Psyllid ID: psy3662

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130--
Protein Sequence
MSGRGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAKGKSNSQEY
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHcccccHHHHHHHccccEEcccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccHHHHHcccccHHHHHHHHHHcccccEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEcHHHHHHHHHccHHHHHHcccEEEccccccccccHHHccccccccccccccccc
Coil and Loop (DISEMBL)
msgrgkggkaktksktrssraglqfpvgrIHRLLRkgnyaervgagAPVYLAAVLEYLVAEVLELAGnaardnkktriipRHIQLAIRNDEELNKLLNGvtiaqggvlpniqavllpkksetakgksnsqey
Flexible Loop (DISEMBL)
msgrgkggkaktksktrssraglqfpvgrihRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAgnaardnkktriiPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAvllpkksetakgksnsqey
Low Complexity Region (SEG)
MsgrgkggkaktksktrssragLQFPVGRIHRLLRKGNYAERVGAGAPvylaavleylvaevlelaGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAKGKSNSQEY
Disordered region (IsUnstruct)
**********************LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLL****************
Disordered Region (DISOPRED)
************************FPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNI*********************
Disordered Region (DISEMBL)
********************AGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKS************
Disordered Region (DISPRO)
*********************GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPK**************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSGRGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAKGKSNSQEY
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	132	2.2.26 [Sep-21-2011]
Q96QV6	131	Histone H2A type 1-A OS=H	yes	N/A	0.984	0.992	0.862	2e-59
P06897	130	Histone H2A type 1 OS=Xen	N/A	N/A	0.939	0.953	0.888	5e-59
P02264	128	Histone H2A OS=Oncorhynch	N/A	N/A	0.931	0.960	0.903	6e-59
Q64523	129	Histone H2A type 2-C OS=M	yes	N/A	0.962	0.984	0.875	8e-59
Q16777	129	Histone H2A type 2-C OS=H	no	N/A	0.962	0.984	0.875	8e-59
A1A4R1	129	Histone H2A type 2-C OS=B	yes	N/A	0.962	0.984	0.875	8e-59
Q4R3X5	129	Histone H2A.J OS=Macaca f	N/A	N/A	0.962	0.984	0.875	1e-58
P13912	129	Histone H2A OS=Cairina mo	N/A	N/A	0.962	0.984	0.875	1e-58
Q8IUE6	130	Histone H2A type 2-B OS=H	yes	N/A	0.969	0.984	0.868	2e-58
Q8CGP7	130	Histone H2A type 1-K OS=M	no	N/A	0.954	0.969	0.884	2e-58

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

 Score =  226 bits (577), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 113/131 (86%), Positives = 123/131 (93%), Gaps = 1/131 (0%)

Query: 1   MSGRGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLV 59
           MSGRGK GGKA+ KSK+RSSRAGLQFPVGRIHRLLRKGNYAER+GAGAPVYLAAVLEYL 
Sbjct: 1   MSGRGKQGGKARAKSKSRSSRAGLQFPVGRIHRLLRKGNYAERIGAGAPVYLAAVLEYLT 60

Query: 60  AEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKK 119
           AE+LELAGNA+RDNKKTRIIPRH+QLAIRNDEELNKLL GVTIAQGGVLPNIQAVLLPKK
Sbjct: 61  AEILELAGNASRDNKKTRIIPRHLQLAIRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKK 120

Query: 120 SETAKGKSNSQ 130
           +E+   K+ S+
Sbjct: 121 TESHHHKAQSK 131

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 =  226 bits (575), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 111/125 (88%), Positives = 120/125 (96%), Gaps = 1/125 (0%)

Query: 1   MSGRGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLV 59
           MSGRGK GGK + K+KTRSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAVLEYL 
Sbjct: 1   MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT 60

Query: 60  AEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKK 119
           AE+LELAGNAARDNKKTRIIPRH+QLA+RNDEELNKLL GVTIAQGGVLPNIQ+VLLPKK
Sbjct: 61  AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQSVLLPKK 120

Query: 120 SETAK 124
           +E+AK
Sbjct: 121 TESAK 125

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

 Score =  225 bits (573), Expect = 6e-59,   Method: Compositional matrix adjust.
 Identities = 112/124 (90%), Positives = 119/124 (95%), Gaps = 1/124 (0%)

Query: 1   MSGRGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLV 59
           MSGRGK GGKA+ K+KTRSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAVLEYL 
Sbjct: 1   MSGRGKTGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT 60

Query: 60  AEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKK 119
           AE+LELAGNAARDNKKTRIIPRH+QLA+RNDEELNKLL GVTIAQGGVLPNIQAVLLPKK
Sbjct: 61  AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKK 120

Query: 120 SETA 123
           +E A
Sbjct: 121 TEKA 124

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

Oncorhynchus mykiss (taxid: 8022)

>sp|Q64523|H2A2C_MOUSE Histone H2A type 2-C OS=Mus musculus GN=Hist2h2ac PE=1 SV=3

 Score =  225 bits (573), Expect = 8e-59,   Method: Compositional matrix adjust.
 Identities = 112/128 (87%), Positives = 121/128 (94%), Gaps = 1/128 (0%)

Query: 1   MSGRGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLV 59
           MSGRGK GGKA+ K+K+RSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVY+AAVLEYL 
Sbjct: 1   MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLT 60

Query: 60  AEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKK 119
           AE+LELAGNAARDNKKTRIIPRH+QLAIRNDEELNKLL  VTIAQGGVLPNIQAVLLPKK
Sbjct: 61  AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKK 120

Query: 120 SETAKGKS 127
           +E+ K KS
Sbjct: 121 TESHKAKS 128

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|Q16777|H2A2C_HUMAN Histone H2A type 2-C OS=Homo sapiens GN=HIST2H2AC PE=1 SV=4

 Score =  225 bits (573), Expect = 8e-59,   Method: Compositional matrix adjust.
 Identities = 112/128 (87%), Positives = 121/128 (94%), Gaps = 1/128 (0%)

Query: 1   MSGRGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLV 59
           MSGRGK GGKA+ K+K+RSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVY+AAVLEYL 
Sbjct: 1   MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLT 60

Query: 60  AEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKK 119
           AE+LELAGNAARDNKKTRIIPRH+QLAIRNDEELNKLL  VTIAQGGVLPNIQAVLLPKK
Sbjct: 61  AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKK 120

Query: 120 SETAKGKS 127
           +E+ K KS
Sbjct: 121 TESHKAKS 128

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|A1A4R1|H2A2C_BOVIN Histone H2A type 2-C OS=Bos taurus GN=HIST2H2AC PE=2 SV=1

 Score =  225 bits (573), Expect = 8e-59,   Method: Compositional matrix adjust.
 Identities = 112/128 (87%), Positives = 121/128 (94%), Gaps = 1/128 (0%)

Query: 1   MSGRGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLV 59
           MSGRGK GGKA+ K+K+RSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVY+AAVLEYL 
Sbjct: 1   MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLT 60

Query: 60  AEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKK 119
           AE+LELAGNAARDNKKTRIIPRH+QLAIRNDEELNKLL  VTIAQGGVLPNIQAVLLPKK
Sbjct: 61  AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKK 120

Query: 120 SETAKGKS 127
           +E+ K KS
Sbjct: 121 TESHKAKS 128

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.

Bos taurus (taxid: 9913)

>sp|Q4R3X5|H2AJ_MACFA Histone H2A.J OS=Macaca fascicularis GN=H2AFJ PE=2 SV=1

 Score =  224 bits (571), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 112/128 (87%), Positives = 120/128 (93%), Gaps = 1/128 (0%)

Query: 1   MSGRGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLV 59
           MSGRGK GGK + K+K+RSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAVLEYL 
Sbjct: 1   MSGRGKQGGKVRAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT 60

Query: 60  AEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKK 119
           AE+LELAGNAARDNKKTRIIPRH+QLAIRNDEELNKLL  VTIAQGGVLPNIQAVLLPKK
Sbjct: 61  AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKK 120

Query: 120 SETAKGKS 127
           +E+ K KS
Sbjct: 121 TESQKAKS 128

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.

Macaca fascicularis (taxid: 9541)

>sp|P13912|H2A_CAIMO Histone H2A OS=Cairina moschata PE=3 SV=2

 Score =  224 bits (571), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 112/128 (87%), Positives = 121/128 (94%), Gaps = 1/128 (0%)

Query: 1   MSGRGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLV 59
           MSGRGK GGKA+ K+K+RSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAVLEYL 
Sbjct: 1   MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT 60

Query: 60  AEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKK 119
           AE+LELAGNAARDNKKTRIIPRH+QLAIRNDEELNKLL  VTIAQGGVLPNIQAVLLPKK
Sbjct: 61  AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKK 120

Query: 120 SETAKGKS 127
           +++ K KS
Sbjct: 121 TDSHKAKS 128

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.

Cairina moschata (taxid: 8855)

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

 Score =  224 bits (570), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 112/129 (86%), Positives = 121/129 (93%), Gaps = 1/129 (0%)

Query: 1   MSGRGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLV 59
           MSGRGK GGKA+ K+K+RSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAVLEYL 
Sbjct: 1   MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT 60

Query: 60  AEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKK 119
           AE+LELAGNAARDNKKTRIIPRH+QLA+RNDEELNKLL GVTIAQGGVLPNIQAVLLPKK
Sbjct: 61  AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKK 120

Query: 120 SETAKGKSN 128
           +E+ K   N
Sbjct: 121 TESHKPGKN 129

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|Q8CGP7|H2A1K_MOUSE Histone H2A type 1-K OS=Mus musculus GN=Hist1h2ak PE=1 SV=3

 Score =  223 bits (569), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 115/130 (88%), Positives = 122/130 (93%), Gaps = 4/130 (3%)

Query: 1   MSGRGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLV 59
           MSGRGK GGKA+ K+KTRSSRAGLQFPVGR+HRLLRKGNY+ERVGAGAPVYLAAVLEYL 
Sbjct: 1   MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLT 60

Query: 60  AEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKK 119
           AE+LELAGNAARDNKKTRIIPRH+QLAIRNDEELNKLL  VTIAQGGVLPNIQAVLLPKK
Sbjct: 61  AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK 120

Query: 120 SET---AKGK 126
           +ET   AKGK
Sbjct: 121 TETHHKAKGK 130

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)

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	132
405975240	133	Histone H2A [Crassostrea gigas]	1.0	0.992	0.879	2e-59
196012824	137	conserved hypothetical protein [Trichopl	1.0	0.963	0.824	1e-58
157674605	136	histone H2A [Artemia franciscana]	1.0	0.970	0.845	2e-58
194719519	142	H2A [Carassius gibelio]	1.0	0.929	0.830	3e-58
283468891	128	histone H2A [Xenoturbella bocki] gi|2834	0.969	1.0	0.856	5e-58
410927072	124	PREDICTED: histone H2A-like [Takifugu ru	0.939	1.0	0.895	5e-58
348544205	124	PREDICTED: histone H2A-like [Oreochromis	0.939	1.0	0.911	6e-58
358255301	215	histone H2A [Clonorchis sinensis]	0.939	0.576	0.895	6e-58
283468900	128	histone H2A [Xenoturbella bocki]	0.969	1.0	0.848	1e-57
326669124	144	PREDICTED: histone H2A-like [Danio rerio	0.954	0.875	0.889	2e-57

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

 Score =  233 bits (594), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 117/133 (87%), Positives = 124/133 (93%), Gaps = 1/133 (0%)

Query: 1   MSGRGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVA 60
           MSGRGKGGK K+K+K+RSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYL A
Sbjct: 1   MSGRGKGGKTKSKAKSRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLAA 60

Query: 61  EVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKS 120
           EVLELAGNAARDNKKTRIIPRH+QLAIRNDEELNKLL+GVTIAQGGVLPNIQAVLLPKK+
Sbjct: 61  EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKT 120

Query: 121 -ETAKGKSNSQEY 132
               K  S SQE+
Sbjct: 121 GSVGKKSSQSQEF 133

Source: Crassostrea gigas

Species: Crassostrea gigas

Genus: Crassostrea

Family: Ostreidae

Order: Ostreoida

Class: Bivalvia

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|196012824|ref|XP_002116274.1| conserved hypothetical protein [Trichoplax adhaerens] gi|190581229|gb|EDV21307.1| conserved hypothetical protein [Trichoplax adhaerens]

 Score =  231 bits (588), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 113/137 (82%), Positives = 126/137 (91%), Gaps = 5/137 (3%)

Query: 1   MSGRGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVA 60
           MSGRGKGGKA+ K+K+RS+RAGLQFPVGR+HR+LRKGNYAERVGAGAPVYLAAV+EYL A
Sbjct: 1   MSGRGKGGKARNKAKSRSTRAGLQFPVGRVHRMLRKGNYAERVGAGAPVYLAAVMEYLAA 60

Query: 61  EVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKS 120
           E+LELAGNAARDNKK RI+PRH+QLAIRNDEELNKLL+GVTIAQGGVLPNIQAVLLPKKS
Sbjct: 61  EILELAGNAARDNKKQRIVPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKS 120

Query: 121 E-----TAKGKSNSQEY 132
           +     + KG S SQEY
Sbjct: 121 KVPIAGSKKGSSQSQEY 137

Source: Trichoplax adhaerens

Species: Trichoplax adhaerens

Genus: Trichoplax

Phylum: Placozoa

Superkingdom: Eukaryota

>gi|157674605|gb|ABV60391.1| histone H2A [Artemia franciscana]

 Score =  229 bits (585), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 115/136 (84%), Positives = 123/136 (90%), Gaps = 4/136 (2%)

Query: 1   MSGRGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVA 60
           M+GRGKGGK K KSK+RS RAGLQFPVGRIHR+L+KGNYAERVGAGAPVYLAAV+EYL A
Sbjct: 1   MTGRGKGGKTKAKSKSRSGRAGLQFPVGRIHRMLKKGNYAERVGAGAPVYLAAVMEYLAA 60

Query: 61  EVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKS 120
           EVLELAGNAARDNKK+RIIPRH+QLAIRNDEELNKLL GVTIAQGGVLPNIQAVLLPKK+
Sbjct: 61  EVLELAGNAARDNKKSRIIPRHLQLAIRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKA 120

Query: 121 E----TAKGKSNSQEY 132
           E     AKG   SQEY
Sbjct: 121 EGASAKAKGGGQSQEY 136

Source: Artemia franciscana

Species: Artemia franciscana

Genus: Artemia

Family: Artemiidae

Order: Anostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194719519|gb|ACF93799.1| H2A [Carassius gibelio]

 Score =  229 bits (583), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 118/142 (83%), Positives = 125/142 (88%), Gaps = 10/142 (7%)

Query: 1   MSGRGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLV 59
           MSGRGK GGKA+ K+KTRSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAVLEYL 
Sbjct: 1   MSGRGKTGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT 60

Query: 60  AEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKK 119
           AE+LELAGNAARDNKKTRIIPRH+QLA+RNDEELNKLL GVTIAQGGVLPNIQAVLLPKK
Sbjct: 61  AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKK 120

Query: 120 SETA---------KGKSNSQEY 132
           +  A         KG S SQEY
Sbjct: 121 TGQAVPSTGKSGKKGSSQSQEY 142

Source: Carassius gibelio

Species: Carassius gibelio

Genus: Carassius

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|283468891|emb|CAP53876.1| histone H2A [Xenoturbella bocki] gi|283468917|emb|CAP53895.1| histone H2A [Xenoturbella bocki]

 Score =  228 bits (582), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 113/132 (85%), Positives = 123/132 (93%), Gaps = 4/132 (3%)

Query: 1   MSGRGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVA 60
           MSGRGKGGK ++K+KTRSSRAGLQFPVGR+HR LRKGNYA+RVGAGAPVYLAAVLEYL A
Sbjct: 1   MSGRGKGGKVRSKAKTRSSRAGLQFPVGRVHRFLRKGNYAQRVGAGAPVYLAAVLEYLTA 60

Query: 61  EVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKS 120
           E+LELAGNAARDNKKTRIIPRH+QLAIRNDEELNKLL GVTIAQGGVLPNIQAVLLPKK+
Sbjct: 61  EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKT 120

Query: 121 ETAKGKSNSQEY 132
               GK+ SQE+
Sbjct: 121 ----GKAKSQEH 128

Source: Xenoturbella bocki

Species: Xenoturbella bocki

Genus: Xenoturbella

Phylum: Xenoturbellida

Superkingdom: Eukaryota

>gi|410927072|ref|XP_003976990.1| PREDICTED: histone H2A-like [Takifugu rubripes]

 Score =  228 bits (582), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 111/124 (89%), Positives = 120/124 (96%)

Query: 1   MSGRGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVA 60
           MSGRGKGGKA+ K+K+RSSRAGLQFPVGR+HRLLRKGNYA+RVGAGAPVYLAAVLEYL A
Sbjct: 1   MSGRGKGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAQRVGAGAPVYLAAVLEYLTA 60

Query: 61  EVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKS 120
           E+LELAGNAARDNKKTRIIPRH+QLA+RNDEELNKLL GVTIAQGGVLPNIQAVLLPKK+
Sbjct: 61  EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKT 120

Query: 121 ETAK 124
           E AK
Sbjct: 121 EKAK 124

Source: Takifugu rubripes

Species: Takifugu rubripes

Genus: Takifugu

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|348544205|ref|XP_003459572.1| PREDICTED: histone H2A-like [Oreochromis niloticus]

 Score =  228 bits (581), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 113/124 (91%), Positives = 118/124 (95%)

Query: 1   MSGRGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVA 60
           MSGRGK GKAK K KTRSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAVLEYL A
Sbjct: 1   MSGRGKTGKAKAKPKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA 60

Query: 61  EVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKS 120
           E+LELAGNAARDNKKTRIIPRH+QLA+RNDEELNKLL GVTIAQGGVLPNIQAVLLPKK+
Sbjct: 61  EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKT 120

Query: 121 ETAK 124
           E AK
Sbjct: 121 EKAK 124

Source: Oreochromis niloticus

Species: Oreochromis niloticus

Genus: Oreochromis

Family: Cichlidae

Order: Perciformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|358255301|dbj|GAA57014.1| histone H2A [Clonorchis sinensis]

 Score =  228 bits (581), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 111/124 (89%), Positives = 119/124 (95%)

Query: 1   MSGRGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVA 60
           MSGRGKGGK++ K+KTRS+RAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAVLEYL A
Sbjct: 91  MSGRGKGGKSRAKAKTRSARAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLAA 150

Query: 61  EVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKS 120
           EVLELAGNAARDNKKTRIIPRH+QLAIRNDEELNKLL GVTIAQGGVLPNIQ+VLLPKK+
Sbjct: 151 EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGGVTIAQGGVLPNIQSVLLPKKA 210

Query: 121 ETAK 124
           E  K
Sbjct: 211 EKPK 214

Source: Clonorchis sinensis

Species: Clonorchis sinensis

Genus: Clonorchis

Family: Opisthorchiidae

Order: Opisthorchiida

Class: Trematoda

Phylum: Platyhelminthes

Superkingdom: Eukaryota

>gi|283468900|emb|CAP53883.1| histone H2A [Xenoturbella bocki]

 Score =  227 bits (578), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 112/132 (84%), Positives = 123/132 (93%), Gaps = 4/132 (3%)

Query: 1   MSGRGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVA 60
           MSGRGKGGK ++K+KTRSSRAGLQFPVGR+HR LRKGNYA+RVGAGAPVYLAAVLEYL A
Sbjct: 1   MSGRGKGGKVRSKAKTRSSRAGLQFPVGRVHRFLRKGNYAQRVGAGAPVYLAAVLEYLTA 60

Query: 61  EVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKS 120
           E+LELAG+AARDNKKTRIIPRH+QLAIRNDEELNKLL GVTIAQGGVLPNIQAVLLPKK+
Sbjct: 61  EILELAGDAARDNKKTRIIPRHLQLAIRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKT 120

Query: 121 ETAKGKSNSQEY 132
               GK+ SQE+
Sbjct: 121 ----GKAKSQEH 128

Source: Xenoturbella bocki

Species: Xenoturbella bocki

Genus: Xenoturbella

Phylum: Xenoturbellida

Superkingdom: Eukaryota

>gi|326669124|ref|XP_001920286.3| PREDICTED: histone H2A-like [Danio rerio]

 Score =  227 bits (578), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 113/127 (88%), Positives = 120/127 (94%), Gaps = 1/127 (0%)

Query: 1   MSGRGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLV 59
           MSGRGK GGKA+ K+KTRSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAVLEYL 
Sbjct: 18  MSGRGKTGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT 77

Query: 60  AEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKK 119
           AE+LELAGNAARDNKKTRIIPRH+QLA+RNDEELNKLL GVTIAQGGVLPNIQAVLLPKK
Sbjct: 78  AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKK 137

Query: 120 SETAKGK 126
           +E A  K
Sbjct: 138 TEKAAKK 144

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

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	132
ZFIN|ZDB-GENE-081205-1	138	zgc:195633 "zgc:195633" [Danio	0.818	0.782	0.731	1.3e-36
ZFIN|ZDB-GENE-050522-93	132	zgc:110434 "zgc:110434" [Danio	0.787	0.787	0.752	2.1e-36
ZFIN|ZDB-GENE-050731-6	130	zgc:114037 "zgc:114037" [Danio	0.787	0.8	0.752	2.1e-36
UNIPROTKB|E1BH22	136	HIST2H2AB "Histone H2A" [Bos t	0.795	0.772	0.745	2.7e-36
UNIPROTKB|L7N0D9	129	H2AFJ "Uncharacterized protein	0.795	0.813	0.752	2.7e-36
UNIPROTKB|Q8IUE6	130	HIST2H2AB "Histone H2A type 2-	0.795	0.807	0.745	2.7e-36
UNIPROTKB|F2Z5L6	130	HIST2H2AB "Histone H2A" [Sus s	0.795	0.807	0.745	2.7e-36
ZFIN|ZDB-GENE-040426-987	142	h2afx "H2A histone family, mem	0.833	0.774	0.697	2.7e-36
UNIPROTKB|G1K330	136	H2AFJ "Histone H2A" [Gallus ga	0.795	0.772	0.752	3.5e-36
UNIPROTKB|P70082	129	H2A-IX "Histone H2A.J" [Gallus	0.795	0.813	0.752	3.5e-36

ZFIN|ZDB-GENE-081205-1 zgc:195633 "zgc:195633" [Danio rerio (taxid:7955)]

 Score = 394 (143.8 bits), Expect = 1.3e-36, P = 1.3e-36
 Identities = 79/108 (73%), Positives = 84/108 (77%)

Query:    23 LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
             LQFPVGR+HRLLRKGNYAERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct:    31 LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 90

Query:    83 IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAKGKSNSQ 130
             +QLA+RNDEELNKLL GVTIAQGGVLPNIQAVLLPKK+E A  K N +
Sbjct:    91 LQLAVRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKTEKAAKKINGK 138

GO:0003677 "DNA binding" evidence=IEA

GO:0000786 "nucleosome" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

ZFIN|ZDB-GENE-050522-93 zgc:110434 "zgc:110434" [Danio rerio (taxid:7955)]

 Score = 392 (143.0 bits), Expect = 2.1e-36, P = 2.1e-36
 Identities = 79/105 (75%), Positives = 84/105 (80%)

Query:    23 LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
             LQFPVGR+HRLLRKGNYA+RVGAGAP                  GNAARDNKKTRIIPRH
Sbjct:    28 LQFPVGRVHRLLRKGNYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 87

Query:    83 IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSE-TAKGK 126
             +QLA+RNDEELNKLL GVTIAQGGVLPNIQAVLLPKK+E  AKGK
Sbjct:    88 LQLAVRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKTEKAAKGK 132

GO:0003677 "DNA binding" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0000786 "nucleosome" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

ZFIN|ZDB-GENE-050731-6 zgc:114037 "zgc:114037" [Danio rerio (taxid:7955)]

 Score = 392 (143.0 bits), Expect = 2.1e-36, P = 2.1e-36
 Identities = 79/105 (75%), Positives = 84/105 (80%)

Query:    23 LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
             LQFPVGR+HRLLRKGNYA+RVGAGAP                  GNAARDNKKTRIIPRH
Sbjct:    26 LQFPVGRVHRLLRKGNYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 85

Query:    83 IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSE-TAKGK 126
             +QLA+RNDEELNKLL GVTIAQGGVLPNIQAVLLPKK+E  AKGK
Sbjct:    86 LQLAVRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKTEKAAKGK 130

GO:0003677 "DNA binding" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0000786 "nucleosome" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

UNIPROTKB|E1BH22 HIST2H2AB "Histone H2A" [Bos taurus (taxid:9913)]

 Score = 391 (142.7 bits), Expect = 2.7e-36, P = 2.7e-36
 Identities = 79/106 (74%), Positives = 85/106 (80%)

Query:    23 LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
             LQFPVGR+HRLLRKGNYAERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct:    30 LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 89

Query:    83 IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAK-GKS 127
             +QLA+RNDEELNKLL GVTIAQGGVLPNIQAVLLPKK+E+ K GK+
Sbjct:    90 LQLAVRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKTESHKPGKN 135

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000786 "nucleosome" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

UNIPROTKB|L7N0D9 H2AFJ "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 391 (142.7 bits), Expect = 2.7e-36, P = 2.7e-36
 Identities = 79/105 (75%), Positives = 83/105 (79%)

Query:    23 LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
             LQFPVGR+HRLLRKGNYAERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct:    24 LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 83

Query:    83 IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAKGKS 127
             +QLAIRNDEELNKLL  VTIAQGGVLPNIQAVLLPKK+E+ K KS
Sbjct:    84 LQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTESQKAKS 128

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000786 "nucleosome" evidence=IEA

UNIPROTKB|Q8IUE6 HIST2H2AB "Histone H2A type 2-B" [Homo sapiens (taxid:9606)]

 Score = 391 (142.7 bits), Expect = 2.7e-36, P = 2.7e-36
 Identities = 79/106 (74%), Positives = 85/106 (80%)

Query:    23 LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
             LQFPVGR+HRLLRKGNYAERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct:    24 LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 83

Query:    83 IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAK-GKS 127
             +QLA+RNDEELNKLL GVTIAQGGVLPNIQAVLLPKK+E+ K GK+
Sbjct:    84 LQLAVRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKTESHKPGKN 129

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0000786 "nucleosome" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|F2Z5L6 HIST2H2AB "Histone H2A" [Sus scrofa (taxid:9823)]

 Score = 391 (142.7 bits), Expect = 2.7e-36, P = 2.7e-36
 Identities = 79/106 (74%), Positives = 85/106 (80%)

Query:    23 LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
             LQFPVGR+HRLLRKGNYAERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct:    24 LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 83

Query:    83 IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAK-GKS 127
             +QLA+RNDEELNKLL GVTIAQGGVLPNIQAVLLPKK+E+ K GK+
Sbjct:    84 LQLAVRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKTESHKPGKN 129

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000786 "nucleosome" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

ZFIN|ZDB-GENE-040426-987 h2afx "H2A histone family, member X" [Danio rerio (taxid:7955)]

 Score = 391 (142.7 bits), Expect = 2.7e-36, P = 2.7e-36
 Identities = 83/119 (69%), Positives = 87/119 (73%)

Query:    23 LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
             LQFPVGR+HRLLRKGNYAERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct:    24 LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 83

Query:    83 IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETA---------KGKSNSQEY 132
             +QLA+RNDEELNKLL GVTIAQGGVLPNIQAVLLPKK+  A         KG S SQEY
Sbjct:    84 LQLAVRNDEELNKLLGGVTIAQGGVLPNIQAVLLPKKTGQAAASSGKSGKKGSSQSQEY 142

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0000786 "nucleosome" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA;IDA

GO:0006281 "DNA repair" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0007126 "meiosis" evidence=IEA

UNIPROTKB|G1K330 H2AFJ "Histone H2A" [Gallus gallus (taxid:9031)]

 Score = 390 (142.3 bits), Expect = 3.5e-36, P = 3.5e-36
 Identities = 79/105 (75%), Positives = 83/105 (79%)

Query:    23 LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
             LQFPVGR+HRLLRKGNYAERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct:    31 LQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLTAEILELAGNAARDNKKTRIIPRH 90

Query:    83 IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAKGKS 127
             +QLAIRNDEELNKLL  VTIAQGGVLPNIQAVLLPKK+E+ K KS
Sbjct:    91 LQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTESHKAKS 135

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0000786 "nucleosome" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|P70082 H2A-IX "Histone H2A.J" [Gallus gallus (taxid:9031)]

 Score = 390 (142.3 bits), Expect = 3.5e-36, P = 3.5e-36
 Identities = 79/105 (75%), Positives = 83/105 (79%)

Query:    23 LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
             LQFPVGR+HRLLRKGNYAERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct:    24 LQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLTAEILELAGNAARDNKKTRIIPRH 83

Query:    83 IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAKGKS 127
             +QLAIRNDEELNKLL  VTIAQGGVLPNIQAVLLPKK+E+ K KS
Sbjct:    84 LQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTESHKAKS 128

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0000786 "nucleosome" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

---

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	0.9024	0.9242	0.9531	yes	N/A
Q93077	H2A1C_HUMAN	No assigned EC number	0.8769	0.9545	0.9692	no	N/A
Q3ZBX9	H2AJ_BOVIN	No assigned EC number	0.875	0.9621	0.9844	yes	N/A
Q00728	H2A4_RAT	No assigned EC number	0.8536	0.9242	0.9384	no	N/A
Q4R3X5	H2AJ_MACFA	No assigned EC number	0.875	0.9621	0.9844	N/A	N/A
Q64522	H2A2B_MOUSE	No assigned EC number	0.8604	0.9696	0.9846	yes	N/A
Q64523	H2A2C_MOUSE	No assigned EC number	0.875	0.9621	0.9844	yes	N/A
P69142	H2AE_PSAMI	No assigned EC number	0.875	0.9090	0.9677	N/A	N/A
P20671	H2A1D_HUMAN	No assigned EC number	0.8769	0.9545	0.9692	no	N/A
P16886	H2AL_STRPU	No assigned EC number	0.8629	0.9318	0.9761	no	N/A
P35061	H2A_ACRFO	No assigned EC number	0.8925	0.9166	0.968	N/A	N/A
P35062	H2A3_CHICK	No assigned EC number	0.8593	0.9621	0.9844	yes	N/A
P70082	H2AJ_CHICK	No assigned EC number	0.8671	0.9621	0.9844	yes	N/A
P22752	H2A1_MOUSE	No assigned EC number	0.8769	0.9545	0.9692	yes	N/A
P0C169	H2A1C_RAT	No assigned EC number	0.8769	0.9545	0.9692	yes	N/A
Q8CGP7	H2A1K_MOUSE	No assigned EC number	0.8846	0.9545	0.9692	no	N/A
Q8CGP6	H2A1H_MOUSE	No assigned EC number	0.8943	0.9242	0.9531	yes	N/A
P13912	H2A_CAIMO	No assigned EC number	0.875	0.9621	0.9844	N/A	N/A
Q8R1M2	H2AJ_MOUSE	No assigned EC number	0.875	0.9621	0.9844	yes	N/A
A1A4R1	H2A2C_BOVIN	No assigned EC number	0.875	0.9621	0.9844	yes	N/A
P0CC09	H2A2A_RAT	No assigned EC number	0.8692	0.9545	0.9692	yes	N/A
Q8IUE6	H2A2B_HUMAN	No assigned EC number	0.8682	0.9696	0.9846	yes	N/A
Q96QV6	H2A1A_HUMAN	No assigned EC number	0.8625	0.9848	0.9923	yes	N/A
P27661	H2AX_MOUSE	No assigned EC number	0.8041	1.0	0.9230	no	N/A
P13630	H2A_PARLI	No assigned EC number	0.8666	0.9090	0.9677	N/A	N/A
Q64598	H2A1F_RAT	No assigned EC number	0.8861	0.9242	0.9384	no	N/A
Q16777	H2A2C_HUMAN	No assigned EC number	0.875	0.9621	0.9844	no	N/A
Q7L7L0	H2A3_HUMAN	No assigned EC number	0.8692	0.9545	0.9692	no	N/A
Q99878	H2A1J_HUMAN	No assigned EC number	0.9024	0.9242	0.9531	yes	N/A
Q9BTM1	H2AJ_HUMAN	No assigned EC number	0.875	0.9621	0.9844	no	N/A
P06897	H2A1_XENLA	No assigned EC number	0.888	0.9393	0.9538	N/A	N/A
P0C0S8	H2A1_HUMAN	No assigned EC number	0.8846	0.9545	0.9692	no	N/A
P0C0S9	H2A1_BOVIN	No assigned EC number	0.8846	0.9545	0.9692	yes	N/A
A9UMV8	H2AJ_RAT	No assigned EC number	0.875	0.9621	0.9844	yes	N/A
P69141	H2A_STRPU	No assigned EC number	0.875	0.9090	0.9677	yes	N/A
P16104	H2AX_HUMAN	No assigned EC number	0.7972	1.0	0.9230	no	N/A
P04735	H2A1_PSAMI	No assigned EC number	0.8536	0.9318	0.984	N/A	N/A
Q6FI13	H2A2A_HUMAN	No assigned EC number	0.8692	0.9545	0.9692	no	N/A
Q7ZUY3	H2AX_DANRE	No assigned EC number	0.9090	0.9090	0.8450	no	N/A
P04908	H2A1B_HUMAN	No assigned EC number	0.8769	0.9545	0.9692	no	N/A
Q6GM86	H2AX_XENLA	No assigned EC number	0.8148	0.9924	0.9424	N/A	N/A
Q6GSS7	H2A2A_MOUSE	No assigned EC number	0.8692	0.9545	0.9692	yes	N/A
Q8BFU2	H2A3_MOUSE	No assigned EC number	0.8692	0.9545	0.9692	yes	N/A
P0C170	H2A1E_RAT	No assigned EC number	0.8846	0.9545	0.9692	yes	N/A
P02269	H2A_ASTRU	No assigned EC number	0.8780	0.9318	0.984	N/A	N/A
Q4FZT6	H2A3_RAT	No assigned EC number	0.8692	0.9545	0.9692	yes	N/A
P02262	H2A1_RAT	No assigned EC number	0.8769	0.9545	0.9692	yes	N/A
P02263	H2A4_CHICK	No assigned EC number	0.8671	0.9621	0.9844	yes	N/A
P02264	H2A_ONCMY	No assigned EC number	0.9032	0.9318	0.9609	N/A	N/A
Q8CGP5	H2A1F_MOUSE	No assigned EC number	0.8943	0.9242	0.9384	no	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	132
PTZ00017	134	PTZ00017, PTZ00017, histone H2A; Provisional	2e-71
cd00074	115	cd00074, H2A, Histone 2A; H2A is a subunit of the	5e-68
PLN00157	132	PLN00157, PLN00157, histone H2A; Provisional	1e-67
smart00414	106	smart00414, H2A, Histone 2A	1e-65
PLN00156	139	PLN00156, PLN00156, histone H2AX; Provisional	3e-59
COG5262	132	COG5262, HTA1, Histone H2A [Chromatin structure an	3e-55
PLN00153	129	PLN00153, PLN00153, histone H2A; Provisional	1e-54
PLN00154	136	PLN00154, PLN00154, histone H2A; Provisional	3e-39
PTZ00252	134	PTZ00252, PTZ00252, histone H2A; Provisional	7e-31
pfam00125	75	pfam00125, Histone, Core histone H2A/H2B/H3/H4	1e-26
PLN00155	58	PLN00155, PLN00155, histone H2A; Provisional	4e-19
COG5247	113	COG5247, BUR6, Class 2 transcription repressor NC2	5e-07
pfam00808	65	pfam00808, CBFD_NFYB_HMF, Histone-like transcripti	7e-04
COG2036	91	COG2036, HHT1, Histones H3 and H4 [Chromatin struc	0.001

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

 Score =  209 bits (534), Expect = 2e-71
 Identities = 97/134 (72%), Positives = 110/134 (82%), Gaps = 3/134 (2%)

Query: 1   MSGRGKGGKAKTKSK---TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEY 57
             G+GK G  K   K   +RS++AGLQFPVGR+HR L+KG YA+RVGAGAPVYLAAVLEY
Sbjct: 1   KGGKGKTGGGKAGKKKPVSRSAKAGLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEY 60

Query: 58  LVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLP 117
           L AEVLELAGNAA+DNKK RI PRHIQLAIRNDEELNKLL GVTIA GGVLPNI  VLLP
Sbjct: 61  LTAEVLELAGNAAKDNKKKRITPRHIQLAIRNDEELNKLLAGVTIASGGVLPNIHKVLLP 120

Query: 118 KKSETAKGKSNSQE 131
           KKS+  +GK  +++
Sbjct: 121 KKSKPKQGKKQNKQ 134

Length = 134

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

 Score =  200 bits (510), Expect = 5e-68
 Identities = 95/113 (84%), Positives = 102/113 (90%)

Query: 7   GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELA 66
           GGK K+K ++RS+RAGLQFPVGRIHR L+KG YAERVGAGAPVYLAAVLEYL AEVLELA
Sbjct: 3   GGKKKSKKRSRSARAGLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELA 62

Query: 67  GNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKK 119
           GNAARDNKK RI PRH+QLA+RNDEELNKLL GVTIA GGVLPNI  VLLPKK
Sbjct: 63  GNAARDNKKKRITPRHLQLAVRNDEELNKLLKGVTIASGGVLPNIHKVLLPKK 115

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 =  200 bits (509), Expect = 1e-67
 Identities = 98/131 (74%), Positives = 110/131 (83%), Gaps = 2/131 (1%)

Query: 1   MSGRGK--GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYL 58
           MSGRGK  GG    K+ +RS++AGLQFPVGRI R L+ G YA RVGAGAPVYLAAVLEYL
Sbjct: 1   MSGRGKRKGGGGGKKATSRSAKAGLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYL 60

Query: 59  VAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPK 118
            AEVLELAGNAARDNKK+RI+PRHIQLA+RNDEEL+KLL GVTIA GGVLPNI +VLLPK
Sbjct: 61  AAEVLELAGNAARDNKKSRIVPRHIQLAVRNDEELSKLLGGVTIAAGGVLPNIHSVLLPK 120

Query: 119 KSETAKGKSNS 129
           KS  +KG+   
Sbjct: 121 KSGKSKGEPKD 131

Length = 132

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

 Score =  194 bits (494), Expect = 1e-65
 Identities = 93/106 (87%), Positives = 98/106 (92%)

Query: 16  TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKK 75
           +RS+RAGLQFPVGRIHRLLRKG YA+RVGAGAPVYLAAVLEYL AEVLELAGNAARDNKK
Sbjct: 1   SRSARAGLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKK 60

Query: 76  TRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSE 121
            RI PRH+QLAIRNDEELNKLL GVTIAQGGVLPNI  VLLPKK+ 
Sbjct: 61  RRITPRHLQLAIRNDEELNKLLKGVTIAQGGVLPNIHKVLLPKKTG 106

Length = 106

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

 Score =  179 bits (454), Expect = 3e-59
 Identities = 98/135 (72%), Positives = 108/135 (80%), Gaps = 3/135 (2%)

Query: 1   MSGRGKGGKAK-TKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLV 59
            + +G  GK K TKS +RSS+AGLQFPVGRI R L+ G YAERVGAGAPVYL+AVLEYL 
Sbjct: 5   GTTKGGRGKPKATKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLA 64

Query: 60  AEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKK 119
           AEVLELAGNAARDNKK RI+PRHIQLA+RNDEEL+KLL  VTIA GGVLPNI   LLPKK
Sbjct: 65  AEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGSVTIAAGGVLPNIHQTLLPKK 124

Query: 120 SETAKGK--SNSQEY 132
               KG   S SQE+
Sbjct: 125 VGKGKGDIGSASQEF 139

Length = 139

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

 Score =  168 bits (427), Expect = 3e-55
 Identities = 97/131 (74%), Positives = 107/131 (81%), Gaps = 4/131 (3%)

Query: 3   GRGKGGKA--KTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVA 60
             GKGGKA     S++RS++AGL FPVGR+ RLL+KGNY  R+GAGAPVYLAAVLEYL A
Sbjct: 3   SGGKGGKAADARVSQSRSAKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAA 62

Query: 61  EVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKS 120
           E+LELAGNAARDNKK RIIPRH+QLAIRNDEELNKLL  VTIAQGGVLPNI   LLPK S
Sbjct: 63  EILELAGNAARDNKKKRIIPRHLQLAIRNDEELNKLLGDVTIAQGGVLPNINPGLLPKSS 122

Query: 121 ETAKGKSNSQE 131
           +  KG   SQE
Sbjct: 123 K--KGSKRSQE 131

Length = 132

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

 Score =  167 bits (423), Expect = 1e-54
 Identities = 97/129 (75%), Positives = 110/129 (85%)

Query: 1   MSGRGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVA 60
           M+GRGKG  +  K+ +RS++AGLQFPVGRI R L+KG YAER+GAGAPVYLAAVLEYL A
Sbjct: 1   MAGRGKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTA 60

Query: 61  EVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKS 120
           EVLELAGNAARDNKK RI+PRHIQLAIRNDEEL KLL  VTIA GGVLPNI AVLLPKK+
Sbjct: 61  EVLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLLGEVTIASGGVLPNIHAVLLPKKT 120

Query: 121 ETAKGKSNS 129
           +  KG+  +
Sbjct: 121 KGGKGEETA 129

Length = 129

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

 Score =  128 bits (322), Expect = 3e-39
 Identities = 73/122 (59%), Positives = 88/122 (72%), Gaps = 2/122 (1%)

Query: 1   MSGRGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVLEYLV 59
            +   K  K K K  +RSSRAGLQFPVGRIHR L++   A  RVGA A VY AA+LEYL 
Sbjct: 15  TAAAAKKDKDKKKPTSRSSRAGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLT 74

Query: 60  AEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKK 119
           AEVLELAGNA++D K  RI PRH+QLAIR DEEL+ L+ G TIA GGV+P+I   L+ K 
Sbjct: 75  AEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIKG-TIAGGGVIPHIHKSLINKS 133

Query: 120 SE 121
           ++
Sbjct: 134 TK 135

Length = 136

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

 Score =  106 bits (267), Expect = 7e-31
 Identities = 58/121 (47%), Positives = 79/121 (65%), Gaps = 2/121 (1%)

Query: 9   KAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGN 68
           KA      RS++AGL FPVGR+  LLR+G YA R+GA   VY+AAVLEYL AE+LEL+  
Sbjct: 10  KASKSGSGRSAKAGLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVK 69

Query: 69  AARDN--KKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAKGK 126
           AA     K  R+ PR + LA+R+D++L  LL  VT+++GGV+P++   L  K     K K
Sbjct: 70  AAAQQAKKPKRLTPRTVTLAVRHDDDLGSLLKNVTLSRGGVMPSLNKALAKKHKSGKKAK 129

Query: 127 S 127
           +
Sbjct: 130 A 130

Length = 134

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

 Score = 94.2 bits (235), Expect = 1e-26
 Identities = 35/75 (46%), Positives = 45/75 (60%), Gaps = 1/75 (1%)

Query: 17 RSSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKK 75
           S    L+ P  R+ R L++G YAE R+ + APV L   LE L+ E+LE AG  AR  K+
Sbjct: 1  SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKR 60

Query: 76 TRIIPRHIQLAIRND 90
            I PR IQLA+R D
Sbjct: 61 KTITPRDIQLAVRLD 75

Length = 75

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

 Score = 74.7 bits (183), Expect = 4e-19
 Identities = 42/58 (72%), Positives = 50/58 (86%)

Query: 1  MSGRGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYL 58
          M+GRGKG  +  K+ +RS++AGLQFPVGRI R L+KG YAER+GAGAPVYLAAVLEYL
Sbjct: 1  MAGRGKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYL 58

Length = 58

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

 Score = 45.0 bits (106), Expect = 5e-07
 Identities = 23/95 (24%), Positives = 42/95 (44%), Gaps = 7/95 (7%)

Query: 11  KTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAA 70
           + K KTR       FP+ R+ ++++      +VG   PV  +  LE  + E++ L+   A
Sbjct: 17  QKKKKTR-------FPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEA 69

Query: 71  RDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQG 105
           R     R+    ++ A  +DE+ + L N       
Sbjct: 70  RKKSSKRMTSEFLKRATESDEKFDFLKNMEQFKNR 104

Length = 113

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

 Score = 35.3 bits (82), Expect = 7e-04
 Identities = 15/63 (23%), Positives = 29/63 (46%)

Query: 25 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQ 84
           P+ R+ R+++    A R+   A   +A  +E  +  +   A    +  K+  I   HI+
Sbjct: 3  LPIARVKRIMKSDPDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAEHIK 62

Query: 85 LAI 87
          LA+
Sbjct: 63 LAV 65

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

>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and dynamics]

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 26/84 (30%), Positives = 39/84 (46%), Gaps = 3/84 (3%)

Query: 5  GKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLE 64
          G  G  + +   RS+   L  P   + R+LRK   AERV + A   L   LE  + E+ E
Sbjct: 2  GAVGLKEIRRYQRSTDLLL--PKAPVRRILRKAG-AERVSSSAIEELQEALEEYLEEIAE 58

Query: 65 LAGNAARDNKKTRIIPRHIQLAIR 88
           A   A   K+  +    I+LA++
Sbjct: 59 DAVELAEHAKRKTVKAEDIKLALK 82

Length = 91

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	132
PLN00153	129	histone H2A; Provisional	100.0
PLN00157	132	histone H2A; Provisional	100.0
PTZ00017	134	histone H2A; Provisional	100.0
PLN00156	139	histone H2AX; Provisional	100.0
PTZ00252	134	histone H2A; Provisional	100.0
KOG1756|consensus	131		100.0
PLN00154	136	histone H2A; Provisional	100.0
cd00074	115	H2A Histone 2A; H2A is a subunit of the nucleosome	100.0
smart00414	106	H2A Histone 2A.	100.0
COG5262	132	HTA1 Histone H2A [Chromatin structure and dynamics	100.0
KOG1757|consensus	131		100.0
PLN00155	58	histone H2A; Provisional	99.89
PF00125	75	Histone: Core histone H2A/H2B/H3/H4 histone h2a si	99.57
PLN00035	103	histone H4; Provisional	99.49
COG5247	113	BUR6 Class 2 transcription repressor NC2, alpha su	99.49
PTZ00015	102	histone H4; Provisional	99.33
KOG1659|consensus	224		99.23
PF00808	65	CBFD_NFYB_HMF: Histone-like transcription factor (	99.19
cd00076	85	H4 Histone H4, one of the four histones, along wit	99.16
COG2036	91	HHT1 Histones H3 and H4 [Chromatin structure and d	99.12
smart00417	74	H4 Histone H4.	99.12
smart00803	65	TAF TATA box binding protein associated factor. TA	99.12
COG5208	286	HAP5 CCAAT-binding factor, subunit C [Transcriptio	98.48
cd07981	72	TAF12 TATA Binding Protein (TBP) Associated Factor	98.38
KOG1657|consensus	236		98.32
KOG3467|consensus	103		98.31
cd07979	117	TAF9 TATA Binding Protein (TBP) Associated Factor	98.26
PF02969	66	TAF: TATA box binding protein associated factor (T	97.86
smart00428	105	H3 Histone H3.	97.82
smart00576	77	BTP Bromodomain transcription factors and PHD doma	97.81
cd08050	343	TAF6 TATA Binding Protein (TBP) Associated Factor	97.74
cd08048	85	TAF11 TATA Binding Protein (TBP) Associated Factor	97.43
PF15511	414	CENP-T: Centromere kinetochore component CENP-T; P	97.08
PF04719	90	TAFII28: hTAFII28-like protein conserved region; I	97.08
PTZ00463	117	histone H2B; Provisional	97.01
KOG0869|consensus	168		96.97
KOG3219|consensus	195		96.95
smart00427	89	H2B Histone H2B.	96.84
PF15630	76	CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C	96.78
PLN00158	116	histone H2B; Provisional	96.75
PLN00160	97	histone H3; Provisional	96.32
PTZ00018	136	histone H3; Provisional	96.23
PF03847	68	TFIID_20kDa: Transcription initiation factor TFIID	96.2
PLN00121	136	histone H3; Provisional	96.18
PLN00161	135	histone H3; Provisional	96.1
KOG0871|consensus	156		96.05
PF02291	129	TFIID-31kDa: Transcription initiation factor IID,	95.98
PF09415	72	CENP-X: CENP-S associating Centromere protein X; I	95.84
PF07524	77	Bromo_TP: Bromodomain associated; InterPro: IPR006	95.61
KOG1658|consensus	162		95.16
KOG0870|consensus	172		95.13
PLN00163	59	histone H4; Provisional	94.87
KOG1142|consensus	258		94.28
KOG1745|consensus	137		93.5
KOG1744|consensus	127		93.19
PF02269	93	TFIID-18kDa: Transcription initiation factor IID,	92.95
cd07978	92	TAF13 The TATA Binding Protein (TBP) Associated Fa	92.71
KOG3334|consensus	148		87.52
COG5094	145	TAF9 Transcription initiation factor TFIID, subuni	85.96
COG5251	199	TAF40 Transcription initiation factor TFIID, subun	80.85

>PLN00153 histone H2A; Provisional

Probab=100.00  E-value=1.3e-50  Score=291.56  Aligned_cols=124  Identities=77%  Similarity=1.159  Sum_probs=117.3

Q ss_pred             CCCCCCCCCCCCccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceech
Q psy3662           1 MSGRGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIP   80 (132)
Q Consensus         1 m~~k~~~~~~~~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp   80 (132)
                      |||++++++.+++..|+|+||||+|||+||+|+|++++|+.||+++|+|||+||||||++||||+|+|.|+++++++|+|
T Consensus         1 m~g~~~~~~~~~k~~srS~ragL~FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItP   80 (129)
T PLN00153          1 MAGRGKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVP   80 (129)
T ss_pred             CCCCCCCCccccCccCcccccCcccchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCh
Confidence            99998765555578999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhcCcHHHHhhhcCCeecCCCcCCCCcccccCCcccccC
Q psy3662          81 RHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAK  124 (132)
Q Consensus        81 ~~i~~AI~~D~EL~~L~~~~~ia~ggv~P~i~~~~~~~k~~~~~  124 (132)
                      +||++||+||+||+.||+++||++|||+|+||++|+|+|.++++
T Consensus        81 rHi~lAI~nDeEL~~Ll~~vTIa~GGV~P~i~~~l~~kk~~~~~  124 (129)
T PLN00153         81 RHIQLAIRNDEELGKLLGEVTIASGGVLPNIHAVLLPKKTKGGK  124 (129)
T ss_pred             HHHHhhccCcHHHHHHHCCCccCCCccCCCcchhhcCcccCCCc
Confidence            99999999999999999999999999999999999999876553

>PLN00157 histone H2A; Provisional

Probab=100.00  E-value=8.2e-50  Score=288.34  Aligned_cols=124  Identities=78%  Similarity=1.182  Sum_probs=116.3

Q ss_pred             CCCCCC--CCCCCCccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCcee
Q psy3662           1 MSGRGK--GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRI   78 (132)
Q Consensus         1 m~~k~~--~~~~~~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~I   78 (132)
                      |||+++  +++.+++..|+|+||||+|||+||+|+|++++|++||+++|+|||+||||||++||||+|+|.|+++++++|
T Consensus         1 ms~~g~~~~~~~~~k~~srS~ragL~FPVgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RI   80 (132)
T PLN00157          1 MSGRGKRKGGGGGKKATSRSAKAGLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRI   80 (132)
T ss_pred             CCCCCCCCCCccCcCCcCcccccCcccchHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccc
Confidence            999876  444556789999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chhhhhhhhcCcHHHHhhhcCCeecCCCcCCCCcccccCCcccccC
Q psy3662          79 IPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAK  124 (132)
Q Consensus        79 tp~~i~~AI~~D~EL~~L~~~~~ia~ggv~P~i~~~~~~~k~~~~~  124 (132)
                      +|+||++||+||+||+.||+++||++|||+|+||++|+|+|..+++
T Consensus        81 tPrHi~lAI~nDeEL~~Ll~~vtIa~GGV~P~i~~~ll~kk~~~~~  126 (132)
T PLN00157         81 VPRHIQLAVRNDEELSKLLGGVTIAAGGVLPNIHSVLLPKKSGKSK  126 (132)
T ss_pred             cHHHHhhcccCcHHHHHHHcCceecCCccCCCcchhhcCCCCCCCC
Confidence            9999999999999999999999999999999999999999875443

>PTZ00017 histone H2A; Provisional

Probab=100.00  E-value=4e-49  Score=285.57  Aligned_cols=127  Identities=76%  Similarity=1.150  Sum_probs=117.1

Q ss_pred             CCCCCCCC-C--CCCccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCce
Q psy3662           1 MSGRGKGG-K--AKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTR   77 (132)
Q Consensus         1 m~~k~~~~-~--~~~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~   77 (132)
                      |+||++.+ +  .+++..|+|+||||+|||+||+|+|++++|++||+++|+|||+||||||++||||+|+|.|+++++++
T Consensus         1 ~~~~~~~~~~~~~~~k~~srS~ragL~FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~R   80 (134)
T PTZ00017          1 KGGKGKTGGGKAGKKKPVSRSAKAGLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKR   80 (134)
T ss_pred             CCCCCcCCCCcccCcCcccccccCCcccchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCe
Confidence            67776532 2  25567899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             echhhhhhhhcCcHHHHhhhcCCeecCCCcCCCCcccccCCcccccCCCC
Q psy3662          78 IIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAKGKS  127 (132)
Q Consensus        78 Itp~~i~~AI~~D~EL~~L~~~~~ia~ggv~P~i~~~~~~~k~~~~~~~~  127 (132)
                      |||+||++||+||+||+.||+++||++|||+|+||++|+|++...++.++
T Consensus        81 ItPrHi~lAI~nDeEL~~Ll~~vtIa~GGV~P~i~~~l~~k~~~~~~~~~  130 (134)
T PTZ00017         81 ITPRHIQLAIRNDEELNKLLAGVTIASGGVLPNIHKVLLPKKSKPKQGKK  130 (134)
T ss_pred             ecHHHHHhhccCcHHHHHHHcCCcccCCccCCCccHhhccCCCCcccccc
Confidence            99999999999999999999999999999999999999999998777644

>PLN00156 histone H2AX; Provisional

Probab=100.00  E-value=4e-49  Score=286.45  Aligned_cols=125  Identities=75%  Similarity=1.095  Sum_probs=115.8

Q ss_pred             CCCCCccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhh
Q psy3662           8 GKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAI   87 (132)
Q Consensus         8 ~~~~~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI   87 (132)
                      ++++++.+|+|+||||+|||+||+|+|++++|+.||+++|+|||+||||||++||||||+|.|+++++++|+|+||++||
T Consensus        13 ~~~~~k~~srS~rAgL~FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAI   92 (139)
T PLN00156         13 KPKATKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAV   92 (139)
T ss_pred             cccccCCcCcccccCcccchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhc
Confidence            34456789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCcHHHHhhhcCCeecCCCcCCCCcccccCCcccccCC--CCCCCCC
Q psy3662          88 RNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAKG--KSNSQEY  132 (132)
Q Consensus        88 ~~D~EL~~L~~~~~ia~ggv~P~i~~~~~~~k~~~~~~--~~~~~~~  132 (132)
                      +||+||+.||+++||++|||+|+||++|+|+|+++++.  .+.+|+|
T Consensus        93 rnDeEL~~Ll~~vTIa~GGV~P~i~~~l~~kk~~~~~~~~~~~~~~~  139 (139)
T PLN00156         93 RNDEELSKLLGSVTIAAGGVLPNIHQTLLPKKVGKGKGDIGSASQEF  139 (139)
T ss_pred             cCcHHHHHHHCCCccCCCccCCCccHhhccccccccccccccccCCC
Confidence            99999999999999999999999999999999866543  3457776

>PTZ00252 histone H2A; Provisional

Probab=100.00  E-value=7.1e-48  Score=277.99  Aligned_cols=126  Identities=48%  Similarity=0.794  Sum_probs=110.8

Q ss_pred             CCCCCCCCCCCCccCC-cccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHh--cCCce
Q psy3662           1 MSGRGKGGKAKTKSKT-RSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARD--NKKTR   77 (132)
Q Consensus         1 m~~k~~~~~~~~~~~s-~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~--~~~k~   77 (132)
                      |+.-++++|+.++..+ +|+||||||||+||+|+|++++|++||+++|+|||+||||||++||||||+|.|++  +++++
T Consensus         1 ~~~~~~~~~~~~~~~~~rS~rAGL~FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~R   80 (134)
T PTZ00252          1 MATPKQAKKKASKSGSGRSAKAGLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKR   80 (134)
T ss_pred             CCCccchhhcccccccccccccCccCchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCccc
Confidence            5543333433334454 99999999999999999999999999999999999999999999999999999976  67889


Q ss_pred             echhhhhhhhcCcHHHHhhhcCCeecCCCcCCCCcccccCCcccccCCC
Q psy3662          78 IIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAKGK  126 (132)
Q Consensus        78 Itp~~i~~AI~~D~EL~~L~~~~~ia~ggv~P~i~~~~~~~k~~~~~~~  126 (132)
                      |+|+||++||+||+||+.||+++||++|||+|+||++|++++.+.++.|
T Consensus        81 ItPrHi~lAIrNDeEL~~Ll~~vTIa~GGVlP~i~~~l~~k~~~~~~~~  129 (134)
T PTZ00252         81 LTPRTVTLAVRHDDDLGSLLKNVTLSRGGVMPSLNKALAKKHKSGKKAK  129 (134)
T ss_pred             ccHHHHHhhccChHHHHHHHcCCccCCCccCCCccHhhccccccCCCCC
Confidence            9999999999999999999999999999999999999999955555443

>KOG1756|consensus

Probab=100.00  E-value=2.7e-46  Score=266.66  Aligned_cols=126  Identities=84%  Similarity=1.219  Sum_probs=116.1

Q ss_pred             CCCCCCCCCC---CCccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCce
Q psy3662           1 MSGRGKGGKA---KTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTR   77 (132)
Q Consensus         1 m~~k~~~~~~---~~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~   77 (132)
                      |+|++++++.   ++...|+|.|+||||||++|+|+|++++|++||+.+|||||+||||||++||+|+|+|.|+++++.+
T Consensus         1 ~s~~~k~gk~~~~~~~~~srs~~agl~fPvgri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~r   80 (131)
T KOG1756|consen    1 MSGRGKGGKAKPRAKAKSSRSSRAGLQFPVGRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTR   80 (131)
T ss_pred             CCccCCCCcccchhhhhcchhhhcccccCHHHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccc
Confidence            6777665532   3456788999999999999999999999999999999999999999999999999999999999999


Q ss_pred             echhhhhhhhcCcHHHHhhhcCCeecCCCcCCCCcccccCCcccccCCC
Q psy3662          78 IIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAKGK  126 (132)
Q Consensus        78 Itp~~i~~AI~~D~EL~~L~~~~~ia~ggv~P~i~~~~~~~k~~~~~~~  126 (132)
                      |+|+||++||+||+||.+|+++|+|++|||+|+||+.++||+..+..++
T Consensus        81 i~PrH~~lAI~NDeEL~~lL~~vtIa~GGvlPnI~~~lLpKk~~~~~~~  129 (131)
T KOG1756|consen   81 ITPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAILLPKKTGKHKSK  129 (131)
T ss_pred             cChHHHHHHHhCcHHHHHHhccceeccCCcccccchhhcccccccCCCC
Confidence            9999999999999999999999999999999999999999988775543

>PLN00154 histone H2A; Provisional

Probab=100.00  E-value=4.2e-46  Score=269.57  Aligned_cols=111  Identities=62%  Similarity=0.908  Sum_probs=105.0

Q ss_pred             CCccCCcccccccccchhHHHHHHhhCC-cccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcC
Q psy3662          11 KTKSKTRSSRAGLQFPVGRIHRLLRKGN-YAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRN   89 (132)
Q Consensus        11 ~~~~~s~s~ragl~fPv~ri~rllk~~~-~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~   89 (132)
                      +++..|+|+||||||||+||+|+|+++. +.+||+.+|+|||+||||||++||||||+|.|+++++++|||+||++||+|
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            4467899999999999999999999986 468999999999999999999999999999999999999999999999999


Q ss_pred             cHHHHhhhcCCeecCCCcCCCCcccccCCcccc
Q psy3662          90 DEELNKLLNGVTIAQGGVLPNIQAVLLPKKSET  122 (132)
Q Consensus        90 D~EL~~L~~~~~ia~ggv~P~i~~~~~~~k~~~  122 (132)
                      |+||+.||+ +||++|||+|+||++|++++.++
T Consensus       105 DeEL~~Ll~-~TIa~GGVlP~i~~~l~~k~~~~  136 (136)
T PLN00154        105 DEELDTLIK-GTIAGGGVIPHIHKSLINKSTKK  136 (136)
T ss_pred             cHHHHHHhc-CCccCCccCCCcchhhcccccCC
Confidence            999999996 69999999999999999997653

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

Probab=100.00  E-value=1.2e-45  Score=262.51  Aligned_cols=111  Identities=84%  Similarity=1.247  Sum_probs=106.8

Q ss_pred             CCCCccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662           9 KAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus         9 ~~~~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      |++++.+|+|+|+||+|||+||+|||+++.+++||+++|+|||+||||||++||+|+|+|.|+++++++|+|+||++||+
T Consensus         5 k~~~~~~s~s~ragL~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~   84 (115)
T cd00074           5 KKKSKKRSRSARAGLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVR   84 (115)
T ss_pred             ccCcCccccccccCccCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHh
Confidence            45567889999999999999999999998899999999999999999999999999999999999999999999999999


Q ss_pred             CcHHHHhhhcCCeecCCCcCCCCcccccCCc
Q psy3662          89 NDEELNKLLNGVTIAQGGVLPNIQAVLLPKK  119 (132)
Q Consensus        89 ~D~EL~~L~~~~~ia~ggv~P~i~~~~~~~k  119 (132)
                      ||+||++||+++||++|||+|+||+.|++++
T Consensus        85 nD~EL~~L~~~vtI~~ggv~p~i~~~l~~~~  115 (115)
T cd00074          85 NDEELNKLLKGVTIASGGVLPNIHKVLLPKK  115 (115)
T ss_pred             ccHHHHHHHcCCcccCCccCCCcchhhcCCC
Confidence            9999999999999999999999999999875

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.

>smart00414 H2A Histone 2A

Probab=100.00  E-value=1.1e-45  Score=259.36  Aligned_cols=106  Identities=88%  Similarity=1.287  Sum_probs=103.3

Q ss_pred             CcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHHHh
Q psy3662          16 TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNK   95 (132)
Q Consensus        16 s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL~~   95 (132)
                      |+|+|+||+|||+||+|+|+++++++||+++|+|||+||||||++||||+|+|.|+++++++|||+||++||+||+|||.
T Consensus         1 srS~ragL~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~nD~EL~~   80 (106)
T smart00414        1 SRSARAGLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRNDEELNK   80 (106)
T ss_pred             CccccCCccCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccCCHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcCCeecCCCcCCCCcccccCCccc
Q psy3662          96 LLNGVTIAQGGVLPNIQAVLLPKKSE  121 (132)
Q Consensus        96 L~~~~~ia~ggv~P~i~~~~~~~k~~  121 (132)
                      ||+++||++|||+|+||++|+|+|++
T Consensus        81 L~~~vti~~ggv~p~i~~~l~~~~~~  106 (106)
T smart00414       81 LLKGVTIAQGGVLPNIHKVLLPKKTG  106 (106)
T ss_pred             HHcCcccCCCccCCCcchhhcccCCC
Confidence            99999999999999999999999763

>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]

Probab=100.00  E-value=3.7e-44  Score=252.78  Aligned_cols=108  Identities=80%  Similarity=1.191  Sum_probs=104.4

Q ss_pred             cCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHH
Q psy3662          14 SKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEEL   93 (132)
Q Consensus        14 ~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL   93 (132)
                      ..|+|.++||+|||+||+|+|+.+++..||+++|+||++||||||++||+|+|+|.|+++++++|+|+||++||+||+||
T Consensus        16 ~~s~sa~agl~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIrnD~EL   95 (132)
T COG5262          16 SQSRSAKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIRNDEEL   95 (132)
T ss_pred             ccchhhhcCccccHHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhcCcHHH
Confidence            56889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhcCCeecCCCcCCCCcccccCCccc
Q psy3662          94 NKLLNGVTIAQGGVLPNIQAVLLPKKSE  121 (132)
Q Consensus        94 ~~L~~~~~ia~ggv~P~i~~~~~~~k~~  121 (132)
                      ++|+++|+|++|||+|+||+.++++..+
T Consensus        96 ~~l~~~~tIa~GGvlp~I~~~ll~k~sk  123 (132)
T COG5262          96 NKLLGDVTIAQGGVLPNINPGLLPKSSK  123 (132)
T ss_pred             HHHhhhheeecCCcccccChhhhhhhhc
Confidence            9999999999999999999999998543

>KOG1757|consensus

Probab=100.00  E-value=1.3e-40  Score=233.27  Aligned_cols=112  Identities=62%  Similarity=0.911  Sum_probs=104.7

Q ss_pred             CCccCCcccccccccchhHHHHHHhhCCcc-cccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcC
Q psy3662          11 KTKSKTRSSRAGLQFPVGRIHRLLRKGNYA-ERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRN   89 (132)
Q Consensus        11 ~~~~~s~s~ragl~fPv~ri~rllk~~~~~-~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~   89 (132)
                      +.+.+|+|.|+||||||+||||.|+....+ .||+.+++||++|+||||++|+||||+|.+++.+.++|||+|+++||+.
T Consensus        17 ~~k~vs~s~raGlqFpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiRG   96 (131)
T KOG1757|consen   17 KAKAVSRSARAGLQFPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG   96 (131)
T ss_pred             hhhhhhHHHhcccccchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheeeecC
Confidence            456789999999999999999999986555 4999999999999999999999999999999999999999999999999


Q ss_pred             cHHHHhhhcCCeecCCCcCCCCcccccCCccccc
Q psy3662          90 DEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETA  123 (132)
Q Consensus        90 D~EL~~L~~~~~ia~ggv~P~i~~~~~~~k~~~~  123 (132)
                      |+|||.|+ ..||++|||+||||++|+.|+++++
T Consensus        97 DeELDtLI-k~TiagGgViPhihk~l~~k~~~~~  129 (131)
T KOG1757|consen   97 DEELDTLI-KATIAGGGVIPHIHKSLINKKGKKK  129 (131)
T ss_pred             cHHHHHHH-HHhhccCccccchHHHHhccccccC
Confidence            99999999 5789999999999999999887654

>PLN00155 histone H2A; Provisional

Probab=99.89  E-value=1.5e-23  Score=131.80  Aligned_cols=58  Identities=72%  Similarity=1.189  Sum_probs=53.1

Q ss_pred             CCCCCCCCCCCCccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHH
Q psy3662           1 MSGRGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYL   58 (132)
Q Consensus         1 m~~k~~~~~~~~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl   58 (132)
                      |||++++++.+++.+|+|+||||||||+||+|+|+++++++||+.+|||||+||||||
T Consensus         1 msg~g~g~~~~~k~~srS~rAgL~FPVgri~r~Lr~g~~a~Rvga~apVYlAAVLEYL   58 (58)
T PLN00155          1 MAGRGKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYL   58 (58)
T ss_pred             CCCCCCCCccccCccCcccccccccchHHHHHHHhcCChhhcccCCcHHHHHHHHHhC
Confidence            8998776555556799999999999999999999999999999999999999999996

>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=99.57  E-value=2.9e-15  Score=98.01  Aligned_cols=73  Identities=44%  Similarity=0.631  Sum_probs=67.2

Q ss_pred             ccccccccchhHHHHHHhhCCccc-ccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCc
Q psy3662          18 SSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRND   90 (132)
Q Consensus        18 s~ragl~fPv~ri~rllk~~~~~~-RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D   90 (132)
                      +.+..+.||+.++.+-+..+.+.. |++.+|.++|.+++||++.+|+++|++.|.++++++|+|+||+.|++.|
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            456778999999999999876664 9999999999999999999999999999999999999999999999765

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 ....

>PLN00035 histone H4; Provisional

Probab=99.49  E-value=4.5e-14  Score=98.61  Aligned_cols=86  Identities=26%  Similarity=0.393  Sum_probs=74.2

Q ss_pred             CCCCCCCCC-------CCCccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy3662           1 MSGRGKGGK-------AKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDN   73 (132)
Q Consensus         1 m~~k~~~~~-------~~~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~   73 (132)
                      |||++++++       ++++++.+.+-++  ||...|.|+++++ .+.|||.++...|..+||.++.+|+..|..+|.|.
T Consensus         1 m~~~~k~~~g~g~~g~kr~~k~~~d~i~~--ipk~~IrRLARr~-GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA   77 (103)
T PLN00035          1 MSGRGKGGKGLGKGGAKRHRKVLRDNIQG--ITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHA   77 (103)
T ss_pred             CCCCCCCCCCCCCCcchHHHHHHHhhhcc--CCHHHHHHHHHHc-CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            888877443       3555566666667  7777899999997 69999999999999999999999999999999999


Q ss_pred             CCceechhhhhhhhcC
Q psy3662          74 KKTRIIPRHIQLAIRN   89 (132)
Q Consensus        74 ~~k~Itp~~i~~AI~~   89 (132)
                      ++++|+++||.+|+..
T Consensus        78 ~RKTV~~~DV~~Alkr   93 (103)
T PLN00035         78 RRKTVTAMDVVYALKR   93 (103)
T ss_pred             CCCcCcHHHHHHHHHH
Confidence            9999999999999853

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

Probab=99.49  E-value=6.9e-14  Score=96.94  Aligned_cols=80  Identities=24%  Similarity=0.460  Sum_probs=76.0

Q ss_pred             ccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHHHhhhcC
Q psy3662          20 RAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNG   99 (132)
Q Consensus        20 ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL~~L~~~   99 (132)
                      +-...||++|++++|+-+.....|+..+||.....||+|+.+|+.+++..|+..+.+|||.++|..|+.+|+.+++|-..
T Consensus        19 ~~ktrFP~ar~KkIMQ~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~   98 (113)
T COG5247          19 KKKTRFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNM   98 (113)
T ss_pred             hhhhcCCHHHHHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHH
Confidence            55668999999999999989999999999999999999999999999999999999999999999999999999998743

>PTZ00015 histone H4; Provisional

Probab=99.33  E-value=3e-12  Score=89.40  Aligned_cols=75  Identities=19%  Similarity=0.311  Sum_probs=65.3

Q ss_pred             CCccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          11 KTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        11 ~~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      +++++.+.+-.|+  |.+.|.||++++ .+.|||.++...+..+||.++.+|+..|..+|.|+++++|+++||.+|+.
T Consensus        19 r~rk~~r~~i~gI--~k~~IrRLarr~-GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlK   93 (102)
T PTZ00015         19 RQKKVLRDNIRGI--TKGAIRRLARRG-GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALK   93 (102)
T ss_pred             hHHHHHhhcccCC--CHHHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHH
Confidence            4444555555664  556799999997 79999999999999999999999999999999999999999999999974

>KOG1659|consensus

Probab=99.23  E-value=1.8e-11  Score=94.69  Aligned_cols=79  Identities=19%  Similarity=0.395  Sum_probs=74.7

Q ss_pred             ccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHHHhhhc
Q psy3662          20 RAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLN   98 (132)
Q Consensus        20 ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL~~L~~   98 (132)
                      +-.-.||++||+++|+.+....+|...+||.+...||.|+.+|+..++..++..+.++++++||..||.+|+.|++|-.
T Consensus         9 ~~~trfp~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk~   87 (224)
T KOG1659|consen    9 KYKTRFPPARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLKE   87 (224)
T ss_pred             hhhccCCHHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHHH
Confidence            3345799999999999999999999999999999999999999999999999999999999999999999999999873

>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=99.19  E-value=8.7e-11  Score=75.15  Aligned_cols=64  Identities=20%  Similarity=0.312  Sum_probs=57.8

Q ss_pred             ccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhh
Q psy3662          24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAI   87 (132)
Q Consensus        24 ~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI   87 (132)
                      .||+++|+|+||......+|+.+|...++...|.|+.+|...|...|...++++|+++||..|+
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            5999999999999866779999999999999999999999999999999999999999999875

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 ....

>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=99.16  E-value=6e-11  Score=80.41  Aligned_cols=76  Identities=20%  Similarity=0.307  Sum_probs=66.6

Q ss_pred             CCccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcC
Q psy3662          11 KTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRN   89 (132)
Q Consensus        11 ~~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~   89 (132)
                      +++++-+.+-+|  +|.+.|.|+.+++ .+.|||.++...+..+||.++.+|+..|..+|.|.++++|+++||.+|+..
T Consensus         2 r~r~~~~~~~~g--i~k~~I~RLarr~-GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr   77 (85)
T cd00076           2 RHRKVLRDNIKG--ITKPAIRRLARRG-GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKR   77 (85)
T ss_pred             chhHHHHHhhcc--CCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence            344555666677  5666799999997 699999999999999999999999999999999999999999999998854

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

Probab=99.12  E-value=1e-10  Score=80.19  Aligned_cols=67  Identities=33%  Similarity=0.420  Sum_probs=62.6

Q ss_pred             cccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          21 AGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        21 agl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      ..+-||+..|.|++++. ..+|||.+|...|..++|-++.+|.+.|...|.|.++++|+++||++|+.
T Consensus        16 ~~~~Lp~apv~Ri~r~~-~~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~   82 (91)
T COG2036          16 TDLLLPKAPVRRILRKA-GAERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALK   82 (91)
T ss_pred             hhhhcCchHHHHHHHHH-hHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHH
Confidence            45678999999999996 67799999999999999999999999999999999999999999999974

>smart00417 H4 Histone H4

Probab=99.12  E-value=8.9e-11  Score=77.67  Aligned_cols=72  Identities=19%  Similarity=0.221  Sum_probs=63.0

Q ss_pred             CccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhh
Q psy3662          12 TKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLA   86 (132)
Q Consensus        12 ~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~A   86 (132)
                      ++++-+.+-.|+  |...|.|+++++ ++.|||.++...+..+||.++.+|+..|..+|.|.++++|+.+||..|
T Consensus         3 ~~~~~~d~i~gI--~k~~IrRLaRr~-GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a   74 (74)
T smart00417        3 HKKVLRDNIQGI--TKPAIRRLARRG-GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA   74 (74)
T ss_pred             hhHHHHhhhcCC--CHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence            445556666675  555699999997 799999999999999999999999999999999999999999999754

>smart00803 TAF TATA box binding protein associated factor

Probab=99.12  E-value=2.6e-10  Score=73.61  Aligned_cols=64  Identities=23%  Similarity=0.271  Sum_probs=60.6

Q ss_pred             ccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        24 ~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      .+|.+.|+|+.+.. +..|||.++...|+..+||.+.+|+..|.++++|++|+++|++||..|+.
T Consensus         2 ~~p~~~i~ria~~~-Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk   65 (65)
T smart00803        2 WLPKETIKDVAESL-GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR   65 (65)
T ss_pred             CCCHHHHHHHHHHC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence            48999999999996 68899999999999999999999999999999999999999999999863

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.

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

Probab=98.48  E-value=2.9e-07  Score=72.11  Aligned_cols=75  Identities=24%  Similarity=0.410  Sum_probs=71.8

Q ss_pred             cccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHHHhhh
Q psy3662          23 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLL   97 (132)
Q Consensus        23 l~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL~~L~   97 (132)
                      +.+|++||+++|+.+....-|++.||+.++.+.|-|++|+.-.|+-.|..+++.++.-.||..|+...+-+++|+
T Consensus       108 h~LPlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLi  182 (286)
T COG5208         108 HNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLI  182 (286)
T ss_pred             ccCcHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHh
Confidence            459999999999998888899999999999999999999999999999999999999999999999999999998

>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=98.38  E-value=1.3e-06  Score=57.14  Aligned_cols=66  Identities=18%  Similarity=0.301  Sum_probs=59.3

Q ss_pred             cchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCc
Q psy3662          25 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRND   90 (132)
Q Consensus        25 fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D   90 (132)
                      ++-..+..++++.....|++.+|...|..++|-|+.+|++.|...|+|.++++|.++||++++..+
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            345678888888655679999999999999999999999999999999999999999999998654

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

>KOG1657|consensus

Probab=98.32  E-value=4.6e-07  Score=71.73  Aligned_cols=78  Identities=21%  Similarity=0.336  Sum_probs=74.0

Q ss_pred             cccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHHHhhhc
Q psy3662          21 AGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLN   98 (132)
Q Consensus        21 agl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL~~L~~   98 (132)
                      ....||++||+++||.+.....|+.+|+|.++.++|+++.|+-..++..+..++++++.-.||..++.+..-+++|+.
T Consensus        71 ~~~~lPlaRiKkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL~D  148 (236)
T KOG1657|consen   71 KNHILPLARIKKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFLRD  148 (236)
T ss_pred             hhccCcHhhccccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccceec
Confidence            356899999999999988889999999999999999999999999999999999999999999999999999999984

>KOG3467|consensus

Probab=98.31  E-value=1.4e-06  Score=59.21  Aligned_cols=85  Identities=28%  Similarity=0.436  Sum_probs=73.0

Q ss_pred             CCCCCCCCC-------CCCccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy3662           1 MSGRGKGGK-------AKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDN   73 (132)
Q Consensus         1 m~~k~~~~~-------~~~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~   73 (132)
                      |+++++++|       ++++++-+.+-+|++-|.  |+|+.+.+ ...||+...-.....++.-++.+++-.|..++.|.
T Consensus         1 Ms~r~~g~KG~~KG~AKrHRK~LsDnIqgitKpa--IRRlARr~-GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HA   77 (103)
T KOG3467|consen    1 MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPA--IRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHA   77 (103)
T ss_pred             CCCcCccccccccchHHHHHHHHHhhccccchHH--HHHHHHhc-CcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            776655433       356667778888999998  99999996 68999999999999999999999999999999999


Q ss_pred             CCceechhhhhhhhc
Q psy3662          74 KKTRIIPRHIQLAIR   88 (132)
Q Consensus        74 ~~k~Itp~~i~~AI~   88 (132)
                      ++++||..|+-.++.
T Consensus        78 KRKTvT~~dvv~~LK   92 (103)
T KOG3467|consen   78 KRKTVTAMDVVYALK   92 (103)
T ss_pred             hhceeeHHHHHHHHH
Confidence            999999999987763

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

Probab=98.26  E-value=2.6e-06  Score=60.78  Aligned_cols=63  Identities=17%  Similarity=0.087  Sum_probs=57.9

Q ss_pred             hHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcH
Q psy3662          28 GRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDE   91 (132)
Q Consensus        28 ~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~   91 (132)
                      --|+++|++. +..+++..++..|...++-++.+|+..|..+|+|.++++|+.+||++||..--
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            3589999995 68899999999999999999999999999999999999999999999996543

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

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

Probab=97.86  E-value=7e-05  Score=48.51  Aligned_cols=64  Identities=22%  Similarity=0.272  Sum_probs=50.3

Q ss_pred             ccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        24 ~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      .||..-|+.+-..- +..-++.+++-.|+.=+||-+.||+..|.+..+|.+|+++|++||+.|++
T Consensus         3 ~~~~esvk~iAes~-Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr   66 (66)
T PF02969_consen    3 VFSQESVKDIAESL-GISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR   66 (66)
T ss_dssp             ---HHHHHHHHHHT-T---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred             cCCHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence            57888888888774 56689999999999999999999999999999999999999999999874

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.

>smart00428 H3 Histone H3

Probab=97.82  E-value=4.5e-05  Score=53.63  Aligned_cols=67  Identities=25%  Similarity=0.308  Sum_probs=58.9

Q ss_pred             cccccchhHHHHHHhhC--Cc----ccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhh
Q psy3662          21 AGLQFPVGRIHRLLRKG--NY----AERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAI   87 (132)
Q Consensus        21 agl~fPv~ri~rllk~~--~~----~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI   87 (132)
                      .+|.+|-..+.|++++-  .+    ..|++++|...|..+.|.++.++++.|...|.|.++.+|+|+|+++|.
T Consensus        26 t~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~   98 (105)
T smart00428       26 TDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLAR   98 (105)
T ss_pred             cccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHH
Confidence            46888888888888751  11    349999999999999999999999999999999999999999999885

>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins

Probab=97.81  E-value=6.9e-05  Score=49.44  Aligned_cols=59  Identities=19%  Similarity=0.156  Sum_probs=54.0

Q ss_pred             HHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcC
Q psy3662          30 IHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRN   89 (132)
Q Consensus        30 i~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~   89 (132)
                      |.++++.. ++.+++.+|...|+.++|-++.+|.+.+-++|.+.+|+..++.||..|+.+
T Consensus        12 Vaqil~~~-Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~   70 (77)
T smart00576       12 VAQILESA-GFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALEN   70 (77)
T ss_pred             HHHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence            56777775 689999999999999999999999999999999999999999999999743

subdomain of archael histone-like transcription factors

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

Probab=97.74  E-value=7.3e-05  Score=61.90  Aligned_cols=60  Identities=18%  Similarity=0.281  Sum_probs=53.9

Q ss_pred             hHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          28 GRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        28 ~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      +-|+-+++.. +..|++.+|...|+..+||.+.+|++.|.+.+++.+|++++++||+.|++
T Consensus         3 ~~i~~ia~~~-Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~   62 (343)
T cd08050           3 ESIKLIAESL-GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALR   62 (343)
T ss_pred             hHHHHHHHHc-CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHH
Confidence            4456666664 68899999999999999999999999999999999999999999999964

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

>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=97.43  E-value=0.00061  Score=46.11  Aligned_cols=63  Identities=25%  Similarity=0.428  Sum_probs=55.2

Q ss_pred             cchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCC---ceechhhhhhhhc
Q psy3662          25 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKK---TRIIPRHIQLAIR   88 (132)
Q Consensus        25 fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~---k~Itp~~i~~AI~   88 (132)
                      ||-..++|++... ..+.|+.+..+.|+++-.-++.||+|.|...-...+.   ..|.|+||+.|..
T Consensus        17 f~k~~iKr~~~~~-~~~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~r   82 (85)
T cd08048          17 FPKAAIKRLIQSV-TGQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYR   82 (85)
T ss_pred             ccHHHHHHHHHHH-cCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHH
Confidence            7777899999885 5689999999999999999999999999988666544   7899999998864

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

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

Probab=97.08  E-value=0.001  Score=56.51  Aligned_cols=72  Identities=13%  Similarity=0.129  Sum_probs=46.4

Q ss_pred             CCccCCcccccccccchhHHHHHHhhC----Ccc-cccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhh
Q psy3662          11 KTKSKTRSSRAGLQFPVGRIHRLLRKG----NYA-ERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRH   82 (132)
Q Consensus        11 ~~~~~s~s~ragl~fPv~ri~rllk~~----~~~-~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~   82 (132)
                      +.+++|+-......+|.+.|++++...    .++ .+|+.+|.-.|..++|||...+.+--.-||.|+|||+|.+.|
T Consensus       338 k~~k~Skhgi~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD  414 (414)
T PF15511_consen  338 KQKKVSKHGIPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD  414 (414)
T ss_dssp             --------------S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred             cccCCCCCCCCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence            455677766667889999999998752    333 499999999999999999999999999999999999999876

>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=97.08  E-value=0.0012  Score=45.22  Aligned_cols=64  Identities=20%  Similarity=0.359  Sum_probs=47.0

Q ss_pred             ccchhHHHHHHhhCCcc-cccccChHHHHHHHHHHHHHHHHHHHHHHHHhc-CCceechhhhhhhhc
Q psy3662          24 QFPVGRIHRLLRKGNYA-ERVGAGAPVYLAAVLEYLVAEVLELAGNAARDN-KKTRIIPRHIQLAIR   88 (132)
Q Consensus        24 ~fPv~ri~rllk~~~~~-~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~-~~k~Itp~~i~~AI~   88 (132)
                      .||-+.|++++... .. +-|+....+.++++-..|+.||+|.|....... ....|+|.||+.|..
T Consensus        23 ~~~k~~ikkli~~~-~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~r   88 (90)
T PF04719_consen   23 SFNKAAIKKLINQV-LGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYR   88 (90)
T ss_dssp             ---HHHHHHHHHHH-HS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHH
T ss_pred             cCCHHHHHHHHHHH-cCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHH
Confidence            48888899999985 44 799999999999999999999999999886554 344799999998863

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.

>PTZ00463 histone H2B; Provisional

Probab=97.01  E-value=0.0045  Score=44.21  Aligned_cols=60  Identities=17%  Similarity=0.217  Sum_probs=52.5

Q ss_pred             HHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          29 RIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        29 ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      .|++.|++-.-..-||..|.-.|...+.-+.+.|...|...|+.+++.+|++++|+.|++
T Consensus        33 YI~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvr   92 (117)
T PTZ00463         33 YIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIR   92 (117)
T ss_pred             HHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHh
Confidence            589999885444578899998999999999999999999999999999999999999984

>KOG0869|consensus

Probab=96.97  E-value=0.0024  Score=47.86  Aligned_cols=66  Identities=15%  Similarity=0.238  Sum_probs=58.2

Q ss_pred             cccchhHHHHHHhhCCcc-cccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          23 LQFPVGRIHRLLRKGNYA-ERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        23 l~fPv~ri~rllk~~~~~-~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      --+|++-|-||||+.--. -+|+.+|..-+--++-.|++-|.-.|...+...+||+|+.+||-+|+.
T Consensus        31 r~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~   97 (168)
T KOG0869|consen   31 RFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMS   97 (168)
T ss_pred             hhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHH
Confidence            458999999999996333 399999999999999889999998898889999999999999999874

>KOG3219|consensus

Probab=96.95  E-value=0.00096  Score=51.45  Aligned_cols=64  Identities=23%  Similarity=0.372  Sum_probs=55.0

Q ss_pred             cccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcC-Cceechhhhhhhh
Q psy3662          23 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNK-KTRIIPRHIQLAI   87 (132)
Q Consensus        23 l~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~-~k~Itp~~i~~AI   87 (132)
                      .-||-+.|++||..-. .+-|+..+.++++++-.-|+.||+|+|.......+ ...+.|.||+.|.
T Consensus       111 s~f~Ka~iKkL~~~it-g~~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~  175 (195)
T KOG3219|consen  111 SAFPKAQIKKLMSSIT-GQSVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAY  175 (195)
T ss_pred             hcCCHHHHHHHHHHHh-CCccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHH
Confidence            4699999999999853 34499999999999999999999999988865544 4569999999987

>smart00427 H2B Histone H2B

Probab=96.84  E-value=0.0043  Score=42.42  Aligned_cols=60  Identities=23%  Similarity=0.303  Sum_probs=52.6

Q ss_pred             HHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          29 RIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        29 ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      .|+|.|++-.-..-|+..|.-.|...+..+...|...|...++.+++.+|++++|+.|++
T Consensus         6 Yi~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvr   65 (89)
T smart00427        6 YIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVR   65 (89)
T ss_pred             HHHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHH
Confidence            588999885434478999999999999999999999999999999999999999999983

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

Probab=96.78  E-value=0.0063  Score=40.37  Aligned_cols=49  Identities=22%  Similarity=0.357  Sum_probs=37.0

Q ss_pred             cChHHHHHHHHHHHHHHHHHHHHH---HHHhcCCceechhhhhhhhcCcHHH
Q psy3662          45 AGAPVYLAAVLEYLVAEVLELAGN---AARDNKKTRIIPRHIQLAIRNDEEL   93 (132)
Q Consensus        45 ~~A~vyLaavLEyl~~eIlelA~~---~A~~~~~k~Itp~~i~~AI~~D~EL   93 (132)
                      .-++.|++++.|-.-..+-.+|..   .|+|.||++|+++|+.+..+.++.|
T Consensus        25 ~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rrn~~L   76 (76)
T PF15630_consen   25 EVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARRNPSL   76 (76)
T ss_dssp             EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT-HHH
T ss_pred             ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhcCCCC
Confidence            356788888888887777777643   4999999999999999999999876

>PLN00158 histone H2B; Provisional

Probab=96.75  E-value=0.0052  Score=43.86  Aligned_cols=61  Identities=25%  Similarity=0.317  Sum_probs=53.3

Q ss_pred             hHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          28 GRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        28 ~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      ..|++.|++-.-..-|+..|.-.|...+..+.+.|...|...++.+++.+|++++|+.|++
T Consensus        31 ~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvr   91 (116)
T PLN00158         31 IYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVR   91 (116)
T ss_pred             HHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHH
Confidence            3689999985444478899999999999999999999999999999999999999999874

>PLN00160 histone H3; Provisional

Probab=96.32  E-value=0.0082  Score=41.65  Aligned_cols=67  Identities=25%  Similarity=0.229  Sum_probs=58.4

Q ss_pred             cccccchhHHHHHHhhCC-----cccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhh
Q psy3662          21 AGLQFPVGRIHRLLRKGN-----YAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAI   87 (132)
Q Consensus        21 agl~fPv~ri~rllk~~~-----~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI   87 (132)
                      .+|.+|-..+.|++++-.     ...|...+|...|--+-|.++-.++|.+.-.|.|.++.+|.|.|++++.
T Consensus        18 t~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~   89 (97)
T PLN00160         18 TDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLAR   89 (97)
T ss_pred             hhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHH
Confidence            468888888888887621     1358999999999999999999999999999999999999999999874

>PTZ00018 histone H3; Provisional

Probab=96.23  E-value=0.0091  Score=43.79  Aligned_cols=66  Identities=26%  Similarity=0.259  Sum_probs=58.1

Q ss_pred             ccccchhHHHHHHhhC----CcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhh
Q psy3662          22 GLQFPVGRIHRLLRKG----NYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAI   87 (132)
Q Consensus        22 gl~fPv~ri~rllk~~----~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI   87 (132)
                      +|.||-..+.|++++-    ....|...+|...|--+-|.++-.++|.+...|.|.++.+|.+.|++++.
T Consensus        60 ~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~  129 (136)
T PTZ00018         60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR  129 (136)
T ss_pred             hhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHH
Confidence            6778888899988862    12359999999999999999999999999999999999999999999874

>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=96.20  E-value=0.018  Score=37.35  Aligned_cols=61  Identities=16%  Similarity=0.329  Sum_probs=48.6

Q ss_pred             HHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcC
Q psy3662          29 RIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRN   89 (132)
Q Consensus        29 ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~   89 (132)
                      ++..++++-.-...+..++...|..+.+-|+.+|+..|...|+|-+..++.+.||+..+..
T Consensus         4 ~l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler   64 (68)
T PF03847_consen    4 KLQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLER   64 (68)
T ss_dssp             HHHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHh
Confidence            5677888865567999999999999999999999999999999999999999999987754

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

>PLN00121 histone H3; Provisional

Probab=96.18  E-value=0.012  Score=43.16  Aligned_cols=66  Identities=26%  Similarity=0.259  Sum_probs=58.0

Q ss_pred             ccccchhHHHHHHhhC----CcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhh
Q psy3662          22 GLQFPVGRIHRLLRKG----NYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAI   87 (132)
Q Consensus        22 gl~fPv~ri~rllk~~----~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI   87 (132)
                      +|.||-..+.|++++-    ....|+..+|...|--+-|.++-.++|.+.-.|.|.++.+|++.|++++.
T Consensus        60 ~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~  129 (136)
T PLN00121         60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR  129 (136)
T ss_pred             ccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHH
Confidence            6778888899988862    12349999999999999999999999999999999999999999999874

>PLN00161 histone H3; Provisional

Probab=96.10  E-value=0.014  Score=42.67  Aligned_cols=67  Identities=25%  Similarity=0.243  Sum_probs=57.9

Q ss_pred             cccccchhHHHHHHhhC--Cc---ccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhh
Q psy3662          21 AGLQFPVGRIHRLLRKG--NY---AERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAI   87 (132)
Q Consensus        21 agl~fPv~ri~rllk~~--~~---~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI   87 (132)
                      .+|.+|-..+.|++++-  .+   ..|+..+|...|--+-|.++-.++|.+.-.|.|.++.+|.|.|++++.
T Consensus        52 t~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~  123 (135)
T PLN00161         52 TELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLAR  123 (135)
T ss_pred             cccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHH
Confidence            36778888888888762  11   358999999999999999999999999999999999999999999874

>KOG0871|consensus

Probab=96.05  E-value=0.021  Score=42.40  Aligned_cols=70  Identities=17%  Similarity=0.250  Sum_probs=60.2

Q ss_pred             ccccccchhHHHHHHhhCCc-ccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcC
Q psy3662          20 RAGLQFPVGRIHRLLRKGNY-AERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRN   89 (132)
Q Consensus        20 ragl~fPv~ri~rllk~~~~-~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~   89 (132)
                      .-.+.+|-.-|..++++.-- .-||..+|-..+-.+.=+|+--|.-.|-..|....+++|.|+|+..|+.+
T Consensus         8 dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~   78 (156)
T KOG0871|consen    8 DDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALEN   78 (156)
T ss_pred             cccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHH
Confidence            45789999999999999633 34999999988888888888888888988999999999999999999854

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

Probab=95.98  E-value=0.028  Score=40.83  Aligned_cols=61  Identities=21%  Similarity=0.151  Sum_probs=43.6

Q ss_pred             hHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcC
Q psy3662          28 GRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRN   89 (132)
Q Consensus        28 ~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~   89 (132)
                      --|+-+|++. +.......++.-|.-..--.+.+||+-|-.+|.|.+++.|+..||++||..
T Consensus        16 ~~i~~iL~~~-Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~   76 (129)
T PF02291_consen   16 RVIHLILKSM-GVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQS   76 (129)
T ss_dssp             HHHHHHHHHT-T---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHH
T ss_pred             HHHHHHHHHc-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHH
Confidence            4477888886 333444445555555555678899999999999999999999999999973

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

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

Probab=95.84  E-value=0.057  Score=35.39  Aligned_cols=61  Identities=21%  Similarity=0.247  Sum_probs=47.9

Q ss_pred             chhHHHHHHhhC--CcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCce-echhhhhhh
Q psy3662          26 PVGRIHRLLRKG--NYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTR-IIPRHIQLA   86 (132)
Q Consensus        26 Pv~ri~rllk~~--~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~-Itp~~i~~A   86 (132)
                      |..=|.|+|+..  ...-||+.+|..-++..|+-|+.|-+-.|...|...+... |..+||+..
T Consensus         1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki   64 (72)
T PF09415_consen    1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKI   64 (72)
T ss_dssp             -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHH
T ss_pred             ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHH
Confidence            445578888852  1234999999999999999999999999999999999888 999999864

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

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

Probab=95.61  E-value=0.048  Score=35.51  Aligned_cols=58  Identities=16%  Similarity=0.174  Sum_probs=51.0

Q ss_pred             HHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          30 IHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        30 i~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      |-.+++.. +...++.+|..-|+.+++.++.+|...+-.+|.+.+|...++.|+..|+.
T Consensus        12 va~il~~~-GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~   69 (77)
T PF07524_consen   12 VAQILKHA-GFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALE   69 (77)
T ss_pred             HHHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence            44556563 57789999999999999999999999999999999999999999998873

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 [, ].

>KOG1658|consensus

Probab=95.16  E-value=0.024  Score=42.41  Aligned_cols=75  Identities=20%  Similarity=0.243  Sum_probs=65.9

Q ss_pred             cccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHHHhhh
Q psy3662          23 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLL   97 (132)
Q Consensus        23 l~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL~~L~   97 (132)
                      .++|++||+.+++......-....+...++..-|-++.++-..++..+....++++.-+++..||..-.|+.++-
T Consensus        58 ~rLpL~rik~vvkl~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~de~~fle  132 (162)
T KOG1658|consen   58 SRLPLARIKQVVKLDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAVDEFAFLE  132 (162)
T ss_pred             hhccHHHHHhhccCCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccchHHHHHHh
Confidence            689999999999986544455566666788899999999999999999999999999999999999999998887

>KOG0870|consensus

Probab=95.13  E-value=0.076  Score=40.15  Aligned_cols=67  Identities=21%  Similarity=0.312  Sum_probs=56.8

Q ss_pred             cccccchhHHHHHHhhCCcccc---cccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          21 AGLQFPVGRIHRLLRKGNYAER---VGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        21 agl~fPv~ri~rllk~~~~~~R---Vs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      ..|-||.+-|.|++++- ..+.   |+.+|-..|+..-=-|+..+.-.|.+.|+++++++|++.|+-.|+.
T Consensus         7 ~dl~lP~AiI~rlvke~-l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~   76 (172)
T KOG0870|consen    7 EDLNLPNAIITRLVKEV-LPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALD   76 (172)
T ss_pred             HHhhccHHHHHHHHHHh-CccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHH
Confidence            35789999999999884 5554   7788888888777778888899999999999999999999998873

>PLN00163 histone H4; Provisional

Probab=94.87  E-value=0.0097  Score=37.58  Aligned_cols=46  Identities=39%  Similarity=0.616  Sum_probs=33.9

Q ss_pred             CCCCCCCCC-------CCCccCCcccccccccchhHHHHHHhhCCcccccccChHH
Q psy3662           1 MSGRGKGGK-------AKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPV   49 (132)
Q Consensus         1 m~~k~~~~~-------~~~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~v   49 (132)
                      |+|++++++       ++++++.+.+-.+++-|.  |.|+.+.+ ...|||...-.
T Consensus         1 m~g~gkggkglGkggaKRhrk~lrd~i~gItKpa--IrRLARRg-GVKRIs~~iY~   53 (59)
T PLN00163          1 MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPA--IRRLARRG-GVKRISGLIYE   53 (59)
T ss_pred             CCCCCCCCCccCCccchhHHHHHHHhhcccchHH--HHHHHHhc-CceeecchhhH
Confidence            787765432       355566777778988887  99999996 68899977443

>KOG1142|consensus

Probab=94.28  E-value=0.087  Score=42.36  Aligned_cols=68  Identities=13%  Similarity=0.235  Sum_probs=60.6

Q ss_pred             cccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCc
Q psy3662          23 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRND   90 (132)
Q Consensus        23 l~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D   90 (132)
                      ..+-.-.++.+++.-.....+..++-.+|.-+.+-|++.|+..|...|+|-+..+|..+||++.++++
T Consensus       153 ~il~k~kl~dLvqqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~  220 (258)
T KOG1142|consen  153 PILSKRKLDDLVQQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERN  220 (258)
T ss_pred             ccccccchhHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeecc
Confidence            34455678899998655678999999999999999999999999999999999999999999999877

>KOG1745|consensus

Probab=93.50  E-value=0.085  Score=38.71  Aligned_cols=66  Identities=27%  Similarity=0.270  Sum_probs=53.2

Q ss_pred             cccchhHHHHHHhh----CCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          23 LQFPVGRIHRLLRK----GNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        23 l~fPv~ri~rllk~----~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      |.++-..+.|+.++    ....-|+.++|...|-...|.++-.+.|.+--.|.|.++.+|.|.||++|..
T Consensus        62 LlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArr  131 (137)
T KOG1745|consen   62 LLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR  131 (137)
T ss_pred             HHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhh
Confidence            44444556666652    2223489999999999999999999999998889999999999999999864

>KOG1744|consensus

Probab=93.19  E-value=0.45  Score=34.50  Aligned_cols=64  Identities=20%  Similarity=0.217  Sum_probs=50.4

Q ss_pred             cccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhh
Q psy3662          21 AGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAI   87 (132)
Q Consensus        21 agl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI   87 (132)
                      -...++|   .|.+++-.-.--|+..+.-.+.+.+-.+...|+..|+..|+-.++.+|+.++|+.|+
T Consensus        37 e~~s~yv---~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~  100 (127)
T KOG1744|consen   37 ESYSEYV---YKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAV  100 (127)
T ss_pred             Cceeeeh---hhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHH
Confidence            3466665   446665222223788888888888888899999999999999999999999999987

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

Probab=92.95  E-value=0.12  Score=35.25  Aligned_cols=62  Identities=11%  Similarity=0.105  Sum_probs=17.7

Q ss_pred             HHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHH
Q psy3662          32 RLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEEL   93 (132)
Q Consensus        32 rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL   93 (132)
                      .+|--.+....-..++...+-.++--.+.+++..|...|...|+++|+.+|+..++++|+.-
T Consensus         9 ~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D~~K   70 (93)
T PF02269_consen    9 QMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKDPKK   70 (93)
T ss_dssp             HHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC-------------------------
T ss_pred             HHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcCHHH
Confidence            33433333344444455555555555555666677777888888999999999999999753

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

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

Probab=92.71  E-value=0.64  Score=31.73  Aligned_cols=63  Identities=11%  Similarity=0.158  Sum_probs=37.4

Q ss_pred             HHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHH
Q psy3662          30 IHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEEL   93 (132)
Q Consensus        30 i~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL   93 (132)
                      |..+|--.+....-..++...+-.++-.++.+++-.|...|. .++.+|+++|+..+|.+|+.=
T Consensus         8 i~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D~~K   70 (92)
T cd07978           8 IRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKDPKK   70 (92)
T ss_pred             HHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcCHHH
Confidence            444554433333333334444444444444455556666665 577788999999999999863

The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy

>KOG3334|consensus

Probab=87.52  E-value=2.4  Score=31.41  Aligned_cols=57  Identities=25%  Similarity=0.321  Sum_probs=41.5

Q ss_pred             HHHHHhhCCcccccccChHHHHHHHHHH---HHHHHHHHHHHHHHhcCCceechhhhhhhhcCc
Q psy3662          30 IHRLLRKGNYAERVGAGAPVYLAAVLEY---LVAEVLELAGNAARDNKKTRIIPRHIQLAIRND   90 (132)
Q Consensus        30 i~rllk~~~~~~RVs~~A~vyLaavLEy---l~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D   90 (132)
                      |+-+|++.+    |.+.-+-.+.-.||+   .+..||+-|.-++.|.++..|..+|+++|+..-
T Consensus        19 i~~iL~s~G----I~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~   78 (148)
T KOG3334|consen   19 IASILKSLG----IQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMR   78 (148)
T ss_pred             HHHHHHHcC----ccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHH
Confidence            677777743    233333334444554   567899999999999999999999999999653

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

Probab=85.96  E-value=3.4  Score=30.05  Aligned_cols=60  Identities=25%  Similarity=0.277  Sum_probs=48.8

Q ss_pred             HHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceech---hhhhhhhcCc
Q psy3662          30 IHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIP---RHIQLAIRND   90 (132)
Q Consensus        30 i~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp---~~i~~AI~~D   90 (132)
                      |+-+|+. ...+--+..++.-|...---.+.++|+-|.-+|.+.|+.-|++   +|+++|+..-
T Consensus        20 ihliL~S-lgi~~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~   82 (145)
T COG5094          20 IHLILRS-LGIEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATK   82 (145)
T ss_pred             HHHHHHh-cCchhhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHH
Confidence            6666665 3566667778877777777789999999999999999998888   9999999654

>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]

Probab=80.85  E-value=2.2  Score=32.69  Aligned_cols=64  Identities=22%  Similarity=0.291  Sum_probs=51.4

Q ss_pred             ccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHh-cCCceechhhhhhhhc
Q psy3662          24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARD-NKKTRIIPRHIQLAIR   88 (132)
Q Consensus        24 ~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~-~~~k~Itp~~i~~AI~   88 (132)
                      -||-..|+.+.-. ...+-|+....+++.++-.-++.||+|+|...-.. .....+.|.|++.|+.
T Consensus       115 ~lnKt~VKKlast-V~nQtVspNi~I~l~g~~KVfvGEiIElA~~Vq~~w~~sgpl~p~h~reayr  179 (199)
T COG5251         115 SLNKTQVKKLAST-VANQTVSPNIRIFLQGVGKVFVGEIIELAMIVQNKWLTSGPLIPFHKREAYR  179 (199)
T ss_pred             CCCHHHHHHHHHH-HhccccCCCeeeeeechhHHHHHHHHHHHHHHHHHhcccCCCChHHHHHHHH
Confidence            4777888888766 36778999999999999999999999999765333 2344689999998874

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	132
2nqb_C	123	Drosophila Nucleosome Structure Length = 123		6e-39
2pyo_C	120	Drosophila Nucleosome Core Length = 120		6e-39
1eqz_A	129	X-Ray Structure Of The Nucleosome Core Particle At		3e-38
1m18_C	129	Ligand Binding Alters The Structure And Dynamics Of		3e-38
2hio_A	128	Histone Octamer (Chicken), Chromosomal Protein Leng		3e-38
3c1b_C	129	The Effect Of H3 K79 Dimethylation And H4 K20 Trime		5e-38
1zbb_C	129	Structure Of The 4_601_167 Tetranucleosome Length =		6e-38
3a6n_C	133	The Nucleosome Containing A Testis-Specific Histone		9e-38
2cv5_C	130	Crystal Structure Of Human Nucleosome Core Particle		1e-37
2f8n_K	149	2.9 Angstrom X-Ray Structure Of Hybrid Macroh2a Nuc		1e-37
1zla_C	129	X-Ray Structure Of A Kaposi's Sarcoma Herpesvirus L		8e-37
3kwq_C	107	Structural Characterization Of H3k56q Nucleosomes A		2e-36
1s32_C	119	Molecular Recognition Of The Nucleosomal 'supergroo		5e-36
1aoi_C	116	Complex Between Nucleosome Core Particle (H3,H4,H2a		5e-36
1kx3_C	128	X-Ray Structure Of The Nucleosome Core Particle, Nc		5e-35
1id3_C	131	Crystal Structure Of The Yeast Nucleosome Core Part		6e-34
1hio_A	95	Histone Octamer (Chicken), Chromosomal Protein, Alp		4e-31
2xql_A	91	Fitting Of The H2a-H2b Histones In The Electron Mic		1e-28
1u35_C	120	Crystal Structure Of The Nucleosome Core Particle C		5e-22
1f66_C	128	2.6 A Crystal Structure Of A Nucleosome Core Partic		1e-16
2jss_A	192	Nmr Structure Of Chaperone Chz1 Complexed With Hist		9e-15

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

Iteration: 1
 Score =  155 bits (392), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 78/99 (78%), Positives = 81/99 (81%)
Query: 23  LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
           LQFPVGRIHRLLRKGNYAERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct: 22  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 81
Query: 83  IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSE 121
           +QLAIRNDEELNKLL+GVTIAQGGVLPNIQAVLLPKK+E
Sbjct: 82  LQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTE 120

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

Iteration: 1
 Score =  155 bits (392), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 78/99 (78%), Positives = 81/99 (81%)
Query: 23  LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
           LQFPVGRIHRLLRKGNYAERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct: 22  LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 81
Query: 83  IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSE 121
           +QLAIRNDEELNKLL+GVTIAQGGVLPNIQAVLLPKK+E
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 =  153 bits (387), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 77/105 (73%), Positives = 83/105 (79%)
Query: 23  LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
           LQFPVGR+HRLLRKGNYAERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct: 24  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 83
Query: 83  IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAKGKS 127
           +QLAIRNDEELNKLL  VTIAQGGVLPNIQAVLLPKK+++ K K+
Sbjct: 84  LQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTDSHKAKA 128

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

Iteration: 1
 Score =  153 bits (386), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 76/102 (74%), Positives = 82/102 (80%)
Query: 23  LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
           LQFPVGR+HRLLRKGNYAERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct: 23  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 82
Query: 83  IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAK 124
           +QLA+RNDEELNKLL  VTIAQGGVLPNIQ+VLLPKK+E+AK
Sbjct: 83  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESAK 124

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

Iteration: 1
 Score =  153 bits (386), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 77/105 (73%), Positives = 83/105 (79%)
Query: 23  LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
           LQFPVGR+HRLLRKGNYAERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct: 23  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 82
Query: 83  IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAKGKS 127
           +QLAIRNDEELNKLL  VTIAQGGVLPNIQAVLLPKK+++ K K+
Sbjct: 83  LQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTDSHKAKA 127

>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 =  152 bits (384), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 75/102 (73%), Positives = 82/102 (80%)
Query: 23  LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
           LQFPVGR+HRLLRKGNYAERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct: 23  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 82
Query: 83  IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAK 124
           +QLA+RNDEELNKLL  VTIAQGGVLPNIQ+VLLPKK+E++K
Sbjct: 83  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSK 124

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

Iteration: 1
 Score =  152 bits (384), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 75/102 (73%), Positives = 82/102 (80%)
Query: 23  LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
           LQFPVGR+HRLLRKGNYAERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct: 23  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 82
Query: 83  IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAK 124
           +QLA+RNDEELNKLL  VTIAQGGVLPNIQ+VLLPKK+E++K
Sbjct: 83  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSK 124

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

Iteration: 1
 Score =  151 bits (382), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 79/107 (73%), Positives = 84/107 (78%), Gaps = 3/107 (2%)
Query: 23  LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
           LQFPVGR+HRLLRKGNY+ERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct: 27  LQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 86
Query: 83  IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSET---AKGK 126
           +QLAIRNDEELNKLL  VTIAQGGVLPNIQAVLLPKK+E+   AKGK
Sbjct: 87  LQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK 133

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

Iteration: 1
 Score =  151 bits (381), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 79/107 (73%), Positives = 84/107 (78%), Gaps = 3/107 (2%)
Query: 23  LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
           LQFPVGR+HRLLRKGNY+ERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct: 24  LQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 83
Query: 83  IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSET---AKGK 126
           +QLAIRNDEELNKLL  VTIAQGGVLPNIQAVLLPKK+E+   AKGK
Sbjct: 84  LQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK 130

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

Iteration: 1
 Score =  151 bits (381), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 79/107 (73%), Positives = 84/107 (78%), Gaps = 3/107 (2%)
Query: 23  LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
           LQFPVGR+HRLLRKGNY+ERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct: 43  LQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 102
Query: 83  IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSET---AKGK 126
           +QLAIRNDEELNKLL  VTIAQGGVLPNIQAVLLPKK+E+   AKGK
Sbjct: 103 LQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK 149

>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 =  148 bits (374), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 73/102 (71%), Positives = 80/102 (78%)
Query: 23  LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
           LQFPVGR+HRLLRKGNYAERVGAGAP                  GN  RDNKKTRIIPRH
Sbjct: 23  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNWERDNKKTRIIPRH 82
Query: 83  IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAK 124
           +QLA+RNDEELNKLL  VTIAQGGVLPNIQ+VLLPKK+E++K
Sbjct: 83  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSK 124

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

Iteration: 1
 Score =  147 bits (370), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 73/98 (74%), Positives = 78/98 (79%)
Query: 23  LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
           LQFPVGR+HRLLRKGNYAERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct: 10  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 69
Query: 83  IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKS 120
           +QLA+RNDEELNKLL  VTIAQGGVLPNIQ+VLLPKK+
Sbjct: 70  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT 107

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

Iteration: 1
 Score =  145 bits (367), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 73/97 (75%), Positives = 77/97 (79%)
Query: 23  LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
           LQFPVGR+HRLLRKGNYAERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct: 23  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 82
Query: 83  IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKK 119
           +QLA+RNDEELNKLL  VTIAQGGVLPNIQ+VLLPKK
Sbjct: 83  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK 119

>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 =  145 bits (367), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 73/97 (75%), Positives = 77/97 (79%)
Query: 23  LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
           LQFPVGR+HRLLRKGNYAERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct: 20  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 79
Query: 83  IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKK 119
           +QLA+RNDEELNKLL  VTIAQGGVLPNIQ+VLLPKK
Sbjct: 80  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK 116

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

Iteration: 1
 Score =  142 bits (358), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 71/95 (74%), Positives = 75/95 (78%)
Query: 23  LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
           LQFPVGR+HRLLRKGNYAERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct: 23  LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 82
Query: 83  IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLP 117
           +QLA+RNDEELNKLL  VTIAQGGVLPNIQ+VLLP
Sbjct: 83  LQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLP 117

>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 =  139 bits (349), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 72/109 (66%), Positives = 79/109 (72%), Gaps = 2/109 (1%)
Query: 23  LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
           L FPVGR+HRLLR+GNYA+R+G+GAP                  GNAARDNKKTRIIPRH
Sbjct: 24  LTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRH 83
Query: 83  IQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAKGKSNSQE 131
           +QLAIRND+ELNKLL  VTIAQGGVLPNI   LLPKKS  AK    SQE
Sbjct: 84  LQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPKKS--AKATKASQE 130

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

Iteration: 1
 Score =  129 bits (324), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 65/87 (74%), Positives = 67/87 (77%)
Query: 23  LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
           LQFPVGR+HRLLRKGNYAERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct: 9   LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 68
Query: 83  IQLAIRNDEELNKLLNGVTIAQGGVLP 109
           +QLAIRNDEELNKLL  VTIAQGGVLP
Sbjct: 69  LQLAIRNDEELNKLLGKVTIAQGGVLP 95

>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 =  121 bits (304), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 61/83 (73%), Positives = 63/83 (75%)
Query: 23  LQFPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRH 82
           LQFPVGR+HRLLRKGNYAERVGAGAP                  GNAARDNKKTRIIPRH
Sbjct: 9   LQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRH 68
Query: 83  IQLAIRNDEELNKLLNGVTIAQG 105
           +QLAIRNDEELNKLL  VTIAQG
Sbjct: 69  LQLAIRNDEELNKLLGKVTIAQG 91

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

Iteration: 1
 Score = 99.4 bits (246), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 52/95 (54%), Positives = 60/95 (63%)
Query: 25  FPVGRIHRLLRKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPRHIQ 84
           FPVGR+ R ++KG+   R+G GAP                   NAARDNKK R+ PRHI 
Sbjct: 23  FPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHIL 82
Query: 85  LAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKK 119
           LA+ NDEELN+LL GVTIA GGVLPNI   LL KK
Sbjct: 83  LAVANDEELNQLLKGVTIASGGVLPNIHPELLAKK 117

>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 = 81.6 bits (200), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 47/100 (47%), Positives = 58/100 (58%), Gaps = 2/100 (2%)
Query: 23  LQFPVGRIHRLLRKGNYAE-RVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPR 81
           LQFPVGRIHR L+    +  RVGA A                   GNA++D K  RI PR
Sbjct: 26  LQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPR 85
Query: 82  HIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSE 121
           H+QLAIR DEEL+ L+   TIA GGV+P+I   L+ KK +
Sbjct: 86  HLQLAIRGDEELDSLIK-ATIAGGGVIPHIHKSLIGKKGQ 124

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

Iteration: 1
 Score = 75.1 bits (183), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 44/90 (48%), Positives = 51/90 (56%), Gaps = 2/90 (2%)
Query: 23  LQFPVGRIHRLL-RKGNYAERVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKTRIIPR 81
           LQFPVGRI R L R      RVG+ A                   GNAA+D K  RI PR
Sbjct: 104 LQFPVGRIKRYLKRHATGRTRVGSKAAIYLTAVLEYLTAEVLELAGNAAKDLKVKRITPR 163
Query: 82  HIQLAIRNDEELNKLLNGVTIAQGGVLPNI 111
           H+QLAIR D+EL+ L+   TIA GGVLP+I
Sbjct: 164 HLQLAIRGDDELDSLIRA-TIASGGVLPHI 192

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	132
1tzy_A	129	Histone H2A-IV; histone-fold, tetramer-dimer-dimer	6e-55
2f8n_K	149	Histone H2A type 1; nucleosome, NCP, macroh2A, his	2e-54
2nqb_C	123	Histone H2A; nucleosome, NCP, chromatin, structura	5e-53
2f8n_G	120	Core histone macro-H2A.1; nucleosome, NCP, macroh2	9e-52
1id3_C	131	Histone H2A.1; nucleosome core particle, chromatin	3e-48
1f66_C	128	Histone H2A.Z; nucleosome, chromatin, histone vari	2e-43
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	3e-29
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	1e-23
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	7e-11
3ksy_A	1049	SOS-1, SON of sevenless homolog 1; RAS, RAS activa	9e-10
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	9e-06
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	1e-04

>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 =  167 bits (423), Expect = 6e-55
 Identities = 111/128 (86%), Positives = 121/128 (94%), Gaps = 1/128 (0%)

Query: 1   MSGRGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLV 59
           MSGRGK GGKA+ K+K+RSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAVLEYL 
Sbjct: 1   MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT 60

Query: 60  AEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKK 119
           AE+LELAGNAARDNKKTRIIPRH+QLAIRNDEELNKLL  VTIAQGGVLPNIQAVLLPKK
Sbjct: 61  AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKK 120

Query: 120 SETAKGKS 127
           +++ K K+
Sbjct: 121 TDSHKAKA 128

>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 =  166 bits (421), Expect = 2e-54
 Identities = 111/131 (84%), Positives = 121/131 (92%), Gaps = 2/131 (1%)

Query: 1   MSGRGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLV 59
           MSGRGK GGKA+ K+KTRSSRAGLQFPVGR+HRLLRKGNY+ERVGAGAPVYLAAVLEYL 
Sbjct: 20  MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLT 79

Query: 60  AEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKK 119
           AE+LELAGNAARDNKKTRIIPRH+QLAIRNDEELNKLL  VTIAQGGVLPNIQAVLLPKK
Sbjct: 80  AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK 139

Query: 120 SETAKGKSNSQ 130
           +E +  K+  +
Sbjct: 140 TE-SHHKAKGK 149

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

 Score =  162 bits (410), Expect = 5e-53
 Identities = 110/120 (91%), Positives = 117/120 (97%)

Query: 2   SGRGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAE 61
           SGRGKGGK K K+K+RS+RAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAV+EYL AE
Sbjct: 1   SGRGKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE 60

Query: 62  VLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSE 121
           VLELAGNAARDNKKTRIIPRH+QLAIRNDEELNKLL+GVTIAQGGVLPNIQAVLLPKK+E
Sbjct: 61  VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTE 120

>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 =  158 bits (401), Expect = 9e-52
 Identities = 78/122 (63%), Positives = 94/122 (77%), Gaps = 2/122 (1%)

Query: 1   MSGRGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVA 60
           MS RG  GK K+   +RS++AG+ FPVGR+ R ++KG+   R+G GAPVY+AAVLEYL A
Sbjct: 1   MSSRG--GKKKSTKTSRSAKAGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTA 58

Query: 61  EVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKS 120
           E+LELA NAARDNKK R+ PRHI LA+ NDEELN+LL GVTIA GGVLPNI   LL KK 
Sbjct: 59  EILELAVNAARDNKKGRVTPRHILLAVANDEELNQLLKGVTIASGGVLPNIHPELLAKKR 118

Query: 121 ET 122
            +
Sbjct: 119 GS 120

>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 =  150 bits (379), Expect = 3e-48
 Identities = 94/127 (74%), Positives = 107/127 (84%), Gaps = 1/127 (0%)

Query: 2   SGRG-KGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVA 60
            G+G K G A   S++RS++AGL FPVGR+HRLLR+GNYA+R+G+GAPVYL AVLEYL A
Sbjct: 2   GGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAA 61

Query: 61  EVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKS 120
           E+LELAGNAARDNKKTRIIPRH+QLAIRND+ELNKLL  VTIAQGGVLPNI   LLPKKS
Sbjct: 62  EILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPKKS 121

Query: 121 ETAKGKS 127
             A   S
Sbjct: 122 AKATKAS 128

>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 =  138 bits (348), Expect = 2e-43
 Identities = 75/125 (60%), Positives = 90/125 (72%), Gaps = 5/125 (4%)

Query: 1   MSGRGKG---GKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAER-VGAGAPVYLAAVLE 56
           M+G   G   GKAKTK+ +RS RAGLQFPVGRIHR L+    +   VGA A VY AA+LE
Sbjct: 1   MAGGKAGKDSGKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILE 60

Query: 57  YLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLL 116
           YL AEVLELAGNA++D K  RI PRH+QLAIR DEEL+ L+   TIA GGV+P+I   L+
Sbjct: 61  YLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIK-ATIAGGGVIPHIHKSLI 119

Query: 117 PKKSE 121
            KK +
Sbjct: 120 GKKGQ 124

>2jss_A Chimera of histone H2B.1 and histone H2A.Z; histone/chaperone complex, intrinsically unfolded protein, chaperone/structural protein complex; NMR {Saccharomyces cerevisiae} SCOP: a.22.1.1 a.22.1.1 Length = 192

 Score =  104 bits (258), Expect = 3e-29
 Identities = 62/102 (60%), Positives = 77/102 (75%), Gaps = 2/102 (1%)

Query: 11  KTKSKTRSSRAGLQFPVGRIHRLLRKGNYAER-VGAGAPVYLAAVLEYLVAEVLELAGNA 69
            T++++ S+RAGLQFPVGRI R L++       VG+ A +YL AVLEYL AEVLELAGNA
Sbjct: 92  STQAQSSSARAGLQFPVGRIKRYLKRHATGRTRVGSKAAIYLTAVLEYLTAEVLELAGNA 151

Query: 70  ARDNKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNI 111
           A+D K  RI PRH+QLAIR D+EL+ L+   TIA GGVLP+I
Sbjct: 152 AKDLKVKRITPRHLQLAIRGDDELDSLI-RATIASGGVLPHI 192

>1jfi_A Transcription regulator NC2 alpha chain; histone, H2A/H2B, tata-DNA, transcription initiation, NC2, negative cofactor, structural genomics, PSI; 2.62A {Homo sapiens} SCOP: a.22.1.3 Length = 98

 Score = 86.5 bits (214), Expect = 1e-23
 Identities = 14/77 (18%), Positives = 34/77 (44%)

Query: 16 TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKK 75
          ++  +   +FP  RI ++++      +V A  PV ++  LE  +  +L+ A    +    
Sbjct: 3  SKKKKYNARFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNA 62

Query: 76 TRIIPRHIQLAIRNDEE 92
            +   H++  I  + +
Sbjct: 63 KTMTTSHLKQCIELEGD 79

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

 Score = 54.2 bits (130), Expect = 7e-11
 Identities = 16/70 (22%), Positives = 32/70 (45%)

Query: 24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHI 83
          + P+ RI ++++     + + A APV  A   +  + E+   A     DNK+  +    I
Sbjct: 19 ELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDI 78

Query: 84 QLAIRNDEEL 93
           +AI   ++ 
Sbjct: 79 AMAITKFDQF 88

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

 Score = 54.4 bits (130), Expect = 9e-10
 Identities = 28/84 (33%), Positives = 48/84 (57%), Gaps = 1/84 (1%)

Query: 10  AKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNA 69
           A++  + R  R  L  PV +IH LL++     ++     VY+ AVLEY+ A++L+L GN 
Sbjct: 90  AQSAIEKRKRRNPLSLPVEKIHPLLKEVL-GYKIDHQVSVYIVAVLEYISADILKLVGNY 148

Query: 70  ARDNKKTRIIPRHIQLAIRNDEEL 93
            R+ +   I  + I++A+  D+ L
Sbjct: 149 VRNIRHYEITKQDIKVAMCADKVL 172

>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 = 41.6 bits (97), Expect = 9e-06
 Identities = 8/88 (9%), Positives = 26/88 (29%), Gaps = 2/88 (2%)

Query: 8  GKAKTKSKTRSSRAG-LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELA 66
          G+ +++             P+ R+  +++       +       +    E  V  +   A
Sbjct: 2  GEPRSQPPVERPPTAETFLPLSRVRTIMKSSMDTGLITNEVLFLMTKCTELFVRHLAGAA 61

Query: 67 GNAARDNKKTRII-PRHIQLAIRNDEEL 93
                 +    +   H+   +  ++ L
Sbjct: 62 YTEEFGQRPGEALKYEHLSQVVNKNKNL 89

>1ku5_A HPHA, archaeal histon; histone fold, DNA binding protein; 2.30A {Pyrococcus horikoshii} SCOP: a.22.1.2 Length = 70

 Score = 37.0 bits (86), Expect = 1e-04
 Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 1/65 (1%)

Query: 25 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQ 84
           P+  + RL+RK   AERV   A   LA  LE    E+ + A   AR   +  +    I+
Sbjct: 7  LPIAPVDRLIRKAG-AERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIK 65

Query: 85 LAIRN 89
          LAI++
Sbjct: 66 LAIKS 70

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	132
1tzy_A	129	Histone H2A-IV; histone-fold, tetramer-dimer-dimer	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
2f8n_K	149	Histone H2A type 1; nucleosome, NCP, macroh2A, his	100.0
1id3_C	131	Histone H2A.1; nucleosome core particle, chromatin	100.0
1f66_C	128	Histone H2A.Z; nucleosome, chromatin, histone vari	100.0
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	100.0
3ksy_A	1049	SOS-1, SON of sevenless homolog 1; RAS, RAS activa	99.91
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	99.89
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	99.8
2yfw_B	103	Histone H4, H4; cell cycle, kinetochore, centromer	99.79
1tzy_D	103	Histone H4-VI; histone-fold, tetramer-dimer-dimer,	99.79
4g92_C	119	HAPE; transcription factor, nucleosome, minor groo	99.78
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	99.71
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	99.53
1id3_B	102	Histone H4; nucleosome core particle, chromatin, p	99.39
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	99.37
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	99.32
2hue_C	84	Histone H4; mini beta sheet, elongated beta sandwh	99.16
1n1j_A	93	NF-YB; histone-like PAIR, DNA binding protein; 1.6	99.07
1taf_B	70	TFIID TBP associated factor 62; transcription init	98.99
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	98.98
3b0c_W	76	CENP-W, centromere protein W; histone fold, DNA bi	98.95
2byk_B	128	Chrac-14; nucleosome sliding, histone fold, DNA-bi	98.87
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	98.79
1taf_A	68	TFIID TBP associated factor 42; transcription init	98.73
1jfi_B	179	DR1 protein, transcription regulator NC2 beta chai	98.51
4dra_A	113	Centromere protein S; DNA binding complex, DNA dam	98.41
3v9r_A	90	MHF1, uncharacterized protein YOL086W-A; histone f	98.39
2hue_B	77	Histone H3; mini beta sheet, elongated beta sandwh	98.38
3nqj_A	82	Histone H3-like centromeric protein A; alpha helix	98.36
3b0b_B	107	CENP-S, centromere protein S; histone fold, DNA bi	98.3
2ly8_A	121	Budding yeast chaperone SCM3; centromere protein,	98.24
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	98.23
3nqu_A	140	Histone H3-like centromeric protein A; alpha helix	98.2
3r45_A	156	Histone H3-like centromeric protein A; histone fol	98.2
2yfv_A	100	Histone H3-like centromeric protein CSE4; cell cyc	98.19
1tzy_C	136	Histone H3; histone-fold, tetramer-dimer-dimer, DN	98.1
3vh5_A	140	CENP-S; histone fold, chromosome segregation, DNA	98.07
2nqb_D	123	Histone H2B; nucleosome, NCP, chromatin, structura	97.89
1tzy_B	126	Histone H2B; histone-fold, tetramer-dimer-dimer, D	97.83
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	97.33
1bh9_B	89	TAFII28; histone fold, tata binding protein, trans	97.05
4dra_E	84	Centromere protein X; DNA binding complex, DNA dam	96.75
3b0b_C	81	CENP-X, centromere protein X; histone fold, DNA bi	96.64
1h3o_B	76	Transcription initiation factor TFIID 20/15 kDa su	95.9
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	95.09
1wwi_A	148	Hypothetical protein TTHA1479; structural genomics	91.14
1k6k_A	143	ATP-dependent CLP protease ATP-binding subunit CLP	87.65
1r4v_A	171	Hypothetical protein AQ_328; structural genomics,	86.75
1khy_A	148	CLPB protein; alpha helix, chaperone; 1.95A {Esche	82.79
3fes_A	145	ATP-dependent CLP endopeptidase; alpha-helical bun	81.75
2y1q_A	150	CLPC N-domain, negative regulator of genetic compe	80.11

>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=8.1e-49  Score=282.80  Aligned_cols=123  Identities=89%  Similarity=1.300  Sum_probs=104.8

Q ss_pred             CCCCCC-CCCCCCccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceec
Q psy3662           1 MSGRGK-GGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRII   79 (132)
Q Consensus         1 m~~k~~-~~~~~~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~It   79 (132)
                      |||+++ +++.+++.+|+|+|+||+|||+||+|||+++++++||+++|+|||+||||||++||+|+|+|.|+++++++|+
T Consensus         1 m~~~~~~~~~~~~~~~srS~ragLqfPV~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krIt   80 (129)
T 1tzy_A            1 MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRII   80 (129)
T ss_dssp             -------------CCCCHHHHHTCSSCHHHHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEEC
T ss_pred             CCCCCCCCCCCCCCCCCccccCceeccHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEc
Confidence            899876 5556667899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhhcCcHHHHhhhcCCeecCCCcCCCCcccccCCccccc
Q psy3662          80 PRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETA  123 (132)
Q Consensus        80 p~~i~~AI~~D~EL~~L~~~~~ia~ggv~P~i~~~~~~~k~~~~  123 (132)
                      |+||++||+||+|||+||+++||++|||+|+||++|++++.++|
T Consensus        81 p~hi~lAI~nDeEL~~L~~~vtIa~ggvlP~i~~~l~~k~~~~~  124 (129)
T 1tzy_A           81 PRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTDSH  124 (129)
T ss_dssp             HHHHHHHHHTSHHHHHHTTTEEETTCCCCCCCCGGGSCC-----
T ss_pred             HHHHHHHHhccHHHHHHhCCCeecCCCcCCCCCHHHcCcccccc
Confidence            99999999999999999999999999999999999999998765

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

Probab=100.00  E-value=1.4e-48  Score=279.56  Aligned_cols=122  Identities=90%  Similarity=1.308  Sum_probs=105.0

Q ss_pred             CCCCCCCCCCCccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechh
Q psy3662           2 SGRGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPR   81 (132)
Q Consensus         2 ~~k~~~~~~~~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~   81 (132)
                      ||+|++++.+++.+|+|+|+||+|||+||+|||+++++++||+++|+|||+||||||++||+|+|+|.|+++++++|+|+
T Consensus         1 ~~~~~~~~~~~~~~s~s~ragL~fPV~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~   80 (123)
T 2nqb_C            1 SGRGKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPR   80 (123)
T ss_dssp             ------------CCCHHHHHTCSSCHHHHHHHHHHTTSCSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHH
T ss_pred             CCCCCCCCCCCCCCCccccCCeeccHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccHH
Confidence            56777677777889999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhcCcHHHHhhhcCCeecCCCcCCCCcccccCCccccc
Q psy3662          82 HIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETA  123 (132)
Q Consensus        82 ~i~~AI~~D~EL~~L~~~~~ia~ggv~P~i~~~~~~~k~~~~  123 (132)
                      ||++||+||+|||+||+++||++|||+|+||++|++|+.+++
T Consensus        81 hi~lAI~nDeEL~~Ll~~vtia~ggvlp~i~~~l~~k~~~~~  122 (123)
T 2nqb_C           81 HLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTEKK  122 (123)
T ss_dssp             HHHHHHHTSHHHHHHTTTEEETTCCCCCCCCGGGSSCC----
T ss_pred             HHHHHHhccHHHHHHhcCceeCCCCcCCCccHHHcCcccccC
Confidence            999999999999999999999999999999999999988765

>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=2.4e-48  Score=277.37  Aligned_cols=119  Identities=66%  Similarity=1.000  Sum_probs=106.0

Q ss_pred             CCCCCCCCCCCCccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceech
Q psy3662           1 MSGRGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIP   80 (132)
Q Consensus         1 m~~k~~~~~~~~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp   80 (132)
                      ||||+  ++.+++.+|+|+|+||+|||+||+|||+++++++||+++|+|||+||||||++||+|+|+|.|+++++++|+|
T Consensus         1 m~~~~--~~~~~~~~srs~ragLqfPV~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~~rItp   78 (120)
T 2f8n_G            1 MSSRG--GKKKSTKTSRSAKAGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTP   78 (120)
T ss_dssp             -----------CCCCCHHHHHTCSSCHHHHHHHHHHHSSSCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECH
T ss_pred             CCCCC--CCCCcCCcCcccccCccCChHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcH
Confidence            89886  3445668999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhcCcHHHHhhhcCCeecCCCcCCCCcccccCCccc
Q psy3662          81 RHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSE  121 (132)
Q Consensus        81 ~~i~~AI~~D~EL~~L~~~~~ia~ggv~P~i~~~~~~~k~~  121 (132)
                      +||++||+||+|||+||+++||++|||+|+||++|++|+.+
T Consensus        79 ~hi~lAI~nDeEL~~Ll~~vtia~ggv~p~i~~~l~~k~~~  119 (120)
T 2f8n_G           79 RHILLAVANDEELNQLLKGVTIASGGVLPNIHPELLAKKRG  119 (120)
T ss_dssp             HHHHHHHHTSHHHHHHTTTEEETTCCCCCCCCGGGSCCC--
T ss_pred             HHHHHHHhcCHHHHHHhCCceECCCCcCCCcCHHHcCCccC
Confidence            99999999999999999999999999999999999999764

>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=5.9e-48  Score=283.69  Aligned_cols=124  Identities=88%  Similarity=1.272  Sum_probs=104.1

Q ss_pred             CCCCCCC-CCCCCccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceec
Q psy3662           1 MSGRGKG-GKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRII   79 (132)
Q Consensus         1 m~~k~~~-~~~~~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~It   79 (132)
                      |||++++ ++.+++.+|+|+|+||+|||+||+|||+++++++||+++|+|||+||||||++||+|+|+|.|+++++++|+
T Consensus        20 ~~~~~~~~~~~~~k~~srS~ragLqFPVgrI~R~LK~~~~a~RVs~~A~VyLAAVLEYL~aEILelAgn~A~~~krkrIt   99 (149)
T 2f8n_K           20 MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRII   99 (149)
T ss_dssp             --------------CCCHHHHHTCSSCHHHHHHHHHHTTSCSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEEC
T ss_pred             cccCCCCCCCCCCCCCCccccCCeeccHHHHHHHHHccccccccCcCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCc
Confidence            8888764 556667899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhhcCcHHHHhhhcCCeecCCCcCCCCcccccCCcccccC
Q psy3662          80 PRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAK  124 (132)
Q Consensus        80 p~~i~~AI~~D~EL~~L~~~~~ia~ggv~P~i~~~~~~~k~~~~~  124 (132)
                      |+||++||+||+|||+||+++||++|||+|+||++|++|+.++++
T Consensus       100 prhI~lAI~nDeEL~~Ll~~vtIa~gGVlP~i~~~l~~k~~~~~~  144 (149)
T 2f8n_K          100 PRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHH  144 (149)
T ss_dssp             HHHHHHHHHHSHHHHHHTTTEEETTCCCCCCCCGGGSCC------
T ss_pred             HHHHHHHHhccHHHHHHhcCceEcCCCCCCCccHHHcCccccccc
Confidence            999999999999999999999999999999999999999987665

>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=3e-47  Score=275.20  Aligned_cols=122  Identities=76%  Similarity=1.154  Sum_probs=107.5

Q ss_pred             CCCCCccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhh
Q psy3662           8 GKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAI   87 (132)
Q Consensus         8 ~~~~~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI   87 (132)
                      ++.+++.+|+|+|+||+|||+||+|||+++++++||+++|+|||+||||||++||+|+|+|.|+++++++|+|+||++||
T Consensus         9 ~~~~~~~~srS~ragLqfPV~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hI~lAI   88 (131)
T 1id3_C            9 GSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRHLQLAI   88 (131)
T ss_dssp             -------CCTTGGGTCSSCHHHHHHHHHTTCSCSEECSSHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHH
T ss_pred             CCCCCCCCCccccCCeecCHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHHHH
Confidence            34456789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCcHHHHhhhcCCeecCCCcCCCCcccccCCcccccCCCCCCCC
Q psy3662          88 RNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAKGKSNSQE  131 (132)
Q Consensus        88 ~~D~EL~~L~~~~~ia~ggv~P~i~~~~~~~k~~~~~~~~~~~~  131 (132)
                      +||+|||+||+++||++|||+|+||++|++|+.++++  +.+|+
T Consensus        89 ~nDeEL~~Ll~~vtIa~ggvlP~i~~~l~~k~~~~~~--~~~~~  130 (131)
T 1id3_C           89 RNDDELNKLLGNVTIAQGGVLPNIHQNLLPKKSAKAT--KASQE  130 (131)
T ss_dssp             HTCHHHHHHTTTEEETTCCCCCCCCGGGSCCSCCSCC-------
T ss_pred             hccHHHHHHhcCceecCCccCCCccHHHcCccccccc--ccccc
Confidence            9999999999999999999999999999999887654  44555

>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=8.6e-47  Score=271.91  Aligned_cols=123  Identities=62%  Similarity=0.914  Sum_probs=99.3

Q ss_pred             CCCCCCC---CCCCCccCCcccccccccchhHHHHHHhhCCcc-cccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCc
Q psy3662           1 MSGRGKG---GKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYA-ERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKT   76 (132)
Q Consensus         1 m~~k~~~---~~~~~~~~s~s~ragl~fPv~ri~rllk~~~~~-~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k   76 (132)
                      |||+..+   ++.+++.+|+|+|+||||||+||+|||++++++ +||+++|+|||+||||||++||+|+|+|.|++++++
T Consensus         1 m~~~~~~~~~~~~~~~~~srS~ragLqfPV~ri~R~Lk~~~~a~~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~k   80 (128)
T 1f66_C            1 MAGGKAGKDSGKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVK   80 (128)
T ss_dssp             ----------------CCCHHHHHTCSSCHHHHHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCS
T ss_pred             CCCCCCCCCCCCcCCCCcCccccCCccCChHHHHHHHHHcccchhhccccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence            7866432   234556789999999999999999999999877 599999999999999999999999999999999999


Q ss_pred             eechhhhhhhhcCcHHHHhhhcCCeecCCCcCCCCcccccCCcccccC
Q psy3662          77 RIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKKSETAK  124 (132)
Q Consensus        77 ~Itp~~i~~AI~~D~EL~~L~~~~~ia~ggv~P~i~~~~~~~k~~~~~  124 (132)
                      +|+|+||++||+||+||++||+ .||++|||+|+||++|++|++++|+
T Consensus        81 rItprhi~lAI~nDeEL~~Ll~-~tia~ggv~P~i~~~l~~k~~~~~~  127 (128)
T 1f66_C           81 RITPRHLQLAIRGDEELDSLIK-ATIAGGGVIPHIHKSLIGKKGQQKT  127 (128)
T ss_dssp             EECHHHHHHHHHHSHHHHHHCC-SEETTCCCCCCCCGGGC--------
T ss_pred             eEcHHHHHHHHhccHHHhhhhc-ceecCCccCCCCCHHhcCcccccCC
Confidence            9999999999999999999995 5999999999999999999988754

>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=2.1e-36  Score=230.55  Aligned_cols=98  Identities=63%  Similarity=0.989  Sum_probs=93.9

Q ss_pred             ccCCcccccccccchhHHHHHHhhCCcc-cccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcH
Q psy3662          13 KSKTRSSRAGLQFPVGRIHRLLRKGNYA-ERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDE   91 (132)
Q Consensus        13 ~~~s~s~ragl~fPv~ri~rllk~~~~~-~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~   91 (132)
                      +.+|+|+|+||+|||+||+|+|++++++ +||+++|+|||+||||||++||+|+|+|.|+++++++|+|+||++||+||+
T Consensus        94 ~~~s~s~ragl~fPv~ri~R~lk~~~~a~~Rv~~~A~vyLaavLEyl~~eIlelA~n~a~~~~~~~I~p~~i~lAi~nD~  173 (192)
T 2jss_A           94 QAQSSSARAGLQFPVGRIKRYLKRHATGRTRVGSKAAIYLTAVLEYLTAEVLELAGNAAKDLKVKRITPRHLQLAIRGDD  173 (192)
T ss_dssp             SSSCHHHHSSCCSCHHHHHHHHHHTTCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCHHHHHHHHHTSH
T ss_pred             ccccccccCCCcCCHHHHHHHHHhcCccccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhccH
Confidence            4579999999999999999999998786 699999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhcCCeecCCCcCCCC
Q psy3662          92 ELNKLLNGVTIAQGGVLPNI  111 (132)
Q Consensus        92 EL~~L~~~~~ia~ggv~P~i  111 (132)
                      |||+||+ .||++|||+|+|
T Consensus       174 eL~~L~~-~ti~~ggv~p~i  192 (192)
T 2jss_A          174 ELDSLIR-ATIASGGVLPHI  192 (192)
T ss_dssp             HHHHHHC-SCCTTTCCSSCC
T ss_pred             HHHHHHh-hhhcCCCcCCCC
Confidence            9999995 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=99.91  E-value=3.1e-25  Score=201.62  Aligned_cols=101  Identities=29%  Similarity=0.467  Sum_probs=82.5

Q ss_pred             CccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcH
Q psy3662          12 TKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDE   91 (132)
Q Consensus        12 ~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~   91 (132)
                      +...|+|+||||+|||+||||+| +++|++||+++|+|||+||||||++||||||||+|++.++.+|+|+||++|++||+
T Consensus        92 ~~~~~~~~~~~l~~pv~~~~~~l-~~~~~~r~~~~~~~y~~avleyl~~~~l~la~~~~~~~~~~~i~p~~~~~ai~~d~  170 (1049)
T 3ksy_A           92 SAIEKRKRRNPLSLPVEKIHPLL-KEVLGYKIDHQVSVYIVAVLEYISADILKLVGNYVRNIRHYEITKQDIKVAMCADK  170 (1049)
T ss_dssp             HHHTTCCCSSSCSSCHHHHHHHH-HHHHCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCBCCHHHHHHHHHHCS
T ss_pred             HhhhcccccCCccccHHHHHHHh-hcccccccCCCCcchhHHHHHHHHHHHHHHHHHHHHHcCCceecCccccccccCCH
Confidence            34578999999999999999999 77899999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhcCCeecCCCcCCCCccc
Q psy3662          92 ELNKLLNGVTIAQGGVLPNIQAV  114 (132)
Q Consensus        92 EL~~L~~~~~ia~ggv~P~i~~~  114 (132)
                      ||..||+.. ...+|++|.....
T Consensus       171 eL~~l~~~d-ee~~~~lp~~~~~  192 (1049)
T 3ksy_A          171 VLMDMFHQD-VEDINILSLTDEE  192 (1049)
T ss_dssp             SHHHHCC----------------
T ss_pred             HHHHHHhhc-cccccCCCCcccc
Confidence            999999655 4566788765543

>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=99.89  E-value=7.6e-24  Score=145.83  Aligned_cols=81  Identities=17%  Similarity=0.357  Sum_probs=62.3

Q ss_pred             cccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHHHhh
Q psy3662          17 RSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKL   96 (132)
Q Consensus        17 ~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL~~L   96 (132)
                      ++.+++++||++||+|+||.+.+..|||.+|++|+++++|||+.||+++|++.|.+.++++|+|+||..||.+|++|++|
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            35688999999999999999988899999999999999999999999999999999999999999999999999999999


Q ss_pred             h
Q psy3662          97 L   97 (132)
Q Consensus        97 ~   97 (132)
                      +
T Consensus        84 ~   84 (98)
T 1jfi_A           84 K   84 (98)
T ss_dssp             -
T ss_pred             H
Confidence            8

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

Probab=99.80  E-value=9e-20  Score=125.13  Aligned_cols=79  Identities=22%  Similarity=0.340  Sum_probs=71.7

Q ss_pred             cccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHHHhhh
Q psy3662          19 SRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLL   97 (132)
Q Consensus        19 ~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL~~L~   97 (132)
                      .-.+++||++||+|+||.+.+..|||.+|++|+++++|||+.+|++.|++.|.+.++++|+++||..||.+|++|++|.
T Consensus        14 ~~~~~~lP~arIkrImK~~~~~~~is~eA~~~laka~E~Fi~~l~~~A~~~a~~~krktI~~~di~~Av~~~e~~~FL~   92 (97)
T 1n1j_B           14 DFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLI   92 (97)
T ss_dssp             ------CCHHHHHHHHTTSTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTCGGGGGGT
T ss_pred             CcCCCcCCHHHHHHHHccCccccccChHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHHhcCcHHHHHH
Confidence            3457899999999999999888999999999999999999999999999999999999999999999999999999998

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

Probab=99.79  E-value=1.4e-19  Score=125.48  Aligned_cols=88  Identities=26%  Similarity=0.402  Sum_probs=62.6

Q ss_pred             CCCCCCCCC-------CCCccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy3662           1 MSGRGKGGK-------AKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDN   73 (132)
Q Consensus         1 m~~k~~~~~-------~~~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~   73 (132)
                      |||||+++|       ++++++++++.++  ||++.|+|+++... ..|||.+|.++|+.+|||++.+|++.|.++|+|+
T Consensus         1 m~~~gk~gkg~~~~~~kr~~~~~r~~~~g--ip~~~I~Rlar~~G-~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~ha   77 (103)
T 2yfw_B            1 MSGRGKGGKGLGKGGAKRHRKILRDNIQG--ITKPAIRRLARRGG-VKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHA   77 (103)
T ss_dssp             -------------------------------CCHHHHHHHHHHTT-CCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCCCCCccchhhhhhhhhcc--CCHHHHHHHHHHcC-ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            888766443       3566778999999  99999999999974 5899999999999999999999999999999999


Q ss_pred             CCceechhhhhhhhcCcH
Q psy3662          74 KKTRIIPRHIQLAIRNDE   91 (132)
Q Consensus        74 ~~k~Itp~~i~~AI~~D~   91 (132)
                      ++++|+++||.+|+.+..
T Consensus        78 kRktvt~~DV~~Alr~~g   95 (103)
T 2yfw_B           78 KRKTVTSLDVVYALKRQG   95 (103)
T ss_dssp             TCSEECHHHHHHHHHHHC
T ss_pred             CCCcCcHHHHHHHHHHcC
Confidence            999999999999998654

>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=99.79  E-value=3.1e-19  Score=123.69  Aligned_cols=87  Identities=26%  Similarity=0.410  Sum_probs=70.0

Q ss_pred             CCCCCCCCC-------CCCccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy3662           1 MSGRGKGGK-------AKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDN   73 (132)
Q Consensus         1 m~~k~~~~~-------~~~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~   73 (132)
                      |||+++++|       ++++++++++.++  ||++.|+|+++... ..|||.+|.++|+.+|||++.+|++.|.++|+|+
T Consensus         1 m~g~gk~~kg~~~~~~kr~~k~~r~~~~g--ip~~~I~Rlar~~G-~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~ha   77 (103)
T 1tzy_D            1 MSGRGKGGKGLGKGGAKRHRKVLRDNIQG--ITKPAIRRLARRGG-VKRISGLIYEETRGVLKVFLENVIRDAVTYTEHA   77 (103)
T ss_dssp             --------------------CCCCCGGGG--SCHHHHHHHHHHTT-CCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCCCCCccccccchhhhccc--CCHHHHHHHHHHcC-ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            888765433       3666789999999  89999999999974 5899999999999999999999999999999999


Q ss_pred             CCceechhhhhhhhcCc
Q psy3662          74 KKTRIIPRHIQLAIRND   90 (132)
Q Consensus        74 ~~k~Itp~~i~~AI~~D   90 (132)
                      ++++|+++||.+|+.+.
T Consensus        78 kRktIt~~DV~~Alr~~   94 (103)
T 1tzy_D           78 KRKTVTAMDVVYALKRQ   94 (103)
T ss_dssp             TCSEECHHHHHHHHHHT
T ss_pred             CCCcCCHHHHHHHHHHc
Confidence            99999999999999754

>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=99.78  E-value=4.7e-19  Score=125.68  Aligned_cols=75  Identities=23%  Similarity=0.363  Sum_probs=72.6

Q ss_pred             cccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHHHhhh
Q psy3662          23 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLL   97 (132)
Q Consensus        23 l~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL~~L~   97 (132)
                      .+||++||+|+||.+.+..+|+.+|++|+++++|||+.+|++.|++.|...++++|+|+||..||.+|++|++|.
T Consensus        40 ~~lPvaRIkrImK~d~~~~~is~eA~v~la~a~E~Fi~~L~~~A~~~a~~~krktI~~~di~~Av~~~e~~dFL~  114 (119)
T 4g92_C           40 HQLPLARIKKVMKADPEVKMISAEAPILFAKGCDVFITELTMRAWIHAEDNKRRTLQRSDIAAALSKSDMFDFLI  114 (119)
T ss_dssp             CSSCHHHHHHHHHTSTTCCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTCGGGGGGT
T ss_pred             CCCCHHHHHHHHhhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccCHHHHHHHHhcCchhhHHH
Confidence            479999999999998889999999999999999999999999999999999999999999999999999999886

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

Probab=99.71  E-value=4.1e-18  Score=123.94  Aligned_cols=85  Identities=13%  Similarity=0.200  Sum_probs=62.4

Q ss_pred             ccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHH-HhcCCceechhhhhhhhcCcH
Q psy3662          13 KSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAA-RDNKKTRIIPRHIQLAIRNDE   91 (132)
Q Consensus        13 ~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A-~~~~~k~Itp~~i~~AI~~D~   91 (132)
                      +..+++.+.+++||++||+|+||.+....+|+.+|+++++.++|+|+.+|++.|++.| ...++++|++.||..||.+++
T Consensus         8 k~~s~~~~~~~~LPlaRIKrIMK~dpdv~~Is~eA~vliakA~ElFI~~Lt~~A~~~a~~~~kRKtI~~~Dl~~AV~~~e   87 (140)
T 2byk_A            8 PPVERPPTAETFLPLSRVRTIMKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNK   87 (140)
T ss_dssp             ---------------------CCSSSSCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHHTCS
T ss_pred             CCCCCCcccCCCCCHHHHHHHHhcCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccCHHHHHHHHhcCc
Confidence            4578888999999999999999998888999999999999999999999999999999 999999999999999999999


Q ss_pred             HHHhhh
Q psy3662          92 ELNKLL   97 (132)
Q Consensus        92 EL~~L~   97 (132)
                      +|++|.
T Consensus        88 ~~dFL~   93 (140)
T 2byk_A           88 NLEFLL   93 (140)
T ss_dssp             TTGGGT
T ss_pred             hhhhHh
Confidence            999998

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

Probab=99.53  E-value=1e-14  Score=107.45  Aligned_cols=71  Identities=18%  Similarity=0.223  Sum_probs=67.8

Q ss_pred             cccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCc
Q psy3662          19 SRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRND   90 (132)
Q Consensus        19 ~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D   90 (132)
                      .+.++.||++.|.|+|+++ +..|||++|.++|+.+||+|+.+|+..|.++|.+.+|++|+++||.+|+.++
T Consensus        77 d~~~l~lP~a~V~Ri~k~~-g~~RVS~~A~~~l~~~le~f~~~I~~~A~~~a~ha~RKTIt~eDV~~Al~~~  147 (154)
T 1f1e_A           77 DYDGELFGRATVRRILKRA-GIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITYS  147 (154)
T ss_dssp             TCCSCCCCHHHHHHHHHHT-TCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             ccccccCCccHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhc
Confidence            4789999999999999998 7899999999999999999999999999999999999999999999999764

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

Probab=99.39  E-value=1.2e-12  Score=90.38  Aligned_cols=79  Identities=18%  Similarity=0.251  Sum_probs=65.0

Q ss_pred             CCCCccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662           9 KAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus         9 ~~~~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      .++++++.+.+..+  +|.+.|.|++++. ...|||.++...|+.+|||++.+|+..|..+|+|.++++|+++||.+|+.
T Consensus        15 ~kr~~k~~r~~i~~--ip~~~I~Rlar~~-Gv~rIS~da~~~l~~~le~fi~~I~~dA~~~a~HakRKTVt~~DV~~ALk   91 (102)
T 1id3_B           15 AKRHRKILRDNIQG--ITKPAIRRLARRG-GVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALK   91 (102)
T ss_dssp             ---------CCGGG--SCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             cchHHHHHHhccCC--CCHHHHHHHHHHc-CchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHH
Confidence            35677788877777  7888899999996 67999999999999999999999999999999999999999999999986


Q ss_pred             Cc
Q psy3662          89 ND   90 (132)
Q Consensus        89 ~D   90 (132)
                      ..
T Consensus        92 r~   93 (102)
T 1id3_B           92 RQ   93 (102)
T ss_dssp             HT
T ss_pred             Hc
Confidence            43

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

Probab=99.37  E-value=1.6e-12  Score=83.81  Aligned_cols=65  Identities=34%  Similarity=0.446  Sum_probs=62.2

Q ss_pred             ccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcC
Q psy3662          24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRN   89 (132)
Q Consensus        24 ~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~   89 (132)
                      .||.+.|+|++++. ...|+|.++...|..++|+++.+|++.|..+|.|.+|++|+++||.+|+++
T Consensus         6 ~lp~a~v~Rl~r~~-g~~ris~~a~~~l~e~~~~~~~~v~~dA~~~a~hakRkTI~~~DV~lA~~~   70 (70)
T 1ku5_A            6 ELPIAPVDRLIRKA-GAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIKS   70 (70)
T ss_dssp             CSCHHHHHHHHHHT-TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHTC
T ss_pred             cCChHHHHHHHHHc-CcceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHC
Confidence            68999999999996 688999999999999999999999999999999999999999999999864

>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=99.32  E-value=5.2e-12  Score=80.75  Aligned_cols=64  Identities=31%  Similarity=0.424  Sum_probs=61.3

Q ss_pred             ccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        24 ~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      .||.++|.|+||+. ...||+.+|...|..++|+++.+|.+.|...|.+.++++|+|+||..|++
T Consensus         2 ~lP~a~v~Ri~k~~-~~~ris~~A~~~l~~a~e~fi~~l~~~A~~~a~~~kRkTI~~~Di~~A~~   65 (68)
T 1b67_A            2 ELPIAPIGRIIKNA-GAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARK   65 (68)
T ss_dssp             CSCHHHHHHHHHHT-TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHGG
T ss_pred             CCCccHHHHHHhcC-CcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHH
Confidence            48999999999998 67899999999999999999999999999999999999999999999985

>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=99.16  E-value=1.5e-10  Score=77.05  Aligned_cols=72  Identities=19%  Similarity=0.257  Sum_probs=65.1

Q ss_pred             CcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCc
Q psy3662          16 TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRND   90 (132)
Q Consensus        16 s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D   90 (132)
                      -+.+..|  +|.+.|+|++++. ...|||.++...|+.++|+++.+|+..|..+++|.++++|+++||.+|+...
T Consensus         4 ~r~~~~~--ip~~~I~Riar~~-Gv~rIs~da~~~l~~~l~~~~~~I~~dA~~~a~ha~RKTvt~~DV~~Alk~~   75 (84)
T 2hue_C            4 LRDNIQG--ITKPAIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ   75 (84)
T ss_dssp             GGGGCCS--SCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTT
T ss_pred             ccccCCC--CCHHHHHHHHHHc-CchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHc
Confidence            3455556  6788899999997 6799999999999999999999999999999999999999999999999764

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

Probab=99.07  E-value=2.9e-10  Score=76.84  Aligned_cols=68  Identities=12%  Similarity=0.283  Sum_probs=62.3

Q ss_pred             cccccchhHHHHHHhhC-CcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          21 AGLQFPVGRIHRLLRKG-NYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        21 agl~fPv~ri~rllk~~-~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      ..+.||.++|.|+||+. ....||+.+|...|+.+.|.|+.+|...|...|.+.+|++|+++||..|+.
T Consensus         5 ~d~~LP~a~i~ri~K~~~~~~~~is~dA~~~l~~a~e~Fi~~l~~~A~~~a~~~kRkTI~~~Dv~~Al~   73 (93)
T 1n1j_A            5 QDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMS   73 (93)
T ss_dssp             --CCCCHHHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHH
T ss_pred             ccccCChhHHHHHHHHhCCccceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHH
Confidence            35789999999999997 334799999999999999999999999999999999999999999999996

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

Probab=98.99  E-value=1.5e-09  Score=70.23  Aligned_cols=65  Identities=11%  Similarity=0.146  Sum_probs=61.8

Q ss_pred             cccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          23 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        23 l~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      -.||+..|+++.+.. +..+|+++|...|+.-+||-+.||++.|.+.++|.+|+++|++||+.|+.
T Consensus         5 s~lp~~~v~~iaes~-Gi~~lsddaa~~LA~dvEyr~~eI~qeA~kfmrHakRk~Lt~~DI~~Alk   69 (70)
T 1taf_B            5 SSISAESMKVIAESI-GVGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLK   69 (70)
T ss_dssp             CCCCHHHHHHHHHHT-TCCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC
T ss_pred             ccCCHHHHHHHHHHC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHc
Confidence            479999999999996 68999999999999999999999999999999999999999999999874

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

Probab=98.98  E-value=1.1e-09  Score=80.64  Aligned_cols=64  Identities=17%  Similarity=0.268  Sum_probs=60.9

Q ss_pred             ccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhh
Q psy3662          24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAI   87 (132)
Q Consensus        24 ~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI   87 (132)
                      -||.+.|.|++|+.-...|||.+|...|+.++|.|+.+|...|.+.|.+.+||+|+++||..|+
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            4899999999999745699999999999999999999999999999999999999999999998

>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=98.95  E-value=1.7e-09  Score=70.58  Aligned_cols=66  Identities=21%  Similarity=0.301  Sum_probs=60.5

Q ss_pred             cccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          23 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        23 l~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      -.||.+.|.|+|++.....+||.+|...|..++|.|+.+|...|...|.+.++++|+++||..|+.
T Consensus         3 ~~LP~A~V~rI~K~~~p~~~is~~A~~~i~~~~~~Fi~~la~eA~~~a~~~~rKTI~~~dI~~A~~   68 (76)
T 3b0c_W            3 RTVPRGTLRKIIKKHKPHLRLAANTDLLVHLSFLLFLHRLAEEARTNAFENKSKIIKPEHTIAAAK   68 (76)
T ss_dssp             -CCCHHHHHHHHHHHCTTCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSBCHHHHHHHHH
T ss_pred             CcccccHHHHHHHHhCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence            368999999999975345799999999999999999999999999999999999999999999984

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

Probab=98.87  E-value=1.8e-09  Score=77.11  Aligned_cols=73  Identities=16%  Similarity=0.150  Sum_probs=62.5

Q ss_pred             ccccchhHHHHHHhh-CCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHHH
Q psy3662          22 GLQFPVGRIHRLLRK-GNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELN   94 (132)
Q Consensus        22 gl~fPv~ri~rllk~-~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL~   94 (132)
                      .+.||+++|.|+|++ .....+||.+|...|+.+.|.|+.+|...|...|.+.+|++|+++||..|+...+-++
T Consensus         7 d~~LP~A~I~rImK~~~pd~~~iS~dA~~~l~ka~e~FI~~lt~~A~~~a~~~kRKTI~~~Dv~~Al~~l~f~~   80 (128)
T 2byk_B            7 DLNLPNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFES   80 (128)
T ss_dssp             ----CCSHHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCTT
T ss_pred             cccCCHHHHHHHHHHhCcccceECHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHcCcHH
Confidence            578999999999996 3346799999999999999999999999999999999999999999999997655333

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

Probab=98.79  E-value=3.3e-09  Score=74.06  Aligned_cols=71  Identities=8%  Similarity=0.059  Sum_probs=61.8

Q ss_pred             ccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHH
Q psy3662          22 GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEEL   93 (132)
Q Consensus        22 gl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL   93 (132)
                      .+-||.+-|.|++++. ...|||.++...|..+++.++.+|...|..+|+|.+|++|+++||.+|++.+..+
T Consensus         5 d~~lP~a~I~Ri~r~~-g~~rIS~~a~~~l~e~l~~f~~~v~~da~~~A~HA~RKTV~~eDV~lalrr~g~~   75 (111)
T 3b0c_T            5 EPEIASSLIKQIFSHY-VKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAGRKTVEMADVELLMRRQGLV   75 (111)
T ss_dssp             -----CHHHHHHHHHH-HCSCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTTSS
T ss_pred             CCCCCHHHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHCCCc
Confidence            3568999999999997 6789999999999999999999999999999999999999999999999876544

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

Probab=98.73  E-value=3e-08  Score=63.65  Aligned_cols=60  Identities=18%  Similarity=0.099  Sum_probs=56.8

Q ss_pred             HHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcC
Q psy3662          29 RIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRN   89 (132)
Q Consensus        29 ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~   89 (132)
                      .|+++|++. +++|++..++.-|...++-.+.+|+..|..+|.|.|+++|+.+||++||+.
T Consensus         6 ~i~~iLk~~-G~~~~~~~v~~~L~e~~~ry~~~il~dA~~~a~HAgrktv~~eDVkLAi~~   65 (68)
T 1taf_A            6 VIMSILKEL-NVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLATEV   65 (68)
T ss_dssp             HHHHHHHHT-TCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             HHHHHHHHC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHh
Confidence            589999996 689999999999999999999999999999999999999999999999963

>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=98.51  E-value=2e-07  Score=69.92  Aligned_cols=78  Identities=15%  Similarity=0.236  Sum_probs=66.2

Q ss_pred             ccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHHHhh
Q psy3662          18 SSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKL   96 (132)
Q Consensus        18 s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL~~L   96 (132)
                      ..-..+.||++.|.|+|++..-..||+.+|...|..+++-|+..|...|...|.+.+|++|+++||..|+. +-+|..+
T Consensus         9 ~~~eD~~LP~A~V~RImK~alp~~rISkDA~~al~ec~~eFI~~LtseA~e~a~~~~RKTI~~eDVl~Al~-~LgF~~f   86 (179)
T 1jfi_B            9 GNDDDLTIPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALE-SLGFGSY   86 (179)
T ss_dssp             ---CCCCCCHHHHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHH-HHTTGGG
T ss_pred             CchhhhhcCHHHHHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH-hcChHHH
Confidence            34456889999999999996224799999999999999999999999999999999999999999999996 4444433

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

Probab=98.41  E-value=5e-07  Score=63.19  Aligned_cols=75  Identities=17%  Similarity=0.203  Sum_probs=63.5

Q ss_pred             ccccccchhHHHHHHhhCCcccc---cccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHHHhh
Q psy3662          20 RAGLQFPVGRIHRLLRKGNYAER---VGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKL   96 (132)
Q Consensus        20 ragl~fPv~ri~rllk~~~~~~R---Vs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL~~L   96 (132)
                      ++.|.+.|++   ++++. ...|   ||.++...|+.+++..+.+|..-+...|+|.||++|+++||.++++.++.|..+
T Consensus        26 Kaal~y~V~r---Ivke~-gaer~~~vS~~ai~aL~El~~~~~~~ia~Dl~~fAkHAgRkTI~~eDV~La~Rr~~~L~~~  101 (113)
T 4dra_A           26 KAAVHYTVGC---LCEEV-ALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARRSNSLLKY  101 (113)
T ss_dssp             HHHHHHHHHH---HHHHH-HHHHTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTCHHHHHH
T ss_pred             HHHHHHHHHH---HHHHH-HHHcCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHhCHHHHHH
Confidence            3455666554   44453 3445   999999999999999999999999999999999999999999999999999887


Q ss_pred             hc
Q psy3662          97 LN   98 (132)
Q Consensus        97 ~~   98 (132)
                      +.
T Consensus       102 l~  103 (113)
T 4dra_A          102 IT  103 (113)
T ss_dssp             HH
T ss_pred             HH
Confidence            75

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

Probab=98.39  E-value=8.8e-07  Score=59.68  Aligned_cols=78  Identities=13%  Similarity=0.027  Sum_probs=63.3

Q ss_pred             cccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHHHhhhcC
Q psy3662          21 AGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNG   99 (132)
Q Consensus        21 agl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL~~L~~~   99 (132)
                      +.|.+-|++|-.=.-+. ....||..+...|+.+++..+.+|.+-+...|+|.||++|+++||.++++.++.|..++.+
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 ARLWIRVEERLQQVLSS-EDIKYTPRFINSLLELAYLQLGEMGSDLQAFARHAGRGVVNKSDLMLYLRKQPDLQERVTQ   89 (90)
T ss_dssp             HHHHHHHHHHHHHHSCS-SCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTCHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHHHh-cCceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhChHHHHHhhc
Confidence            44555665554333111 1246999999999999999999999999999999999999999999999999999998754

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

Probab=98.38  E-value=8.6e-07  Score=58.12  Aligned_cols=66  Identities=26%  Similarity=0.259  Sum_probs=59.2

Q ss_pred             cccchhHHHHHHhhC----CcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          23 LQFPVGRIHRLLRKG----NYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        23 l~fPv~ri~rllk~~----~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      |.+|...+.|++++-    ....|++++|...|..+.|.++-++.|.+...|.|.++.+|+|+||++|..
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            568888899998873    135799999999999999999999999999999999999999999999863

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

Probab=98.36  E-value=7.3e-07  Score=59.11  Aligned_cols=66  Identities=23%  Similarity=0.158  Sum_probs=59.2

Q ss_pred             cccchhHHHHHHhhCC------cccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          23 LQFPVGRIHRLLRKGN------YAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        23 l~fPv~ri~rllk~~~------~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      |.+|...+.|++++-.      ...|++++|...|..+.|.++-++.|-|...|.|.++.+|+|+||++|.+
T Consensus         2 lLI~klPF~RLVREI~~~~~~~~~~R~q~~Al~aLQea~E~ylv~Lfeda~lcAiHAkRvTi~~kDiqLa~r   73 (82)
T 3nqj_A            2 LLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARR   73 (82)
T ss_dssp             CSSCHHHHHHHHHHHHHHHHSSCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHH
T ss_pred             CCcccccHHHHHHHHHHHhccCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHHHHHHHH
Confidence            4678888999998743      35699999999999999999999999999999999999999999999863

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

Probab=98.30  E-value=1.4e-06  Score=60.41  Aligned_cols=77  Identities=13%  Similarity=0.153  Sum_probs=62.0

Q ss_pred             cccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHHHhhhc
Q psy3662          21 AGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLN   98 (132)
Q Consensus        21 agl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL~~L~~   98 (132)
                      +.|.+-|++|-+-.-.. ...||+..+...|+.+++.++.+|..-+..+|+|.||++|+++||.++++.++.|...+.
T Consensus        19 aal~~~V~rI~~~~g~~-~~~~vs~~~i~aL~E~~~~~~~~ia~Da~~fA~HAgRkTI~~eDV~La~Rrn~~l~~~l~   95 (107)
T 3b0b_B           19 AAVHYTTGCLCQDVAED-KGVLFSKQTVAAISEITFRQCENFARDLEMFARHAKRSTITSEDVKLLARRSNSLLKYIT   95 (107)
T ss_dssp             HHHHHHHHHHHHHHHHH-HTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhh-cCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcCcCCHHHHHHHHHhCHHHHHHHH
Confidence            34555554443322111 125999999999999999999999999999999999999999999999999999987664

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

Probab=98.24  E-value=2.2e-06  Score=60.61  Aligned_cols=51  Identities=14%  Similarity=0.165  Sum_probs=48.6

Q ss_pred             CcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          38 NYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        38 ~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      .++.|||.++...+..+||.++.+|+..|..++.|.++|+||++||.+|++
T Consensus        60 gGvkRIS~~iy~e~r~vl~~~l~~i~rdav~yaehA~RKTVta~DV~~Alk  110 (121)
T 2ly8_A           60 RGSKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALK  110 (121)
T ss_dssp             CCSSCCSSCHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCBCHHHHHHHHH
T ss_pred             cCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHH
Confidence            367899999999999999999999999999999999999999999999975

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

Probab=98.23  E-value=7.6e-07  Score=69.17  Aligned_cols=60  Identities=15%  Similarity=0.129  Sum_probs=55.4

Q ss_pred             HHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCc
Q psy3662          30 IHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRND   90 (132)
Q Consensus        30 i~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D   90 (132)
                      +.|+++++ .+.|||.++...+..+||.++.+|+..|..+|.+.++++||++||.+|+..-
T Consensus       167 ~~RlaRrg-GVkRIS~~iyeelr~vLe~fle~IirdAv~yaeHA~RKTVta~DV~~ALKr~  226 (235)
T 2l5a_A          167 DEEDGDKG-GVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQ  226 (235)
T ss_dssp             CCTTSCCT-TCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHH
T ss_pred             HHHHhhcC-CchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHhc
Confidence            45888886 6899999999999999999999999999999999999999999999998643

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

Probab=98.20  E-value=2.4e-06  Score=61.75  Aligned_cols=68  Identities=22%  Similarity=0.149  Sum_probs=61.4

Q ss_pred             cccccchhHHHHHHhhCC------cccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          21 AGLQFPVGRIHRLLRKGN------YAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        21 agl~fPv~ri~rllk~~~------~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      .+|.||...|.|++++-.      ...|++++|...|..+.|.++.+++|.|...|.|.++.+|+|+||++|..
T Consensus        58 t~LLIpKlPF~RLVREI~~~~~~~~~~Rfq~~Al~ALQEAaEayLv~LFEdanlcAiHAkRVTIm~kDiqLArr  131 (140)
T 3nqu_A           58 THLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARR  131 (140)
T ss_dssp             -CCCSCTTHHHHHHHHHHHHHHTTCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             cccccccccHHHHHHHHHHHhcccccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHHHH
Confidence            478899999999998743      35799999999999999999999999999999999999999999999864

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

Probab=98.20  E-value=2e-06  Score=63.06  Aligned_cols=71  Identities=21%  Similarity=0.125  Sum_probs=62.7

Q ss_pred             cccccchhHHHHHHhhCC------cccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcH
Q psy3662          21 AGLQFPVGRIHRLLRKGN------YAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDE   91 (132)
Q Consensus        21 agl~fPv~ri~rllk~~~------~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~   91 (132)
                      .+|.||...|.|++++..      ...|++++|...|..+.|.++.+++|.|...|.|.++.+|+|+||++|..--.
T Consensus        74 teLLIpKlPF~RLVREIa~~~~~~~~lRfqs~Al~ALQEAaEayLV~LFEdanLcAiHAkRVTIm~kDIqLArrIrg  150 (156)
T 3r45_A           74 THLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIRG  150 (156)
T ss_dssp             -CCCSCHHHHHHHHHHHHHTTTTTCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSEECHHHHHHHHHHHH
T ss_pred             cccccccccHHHHHHHHHHHhccCccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHHHHHcc
Confidence            478899999999998732      25699999999999999999999999999999999999999999999875433

>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=98.19  E-value=2.9e-06  Score=58.18  Aligned_cols=68  Identities=24%  Similarity=0.194  Sum_probs=57.9

Q ss_pred             cccccchhHHHHHHhhCC-------cccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          21 AGLQFPVGRIHRLLRKGN-------YAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        21 agl~fPv~ri~rllk~~~-------~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      .+|.+|...+.|++++-.       ...|++++|...|..+.|.++-+++|.+...|.|.++.+|+|.||++|..
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            578899999999998732       15699999999999999999999999999999999999999999999863

>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=98.10  E-value=6.8e-06  Score=59.13  Aligned_cols=68  Identities=26%  Similarity=0.272  Sum_probs=61.2

Q ss_pred             cccccchhHHHHHHhhC----CcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          21 AGLQFPVGRIHRLLRKG----NYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        21 agl~fPv~ri~rllk~~----~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      .+|.||...|.|++++-    ....|++++|...|..+.|.++-+++|.+...|.|.++.+|.|+||++|..
T Consensus        59 t~lLIpk~PF~RLVREI~~~~~~~~R~q~~Al~aLQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa~r  130 (136)
T 1tzy_C           59 TELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR  130 (136)
T ss_dssp             CSCCSCHHHHHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             hhhhhccchHHHHHHHHHHHhhhhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHhHHHHHH
Confidence            36789999999999874    124699999999999999999999999999999999999999999999863

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

Probab=98.07  E-value=5.5e-06  Score=59.81  Aligned_cols=79  Identities=14%  Similarity=0.174  Sum_probs=64.2

Q ss_pred             ccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHHHhhhcC
Q psy3662          20 RAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLNG   99 (132)
Q Consensus        20 ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL~~L~~~   99 (132)
                      ++.|.+-|++|-.=.-.. ....|+.++...|+.+++.++.+|..-+..+|+|.||++|+++||.++++.++.|..++..
T Consensus        18 KaAl~y~VgkIvee~~~~-~~~~vS~~ai~aL~El~~~~~e~ia~DLe~FAkHAGRKTI~~eDVkLa~Rrn~~L~~~L~~   96 (140)
T 3vh5_A           18 RAAVHYTTGALAQDVAED-KGVLFSKQTVAAISEITFRQAENFARDLEMFARHAKRSTITSEDVKLLARRSNSLLKYITQ   96 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHH-HTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHh-cCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhCHHHHHHHHH
Confidence            345556665554322111 1236999999999999999999999999999999999999999999999999999998853

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

Probab=97.89  E-value=2.5e-05  Score=55.18  Aligned_cols=60  Identities=20%  Similarity=0.221  Sum_probs=54.9

Q ss_pred             hHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhh
Q psy3662          28 GRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAI   87 (132)
Q Consensus        28 ~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI   87 (132)
                      ..|+++|++-.-...||+.|...|..+++.+...|...|...|+.+++++|++++|+.|+
T Consensus        37 ~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtAv   96 (123)
T 2nqb_D           37 IYIYTVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAV   96 (123)
T ss_dssp             HHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHH
Confidence            468999998533348999999999999999999999999999999999999999999998

>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=97.83  E-value=3.6e-05  Score=54.62  Aligned_cols=64  Identities=17%  Similarity=0.256  Sum_probs=57.1

Q ss_pred             cccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhh
Q psy3662          23 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAI   87 (132)
Q Consensus        23 l~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI   87 (132)
                      -.|.+ .|+++|++-.-...||+.|...|..+++.+...|...|...|+.+++++||+++|+.|+
T Consensus        36 esy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtAv   99 (126)
T 1tzy_B           36 ESYSI-YVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAV   99 (126)
T ss_dssp             CCCHH-HHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHH
T ss_pred             ccHHH-HHHHHHHHhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence            34555 79999999533348999999999999999999999999999999999999999999998

>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=97.33  E-value=0.00034  Score=52.65  Aligned_cols=61  Identities=23%  Similarity=0.281  Sum_probs=55.2

Q ss_pred             hHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          28 GRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        28 ~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      ..|+|+|++..-...||..|..+|...+..++..|...|...+..+++++||++||+.|++
T Consensus         7 ~yi~kvLkqv~p~~~iS~~Am~~m~s~v~di~~rIa~eA~~L~~~~~r~Tit~~eIq~Avr   67 (192)
T 2jss_A            7 SYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVR   67 (192)
T ss_dssp             HHHHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCSCCHHHHHHHHH
T ss_pred             HHHHHHHcccCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Confidence            3689999986434689999999999999999999999999999999999999999999985

>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=97.05  E-value=0.0012  Score=44.02  Aligned_cols=64  Identities=23%  Similarity=0.387  Sum_probs=54.8

Q ss_pred             ccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhc-CCceechhhhhhhhc
Q psy3662          24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDN-KKTRIIPRHIQLAIR   88 (132)
Q Consensus        24 ~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~-~~k~Itp~~i~~AI~   88 (132)
                      .||-..|+|++..- ....|+.+..+.|+++--.|+.||+|.|....... ....|.|.||+.|..
T Consensus        16 ~f~k~~vKrl~~~~-~~~~v~~~v~i~v~glaKvfVgelVE~A~~V~~~~~~~~Pl~P~HireA~r   80 (89)
T 1bh9_B           16 AFPKAAIKRLIQSI-TGTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVR   80 (89)
T ss_dssp             CCCHHHHHHHHHHH-HSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHH-cCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHH
Confidence            57777799999874 57799999999999999999999999999986665 455899999999873

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

Probab=96.75  E-value=0.0066  Score=40.11  Aligned_cols=68  Identities=19%  Similarity=0.198  Sum_probs=57.0

Q ss_pred             ccccccchhHHHHHHhhCC--cccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhh
Q psy3662          20 RAGLQFPVGRIHRLLRKGN--YAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAI   87 (132)
Q Consensus        20 ragl~fPv~ri~rllk~~~--~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI   87 (132)
                      .++..||..=|.|+|+..-  ...||+.+|...++..|+.|+.|.+..|...|...+...|..+|++...
T Consensus         8 ~~~~~i~~~li~ril~~~F~~~kTkIs~dAl~l~aeyl~iFV~EAv~RA~~~a~~e~~~~le~e~LEki~   77 (84)
T 4dra_E            8 GAGSGFRKELVSRLLHLHFKDDKTKVSGDALQLMVELLKVFVVEAAVRGVRQAQAEDALRVDVDQLEKVL   77 (84)
T ss_dssp             ---CCCCHHHHHHHHHTTCSSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHhcCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHH
Confidence            3467899999999999631  1249999999999999999999999999999998888899999999643

>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=96.64  E-value=0.0094  Score=39.06  Aligned_cols=65  Identities=23%  Similarity=0.250  Sum_probs=56.6

Q ss_pred             ccccchhHHHHHHhhCC--cccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhh
Q psy3662          22 GLQFPVGRIHRLLRKGN--YAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLA   86 (132)
Q Consensus        22 gl~fPv~ri~rllk~~~--~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~A   86 (132)
                      +..||..=|.|+|+..-  ...||+.+|..-++..|+.|+.|.+..|...|...+...|..+|++..
T Consensus         6 ~~~~~~~lI~ril~~~f~~~ktrI~~dAl~l~aeyl~iFV~EAv~RA~~~a~~e~~~~le~~~LEki   72 (81)
T 3b0b_C            6 EGGFRKETVERLLRLHFRDGRTRVNGDALLLMAELLKVFVREAAARAARQAQAEDLEKVDIEHVEKV   72 (81)
T ss_dssp             -CCCCHHHHHHHHHHHCCSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHhccCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeecHHHHHHH
Confidence            45799999999999731  134999999999999999999999999999998889899999999974

>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=95.90  E-value=0.022  Score=36.84  Aligned_cols=66  Identities=17%  Similarity=0.283  Sum_probs=59.1

Q ss_pred             ccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcC
Q psy3662          24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRN   89 (132)
Q Consensus        24 ~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~   89 (132)
                      .++-.++..++++-.....+..++-..|..+.+-|+..+++.|...|+|-+..++.+.|+++.+..
T Consensus         5 vl~k~~L~~Lv~~idp~~~ld~~vee~ll~lADdFV~~V~~~ac~lAKhR~s~~le~kDvql~Ler   70 (76)
T 1h3o_B            5 VLTKKKLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLER   70 (76)
T ss_dssp             SSCHHHHHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHH
T ss_pred             cccHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHh
Confidence            567788999999865567999999999999999999999999999999999999999999987643

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

Probab=95.09  E-value=0.035  Score=42.97  Aligned_cols=66  Identities=23%  Similarity=0.166  Sum_probs=54.7

Q ss_pred             ccccchhHHHHHHhhC----Cc---ccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhh
Q psy3662          22 GLQFPVGRIHRLLRKG----NY---AERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAI   87 (132)
Q Consensus        22 gl~fPv~ri~rllk~~----~~---~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI   87 (132)
                      .|.+|-.++.|++++-    ..   ..|..++|...|.-+-|.++-.++|-+.-.|.|.++.+|.|.|+++|-
T Consensus         9 ~~lI~KlPFqRLVREIaq~~~~~~~~lRfqs~Al~ALQEAaEayLV~LFEd~nLcaiHAkRVTim~kDiqLar   81 (235)
T 2l5a_A            9 KLLISKIPFARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMKKDMQLAR   81 (235)
T ss_dssp             --CCSCCHHHHHHHHHHHTSCGGGTTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTSGGGTTHHHHHH
T ss_pred             cccccCccHHHHHHHHHHHhccCCccceecHHHHHHHHHHHHHHHHHHHhhhHHHHhcccccccchhhHHHHH
Confidence            4677777788877651    11   248899999999999999999999999999999999999999999983

>1wwi_A Hypothetical protein TTHA1479; structural genomics, unknown function, riken structural genomics/proteomics initiative, RSGI; 1.58A {Thermus thermophilus HB8} SCOP: a.22.1.4 PDB: 1wws_A

Probab=91.14  E-value=0.68  Score=33.37  Aligned_cols=60  Identities=18%  Similarity=0.237  Sum_probs=52.5

Q ss_pred             ccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhh
Q psy3662          24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQ   84 (132)
Q Consensus        24 ~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~   84 (132)
                      .+++.+++++++.. ..--|..+-.--+..++|--+.+++..|-..|+.+++..|.|.|+-
T Consensus         2 vm~~~~~e~lFR~a-a~LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~n~RdvI~~~DLP   61 (148)
T 1wwi_A            2 LMKVAEFERLFRQA-AGLDVDKNDLKRVSDFLRNKLYDLLAVAERNAKYNGRDLIFEPDLP   61 (148)
T ss_dssp             CSCHHHHHHHHHHH-HCCCCCGGGHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECGGGSC
T ss_pred             cCCHHHHHHHHHHH-hccCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeeccccCC
Confidence            57889999999985 3446778888888999999999999999999999999999999975

>1k6k_A ATP-dependent CLP protease ATP-binding subunit CLPA; chaperone, ATPase, adaptor binding, X-RAY, structure, N-domain, hydrolase; 1.80A {Escherichia coli} SCOP: a.174.1.1 PDB: 1r6c_X 1r6o_A* 1r6q_A* 1mg9_B* 1lzw_B* 1mbx_A* 1mbv_A 1mbu_A*

Probab=87.65  E-value=0.71  Score=31.43  Aligned_cols=40  Identities=20%  Similarity=0.289  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHHHhhhc
Q psy3662          59 VAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLN   98 (132)
Q Consensus        59 ~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL~~L~~   98 (132)
                      +.++++.|.+.|...+...|+|+||-+|+-.+++...++.
T Consensus         6 ~~~~l~~A~~~A~~~~~~~i~~eHlLlaLl~~~~~~~iL~   45 (143)
T 1k6k_A            6 LELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALE   45 (143)
T ss_dssp             HHHHHHHHHHHHHHHTBSEECHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCCcCHHHHHHHHHcCchHHHHHH
Confidence            4578899999999999999999999999988877666554

>1r4v_A Hypothetical protein AQ_328; structural genomics, all-alpha, histon fold, PSI, protein ST initiative, midwest center for structural genomics; HET: MSE; 1.90A {Aquifex aeolicus} SCOP: a.22.1.4

Probab=86.75  E-value=0.67  Score=34.12  Aligned_cols=60  Identities=12%  Similarity=0.056  Sum_probs=53.0

Q ss_pred             ccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhh
Q psy3662          24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQ   84 (132)
Q Consensus        24 ~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~   84 (132)
                      .+++.+++|+++.. ..--|..+-.--+..+++--+.+++..|-..|+.++|..|.|.|+-
T Consensus        26 vmg~~kferlFR~a-agLDvdK~d~kr~~d~V~~Kl~DLl~va~~~Ak~NgRDvI~~~DLP   85 (171)
T 1r4v_A           26 PKGFDKLDHYFRTE-LDIDLTDETIELLLNSVKAAFGKLFYGAEQRARWNGRDFIALADLN   85 (171)
T ss_dssp             CTTHHHHHHHHHHH-HCCCCCHHHHHHHHHHHHHHHHHTTTTHHHHHHHTTCSEECGGGSC
T ss_pred             cCChHHHHHHHHHH-hccCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeeccccCC
Confidence            88999999999985 3446777777788899999999999999999999999999999975

>1khy_A CLPB protein; alpha helix, chaperone; 1.95A {Escherichia coli} SCOP: a.174.1.1

Probab=82.79  E-value=1  Score=30.70  Aligned_cols=33  Identities=27%  Similarity=0.220  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHHHhcCCceechhhhhhhhcCcH
Q psy3662          59 VAEVLELAGNAARDNKKTRIIPRHIQLAIRNDE   91 (132)
Q Consensus        59 ~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~   91 (132)
                      +.++++.|...|...+...|+|+||-+|+-.++
T Consensus        10 ~~~~l~~A~~~A~~~~~~~i~~eHlLlaLl~~~   42 (148)
T 1khy_A           10 FQLALADAQSLALGHDNQFIEPLHLMSALLNQE   42 (148)
T ss_dssp             HHHHHHHHHHHHHHTTCSSBCHHHHHHHHHTCT
T ss_pred             HHHHHHHHHHHHHHcCCCccCHHHHHHHHHcCC
Confidence            357889999999999999999999999997665

>3fes_A ATP-dependent CLP endopeptidase; alpha-helical bundles, structural genomics, PSI-2, protein S initiative; HET: PG4 EPE; 1.82A {Clostridium difficile}

Probab=81.75  E-value=0.78  Score=31.71  Aligned_cols=39  Identities=23%  Similarity=0.294  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHHHHhcCCceechhhhhhhhcCcH--HHHhhh
Q psy3662          59 VAEVLELAGNAARDNKKTRIIPRHIQLAIRNDE--ELNKLL   97 (132)
Q Consensus        59 ~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~--EL~~L~   97 (132)
                      +.++++.|.+.|...+...|+|+||-+|+-.++  ....++
T Consensus        12 a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~~~~~iL   52 (145)
T 3fes_A           12 AKKAIDLAFESAKSLGHNIVGSEHILLGLLREEEGIAAKVL   52 (145)
T ss_dssp             HHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHCSSHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCCccHHHHHHHHHhCCCChHHHHH
Confidence            457889999999999999999999999997654  344444

>2y1q_A CLPC N-domain, negative regulator of genetic competence CLPC/MEC; transcription, proteolysis; 1.50A {Bacillus subtilis} PDB: 2y1r_A* 2k77_A

Probab=80.11  E-value=1.3  Score=30.38  Aligned_cols=39  Identities=31%  Similarity=0.309  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHHHHhcCCceechhhhhhhhcCcHH--HHhhh
Q psy3662          59 VAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEE--LNKLL   97 (132)
Q Consensus        59 ~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~E--L~~L~   97 (132)
                      +.++++.|.+.|...+...|+|+||-+|+-.+++  ...++
T Consensus        10 ~~~al~~A~~~A~~~~h~~i~~eHlLlaLl~~~~~~~~~iL   50 (150)
T 2y1q_A           10 AQKVLALAQEEALRLGHNNIGTEHILLGLVREGEGIAAKAL   50 (150)
T ss_dssp             HHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHCSSHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCCccHHHHHHHHHhCCCCHHHHHH
Confidence            3578889999999999999999999999966543  44444

---

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	132
d1tzya_	106	a.22.1.1 (A:) Histone H2A {Chicken (Gallus gallus)	4e-63
d1u35c1	106	a.22.1.1 (C:814-919) macro-H2A.1, histone domain {	6e-62
d1f66c_	103	a.22.1.1 (C:) Histone H2A {Human (Homo sapiens), v	2e-52
d1q9ca_	172	a.22.1.3 (A:) Histone domain of Son of sevenless p	2e-46
d1jfia_	66	a.22.1.3 (A:) Negative cofactor 2, NC2, alpha chai	5e-24
d1n1jb_	78	a.22.1.3 (B:) Nuclear transcription factor Y subun	2e-22
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	4e-15
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	2e-11
d1htaa_	68	a.22.1.2 (A:) Archaeal histone {Archaeon Methanoth	1e-06
d1ku5a_	66	a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococc	1e-04

>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 =  186 bits (473), Expect = 4e-63
 Identities = 98/106 (92%), Positives = 103/106 (97%)

Query: 13  KSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARD 72
           K+K+RSSRAGLQFPVGR+HRLLRKGNYAERVGAGAPVYLAAVLEYL AE+LELAGNAARD
Sbjct: 1   KAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARD 60

Query: 73  NKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPK 118
           NKKTRIIPRH+QLAIRNDEELNKLL  VTIAQGGVLPNIQAVLLPK
Sbjct: 61  NKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPK 106

>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 =  183 bits (465), Expect = 6e-62
 Identities = 71/105 (67%), Positives = 85/105 (80%)

Query: 15  KTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNK 74
            +RS++AG+ FPVGR+ R ++KG+   R+G GAPVY+AAVLEYL AE+LELA NAARDNK
Sbjct: 2   TSRSAKAGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNK 61

Query: 75  KTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLLPKK 119
           K R+ PRHI LA+ NDEELN+LL GVTIA GGVLPNI   LL KK
Sbjct: 62  KGRVTPRHILLAVANDEELNQLLKGVTIASGGVLPNIHPELLAKK 106

>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 = 2e-52
 Identities = 65/104 (62%), Positives = 78/104 (75%), Gaps = 2/104 (1%)

Query: 14  SKTRSSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVLEYLVAEVLELAGNAARD 72
           + +RS RAGLQFPVGRIHR L+    +  RVGA A VY AA+LEYL AEVLELAGNA++D
Sbjct: 1   AVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKD 60

Query: 73  NKKTRIIPRHIQLAIRNDEELNKLLNGVTIAQGGVLPNIQAVLL 116
            K  RI PRH+QLAIR DEEL+ L+   TIA GGV+P+I   L+
Sbjct: 61  LKVKRITPRHLQLAIRGDEELDSLI-KATIAGGGVIPHIHKSLI 103

>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 =  146 bits (369), Expect = 2e-46
 Identities = 29/96 (30%), Positives = 52/96 (54%), Gaps = 1/96 (1%)

Query: 3   GRGKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEV 62
            +     A++  + R  R  L  PV +IH LL++     ++     VY+ AVLEY+ A++
Sbjct: 78  DKWAIADAQSAIEKRKRRNPLSLPVEKIHPLLKEV-LGYKIDHQVSVYIVAVLEYISADI 136

Query: 63  LELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLLN 98
           L+LAGN  R+ +   I  + I++A+  D+ L  + +
Sbjct: 137 LKLAGNYVRNIRHYEITKQDIKVAMCADKVLMDMFH 172

>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 = 85.9 bits (213), Expect = 5e-24
 Identities = 14/64 (21%), Positives = 29/64 (45%)

Query: 24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHI 83
          +FP  RI ++++      +V A  PV ++  LE  +  +L+ A    +      +   H+
Sbjct: 2  RFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHL 61

Query: 84 QLAI 87
          +  I
Sbjct: 62 KQCI 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 = 82.2 bits (203), Expect = 2e-22
 Identities = 18/75 (24%), Positives = 36/75 (48%)

Query: 26  PVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQL 85
           P+ RI ++++     + + A APV  A   +  + E+   A     DNK+  +    I +
Sbjct: 2   PLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAM 61

Query: 86  AIRNDEELNKLLNGV 100
           AI   ++ + L++ V
Sbjct: 62  AITKFDQFDFLIDIV 76

>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 = 65.2 bits (159), Expect = 4e-15
 Identities = 13/76 (17%), Positives = 28/76 (36%), Gaps = 1/76 (1%)

Query: 14  SKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDN 73
            +      G  F    + R+L++    ER  + A      ++     E+ E A   A ++
Sbjct: 69  VEGVEDYDGELFGRATVRRILKRAG-IERASSDAVDLYNKLICRATEELGEKAAEYADED 127

Query: 74  KKTRIIPRHIQLAIRN 89
            +  +    ++ AI  
Sbjct: 128 GRKTVQGEDVEKAITY 143

>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} Length = 151

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon Methanopyrus kandleri [TaxId: 2320]

 Score = 55.2 bits (133), Expect = 2e-11
 Identities = 11/65 (16%), Positives = 24/65 (36%)

Query: 24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHI 83
          + P   I R+ R+G    R+   A   +   +  +   V   A +    + K  ++  H+
Sbjct: 1  ELPKAAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHL 60

Query: 84 QLAIR 88
          +    
Sbjct: 61 KALAD 65

>d1htaa_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanothermus fervidus, histone A [TaxId: 2180]} Length = 68

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon Methanothermus fervidus, histone A [TaxId: 2180]

 Score = 40.9 bits (96), Expect = 1e-06
 Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 1/65 (1%)

Query: 24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHI 83
          + P+  I R+++    AERV   A + LA VLE +  E+   A   A+   +  I    I
Sbjct: 3  ELPIAPIGRIIKNAG-AERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDI 61

Query: 84 QLAIR 88
          +LA +
Sbjct: 62 ELARK 66

>d1ku5a_ a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococcus horikoshii) [TaxId: 53953]} Length = 66

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon (Pyrococcus horikoshii) [TaxId: 53953]

 Score = 35.5 bits (82), Expect = 1e-04
 Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 1/66 (1%)

Query: 24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHI 83
          + P+  + RL+RK   AERV   A   LA  LE    E+ + A   AR   +  +    I
Sbjct: 2  ELPIAPVDRLIRKAG-AERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDI 60

Query: 84 QLAIRN 89
          +LAI++
Sbjct: 61 KLAIKS 66

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	132
d1tzya_	106	Histone H2A {Chicken (Gallus gallus), erythrocytes	100.0
d1u35c1	106	macro-H2A.1, histone domain {Human (Homo sapiens)	100.0
d1f66c_	103	Histone H2A {Human (Homo sapiens), variant H2A.Z [	100.0
d1q9ca_	172	Histone domain of Son of sevenless protein {Human	99.96
d1jfia_	66	Negative cofactor 2, NC2, alpha chain {Human (Homo	99.67
d1n1jb_	78	Nuclear transcription factor Y subunit gamma (Nf-Y	99.57
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	99.44
d1ku5a_	66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	99.3
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	99.28
d1n1ja_	87	Nuclear transcription factor Y subunit beta (Nf-Yb	99.1
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	98.94
d2huec1	82	Histone H4 {African clawed frog (Xenopus laevis) [	98.88
d1jfib_	135	Negative cofactor 2, NC2, beta chain {Human (Homo	98.84
d2byka1	72	Chrac-16 {Fruit fly (Drosophila melanogaster) [Tax	98.59
d2bykb1	89	Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax	98.57
d1tzyc_	95	Histone H3 {Chicken (Gallus gallus), erythrocytes	97.63
d1tafb_	70	TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta	97.44
d1tzyb_	92	Histone H2B {Chicken (Gallus gallus), erythrocytes	97.35
d1bh9b_	89	TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]}	97.16
d1tafa_	68	TAF(II)42 {Fruit fly (Drosophila melanogaster) [Ta	96.52
d1h3ob_	74	TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom	95.31
d1k6ka_	142	N-terminal, ClpS-binding domain of ClpA, an Hsp100	91.61
d1wwia1	148	Hypothetical protein TTHA1479 {Thermus thermophilu	91.51
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	88.93
d1khya_	139	N-terminal domain of ClpB (heat shock protein F84.	86.8
d1qvra1	145	N-terminal domain of ClpB (heat shock protein F84.	86.35
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	83.94

>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=4.4e-47  Score=263.29  Aligned_cols=106  Identities=92%  Similarity=1.327  Sum_probs=103.6

Q ss_pred             ccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHH
Q psy3662          13 KSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEE   92 (132)
Q Consensus        13 ~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~E   92 (132)
                      |.+|+|+||||+|||++|+|+|+++++++||+++|+|||+||||||++||||+|||+|+++++++|||+||++||+||+|
T Consensus         1 k~~Srs~rAgL~FpV~rv~r~Lk~~~~~~rv~~~apVylaAVLEYLtaEiLELAgn~a~~~k~~rItPrhi~lAirnDee   80 (106)
T d1tzya_           1 KAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEE   80 (106)
T ss_dssp             CCCCHHHHHTCSSCHHHHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHTSHH
T ss_pred             CCccccccCCccCChHHHHHHHHcCccccccCCCchHHHHHHHHHHHHHHHHHhhHHHHhcCCceecchhhhhcccCHHH
Confidence            35799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhcCCeecCCCcCCCCcccccCC
Q psy3662          93 LNKLLNGVTIAQGGVLPNIQAVLLPK  118 (132)
Q Consensus        93 L~~L~~~~~ia~ggv~P~i~~~~~~~  118 (132)
                      |+.||.++||++|||+|+||++|+||
T Consensus        81 L~~L~~~vtI~~GGv~P~Ih~~Llpk  106 (106)
T d1tzya_          81 LNKLLGKVTIAQGGVLPNIQAVLLPK  106 (106)
T ss_dssp             HHHHTTTEEETTCCCCCCCCGGGSCC
T ss_pred             HHHHHcCCeecCCCccCccCHhhcCC
Confidence            99999999999999999999999986

>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=4.9e-47  Score=263.14  Aligned_cols=106  Identities=67%  Similarity=1.024  Sum_probs=103.5

Q ss_pred             cCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHH
Q psy3662          14 SKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEEL   93 (132)
Q Consensus        14 ~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL   93 (132)
                      +.|||+||||+|||+||+|+|+++++++||+++|||||+||||||++||||+|+|+|.++++++|+|+||++||+||+||
T Consensus         1 k~srs~ragL~FpV~ri~r~Lk~~~~~~rv~~~apVylaAVLEYL~aEILELAgn~a~~~k~~rItprhi~lairnD~EL   80 (106)
T d1u35c1           1 KTSRSAKAGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILLAVANDEEL   80 (106)
T ss_dssp             CCCHHHHHTCSSCHHHHHHHHHHHSTTSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHSHHH
T ss_pred             CCCccccCCcccCHHHHHHHHhCCCCccccCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCeeecchhhhcccCHHHH
Confidence            36889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhcCCeecCCCcCCCCcccccCCc
Q psy3662          94 NKLLNGVTIAQGGVLPNIQAVLLPKK  119 (132)
Q Consensus        94 ~~L~~~~~ia~ggv~P~i~~~~~~~k  119 (132)
                      +.||+++||++|||+|+||++|+|||
T Consensus        81 ~~L~~~vtI~~GGv~p~Ih~~Ll~kk  106 (106)
T d1u35c1          81 NQLLKGVTIASGGVLPNIHPELLAKK  106 (106)
T ss_dssp             HHHTTTEEETTCCCCCCCCGGGSCCC
T ss_pred             HHHHcCCeEeCCcccCCcCHHhcCCC
Confidence            99999999999999999999999986

>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=3.1e-44  Score=248.26  Aligned_cols=101  Identities=64%  Similarity=0.962  Sum_probs=97.8

Q ss_pred             CCcccccccccchhHHHHHHhhCCccc-ccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHH
Q psy3662          15 KTRSSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEEL   93 (132)
Q Consensus        15 ~s~s~ragl~fPv~ri~rllk~~~~~~-RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL   93 (132)
                      +|||+||||+|||+||+|||+++++++ ||+++|||||+||||||++||||+|+|.|.++++++|||+||++||+||+||
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            689999999999999999999998986 6999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhcCCeecCCCcCCCCccccc
Q psy3662          94 NKLLNGVTIAQGGVLPNIQAVLL  116 (132)
Q Consensus        94 ~~L~~~~~ia~ggv~P~i~~~~~  116 (132)
                      +.|| ++||++|||+|+||++|+
T Consensus        82 ~~L~-~vti~~GGv~p~I~~~Ll  103 (103)
T d1f66c_          82 DSLI-KATIAGGGVIPHIHKSLI  103 (103)
T ss_dssp             HHHC-CSEETTCCCCCCCCGGGC
T ss_pred             HHHh-CeEeeCCeecccccHhhC
Confidence            9999 599999999999999985

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

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

Probab=99.96  E-value=5e-30  Score=190.47  Aligned_cols=86  Identities=33%  Similarity=0.563  Sum_probs=74.5

Q ss_pred             CccCCcccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcH
Q psy3662          12 TKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDE   91 (132)
Q Consensus        12 ~~~~s~s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~   91 (132)
                      +...|++.|+||+|||++|+|+||++ +++|||++|+|||+||||||++||+|+|+|+|+++++++|||+||++||+||+
T Consensus        87 ~~~~srs~ragL~fPV~rv~rlLk~~-~a~RVs~~A~vyLaavLEyl~aeILelAgn~a~~~krkrItp~dI~lAi~nD~  165 (172)
T d1q9ca_          87 SAIEKRKRRNPLSLPVEKIHPLLKEV-LGYKIDHQVSVYIVAVLEYISADILKLAGNYVRNIRHYEITKQDIKVAMCADK  165 (172)
T ss_dssp             HHHC--------CCCHHHHHHHHHHH-HSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSBCCHHHHHHHHHTCH
T ss_pred             HHHhccccccCceecHHHHHHHHHhc-cccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCceecHHHHHHHHhCCH
Confidence            34578999999999999999999996 89999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhc
Q psy3662          92 ELNKLLN   98 (132)
Q Consensus        92 EL~~L~~   98 (132)
                      ||+.||+
T Consensus       166 eL~~Lf~  172 (172)
T d1q9ca_         166 VLMDMFH  172 (172)
T ss_dssp             HHHHHCC
T ss_pred             HHHHhhC
Confidence            9999984

>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=99.67  E-value=5.3e-17  Score=102.45  Aligned_cols=65  Identities=22%  Similarity=0.464  Sum_probs=59.8

Q ss_pred             ccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        24 ~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      +||++||+|+||.+....+||.+|+++++.++|||+.++++.|++.|...++++|+++||..||+
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            69999999999998888999999999999999999999999999999999999999999999884

>d1n1jb_ a.22.1.3 (B:) Nuclear transcription factor Y subunit gamma (Nf-Yc2) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Nuclear transcription factor Y subunit gamma (Nf-Yc2)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=3.6e-15  Score=96.49  Aligned_cols=73  Identities=23%  Similarity=0.397  Sum_probs=70.3

Q ss_pred             cchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHHHhhh
Q psy3662          25 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLL   97 (132)
Q Consensus        25 fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL~~L~   97 (132)
                      +|+++|+|+||.+....+|+.+|+++++.++|+|+.++.+.|.+.|...++++|+++||..|++++++|++|.
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            6999999999987778899999999999999999999999999999999999999999999999999998886

>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=99.44  E-value=1e-13  Score=99.84  Aligned_cols=70  Identities=19%  Similarity=0.232  Sum_probs=66.3

Q ss_pred             ccccccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          18 SSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        18 s~ragl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      ..++++.||.++|+|++++. ...|||.+|.++|+.++|||+.+|++.|.++|.+.++++|+|+||..|+.
T Consensus        73 ~~~~~~~fp~a~IkRi~k~~-g~~ris~dA~~~l~~~~E~fi~~l~~~A~~~a~~~kRkTI~~~DI~~Av~  142 (151)
T d1f1ea_          73 EDYDGELFGRATVRRILKRA-GIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAIT  142 (151)
T ss_dssp             TTCCSCCCCHHHHHHHHHHT-TCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             cccccCccCHHHHHHHHHcC-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHH
Confidence            45789999999999999986 68899999999999999999999999999999999999999999999984

>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=99.30  E-value=3.5e-12  Score=79.75  Aligned_cols=65  Identities=34%  Similarity=0.446  Sum_probs=61.7

Q ss_pred             ccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcC
Q psy3662          24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRN   89 (132)
Q Consensus        24 ~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~   89 (132)
                      ++|.++|.|+++++ ...||+.+|...+..++|.|+.++...|..+|.+.+|++|+++||..|+++
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 ELPIAPVDRLIRKA-GAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIKS   66 (66)
T ss_dssp             CSCHHHHHHHHHHT-TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHhC-cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhC
Confidence            68999999999997 567999999999999999999999999999999999999999999999864

>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=99.28  E-value=3.7e-12  Score=79.94  Aligned_cols=64  Identities=31%  Similarity=0.424  Sum_probs=60.9

Q ss_pred             ccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        24 ~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      .+|.++|+|+++++ ...||+.+|...++.++|+|+.+|++.|..+|.+.+|++|+++||..|++
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            38999999999996 67899999999999999999999999999999999999999999999985

>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=99.10  E-value=6e-11  Score=77.74  Aligned_cols=74  Identities=11%  Similarity=0.209  Sum_probs=66.5

Q ss_pred             cccchhHHHHHHhhC-CcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHHHhh
Q psy3662          23 LQFPVGRIHRLLRKG-NYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKL   96 (132)
Q Consensus        23 l~fPv~ri~rllk~~-~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL~~L   96 (132)
                      |.||.++|.|+|++. ....+|+.+|...++.+.|.|+.++...|.+.|...++++|+++||..|+.+.+-++++
T Consensus         1 l~LP~a~v~ri~K~~~p~~~~is~ea~~~i~~a~e~Fi~~lt~~A~~~a~~~~rKTI~~~dv~~Al~~~~~~~fl   75 (87)
T d1n1ja_           1 IYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYV   75 (87)
T ss_dssp             CCCCHHHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTTCGGGH
T ss_pred             CCCcHhHHHHHHHHhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHcCcHhHH
Confidence            569999999999964 35679999999999999999999999999999999999999999999999887654443

>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=98.94  E-value=8.3e-10  Score=78.96  Aligned_cols=65  Identities=17%  Similarity=0.263  Sum_probs=61.2

Q ss_pred             ccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        24 ~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      .||++.|.|+|++.-...|||.+|...|..++++++..|...|.+.|.+.++++|+|+||+.|+.
T Consensus         1 ~lP~a~I~rilk~~~~~~ris~da~~~l~~~~~~~~~~Ia~eA~~l~~~~~rKTi~~edi~~a~~   65 (151)
T d1f1ea_           1 ELPKAAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALAD   65 (151)
T ss_dssp             CCCHHHHHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHH
T ss_pred             CCCccHHHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence            48999999999986567899999999999999999999999999999999999999999999973

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

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H4
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=98.88  E-value=3.6e-09  Score=68.59  Aligned_cols=66  Identities=18%  Similarity=0.232  Sum_probs=61.0

Q ss_pred             cchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcH
Q psy3662          25 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDE   91 (132)
Q Consensus        25 fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~   91 (132)
                      +|-.-|.|++++. ...|||.++...|+.++||++.+|+..|..++.|+++++||++||.+|++..-
T Consensus        10 I~k~~i~Riar~~-Gv~ris~d~~~~l~~~l~~~l~~i~~~a~~~~~hakRKTvt~~DV~~Alkr~g   75 (82)
T d2huec1          10 ITKPAIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQG   75 (82)
T ss_dssp             SCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTTC
T ss_pred             cCHHHHHHHHHHc-CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHhcC
Confidence            5566799999996 68999999999999999999999999999999999999999999999997653

>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=98.84  E-value=1.6e-09  Score=76.14  Aligned_cols=70  Identities=17%  Similarity=0.243  Sum_probs=64.5

Q ss_pred             ccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCcH
Q psy3662          22 GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRNDE   91 (132)
Q Consensus        22 gl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~   91 (132)
                      .+.||.++|.|+|+..-...+|+.+|...++.+.|.|+..|...|...|...+|++|+++||..|+.+-+
T Consensus         2 dl~LP~a~I~kI~K~~~~~~~is~dA~~~i~~a~~~Fi~~lt~~A~~~a~~~~RkTi~~~Dv~~Al~~~~   71 (135)
T d1jfib_           2 DLTIPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALESLG   71 (135)
T ss_dssp             CCCCCHHHHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHT
T ss_pred             cccccHHHHHHHHhhCCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHcC
Confidence            3789999999999996556799999999999999999999999999999999999999999999997533

>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=98.59  E-value=1.9e-08  Score=63.53  Aligned_cols=64  Identities=11%  Similarity=0.130  Sum_probs=56.9

Q ss_pred             HhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHH-hcCCceechhhhhhhhcCcHHHHhhh
Q psy3662          34 LRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAAR-DNKKTRIIPRHIQLAIRNDEELNKLL   97 (132)
Q Consensus        34 lk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~-~~~~k~Itp~~i~~AI~~D~EL~~L~   97 (132)
                      ||.+.....|+.+|++.++..+|.|+.++.+.|...+. +.++++|++.||..||.+++.|++|-
T Consensus         1 Mk~d~dv~~is~ea~~lvskAtElFi~~L~~~a~~~a~~~~~~ktl~~~dl~~aV~~~~~f~FL~   65 (72)
T d2byka1           1 MKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEFLL   65 (72)
T ss_dssp             CCSSSSCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHHTCSTTGGGT
T ss_pred             CCCCHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCccccHHHHHHHHccCchhhHHH
Confidence            45556778999999999999999999999999988875 45568999999999999999999887

>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=98.57  E-value=5.7e-08  Score=63.40  Aligned_cols=64  Identities=17%  Similarity=0.198  Sum_probs=59.1

Q ss_pred             chhHHHHHHhhC-CcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcC
Q psy3662          26 PVGRIHRLLRKG-NYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRN   89 (132)
Q Consensus        26 Pv~ri~rllk~~-~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~   89 (132)
                      |.++|.|+|++. ....+|+.+|...++.+.|.|+..+...|...|...++++|+++||..|+.+
T Consensus         1 P~a~i~ri~K~~~p~~~~iskeA~~~i~~aae~FI~~lt~~A~~~a~~~~rKtI~~~dv~~Al~~   65 (89)
T d2bykb1           1 PNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTE   65 (89)
T ss_dssp             CCSHHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHH
T ss_pred             CccHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence            889999999963 3567999999999999999999999999999999999999999999999964

>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=97.63  E-value=8.3e-05  Score=48.77  Aligned_cols=68  Identities=25%  Similarity=0.248  Sum_probs=60.1

Q ss_pred             ccccccchhHHHHHHhhC----CcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhh
Q psy3662          20 RAGLQFPVGRIHRLLRKG----NYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAI   87 (132)
Q Consensus        20 ragl~fPv~ri~rllk~~----~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI   87 (132)
                      -.+|.+|-..+.|++++-    ....|+..+|...|-.+.|.++-++++.|...|.|.++.+|+|.|+++|.
T Consensus        17 st~lLIpk~pF~RLVRei~~~~~~~~r~~~~Al~aLQea~E~yLv~lfeda~~~a~HakRvTl~~kD~~Lar   88 (95)
T d1tzyc_          17 STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR   88 (95)
T ss_dssp             CCSCCSCHHHHHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHH
T ss_pred             CcccccccccHHHHHHHHHHhcCCCCEeeHHHHHHHHHHHHHHHHHHHHHhHHHHHhcCCCcCCHHHHHHHH
Confidence            357889999999999862    12349999999999999999999999999999999999999999999875

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

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

Probab=97.44  E-value=0.00032  Score=43.44  Aligned_cols=66  Identities=12%  Similarity=0.177  Sum_probs=60.3

Q ss_pred             ccccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          22 GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        22 gl~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      +-.||..-|+-+...- +..-++.+++-.|+-=+||=+.||++.|.+.-+|.+|+++|.+||..|++
T Consensus         4 ~S~~~~esik~iAeS~-Gi~~l~de~a~~LA~DveYRl~eiiQeA~KFMrhskR~~Ltt~Did~ALk   69 (70)
T d1tafb_           4 GSSISAESMKVIAESI-GVGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLK   69 (70)
T ss_dssp             SCCCCHHHHHHHHHHT-TCCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC
T ss_pred             cccCCHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcCcHHHHHHHHc
Confidence            4578999999888774 57789999999999999999999999999999999999999999999874

>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=97.35  E-value=0.00022  Score=46.39  Aligned_cols=60  Identities=20%  Similarity=0.266  Sum_probs=54.8

Q ss_pred             HHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          29 RIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        29 ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      .|+|.|++-.-...|++.|...|..++..+...|...|...|+.+++++|+.++|+.|+.
T Consensus         8 Yi~kVLKqVhp~~giS~kam~imnsfvndiferIa~EA~~La~~~kr~TitsreIqtAvr   67 (92)
T d1tzyb_           8 YVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVR   67 (92)
T ss_dssp             HHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             HHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHH
Confidence            588999985445589999999999999999999999999999999999999999999984

>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=97.16  E-value=0.0004  Score=44.89  Aligned_cols=64  Identities=23%  Similarity=0.387  Sum_probs=55.7

Q ss_pred             ccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhc-CCceechhhhhhhhc
Q psy3662          24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDN-KKTRIIPRHIQLAIR   88 (132)
Q Consensus        24 ~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~-~~k~Itp~~i~~AI~   88 (132)
                      .||-+.|+|++..- ..+.|+....+.++++-.-|+.||+|.|....... ....|.|+||..|..
T Consensus        16 ~~~K~~vkrl~~~~-~g~sv~~~v~i~v~giaKvFvGEiVE~A~~V~~~~~e~~PL~P~HireA~r   80 (89)
T d1bh9b_          16 AFPKAAIKRLIQSI-TGTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVR   80 (89)
T ss_dssp             CCCHHHHHHHHHHH-HSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHH-cCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCcHHHHHHHH
Confidence            38889999999985 57899999999999999999999999999886554 445799999999874

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

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

Probab=96.52  E-value=0.005  Score=37.63  Aligned_cols=58  Identities=19%  Similarity=0.126  Sum_probs=42.9

Q ss_pred             HHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          30 IHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        30 i~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      |+-+|++. ...-...-++.-|--..--.+.+||+-|.-++.|.+++.|+.+|+++||+
T Consensus         7 i~~iL~~~-GV~~yeprV~~qlLef~yRYtt~VL~DA~vys~HA~k~~id~dDVkLAi~   64 (68)
T d1tafa_           7 IMSILKEL-NVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLATE   64 (68)
T ss_dssp             HHHHHHHT-TCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHH
T ss_pred             HHHHHHHc-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHH
Confidence            66677775 33333333444444444556889999999999999999999999999996

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

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

Probab=95.31  E-value=0.024  Score=35.01  Aligned_cols=66  Identities=17%  Similarity=0.296  Sum_probs=57.7

Q ss_pred             cchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhhhhcCc
Q psy3662          25 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQLAIRND   90 (132)
Q Consensus        25 fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D   90 (132)
                      |.-.++..++++-.-...+..++-..|..+.+-|+..++..|...|++-+..+|.+.||++.+..+
T Consensus         4 l~K~~L~eLv~~idp~~~ld~~vee~ll~iADdFV~~V~~~ac~lAKhR~s~~le~kDvql~LeR~   69 (74)
T d1h3ob_           4 LTKKKLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLERQ   69 (74)
T ss_dssp             SCHHHHHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCcHHHHHHHHHhh
Confidence            445678888888655678999999999999999999999999999999999999999999876543

>d1k6ka_ a.174.1.1 (A:) N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone
species: Escherichia coli [TaxId: 562]

Probab=91.61  E-value=0.11  Score=33.98  Aligned_cols=39  Identities=21%  Similarity=0.289  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHHHHhcCCceechhhhhhhhcCcHHHHhhh
Q psy3662          59 VAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEELNKLL   97 (132)
Q Consensus        59 ~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~EL~~L~   97 (132)
                      +.++|..|.+.|...+...|+|+||-+|+-+|++...++
T Consensus         6 l~~~l~~A~~~A~~~~h~~i~~EHLL~aLl~~~~~~~~l   44 (142)
T d1k6ka_           6 LELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREAL   44 (142)
T ss_dssp             HHHHHHHHHHHHHHHTBSEECHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCcccHHHHHHHHHhchhHHHHH
Confidence            356788999999999999999999999999998865544

>d1wwia1 a.22.1.4 (A:1-148) Hypothetical protein TTHA1479 {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Bacterial histone-fold protein
domain: Hypothetical protein TTHA1479
species: Thermus thermophilus [TaxId: 274]

Probab=91.51  E-value=0.28  Score=33.67  Aligned_cols=61  Identities=18%  Similarity=0.248  Sum_probs=53.0

Q ss_pred             ccchhHHHHHHhhCCcccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCceechhhhhh
Q psy3662          24 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVLEYLVAEVLELAGNAARDNKKTRIIPRHIQL   85 (132)
Q Consensus        24 ~fPv~ri~rllk~~~~~~RVs~~A~vyLaavLEyl~~eIlelA~~~A~~~~~k~Itp~~i~~   85 (132)
                      ..|+++++++++.. ..--|..+-.--+..+++--+.+++..|-..|+.+++..|.|.|+-.
T Consensus         2 ~m~~~k~e~~FR~a-a~LdvdK~d~~r~~d~V~~Kl~DLllva~~~A~~n~RdvI~~~DLPI   62 (148)
T d1wwia1           2 LMKVAEFERLFRQA-AGLDVDKNDLKRVSDFLRNKLYDLLAVAERNAKYNGRDLIFEPDLPI   62 (148)
T ss_dssp             CSCHHHHHHHHHHH-HCCCCCGGGHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECGGGSCC
T ss_pred             CCcHHHHHHHHHHH-hccCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeeccccCCc
Confidence            46899999999985 34467888888889999999999999999999999999999999753

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

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

Probab=88.93  E-value=0.19  Score=35.12  Aligned_cols=31  Identities=13%  Similarity=0.184  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHHhcCCceechhhhhhhhcCc
Q psy3662          60 AEVLELAGNAARDNKKTRIIPRHIQLAIRND   90 (132)
Q Consensus        60 ~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D   90 (132)
                      -+++..|...|...+...||++|++.|+..|
T Consensus       257 i~~l~~a~~~A~~~~~~~It~~~V~~A~~e~  287 (287)
T d1w5sa2         257 IVALKMACEMAEAMGRDSLSEDLVRKAVSEN  287 (287)
T ss_dssp             HHHHHHHHHHHHHTTCSSCCHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcCCCCCCHHHHHHHHhcC
Confidence            3578888888988899999999999998754

>d1khya_ a.174.1.1 (A:) N-terminal domain of ClpB (heat shock protein F84.1) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal domain of ClpB (heat shock protein F84.1)
species: Escherichia coli [TaxId: 562]

Probab=86.80  E-value=0.25  Score=31.92  Aligned_cols=39  Identities=28%  Similarity=0.266  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHHhcCCceechhhhhhhhcCcHH--HHhhh
Q psy3662          59 VAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEE--LNKLL   97 (132)
Q Consensus        59 ~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~E--L~~L~   97 (132)
                      +.+++..|-..|...+...|+|+||-+|+-+|++  ...++
T Consensus         7 ~~~~l~~A~~~A~~~~h~~v~~eHlL~all~~~~~~~~~iL   47 (139)
T d1khya_           7 FQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLL   47 (139)
T ss_dssp             HHHHHHHHHHHHHHTTCSSBCHHHHHHHHHTCTTCSHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCcccHHHHHHHHHhCcccHHHHHH
Confidence            4578899999999999999999999999987654  34444

>d1qvra1 a.174.1.1 (A:4-148) N-terminal domain of ClpB (heat shock protein F84.1) {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal domain of ClpB (heat shock protein F84.1)
species: Thermus thermophilus [TaxId: 274]

Probab=86.35  E-value=0.36  Score=31.99  Aligned_cols=40  Identities=28%  Similarity=0.228  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHHHhcCCceechhhhhhhhcCcHH--HHhhhc
Q psy3662          59 VAEVLELAGNAARDNKKTRIIPRHIQLAIRNDEE--LNKLLN   98 (132)
Q Consensus        59 ~~eIlelA~~~A~~~~~k~Itp~~i~~AI~~D~E--L~~L~~   98 (132)
                      +.++++.|-+.|...+...|+|+||-.|+-+|++  +..++.
T Consensus         7 a~~~l~~A~~~A~~~~~~~i~~~HlL~all~~~~~~~~~iL~   48 (145)
T d1qvra1           7 AREALAQAQVLAQRMKHQAIDLPHLWAVLLKDERSLAWRLLE   48 (145)
T ss_dssp             HHHHHHHHHHHHHHTTCSEECHHHHHHHHCCSSSSHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCcccHHHHHHHHHcCCcchHHHHHH
Confidence            4578999999999999999999999999987664  566664

>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=83.94  E-value=1  Score=30.79  Aligned_cols=29  Identities=21%  Similarity=0.389  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHHHhcCCceechhhhhhhhc
Q psy3662          60 AEVLELAGNAARDNKKTRIIPRHIQLAIR   88 (132)
Q Consensus        60 ~eIlelA~~~A~~~~~k~Itp~~i~~AI~   88 (132)
                      .++++.|...|...++.+|+++||+.|..
T Consensus       243 ~~ll~~a~~~A~~~~~~~I~~edv~~A~~  271 (276)
T d1fnna2         243 IDILYRSAYAAQQNGRKHIAPEDVRKSSK  271 (276)
T ss_dssp             HHHHHHHHHHHHHTTCSSCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCcCHHHHHHHHH
Confidence            46778898899999999999999999874