bits (285), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 51/56 (91%), Positives = 55/56 (98%)
Query: 388 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT 443
           ESY+IY+YKVLKQVHPDTG+SSKAMSIMNSFVNDIFERIA E+SRLAHYNKRSTIT
Sbjct: 35  ESYSIYVYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAGEASRLAHYNKRSTIT 90

>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 =  168 bits (425), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 79/84 (94%), Positives = 83/84 (98%)
Query: 34  ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 93
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTITSREI
Sbjct: 9   ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 68
Query: 94  QTAVRLLLPGELAKHAVSEGTKAV 117
           QTAVRLLLPGELAKHAVSEGTKAV
Sbjct: 69  QTAVRLLLPGELAKHAVSEGTKAV 92

>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 =  114 bits (284), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 51/56 (91%), Positives = 55/56 (98%)
Query: 388 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT 443
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTIT
Sbjct: 9   ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTIT 64

>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 = 9e-42,   Method: Compositional matrix adjust.
 Identities = 77/89 (86%), Positives = 85/89 (95%)
Query: 143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
           L FPVGR+HRLLR+GNYA+R+G+GAPVYL AV+EYLAAE+LELAGNAARDNKKTRIIPRH
Sbjct: 24  LTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRH 83
Query: 203 LQLAIRNDEELNKLLSGVTIAQGGVLPNI 231
           LQLAIRND+ELNKLL  VTIAQGGVLPNI
Sbjct: 84  LQLAIRNDDELNKLLGNVTIAQGGVLPNI 112

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

Iteration: 1
 Score =  167 bits (423), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 79/84 (94%), Positives = 83/84 (98%)
Query: 34  ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 93
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTITSREI
Sbjct: 3   ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 62
Query: 94  QTAVRLLLPGELAKHAVSEGTKAV 117
           QTAVRLLLPGELAKHAVSEGTKAV
Sbjct: 63  QTAVRLLLPGELAKHAVSEGTKAV 86

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

Iteration: 1
 Score =  113 bits (283), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 51/56 (91%), Positives = 55/56 (98%)
Query: 388 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT 443
           ESYAIY+YKVLKQVHPDTG+SSKAMSIMNSFVND+FERIA E+SRLAHYNKRSTIT
Sbjct: 3   ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTIT 58

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

Iteration: 1
 Score =  166 bits (420), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 78/84 (92%), Positives = 82/84 (97%)
Query: 34  ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 93
           ESY+IY+YKVLKQVHPDTG+SSKAM IMNSFVNDIFERIA E+SRLAHYNKRSTITSREI
Sbjct: 39  ESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREI 98
Query: 94  QTAVRLLLPGELAKHAVSEGTKAV 117
           QTAVRLLLPGELAKHAVSEGTKAV
Sbjct: 99  QTAVRLLLPGELAKHAVSEGTKAV 122

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

Iteration: 1
 Score =  112 bits (280), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 50/56 (89%), Positives = 54/56 (96%)
Query: 388 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT 443
           ESY+IY+YKVLKQVHPDTG+SSKAM IMNSFVNDIFERIA E+SRLAHYNKRSTIT
Sbjct: 39  ESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTIT 94

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

Iteration: 1
 Score =  166 bits (419), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 78/84 (92%), Positives = 82/84 (97%)
Query: 34  ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 93
           ESY+IY+YKVLKQVHPDTG+SSKAM IMNSFVNDIFERIA E+SRLAHYNKRSTITSREI
Sbjct: 35  ESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREI 94
Query: 94  QTAVRLLLPGELAKHAVSEGTKAV 117
           QTAVRLLLPGELAKHAVSEGTKAV
Sbjct: 95  QTAVRLLLPGELAKHAVSEGTKAV 118

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

Iteration: 1
 Score =  112 bits (279), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 50/56 (89%), Positives = 54/56 (96%)
Query: 388 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT 443
           ESY+IY+YKVLKQVHPDTG+SSKAM IMNSFVNDIFERIA E+SRLAHYNKRSTIT
Sbjct: 35  ESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTIT 90

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

Iteration: 1
 Score =  166 bits (419), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 77/84 (91%), Positives = 82/84 (97%)
Query: 34  ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 93
           ESY++Y+YKVLKQVHPDTG+SSKAM IMNSFVNDIFERIA E+SRLAHYNKRSTITSREI
Sbjct: 36  ESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREI 95
Query: 94  QTAVRLLLPGELAKHAVSEGTKAV 117
           QTAVRLLLPGELAKHAVSEGTKAV
Sbjct: 96  QTAVRLLLPGELAKHAVSEGTKAV 119

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

Iteration: 1
 Score =  112 bits (279), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 49/56 (87%), Positives = 54/56 (96%)
Query: 388 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT 443
           ESY++Y+YKVLKQVHPDTG+SSKAM IMNSFVNDIFERIA E+SRLAHYNKRSTIT
Sbjct: 36  ESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTIT 91

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

Iteration: 1
 Score =  166 bits (419), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 78/84 (92%), Positives = 82/84 (97%)
Query: 34  ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 93
           ESY+IY+YKVLKQVHPDTG+SSKAM IMNSFVNDIFERIA E+SRLAHYNKRSTITSREI
Sbjct: 36  ESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREI 95
Query: 94  QTAVRLLLPGELAKHAVSEGTKAV 117
           QTAVRLLLPGELAKHAVSEGTKAV
Sbjct: 96  QTAVRLLLPGELAKHAVSEGTKAV 119

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

Iteration: 1
 Score =  112 bits (279), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 50/56 (89%), Positives = 54/56 (96%)
Query: 388 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT 443
           ESY+IY+YKVLKQVHPDTG+SSKAM IMNSFVNDIFERIA E+SRLAHYNKRSTIT
Sbjct: 36  ESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTIT 91

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

Iteration: 1
 Score =  166 bits (419), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 77/84 (91%), Positives = 83/84 (98%)
Query: 34  ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 93
           ESY+IY+YKVLKQVHPDTG+SSKAM IMNSFVNDIFERIA+E+SRLAHYNKRSTITSRE+
Sbjct: 36  ESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIASEASRLAHYNKRSTITSREV 95
Query: 94  QTAVRLLLPGELAKHAVSEGTKAV 117
           QTAVRLLLPGELAKHAVSEGTKAV
Sbjct: 96  QTAVRLLLPGELAKHAVSEGTKAV 119

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

Iteration: 1
 Score =  112 bits (280), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 50/56 (89%), Positives = 55/56 (98%)
Query: 388 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT 443
           ESY+IY+YKVLKQVHPDTG+SSKAM IMNSFVNDIFERIA+E+SRLAHYNKRSTIT
Sbjct: 36  ESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIASEASRLAHYNKRSTIT 91

>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 =  162 bits (411), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 77/83 (92%), Positives = 81/83 (97%)
Query: 35  SYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQ 94
           SY+IY+YKVLKQVHPDTG+SSKAM IMNSFVNDIFERIA E+SRLAHYNKRSTITSREIQ
Sbjct: 1   SYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQ 60
Query: 95  TAVRLLLPGELAKHAVSEGTKAV 117
           TAVRLLLPGELAKHAVSEGTKAV
Sbjct: 61  TAVRLLLPGELAKHAVSEGTKAV 83

>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 =  108 bits (271), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 49/55 (89%), Positives = 53/55 (96%)
Query: 389 SYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT 443
           SY+IY+YKVLKQVHPDTG+SSKAM IMNSFVNDIFERIA E+SRLAHYNKRSTIT
Sbjct: 1   SYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTIT 55

>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 =  162 bits (409), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 77/83 (92%), Positives = 80/83 (96%)
Query: 143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202
           LQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRH
Sbjct: 9   LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 68
Query: 203 LQLAIRNDEELNKLLSGVTIAQG 225
           LQLAIRNDEELNKLL  VTIAQG
Sbjct: 69  LQLAIRNDEELNKLLGKVTIAQG 91

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

Iteration: 1
 Score =  160 bits (406), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 76/84 (90%), Positives = 80/84 (95%)
Query: 34  ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 93
           ESY+IY+YKVLKQVHPDTG+SSKA  I NSFVNDIFERIA E+SRLAHYNKRSTITSREI
Sbjct: 39  ESYSIYVYKVLKQVHPDTGISSKAXGIXNSFVNDIFERIAGEASRLAHYNKRSTITSREI 98
Query: 94  QTAVRLLLPGELAKHAVSEGTKAV 117
           QTAVRLLLPGELAKHAVSEGTKAV
Sbjct: 99  QTAVRLLLPGELAKHAVSEGTKAV 122

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

Iteration: 1
 Score =  107 bits (266), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 48/56 (85%), Positives = 52/56 (92%)
Query: 388 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT 443
           ESY+IY+YKVLKQVHPDTG+SSKA  I NSFVNDIFERIA E+SRLAHYNKRSTIT
Sbjct: 39  ESYSIYVYKVLKQVHPDTGISSKAXGIXNSFVNDIFERIAGEASRLAHYNKRSTIT 94

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

Iteration: 1
 Score =  157 bits (396), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 75/83 (90%), Positives = 79/83 (95%)
Query: 35  SYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQ 94
           SY+IY+YKVLKQVHPDTG+SSKAM  MNSFVNDIFERIA  +SRLAHYNKRSTITSREIQ
Sbjct: 1   SYSIYVYKVLKQVHPDTGISSKAMGSMNSFVNDIFERIAGLASRLAHYNKRSTITSREIQ 60
Query: 95  TAVRLLLPGELAKHAVSEGTKAV 117
           TAVRLLLPGELAKHAVSEGTKAV
Sbjct: 61  TAVRLLLPGELAKHAVSEGTKAV 83

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

Iteration: 1
 Score =  103 bits (256), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 47/55 (85%), Positives = 51/55 (92%)
Query: 389 SYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT 443
           SY+IY+YKVLKQVHPDTG+SSKAM  MNSFVNDIFERIA  +SRLAHYNKRSTIT
Sbjct: 1   SYSIYVYKVLKQVHPDTGISSKAMGSMNSFVNDIFERIAGLASRLAHYNKRSTIT 55

>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 =  149 bits (375), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 67/84 (79%), Positives = 79/84 (94%)
Query: 34  ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREI 93
           E+Y+ YIYKVLKQ HPDTG+S K+MSI+NSFVNDIFERIA E+S+LA YNK+STI++REI
Sbjct: 38  ETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREI 97
Query: 94  QTAVRLLLPGELAKHAVSEGTKAV 117
           QTAVRL+LPGELAKHAVSEGT+AV
Sbjct: 98  QTAVRLILPGELAKHAVSEGTRAV 121

>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 = 97.8 bits (242), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 42/56 (75%), Positives = 51/56 (91%)
Query: 388 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT 443
           E+Y+ YIYKVLKQ HPDTG+S K+MSI+NSFVNDIFERIA E+S+LA YNK+STI+
Sbjct: 38  ETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTIS 93

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

Iteration: 1
 Score =  130 bits (328), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 61/88 (69%), Positives = 73/88 (82%)
Query: 145 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQ 204
           FPVGR+ R ++KG+   R+G GAPVY+AAV+EYL AE+LELA NAARDNKK R+ PRH+ 
Sbjct: 23  FPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHIL 82
Query: 205 LAIRNDEELNKLLSGVTIAQGGVLPNIQ 232
           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 =  112 bits (281), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 60/101 (59%), Positives = 73/101 (72%), Gaps = 2/101 (1%)
Query: 143 LQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPR 201
           LQFPVGRIHR L+    +  RVGA A VY AA++EYL AEVLELAGNA++D K  RI PR
Sbjct: 26  LQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPR 85
Query: 202 HLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTHQ 242
           HLQLAIR DEEL+ L+   TIA GGV+P+I    + ++  Q
Sbjct: 86  HLQLAIRGDEELDSLIK-ATIAGGGVIPHIHKSLIGKKGQQ 125

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 37/172 (21%), Positives = 73/172 (42%), Gaps = 28/172 (16%)
Query: 42  KVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLL 101
           KV  QVHP    +  A+  +   +  +   +     R          ++ +++  V+   
Sbjct: 29  KVQGQVHPTLESNDDALQYVEELILQLLNXLCQAQPR----------SASDVEERVQKSF 78
Query: 102 PGELAKHAVSEGTKAVXXXXXXXXXXXXXXXXXXXXXXXXXLQFPVGRIHRLLRKGNYAE 161
           P  + K A+++   A+                         L  PV +IH LL++     
Sbjct: 79  PHPIDKWAIADAQSAIEKRKRRNP-----------------LSLPVEKIHPLLKEV-LGY 120
Query: 162 RVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEEL 213
           ++     VY+ AV+EY++A++L+LAGN  R+ +   I  + +++A   D+ L
Sbjct: 121 KIDHQVSVYIVAVLEYISADILKLAGNYVRNIRHYEITKQDIKVAXCADKVL 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 = 36/172 (20%), Positives = 73/172 (42%), Gaps = 28/172 (16%)
Query: 42  KVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLL 101
           KV  QVHP    +  A+  +   +  +   +     R          ++ +++  V+   
Sbjct: 29  KVQGQVHPTLESNDDALQYVEELILQLLNMLCQAQPR----------SASDVEERVQKSF 78
Query: 102 PGELAKHAVSEGTKAVXXXXXXXXXXXXXXXXXXXXXXXXXLQFPVGRIHRLLRKGNYAE 161
           P  + K A+++   A+                         L  PV +IH LL++     
Sbjct: 79  PHPIDKWAIADAQSAIEKRKRRNP-----------------LSLPVEKIHPLLKEV-LGY 120
Query: 162 RVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEEL 213
           ++     VY+ AV+EY++A++L+L GN  R+ +   I  + +++A+  D+ L
Sbjct: 121 KIDHQVSVYIVAVLEYISADILKLVGNYVRNIRHYEITKQDIKVAMCADKVL 172

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	475
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	2e-63
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	2e-23
2nqb_D	123	Histone H2B; nucleosome, NCP, chromatin, structura	2e-52
2nqb_D	123	Histone H2B; nucleosome, NCP, chromatin, structura	7e-30
1tzy_B	126	Histone H2B; histone-fold, tetramer-dimer-dimer, D	3e-47
1tzy_B	126	Histone H2B; histone-fold, tetramer-dimer-dimer, D	2e-25
2f8n_K	149	Histone H2A type 1; nucleosome, NCP, macroh2A, his	1e-45
2nqb_C	123	Histone H2A; nucleosome, NCP, chromatin, structura	9e-45
1tzy_A	129	Histone H2A-IV; histone-fold, tetramer-dimer-dimer	3e-44
2f8n_G	120	Core histone macro-H2A.1; nucleosome, NCP, macroh2	4e-43
1id3_C	131	Histone H2A.1; nucleosome core particle, chromatin	2e-40
1f66_C	128	Histone H2A.Z; nucleosome, chromatin, histone vari	2e-35
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	2e-20
3ksy_A	1049	SOS-1, SON of sevenless homolog 1; RAS, RAS activa	1e-13
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-11
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	6e-09
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	2e-04
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	5e-04

>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 =  203 bits (515), Expect = 2e-63
 Identities = 135/201 (67%), Positives = 161/201 (80%), Gaps = 10/201 (4%)

Query: 32  RKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSR 91
           RKE+Y+ YIYKVLKQ HPDTG+S K+MSI+NSFVNDIFERIA E+S+LA YNK+STI++R
Sbjct: 1   RKETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAR 60

Query: 92  EIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSKGKGGKAKTKSKTRSSRAGLQFPVGRIH 151
           EIQTAVRL+LPGELAKHAVSEGT+AVTKY+SS           ++ S+RAGLQFPVGRI 
Sbjct: 61  EIQTAVRLILPGELAKHAVSEGTRAVTKYSSSTQA--------QSSSARAGLQFPVGRIK 112

Query: 152 RLLRKGNYAER-VGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND 210
           R L++       VG+ A +YL AV+EYL AEVLELAGNAA+D K  RI PRHLQLAIR D
Sbjct: 113 RYLKRHATGRTRVGSKAAIYLTAVLEYLTAEVLELAGNAAKDLKVKRITPRHLQLAIRGD 172

Query: 211 EELNKLLSGVTIAQGGVLPNI 231
           +EL+ L+   TIA GGVLP+I
Sbjct: 173 DELDSLI-RATIASGGVLPHI 192

>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 = 96.8 bits (239), Expect = 2e-23
 Identities = 44/85 (51%), Positives = 54/85 (63%)

Query: 386 RKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKD 445
           RKE+Y+ YIYKVLKQ HPDTG+S K+MSI+NSFVNDIFERIA E+S+LA YNK+STI+  
Sbjct: 1   RKETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAR 60

Query: 446 LCPSVCLYSYTLYERTCVTLWACTH 470
              +                     
Sbjct: 61  EIQTAVRLILPGELAKHAVSEGTRA 85

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

 Score =  172 bits (436), Expect = 2e-52
 Identities = 111/120 (92%), Positives = 116/120 (96%)

Query: 5   KSSGKAVKKAGKAQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSF 64
           K+SGKA KKAGKAQKNI K+DKKKK +RKESYAIYIY VLKQVHPDTG+SSKAMSIMNSF
Sbjct: 4   KTSGKAAKKAGKAQKNITKTDKKKKRKRKESYAIYIYTVLKQVHPDTGISSKAMSIMNSF 63

Query: 65  VNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 124
           VNDIFERIAAE+SRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
Sbjct: 64  VNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 123

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

 Score =  112 bits (280), Expect = 7e-30
 Identities = 77/86 (89%), Positives = 82/86 (95%)

Query: 359 KSSGKAVKKAGKAQKNITKSDKKKKPRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSF 418
           K+SGKA KKAGKAQKNITK+DKKKK +RKESYAIYIY VLKQVHPDTG+SSKAMSIMNSF
Sbjct: 4   KTSGKAAKKAGKAQKNITKTDKKKKRKRKESYAIYIYTVLKQVHPDTGISSKAMSIMNSF 63

Query: 419 VNDIFERIAAESSRLAHYNKRSTITK 444
           VNDIFERIAAE+SRLAHYNKRSTIT 
Sbjct: 64  VNDIFERIAAEASRLAHYNKRSTITS 89

>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 =  158 bits (401), Expect = 3e-47
 Identities = 99/126 (78%), Positives = 104/126 (82%), Gaps = 2/126 (1%)

Query: 1   MAAGKSSGKAVKKAGK--AQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAM 58
           M     S  A KK  K    K   K DKK+K  RKESY+IY+YKVLKQVHPDTG+SSKAM
Sbjct: 1   MPEPAKSAPAPKKGSKKAVTKTQKKGDKKRKKSRKESYSIYVYKVLKQVHPDTGISSKAM 60

Query: 59  SIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT 118
            IMNSFVNDIFERIA E+SRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
Sbjct: 61  GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT 120

Query: 119 KYTSSK 124
           KYTSSK
Sbjct: 121 KYTSSK 126

>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 = 99.9 bits (248), Expect = 2e-25
 Identities = 64/92 (69%), Positives = 69/92 (75%), Gaps = 2/92 (2%)

Query: 355 MAAGKSSGKAVKKAGK--AQKNITKSDKKKKPRRKESYAIYIYKVLKQVHPDTGVSSKAM 412
           M     S  A KK  K    K   K DKK+K  RKESY+IY+YKVLKQVHPDTG+SSKAM
Sbjct: 1   MPEPAKSAPAPKKGSKKAVTKTQKKGDKKRKKSRKESYSIYVYKVLKQVHPDTGISSKAM 60

Query: 413 SIMNSFVNDIFERIAAESSRLAHYNKRSTITK 444
            IMNSFVNDIFERIA E+SRLAHYNKRSTIT 
Sbjct: 61  GIMNSFVNDIFERIAGEASRLAHYNKRSTITS 92

>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 =  155 bits (392), Expect = 1e-45
 Identities = 103/133 (77%), Positives = 110/133 (82%), Gaps = 1/133 (0%)

Query: 103 GELAKHAVSEGTKAVTKYTSSKGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAE 161
           G    H             S +GK GGKA+ K+KTRSSRAGLQFPVGR+HRLLRKGNY+E
Sbjct: 2   GSSHHHHHHSSGLVPRGSMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSE 61

Query: 162 RVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVT 221
           RVGAGAPVYLAAV+EYL AE+LELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLL  VT
Sbjct: 62  RVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVT 121

Query: 222 IAQGGVLPNIQAV 234
           IAQGGVLPNIQAV
Sbjct: 122 IAQGGVLPNIQAV 134

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

 Score =  151 bits (383), Expect = 9e-45
 Identities = 106/113 (93%), Positives = 110/113 (97%)

Query: 122 SSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE 181
           S +GKGGK K K+K+RS+RAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE
Sbjct: 1   SGRGKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE 60

Query: 182 VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV 234
           VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV
Sbjct: 61  VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV 113

>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 =  150 bits (380), Expect = 3e-44
 Identities = 101/114 (88%), Positives = 108/114 (94%), Gaps = 1/114 (0%)

Query: 122 SSKGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA 180
           S +GK GGKA+ K+K+RSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL A
Sbjct: 2   SGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA 61

Query: 181 EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV 234
           E+LELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLL  VTIAQGGVLPNIQAV
Sbjct: 62  EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAV 115

>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 =  147 bits (371), Expect = 4e-43
 Identities = 69/110 (62%), Positives = 87/110 (79%)

Query: 125 GKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLE 184
            +GGK K+   +RS++AG+ FPVGR+ R ++KG+   R+G GAPVY+AAV+EYL AE+LE
Sbjct: 3   SRGGKKKSTKTSRSAKAGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILE 62

Query: 185 LAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV 234
           LA NAARDNKK R+ PRH+ LA+ NDEELN+LL GVTIA GGVLPNI   
Sbjct: 63  LAVNAARDNKKGRVTPRHILLAVANDEELNQLLKGVTIASGGVLPNIHPE 112

>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 =  140 bits (354), Expect = 2e-40
 Identities = 86/110 (78%), Positives = 98/110 (89%)

Query: 125 GKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLE 184
           GK G A   S++RS++AGL FPVGR+HRLLR+GNYA+R+G+GAPVYL AV+EYLAAE+LE
Sbjct: 6   GKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILE 65

Query: 185 LAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV 234
           LAGNAARDNKKTRIIPRHLQLAIRND+ELNKLL  VTIAQGGVLPNI   
Sbjct: 66  LAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQN 115

>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 =  127 bits (319), Expect = 2e-35
 Identities = 69/113 (61%), Positives = 82/113 (72%), Gaps = 2/113 (1%)

Query: 123 SKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAER-VGAGAPVYLAAVMEYLAAE 181
           +    GKAKTK+ +RS RAGLQFPVGRIHR L+    +   VGA A VY AA++EYL AE
Sbjct: 6   AGKDSGKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAE 65

Query: 182 VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV 234
           VLELAGNA++D K  RI PRHLQLAIR DEEL+ L+   TIA GGV+P+I   
Sbjct: 66  VLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLI-KATIAGGGVIPHIHKS 117

>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 = 84.9 bits (210), Expect = 2e-20
 Identities = 14/77 (18%), Positives = 33/77 (42%)

Query: 136 TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKK 195
           ++  +   +FP  RI ++++      +V A  PV ++  +E     +L+ A    +    
Sbjct: 3   SKKKKYNARFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNA 62

Query: 196 TRIIPRHLQLAIRNDEE 212
             +   HL+  I  + +
Sbjct: 63  KTMTTSHLKQCIELEGD 79

>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 = 72.9 bits (178), Expect = 1e-13
 Identities = 39/174 (22%), Positives = 77/174 (44%), Gaps = 28/174 (16%)

Query: 40  IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL 99
           + KV  QVHP    +  A+  +   +  +   +     R          ++ +++  V+ 
Sbjct: 27  LKKVQGQVHPTLESNDDALQYVEELILQLLNMLCQAQPR----------SASDVEERVQK 76

Query: 100 LLPGELAKHAVSEGTKAVTKYTSSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNY 159
             P  + K A+++   A+ K                 R  R  L  PV +IH LL++   
Sbjct: 77  SFPHPIDKWAIADAQSAIEK-----------------RKRRNPLSLPVEKIHPLLKEVL- 118

Query: 160 AERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEEL 213
             ++     VY+ AV+EY++A++L+L GN  R+ +   I  + +++A+  D+ L
Sbjct: 119 GYKIDHQVSVYIVAVLEYISADILKLVGNYVRNIRHYEITKQDIKVAMCADKVL 172

>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 = 64.5 bits (156), Expect = 4e-11
 Identities = 65/477 (13%), Positives = 125/477 (26%), Gaps = 160/477 (33%)

Query: 42  KVLKQVHPDTGV-------SSKAMSIMNSFVND--------IFERIAAESSRLAHYNKRS 86
            ++      +G         SK   ++  FV +        +   I  E        + S
Sbjct: 53  HIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTE------QRQPS 106

Query: 87  TITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSKGKGGKAKTKSKTRSSRAGLQFP 146
            +T   I+   RL               +   KY  S+ +                   P
Sbjct: 107 MMTRMYIEQRDRL-----------YNDNQVFAKYNVSRLQ-------------------P 136

Query: 147 VGRIHRLLRKGNYAERV------GAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIP 200
             ++ + L +   A+ V      G+G           +A +V           K    + 
Sbjct: 137 YLKLRQALLELRPAKNVLIDGVLGSGKTW--------VALDVC-------LSYKVQCKMD 181

Query: 201 RH---LQLAIRNDEE-----LNKLLSGVTIAQGGVLPNIQAVRVLEQTHQVGLASLLQGH 252
                L L   N  E     L KLL  +         +   +++   + Q  L  LL+  
Sbjct: 182 FKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK 241

Query: 253 -HGRALEAQRVDDVHGGDGLSLGVLGVGDGVADHVLEEHLENATGLLVDESGNTLDSTST 311
            +   L             L   VL     V +    +          + S   L   +T
Sbjct: 242 PYENCL-------------L---VL---LNVQN---AKAWN-----AFNLSCKIL--LTT 272

Query: 312 RQTTDGGLGDSLDV--VTEYFPVPLGASFS--ESLS------SLTTADL---------LS 352
           R      + D L     T         + +  E  S           DL           
Sbjct: 273 R---FKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRR 329

Query: 353 ITMAAGKSSGKAVKKAGKAQ-KNITKSDKKKKPR-RKESYAIYIYKVLKQ------VHP- 403
           +++ A         + G A   N    +  K     + S  +      ++      V P 
Sbjct: 330 LSIIA------ESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPP 383

Query: 404 DTGVSSKAMSIM--NSFVNDIFERIAAESSRLAHYNKRSTITKDLCPSVCLYSYTLY 458
              + +  +S++  +   +D+   +  +        K S + K         + ++ 
Sbjct: 384 SAHIPTILLSLIWFDVIKSDV-MVVVNKLH------KYSLVEKQPKE----STISIP 429

>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 = 42.9 bits (100), Expect = 2e-04
 Identities = 34/248 (13%), Positives = 72/248 (29%), Gaps = 69/248 (27%)

Query: 19  KNIAKSDKKKKHR-RKESYAIYIYKVLKQ------VHP-DTGVSSKAMSIM--NSFVNDI 68
            N    +  K     + S  +      ++      V P    + +  +S++  +   +D+
Sbjct: 345 DNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDV 404

Query: 69  FERIAAE---SSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSKG 125
              +  +    S +    K STI+   I   +++ L  E A H        V  Y   K 
Sbjct: 405 -MVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHR-----SIVDHYNIPKT 458

Query: 126 KGGKAKT--------------------------------------KSKTRSSRAGLQFPV 147
                                                        + K R          
Sbjct: 459 FDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASG 518

Query: 148 GRIHRLLRKGNYAERVGAGAPVY---LAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQ 204
             ++ L +   Y   +    P Y   + A++++L     ++  N     K T +    L+
Sbjct: 519 SILNTLQQLKFYKPYICDNDPKYERLVNAILDFL----PKIEENLICS-KYTDL----LR 569

Query: 205 LAIRNDEE 212
           +A+  ++E
Sbjct: 570 IALMAEDE 577

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

 Score = 52.3 bits (125), Expect = 6e-09
 Identities = 15/70 (21%), Positives = 31/70 (44%)

Query: 144 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHL 203
           + P+ RI ++++     + + A APV  A   +    E+   A     DNK+  +    +
Sbjct: 19  ELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDI 78

Query: 204 QLAIRNDEEL 213
            +AI   ++ 
Sbjct: 79  AMAITKFDQF 88

>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 = 2e-04
 Identities = 8/88 (9%), Positives = 25/88 (28%), Gaps = 2/88 (2%)

Query: 128 GKAKTKSKTRSSRAG-LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELA 186
           G+ +++             P+ R+  +++       +       +    E     +   A
Sbjct: 2   GEPRSQPPVERPPTAETFLPLSRVRTIMKSSMDTGLITNEVLFLMTKCTELFVRHLAGAA 61

Query: 187 GNAARDNKKTRII-PRHLQLAIRNDEEL 213
                  +    +   HL   +  ++ L
Sbjct: 62  YTEEFGQRPGEALKYEHLSQVVNKNKNL 89

>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 = 40.8 bits (94), Expect = 5e-04
 Identities = 17/98 (17%), Positives = 36/98 (36%), Gaps = 4/98 (4%)

Query: 5   KSSGKAVKKAGKAQKNIAKSDKKKKHRRKESYAIYIYKV----LKQVHPDTGVSSKAMSI 60
             +G+ V+  G  +   A +  K K  +  S    I  +             +S      
Sbjct: 127 LKTGEIVEDNGHIKTLTANNSTKDKRTKYTSVLRDIIDISDEEDGDKGGVKRISGLIYEE 186

Query: 61  MNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR 98
           + + +    E +  +S     + KR T+TS ++  A++
Sbjct: 187 VRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALK 224

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	475
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	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
2nqb_D	123	Histone H2B; nucleosome, NCP, chromatin, structura	100.0
1id3_C	131	Histone H2A.1; nucleosome core particle, chromatin	100.0
1tzy_A	129	Histone H2A-IV; histone-fold, tetramer-dimer-dimer	100.0
1tzy_B	126	Histone H2B; histone-fold, tetramer-dimer-dimer, D	100.0
2f8n_K	149	Histone H2A type 1; nucleosome, NCP, macroh2A, his	100.0
1f66_C	128	Histone H2A.Z; nucleosome, chromatin, histone vari	100.0
1tzy_B	126	Histone H2B; histone-fold, tetramer-dimer-dimer, D	100.0
2nqb_D	123	Histone H2B; nucleosome, NCP, chromatin, structura	100.0
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	99.85
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	99.72
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	99.61
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	99.49
4g92_C	119	HAPE; transcription factor, nucleosome, minor groo	99.45
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	99.28
1tzy_D	103	Histone H4-VI; histone-fold, tetramer-dimer-dimer,	99.13
2yfw_B	103	Histone H4, H4; cell cycle, kinetochore, centromer	99.1
3b0c_W	76	CENP-W, centromere protein W; histone fold, DNA bi	99.09
3b0c_W	76	CENP-W, centromere protein W; histone fold, DNA bi	99.05
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	98.43
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	98.24
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	98.24
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	98.17
1tzy_D	103	Histone H4-VI; histone-fold, tetramer-dimer-dimer,	97.74
2yfw_B	103	Histone H4, H4; cell cycle, kinetochore, centromer	97.7
1id3_B	102	Histone H4; nucleosome core particle, chromatin, p	97.56
1n1j_A	93	NF-YB; histone-like PAIR, DNA binding protein; 1.6	97.51
1id3_B	102	Histone H4; nucleosome core particle, chromatin, p	97.27
1dbh_A	354	Protein (human SOS 1); guanine nucleotide exchange	97.26
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	97.21
2hue_C	84	Histone H4; mini beta sheet, elongated beta sandwh	97.15
2byk_B	128	Chrac-14; nucleosome sliding, histone fold, DNA-bi	97.11
1n1j_A	93	NF-YB; histone-like PAIR, DNA binding protein; 1.6	97.03
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	96.96
1jfi_B	179	DR1 protein, transcription regulator NC2 beta chai	96.84
1id3_C	131	Histone H2A.1; nucleosome core particle, chromatin	96.82
1taf_B	70	TFIID TBP associated factor 62; transcription init	96.79
2hue_C	84	Histone H4; mini beta sheet, elongated beta sandwh	96.76
2nqb_C	123	Histone H2A; nucleosome, NCP, chromatin, structura	96.61
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	96.52
2byk_B	128	Chrac-14; nucleosome sliding, histone fold, DNA-bi	96.4
2f8n_G	120	Core histone macro-H2A.1; nucleosome, NCP, macroh2	96.21
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	96.12
1f66_C	128	Histone H2A.Z; nucleosome, chromatin, histone vari	96.03
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	96.01
4g92_C	119	HAPE; transcription factor, nucleosome, minor groo	96.01
1tzy_A	129	Histone H2A-IV; histone-fold, tetramer-dimer-dimer	95.97
2f8n_K	149	Histone H2A type 1; nucleosome, NCP, macroh2A, his	95.95
1taf_B	70	TFIID TBP associated factor 62; transcription init	95.85
1taf_A	68	TFIID TBP associated factor 42; transcription init	95.85
1jfi_B	179	DR1 protein, transcription regulator NC2 beta chai	95.81
2hue_B	77	Histone H3; mini beta sheet, elongated beta sandwh	95.75
3v9r_A	90	MHF1, uncharacterized protein YOL086W-A; histone f	95.68
1h3o_B	76	Transcription initiation factor TFIID 20/15 kDa su	95.59
1taf_A	68	TFIID TBP associated factor 42; transcription init	95.51
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	95.31
1tzy_C	136	Histone H3; histone-fold, tetramer-dimer-dimer, DN	94.96
3v9r_A	90	MHF1, uncharacterized protein YOL086W-A; histone f	94.87
4dra_A	113	Centromere protein S; DNA binding complex, DNA dam	94.71
3b0b_B	107	CENP-S, centromere protein S; histone fold, DNA bi	94.58
3nqj_A	82	Histone H3-like centromeric protein A; alpha helix	94.46
2yfv_A	100	Histone H3-like centromeric protein CSE4; cell cyc	94.4
3b0b_B	107	CENP-S, centromere protein S; histone fold, DNA bi	94.36
3vh5_A	140	CENP-S; histone fold, chromosome segregation, DNA	94.12
4dra_A	113	Centromere protein S; DNA binding complex, DNA dam	93.91
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	93.68
3nqj_A	82	Histone H3-like centromeric protein A; alpha helix	93.56
3jv3_A	283	Intersectin-1; SH3 domain, DH domain, guanine nucl	93.46
2hue_B	77	Histone H3; mini beta sheet, elongated beta sandwh	93.38
2ly8_A	121	Budding yeast chaperone SCM3; centromere protein,	93.34
3vh5_A	140	CENP-S; histone fold, chromosome segregation, DNA	93.15
2dfk_A	402	Collybistin II; DH domain, PH domain, cell cycle;	92.89
3nqu_A	140	Histone H3-like centromeric protein A; alpha helix	92.75
3r45_A	156	Histone H3-like centromeric protein A; histone fol	92.63
3nqu_A	140	Histone H3-like centromeric protein A; alpha helix	92.45
3r45_A	156	Histone H3-like centromeric protein A; histone fol	92.45
1txd_A	385	RHO guanine nucleotide exchange factor 12; helical	92.43
3jzy_A	510	Intersectin 2; C2 domain, structural genomics cons	92.37
2yfv_A	100	Histone H3-like centromeric protein CSE4; cell cyc	92.13
1tzy_C	136	Histone H3; histone-fold, tetramer-dimer-dimer, DN	91.52
2z0q_A	346	XPLN, RHO guanine nucleotide exchange factor 3; DH	91.27
1bh9_B	89	TAFII28; histone fold, tata binding protein, trans	89.88
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	89.79
2ly8_A	121	Budding yeast chaperone SCM3; centromere protein,	89.73
1foe_A	377	T-lymphoma invasion and metastasis inducing protei	89.22
2pz1_A	466	RHO guanine nucleotide exchange factor 4; helical	89.1
1h3o_B	76	Transcription initiation factor TFIID 20/15 kDa su	86.79
2vrw_B	406	P95VAV, VAV1, proto-oncogene VAV; lipoprotein, GTP	85.9
1by1_A	209	Protein (PIX); RHO-GTPase exchange factor, transpo	85.63
1nty_A	311	Triple functional domain protein; DBL, pleckstrin,	85.47
3p6a_A	377	RHO guanine nucleotide exchange factor 1; regulati	84.94
3b0b_C	81	CENP-X, centromere protein X; histone fold, DNA bi	83.93
4dra_E	84	Centromere protein X; DNA binding complex, DNA dam	83.64
2rgn_B	354	RHOA/RAC/CDC42 exchange factor; heterotrimeric G-p	83.29
3mpx_A	434	FYVE, rhogef and PH domain-containing protein 5; s	82.76
1xcg_A	368	PDZ-rhogef, RHO guanine nucleotide exchange factor	82.02
3odw_A	536	RHO guanine nucleotide exchange factor 1; regulati	80.28

>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=2.3e-63  Score=470.61  Aligned_cols=191  Identities=71%  Similarity=1.070  Sum_probs=184.1

Q ss_pred             CchhHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHHHHHH
Q psy17765         32 RKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVS  111 (475)
Q Consensus        32 ~~~sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaKhAvs  111 (475)
                      ++++|++||||||||||||++||++||++||+|++|+|+||+.||++|+.+++++|||++|||+||+++|||+|+|||++
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            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhhhhhccccCCCCCCCCCCccCcCCCCCcccchhHHHHHHhhcCcc-cccCCChhHHHHHHHHHHHHHHHHHHhHHH
Q psy17765        112 EGTKAVTKYTSSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYA-ERVGAGAPVYLAAVMEYLAAEVLELAGNAA  190 (475)
Q Consensus       112 eG~kAV~ky~sSkg~~~k~~~~~~srSsRagL~FPVsRi~r~Lke~~~~-~RI~~~A~VYLaAVLEYLtaEILELAgn~A  190 (475)
                      +|++|+++|++++        +.+++|+|+||||||+||+|||++++++ +||+++|+|||+||||||++||||+|||+|
T Consensus        81 eG~kAv~k~~~sk--------~~~s~s~ragl~fPv~ri~R~lk~~~~a~~Rv~~~A~vyLaavLEyl~~eIlelA~n~a  152 (192)
T 2jss_A           81 EGTRAVTKYSSST--------QAQSSSARAGLQFPVGRIKRYLKRHATGRTRVGSKAAIYLTAVLEYLTAEVLELAGNAA  152 (192)
T ss_dssp             HHHHHHHHHHHHC--------SSSCHHHHSSCCSCHHHHHHHHHHTTCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhcccc--------ccccccccCCCcCCHHHHHHHHHhcCccccccccChHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999998874        2458999999999999999999999886 799999999999999999999999999999


Q ss_pred             HhcCCcccchhHHHHHHhccHHHHhhhcCceecCCcccCCc
Q psy17765        191 RDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNI  231 (475)
Q Consensus       191 ~~~k~~rItP~hI~lAI~nD~EL~~Lf~~~tIa~gGV~p~i  231 (475)
                      +++++++|+|+||++||+||+|||.||+ +||++|||+|+|
T Consensus       153 ~~~~~~~I~p~~i~lAi~nD~eL~~L~~-~ti~~ggv~p~i  192 (192)
T 2jss_A          153 KDLKVKRITPRHLQLAIRGDDELDSLIR-ATIASGGVLPHI  192 (192)
T ss_dssp             HHHTCSSCCHHHHHHHHHTSHHHHHHHC-SCCTTTCCSSCC
T ss_pred             HhcCCCccCHHHHHHHHhccHHHHHHHh-hhhcCCCcCCCC
Confidence            9999999999999999999999999996 699999999997

>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=100.00  E-value=1.1e-44  Score=412.63  Aligned_cols=266  Identities=21%  Similarity=0.306  Sum_probs=228.2

Q ss_pred             ccccCchhHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHH
Q psy17765         28 KKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAK  107 (475)
Q Consensus        28 ~~~k~~~sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaK  107 (475)
                      -..||++.|...|+||+.||||++++..+|+.++++++.+++..||.       .   .+.|+.||+.+|..+||++|++
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~---~~~~~~~~~~~~~~~~~~~~~~   84 (1049)
T 3ksy_A           15 NAPKWRGLLVPALKKVQGQVHPTLESNDDALQYVEELILQLLNMLCQ-------A---QPRSASDVEERVQKSFPHPIDK   84 (1049)
T ss_dssp             CCTTSSSSSHHHHHHHHHHHCTTSBCCHHHHHHHHHHHHHHHHHHHH-------T---CCCSHHHHHHHHHHHSCTTHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHhCCCCCccHhHHHHHHHHHHHHHHHHhc-------C---CCccHHHHHHHHHHhCCCchHH
Confidence            36799999999999999999999999999999999999988877653       3   3459999999999999999999


Q ss_pred             HHHHHhhhhhhhccccCCCCCCCCCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHh
Q psy17765        108 HAVSEGTKAVTKYTSSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAG  187 (475)
Q Consensus       108 hAvseG~kAV~ky~sSkg~~~k~~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAg  187 (475)
                      ||+.++..++..                 +|+|||||||||||||+| +|+|++||+++||||||||||||++|||||||
T Consensus        85 ~~~~~~~~~~~~-----------------~~~~~~l~~pv~~~~~~l-~~~~~~r~~~~~~~y~~avleyl~~~~l~la~  146 (1049)
T 3ksy_A           85 WAIADAQSAIEK-----------------RKRRNPLSLPVEKIHPLL-KEVLGYKIDHQVSVYIVAVLEYISADILKLVG  146 (1049)
T ss_dssp             HHHHHHHHHHTT-----------------CCCSSSCSSCHHHHHHHH-HHHHCSCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhc-----------------ccccCCccccHHHHHHHh-hcccccccCCCCcchhHHHHHHHHHHHHHHHH
Confidence            999999888764                 788999999999999999 89999999999999999999999999999999


Q ss_pred             HHHHhcCCcccchhHHHHHHhccHHHHhhhcCceecCCcccCCccccccccccccccccccccCCCCCccccccccccCC
Q psy17765        188 NAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQTHQVGLASLLQGHHGRALEAQRVDDVHG  267 (475)
Q Consensus       188 n~A~~~k~~rItP~hI~lAI~nD~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  267 (475)
                      |+|+++++.+|+|+||++||+||+||+.||++.. ..+|++|...                                   
T Consensus       147 ~~~~~~~~~~i~p~~~~~ai~~d~eL~~l~~~de-e~~~~lp~~~-----------------------------------  190 (1049)
T 3ksy_A          147 NYVRNIRHYEITKQDIKVAMCADKVLMDMFHQDV-EDINILSLTD-----------------------------------  190 (1049)
T ss_dssp             HHHHHTTCCBCCHHHHHHHHHHCSSHHHHCC-------------------------------------------------
T ss_pred             HHHHHcCCceecCccccccccCCHHHHHHHhhcc-ccccCCCCcc-----------------------------------
Confidence            9999999999999999999999999999997542 3445555311                                   


Q ss_pred             CCCCcccccccccchhhh----------------hhHHHHHHhcccccc-----ccccccccccccccccCCcchhhhhc
Q psy17765        268 GDGLSLGVLGVGDGVADH----------------VLEEHLENATGLLVD-----ESGNTLDSTSTRQTTDGGLGDSLDVV  326 (475)
Q Consensus       268 ~~~~~~g~l~~~~~v~d~----------------Vfre~l~~~~~l~~~-----~f~n~ld~~e~~~~~~g~leD~le~~  326 (475)
                      +++.+.+.++|.++|.++                +|.++|....+++.+     ||+||-+|+++.+.|+..|++.+++.
T Consensus       191 ~~~~~~~~~~~revI~ELi~TE~~YV~~L~~l~~~y~~pL~~~~~~l~~~~~~~IF~Ni~~I~~~h~~fL~~Le~~~~~~  270 (1049)
T 3ksy_A          191 EEPSTSGEQTYYDLVKAFMAEIRQYIRELNLIIKVFREPFVSNSKLFSANDVENIFSRIVDIHELSVKLLGHIEDTVEMT  270 (1049)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHCTTTSCHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             ccCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCccCCCHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhcc
Confidence            123345678888888776                788888876555554     99999999999999999999999998


Q ss_pred             cccCCCCcccchhhhccccccchhhhhhhcc
Q psy17765        327 TEYFPVPLGASFSESLSSLTTADLLSITMAA  357 (475)
Q Consensus       327 ~e~~~~p~~gs~fe~la~~~~~~~~~~~m~~  357 (475)
                      +++.+.+.+|.||.++++...|++|+.|...
T Consensus       271 ~~~~~~~~IgdiFl~~~~~~~F~~Y~~Yc~n  301 (1049)
T 3ksy_A          271 DEGSPHPLVGSCFEDLAEELAFDPYESYARD  301 (1049)
T ss_dssp             CSSSSSCCCHHHHHHHHHTTTTSHHHHHHHH
T ss_pred             ccCCchhhHHHHHHHHHHHhhhhHHHHHHHh
Confidence            8877889999999999998899999999765

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

Probab=100.00  E-value=3.6e-40  Score=292.30  Aligned_cols=117  Identities=91%  Similarity=1.282  Sum_probs=105.1

Q ss_pred             CCCCCCCCCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHH
Q psy17765        124 KGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHL  203 (475)
Q Consensus       124 kg~~~k~~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI  203 (475)
                      +|+|+|.+++.+|+|+||||||||+||+|||++++|++||+++|+|||+||||||++||||+|+|+|+++++++|+|+||
T Consensus         3 ~~~~~~~~~~~~s~s~ragL~fPV~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hi   82 (123)
T 2nqb_C            3 RGKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHL   82 (123)
T ss_dssp             ----------CCCHHHHHTCSSCHHHHHHHHHHTTSCSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHH
T ss_pred             CCCCCCCCCCCCCccccCCeeccHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHH
Confidence            35667777788999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhccHHHHhhhcCceecCCcccCCcccccccccc
Q psy17765        204 QLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT  240 (475)
Q Consensus       204 ~lAI~nD~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~  240 (475)
                      ++||+||+|||.||+++||++|||+|+||++|+|+++
T Consensus        83 ~lAI~nDeEL~~Ll~~vtia~ggvlp~i~~~l~~k~~  119 (123)
T 2nqb_C           83 QLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKT  119 (123)
T ss_dssp             HHHHHTSHHHHHHTTTEEETTCCCCCCCCGGGSSCC-
T ss_pred             HHHHhccHHHHHHhcCceeCCCCcCCCccHHHcCccc
Confidence            9999999999999999999999999999999999987

>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=4.4e-40  Score=290.62  Aligned_cols=115  Identities=60%  Similarity=0.964  Sum_probs=106.5

Q ss_pred             CCCCCCCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHH
Q psy17765        126 KGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQL  205 (475)
Q Consensus       126 ~~~k~~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~l  205 (475)
                      +|||++++.+|+|+||||||||+||+|||++++|++||+++|+|||+||||||++||||+|+|+|+++++++|+|+||++
T Consensus         4 ~~~~~~~~~~srs~ragLqfPV~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~~rItp~hi~l   83 (120)
T 2f8n_G            4 RGGKKKSTKTSRSAKAGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILL   83 (120)
T ss_dssp             ------CCCCCHHHHHTCSSCHHHHHHHHHHHSSSCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHH
T ss_pred             CCCCCCcCCcCcccccCccCChHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHH
Confidence            34666677889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhccHHHHhhhcCceecCCcccCCcccccccccc
Q psy17765        206 AIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT  240 (475)
Q Consensus       206 AI~nD~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~  240 (475)
                      ||+||+|||.||+++||++|||+|+||++|+|+++
T Consensus        84 AI~nDeEL~~Ll~~vtia~ggv~p~i~~~l~~k~~  118 (120)
T 2f8n_G           84 AVANDEELNQLLKGVTIASGGVLPNIHPELLAKKR  118 (120)
T ss_dssp             HHHTSHHHHHHTTTEEETTCCCCCCCCGGGSCCC-
T ss_pred             HHhcCHHHHHHhCCceECCCCcCCCcCHHHcCCcc
Confidence            99999999999999999999999999999999986

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

Probab=100.00  E-value=7.4e-40  Score=288.14  Aligned_cols=120  Identities=90%  Similarity=1.169  Sum_probs=92.7

Q ss_pred             CCCC--cchhhhhhccccccccccccccccCchhHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy17765          4 GKSS--GKAVKKAGKAQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAH   81 (475)
Q Consensus         4 m~~k--~~~~~k~gka~~~~~~~~kk~~~k~~~sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~   81 (475)
                      |||+  .+++++.+|+..+..++++|++++++++|+.||||||||||||++||++||++||+||+||||||+.||++|++
T Consensus         1 ~~~~~~~~~~k~~~~~~~~~~~~~~k~~~~~~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~   80 (123)
T 2nqb_D            1 IPPKTSGKAAKKAGKAQKNITKTDKKKKRKRKESYAIYIYTVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAH   80 (123)
T ss_dssp             ----------------------------CCCCCCSHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcccccccccccccCCCCCCCCccccchHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6776  34444555554444456677788899999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCChHHHHHHHHHhCcHHHHHHHHHHhhhhhhhcccc
Q psy17765         82 YNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS  123 (475)
Q Consensus        82 ~~kr~TlT~rdIqtAVrllLPgeLaKhAvseG~kAV~ky~sS  123 (475)
                      +|+|+|||+||||+||||+|||||+|||++||++||++|+++
T Consensus        81 ~nkr~TitsreIqtAvrLlLpGELaKhAvseGtkAV~ky~ss  122 (123)
T 2nqb_D           81 YNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS  122 (123)
T ss_dssp             HTTCCEECHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             hcCCCcCCHHHHHHHHHHhCcHHHHHHHHHHHHHHHhcccCC
Confidence            999999999999999999999999999999999999999876

>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=2.4e-39  Score=289.81  Aligned_cols=115  Identities=74%  Similarity=1.144  Sum_probs=105.1

Q ss_pred             CCCCCCCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHH
Q psy17765        126 KGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQL  205 (475)
Q Consensus       126 ~~~k~~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~l  205 (475)
                      ++++.+++.+|+|+||||||||+||+|||++++|++||+++|+|||+||||||++||||+|+|+|+++++++|+|+||++
T Consensus         7 ~~~~~~~~~~srS~ragLqfPV~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hI~l   86 (131)
T 1id3_C            7 KAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRHLQL   86 (131)
T ss_dssp             ---------CCTTGGGTCSSCHHHHHHHHHTTCSCSEECSSHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHH
T ss_pred             CCCCCCCCCCCccccCCeecCHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHH
Confidence            34555667889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhccHHHHhhhcCceecCCcccCCcccccccccc
Q psy17765        206 AIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT  240 (475)
Q Consensus       206 AI~nD~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~  240 (475)
                      ||+||+|||.||+++||++|||+|+||++|+|+++
T Consensus        87 AI~nDeEL~~Ll~~vtIa~ggvlP~i~~~l~~k~~  121 (131)
T 1id3_C           87 AIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPKKS  121 (131)
T ss_dssp             HHHTCHHHHHHTTTEEETTCCCCCCCCGGGSCCSC
T ss_pred             HHhccHHHHHHhcCceecCCccCCCccHHHcCccc
Confidence            99999999999999999999999999999999988

>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=2.7e-39  Score=288.81  Aligned_cols=114  Identities=87%  Similarity=1.252  Sum_probs=104.9

Q ss_pred             CCCCCCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHH
Q psy17765        127 GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLA  206 (475)
Q Consensus       127 ~~k~~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lA  206 (475)
                      +++.+++.+|+|+|+||||||+||+|||++++|++||+++|+|||+||||||++||||+|+|+|+++++++|+|+||++|
T Consensus         8 ~~~~~~~~~srS~ragLqfPV~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hi~lA   87 (129)
T 1tzy_A            8 GGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLA   87 (129)
T ss_dssp             ------CCCCHHHHHTCSSCHHHHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             CCCCCCCCCCccccCceeccHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEcHHHHHHH
Confidence            45666678899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhccHHHHhhhcCceecCCcccCCcccccccccc
Q psy17765        207 IRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT  240 (475)
Q Consensus       207 I~nD~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~  240 (475)
                      |+||+|||.||+++||++|||+|+||++|+|+++
T Consensus        88 I~nDeEL~~L~~~vtIa~ggvlP~i~~~l~~k~~  121 (129)
T 1tzy_A           88 IRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKT  121 (129)
T ss_dssp             HHTSHHHHHHTTTEEETTCCCCCCCCGGGSCC--
T ss_pred             HhccHHHHHHhCCCeecCCCcCCCCCHHHcCccc
Confidence            9999999999999999999999999999999987

>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=3.7e-39  Score=284.74  Aligned_cols=101  Identities=90%  Similarity=1.223  Sum_probs=91.0

Q ss_pred             cccccccccCchhHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCc
Q psy17765         23 KSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLP  102 (475)
Q Consensus        23 ~~~kk~~~k~~~sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLP  102 (475)
                      ++++|++++++++|++||||||||||||++||++||++|||||+||||||+.||++|+++|+|+|||+||||+||||+||
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            45567778899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhhhhhhcccc
Q psy17765        103 GELAKHAVSEGTKAVTKYTSS  123 (475)
Q Consensus       103 geLaKhAvseG~kAV~ky~sS  123 (475)
                      |||+|||++||++||++|+++
T Consensus       105 GELaKhAvseGtkAV~ky~ss  125 (126)
T 1tzy_B          105 GELAKHAVSEGTKAVTKYTSS  125 (126)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHhcccCC
Confidence            999999999999999999876

>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=1.5e-38  Score=289.63  Aligned_cols=113  Identities=87%  Similarity=1.243  Sum_probs=104.2

Q ss_pred             CCCCCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHH
Q psy17765        128 GKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAI  207 (475)
Q Consensus       128 ~k~~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI  207 (475)
                      +|.+++.+|+|+||||||||+||+||||+++|++||+++|+|||+||||||++||||+|+|+|+++++++|+|+||++||
T Consensus        28 ~~~~~k~~srS~ragLqFPVgrI~R~LK~~~~a~RVs~~A~VyLAAVLEYL~aEILelAgn~A~~~krkrItprhI~lAI  107 (149)
T 2f8n_K           28 GKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAI  107 (149)
T ss_dssp             ------CCCHHHHHTCSSCHHHHHHHHHHTTSCSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHH
T ss_pred             CCCCCCCCCccccCCeeccHHHHHHHHHccccccccCcCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHH
Confidence            56666788999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccHHHHhhhcCceecCCcccCCcccccccccc
Q psy17765        208 RNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT  240 (475)
Q Consensus       208 ~nD~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~  240 (475)
                      +||+|||.||+++||++|||+|+||++|+|+++
T Consensus       108 ~nDeEL~~Ll~~vtIa~gGVlP~i~~~l~~k~~  140 (149)
T 2f8n_K          108 RNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKT  140 (149)
T ss_dssp             HHSHHHHHHTTTEEETTCCCCCCCCGGGSCC--
T ss_pred             hccHHHHHHhcCceEcCCCCCCCccHHHcCccc
Confidence            999999999999999999999999999999987

>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=3.1e-38  Score=281.62  Aligned_cols=112  Identities=63%  Similarity=0.910  Sum_probs=99.5

Q ss_pred             CCCCCCccCcCCCCCcccchhHHHHHHhhcCcc-cccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHH
Q psy17765        128 GKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYA-ERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLA  206 (475)
Q Consensus       128 ~k~~~~~~srSsRagL~FPVsRi~r~Lke~~~~-~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lA  206 (475)
                      ++.+++.+|+|+||||||||+||||||++++|+ +||+++|+|||+||||||++||||+|+|+|+++++++|+|+||++|
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            344556789999999999999999999999987 5999999999999999999999999999999999999999999999


Q ss_pred             HhccHHHHhhhcCceecCCcccCCcccccccccc
Q psy17765        207 IRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT  240 (475)
Q Consensus       207 I~nD~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~  240 (475)
                      |+||+||+.||+ +||++|||+|+||++|+|+++
T Consensus        91 I~nDeEL~~Ll~-~tia~ggv~P~i~~~l~~k~~  123 (128)
T 1f66_C           91 IRGDEELDSLIK-ATIAGGGVIPHIHKSLIGKKG  123 (128)
T ss_dssp             HHHSHHHHHHCC-SEETTCCCCCCCCGGGC----
T ss_pred             HhccHHHhhhhc-ceecCCccCCCCCHHhcCccc
Confidence            999999999996 599999999999999999987

>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=2.2e-35  Score=260.73  Aligned_cols=77  Identities=77%  Similarity=1.061  Sum_probs=66.0

Q ss_pred             ccCCccCcCCCccceeehhhhhccccCCCCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCCcCCCCCc-hhheehc
Q psy17765        377 KSDKKKKPRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDL-CPSVCLY  453 (475)
Q Consensus       377 ~~~~k~~~~~~esy~~Yi~kvLkqvhp~~giS~kam~imnsfv~Diferia~Eas~L~~~~kr~Tltsr~-~~~~~~~  453 (475)
                      +.++|++++|+|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+|+|||+|| |+||+|+
T Consensus        25 ~~~~k~~~~~~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtAvrLl  102 (126)
T 1tzy_B           25 KGDKKRKKSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLL  102 (126)
T ss_dssp             ---------CCCCCHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             CCCCCccccccccHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            4456677889999999999999999999999999999999999999999999999999999999999986 8899884

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

Probab=100.00  E-value=2.7e-35  Score=259.21  Aligned_cols=92  Identities=84%  Similarity=1.092  Sum_probs=67.7

Q ss_pred             ccchhccccccccccccCCccCcCCCccceeehhhhhccccCCCCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCCcC
Q psy17765        362 GKAVKKAGKAQKNITKSDKKKKPRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRST  441 (475)
Q Consensus       362 ~k~~~~~~~~~~~~~~~~~k~~~~~~esy~~Yi~kvLkqvhp~~giS~kam~imnsfv~Diferia~Eas~L~~~~kr~T  441 (475)
                      .+++++.++......+.++|++++|+|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+|+|
T Consensus         7 ~~~~k~~~~~~~~~~~~~~k~~~~~~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~T   86 (123)
T 2nqb_D            7 GKAAKKAGKAQKNITKTDKKKKRKRKESYAIYIYTVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRST   86 (123)
T ss_dssp             ----------------------CCCCCCSHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCE
T ss_pred             CcccccccccccccCCCCCCCCccccchHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc
Confidence            34444443333222345567778899999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCc-hhheehc
Q psy17765        442 ITKDL-CPSVCLY  453 (475)
Q Consensus       442 ltsr~-~~~~~~~  453 (475)
                      ||+|| |+||+|+
T Consensus        87 itsreIqtAvrLl   99 (123)
T 2nqb_D           87 ITSREIQTAVRLL   99 (123)
T ss_dssp             ECHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHh
Confidence            99986 8899884

>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=99.85  E-value=7.8e-23  Score=193.39  Aligned_cols=68  Identities=68%  Similarity=0.982  Sum_probs=65.1

Q ss_pred             CCccceeehhhhhccccCCCCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCCcCCCCCc-hhheehc
Q psy17765        386 RKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDL-CPSVCLY  453 (475)
Q Consensus       386 ~~esy~~Yi~kvLkqvhp~~giS~kam~imnsfv~Diferia~Eas~L~~~~kr~Tltsr~-~~~~~~~  453 (475)
                      |+|+|+.||||||||||||+|||++||.+|||||+|+|||||.||++|++||+|+|||+|| |+||+|+
T Consensus         1 ~~~~~~~yi~kvLkqv~p~~~iS~~Am~~m~s~v~di~~rIa~eA~~L~~~~~r~Tit~~eIq~Avrl~   69 (192)
T 2jss_A            1 RKETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLI   69 (192)
T ss_dssp             CCSTTHHHHHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCSCCHHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHcccCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHh
Confidence            4799999999999999999999999999999999999999999999999999999999987 7898874

>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=99.72  E-value=4.2e-18  Score=145.27  Aligned_cols=82  Identities=17%  Similarity=0.345  Sum_probs=62.5

Q ss_pred             cCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHHHhh
Q psy17765        137 RSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKL  216 (475)
Q Consensus       137 rSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL~~L  216 (475)
                      ++.+++++||++||+|+||.+.+..||+..|++|+++++|||+.||+++|++.|+++++++|+|+||..||++|++|+.|
T Consensus         4 ~~kk~~~~fPvaRIkrimK~~~~~~~vs~~A~v~la~a~E~Fi~el~~~A~~~a~~~krktI~~~di~~av~~~e~l~FL   83 (98)
T 1jfi_A            4 KKKKYNARFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQCIELEGDPAAN   83 (98)
T ss_dssp             ------CCCCHHHHHHHHTTSTTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC---CBCHHHHHTTCC--------
T ss_pred             cccccCCCCChHHHHHHHHcCccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHhcCchhhHH
Confidence            45688999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hc
Q psy17765        217 LS  218 (475)
Q Consensus       217 f~  218 (475)
                      +.
T Consensus        84 ~d   85 (98)
T 1jfi_A           84 KA   85 (98)
T ss_dssp             --
T ss_pred             Hh
Confidence            85

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

Probab=99.61  E-value=5.7e-15  Score=135.36  Aligned_cols=140  Identities=17%  Similarity=0.219  Sum_probs=126.2

Q ss_pred             HHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHHHHHHHhhhhh
Q psy17765         38 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAV  117 (475)
Q Consensus        38 ~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaKhAvseG~kAV  117 (475)
                      .-|.|++|+.-|...||.+|-.-+...+..+...|+.+|..++...+|+|++..||..|+..+            |   +
T Consensus         8 a~V~Riik~~lg~~rVS~dA~~~l~~~l~~f~~~i~~~A~~~a~ha~RKTv~a~DV~~a~~~l------------g---~   72 (154)
T 1f1e_A            8 AAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADVL------------M---V   72 (154)
T ss_dssp             HHHHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHHH------------T---C
T ss_pred             cHHHHHHHhcCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhc------------c---c
Confidence            458899999888899999999999999999999999999999999999999999998887432            1   1


Q ss_pred             hhccccCCCCCCCCCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcc
Q psy17765        118 TKYTSSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTR  197 (475)
Q Consensus       118 ~ky~sSkg~~~k~~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~r  197 (475)
                      ..|                 -.+.++.||++.|.|+||++ ...||++.|..+|+.+||+++.+|.+.|.++|++.++++
T Consensus        73 ~~v-----------------~d~~~l~lP~a~V~Ri~k~~-g~~RVS~~A~~~l~~~le~f~~~I~~~A~~~a~ha~RKT  134 (154)
T 1f1e_A           73 EGV-----------------EDYDGELFGRATVRRILKRA-GIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKT  134 (154)
T ss_dssp             TTS-----------------TTCCSCCCCHHHHHHHHHHT-TCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSE
T ss_pred             ccC-----------------CccccccCCccHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCc
Confidence            111                 13568999999999999998 788999999999999999999999999999999999999


Q ss_pred             cchhHHHHHHhcc
Q psy17765        198 IIPRHLQLAIRND  210 (475)
Q Consensus       198 ItP~hI~lAI~nD  210 (475)
                      |+++||.+|+.++
T Consensus       135 It~eDV~~Al~~~  147 (154)
T 1f1e_A          135 VQGEDVEKAITYS  147 (154)
T ss_dssp             ECHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHhc
Confidence            9999999999876

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

Probab=99.49  E-value=5.2e-14  Score=119.65  Aligned_cols=78  Identities=21%  Similarity=0.339  Sum_probs=72.2

Q ss_pred             CCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHHHhhhc
Q psy17765        141 AGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLS  218 (475)
Q Consensus       141 agL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL~~Lf~  218 (475)
                      .+++||++||+|+||.+.+..||+..|++|++.++||++.++++.|++.|++.++++|+++||..||++|++|+.|..
T Consensus        16 ~~~~lP~arIkrImK~~~~~~~is~eA~~~laka~E~Fi~~l~~~A~~~a~~~krktI~~~di~~Av~~~e~~~FL~d   93 (97)
T 1n1j_B           16 RVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLID   93 (97)
T ss_dssp             ----CCHHHHHHHHTTSTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTCGGGGGGTT
T ss_pred             CCCcCCHHHHHHHHccCccccccChHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHHhcCcHHHHHHh
Confidence            368999999999999999989999999999999999999999999999999999999999999999999999999884

>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=99.45  E-value=1.3e-13  Score=121.36  Aligned_cols=76  Identities=21%  Similarity=0.319  Sum_probs=72.8

Q ss_pred             CcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHHHhhh
Q psy17765        142 GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLL  217 (475)
Q Consensus       142 gL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL~~Lf  217 (475)
                      ..+||++||+|+||.+.+..+|+..|++|+++++||++.+|++.|++.|++.++++|+|+||..||++|++|+.|-
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            3689999999999999999999999999999999999999999999999999999999999999999999998665

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

Probab=99.28  E-value=2.3e-12  Score=116.45  Aligned_cols=84  Identities=13%  Similarity=0.199  Sum_probs=62.4

Q ss_pred             ccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHH-HhcCCcccchhHHHHHHhccHH
Q psy17765        134 SKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAA-RDNKKTRIIPRHLQLAIRNDEE  212 (475)
Q Consensus       134 ~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A-~~~k~~rItP~hI~lAI~nD~E  212 (475)
                      ..+++.+.+++||++||+|+||.+....+|+..|+++++.++|||+.++.+.|++.| ...++++|+++||..||.++++
T Consensus         9 ~~s~~~~~~~~LPlaRIKrIMK~dpdv~~Is~eA~vliakA~ElFI~~Lt~~A~~~a~~~~kRKtI~~~Dl~~AV~~~e~   88 (140)
T 2byk_A            9 PVERPPTAETFLPLSRVRTIMKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKN   88 (140)
T ss_dssp             --------------------CCSSSSCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHHTCST
T ss_pred             CCCCCcccCCCCCHHHHHHHHhcCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccCHHHHHHHHhcCch
Confidence            356788899999999999999999999999999999999999999999999999999 9999999999999999999999


Q ss_pred             HHhhh
Q psy17765        213 LNKLL  217 (475)
Q Consensus       213 L~~Lf  217 (475)
                      |..|.
T Consensus        89 ~dFL~   93 (140)
T 2byk_A           89 LEFLL   93 (140)
T ss_dssp             TGGGT
T ss_pred             hhhHh
Confidence            99988

>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=99.13  E-value=8.8e-11  Score=100.78  Aligned_cols=78  Identities=17%  Similarity=0.239  Sum_probs=70.4

Q ss_pred             CCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhcc
Q psy17765        131 KTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND  210 (475)
Q Consensus       131 ~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD  210 (475)
                      +.+..++++.++  ||+..|+|+++.+.+ .||+..+..+|+.+|||++.+|++.|.+++++.++++|+|+||.+|+++.
T Consensus        18 r~~k~~r~~~~g--ip~~~I~Rlar~~G~-~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktIt~~DV~~Alr~~   94 (103)
T 1tzy_D           18 RHRKVLRDNIQG--ITKPAIRRLARRGGV-KRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ   94 (103)
T ss_dssp             ---CCCCCGGGG--SCHHHHHHHHHHTTC-CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHT
T ss_pred             ccccchhhhccc--CCHHHHHHHHHHcCc-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHc
Confidence            345568888888  999999999999876 79999999999999999999999999999999999999999999999976


Q ss_pred             H
Q psy17765        211 E  211 (475)
Q Consensus       211 ~  211 (475)
                      .
T Consensus        95 g   95 (103)
T 1tzy_D           95 G   95 (103)
T ss_dssp             T
T ss_pred             C
Confidence            4

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

Probab=99.10  E-value=1.3e-10  Score=99.75  Aligned_cols=79  Identities=16%  Similarity=0.238  Sum_probs=63.4

Q ss_pred             CCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhcc
Q psy17765        131 KTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND  210 (475)
Q Consensus       131 ~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD  210 (475)
                      +.+..++++.++  ||+..|+|+++.+.+ .||+..+..+|+.+|||++.+|++.|.+++++.++++|+|+||.+|+++.
T Consensus        18 r~~~~~r~~~~g--ip~~~I~Rlar~~G~-~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktvt~~DV~~Alr~~   94 (103)
T 2yfw_B           18 RHRKILRDNIQG--ITKPAIRRLARRGGV-KRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQ   94 (103)
T ss_dssp             --------------CCHHHHHHHHHHTTC-CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             chhhhhhhhhcc--CCHHHHHHHHHHcCc-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHc
Confidence            334556888888  999999999999877 79999999999999999999999999999999999999999999999976


Q ss_pred             HH
Q psy17765        211 EE  212 (475)
Q Consensus       211 ~E  212 (475)
                      .+
T Consensus        95 g~   96 (103)
T 2yfw_B           95 GR   96 (103)
T ss_dssp             C-
T ss_pred             CC
Confidence            43

>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=99.09  E-value=9.8e-11  Score=95.21  Aligned_cols=66  Identities=18%  Similarity=0.220  Sum_probs=63.0

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCc
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLP  102 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLP  102 (475)
                      ...|+|++|+++|+..||.+|+..|+.++.+++++|+.||..+|..++|+||+.+||+.|++.+|-
T Consensus         7 ~A~V~rI~K~~~p~~~is~~A~~~i~~~~~~Fi~~la~eA~~~a~~~~rKTI~~~dI~~A~~~ll~   72 (76)
T 3b0c_W            7 RGTLRKIIKKHKPHLRLAANTDLLVHLSFLLFLHRLAEEARTNAFENKSKIIKPEHTIAAAKVILK   72 (76)
T ss_dssp             HHHHHHHHHHHCTTCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSBCHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHhCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHH
Confidence            357999999999999999999999999999999999999999999999999999999999999863

>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=99.05  E-value=2.3e-11  Score=98.96  Aligned_cols=61  Identities=16%  Similarity=0.171  Sum_probs=56.4

Q ss_pred             eehhhhhccccCCCCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCCcCCCCCc-hhheeh
Q psy17765        392 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDL-CPSVCL  452 (475)
Q Consensus       392 ~Yi~kvLkqvhp~~giS~kam~imnsfv~Diferia~Eas~L~~~~kr~Tltsr~-~~~~~~  452 (475)
                      .+|+|++||+|||.+||++|+.+|+.++++++++||.||+.+|++++|.||++++ +.|+..
T Consensus         8 A~V~rI~K~~~p~~~is~~A~~~i~~~~~~Fi~~la~eA~~~a~~~~rKTI~~~dI~~A~~~   69 (76)
T 3b0c_W            8 GTLRKIIKKHKPHLRLAANTDLLVHLSFLLFLHRLAEEARTNAFENKSKIIKPEHTIAAAKV   69 (76)
T ss_dssp             HHHHHHHHHHCTTCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSBCHHHHHHHHHH
T ss_pred             cHHHHHHHHhCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence            4699999999999999999999999999999999999999999999999999987 555543

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

Probab=98.43  E-value=4.9e-07  Score=82.90  Aligned_cols=64  Identities=20%  Similarity=0.285  Sum_probs=60.5

Q ss_pred             ccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHH
Q psy17765        144 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAI  207 (475)
Q Consensus       144 ~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI  207 (475)
                      -+|..-|.|++|++--..||+..|...|+.++|.+..+|...|.++|.+.+++.|+++||..|+
T Consensus         4 ~LP~a~V~Riik~~lg~~rVS~dA~~~l~~~l~~f~~~i~~~A~~~a~ha~RKTv~a~DV~~a~   67 (154)
T 1f1e_A            4 ELPKAAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALA   67 (154)
T ss_dssp             CCCHHHHHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHH
T ss_pred             cCCccHHHHHHHhcCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHH
Confidence            4899999999999855699999999999999999999999999999999999999999999887

>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=98.24  E-value=2e-06  Score=67.93  Aligned_cols=65  Identities=28%  Similarity=0.413  Sum_probs=61.4

Q ss_pred             ccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhc
Q psy17765        144 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN  209 (475)
Q Consensus       144 ~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~n  209 (475)
                      .||..+|.|+||+. ...||++.|...|.-++|++..+|.+-|...|.+.+++.|+|+||+.|++.
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 678999999999999999999999999999999999999999999999863

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

Probab=98.24  E-value=2e-06  Score=68.47  Aligned_cols=66  Identities=32%  Similarity=0.417  Sum_probs=62.0

Q ss_pred             cccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhc
Q psy17765        143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN  209 (475)
Q Consensus       143 L~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~n  209 (475)
                      ..||.+.|+|++|++ -..|++..+...|..++|+++.+|++-|..+|.+.+++.|+++||++|+++
T Consensus         5 ~~lp~a~v~Rl~r~~-g~~ris~~a~~~l~e~~~~~~~~v~~dA~~~a~hakRkTI~~~DV~lA~~~   70 (70)
T 1ku5_A            5 GELPIAPVDRLIRKA-GAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIKS   70 (70)
T ss_dssp             CCSCHHHHHHHHHHT-TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHTC
T ss_pred             ccCChHHHHHHHHHc-CcceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHC
Confidence            368999999999986 468999999999999999999999999999999999999999999999875

>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=98.17  E-value=2.2e-06  Score=67.61  Aligned_cols=62  Identities=26%  Similarity=0.351  Sum_probs=58.3

Q ss_pred             HHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765         38 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  100 (475)
Q Consensus        38 ~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll  100 (475)
                      .-|.|++|++ ++..||++|+..|...+..+++.|+.+|...+...+|+||+.+||+.|++.+
T Consensus         6 a~v~Ri~k~~-~~~ris~~A~~~l~~a~e~fi~~l~~~A~~~a~~~kRkTI~~~Di~~A~~~l   67 (68)
T 1b67_A            6 APIGRIIKNA-GAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARKMF   67 (68)
T ss_dssp             HHHHHHHHHT-TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHGGGG
T ss_pred             cHHHHHHhcC-CcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhc
Confidence            4588999999 8899999999999999999999999999999999999999999999998864

>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=97.74  E-value=5e-05  Score=64.96  Aligned_cols=66  Identities=12%  Similarity=0.120  Sum_probs=60.7

Q ss_pred             hhHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765         34 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  100 (475)
Q Consensus        34 ~sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll  100 (475)
                      +--...|.|+++..-. ..||.++...|...+..+++.|+.+|..++.+++|+|+|.+||+.|++.+
T Consensus        29 gip~~~I~Rlar~~G~-~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktIt~~DV~~Alr~~   94 (103)
T 1tzy_D           29 GITKPAIRRLARRGGV-KRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ   94 (103)
T ss_dssp             GSCHHHHHHHHHHTTC-CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHT
T ss_pred             cCCHHHHHHHHHHcCc-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHc
Confidence            3346889999999876 57999999999999999999999999999999999999999999999975

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

Probab=97.70  E-value=5.2e-05  Score=64.89  Aligned_cols=64  Identities=14%  Similarity=0.167  Sum_probs=59.7

Q ss_pred             HHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765         36 YAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  100 (475)
Q Consensus        36 f~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll  100 (475)
                      =...|.|+++..-. ..||.++.+.|...+..+++.|+.+|..++.+++|+|+|.+||+.|++.+
T Consensus        31 p~~~I~Rlar~~G~-~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktvt~~DV~~Alr~~   94 (103)
T 2yfw_B           31 TKPAIRRLARRGGV-KRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQ   94 (103)
T ss_dssp             CHHHHHHHHHHTTC-CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCc-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHc
Confidence            46789999999876 57999999999999999999999999999999999999999999999976

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

Probab=97.56  E-value=0.0002  Score=61.32  Aligned_cols=72  Identities=18%  Similarity=0.260  Sum_probs=63.1

Q ss_pred             CcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhcc
Q psy17765        136 TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND  210 (475)
Q Consensus       136 srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD  210 (475)
                      .+-+-.+  +|..-|.|+++.+. ..||+..+..-|..++||+..+|+.-|..+++..+++.|+++||..|+...
T Consensus        22 ~r~~i~~--ip~~~I~Rlar~~G-v~rIS~da~~~l~~~le~fi~~I~~dA~~~a~HakRKTVt~~DV~~ALkr~   93 (102)
T 1id3_B           22 LRDNIQG--ITKPAIRRLARRGG-VKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQ   93 (102)
T ss_dssp             --CCGGG--SCHHHHHHHHHHTT-CCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHT
T ss_pred             HHhccCC--CCHHHHHHHHHHcC-chhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHc
Confidence            3443433  89999999999864 489999999999999999999999999999999999999999999999855

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

Probab=97.51  E-value=0.0002  Score=59.85  Aligned_cols=67  Identities=10%  Similarity=0.262  Sum_probs=62.3

Q ss_pred             CcccchhHHHHHHhhc-CcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765        142 GLQFPVGRIHRLLRKG-NYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  208 (475)
Q Consensus       142 gL~FPVsRi~r~Lke~-~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~  208 (475)
                      .+.||.++|.|+||+. ....||+..|...|+-+.|.+..+|.+-|...|.+.+++.|+++||..|+.
T Consensus         6 d~~LP~a~i~ri~K~~~~~~~~is~dA~~~l~~a~e~Fi~~l~~~A~~~a~~~kRkTI~~~Dv~~Al~   73 (93)
T 1n1j_A            6 DIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMS   73 (93)
T ss_dssp             -CCCCHHHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHH
T ss_pred             cccCChhHHHHHHHHhCCccceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHH
Confidence            5899999999999987 345799999999999999999999999999999999999999999999997

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

Probab=97.27  E-value=0.00044  Score=59.19  Aligned_cols=64  Identities=16%  Similarity=0.176  Sum_probs=58.7

Q ss_pred             HHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765         36 YAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  100 (475)
Q Consensus        36 f~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll  100 (475)
                      =...|.|+.+..-+ ..||.++.+.+...+..+++.|+.+|..++.+.+|+|+|..||..|++.+
T Consensus        30 p~~~I~Rlar~~Gv-~rIS~da~~~l~~~le~fi~~I~~dA~~~a~HakRKTVt~~DV~~ALkr~   93 (102)
T 1id3_B           30 TKPAIRRLARRGGV-KRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQ   93 (102)
T ss_dssp             CHHHHHHHHHHTTC-CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHcCc-hhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHc
Confidence            36789999998744 56999999999999999999999999999999999999999999999875

>1dbh_A Protein (human SOS 1); guanine nucleotide exchange factor, gene regulation; 2.30A {Homo sapiens} SCOP: a.87.1.1 b.55.1.1 PDB: 1pms_A 1awe_A

Probab=97.26  E-value=2.7e-05  Score=77.82  Aligned_cols=72  Identities=19%  Similarity=0.165  Sum_probs=63.0

Q ss_pred             hhHHHHHHhcccccc-----ccccccccccccccccCCcchhhhhccccCCCCcccchhhhccccccchhhhhhhcc
Q psy17765        286 VLEEHLENATGLLVD-----ESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAA  357 (475)
Q Consensus       286 Vfre~l~~~~~l~~~-----~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~~~~~~~~~~~m~~  357 (475)
                      +|.++|.....++.+     ||+||-+|+++...|+..|++.+++.+++.+++.+|.||.++++...|++|+.|...
T Consensus        28 ~y~~~l~~~~~~l~~~~~~~iF~ni~~I~~~h~~fl~~L~~~~~~~~~~~~~~~ig~~f~~~~~~~~f~~Y~~Y~~n  104 (354)
T 1dbh_A           28 VFREPFVSNSKLFSANDVENIFSRIVDIHELSVKLLGHIEDTVEMTDEGSPHPLVGSCFEDLAEELAFDPYESYARD  104 (354)
T ss_dssp             TTTHHHHHCTTTCCHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHTCCTTSSSCCCHHHHHHHHHTTTTHHHHHHHHH
T ss_pred             HHHHHHHhCcCCCCHHHHHHHHcCHHHHHHHHHHHHHHHHHHHhccccCCccchHHHHHHHHhHHhhhhHHHHHHHh
Confidence            788888876555554     999999999999999999999999988877889999999999987679999999775

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

Probab=97.21  E-value=0.00065  Score=53.85  Aligned_cols=60  Identities=17%  Similarity=0.330  Sum_probs=55.1

Q ss_pred             HHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHH
Q psy17765         38 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR   98 (475)
Q Consensus        38 ~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVr   98 (475)
                      ..|.|++|.. ....+|.++...+..++..+++.|+.+|...+.+.+|+|++.+||+.|++
T Consensus        10 a~v~Rl~r~~-g~~ris~~a~~~l~e~~~~~~~~v~~dA~~~a~hakRkTI~~~DV~lA~~   69 (70)
T 1ku5_A           10 APVDRLIRKA-GAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIK   69 (70)
T ss_dssp             HHHHHHHHHT-TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHT
T ss_pred             HHHHHHHHHc-CcceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence            3588888886 46789999999999999999999999999999999999999999999875

>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=97.15  E-value=0.0011  Score=54.54  Aligned_cols=65  Identities=17%  Similarity=0.234  Sum_probs=61.1

Q ss_pred             cchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhcc
Q psy17765        145 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND  210 (475)
Q Consensus       145 FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD  210 (475)
                      +|..-|.|+++.+. ..||+..+.--|..++||...+|+.-|..++++.+++.|+++||..|+...
T Consensus        11 ip~~~I~Riar~~G-v~rIs~da~~~l~~~l~~~~~~I~~dA~~~a~ha~RKTvt~~DV~~Alk~~   75 (84)
T 2hue_C           11 ITKPAIRRLARRGG-VKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ   75 (84)
T ss_dssp             SCHHHHHHHHHHTT-CCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTT
T ss_pred             CCHHHHHHHHHHcC-chhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHc
Confidence            78999999999875 489999999999999999999999999999999999999999999999865

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

Probab=97.11  E-value=0.00055  Score=60.80  Aligned_cols=71  Identities=17%  Similarity=0.171  Sum_probs=61.5

Q ss_pred             CcccchhHHHHHHhh-cCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHH
Q psy17765        142 GLQFPVGRIHRLLRK-GNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEE  212 (475)
Q Consensus       142 gL~FPVsRi~r~Lke-~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~E  212 (475)
                      .+.||.++|.|+|++ ..-..+|+..|...|+-+.|.+..+|-..|...|.+.+++.|+++||..|+...+-
T Consensus         7 d~~LP~A~I~rImK~~~pd~~~iS~dA~~~l~ka~e~FI~~lt~~A~~~a~~~kRKTI~~~Dv~~Al~~l~f   78 (128)
T 2byk_B            7 DLNLPNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDF   78 (128)
T ss_dssp             ----CCSHHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTC
T ss_pred             cccCCHHHHHHHHHHhCcccceECHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHcCc
Confidence            578999999999996 44468999999999999999999999999999999999999999999999997653

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

Probab=97.03  E-value=0.0017  Score=54.20  Aligned_cols=66  Identities=23%  Similarity=0.362  Sum_probs=59.6

Q ss_pred             HHHHHHhhccCCC-CCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh-CcH
Q psy17765         38 IYIYKVLKQVHPD-TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL-LPG  103 (475)
Q Consensus        38 ~yI~KVLKQVhPd-~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll-LPg  103 (475)
                      ..|.|+.|..-|+ ..||.+|...|...+..++..|+.+|...|...+|+||+..||..|++.+ |..
T Consensus        12 a~i~ri~K~~~~~~~~is~dA~~~l~~a~e~Fi~~l~~~A~~~a~~~kRkTI~~~Dv~~Al~~l~F~~   79 (93)
T 1n1j_A           12 ANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDS   79 (93)
T ss_dssp             HHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTTCGG
T ss_pred             hHHHHHHHHhCCccceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHcCcHh
Confidence            4689999999775 67999999999999999999999999999999999999999999999865 443

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

Probab=96.96  E-value=0.015  Score=56.46  Aligned_cols=175  Identities=18%  Similarity=0.223  Sum_probs=117.2

Q ss_pred             CchhHHHHHHHHhhccCC---CCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh----CcHH
Q psy17765         32 RKESYAIYIYKVLKQVHP---DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL----LPGE  104 (475)
Q Consensus        32 ~~~sf~~yI~KVLKQVhP---d~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll----LPge  104 (475)
                      ++-.|+..++.+.....+   ++.+++.|+.-|..-....+..+-+.+.-.+...+|-||.++|||-|-|+-    -|.+
T Consensus        13 ~KlPFqRLVREIaq~~~~~~~~lRfqs~Al~ALQEAaEayLV~LFEd~nLcaiHAkRVTim~kDiqLarrirg~~~~p~e   92 (235)
T 2l5a_A           13 SKIPFARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMKKDMQLARRIRGQFLVPRG   92 (235)
T ss_dssp             SCCHHHHHHHHHHHTSCGGGTTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTSGGGTTHHHHHHTSSCSCCCCSS
T ss_pred             cCccHHHHHHHHHHHhccCCccceecHHHHHHHHHHHHHHHHHHHhhhHHHHhcccccccchhhHHHHHHHhhccCCchh
Confidence            466799999999888765   789999999888776666666665566666678899999999999998874    2332


Q ss_pred             HH-HHHH-----HHhh-hhhhhccccCCC--------------CCCCCCCccCcCCC-----------CCcccchhHHHH
Q psy17765        105 LA-KHAV-----SEGT-KAVTKYTSSKGK--------------GGKAKTKSKTRSSR-----------AGLQFPVGRIHR  152 (475)
Q Consensus       105 La-KhAv-----seG~-kAV~ky~sSkg~--------------~~k~~~~~~srSsR-----------agL~FPVsRi~r  152 (475)
                      +. +++-     ..-. .-+.||.+-.+.              -|.-+....-.+.+           .-++  ++ +.|
T Consensus        93 vme~~~~~~~~~k~~~~~i~~ky~~~~~~gd~idl~tG~iv~dnGh~~~l~~~~~~~~~~~r~~~vLrD~i~--i~-~~R  169 (235)
T 2l5a_A           93 SMERHKLADENMRKVWSNIISKYESIEEQGDLVDLKTGEIVEDNGHIKTLTANNSTKDKRTKYTSVLRDIID--IS-DEE  169 (235)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHHHTTCCCCSCCCSSSSCCCCCCCCCCCSCCCCCGGGCCSSTHHHHHHHHHH--HT-CCT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcccCCCCcccCCCCceeeeCcHHHHhhcCCCCCccchhHHHHHHHhhc--cc-HHH
Confidence            22 2221     1111 223466442211              11111111000000           0011  11 224


Q ss_pred             HHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhcc
Q psy17765        153 LLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND  210 (475)
Q Consensus       153 ~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD  210 (475)
                      +.+.+. ..||+..+..-+..+||.+..+|+.-|..++...+++.|++.||..|+..-
T Consensus       170 laRrgG-VkRIS~~iyeelr~vLe~fle~IirdAv~yaeHA~RKTVta~DV~~ALKr~  226 (235)
T 2l5a_A          170 DGDKGG-VKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQ  226 (235)
T ss_dssp             TSCCTT-CCTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHH
T ss_pred             HhhcCC-chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHhc
Confidence            444433 379999999999999999999999999999999999999999999998744

>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=96.84  E-value=0.0025  Score=59.71  Aligned_cols=69  Identities=17%  Similarity=0.331  Sum_probs=63.1

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh-CcHHH
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL-LPGEL  105 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll-LPgeL  105 (475)
                      ..-|.|+.|++-|+..||.+|...|...+..+...|+.+|..+|...+|+||+..||..|+.-+ |++-+
T Consensus        18 ~A~V~RImK~alp~~rISkDA~~al~ec~~eFI~~LtseA~e~a~~~~RKTI~~eDVl~Al~~LgF~~fv   87 (179)
T 1jfi_B           18 RAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALESLGFGSYI   87 (179)
T ss_dssp             HHHHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHTTGGGH
T ss_pred             HHHHHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhcChHHHH
Confidence            4568999999999889999999999999999999999999999999999999999999999987 66533

>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=96.82  E-value=0.002  Score=57.51  Aligned_cols=69  Identities=22%  Similarity=0.249  Sum_probs=60.7

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHH
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAK  107 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaK  107 (475)
                      ...|+|+|++..---.|+..|..+|...+..+...|.+.|...++.+++++|+++|||.||+-  ..||.+
T Consensus        28 V~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hI~lAI~n--DeEL~~   96 (131)
T 1id3_C           28 VGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRHLQLAIRN--DDELNK   96 (131)
T ss_dssp             HHHHHHHHHTTCSCSEECSSHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT--CHHHHH
T ss_pred             HHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHHHHhc--cHHHHH
Confidence            578999999975555899999999999999999999999999999999999999999999995  445543

>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=96.79  E-value=0.0032  Score=50.54  Aligned_cols=65  Identities=9%  Similarity=0.146  Sum_probs=59.9

Q ss_pred             cccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765        143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  208 (475)
Q Consensus       143 L~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~  208 (475)
                      -.||+.-|.++.+.-. ..+++..+..-|+--+||-..||++-|.+.+++.++++++.+||..|++
T Consensus         5 s~lp~~~v~~iaes~G-i~~lsddaa~~LA~dvEyr~~eI~qeA~kfmrHakRk~Lt~~DI~~Alk   69 (70)
T 1taf_B            5 SSISAESMKVIAESIG-VGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLK   69 (70)
T ss_dssp             CCCCHHHHHHHHHHTT-CCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC
T ss_pred             ccCCHHHHHHHHHHCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHc
Confidence            4789999999998644 4799999999999999999999999999999999999999999999975

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

Probab=96.76  E-value=0.0017  Score=53.46  Aligned_cols=65  Identities=12%  Similarity=0.126  Sum_probs=58.3

Q ss_pred             hHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765         35 SYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  100 (475)
Q Consensus        35 sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll  100 (475)
                      -=...|.|+.+..-. ..||.++.+.+...+...++.|+.+|..++.+.+|+|+|..||..|++..
T Consensus        11 ip~~~I~Riar~~Gv-~rIs~da~~~l~~~l~~~~~~I~~dA~~~a~ha~RKTvt~~DV~~Alk~~   75 (84)
T 2hue_C           11 ITKPAIRRLARRGGV-KRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ   75 (84)
T ss_dssp             SCHHHHHHHHHHTTC-CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTT
T ss_pred             CCHHHHHHHHHHcCc-hhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHc
Confidence            345679999998754 56999999999999999999999999999999999999999999998864

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

Probab=96.61  E-value=0.0029  Score=55.88  Aligned_cols=69  Identities=22%  Similarity=0.235  Sum_probs=61.1

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHH
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAK  107 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaK  107 (475)
                      ...|+|+|++..---.|+..|..+|...+..+...|.+.|...+..+++++||++|||.||+-  ..||..
T Consensus        26 V~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hi~lAI~n--DeEL~~   94 (123)
T 2nqb_C           26 VGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN--DEELNK   94 (123)
T ss_dssp             HHHHHHHHHHTTSCSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT--SHHHHH
T ss_pred             HHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHHHHHhc--cHHHHH
Confidence            578999999985556899999999999999999999999999999999999999999999996  555543

>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=96.52  E-value=0.0033  Score=54.46  Aligned_cols=62  Identities=16%  Similarity=0.267  Sum_probs=56.8

Q ss_pred             HHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765         38 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  100 (475)
Q Consensus        38 ~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll  100 (475)
                      ..|+|+.+.. ....||.++...+..++..+++.|+.+|..++.+.+|+|++..||..|++..
T Consensus        11 a~I~Ri~r~~-g~~rIS~~a~~~l~e~l~~f~~~v~~da~~~A~HA~RKTV~~eDV~lalrr~   72 (111)
T 3b0c_T           11 SLIKQIFSHY-VKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAGRKTVEMADVELLMRRQ   72 (111)
T ss_dssp             HHHHHHHHHH-HCSCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHT
T ss_pred             HHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHC
Confidence            4678877776 6778999999999999999999999999999999999999999999999873

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

Probab=96.40  E-value=0.007  Score=53.65  Aligned_cols=65  Identities=23%  Similarity=0.324  Sum_probs=59.1

Q ss_pred             HHHHHhhccCCC-CCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh-CcH
Q psy17765         39 YIYKVLKQVHPD-TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL-LPG  103 (475)
Q Consensus        39 yI~KVLKQVhPd-~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll-LPg  103 (475)
                      .|.|+.|+.-|+ ..||.+|...|...+.-+...|+.+|..+|...+|+||+..||..|+..+ |..
T Consensus        14 ~I~rImK~~~pd~~~iS~dA~~~l~ka~e~FI~~lt~~A~~~a~~~kRKTI~~~Dv~~Al~~l~f~~   80 (128)
T 2byk_B           14 VIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFES   80 (128)
T ss_dssp             HHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCTT
T ss_pred             HHHHHHHHhCcccceECHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHcCcHH
Confidence            589999987775 57999999999999999999999999999999999999999999999988 443

>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=96.21  E-value=0.0063  Score=53.50  Aligned_cols=69  Identities=23%  Similarity=0.244  Sum_probs=60.9

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHH
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAK  107 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaK  107 (475)
                      ...|+|.|+...--..|+..|-.+|...+..+...|.+.|...++.+++++||+++||.||+-  ..||.+
T Consensus        25 V~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~~rItp~hi~lAI~n--DeEL~~   93 (120)
T 2f8n_G           25 VGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILLAVAN--DEELNQ   93 (120)
T ss_dssp             HHHHHHHHHHHSSSCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT--SHHHHH
T ss_pred             hHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHHHHhc--CHHHHH
Confidence            568999999987666899999999999999999999999999999999999999999999996  555544

>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=96.12  E-value=0.0053  Score=53.21  Aligned_cols=72  Identities=8%  Similarity=0.046  Sum_probs=61.7

Q ss_pred             CcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHHH
Q psy17765        142 GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELN  214 (475)
Q Consensus       142 gL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL~  214 (475)
                      .+.+|-+-|.|+++.+ -..||+..+..-|..+++.++.+|..-|..+|++.+++.|+++||.+|++.+..+.
T Consensus         5 d~~lP~a~I~Ri~r~~-g~~rIS~~a~~~l~e~l~~f~~~v~~da~~~A~HA~RKTV~~eDV~lalrr~g~~~   76 (111)
T 3b0c_T            5 EPEIASSLIKQIFSHY-VKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAGRKTVEMADVELLMRRQGLVT   76 (111)
T ss_dssp             -----CHHHHHHHHHH-HCSCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTTSSB
T ss_pred             CCCCCHHHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHCCCcc
Confidence            4689999999999986 45799999999999999999999999999999999999999999999999876553

>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=96.03  E-value=0.012  Score=52.30  Aligned_cols=70  Identities=20%  Similarity=0.140  Sum_probs=60.7

Q ss_pred             HHHHHHHhhccCCC-CCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHHH
Q psy17765         37 AIYIYKVLKQVHPD-TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKH  108 (475)
Q Consensus        37 ~~yI~KVLKQVhPd-~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaKh  108 (475)
                      ...|+|.|+....- ..|+..|-.+|...+..+...|.+.|...+..+++++||+++||.||+-  ..||..-
T Consensus        30 V~ri~R~Lk~~~~a~~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItprhi~lAI~n--DeEL~~L  100 (128)
T 1f66_C           30 VGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG--DEELDSL  100 (128)
T ss_dssp             HHHHHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHH--SHHHHHH
T ss_pred             hHHHHHHHHHcccchhhccccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEcHHHHHHHHhc--cHHHhhh
Confidence            56899999987643 4799999999999999999999999999999999999999999999997  5666543

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

Probab=96.01  E-value=0.014  Score=49.14  Aligned_cols=62  Identities=19%  Similarity=0.188  Sum_probs=56.2

Q ss_pred             HHHHHHHhhccCCCC-CcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         37 AIYIYKVLKQVHPDT-GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~-~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      ...|+|++|.- |+. .||.+|...|.-.+..+...|+.+|...+..++|+||+.+||+.||+-
T Consensus        22 ~arIkrImK~~-~~~~~is~eA~~~laka~E~Fi~~l~~~A~~~a~~~krktI~~~di~~Av~~   84 (97)
T 1n1j_B           22 LARIKKIMKLD-EDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITK   84 (97)
T ss_dssp             HHHHHHHHTTS-TTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTT
T ss_pred             HHHHHHHHccC-ccccccChHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHHhc
Confidence            46799999986 774 599999999999999999999999999999999999999999999875

>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=96.01  E-value=0.011  Score=51.73  Aligned_cols=63  Identities=21%  Similarity=0.151  Sum_probs=56.1

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      ...|+|++|.......||.+|..++.--+.-+...|+.+|...|..++|+||+.+||..||+-
T Consensus        44 vaRIkrImK~d~~~~~is~eA~v~la~a~E~Fi~~L~~~A~~~a~~~krktI~~~di~~Av~~  106 (119)
T 4g92_C           44 LARIKKVMKADPEVKMISAEAPILFAKGCDVFITELTMRAWIHAEDNKRRTLQRSDIAAALSK  106 (119)
T ss_dssp             HHHHHHHHHTSTTCCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTT
T ss_pred             HHHHHHHHhhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccCHHHHHHHHhc
Confidence            567999999863334699999999999999999999999999999999999999999999975

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

Probab=95.97  E-value=0.011  Score=52.46  Aligned_cols=69  Identities=22%  Similarity=0.237  Sum_probs=60.8

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHH
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAK  107 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaK  107 (475)
                      ...|+|+|++..---.|+..|-.+|...+..+...|.+.|...+..+++++||++|||.||+-  ..||..
T Consensus        28 V~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hi~lAI~n--DeEL~~   96 (129)
T 1tzy_A           28 VGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRN--DEELNK   96 (129)
T ss_dssp             HHHHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT--SHHHHH
T ss_pred             HHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEcHHHHHHHHhc--cHHHHH
Confidence            568999999975556899999999999999999999999999999999999999999999995  445543

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

Probab=95.95  E-value=0.015  Score=52.91  Aligned_cols=69  Identities=22%  Similarity=0.240  Sum_probs=61.1

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHH
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAK  107 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaK  107 (475)
                      ...|+|+|++..---.|+..|-.+|...+..+...|.+.|...++.+++++|++++||.||+-  ..||.+
T Consensus        47 VgrI~R~LK~~~~a~RVs~~A~VyLAAVLEYL~aEILelAgn~A~~~krkrItprhI~lAI~n--DeEL~~  115 (149)
T 2f8n_K           47 VGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRN--DEELNK  115 (149)
T ss_dssp             HHHHHHHHHHTTSCSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH--SHHHHH
T ss_pred             HHHHHHHHHccccccccCcCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHhc--cHHHHH
Confidence            568999999986666899999999999999999999999999999999999999999999996  555544

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

Probab=95.85  E-value=0.021  Score=45.82  Aligned_cols=61  Identities=15%  Similarity=0.260  Sum_probs=53.1

Q ss_pred             HHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         38 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        38 ~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      ..|.++.+++-= ..+|.++...|-.-+..-+..|++||.++++..+|+|+|..||..|+++
T Consensus        10 ~~v~~iaes~Gi-~~lsddaa~~LA~dvEyr~~eI~qeA~kfmrHakRk~Lt~~DI~~Alk~   70 (70)
T 1taf_B           10 ESMKVIAESIGV-GSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLKV   70 (70)
T ss_dssp             HHHHHHHHHTTC-CCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC-
T ss_pred             HHHHHHHHHCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHcC
Confidence            357777777742 3689999999999999999999999999999999999999999998763

>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=95.85  E-value=0.023  Score=45.34  Aligned_cols=60  Identities=18%  Similarity=0.106  Sum_probs=55.1

Q ss_pred             HHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhc
Q psy17765        149 RIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN  209 (475)
Q Consensus       149 Ri~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~n  209 (475)
                      -|+++|++.. ..+++..++.-|.-.+|-.+.+|++-|..+|.+.+++.|+.+||++||..
T Consensus         6 ~i~~iLk~~G-~~~~~~~v~~~L~e~~~ry~~~il~dA~~~a~HAgrktv~~eDVkLAi~~   65 (68)
T 1taf_A            6 VIMSILKELN-VQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLATEV   65 (68)
T ss_dssp             HHHHHHHHTT-CCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             HHHHHHHHCC-CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHh
Confidence            5788998744 47999999999999999999999999999999999999999999999974

>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=95.81  E-value=0.017  Score=54.00  Aligned_cols=76  Identities=16%  Similarity=0.229  Sum_probs=65.0

Q ss_pred             CCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHHHhhh
Q psy17765        141 AGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLL  217 (475)
Q Consensus       141 agL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL~~Lf  217 (475)
                      ..+.||.+.|.|+|++..-..||+..|...|+-+.+-+...|-..|...|.+.+++.|+++||..|+. +-++..+.
T Consensus        12 eD~~LP~A~V~RImK~alp~~rISkDA~~al~ec~~eFI~~LtseA~e~a~~~~RKTI~~eDVl~Al~-~LgF~~fv   87 (179)
T 1jfi_B           12 DDLTIPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALE-SLGFGSYI   87 (179)
T ss_dssp             CCCCCCHHHHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHH-HHTTGGGH
T ss_pred             hhhhcCHHHHHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH-hcChHHHH
Confidence            46899999999999986435799999999999999999999988888889999999999999999998 44444433

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

Probab=95.75  E-value=0.028  Score=45.92  Aligned_cols=67  Identities=19%  Similarity=0.245  Sum_probs=59.8

Q ss_pred             chhHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         33 KESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        33 ~~sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      +-.|+.-++.+.....++..+++.|+.-|..-....+..+.+++..++.+.+|.|+.++|||-|.++
T Consensus         6 k~PF~RLVRei~~~~~~~~R~q~~Al~aLQea~Eaylv~lfeda~l~A~HAkRvTi~~kDiqLa~ri   72 (77)
T 2hue_B            6 KLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRI   72 (77)
T ss_dssp             HHHHHHHHHHHHHTTCSSCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHcCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHhhHHHHHHH
Confidence            3457777888877777889999999999999999999999999999999999999999999999886

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

Probab=95.68  E-value=0.016  Score=48.54  Aligned_cols=78  Identities=14%  Similarity=0.028  Sum_probs=59.6

Q ss_pred             CCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHHHhhhcC
Q psy17765        141 AGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSG  219 (475)
Q Consensus       141 agL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL~~Lf~~  219 (475)
                      +.|.+-|++|=.-.-+ ..+..++..+..-|+.+++..+.+|.+=+...|++.+++.|++.||.++++.++.|..++.+
T Consensus        12 aal~~~V~ki~~e~~~-~~g~~vs~~~i~aL~e~~~~~~~~ia~Dl~~fA~HAgRkTI~~eDV~L~~Rrn~~L~~~l~~   89 (90)
T 3v9r_A           12 ARLWIRVEERLQQVLS-SEDIKYTPRFINSLLELAYLQLGEMGSDLQAFARHAGRGVVNKSDLMLYLRKQPDLQERVTQ   89 (90)
T ss_dssp             HHHHHHHHHHHHHHSC-SSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTCHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHHH-hcCceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhChHHHHHhhc
Confidence            4577777776543311 11245777777777777777777778777888999999999999999999999999998764

>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=95.59  E-value=0.036  Score=45.16  Aligned_cols=62  Identities=16%  Similarity=0.355  Sum_probs=57.2

Q ss_pred             HHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765         39 YIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  100 (475)
Q Consensus        39 yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll  100 (475)
                      -|...++||-|+..+..++-+.|-.+..++.+.++..|++|+.+.+..|+.++|||......
T Consensus        10 ~L~~Lv~~idp~~~ld~~vee~ll~lADdFV~~V~~~ac~lAKhR~s~~le~kDvql~Ler~   71 (76)
T 1h3o_B           10 KLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLERQ   71 (76)
T ss_dssp             HHHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHhh
Confidence            37788899999999999999999999999999999999999999999999999999887653

>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=95.51  E-value=0.047  Score=43.51  Aligned_cols=63  Identities=16%  Similarity=0.252  Sum_probs=55.3

Q ss_pred             HHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhC
Q psy17765         38 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLL  101 (475)
Q Consensus        38 ~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllL  101 (475)
                      ..|.++||..-= ...+..+...|-.|+.+....|+.+|..++.+.+|+|++..||+.|++..+
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            457888887532 367999999999999999999999999999999999999999999998653

>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=95.31  E-value=0.018  Score=48.71  Aligned_cols=62  Identities=13%  Similarity=0.278  Sum_probs=52.1

Q ss_pred             HHHHHHHhhccCCC-CCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         37 AIYIYKVLKQVHPD-TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        37 ~~yI~KVLKQVhPd-~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      ...|+|++|. .|+ ..||.+|.-++.-.+..+...|+.+|...+..++++||+.+||+.||+-
T Consensus        14 vaRIkrimK~-~~~~~~vs~~A~v~la~a~E~Fi~el~~~A~~~a~~~krktI~~~di~~av~~   76 (98)
T 1jfi_A           14 PARIKKIMQT-DEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQCIEL   76 (98)
T ss_dssp             HHHHHHHHTT-STTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC---CBCHHHHHTTCC-
T ss_pred             hHHHHHHHHc-CccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHhc
Confidence            5679999997 556 5699999999999999999999999999999999999999999988865

>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=94.96  E-value=0.05  Score=48.82  Aligned_cols=64  Identities=19%  Similarity=0.251  Sum_probs=56.6

Q ss_pred             HHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         36 YAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        36 f~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      |+-.++.+.....+++.++++|+.-|..-..+.+..|.+++..++.+.++.||.++|||-|.++
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            6666666666666889999999999999999999999999999999999999999999999887

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

Probab=94.87  E-value=0.048  Score=45.72  Aligned_cols=64  Identities=13%  Similarity=0.159  Sum_probs=54.7

Q ss_pred             HHHHHHHHhhccCC--CCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         36 YAIYIYKVLKQVHP--DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        36 f~~yI~KVLKQVhP--d~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      .--.+-|+..++-+  +..+|.+++.-|..++.+.++.|+.++..++...+|+||+..||..++|.
T Consensus        14 l~~~V~ki~~e~~~~~g~~vs~~~i~aL~e~~~~~~~~ia~Dl~~fA~HAgRkTI~~eDV~L~~Rr   79 (90)
T 3v9r_A           14 LWIRVEERLQQVLSSEDIKYTPRFINSLLELAYLQLGEMGSDLQAFARHAGRGVVNKSDLMLYLRK   79 (90)
T ss_dssp             HHHHHHHHHHHHSCSSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHhcCceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHh
Confidence            33445566666644  35699999999999999999999999999999999999999999998887

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

Probab=94.71  E-value=0.031  Score=48.70  Aligned_cols=79  Identities=15%  Similarity=0.179  Sum_probs=64.5

Q ss_pred             CCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHHHhhhcC
Q psy17765        140 RAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSG  219 (475)
Q Consensus       140 RagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL~~Lf~~  219 (475)
                      ++.|.+.|+||-+---..+ ...++..+..-|+-+++..+.+|.+-+...|+..+++.|++.||.++++.++.|..+++.
T Consensus        26 Kaal~y~V~rIvke~gaer-~~~vS~~ai~aL~El~~~~~~~ia~Dl~~fAkHAgRkTI~~eDV~La~Rr~~~L~~~l~~  104 (113)
T 4dra_A           26 KAAVHYTVGCLCEEVALDK-EMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARRSNSLLKYITD  104 (113)
T ss_dssp             HHHHHHHHHHHHHHHHHHH-TCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHc-CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHhCHHHHHHHHH
Confidence            4668999998865432211 234888888888888888888888888889999999999999999999999999988763

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

Probab=94.58  E-value=0.033  Score=48.12  Aligned_cols=78  Identities=14%  Similarity=0.184  Sum_probs=65.0

Q ss_pred             CCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHHHhhhc
Q psy17765        140 RAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLS  218 (475)
Q Consensus       140 RagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL~~Lf~  218 (475)
                      ++.|.+-|+||-+---. ....|++..+..-|+-+++..+.+|.+-+..+|++.+++.|+++||.++++.++.|.+.++
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            34588888887654322 1235899999999999998889999999999999999999999999999999999987765

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

Probab=94.46  E-value=0.098  Score=43.14  Aligned_cols=67  Identities=12%  Similarity=0.155  Sum_probs=57.0

Q ss_pred             hhHHHHHHHHhhccC--CCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765         34 ESYAIYIYKVLKQVH--PDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  100 (475)
Q Consensus        34 ~sf~~yI~KVLKQVh--Pd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll  100 (475)
                      -.|+.-++.+-.+..  .+..++++|+.-+..-..+.+..+.+++...+.+.+|.|+.++|||-|.|+-
T Consensus         7 lPF~RLVREI~~~~~~~~~~R~q~~Al~aLQea~E~ylv~Lfeda~lcAiHAkRvTi~~kDiqLa~rir   75 (82)
T 3nqj_A            7 LPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIR   75 (82)
T ss_dssp             HHHHHHHHHHHHHHHSSCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHhccCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHHHHHHHHHc
Confidence            446777777766555  3678999999999999999999999999988999999999999999998873

>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=94.40  E-value=0.085  Score=45.02  Aligned_cols=67  Identities=21%  Similarity=0.222  Sum_probs=57.6

Q ss_pred             chhHHHHHHHHhhccCC---CCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         33 KESYAIYIYKVLKQVHP---DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        33 ~~sf~~yI~KVLKQVhP---d~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      +-.|+--++.+.....+   +..+++.|+.-|..-..+.+..+.+++..++.+.+|.|+.++|||-|.++
T Consensus        30 k~PF~RLVREI~~~~~~~~~~~R~q~~Al~ALQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa~ri   99 (100)
T 2yfv_A           30 RMPFARLVKEVTDQFTTESEPLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARRI   99 (100)
T ss_dssp             HHHHHHHHHHHHHTTC-----CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHC
T ss_pred             cccHHHHHHHHHHHhccccchhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHHHh
Confidence            44588888888877766   78899999999999999999999999999999999999999999999875

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

Probab=94.36  E-value=0.035  Score=47.92  Aligned_cols=65  Identities=20%  Similarity=0.150  Sum_probs=56.1

Q ss_pred             HHHHHHHHhhccCC--CCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765         36 YAIYIYKVLKQVHP--DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  100 (475)
Q Consensus        36 f~~yI~KVLKQVhP--d~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll  100 (475)
                      .-..+-|+.++.--  +..+|.+++..|..++.+.++.|+.++..++.+.+|+||+..||..|+|..
T Consensus        21 l~~~V~rI~~~~g~~~~~~vs~~~i~aL~E~~~~~~~~ia~Da~~fA~HAgRkTI~~eDV~La~Rrn   87 (107)
T 3b0b_B           21 VHYTTGCLCQDVAEDKGVLFSKQTVAAISEITFRQCENFARDLEMFARHAKRSTITSEDVKLLARRS   87 (107)
T ss_dssp             HHHHHHHHHHHHHHHHTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHHhhhcCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcCcCCHHHHHHHHHhC
Confidence            44456677766632  467999999999999999999999999999999999999999999999873

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

Probab=94.12  E-value=0.1  Score=46.95  Aligned_cols=68  Identities=22%  Similarity=0.201  Sum_probs=56.7

Q ss_pred             HHHHHhhcc--CCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHHH
Q psy17765         39 YIYKVLKQV--HPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKH  108 (475)
Q Consensus        39 yI~KVLKQV--hPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaKh  108 (475)
                      .+-|+.+++  ..++.+|.+++..|..++.+.++.|+.++..++...+|+||+..||..++|.  -..|..+
T Consensus        24 ~VgkIvee~~~~~~~~vS~~ai~aL~El~~~~~e~ia~DLe~FAkHAGRKTI~~eDVkLa~Rr--n~~L~~~   93 (140)
T 3vh5_A           24 TTGALAQDVAEDKGVLFSKQTVAAISEITFRQAENFARDLEMFARHAKRSTITSEDVKLLARR--SNSLLKY   93 (140)
T ss_dssp             HHHHHHHHHHHHHTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTT--SHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHh--CHHHHHH
Confidence            344555555  2356799999999999999999999999999999999999999999999998  4455444

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

Probab=93.91  E-value=0.061  Score=46.88  Aligned_cols=63  Identities=16%  Similarity=0.214  Sum_probs=55.1

Q ss_pred             HHHHHHHhhccC--CCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         37 AIYIYKVLKQVH--PDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        37 ~~yI~KVLKQVh--Pd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      --.+.|+++++-  .+..+|.+++.-|..++.+.++.|+.++..++...+|+||+..||..++|.
T Consensus        30 ~y~V~rIvke~gaer~~~vS~~ai~aL~El~~~~~~~ia~Dl~~fAkHAgRkTI~~eDV~La~Rr   94 (113)
T 4dra_A           30 HYTVGCLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARR   94 (113)
T ss_dssp             HHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHh
Confidence            344667776663  246799999999999999999999999999999999999999999999887

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

Probab=93.68  E-value=0.11  Score=46.60  Aligned_cols=62  Identities=10%  Similarity=0.125  Sum_probs=50.0

Q ss_pred             HHHHHHHhhccCCCC-CcChHHHHHHHHHHHHHHHHHHHHHhhhh-hcCCCCCCChHHHHHHHHH
Q psy17765         37 AIYIYKVLKQVHPDT-GVSSKAMSIMNSFVNDIFERIAAESSRLA-HYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~-~IS~~Am~imns~v~diferIa~EA~~L~-~~~kr~TlT~rdIqtAVrl   99 (475)
                      ...|+|++|.- |+. .||.+|.-+|.--+--++..|+.+|...+ ..++|+||+.+||..||..
T Consensus        22 laRIKrIMK~d-pdv~~Is~eA~vliakA~ElFI~~Lt~~A~~~a~~~~kRKtI~~~Dl~~AV~~   85 (140)
T 2byk_A           22 LSRVRTIMKSS-MDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNK   85 (140)
T ss_dssp             -------CCSS-SSCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHHT
T ss_pred             HHHHHHHHhcC-cccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccCHHHHHHHHhc
Confidence            56799999986 775 59999999999988888999999999999 9999999999999999974

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

Probab=93.56  E-value=0.14  Score=42.18  Aligned_cols=67  Identities=22%  Similarity=0.123  Sum_probs=55.7

Q ss_pred             cccchhHHHHHHhhcC------cccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhc
Q psy17765        143 LQFPVGRIHRLLRKGN------YAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN  209 (475)
Q Consensus       143 L~FPVsRi~r~Lke~~------~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~n  209 (475)
                      |.+|.--|.|+.|+-.      ...|+.++|..-|--..|....++.|-+...|.+.++..|.|+||++|.+-
T Consensus         2 lLI~klPF~RLVREI~~~~~~~~~~R~q~~Al~aLQea~E~ylv~Lfeda~lcAiHAkRvTi~~kDiqLa~ri   74 (82)
T 3nqj_A            2 LLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRI   74 (82)
T ss_dssp             CSSCHHHHHHHHHHHHHHHHSSCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             CCcccccHHHHHHHHHHHhccCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHHHHHHHHH
Confidence            3455555666666532      356999999999999999999999999999999999999999999999763

>3jv3_A Intersectin-1; SH3 domain, DH domain, guanine nucleotide exchange factor, autoinhibition, domain-swapped, cell junction, cell project endocytosis; 2.40A {Mus musculus} PDB: 3gf9_A

Probab=93.46  E-value=0.011  Score=56.54  Aligned_cols=70  Identities=10%  Similarity=-0.073  Sum_probs=55.3

Q ss_pred             hhHHHHHHhccccc----cccccccccccccccccCCcchhhhhccccCCCCcccchhhhccccccchhhhhhhcc
Q psy17765        286 VLEEHLENATGLLV----DESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAA  357 (475)
Q Consensus       286 Vfre~l~~~~~l~~----~~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~~~~~~~~~~~m~~  357 (475)
                      +|.++|.....+..    .||+|+-+|+++.+.|+..|++.+....++.++..+|.||..+++.  +++|..|...
T Consensus       107 ~y~~~l~~~~~l~~~~~~~iF~ni~~i~~~~~~fl~~L~~~~~~~~~~~~~~~ig~~f~~~~~~--~~~Y~~Y~~~  180 (283)
T 3jv3_A          107 IFQKPLTESELLTEKEVAMIFVNWKELIMCNIKLLKALRVRKKMSGEKMPVKMIGDILSAQLPH--MQPYIRFCSC  180 (283)
T ss_dssp             HTTHHHHTTCSSCHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHCTTCCCCCCHHHHHHHGGG--GTHHHHHHHH
T ss_pred             HHHhhccccCCCCHHHHHHHccCHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHhh--chhHHHHHcC
Confidence            56666654332222    2999999999999999999999998877777889999999887764  7899988654

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

Probab=93.38  E-value=0.18  Score=41.07  Aligned_cols=66  Identities=24%  Similarity=0.241  Sum_probs=55.4

Q ss_pred             cccchhHHHHHHhhc----CcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765        143 LQFPVGRIHRLLRKG----NYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  208 (475)
Q Consensus       143 L~FPVsRi~r~Lke~----~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~  208 (475)
                      |.+|.-=|.|++|+-    .-..|+.++|..-|--..|....++.|-+...|.+.++..|.|+||++|.+
T Consensus         2 lli~k~PF~RLVRei~~~~~~~~R~q~~Al~aLQea~Eaylv~lfeda~l~A~HAkRvTi~~kDiqLa~r   71 (77)
T 2hue_B            2 ALIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARR   71 (77)
T ss_dssp             CCSCHHHHHHHHHHHHHTTCSSCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             CccccchHHHHHHHHHHHcCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHhhHHHHHH
Confidence            455666666666653    124799999999999999999999999999999999999999999999975

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

Probab=93.34  E-value=0.12  Score=45.63  Aligned_cols=48  Identities=19%  Similarity=0.271  Sum_probs=45.7

Q ss_pred             CcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         52 GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        52 ~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      .||..+.+-+...+.+.++.|+.+|..++.+.+|+|+|..||.-|++.
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            499999999999999999999999999999999999999999998876

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

Probab=93.15  E-value=0.089  Score=47.40  Aligned_cols=79  Identities=15%  Similarity=0.194  Sum_probs=64.4

Q ss_pred             CCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHHHhhhcC
Q psy17765        140 RAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSG  219 (475)
Q Consensus       140 RagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL~~Lf~~  219 (475)
                      ++.|.+-|++|-.-.-. .....++..+..-|+-+++..+.+|..=+-.+|++.+++.|++.||.++++.++.|..++..
T Consensus        18 KaAl~y~VgkIvee~~~-~~~~~vS~~ai~aL~El~~~~~e~ia~DLe~FAkHAGRKTI~~eDVkLa~Rrn~~L~~~L~~   96 (140)
T 3vh5_A           18 RAAVHYTTGALAQDVAE-DKGVLFSKQTVAAISEITFRQAENFARDLEMFARHAKRSTITSEDVKLLARRSNSLLKYITQ   96 (140)
T ss_dssp             HHHHHHHHHHHHHHHHH-HHTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH-hcCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhCHHHHHHHHH
Confidence            35588888887654311 12346888888888888888888888888889999999999999999999999999988764

>2dfk_A Collybistin II; DH domain, PH domain, cell cycle; 2.15A {Rattus norvegicus} SCOP: a.87.1.1 b.55.1.1

Probab=92.89  E-value=0.012  Score=60.01  Aligned_cols=68  Identities=9%  Similarity=-0.120  Sum_probs=51.2

Q ss_pred             hhHHHHHHhcccccc-----ccccccccccccccccCCcchhhhhccccCCCCcccchhhhccccccchhhhhhhcc
Q psy17765        286 VLEEHLENATGLLVD-----ESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAA  357 (475)
Q Consensus       286 Vfre~l~~~~~l~~~-----~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~~~~~~~~~~~m~~  357 (475)
                      +|.++|.....++.+     ||+||-+|+++...|+..|++.++-  .+...+.+|.||.++++  .|++|+.|...
T Consensus        66 ~y~~pl~~~~~~l~~~~~~~iF~ni~~I~~~h~~fL~~Le~~~~~--~~~~~~~ig~ifl~~~~--~f~~Y~~Y~~n  138 (402)
T 2dfk_A           66 GYLKQCRKRRDMFSDEQLKVIFGNIEDIYRFQMGFVRDLEKQYNN--DDPHLSEIGPCFLEHQD--GFWIYSEYCNN  138 (402)
T ss_dssp             HTHHHHHHCTTTCCHHHHHHHHTTHHHHHHHHHHHHHHHHHHCCS--SCGGGCCCHHHHHHTTT--GGGHHHHHHHH
T ss_pred             HHHHHHHhCcCCCCHHHHHHHHhcHHHHHHHHHHHHHHHHHHHcc--CCCchhhHHHHHHHHHh--hhHHHHHHHHh
Confidence            566666554444443     9999999999999999999887643  12224689999999875  58999999765

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

Probab=92.75  E-value=0.21  Score=45.01  Aligned_cols=65  Identities=12%  Similarity=0.172  Sum_probs=54.6

Q ss_pred             HHHHHHHHhhccC--CCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765         36 YAIYIYKVLKQVH--PDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  100 (475)
Q Consensus        36 f~~yI~KVLKQVh--Pd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll  100 (475)
                      |+-.++.+-.+..  -++.++.+|+..|..-..+.+..|.+++..++.+.++.||..+|||-|.++-
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            6666666655444  3678999999999999999999999999988899999999999999999873

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

Probab=92.63  E-value=0.21  Score=45.75  Aligned_cols=64  Identities=13%  Similarity=0.190  Sum_probs=54.7

Q ss_pred             HHHHHHHHhhccCC--CCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         36 YAIYIYKVLKQVHP--DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        36 f~~yI~KVLKQVhP--d~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      |+-.++.+..+..+  ++.++.+|+..|..-..+.+..|.++|..++...++.||..+|||-|.++
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            66666666655553  57899999999999999999999999988888899999999999999988

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

Probab=92.45  E-value=0.2  Score=45.10  Aligned_cols=69  Identities=22%  Similarity=0.115  Sum_probs=60.3

Q ss_pred             CCcccchhHHHHHHhhcC------cccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhc
Q psy17765        141 AGLQFPVGRIHRLLRKGN------YAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN  209 (475)
Q Consensus       141 agL~FPVsRi~r~Lke~~------~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~n  209 (475)
                      .+|.+|.--|.|+++|-.      ...|+.++|..-|--+.|....++.|-+...|.+.++..|.|+||++|.+=
T Consensus        58 t~LLIpKlPF~RLVREI~~~~~~~~~~Rfq~~Al~ALQEAaEayLv~LFEdanlcAiHAkRVTIm~kDiqLArri  132 (140)
T 3nqu_A           58 THLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRI  132 (140)
T ss_dssp             -CCCSCTTHHHHHHHHHHHHHHTTCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             cccccccccHHHHHHHHHHHhcccccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHHHHh
Confidence            468899888888888733      257999999999999999999999999999999999999999999999763

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

Probab=92.45  E-value=0.17  Score=46.40  Aligned_cols=72  Identities=21%  Similarity=0.092  Sum_probs=61.8

Q ss_pred             CCcccchhHHHHHHhhcC------cccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHH
Q psy17765        141 AGLQFPVGRIHRLLRKGN------YAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEE  212 (475)
Q Consensus       141 agL~FPVsRi~r~Lke~~------~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~E  212 (475)
                      .+|.+|.--|.|+++|-.      ...|+.++|..-|--+.|..+.++.|-|...|...++..|.|+||++|.+=-.|
T Consensus        74 teLLIpKlPF~RLVREIa~~~~~~~~lRfqs~Al~ALQEAaEayLV~LFEdanLcAiHAkRVTIm~kDIqLArrIrg~  151 (156)
T 3r45_A           74 THLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIRGL  151 (156)
T ss_dssp             -CCCSCHHHHHHHHHHHHHTTTTTCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSEECHHHHHHHHHHHHH
T ss_pred             cccccccccHHHHHHHHHHHhccCccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHHHHHccc
Confidence            468999999999988732      246999999999999999999999999988899999999999999999864333

>1txd_A RHO guanine nucleotide exchange factor 12; helical bundle (DH), beta sandwich (PH), signaling protein; 2.13A {Homo sapiens} SCOP: a.87.1.1 b.55.1.1 PDB: 1x86_A

Probab=92.43  E-value=0.019  Score=57.89  Aligned_cols=70  Identities=9%  Similarity=-0.121  Sum_probs=55.7

Q ss_pred             hhHHHHHHhccccc-----cccccccccccccccccCCcchhhhhccccCCCCcccchhhhccc---cccc-hhhhhhhc
Q psy17765        286 VLEEHLENATGLLV-----DESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSS---LTTA-DLLSITMA  356 (475)
Q Consensus       286 Vfre~l~~~~~l~~-----~~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~---~~~~-~~~~~~m~  356 (475)
                      +|.++|.... ++.     .||+|+-+|+++. .++..|++.++..+++...+.+|.||.++.+   .+.| ++|+.|..
T Consensus        49 ~f~~~l~~~~-~l~~~~~~~iF~ni~~I~~~h-~fL~~l~~~~~~~~~~~~~~~ig~~fl~~~~~~~~~~f~~~Y~~Y~~  126 (385)
T 1txd_A           49 VFYQRVSREG-ILSPSELRKIFSNLEDILQLH-IGLNEQMKAVRKRNETSVIDQIGEDLLTWFSGPGEEKLKHAAATFCS  126 (385)
T ss_dssp             HTHHHHHHHT-CSCHHHHHHHHTTHHHHHHHH-HHHHHHHHHHHTTCTTCCCCCCHHHHHHHHSTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhcC-CCCHHHHHHHhcCHHHHHHHH-HHHHHHHHHHHHhhcCCCcccHHHHHHHHccchhHHHHHHHHHHHHH
Confidence            7788887633 333     2999999999999 9999999988776776678899999999875   3566 89998866


Q ss_pred             c
Q psy17765        357 A  357 (475)
Q Consensus       357 ~  357 (475)
                      .
T Consensus       127 n  127 (385)
T 1txd_A          127 N  127 (385)
T ss_dssp             T
T ss_pred             c
Confidence            5

>3jzy_A Intersectin 2; C2 domain, structural genomics consortium (SGC), endocytosis; 1.56A {Homo sapiens} PDB: 3qbv_B* 1ki1_B

Probab=92.37  E-value=0.024  Score=58.68  Aligned_cols=137  Identities=12%  Similarity=0.088  Sum_probs=0.0

Q ss_pred             hhHHHHHHhccc----cccccccccccccccccccCCcchhhhhccccCCCCcccchhhhccccccchhhhhhhccCCcC
Q psy17765        286 VLEEHLENATGL----LVDESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAAGKSS  361 (475)
Q Consensus       286 Vfre~l~~~~~l----~~~~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~~~~~~~~~~~m~~~~~~  361 (475)
                      +|.++|.....+    ...||+|+-+|+++.+.|+..|++.+....++.++..+|.||..+++  .+++|..|......+
T Consensus        52 ~y~~~l~~~~~l~~~~~~~iF~ni~~i~~~h~~fl~~L~~~~~~~~~~~~~~~ig~~f~~~~~--~~~~Y~~Y~~~~~~a  129 (510)
T 3jzy_A           52 VFQKRMAESGFLTEGEMALIFVNWKELIMSNTKLLKALRVRKKTGGEKMPVQMIGDILAAELS--HMQAYIRFCSCQLNG  129 (510)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHhhcCCCCHHHHHHHccCHHHHHHHHHHHHHHHHHHHhccCCCCchhhHHHHHHHHhH--HHHHHHHHHHhHHHH
Confidence            666777653222    22399999999999999999999998877777778899999988764  578999887653211


Q ss_pred             ccchhccccccccc---cccCCccCc--------------CCCccceeehhhhhcc---ccCCCCCchHHHHHHhhHHHH
Q psy17765        362 GKAVKKAGKAQKNI---TKSDKKKKP--------------RRKESYAIYIYKVLKQ---VHPDTGVSSKAMSIMNSFVND  421 (475)
Q Consensus       362 ~k~~~~~~~~~~~~---~~~~~k~~~--------------~~~esy~~Yi~kvLkq---vhp~~giS~kam~imnsfv~D  421 (475)
                      ...-....+..+.-   -+.......              .|-..|...+-.+||.   -|||..-=.+|...|..++..
T Consensus       130 ~~~l~~~~~~~~~f~~~~~~~~~~~~~~~l~L~~~L~~PvQRi~rY~LLL~~llk~t~~~~~d~~~l~~A~~~i~~v~~~  209 (510)
T 3jzy_A          130 AALLQQKTDEDTDFKEFLKKLASDPRCKGMPLSSFLLKPMQRITRYPLLIRSILENTPESHADHSSLKLALERAEELCSQ  209 (510)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHhCccccCCCHHHHhChhhhhhcCcHHHHHHHHhcCCCCCccHHHHHHHHHHHHHHHHH
Confidence            11111100000000   000000011              1223455555555664   378877778888888877765


Q ss_pred             HHh
Q psy17765        422 IFE  424 (475)
Q Consensus       422 ife  424 (475)
                      +=+
T Consensus       210 in~  212 (510)
T 3jzy_A          210 VNE  212 (510)
T ss_dssp             ---
T ss_pred             HHH
Confidence            543

>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=92.13  E-value=0.22  Score=42.50  Aligned_cols=68  Identities=24%  Similarity=0.222  Sum_probs=56.8

Q ss_pred             CCcccchhHHHHHHhhcC--c-----ccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765        141 AGLQFPVGRIHRLLRKGN--Y-----AERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  208 (475)
Q Consensus       141 agL~FPVsRi~r~Lke~~--~-----~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~  208 (475)
                      .+|.+|.--|.|+.++-.  +     ..|+.++|..-|--..|....++.|-+...|...++..|.|.||++|.+
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            368999999999888742  1     4799999999999999999999999999999999999999999999974

>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=91.52  E-value=0.36  Score=43.26  Aligned_cols=67  Identities=25%  Similarity=0.250  Sum_probs=59.8

Q ss_pred             CcccchhHHHHHHhhcC----cccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765        142 GLQFPVGRIHRLLRKGN----YAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  208 (475)
Q Consensus       142 gL~FPVsRi~r~Lke~~----~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~  208 (475)
                      +|.+|.--|.|++++-.    -..|+.++|..-|.-..|....++.|-+...|.+.++..|.|.||++|.+
T Consensus        60 ~lLIpk~PF~RLVREI~~~~~~~~R~q~~Al~aLQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa~r  130 (136)
T 1tzy_C           60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR  130 (136)
T ss_dssp             SCCSCHHHHHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             hhhhccchHHHHHHHHHHHhhhhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHhHHHHHH
Confidence            58999999999888741    24799999999999999999999999999999999999999999999975

>2z0q_A XPLN, RHO guanine nucleotide exchange factor 3; DH-PH domain, alternative splicing, cytoplasm, guanine- nucleotide releasing factor; 1.79A {Mus musculus} PDB: 3eo2_A

Probab=91.27  E-value=0.036  Score=54.91  Aligned_cols=67  Identities=4%  Similarity=-0.157  Sum_probs=52.5

Q ss_pred             hhHHHHHHhccccc----cccccccccccccccccCCcchhhhhccccCCCCcccchhhhccccccchhhhhhhcc
Q psy17765        286 VLEEHLENATGLLV----DESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAA  357 (475)
Q Consensus       286 Vfre~l~~~~~l~~----~~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~~~~~~~~~~~m~~  357 (475)
                      +|.++|....-+..    .||+|+-+|+++...|+..|++.+.-   +...+.+|.||.++++  .|++|+.|...
T Consensus        44 ~y~~~l~~~~~l~~~~~~~iF~ni~~i~~~h~~fl~~L~~~~~~---~~~~~~ig~~f~~~~~--~~~~Y~~Y~~n  114 (346)
T 2z0q_A           44 AYHDPMLKLSIMTEQELNQIFGTLDSLIPLHEELLSQLRDVRKP---DGSTEHVGPILVGWLP--CLSSYDSYCSN  114 (346)
T ss_dssp             HTHHHHHHTTSSCHHHHHHHHTTHHHHHHHHHHHHHHHHHHCCT---TSCCSCCHHHHHHHGG--GGGHHHHHHHH
T ss_pred             HHHHHHHhCCCCCHHHHHHHhccHHHHHHHHHHHHHHHHHHhcc---CCccchHHHHHHHHhh--HHHHHHHHHHC
Confidence            67777776532222    29999999999999999999987653   3457889999999876  47899999765

>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=89.88  E-value=0.63  Score=38.75  Aligned_cols=64  Identities=22%  Similarity=0.372  Sum_probs=53.5

Q ss_pred             ccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcC-CcccchhHHHHHHh
Q psy17765        144 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNK-KTRIIPRHLQLAIR  208 (475)
Q Consensus       144 ~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k-~~rItP~hI~lAI~  208 (475)
                      .||=..+.|+++. ...+.++....+-++++---++.||.|.|.......+ ...|.|.||..|.+
T Consensus        16 ~f~k~~vKrl~~~-~~~~~v~~~v~i~v~glaKvfVgelVE~A~~V~~~~~~~~Pl~P~HireA~r   80 (89)
T 1bh9_B           16 AFPKAAIKRLIQS-ITGTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVR   80 (89)
T ss_dssp             CCCHHHHHHHHHH-HHSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCHHHHHHHHH
T ss_pred             cCCHHHHHHHHHH-HcCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHH
Confidence            4667778888864 5678999999999999999999999999988876553 55899999998865

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

Probab=89.79  E-value=0.49  Score=45.90  Aligned_cols=49  Identities=18%  Similarity=0.255  Sum_probs=46.8

Q ss_pred             CcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765         52 GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  100 (475)
Q Consensus        52 ~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll  100 (475)
                      .||..+.+-+...+..+++.|+.+|..++.+.+|+|+|+.||.-|++..
T Consensus       178 RIS~~iyeelr~vLe~fle~IirdAv~yaeHA~RKTVta~DV~~ALKr~  226 (235)
T 2l5a_A          178 RISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQ  226 (235)
T ss_dssp             TTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHhc
Confidence            4999999999999999999999999999999999999999999999864

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

Probab=89.73  E-value=0.68  Score=40.73  Aligned_cols=49  Identities=12%  Similarity=0.154  Sum_probs=46.6

Q ss_pred             cccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhc
Q psy17765        161 ERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN  209 (475)
Q Consensus       161 ~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~n  209 (475)
                      .||+..+..-+..+||.+..+|+.-|..++...+++.|+..||..|+..
T Consensus        63 kRIS~~iy~e~r~vl~~~l~~i~rdav~yaehA~RKTVta~DV~~Alkr  111 (121)
T 2ly8_A           63 KRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKR  111 (121)
T ss_dssp             SCCSSCHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCBCHHHHHHHHHH
T ss_pred             cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHh
Confidence            6999999999999999999999999999999999999999999999864

>1foe_A T-lymphoma invasion and metastasis inducing protein 1; DBL homology domain, pleckstrin homology domain, GTPase, guanine nucleotide exchange factor; 2.80A {Mus musculus} SCOP: a.87.1.1 b.55.1.1

Probab=89.22  E-value=0.035  Score=55.76  Aligned_cols=71  Identities=15%  Similarity=-0.048  Sum_probs=53.3

Q ss_pred             hhHHHHHHhccccc----cccccccccccccccccCCcchhhhhcccc----------CCCCcccchhhhccccccchhh
Q psy17765        286 VLEEHLENATGLLV----DESGNTLDSTSTRQTTDGGLGDSLDVVTEY----------FPVPLGASFSESLSSLTTADLL  351 (475)
Q Consensus       286 Vfre~l~~~~~l~~----~~f~n~ld~~e~~~~~~g~leD~le~~~e~----------~~~p~~gs~fe~la~~~~~~~~  351 (475)
                      +|.++|....-+..    .||+||-+|+++...|+..|++.++..++.          ..++.+|.||.++++  .|++|
T Consensus        36 ~y~~pl~~~~~l~~~~~~~iF~ni~~I~~~h~~fl~~L~~~~~~~~~~~~~~~~~~~~~~~~~ig~~f~~~~~--~f~~Y  113 (377)
T 1foe_A           36 RYLKPLQKETFLTQDELDVLFGNLTEMVEFQVEFLKTLEDGVRLVPDLEKLEKVDQFKKVLFSLGGSFLYYAD--RFKLY  113 (377)
T ss_dssp             HTHHHHHTSSSSCHHHHHHHHSSHHHHHHHHHHHHHHHHHHHTTSSCGGGCCSGGGGHHHHHHHHHHHHHHTT--GGGGH
T ss_pred             HHHHHHHhcCCCCHHHHHHHHhCHHHHHHHHHHHHHHHHHHHhcCCcchhhhhhhhhhhHHHHHHHHHHHHHH--HHHHH
Confidence            67788876432222    299999999999999999999988754321          123579999999976  58999


Q ss_pred             hhhhccC
Q psy17765        352 SITMAAG  358 (475)
Q Consensus       352 ~~~m~~~  358 (475)
                      +.|....
T Consensus       114 ~~Y~~n~  120 (377)
T 1foe_A          114 SAFCASH  120 (377)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHhH
Confidence            9997653

>2pz1_A RHO guanine nucleotide exchange factor 4; helical bundle, beta barrel, beta sandwich, signaling protei; 2.25A {Homo sapiens} PDB: 2dx1_A 3nmz_D 3nmx_D

Probab=89.10  E-value=0.045  Score=56.59  Aligned_cols=68  Identities=9%  Similarity=-0.033  Sum_probs=51.4

Q ss_pred             hhHHHHHHhcccccc-----ccccccccccccccccCCcchhhhhccccCCCCcccchhhhccccccchhhhhhhcc
Q psy17765        286 VLEEHLENATGLLVD-----ESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAA  357 (475)
Q Consensus       286 Vfre~l~~~~~l~~~-----~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~~~~~~~~~~~m~~  357 (475)
                      +|.++|.....++.+     ||+||-+|+++...|+..|++.++-  ++.....+|.||..+++  .|++|+.|...
T Consensus       143 ~y~~~l~~~~~~l~~~~~~~iF~ni~~I~~~h~~fL~~Le~~~~~--~~~~~~~ig~~fl~~~~--~f~~Y~~Y~~n  215 (466)
T 2pz1_A          143 GYVRQCRKRADMFSEEQLRTIFGNIEDIYRCQKAFVKALEQRFNR--ERPHLSELGACFLEHQA--DFQIYSEYCNN  215 (466)
T ss_dssp             HTHHHHHHCTTTCCHHHHHHHHTTHHHHHHHHHHHHHHHHHHCCS--SCGGGCCCHHHHHHTHH--HHTTHHHHHHH
T ss_pred             HHHHHHhhCcCCCCHHHHHHHHcCHHHHHHHHHHHHHHHHHHHcc--CCCccchHHHHHHHhhH--HHHHHHHHHHh
Confidence            556666554445543     9999999999999999999887653  22224689999999874  68999999765

>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=86.79  E-value=0.33  Score=39.43  Aligned_cols=55  Identities=16%  Similarity=0.340  Sum_probs=49.1

Q ss_pred             hhhhhccccCCCCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCCcCCCCCchh
Q psy17765        394 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDLCP  448 (475)
Q Consensus       394 i~kvLkqvhp~~giS~kam~imnsfv~Diferia~Eas~L~~~~kr~Tltsr~~~  448 (475)
                      +-..++||-|...|...+...+-.+.+|.-+.+..-|++||++.+-.||..++++
T Consensus        11 L~~Lv~~idp~~~ld~~vee~ll~lADdFV~~V~~~ac~lAKhR~s~~le~kDvq   65 (76)
T 1h3o_B           11 LQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQ   65 (76)
T ss_dssp             HHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHH
T ss_pred             HHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCccHHHHH
Confidence            5567899999999999999988888888888889999999999999999998864

>2vrw_B P95VAV, VAV1, proto-oncogene VAV; lipoprotein, GTP-binding, metal-binding, phosphoprotein, exchange factor, RAC, GTPase, membrane domain; 1.85A {Mus musculus} PDB: 3bji_A 1f5x_A

Probab=85.90  E-value=0.086  Score=53.50  Aligned_cols=63  Identities=11%  Similarity=-0.127  Sum_probs=50.6

Q ss_pred             hhHHHHHHhccccc-----cccccccccccccccccCCcchhhhhccccCCCCcccchhhhccccccchhhhhhhcc
Q psy17765        286 VLEEHLENATGLLV-----DESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAA  357 (475)
Q Consensus       286 Vfre~l~~~~~l~~-----~~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~~~~~~~~~~~m~~  357 (475)
                      +|.++|..   .+.     .||+||-+|+++...|+..|++.++.    ...+.+|.||.++++  .|++|+.|...
T Consensus        50 ~f~~~l~~---~l~~~~~~~iF~ni~~i~~~h~~fl~~L~~~~~~----~~~~~ig~~f~~~~~--~~~~Y~~Y~~n  117 (406)
T 2vrw_B           50 HFMKPLQR---FLKPQDMETIFVNIEELFSVHTHFLKELKDALAG----PGATTLYQVFIKYKE--RFLVYGRYCSQ  117 (406)
T ss_dssp             HTHHHHTT---TSCHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHS----GGGTTHHHHHHHHTT--GGGHHHHHHHH
T ss_pred             HHHHHHHH---hCCHHHHHHHhcCHHHHHHHHHHHHHHHHHHhcC----CCccHHHHHHHHHHH--HHHHHHHHHHh
Confidence            66677754   233     29999999999999999999998874    235789999999976  48999999765

>1by1_A Protein (PIX); RHO-GTPase exchange factor, transport protein; NMR {Homo sapiens} SCOP: a.87.1.1

Probab=85.63  E-value=0.078  Score=49.05  Aligned_cols=135  Identities=15%  Similarity=0.070  Sum_probs=79.6

Q ss_pred             hhHHHHHHhccc----cccccccccccccccccccCCcchhhhhccccCCCCcccchhhhccccccch-hhhhhhccCCc
Q psy17765        286 VLEEHLENATGL----LVDESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTAD-LLSITMAAGKS  360 (475)
Q Consensus       286 Vfre~l~~~~~l----~~~~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~~~~~~-~~~~~m~~~~~  360 (475)
                      +|.++|....-+    ...+|+|+-+|+++...|+..|++.++.   ......+|.||.++++  .|. +|+.|......
T Consensus        38 ~y~~pl~~~~~l~~~~~~~iF~ni~~i~~~h~~fl~~L~~~~~~---~~~~~~ig~~f~~~~~--~f~~~Y~~Y~~n~~~  112 (209)
T 1by1_A           38 TYLRPLQTSEKLSSANISYLMGNLEEICSFQQMLVQSLEECTKL---PEAQQRVGGCFLNLMP--QMKTLYLTYCANHPS  112 (209)
T ss_dssp             HHHHHHTTTSSSSSSGGGTTHHHHHHHHHHHHHHHHHHHHHHHT---TCSSCCHHHHHHHHHH--HHHHHHHHHHHHHHH
T ss_pred             HHHHHhhccCCCCHHHHHHHHcCHHHHHHHHHHHHHHHHHHHcC---CcchhhHHHHHHHHHH--HHHHHHHHHHHHHHH
Confidence            677777653212    2239999999999999999999998764   2346789999999875  474 99888665311


Q ss_pred             Cccchhccc----cccccc-cccCCc--------cCcCCCccceeehhhhhcc---ccCCCCCchHHHHHHhhHHHHHHh
Q psy17765        361 SGKAVKKAG----KAQKNI-TKSDKK--------KKPRRKESYAIYIYKVLKQ---VHPDTGVSSKAMSIMNSFVNDIFE  424 (475)
Q Consensus       361 ~~k~~~~~~----~~~~~~-~~~~~k--------~~~~~~esy~~Yi~kvLkq---vhp~~giS~kam~imnsfv~Dife  424 (475)
                      +...-.+..    +--+.. ....++        +--.|--.|...+-.+||.   -|||..-=.+|...|..+++.|=|
T Consensus       113 a~~~l~~~~~~f~~fl~~~~~~~~~~l~L~s~Li~PvQRi~rY~LLL~~Llk~t~~~h~d~~~l~~Al~~i~~v~~~iNe  192 (209)
T 1by1_A          113 AVNVLTEHSEELGEFMETKGASSPGILVLTTGLSKPFMRLDKYPTLLKELERHMEDYHTDRQDIQKSMAAFKNLSAQCQE  192 (209)
T ss_dssp             HHHHHHHHTTTHHHHTTTTCCCSSTTTHHHHHTTSTTTGGGTHHHHHHHHHHSSCCCSSSTHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCHHHHHHHHHhcCCCCCcCCHHHHhhHHHHHHhHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHH
Confidence            111100000    000000 000000        0011233455555556664   377777778888888888776654


Q ss_pred             H
Q psy17765        425 R  425 (475)
Q Consensus       425 r  425 (475)
                      .
T Consensus       193 ~  193 (209)
T 1by1_A          193 V  193 (209)
T ss_dssp             H
T ss_pred             H
Confidence            3

>1nty_A Triple functional domain protein; DBL, pleckstrin, GEF, RHO, GTPase, guanine-nucleotide releas factor, phosphorylation, signaling protein; 1.70A {Homo sapiens} SCOP: a.87.1.1 b.55.1.1 PDB: 2nz8_B 2kr9_A

Probab=85.47  E-value=0.14  Score=50.06  Aligned_cols=64  Identities=5%  Similarity=-0.137  Sum_probs=49.1

Q ss_pred             hhHHHHHHhcc-cc-------ccccccccccccccc-cccCCcchhhhhccccCCCCcccchhhhccccccchhhhhhhc
Q psy17765        286 VLEEHLENATG-LL-------VDESGNTLDSTSTRQ-TTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMA  356 (475)
Q Consensus       286 Vfre~l~~~~~-l~-------~~~f~n~ld~~e~~~-~~~g~leD~le~~~e~~~~p~~gs~fe~la~~~~~~~~~~~m~  356 (475)
                      +|.++|..... +.       ..||+|+-+|+++.. .|+..|++..+.      .+.+|.||..+++  .|++|+.|..
T Consensus        34 ~y~~~l~~~~~~l~~~~~~~~~~iF~ni~~i~~~h~~~fl~~L~~~~~~------~~~ig~~f~~~~~--~~~~Y~~Y~~  105 (311)
T 1nty_A           34 TYLWEMTSGVEEIPPGIVNKELIIFGNMQEIYEFHNNIFLKELEKYEQL------PEDVGHCFVTWAD--KFQMYVTYCK  105 (311)
T ss_dssp             HHHHHHHHCCSCCCTTTTTCHHHHHTTHHHHHHHHHHTHHHHHHHTTTC------GGGTHHHHHHTTT--TTHHHHHHHH
T ss_pred             HHHHHHHhhccCCChhhhhhHHHhhcCHHHHHHHHHHHHHHHHHHHHCC------HHHHHHHHHHHHH--HhHHHHHHHh
Confidence            78888876332 11       239999999999998 499988886532      3689999999886  5799998866


Q ss_pred             c
Q psy17765        357 A  357 (475)
Q Consensus       357 ~  357 (475)
                      .
T Consensus       106 n  106 (311)
T 1nty_A          106 N  106 (311)
T ss_dssp             H
T ss_pred             C
Confidence            5

>3p6a_A RHO guanine nucleotide exchange factor 1; regulation of RHOA GTPase, rhogef, DH, PH, signaling PR; 2.50A {Homo sapiens} PDB: 3odo_A

Probab=84.94  E-value=0.12  Score=51.52  Aligned_cols=70  Identities=3%  Similarity=-0.195  Sum_probs=50.0

Q ss_pred             hhHHHHHHhccccc----cccccccccccccccccCCcchhhhhccccCCCCcccchhhhccccc---cc-hhhhhhhcc
Q psy17765        286 VLEEHLENATGLLV----DESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLT---TA-DLLSITMAA  357 (475)
Q Consensus       286 Vfre~l~~~~~l~~----~~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~~~---~~-~~~~~~m~~  357 (475)
                      +|.++|....-+..    .||+|+-+|+++.+.++..|++.+.  +.+..++.+|.||...++-.   .| ++|+.|...
T Consensus        52 ~y~~~l~~~~~l~~~~~~~iF~ni~~I~~~h~~fl~~L~~~~~--~~~~~~~~ig~~fl~~~~~~~~~~~~~~Y~~Y~~n  129 (377)
T 3p6a_A           52 LFFQPMAECLFFPLEELQNIFPSLDELIEVHSLFLDRLMKRRQ--ESGYLIEEIGDVLLARFDGAEGSWFQKISSRFCSR  129 (377)
T ss_dssp             HTHHHHHHHTSSCHHHHHHHSTTHHHHHHHHHHHHHHHHHHHH--HC--CCCCCHHHHHHHHSHHHHHHHHHHHHHHHHT
T ss_pred             HHHHhhhhcCCCCHHHHHHHHccHHHHHHHHHHHHHHHHHHHh--ccCCCCCcHHHHHHHHhcchhhHHHHHHHHHHHHh
Confidence            67777765432222    2999999999999999988887654  23345789999999987642   23 788888665

>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=83.93  E-value=2.6  Score=34.54  Aligned_cols=64  Identities=20%  Similarity=0.223  Sum_probs=55.8

Q ss_pred             CcccchhHHHHHHhhcC--cccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHH
Q psy17765        142 GLQFPVGRIHRLLRKGN--YAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQL  205 (475)
Q Consensus       142 gL~FPVsRi~r~Lke~~--~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~l  205 (475)
                      +..||..-|+++|+..-  -..||+..|-.-++..|+-++.|.+..|...|+..+...|..+||+.
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            46899999999998732  23699999999999999999999999999998888888999999986

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

Probab=83.64  E-value=3.3  Score=34.23  Aligned_cols=66  Identities=18%  Similarity=0.173  Sum_probs=55.2

Q ss_pred             CCCcccchhHHHHHHhhcC--cccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHH
Q psy17765        140 RAGLQFPVGRIHRLLRKGN--YAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQL  205 (475)
Q Consensus       140 RagL~FPVsRi~r~Lke~~--~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~l  205 (475)
                      .++..||..-|.|+|+..-  -..||+..|---++..|+-++.|.+-.|...|...+...|..+||+.
T Consensus         8 ~~~~~i~~~li~ril~~~F~~~kTkIs~dAl~l~aeyl~iFV~EAv~RA~~~a~~e~~~~le~e~LEk   75 (84)
T 4dra_E            8 GAGSGFRKELVSRLLHLHFKDDKTKVSGDALQLMVELLKVFVVEAAVRGVRQAQAEDALRVDVDQLEK   75 (84)
T ss_dssp             ---CCCCHHHHHHHHHTTCSSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHhcCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHH
Confidence            4578999999999999432  23699999999999999999999999999888877777899999985

>2rgn_B RHOA/RAC/CDC42 exchange factor; heterotrimeric G-protein, small molecular weight G-protein, complex, protein-protein complex, rhogef, galphaq; HET: GDP; 3.50A {Homo sapiens}

Probab=83.29  E-value=0.17  Score=50.53  Aligned_cols=65  Identities=9%  Similarity=-0.120  Sum_probs=50.7

Q ss_pred             hhHHHHHHhc--ccc----cccccccccccccccc-ccCCcchhhhhccccCCCCcccchhhhccccccchhhhhhhccC
Q psy17765        286 VLEEHLENAT--GLL----VDESGNTLDSTSTRQT-TDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAAG  358 (475)
Q Consensus       286 Vfre~l~~~~--~l~----~~~f~n~ld~~e~~~~-~~g~leD~le~~~e~~~~p~~gs~fe~la~~~~~~~~~~~m~~~  358 (475)
                      +|.++|....  ..+    ..||+||-+|+++... |+..|++.++-      .+.+|.||.++++  .|++|+.|....
T Consensus        37 ~y~~~l~~~~~p~~l~~~~~~iF~ni~~I~~~h~~~fl~~L~~~~~~------~~~ig~~fl~~~~--~f~~Y~~Y~~n~  108 (354)
T 2rgn_B           37 GYMATMAAQGVPESLRGRDRIVFGNIQQIYEWHRDYFLQELQRCLKD------PDWLAQLFIKHER--RLHMYVVYCQNK  108 (354)
T ss_dssp             THHHHHHHHCCCSSSGGGHHHHHTTHHHHHHHHHHTHHHHHHHHHSC------GGGHHHHHHHTTT--TTHHHHHHHHTS
T ss_pred             HHHHHHHhcCCchhhhhhHHHHhhCHHHHHHHHHHHHHHHHHHHHcC------HHHHHHHHHHhHH--HHHHHHHHHhCc
Confidence            6788887642  112    2399999999999998 89999887642      3689999999976  589999997764

>3mpx_A FYVE, rhogef and PH domain-containing protein 5; structural genomics consortium, DH domain, SGC, L binding protein; 2.80A {Homo sapiens}

Probab=82.76  E-value=0.16  Score=51.81  Aligned_cols=52  Identities=10%  Similarity=-0.160  Sum_probs=45.0

Q ss_pred             ccccccccccccccccCCcchhhhhccccCCCCcccchhhhccccccchhhhhhhcc
Q psy17765        301 ESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAA  357 (475)
Q Consensus       301 ~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~~~~~~~~~~~m~~  357 (475)
                      ||+||.+|+++.+.|+..|++.++.-   ...+.+|.||..+++.  +++|..|...
T Consensus        75 iF~ni~~I~~~h~~fL~~L~~~~~~~---~~~~~ig~ifl~~~~~--~~~Y~~Y~~n  126 (434)
T 3mpx_A           75 GLSELPAIHDLHQGILEELEERLSNW---ESQQKVADVFLAREQG--FDHHATHILQ  126 (434)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTT---TTCCCCTHHHHTTTTT--HHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHHHHHHHHHhc---cCcccHHHHHHHhhHH--HHHHHHHHHh
Confidence            99999999999999999999988753   3468999999999875  8899988664

>1xcg_A PDZ-rhogef, RHO guanine nucleotide exchange factor 11; X-RAY crystallography, regulation of RHOA GTPase, protein complex; 2.50A {Homo sapiens} SCOP: a.87.1.1 b.55.1.1 PDB: 3kz1_A*

Probab=82.02  E-value=0.21  Score=49.65  Aligned_cols=68  Identities=4%  Similarity=-0.094  Sum_probs=50.4

Q ss_pred             hhHHHHHHhccccc-----cccccccccccccccccCCcchhhhhccccCCCCcccchhhhccc----cccchhhhhhhc
Q psy17765        286 VLEEHLENATGLLV-----DESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSS----LTTADLLSITMA  356 (475)
Q Consensus       286 Vfre~l~~~~~l~~-----~~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~----~~~~~~~~~~m~  356 (475)
                      +|.++|.... ++.     .||+|+-+|+++...++..|++.++   ++..++.+|.||.+...    ..-+++|..|..
T Consensus        46 ~f~~~l~~~~-~l~~~~~~~iF~ni~~i~~~h~~fl~~L~~~~~---~~~~~~~ig~~f~~~~~~~~~~~~~~~Y~~Y~~  121 (368)
T 1xcg_A           46 IFYQRMKKEN-LMPREELARLFPNLPELIEIHNSWCEAMKKLRE---EGPIIKEISDLMLARFDGPAREELQQVAAQFCS  121 (368)
T ss_dssp             HTHHHHHHTT-SSCHHHHHHHSSSHHHHHHHHHHHHHHHHHHHH---TCSSCCCCHHHHHHHHSHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHhcC-CCCHHHHHHHhCCHHHHHHHHHHHHHHHHHHHh---cCCCcCcHHHHHHHHccchhHHHHHHHHHHHHh
Confidence            6777777643 332     2999999999999999998887654   44456789999988543    124788888865


Q ss_pred             c
Q psy17765        357 A  357 (475)
Q Consensus       357 ~  357 (475)
                      .
T Consensus       122 ~  122 (368)
T 1xcg_A          122 Y  122 (368)
T ss_dssp             T
T ss_pred             h
Confidence            4

>3odw_A RHO guanine nucleotide exchange factor 1; regulation of RHOA GTPase, rhogef, DH, PH, signaling PR; 3.20A {Homo sapiens} PDB: 3odx_A

Probab=80.28  E-value=0.24  Score=52.71  Aligned_cols=69  Identities=3%  Similarity=-0.195  Sum_probs=48.4

Q ss_pred             hhHHHHHHhcccccc-----ccccccccccccccccCCcchhhhhccccCCCCcccchhhhcccc---ccc-hhhhhhhc
Q psy17765        286 VLEEHLENATGLLVD-----ESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSL---TTA-DLLSITMA  356 (475)
Q Consensus       286 Vfre~l~~~~~l~~~-----~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~~---~~~-~~~~~~m~  356 (475)
                      +|.++|.... ++.+     ||+||.+|+++.+.|+..|++.+.  +.+..++.+|.||..+++-   +.| ++|..|..
T Consensus       205 ~y~~pl~~~~-~l~~~~~~~IF~nie~I~~~h~~fL~~L~~~~~--~~~~~~~~Igdifl~~~~~~~~~~f~~~Y~~Y~~  281 (536)
T 3odw_A          205 LFFQPMAECL-FFPLEELQNIFPSLDELIEVHSLFLDRLMKRRQ--ESGYLIEEIGDVLLARFDGAEGSWFQKISSRFCS  281 (536)
T ss_dssp             HTHHHHHHTT-SSCHHHHHHHSTTHHHHHHHHHHHHHHHHHHHH--TC---CCCCHHHHHHHHSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcC-CCCHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH--hcCcccccHHHHHHHHcchhhhHHHHHHHHHHHh
Confidence            5666666532 2332     999999999999999988887543  2234578999999998763   224 78888876


Q ss_pred             c
Q psy17765        357 A  357 (475)
Q Consensus       357 ~  357 (475)
                      .
T Consensus       282 n  282 (536)
T 3odw_A          282 R  282 (536)
T ss_dssp             T
T ss_pred             h
Confidence            5

---

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	475
d1q9ca_	172	a.22.1.3 (A:) Histone domain of Son of sevenless p	1e-67
d1q9ca_	172	a.22.1.3 (A:) Histone domain of Son of sevenless p	2e-12
d1tzya_	106	a.22.1.1 (A:) Histone H2A {Chicken (Gallus gallus)	4e-57
d1tzyb_	92	a.22.1.1 (B:) Histone H2B {Chicken (Gallus gallus)	2e-55
d1tzyb_	92	a.22.1.1 (B:) Histone H2B {Chicken (Gallus gallus)	8e-31
d1u35c1	106	a.22.1.1 (C:814-919) macro-H2A.1, histone domain {	2e-54
d1f66c_	103	a.22.1.1 (C:) Histone H2A {Human (Homo sapiens), v	5e-48
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	1e-34
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	5e-14
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	3e-10
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	3e-04
d1jfia_	66	a.22.1.3 (A:) Negative cofactor 2, NC2, alpha chai	9e-22
d1jfia_	66	a.22.1.3 (A:) Negative cofactor 2, NC2, alpha chai	0.001
d1n1jb_	78	a.22.1.3 (B:) Nuclear transcription factor Y subun	3e-19

>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 =  212 bits (541), Expect = 1e-67
 Identities = 40/192 (20%), Positives = 83/192 (43%), Gaps = 28/192 (14%)

Query: 26  KKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR 85
           ++   + +      + KV  QVHP    +  A+  +   +  +   +     R       
Sbjct: 8   EENAPKWRGLLVPALKKVQGQVHPTLESNDDALQYVEELILQLLNMLCQAQPR------- 60

Query: 86  STITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSKGKGGKAKTKSKTRSSRAGLQF 145
              ++ +++  V+   P  + K A+++   A+ K                 R  R  L  
Sbjct: 61  ---SASDVEERVQKSFPHPIDKWAIADAQSAIEK-----------------RKRRNPLSL 100

Query: 146 PVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQL 205
           PV +IH LL++     ++     VY+ AV+EY++A++L+LAGN  R+ +   I  + +++
Sbjct: 101 PVEKIHPLLKEV-LGYKIDHQVSVYIVAVLEYISADILKLAGNYVRNIRHYEITKQDIKV 159

Query: 206 AIRNDEELNKLL 217
           A+  D+ L  + 
Sbjct: 160 AMCADKVLMDMF 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 = 63.3 bits (154), Expect = 2e-12
 Identities = 10/56 (17%), Positives = 21/56 (37%)

Query: 380 KKKKPRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAH 435
           ++  P+ +      + KV  QVHP    +  A+  +   +  +   +     R A 
Sbjct: 8   EENAPKWRGLLVPALKKVQGQVHPTLESNDDALQYVEELILQLLNMLCQAQPRSAS 63

>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 =  182 bits (464), Expect = 4e-57
 Identities = 94/102 (92%), Positives = 99/102 (97%)

Query: 133 KSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARD 192
           K+K+RSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAV+EYL AE+LELAGNAARD
Sbjct: 1   KAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARD 60

Query: 193 NKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV 234
           NKKTRIIPRHLQLAIRNDEELNKLL  VTIAQGGVLPNIQAV
Sbjct: 61  NKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAV 102

>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 =  177 bits (451), Expect = 2e-55
 Identities = 86/92 (93%), Positives = 90/92 (97%)

Query: 32  RKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSR 91
           RKESY+IY+YKVLKQVHPDTG+SSKAM IMNSFVNDIFERIA E+SRLAHYNKRSTITSR
Sbjct: 1   RKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSR 60

Query: 92  EIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS 123
           EIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS
Sbjct: 61  EIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS 92

>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 =  112 bits (281), Expect = 8e-31
 Identities = 52/59 (88%), Positives = 56/59 (94%)

Query: 386 RKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITK 444
           RKESY+IY+YKVLKQVHPDTG+SSKAM IMNSFVNDIFERIA E+SRLAHYNKRSTIT 
Sbjct: 1   RKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITS 59

>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 =  175 bits (445), Expect = 2e-54
 Identities = 65/100 (65%), Positives = 81/100 (81%)

Query: 135 KTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNK 194
            +RS++AG+ FPVGR+ R ++KG+   R+G GAPVY+AAV+EYL AE+LELA NAARDNK
Sbjct: 2   TSRSAKAGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNK 61

Query: 195 KTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV 234
           K R+ PRH+ LA+ NDEELN+LL GVTIA GGVLPNI   
Sbjct: 62  KGRVTPRHILLAVANDEELNQLLKGVTIASGGVLPNIHPE 101

>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 =  158 bits (402), Expect = 5e-48
 Identities = 64/102 (62%), Positives = 76/102 (74%), Gaps = 2/102 (1%)

Query: 134 SKTRSSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVMEYLAAEVLELAGNAARD 192
           + +RS RAGLQFPVGRIHR L+    +  RVGA A VY AA++EYL AEVLELAGNA++D
Sbjct: 1   AVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKD 60

Query: 193 NKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAV 234
            K  RI PRHLQLAIR DEEL+ L+   TIA GGV+P+I   
Sbjct: 61  LKVKRITPRHLQLAIRGDEELDSLI-KATIAGGGVIPHIHKS 101

>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 =  124 bits (314), Expect = 1e-34
 Identities = 23/170 (13%), Positives = 56/170 (32%), Gaps = 33/170 (19%)

Query: 40  IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL 99
           I ++ +Q   +  +S  A   +  FV  + E +A  +  +   + + T+    ++    +
Sbjct: 7   IERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADV 66

Query: 100 LLPGELAKHAVSEGTKAVTKYTSSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNY 159
           L+   +  +                                 G  F    + R+L++   
Sbjct: 67  LMVEGVEDYD--------------------------------GELFGRATVRRILKRAG- 93

Query: 160 AERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN 209
            ER  + A      ++     E+ E A   A ++ +  +    ++ AI  
Sbjct: 94  IERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITY 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 = 67.1 bits (164), Expect = 5e-14
 Identities = 9/52 (17%), Positives = 24/52 (46%)

Query: 394 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKD 445
           I ++ +Q   +  +S  A   +  FV  + E +A  +  +   + + T+ ++
Sbjct: 7   IERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEE 58

>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 = 3e-10
 Identities = 13/65 (20%), Positives = 25/65 (38%)

Query: 144 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHL 203
           + P   I R+ R+G    R+   A   +   +  +A  V   A +    + K  ++  HL
Sbjct: 1   ELPKAAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHL 60

Query: 204 QLAIR 208
           +    
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 = 39.0 bits (91), Expect = 3e-04
 Identities = 13/55 (23%), Positives = 27/55 (49%), Gaps = 2/55 (3%)

Query: 53  VSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLP--GEL 105
            SS A+ + N  +    E +  +++  A  + R T+   +++ A+   +P  GEL
Sbjct: 97  ASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITYSMPKGGEL 151

>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 = 86.3 bits (214), Expect = 9e-22
 Identities = 14/64 (21%), Positives = 28/64 (43%)

Query: 144 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHL 203
           +FP  RI ++++      +V A  PV ++  +E     +L+ A    +      +   HL
Sbjct: 2   RFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHL 61

Query: 204 QLAI 207
           +  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 = 35.1 bits (81), Expect = 0.001
 Identities = 7/58 (12%), Positives = 25/58 (43%)

Query: 40 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAV 97
          I K+++       V++    I++  +    E +  ++ ++       T+T+  ++  +
Sbjct: 8  IKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQCI 65

>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 = 79.5 bits (196), Expect = 3e-19
 Identities = 17/75 (22%), Positives = 34/75 (45%)

Query: 146 PVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQL 205
           P+ RI ++++     + + A APV  A   +    E+   A     DNK+  +    + +
Sbjct: 2   PLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAM 61

Query: 206 AIRNDEELNKLLSGV 220
           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	475
d1q9ca_	172	Histone domain of Son of sevenless protein {Human	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
d1tzyb_	92	Histone H2B {Chicken (Gallus gallus), erythrocytes	100.0
d1tzyb_	92	Histone H2B {Chicken (Gallus gallus), erythrocytes	99.97
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	99.89
d1jfia_	66	Negative cofactor 2, NC2, alpha chain {Human (Homo	99.2
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	99.09
d1n1jb_	78	Nuclear transcription factor Y subunit gamma (Nf-Y	98.89
d1q9ca_	172	Histone domain of Son of sevenless protein {Human	98.71
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	98.07
d1ku5a_	66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	98.04
d1n1ja_	87	Nuclear transcription factor Y subunit beta (Nf-Yb	97.83
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	97.6
d1dbha1	207	Son of sevenless-1 (sos-1) {Human (Homo sapiens) [	97.45
d1jfib_	135	Negative cofactor 2, NC2, beta chain {Human (Homo	97.27
d1ku5a_	66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	97.26
d1n1ja_	87	Nuclear transcription factor Y subunit beta (Nf-Yb	96.83
d1jfia_	66	Negative cofactor 2, NC2, alpha chain {Human (Homo	96.64
d1jfib_	135	Negative cofactor 2, NC2, beta chain {Human (Homo	96.57
d2bykb1	89	Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax	96.56
d2byka1	72	Chrac-16 {Fruit fly (Drosophila melanogaster) [Tax	96.53
d2bykb1	89	Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax	96.52
d1n1jb_	78	Nuclear transcription factor Y subunit gamma (Nf-Y	96.02
d2huec1	82	Histone H4 {African clawed frog (Xenopus laevis) [	95.98
d1tzyc_	95	Histone H3 {Chicken (Gallus gallus), erythrocytes	95.57
d2huec1	82	Histone H4 {African clawed frog (Xenopus laevis) [	95.57
d1h3ob_	74	TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom	94.98
d1tzya_	106	Histone H2A {Chicken (Gallus gallus), erythrocytes	93.35
d1u35c1	106	macro-H2A.1, histone domain {Human (Homo sapiens)	93.3
d1f66c_	103	Histone H2A {Human (Homo sapiens), variant H2A.Z [	90.76
d1bh9b_	89	TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]}	90.4
d1ki1b1	210	GEF of intersectin {Human (Homo sapiens) [TaxId: 9	90.36
d1tafb_	70	TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta	90.25
d1tzyc_	95	Histone H3 {Chicken (Gallus gallus), erythrocytes	89.03
d2dfka1	203	Rho guanine nucleotide exchange factor 9, Collybis	85.75
d2byka1	72	Chrac-16 {Fruit fly (Drosophila melanogaster) [Tax	83.73
d1h3ob_	74	TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom	82.75
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	81.35

>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=100.00  E-value=1.2e-47  Score=354.59  Aligned_cols=162  Identities=24%  Similarity=0.446  Sum_probs=147.5

Q ss_pred             cccCchhHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHHH
Q psy17765         29 KHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKH  108 (475)
Q Consensus        29 ~~k~~~sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaKh  108 (475)
                      .++|++.|..||+|||+||||+++|+++|+++||+|++++|++|+.          ..|.|++|||.+|+++||++|++|
T Consensus        11 ~~~w~g~f~~~i~KVl~qvhP~l~i~~~Al~~i~~~i~~ll~~L~~----------~~p~sv~dVe~~v~~~fp~~i~~~   80 (172)
T d1q9ca_          11 APKWRGLLVPALKKVQGQVHPTLESNDDALQYVEELILQLLNMLCQ----------AQPRSASDVEERVQKSFPHPIDKW   80 (172)
T ss_dssp             HHHHTTSSHHHHHHHHHHHCSSSBCCHHHHHHHHHHHHHHHHHHHT----------TCCCSTTHHHHHHHHSSCTTHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHHHHHHHHHc----------cCCccHHHHHHHHHHhCCchHHHH
Confidence            5689999999999999999999999999999999999999999762          456799999999999999999999


Q ss_pred             HHHHhhhhhhhccccCCCCCCCCCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhH
Q psy17765        109 AVSEGTKAVTKYTSSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGN  188 (475)
Q Consensus       109 AvseG~kAV~ky~sSkg~~~k~~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn  188 (475)
                      |++++.+++.+                 +|+|+||+|||+||+|+||++ +++||+++|+|||+||||||++||||+|||
T Consensus        81 ai~~a~~~~~s-----------------rs~ragL~fPV~rv~rlLk~~-~a~RVs~~A~vyLaavLEyl~aeILelAgn  142 (172)
T d1q9ca_          81 AIADAQSAIEK-----------------RKRRNPLSLPVEKIHPLLKEV-LGYKIDHQVSVYIVAVLEYISADILKLAGN  142 (172)
T ss_dssp             HHHHHHHHHC-------------------------CCCHHHHHHHHHHH-HSSCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhc-----------------cccccCceecHHHHHHHHHhc-cccccccchHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999864                 688999999999999999986 899999999999999999999999999999


Q ss_pred             HHHhcCCcccchhHHHHHHhccHHHHhhhc
Q psy17765        189 AARDNKKTRIIPRHLQLAIRNDEELNKLLS  218 (475)
Q Consensus       189 ~A~~~k~~rItP~hI~lAI~nD~EL~~Lf~  218 (475)
                      +|+++++++|+|+||++||+||+||++||+
T Consensus       143 ~a~~~krkrItp~dI~lAi~nD~eL~~Lf~  172 (172)
T d1q9ca_         143 YVRNIRHYEITKQDIKVAMCADKVLMDMFH  172 (172)
T ss_dssp             HHHHHTCSBCCHHHHHHHHHTCHHHHHHCC
T ss_pred             HHHHcCCceecHHHHHHHHhCCHHHHHhhC
Confidence            999999999999999999999999999994

>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=1.7e-42  Score=297.29  Aligned_cols=105  Identities=89%  Similarity=1.267  Sum_probs=103.1

Q ss_pred             ccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHH
Q psy17765        134 SKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEEL  213 (475)
Q Consensus       134 ~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL  213 (475)
                      .+|||+|||||||||||||+||+++|++||+++|||||+||||||++||||||||+|++++++||+|+||++||+||+||
T Consensus         2 ~~Srs~rAgL~FpV~rv~r~Lk~~~~~~rv~~~apVylaAVLEYLtaEiLELAgn~a~~~k~~rItPrhi~lAirnDeeL   81 (106)
T d1tzya_           2 AKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEEL   81 (106)
T ss_dssp             CCCHHHHHTCSSCHHHHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHTSHHH
T ss_pred             CccccccCCccCChHHHHHHHHcCccccccCCCchHHHHHHHHHHHHHHHHHhhHHHHhcCCceecchhhhhcccCHHHH
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhcCceecCCcccCCcccccccc
Q psy17765        214 NKLLSGVTIAQGGVLPNIQAVRVLE  238 (475)
Q Consensus       214 ~~Lf~~~tIa~gGV~p~i~~~ll~~  238 (475)
                      ++||+++||++|||+|+||++||||
T Consensus        82 ~~L~~~vtI~~GGv~P~Ih~~Llpk  106 (106)
T d1tzya_          82 NKLLGKVTIAQGGVLPNIQAVLLPK  106 (106)
T ss_dssp             HHHTTTEEETTCCCCCCCCGGGSCC
T ss_pred             HHHHcCCeecCCCccCccCHhhcCC
Confidence            9999999999999999999999986

>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=3.2e-42  Score=295.73  Aligned_cols=105  Identities=62%  Similarity=0.982  Sum_probs=103.2

Q ss_pred             cCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHHH
Q psy17765        135 KTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELN  214 (475)
Q Consensus       135 ~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL~  214 (475)
                      .|||+|||||||||||||+|++++|++||+++||||||||||||++||||||||+|++++++||+|+||++||+||+||+
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            47899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhcCceecCCcccCCccccccccc
Q psy17765        215 KLLSGVTIAQGGVLPNIQAVRVLEQ  239 (475)
Q Consensus       215 ~Lf~~~tIa~gGV~p~i~~~ll~~~  239 (475)
                      +||+++||++|||+|+||++|||+|
T Consensus        82 ~L~~~vtI~~GGv~p~Ih~~Ll~kk  106 (106)
T d1u35c1          82 QLLKGVTIASGGVLPNIHPELLAKK  106 (106)
T ss_dssp             HHTTTEEETTCCCCCCCCGGGSCCC
T ss_pred             HHHcCCeEeCCcccCCcCHHhcCCC
Confidence            9999999999999999999999986

>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=8.3e-40  Score=279.72  Aligned_cols=101  Identities=63%  Similarity=0.949  Sum_probs=97.7

Q ss_pred             cCcCCCCCcccchhHHHHHHhhcCccc-ccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHH
Q psy17765        135 KTRSSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEEL  213 (475)
Q Consensus       135 ~srSsRagL~FPVsRi~r~Lke~~~~~-RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL  213 (475)
                      .|||+|||||||||||||||++++|++ ||+++|||||+||||||++||||+|||++++++++||||+||++||+||+||
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            578999999999999999999999985 7999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhcCceecCCcccCCcccccc
Q psy17765        214 NKLLSGVTIAQGGVLPNIQAVRV  236 (475)
Q Consensus       214 ~~Lf~~~tIa~gGV~p~i~~~ll  236 (475)
                      |+||+ +||++|||+|+||++||
T Consensus        82 ~~L~~-vti~~GGv~p~I~~~Ll  103 (103)
T d1f66c_          82 DSLIK-ATIAGGGVIPHIHKSLI  103 (103)
T ss_dssp             HHHCC-SEETTCCCCCCCCGGGC
T ss_pred             HHHhC-eEeeCCeecccccHhhC
Confidence            99995 99999999999999986

>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=1.5e-36  Score=254.12  Aligned_cols=92  Identities=93%  Similarity=1.267  Sum_probs=90.0

Q ss_pred             CchhHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHHHHHH
Q psy17765         32 RKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVS  111 (475)
Q Consensus        32 ~~~sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaKhAvs  111 (475)
                      |+++|+.||||||||||||+|||++||.+||+||+|+|||||.||++|+++++|+|||+||||+||+++|||||+|||++
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            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Hhhhhhhhcccc
Q psy17765        112 EGTKAVTKYTSS  123 (475)
Q Consensus       112 eG~kAV~ky~sS  123 (475)
                      ||++||++|++|
T Consensus        81 eGtkAv~ky~ss   92 (92)
T d1tzyb_          81 EGTKAVTKYTSS   92 (92)
T ss_dssp             HHHHHHHHHHHC
T ss_pred             HHHHHHHHhccC
Confidence            999999999865

>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=99.97  E-value=8.3e-33  Score=231.36  Aligned_cols=68  Identities=79%  Similarity=1.104  Sum_probs=65.6

Q ss_pred             CCccceeehhhhhccccCCCCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCCcCCCCCc-hhheehc
Q psy17765        386 RKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDL-CPSVCLY  453 (475)
Q Consensus       386 ~~esy~~Yi~kvLkqvhp~~giS~kam~imnsfv~Diferia~Eas~L~~~~kr~Tltsr~-~~~~~~~  453 (475)
                      |+|+|++||||||||||||+|||++||+||||||||||||||.||++|++||||+|||+|| |+||+|+
T Consensus         1 R~esy~~Yi~kVLKqVhp~~giS~kam~imnsfvndiferIa~EA~~La~~~kr~TitsreIqtAvrL~   69 (92)
T d1tzyb_           1 RKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLL   69 (92)
T ss_dssp             CCCCCHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999999999999999999999999986 8899883

>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=99.89  E-value=4.5e-23  Score=186.05  Aligned_cols=139  Identities=17%  Similarity=0.227  Sum_probs=130.1

Q ss_pred             HHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHHHHHHHhhhhh
Q psy17765         38 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAV  117 (475)
Q Consensus        38 ~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaKhAvseG~kAV  117 (475)
                      ..|+||+||++|+.+||.+|+++|++++++++++|+.||..||.+++|+|++.+||+.|++.++++++.+          
T Consensus         5 a~I~rilk~~~~~~ris~da~~~l~~~~~~~~~~Ia~eA~~l~~~~~rKTi~~edi~~a~~~~~~~~~~~----------   74 (151)
T d1f1ea_           5 AAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADVLMVEGVED----------   74 (151)
T ss_dssp             HHHHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHHHTCTTSTT----------
T ss_pred             cHHHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhcccccccc----------
Confidence            4699999999999999999999999999999999999999999999999999999999999988766643          


Q ss_pred             hhccccCCCCCCCCCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcc
Q psy17765        118 TKYTSSKGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTR  197 (475)
Q Consensus       118 ~ky~sSkg~~~k~~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~r  197 (475)
                                            ++++.||+++|.|++++. -..||+..|..+|+.++||++.+|++.|.++|.+.+++.
T Consensus        75 ----------------------~~~~~fp~a~IkRi~k~~-g~~ris~dA~~~l~~~~E~fi~~l~~~A~~~a~~~kRkT  131 (151)
T d1f1ea_          75 ----------------------YDGELFGRATVRRILKRA-GIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKT  131 (151)
T ss_dssp             ----------------------CCSCCCCHHHHHHHHHHT-TCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSE
T ss_pred             ----------------------cccCccCHHHHHHHHHcC-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence                                  347899999999999975 467999999999999999999999999999999999999


Q ss_pred             cchhHHHHHHhc
Q psy17765        198 IIPRHLQLAIRN  209 (475)
Q Consensus       198 ItP~hI~lAI~n  209 (475)
                      |+|+||+.||+.
T Consensus       132 I~~~DI~~Av~~  143 (151)
T d1f1ea_         132 VQGEDVEKAITY  143 (151)
T ss_dssp             ECHHHHHHHHHH
T ss_pred             CCHHHHHHHHHH
Confidence            999999999974

>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=99.20  E-value=8.6e-12  Score=96.92  Aligned_cols=65  Identities=22%  Similarity=0.449  Sum_probs=59.6

Q ss_pred             ccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765        144 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  208 (475)
Q Consensus       144 ~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~  208 (475)
                      +||++||+++||.+....+|+..|+++++.++|||+.++++.|++.++..++++|+|+||..||.
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            69999999999999999999999999999999999999999999999999999999999998863

>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=99.09  E-value=1e-11  Score=111.06  Aligned_cols=59  Identities=15%  Similarity=0.213  Sum_probs=55.1

Q ss_pred             hhhhhccccCCCCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCCcCCCCCch-hheeh
Q psy17765        394 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDLC-PSVCL  452 (475)
Q Consensus       394 i~kvLkqvhp~~giS~kam~imnsfv~Diferia~Eas~L~~~~kr~Tltsr~~-~~~~~  452 (475)
                      |+|+|||+||+.+||.+||.+||+|++|+|++||.||..|+.+++|.||+++++ .++++
T Consensus         7 I~rilk~~~~~~ris~da~~~l~~~~~~~~~~Ia~eA~~l~~~~~rKTi~~edi~~a~~~   66 (151)
T d1f1ea_           7 IERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADV   66 (151)
T ss_dssp             HHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHH
T ss_pred             HHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHh
Confidence            899999999999999999999999999999999999999999999999999874 44454

>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=98.89  E-value=1.8e-09  Score=85.79  Aligned_cols=73  Identities=22%  Similarity=0.377  Sum_probs=69.5

Q ss_pred             cchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHHHhhh
Q psy17765        145 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLL  217 (475)
Q Consensus       145 FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL~~Lf  217 (475)
                      +|++||.|+||......+|+..|+++++.++|+++.++.+.|++.|++.+++.|+++||..||+++++++.|-
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            6999999999988788999999999999999999999999999999999999999999999999999987765

>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=98.71  E-value=2.1e-09  Score=97.95  Aligned_cols=56  Identities=14%  Similarity=0.166  Sum_probs=48.4

Q ss_pred             CccceeehhhhhccccCCCCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCCcCCCCCc-hhheeh
Q psy17765        387 KESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDL-CPSVCL  452 (475)
Q Consensus       387 ~esy~~Yi~kvLkqvhp~~giS~kam~imnsfv~Diferia~Eas~L~~~~kr~Tltsr~-~~~~~~  452 (475)
                      +..|..||+|||+||||++||+.+||.+||+|++++|++|+          ...+.|.+| +.+|++
T Consensus        15 ~g~f~~~i~KVl~qvhP~l~i~~~Al~~i~~~i~~ll~~L~----------~~~p~sv~dVe~~v~~   71 (172)
T d1q9ca_          15 RGLLVPALKKVQGQVHPTLESNDDALQYVEELILQLLNMLC----------QAQPRSASDVEERVQK   71 (172)
T ss_dssp             TTSSHHHHHHHHHHHCSSSBCCHHHHHHHHHHHHHHHHHHH----------TTCCCSTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHHHHHHHHH----------ccCCccHHHHHHHHHH
Confidence            45899999999999999999999999999999999999997          255667776 555554

>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=98.07  E-value=3.7e-06  Score=64.50  Aligned_cols=64  Identities=28%  Similarity=0.431  Sum_probs=60.0

Q ss_pred             ccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765        144 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  208 (475)
Q Consensus       144 ~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~  208 (475)
                      .+|.++|.|+++.+ ...||+..+...++-++|++..+|.+-|..++.+.+++.|+++||..|+.
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            37999999999986 45799999999999999999999999999999999999999999999985

>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=98.04  E-value=4.2e-06  Score=63.98  Aligned_cols=65  Identities=32%  Similarity=0.468  Sum_probs=61.2

Q ss_pred             ccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhc
Q psy17765        144 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN  209 (475)
Q Consensus       144 ~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~n  209 (475)
                      ++|.++|.|+++.+. ..||+..|...+.-++|.+..++.+-|..++...+++.|+++||..|+.+
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            689999999999874 47999999999999999999999999999999999999999999999875

>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=97.83  E-value=1.4e-05  Score=64.14  Aligned_cols=71  Identities=10%  Similarity=0.190  Sum_probs=64.9

Q ss_pred             cccchhHHHHHHhhc-CcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHH
Q psy17765        143 LQFPVGRIHRLLRKG-NYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEEL  213 (475)
Q Consensus       143 L~FPVsRi~r~Lke~-~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL  213 (475)
                      |.||.++|.|+||+. ....+|+..|...++...|.+...+.+.|.+.|.+.+++.|+|+||..|+.+.+-+
T Consensus         1 l~LP~a~v~ri~K~~~p~~~~is~ea~~~i~~a~e~Fi~~lt~~A~~~a~~~~rKTI~~~dv~~Al~~~~~~   72 (87)
T d1n1ja_           1 IYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFD   72 (87)
T ss_dssp             CCCCHHHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTTCG
T ss_pred             CCCcHhHHHHHHHHhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHcCcH
Confidence            579999999999965 35679999999999999999999999999999999999999999999999987643

>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=97.60  E-value=9.6e-05  Score=56.35  Aligned_cols=62  Identities=26%  Similarity=0.355  Sum_probs=56.7

Q ss_pred             HHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765         38 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  100 (475)
Q Consensus        38 ~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll  100 (475)
                      ..|+|+.|...+ ..||.++...+...+..++..|+.+|...+...+|+|++.+||..|++.+
T Consensus         7 a~I~ri~k~~~~-~ris~ea~~~l~~~~e~fi~~l~~~a~~~a~~~kRkTi~~~DV~~Alk~~   68 (68)
T d1htaa_           7 APIGRIIKNAGA-ERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARKMF   68 (68)
T ss_dssp             HHHHHHHHHTTC-SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHTC
T ss_pred             HHHHHHHHHCCc-chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHhC
Confidence            468889998755 57999999999999999999999999999999999999999999999863

>d1dbha1 a.87.1.1 (A:198-404) Son of sevenless-1 (sos-1) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DBL homology domain (DH-domain)
superfamily: DBL homology domain (DH-domain)
family: DBL homology domain (DH-domain)
domain: Son of sevenless-1 (sos-1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.45  E-value=5.2e-06  Score=74.13  Aligned_cols=71  Identities=20%  Similarity=0.169  Sum_probs=64.1

Q ss_pred             hhHHHHHHhcccccc-----ccccccccccccccccCCcchhhhhccccCCCCcccchhhhccccccchhhhhhhc
Q psy17765        286 VLEEHLENATGLLVD-----ESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMA  356 (475)
Q Consensus       286 Vfre~l~~~~~l~~~-----~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~~~~~~~~~~~m~  356 (475)
                      +|.++|.....++..     ||+|+-+|+++.+.++..|+++++..++..+.|.+|.||.+++....|++|..|..
T Consensus        28 ~y~~pl~~~~~~~~~~~v~~iF~ni~~I~~~h~~fl~~Le~~~~~~~~~~~~~~ig~~f~~~~~~~~f~~Y~~Y~~  103 (207)
T d1dbha1          28 VFREPFVSNSKLFSANDVENIFSRIVDIHELSVKLLGHIEDTVEMTDEGSPHPLVGSCFEDLAEELAFDPYESYAR  103 (207)
T ss_dssp             TTTHHHHHCTTTCCHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHTCCTTSSSCCCHHHHHHHHHTTTTHHHHHHHH
T ss_pred             HHHHHHHhCccCCCHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHccccCCccchHHHHHHHHhHHhcccHHHHHHH
Confidence            788999887766654     99999999999999999999999999998899999999999998888999998864

>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=97.27  E-value=0.00021  Score=61.75  Aligned_cols=69  Identities=17%  Similarity=0.228  Sum_probs=64.8

Q ss_pred             CcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhcc
Q psy17765        142 GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND  210 (475)
Q Consensus       142 gL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD  210 (475)
                      .|.||.++|.|+++..--..+|+..|...++-+.|.++..|...|...|...+++.|++.||..|+.+-
T Consensus         2 dl~LP~a~I~kI~K~~~~~~~is~dA~~~i~~a~~~Fi~~lt~~A~~~a~~~~RkTi~~~Dv~~Al~~~   70 (135)
T d1jfib_           2 DLTIPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALESL   70 (135)
T ss_dssp             CCCCCHHHHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             cccccHHHHHHHHhhCCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHc
Confidence            478999999999999776789999999999999999999999999999999999999999999999964

>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=97.26  E-value=0.00025  Score=53.74  Aligned_cols=60  Identities=17%  Similarity=0.335  Sum_probs=55.5

Q ss_pred             HHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHH
Q psy17765         38 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR   98 (475)
Q Consensus        38 ~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVr   98 (475)
                      ..|+|+.|...| ..||.+|...+......++..|+.+|...+...+|+||+.+||..|++
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            468899998765 589999999999999999999999999999999999999999999875

>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=96.83  E-value=0.0015  Score=51.97  Aligned_cols=63  Identities=24%  Similarity=0.370  Sum_probs=58.3

Q ss_pred             HHHHHHhhccCCC-CCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765         38 IYIYKVLKQVHPD-TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  100 (475)
Q Consensus        38 ~yI~KVLKQVhPd-~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll  100 (475)
                      ..|.|+.|+.-|+ ..||.+|...|.....-+...|+.+|...+...+|+||+..||..|+..+
T Consensus         6 a~v~ri~K~~~p~~~~is~ea~~~i~~a~e~Fi~~lt~~A~~~a~~~~rKTI~~~dv~~Al~~~   69 (87)
T d1n1ja_           6 ANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTL   69 (87)
T ss_dssp             HHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHT
T ss_pred             hHHHHHHHHhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHc
Confidence            4589999988665 56999999999999999999999999999999999999999999999987

>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=96.64  E-value=0.0013  Score=49.76  Aligned_cols=60  Identities=12%  Similarity=0.209  Sum_probs=50.9

Q ss_pred             HHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHH
Q psy17765         38 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAV   97 (475)
Q Consensus        38 ~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAV   97 (475)
                      ..|+|++|.......||.+|...|.-....+...|+.+|...+..++|+||+.+||..||
T Consensus         6 srVkkimk~~~~~~~is~~A~~~~~~a~E~Fi~~l~~~A~~~a~~~krktI~~~dl~~ai   65 (66)
T d1jfia_           6 ARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQCI   65 (66)
T ss_dssp             HHHHHHHTTSTTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC---CBCHHHHHTTC
T ss_pred             HHHHHHHhcCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHh
Confidence            468999998744457999999999999999999999999999999999999999998775

>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=96.57  E-value=0.0023  Score=54.93  Aligned_cols=63  Identities=19%  Similarity=0.361  Sum_probs=60.1

Q ss_pred             HHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765         38 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  100 (475)
Q Consensus        38 ~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll  100 (475)
                      .-|.|+.|..-|+..||.+|...|.....-++..|+.+|...|...+|+||+..||..|+..+
T Consensus         8 a~I~kI~K~~~~~~~is~dA~~~i~~a~~~Fi~~lt~~A~~~a~~~~RkTi~~~Dv~~Al~~~   70 (135)
T d1jfib_           8 AAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALESL   70 (135)
T ss_dssp             HHHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             HHHHHHHhhCCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHc
Confidence            458999999999999999999999999999999999999999999999999999999999987

>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=96.56  E-value=0.0015  Score=52.12  Aligned_cols=65  Identities=17%  Similarity=0.182  Sum_probs=59.4

Q ss_pred             chhHHHHHHhhc-CcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhcc
Q psy17765        146 PVGRIHRLLRKG-NYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND  210 (475)
Q Consensus       146 PVsRi~r~Lke~-~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD  210 (475)
                      |.++|.|+|++. .-..+|+..|...++-+.|.++..+.+.|...|...+++.|+++||..|+.+-
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            789999999864 34579999999999999999999999999999999999999999999999853

>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=96.53  E-value=0.0013  Score=50.89  Aligned_cols=64  Identities=11%  Similarity=0.105  Sum_probs=54.2

Q ss_pred             hhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHh-cCCcccchhHHHHHHhccHHHHhhhc
Q psy17765        155 RKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARD-NKKTRIIPRHLQLAIRNDEELNKLLS  218 (475)
Q Consensus       155 ke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~-~k~~rItP~hI~lAI~nD~EL~~Lf~  218 (475)
                      |-+.....|+..|++.++-..|.++.++.+.|.+.+.. .+++.|++.||..||.+++.|+.|-.
T Consensus         2 k~d~dv~~is~ea~~lvskAtElFi~~L~~~a~~~a~~~~~~ktl~~~dl~~aV~~~~~f~FL~d   66 (72)
T d2byka1           2 KSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEFLLQ   66 (72)
T ss_dssp             CSSSSCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHHTCSTTGGGTT
T ss_pred             CCCHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCccccHHHHHHHHccCchhhHHHH
Confidence            34455678999999999999999999999999877754 45578999999999999999887653

>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=96.52  E-value=0.0026  Score=50.72  Aligned_cols=65  Identities=23%  Similarity=0.324  Sum_probs=58.2

Q ss_pred             HHHHHhhccCCC-CCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh-CcH
Q psy17765         39 YIYKVLKQVHPD-TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL-LPG  103 (475)
Q Consensus        39 yI~KVLKQVhPd-~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll-LPg  103 (475)
                      -|.|+.|+.-|+ ..||++|...+.....-++..|+.+|...+..++|+||+..||..|+..+ |..
T Consensus         4 ~i~ri~K~~~p~~~~iskeA~~~i~~aae~FI~~lt~~A~~~a~~~~rKtI~~~dv~~Al~~~~f~~   70 (89)
T d2bykb1           4 VIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFES   70 (89)
T ss_dssp             HHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCTT
T ss_pred             HHHHHHHHhCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHCCcHH
Confidence            478999987555 67999999999999999999999999999999999999999999999987 443

>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=96.02  E-value=0.0072  Score=46.69  Aligned_cols=62  Identities=19%  Similarity=0.224  Sum_probs=55.1

Q ss_pred             HHHHHHhhccCCC-CCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765         38 IYIYKVLKQVHPD-TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL  100 (475)
Q Consensus        38 ~yI~KVLKQVhPd-~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll  100 (475)
                      ..|+|+.|. .|+ ..+|++|...+.--..-+...|+.+|..-+..++|+||+.+||..||+..
T Consensus         4 srVkrImK~-~~~~~~is~ea~~~i~~a~E~Fi~~l~~~A~~~a~~~~rkti~~~dl~~av~~~   66 (78)
T d1n1jb_           4 ARIKKIMKL-DEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKF   66 (78)
T ss_dssp             HHHHHHHTT-STTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTC
T ss_pred             HHHHHHHhc-CCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHhcC
Confidence            458899886 566 56999999999999999999999999999999999999999999998753

>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=0.0044  Score=49.00  Aligned_cols=63  Identities=13%  Similarity=0.142  Sum_probs=55.1

Q ss_pred             HHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         36 YAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        36 f~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      -...|.|+.+..- --.||.++.+.+...+.+.++.|+.+|..++...+|+|+|..||..|++.
T Consensus        11 ~k~~i~Riar~~G-v~ris~d~~~~l~~~l~~~l~~i~~~a~~~~~hakRKTvt~~DV~~Alkr   73 (82)
T d2huec1          11 TKPAIRRLARRGG-VKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKR   73 (82)
T ss_dssp             CHHHHHHHHHHTT-CCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTT
T ss_pred             CHHHHHHHHHHcC-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHh
Confidence            3457888887752 23599999999999999999999999999999999999999999998874

>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=95.57  E-value=0.013  Score=47.62  Aligned_cols=68  Identities=21%  Similarity=0.263  Sum_probs=63.4

Q ss_pred             CchhHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         32 RKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        32 ~~~sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      ++-.|+-.++.+.....+++.++.+|+..|..-..+.+..+-+.|..++.+.+|-|++++|++-|.++
T Consensus        23 pk~pF~RLVRei~~~~~~~~r~~~~Al~aLQea~E~yLv~lfeda~~~a~HakRvTl~~kD~~Larri   90 (95)
T d1tzyc_          23 RKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI   90 (95)
T ss_dssp             CHHHHHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             ccccHHHHHHHHHHhcCCCCEeeHHHHHHHHHHHHHHHHHHHHHhHHHHHhcCCCcCCHHHHHHHHHH
Confidence            35679999999999999999999999999999999999999999999999999999999999998876

>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=95.57  E-value=0.018  Score=45.30  Aligned_cols=66  Identities=17%  Similarity=0.226  Sum_probs=58.9

Q ss_pred             cchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccH
Q psy17765        145 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDE  211 (475)
Q Consensus       145 FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~  211 (475)
                      +|-.-|.|+.+.+. ..||+..+.--|..++||...+|+.-|...+...+++.|+++||..|++...
T Consensus        10 I~k~~i~Riar~~G-v~ris~d~~~~l~~~l~~~l~~i~~~a~~~~~hakRKTvt~~DV~~Alkr~g   75 (82)
T d2huec1          10 ITKPAIRRLARRGG-VKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQG   75 (82)
T ss_dssp             SCHHHHHHHHHHTT-CCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTTC
T ss_pred             cCHHHHHHHHHHcC-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHhcC
Confidence            56667888888754 4699999999999999999999999999999999999999999999998653

>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=94.98  E-value=0.035  Score=43.12  Aligned_cols=61  Identities=16%  Similarity=0.369  Sum_probs=56.3

Q ss_pred             HHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         39 YIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        39 yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      -|...++|+-|+..+..++-+.+-.+..++.+.++.-|++||.+.+..|+.++|||.....
T Consensus         8 ~L~eLv~~idp~~~ld~~vee~ll~iADdFV~~V~~~ac~lAKhR~s~~le~kDvql~LeR   68 (74)
T d1h3ob_           8 KLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLER   68 (74)
T ss_dssp             HHHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCcHHHHHHHHHh
Confidence            3677889999999999999999999999999999999999999999999999999987765

>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=93.35  E-value=0.077  Score=43.70  Aligned_cols=70  Identities=21%  Similarity=0.224  Sum_probs=57.2

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHHH
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKH  108 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaKh  108 (475)
                      ...|+|.|++.+-...++..|--+|...+..+...|.+.|..-++.+++..||+++||-||+-  ..||.+-
T Consensus        15 V~rv~r~Lk~~~~~~rv~~~apVylaAVLEYLtaEiLELAgn~a~~~k~~rItPrhi~lAirn--DeeL~~L   84 (106)
T d1tzya_          15 VGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRN--DEELNKL   84 (106)
T ss_dssp             HHHHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT--SHHHHHH
T ss_pred             hHHHHHHHHcCccccccCCCchHHHHHHHHHHHHHHHHHhhHHHHhcCCceecchhhhhcccC--HHHHHHH
Confidence            456999999976666889999888888887777777777777888999999999999999986  4555543

>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=93.30  E-value=0.06  Score=44.37  Aligned_cols=69  Identities=23%  Similarity=0.244  Sum_probs=59.0

Q ss_pred             HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHH
Q psy17765         37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAK  107 (475)
Q Consensus        37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaK  107 (475)
                      ...|+|.|++-+....|+..|--+|...+..+...|.+.|..-++.+++..||+++||-||+-  ..||.+
T Consensus        14 V~ri~r~Lk~~~~~~rv~~~apVylaAVLEYL~aEILELAgn~a~~~k~~rItprhi~lairn--D~EL~~   82 (106)
T d1u35c1          14 VGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILLAVAN--DEELNQ   82 (106)
T ss_dssp             HHHHHHHHHHHSTTSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH--SHHHHH
T ss_pred             HHHHHHHHhCCCCccccCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCeeecchhhhcccC--HHHHHH
Confidence            356899999987777899999999999888888888888888899999999999999999987  455544

>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=90.76  E-value=0.24  Score=40.30  Aligned_cols=69  Identities=20%  Similarity=0.141  Sum_probs=56.2

Q ss_pred             HHHHHHhhccCCC-CCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHHH
Q psy17765         38 IYIYKVLKQVHPD-TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKH  108 (475)
Q Consensus        38 ~yI~KVLKQVhPd-~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaKh  108 (475)
                      ..|+|.|+..+-. ..|+..|--+|...+..+...|.+.|..-+..+++..||+++|+-||+-  ..||.+-
T Consensus        15 grv~r~L~~~~~~~~rv~~~A~VyLaAvLEYL~aEILelagn~a~~~~~~rItpr~l~lai~n--D~EL~~L   84 (103)
T d1f66c_          15 GRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG--DEELDSL   84 (103)
T ss_dssp             HHHHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHH--SHHHHHH
T ss_pred             HHHHHHHhccCccceecCCCceeeHHHHHHHHHHHHHHHhhhhhccCCCCeeechhhhccccC--cHHHHHH
Confidence            4578888877654 3488889888888888888888888888888999999999999999997  5666553

>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=90.40  E-value=0.26  Score=39.28  Aligned_cols=63  Identities=22%  Similarity=0.379  Sum_probs=55.5

Q ss_pred             cchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcC-CcccchhHHHHHHh
Q psy17765        145 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNK-KTRIIPRHLQLAIR  208 (475)
Q Consensus       145 FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k-~~rItP~hI~lAI~  208 (475)
                      ||=+.|.++++. ..++.|+....+.++++---+..||+|.|.......+ ...|.|.||..|.+
T Consensus        17 ~~K~~vkrl~~~-~~g~sv~~~v~i~v~giaKvFvGEiVE~A~~V~~~~~e~~PL~P~HireA~r   80 (89)
T d1bh9b_          17 FPKAAIKRLIQS-ITGTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVR   80 (89)
T ss_dssp             CCHHHHHHHHHH-HHSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCHHHHHHHHH
T ss_pred             CCHHHHHHHHHH-HcCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCcHHHHHHHH
Confidence            888999999986 5678999999999999999999999999988865544 45899999999876

>d1ki1b1 a.87.1.1 (B:1229-1438) GEF of intersectin {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DBL homology domain (DH-domain)
superfamily: DBL homology domain (DH-domain)
family: DBL homology domain (DH-domain)
domain: GEF of intersectin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.36  E-value=0.024  Score=49.69  Aligned_cols=135  Identities=12%  Similarity=0.104  Sum_probs=83.4

Q ss_pred             hhHHHHHHhcccccc----ccccccccccccccccCCcchhhhhccccCCCCcccchhhhccccccchhhhhhhccCCcC
Q psy17765        286 VLEEHLENATGLLVD----ESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAAGKSS  361 (475)
Q Consensus       286 Vfre~l~~~~~l~~~----~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~~~~~~~~~~~m~~~~~~  361 (475)
                      +|.++|....-+..+    +|+|+-+|.++...++..|+..++...+..++..+|.||..+..  .+++|..|++.-...
T Consensus        34 ~y~~~l~~~~~l~~~~~~~lF~~i~~l~~~h~~~l~~L~~~~~~~~~~~~~~~ig~~f~~~~~--~~~~Y~~Y~~~~~~~  111 (210)
T d1ki1b1          34 IFQKPLMESELLTEKEVAMIFVNWKELIMCNIKLLKALRVRKKMSGEKMPVKMIGDILSAQLP--HMQPYIRFCSRQLNG  111 (210)
T ss_dssp             HTHHHHHHHTSSCHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHCTTSCCCCCHHHHHHHGG--GGTHHHHHHHHHHHH
T ss_pred             HHHHHHhhcCCCCHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHccccccchhHHHHHHHHHHH--HhhHHHHHHHcChHH
Confidence            567777664322222    99999999999999999999999988887788899999998865  478999887642111


Q ss_pred             ccchhccccc--------cc-cccccCCcc--------CcCCCccceeehhhhhccc---cCCCCCchHHHHHHhhHHHH
Q psy17765        362 GKAVKKAGKA--------QK-NITKSDKKK--------KPRRKESYAIYIYKVLKQV---HPDTGVSSKAMSIMNSFVND  421 (475)
Q Consensus       362 ~k~~~~~~~~--------~~-~~~~~~~k~--------~~~~~esy~~Yi~kvLkqv---hp~~giS~kam~imnsfv~D  421 (475)
                      ...-.+..+.        +. ......++-        --.|-..|...+-.++|..   |||...=..|...+..++..
T Consensus       112 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~PvqRl~rY~llL~~l~k~t~~~~~d~~~l~~a~~~~~~~~~~  191 (210)
T d1ki1b1         112 AALIQQKTDEAPDFKEFVKRLEMDPRCKGMPLSSFILKPMQRVTRYPLIIKNILENTPENHPDHSHLKHALEKAEELCSQ  191 (210)
T ss_dssp             HHHHHHHHHHCHHHHHHHHHHHTSGGGTTCCHHHHTTHHHHHHHHHHHHHHHHHTTSCTTSTTHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhcHHHHHHHHHHhhCcccccCCHHHHHHhHHhHHHHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHH
Confidence            1100000000        00 000000000        0012234667777777765   67766667777777777554


Q ss_pred             H
Q psy17765        422 I  422 (475)
Q Consensus       422 i  422 (475)
                      +
T Consensus       192 v  192 (210)
T d1ki1b1         192 V  192 (210)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=90.25  E-value=0.29  Score=37.38  Aligned_cols=48  Identities=19%  Similarity=0.356  Sum_probs=42.2

Q ss_pred             CcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765         52 GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL   99 (475)
Q Consensus        52 ~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl   99 (475)
                      .++.++...|..=+..=+..|.+||.++++..+|.++|.+||-.|.|+
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            478888888888787778899999999999999999999999998764

>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=89.03  E-value=0.51  Score=37.84  Aligned_cols=67  Identities=25%  Similarity=0.255  Sum_probs=58.7

Q ss_pred             CcccchhHHHHHHhhc----CcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765        142 GLQFPVGRIHRLLRKG----NYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR  208 (475)
Q Consensus       142 gL~FPVsRi~r~Lke~----~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~  208 (475)
                      +|.+|-.-|.|+.++-    ....|+.++|-..|=-..|....+++|-|...|.+.++..|+|.|+++|.+
T Consensus        19 ~lLIpk~pF~RLVRei~~~~~~~~r~~~~Al~aLQea~E~yLv~lfeda~~~a~HakRvTl~~kD~~Larr   89 (95)
T d1tzyc_          19 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR   89 (95)
T ss_dssp             SCCSCHHHHHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             ccccccccHHHHHHHHHHhcCCCCEeeHHHHHHHHHHHHHHHHHHHHHhHHHHHhcCCCcCCHHHHHHHHH
Confidence            5889999999988872    123699999999999999999999999999999999999999999998864

>d2dfka1 a.87.1.1 (A:37-239) Rho guanine nucleotide exchange factor 9, Collybistin {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DBL homology domain (DH-domain)
superfamily: DBL homology domain (DH-domain)
family: DBL homology domain (DH-domain)
domain: Rho guanine nucleotide exchange factor 9, Collybistin
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=85.75  E-value=0.046  Score=47.69  Aligned_cols=68  Identities=9%  Similarity=-0.120  Sum_probs=50.9

Q ss_pred             hhHHHHHHhcccccc-----ccccccccccccccccCCcchhhhhccccCCCCcccchhhhccccccchhhhhhhcc
Q psy17765        286 VLEEHLENATGLLVD-----ESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAA  357 (475)
Q Consensus       286 Vfre~l~~~~~l~~~-----~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~~~~~~~~~~~m~~  357 (475)
                      +|.++|......+.+     +|+|+-+++++...++..|++.++-  .+...+.+|.||..+.+  .+++|..|+..
T Consensus        39 ~y~~~l~~~~~~l~~~~~~~lF~ni~~l~~~h~~~l~~L~~~~~~--~~~~~~~ig~~f~~~~~--~~~~Y~~Y~~~  111 (203)
T d2dfka1          39 GYLKQCRKRRDMFSDEQLKVIFGNIEDIYRFQMGFVRDLEKQYNN--DDPHLSEIGPCFLEHQD--GFWIYSEYCNN  111 (203)
T ss_dssp             HTHHHHHHCTTTCCHHHHHHHHTTHHHHHHHHHHHHHHHHHHCCS--SCGGGCCCHHHHHHTTT--GGGHHHHHHHH
T ss_pred             HHHHHHHhccCCCCHHHHHHHHhhHHHHHHHHHHHHHHHHHHHcc--CCccHHHHHHHHHHHHH--hHHHHHHHHHh
Confidence            666667665555544     9999999999999988888776542  33345789999988765  57899999765

>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=83.73  E-value=1.3  Score=33.27  Aligned_cols=55  Identities=11%  Similarity=0.169  Sum_probs=43.2

Q ss_pred             ccCCCCC-cChHHHHHHHHHHHHHHHHHHHHHhhhhh-cCCCCCCChHHHHHHHHHh
Q psy17765         46 QVHPDTG-VSSKAMSIMNSFVNDIFERIAAESSRLAH-YNKRSTITSREIQTAVRLL  100 (475)
Q Consensus        46 QVhPd~~-IS~~Am~imns~v~diferIa~EA~~L~~-~~kr~TlT~rdIqtAVrll  100 (475)
                      |--||.+ ||++|.-.+.--..-+.+.++.+|...+. .++++|++..||..||...
T Consensus         2 k~d~dv~~is~ea~~lvskAtElFi~~L~~~a~~~a~~~~~~ktl~~~dl~~aV~~~   58 (72)
T d2byka1           2 KSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKN   58 (72)
T ss_dssp             CSSSSCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHHTC
T ss_pred             CCCHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCccccHHHHHHHHccC
Confidence            3467775 88888888877777778888999877664 5566899999999998753

>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=82.75  E-value=0.31  Score=37.55  Aligned_cols=55  Identities=16%  Similarity=0.340  Sum_probs=46.0

Q ss_pred             hhhhhccccCCCCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCCcCCCCCchh
Q psy17765        394 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDLCP  448 (475)
Q Consensus       394 i~kvLkqvhp~~giS~kam~imnsfv~Diferia~Eas~L~~~~kr~Tltsr~~~  448 (475)
                      +...++||-|+..|...+-.++--+.+|--+.+..-|.+||++.+-.||..++++
T Consensus         9 L~eLv~~idp~~~ld~~vee~ll~iADdFV~~V~~~ac~lAKhR~s~~le~kDvq   63 (74)
T d1h3ob_           9 LQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQ   63 (74)
T ss_dssp             HHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHH
T ss_pred             HHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCcHHHHH
Confidence            5567899999999999998777666666666677889999999999999998865

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

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

Probab=81.35  E-value=2.1  Score=36.72  Aligned_cols=66  Identities=14%  Similarity=0.147  Sum_probs=51.0

Q ss_pred             HHHHHHHHhhccCCCCCcChHHHHHHHHHH------------HHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhC
Q psy17765         36 YAIYIYKVLKQVHPDTGVSSKAMSIMNSFV------------NDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLL  101 (475)
Q Consensus        36 f~~yI~KVLKQVhPd~~IS~~Am~imns~v------------~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllL  101 (475)
                      ...++.+.++..+.+..++.++++.+....            -+-...++++|..++..+.+.++|.+||+.|.+.++
T Consensus       197 ~~~il~~r~~~~~~~~~~~~~~l~~ia~~~~~~~~~~~~~G~~R~a~~ll~~a~~~A~~~~~~~I~~edv~~A~~~~~  274 (276)
T d1fnna2         197 IFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPEDVRKSSKEVL  274 (276)
T ss_dssp             HHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHhcccccccHHHHHHHHHHhhhhhhhhhcCCCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHh
Confidence            455667777777777788999988876553            123455677888899889999999999999998875