Citrus Sinensis ID: 032523

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------14
Protein Sequence
MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGKGREDIGSASQEF
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHcccEEEccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccHHHHHcccccHHHHHHHHHHcccccEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEcHHHHHHHHHHcHHHHHHcccEEEccccccccccHHHccccccccccccccccccc
Coil and Loop (DISEMBL)
mssagstkggrgkpkstksisrshkaglqfpVGRIARFLKAGkyadrvgagaPVYLSAVLEYLAAEVLELAGnaardnkknrivprHIQLAVRNDEELSKLLGTVtianggvlpnihqnllprkmgkgredigsasqef
Flexible Loop (DISEMBL)
mssagstkggrgkpkstksisrshkaglqfpvGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAgnaardnkknrivPRHIQLAVRNDEELSKLLGTvtianggvlpnihqnllprkmgkgredigsasqef
Low Complexity Region (SEG)
MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPvylsavleylaaevlelaGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGKGREDIGSASQEF
Disordered region (IsUnstruct)
**************************GLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNL*******************
Disordered Region (DISOPRED)
****************************QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNI***********************
Disordered Region (DISEMBL)
************************KAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMG*************
Disordered Region (DISPRO)
**************************GLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPR****************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGKGREDIGSASQEF
Positional Conservation
no confident homologs detected

---

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	139	2.2.26 [Sep-21-2011]
O65759	139	Histone H2AX OS=Cicer ari	N/A	no	1.0	1.0	0.884	4e-67
Q9S9K7	142	Probable histone H2AXb OS	yes	no	1.0	0.978	0.880	5e-66
O04848	142	Probable histone H2AXa OS	yes	no	0.978	0.957	0.889	9e-66
P35063	138	Histone H2AX OS=Picea abi	N/A	no	0.992	1.0	0.884	3e-64
Q2QPG9	138	Probable histone H2AXb OS	yes	no	0.863	0.869	0.891	2e-56
A2ZL69	138	Probable histone H2AXb OS	N/A	no	0.863	0.869	0.891	2e-56
Q8LLP5	137	Probable histone H2AXa OS	no	no	0.906	0.919	0.866	5e-55
A2XLI0	137	Probable histone H2AXa OS	N/A	no	0.906	0.919	0.866	5e-55
Q9LD28	130	Histone H2A.6 OS=Arabidop	no	no	0.920	0.984	0.796	5e-51
O81826	131	Probable histone H2A.3 OS	no	no	0.863	0.916	0.822	5e-51

>sp|O65759|H2AX_CICAR Histone H2AX OS=Cicer arietinum GN=HIS2A PE=2 SV=1

 Score =  252 bits (644), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 123/139 (88%), Positives = 133/139 (95%)

Query: 1   MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVL 60
           MSS  +TKGGRGKPK++KS+SRS KAGLQFPVGRIARFLKAGKYA+RVGAGAPVYLSAVL
Sbjct: 1   MSSTATTKGGRGKPKASKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVL 60

Query: 61  EYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNL 120
           EYLAAEVLELAGNAARDNK NRIVPRHIQLAVRNDEELSKLLG+VTIANGGVLPNIHQ L
Sbjct: 61  EYLAAEVLELAGNAARDNKNNRIVPRHIQLAVRNDEELSKLLGSVTIANGGVLPNIHQTL 120

Query: 121 LPRKMGKGREDIGSASQEF 139
           LP+K+GKG+ +IGSASQEF
Sbjct: 121 LPKKVGKGKGEIGSASQEF 139

Variant histone H2A which replaces conventional H2A in a subset of nucleosomes. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. Required for checkpoint-mediated arrest of cell cycle progression in response to low doses of ionizing radiation and for efficient repair of DNA double strand breaks (DSBs) specifically when modified by C-terminal phosphorylation.
Cicer arietinum (taxid: 3827)

>sp|Q9S9K7|H2AXB_ARATH Probable histone H2AXb OS=Arabidopsis thaliana GN=At1g54690 PE=1 SV=1

 Score =  249 bits (635), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 125/142 (88%), Positives = 133/142 (93%), Gaps = 3/142 (2%)

Query: 1   MSS---AGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLS 57
           MSS   +G+TKGGRGKPK+TKS+SRS KAGLQFPVGRIARFLKAGKYA+RVGAGAPVYLS
Sbjct: 1   MSSGAGSGTTKGGRGKPKATKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLS 60

Query: 58  AVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIH 117
           AVLEYLAAEVLELAGNAARDNKK RIVPRHIQLAVRNDEELSKLLG+VTIANGGVLPNIH
Sbjct: 61  AVLEYLAAEVLELAGNAARDNKKTRIVPRHIQLAVRNDEELSKLLGSVTIANGGVLPNIH 120

Query: 118 QNLLPRKMGKGREDIGSASQEF 139
           Q LLP K+GK + DIGSASQEF
Sbjct: 121 QTLLPSKVGKNKGDIGSASQEF 142

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

Arabidopsis thaliana (taxid: 3702)

>sp|O04848|H2AXA_ARATH Probable histone H2AXa OS=Arabidopsis thaliana GN=At1g08880 PE=1 SV=1

 Score =  248 bits (632), Expect = 9e-66,   Method: Compositional matrix adjust.
 Identities = 121/136 (88%), Positives = 130/136 (95%)

Query: 4   AGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYL 63
           +G+TKGGRGKPK+TKS+SRS KAGLQFPVGRIARFLK+GKYA+RVGAGAPVYLSAVLEYL
Sbjct: 7   SGTTKGGRGKPKATKSVSRSSKAGLQFPVGRIARFLKSGKYAERVGAGAPVYLSAVLEYL 66

Query: 64  AAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPR 123
           AAEVLELAGNAARDNKK RIVPRHIQLAVRNDEELSKLLG+VTIANGGVLPNIHQ LLP 
Sbjct: 67  AAEVLELAGNAARDNKKTRIVPRHIQLAVRNDEELSKLLGSVTIANGGVLPNIHQTLLPS 126

Query: 124 KMGKGREDIGSASQEF 139
           K+GK + DIGSASQEF
Sbjct: 127 KVGKNKGDIGSASQEF 142

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

Arabidopsis thaliana (taxid: 3702)

>sp|P35063|H2AX_PICAB Histone H2AX OS=Picea abies PE=2 SV=1

 Score =  243 bits (619), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 123/139 (88%), Positives = 131/139 (94%), Gaps = 1/139 (0%)

Query: 1   MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVL 60
           MSS+G+ KGGRGK KSTKS+SRS KAGLQFPVGRIARFLKAGKYA+RVGAGAPVYL+AVL
Sbjct: 1   MSSSGA-KGGRGKAKSTKSVSRSQKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLAAVL 59

Query: 61  EYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNL 120
           EYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLG VTIANGGVLPNIHQ L
Sbjct: 60  EYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGAVTIANGGVLPNIHQVL 119

Query: 121 LPRKMGKGREDIGSASQEF 139
           LP+K GK + +IGSASQEF
Sbjct: 120 LPKKSGKDKGEIGSASQEF 138

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

Picea abies (taxid: 3329)

>sp|Q2QPG9|H2AXB_ORYSJ Probable histone H2AXb OS=Oryza sativa subsp. japonica GN=Os12g0530000 PE=2 SV=1

 Score =  217 bits (552), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 107/120 (89%), Positives = 113/120 (94%)

Query: 20  ISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNK 79
           +SRS KAGLQFPVGRIAR+LKAGKYA+RVGAGAPVYLSAVLEYLAAEVLELAGNAARDNK
Sbjct: 19  VSRSSKAGLQFPVGRIARYLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNK 78

Query: 80  KNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGKGREDIGSASQEF 139
           KNRIVPRHIQLAVRNDEELS+LLG VTIA GGVLPNIHQ LLP+K GK + DIGSASQEF
Sbjct: 79  KNRIVPRHIQLAVRNDEELSRLLGAVTIAAGGVLPNIHQTLLPKKGGKDKADIGSASQEF 138

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

Oryza sativa subsp. japonica (taxid: 39947)

>sp|A2ZL69|H2AXB_ORYSI Probable histone H2AXb OS=Oryza sativa subsp. indica GN=OsI_037312 PE=3 SV=1

 Score =  217 bits (552), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 107/120 (89%), Positives = 113/120 (94%)

Query: 20  ISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNK 79
           +SRS KAGLQFPVGRIAR+LKAGKYA+RVGAGAPVYLSAVLEYLAAEVLELAGNAARDNK
Sbjct: 19  VSRSSKAGLQFPVGRIARYLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNK 78

Query: 80  KNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGKGREDIGSASQEF 139
           KNRIVPRHIQLAVRNDEELS+LLG VTIA GGVLPNIHQ LLP+K GK + DIGSASQEF
Sbjct: 79  KNRIVPRHIQLAVRNDEELSRLLGAVTIAAGGVLPNIHQTLLPKKGGKDKADIGSASQEF 138

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

Oryza sativa subsp. indica (taxid: 39946)

>sp|Q8LLP5|H2AXA_ORYSJ Probable histone H2AXa OS=Oryza sativa subsp. japonica GN=Os03g0721900 PE=3 SV=1

 Score =  212 bits (540), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 110/127 (86%), Positives = 118/127 (92%), Gaps = 1/127 (0%)

Query: 13  KPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAG 72
           K K+TK++SRS KAGLQFPVGRIAR+LKAGKYA+RVGAGAPVYLSAVLEYLAAEVLELAG
Sbjct: 12  KAKTTKAVSRSSKAGLQFPVGRIARYLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAG 71

Query: 73  NAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGKGREDI 132
           NAARDNKKNRIVPRHIQLAVRNDEELS+LLGTVTIA GGVLPNI Q LLP+K   G+ DI
Sbjct: 72  NAARDNKKNRIVPRHIQLAVRNDEELSRLLGTVTIAAGGVLPNIQQVLLPKKG-GGKGDI 130

Query: 133 GSASQEF 139
           GSASQEF
Sbjct: 131 GSASQEF 137

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

Oryza sativa subsp. japonica (taxid: 39947)

>sp|A2XLI0|H2AXA_ORYSI Probable histone H2AXa OS=Oryza sativa subsp. indica GN=OsI_012923 PE=3 SV=1

 Score =  212 bits (540), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 110/127 (86%), Positives = 118/127 (92%), Gaps = 1/127 (0%)

Query: 13  KPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAG 72
           K K+TK++SRS KAGLQFPVGRIAR+LKAGKYA+RVGAGAPVYLSAVLEYLAAEVLELAG
Sbjct: 12  KAKTTKAVSRSSKAGLQFPVGRIARYLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAG 71

Query: 73  NAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGKGREDI 132
           NAARDNKKNRIVPRHIQLAVRNDEELS+LLGTVTIA GGVLPNI Q LLP+K   G+ DI
Sbjct: 72  NAARDNKKNRIVPRHIQLAVRNDEELSRLLGTVTIAAGGVLPNIQQVLLPKKG-GGKGDI 130

Query: 133 GSASQEF 139
           GSASQEF
Sbjct: 131 GSASQEF 137

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

Oryza sativa subsp. indica (taxid: 39946)

>sp|Q9LD28|H2A6_ARATH Histone H2A.6 OS=Arabidopsis thaliana GN=RAT5 PE=1 SV=1

 Score =  199 bits (505), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 106/133 (79%), Positives = 113/133 (84%), Gaps = 5/133 (3%)

Query: 1   MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVL 60
           M+  G T G  G  K+T   SRS KAGLQFPVGRIARFLKAGKYA+RVGAGAPVYL+AVL
Sbjct: 1   MAGRGKTLGSGGAKKAT---SRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLAAVL 57

Query: 61  EYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNL 120
           EYLAAEVLELAGNAARDNKK RIVPRHIQLAVRNDEELSKLLG VTIANGGV+PNIH  L
Sbjct: 58  EYLAAEVLELAGNAARDNKKTRIVPRHIQLAVRNDEELSKLLGDVTIANGGVMPNIHNLL 117

Query: 121 LPRKMG--KGRED 131
           LP+K G  K +ED
Sbjct: 118 LPKKAGASKPQED 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. Required for the T-DNA integration step of plant transformation by Agrobacterium. May play an important role in illegitimate recombination.

Arabidopsis thaliana (taxid: 3702)

>sp|O81826|H2A3_ARATH Probable histone H2A.3 OS=Arabidopsis thaliana GN=At4g27230 PE=1 SV=1

 Score =  199 bits (505), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 102/124 (82%), Positives = 108/124 (87%), Gaps = 4/124 (3%)

Query: 10  GRGKP----KSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAA 65
           GRGK      + KS SRS KAGLQFPVGRIARFLKAGKYA+RVGAGAPVYL+AVLEYLAA
Sbjct: 3   GRGKQLGSGAAKKSTSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLAAVLEYLAA 62

Query: 66  EVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKM 125
           EVLELAGNAARDNKK RIVPRHIQLAVRNDEELSKLLG VTIANGGV+PNIH  LLP+K 
Sbjct: 63  EVLELAGNAARDNKKTRIVPRHIQLAVRNDEELSKLLGDVTIANGGVMPNIHNLLLPKKA 122

Query: 126 GKGR 129
           G  +
Sbjct: 123 GSSK 126

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.

Arabidopsis thaliana (taxid: 3702)

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	139
357512103	139	Histone H2A [Medicago truncatula] gi|357	1.0	1.0	0.906	1e-66
225451096	139	PREDICTED: histone H2AX [Vitis vinifera]	1.0	1.0	0.906	1e-66
449435726	140	PREDICTED: probable histone H2AXb-like [	0.992	0.985	0.913	1e-66
449462308	139	PREDICTED: histone H2AX-like [Cucumis sa	1.0	1.0	0.906	4e-66
224131422	142	histone 2 [Populus trichocarpa] gi|22283	0.964	0.943	0.925	6e-66
351724209	140	uncharacterized protein LOC100305465 [Gl	0.992	0.985	0.898	1e-65
224123274	142	histone 2 [Populus trichocarpa] gi|22285	0.964	0.943	0.917	3e-65
255559382	139	histone h2a, putative [Ricinus communis]	0.992	0.992	0.921	3e-65
15214035	139	RecName: Full=Histone H2AX gi|3204129|em	1.0	1.0	0.884	3e-65
297849188	142	hypothetical protein ARALYDRAFT_888122 [	0.978	0.957	0.904	1e-64

>gi|357512103|ref|XP_003626340.1| Histone H2A [Medicago truncatula] gi|357512107|ref|XP_003626342.1| Histone H2A [Medicago truncatula] gi|124360158|gb|ABN08174.1| Histone H2A; Histone-fold [Medicago truncatula] gi|124360160|gb|ABN08176.1| Histone H2A; Histone-fold [Medicago truncatula] gi|355501355|gb|AES82558.1| Histone H2A [Medicago truncatula] gi|355501357|gb|AES82560.1| Histone H2A [Medicago truncatula] gi|388498640|gb|AFK37386.1| unknown [Medicago truncatula]

 Score =  257 bits (657), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 126/139 (90%), Positives = 134/139 (96%)

Query: 1   MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVL 60
           MSS G+TKGGRGKPK+ KS+SRS KAGLQFPVGRIARFLKAGKYA+RVGAGAPVYLSAVL
Sbjct: 1   MSSTGTTKGGRGKPKAAKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVL 60

Query: 61  EYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNL 120
           EYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQ L
Sbjct: 61  EYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQTL 120

Query: 121 LPRKMGKGREDIGSASQEF 139
           LP+K+GKG+ +IGSASQEF
Sbjct: 121 LPKKVGKGKGEIGSASQEF 139

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225451096|ref|XP_002265878.1| PREDICTED: histone H2AX [Vitis vinifera] gi|147815277|emb|CAN70026.1| hypothetical protein VITISV_030174 [Vitis vinifera]

 Score =  257 bits (656), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 126/139 (90%), Positives = 134/139 (96%)

Query: 1   MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVL 60
           MSS GSTKGGRGKPK++KS+SRS KAGLQFPVGRIARFLKAGKYA+RVGAGAPVYLSAVL
Sbjct: 1   MSSTGSTKGGRGKPKASKSVSRSQKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVL 60

Query: 61  EYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNL 120
           EYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLG+VTIANGGVLPNIHQ L
Sbjct: 61  EYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGSVTIANGGVLPNIHQTL 120

Query: 121 LPRKMGKGREDIGSASQEF 139
           LP+K GKG+ +IGSASQEF
Sbjct: 121 LPKKTGKGKGEIGSASQEF 139

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449435726|ref|XP_004135645.1| PREDICTED: probable histone H2AXb-like [Cucumis sativus] gi|449485770|ref|XP_004157270.1| PREDICTED: probable histone H2AXb-like [Cucumis sativus]

 Score =  257 bits (656), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 126/138 (91%), Positives = 134/138 (97%)

Query: 2   SSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLE 61
           S+ GSTKGGRGKPK+TKS+SRSHKAGLQFPVGRIARFLKAGKYA+RVGAGAPVYLSAVLE
Sbjct: 3   STGGSTKGGRGKPKATKSVSRSHKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLE 62

Query: 62  YLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLL 121
           YLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLG+VTIANGGVLPNIHQ LL
Sbjct: 63  YLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGSVTIANGGVLPNIHQTLL 122

Query: 122 PRKMGKGREDIGSASQEF 139
           P+K+GK + DIGSASQEF
Sbjct: 123 PKKVGKDKGDIGSASQEF 140

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462308|ref|XP_004148883.1| PREDICTED: histone H2AX-like [Cucumis sativus] gi|449528788|ref|XP_004171385.1| PREDICTED: histone H2AX-like [Cucumis sativus]

 Score =  255 bits (652), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 126/139 (90%), Positives = 132/139 (94%)

Query: 1   MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVL 60
           MSS+ STKGGRGKPK+TKS+SRS KAGLQFPVGRIARFLKAGKYA+RVGAGAPVYLSAVL
Sbjct: 1   MSSSASTKGGRGKPKATKSVSRSQKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVL 60

Query: 61  EYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNL 120
           EYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLG VTIANGGVLPNIHQ L
Sbjct: 61  EYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGDVTIANGGVLPNIHQTL 120

Query: 121 LPRKMGKGREDIGSASQEF 139
           LP+K G G+ DIGSASQEF
Sbjct: 121 LPKKAGSGKGDIGSASQEF 139

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224131422|ref|XP_002328535.1| histone 2 [Populus trichocarpa] gi|222838250|gb|EEE76615.1| histone 2 [Populus trichocarpa]

 Score =  254 bits (650), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 124/134 (92%), Positives = 132/134 (98%)

Query: 6   STKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAA 65
           STKGGRGKPK++KS+SRSHKAGLQFPVGRIARFLKAGKYA+RVGAGAPVYLSAVLEYLAA
Sbjct: 9   STKGGRGKPKASKSVSRSHKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAA 68

Query: 66  EVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKM 125
           EVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLG+VTIANGGVLPNIHQ LLP+K+
Sbjct: 69  EVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGSVTIANGGVLPNIHQTLLPKKV 128

Query: 126 GKGREDIGSASQEF 139
           GKG+ DIGSASQEF
Sbjct: 129 GKGKGDIGSASQEF 142

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351724209|ref|NP_001235770.1| uncharacterized protein LOC100305465 [Glycine max] gi|255625587|gb|ACU13138.1| unknown [Glycine max]

 Score =  254 bits (648), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 124/138 (89%), Positives = 134/138 (97%)

Query: 2   SSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLE 61
           S+ GSTKGGRGKPK++KS+SRS KAGLQFPVGRIARFLKAGKYA+RVGAGAPVYLSAVLE
Sbjct: 3   STGGSTKGGRGKPKASKSVSRSQKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLE 62

Query: 62  YLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLL 121
           YLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLG+VTIANGGVLPNIHQ LL
Sbjct: 63  YLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGSVTIANGGVLPNIHQTLL 122

Query: 122 PRKMGKGREDIGSASQEF 139
           P+K+GKG+ +IGSASQEF
Sbjct: 123 PKKVGKGKGEIGSASQEF 140

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224123274|ref|XP_002319038.1| histone 2 [Populus trichocarpa] gi|222857414|gb|EEE94961.1| histone 2 [Populus trichocarpa]

 Score =  252 bits (644), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 123/134 (91%), Positives = 131/134 (97%)

Query: 6   STKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAA 65
           STKGGRGKPK++KS+SRS KAGLQFPVGRIARFLKAGKYA+RVGAGAPVYL+AVLEYLAA
Sbjct: 9   STKGGRGKPKASKSVSRSQKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLAAVLEYLAA 68

Query: 66  EVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKM 125
           EVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLG+VTIANGGVLPNIHQ LLP+KM
Sbjct: 69  EVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGSVTIANGGVLPNIHQTLLPKKM 128

Query: 126 GKGREDIGSASQEF 139
           GKG+ DIGSASQEF
Sbjct: 129 GKGKGDIGSASQEF 142

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255559382|ref|XP_002520711.1| histone h2a, putative [Ricinus communis] gi|223540096|gb|EEF41673.1| histone h2a, putative [Ricinus communis]

 Score =  252 bits (644), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 129/140 (92%), Positives = 134/140 (95%), Gaps = 2/140 (1%)

Query: 1   MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVL 60
           MSS G+TKGGRGKPKS+KS+SRS KAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVL
Sbjct: 1   MSSGGATKGGRGKPKSSKSVSRSQKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVL 60

Query: 61  EYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNL 120
           EYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNL
Sbjct: 61  EYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNL 120

Query: 121 LPRKMGKGRED-IGSASQEF 139
           LP+K  KG+ D IGSASQEF
Sbjct: 121 LPKK-AKGKGDVIGSASQEF 139

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15214035|sp|O65759.1|H2AX_CICAR RecName: Full=Histone H2AX gi|3204129|emb|CAA07234.1| histone H2A [Cicer arietinum]

 Score =  252 bits (644), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 123/139 (88%), Positives = 133/139 (95%)

Query: 1   MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVL 60
           MSS  +TKGGRGKPK++KS+SRS KAGLQFPVGRIARFLKAGKYA+RVGAGAPVYLSAVL
Sbjct: 1   MSSTATTKGGRGKPKASKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVL 60

Query: 61  EYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNL 120
           EYLAAEVLELAGNAARDNK NRIVPRHIQLAVRNDEELSKLLG+VTIANGGVLPNIHQ L
Sbjct: 61  EYLAAEVLELAGNAARDNKNNRIVPRHIQLAVRNDEELSKLLGSVTIANGGVLPNIHQTL 120

Query: 121 LPRKMGKGREDIGSASQEF 139
           LP+K+GKG+ +IGSASQEF
Sbjct: 121 LPKKVGKGKGEIGSASQEF 139

Source: Cicer arietinum

Species: Cicer arietinum

Genus: Cicer

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297849188|ref|XP_002892475.1| hypothetical protein ARALYDRAFT_888122 [Arabidopsis lyrata subsp. lyrata] gi|297338317|gb|EFH68734.1| hypothetical protein ARALYDRAFT_888122 [Arabidopsis lyrata subsp. lyrata]

 Score =  251 bits (640), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 123/136 (90%), Positives = 131/136 (96%)

Query: 4   AGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYL 63
           +G+TKGGRGKPK+TKS+SRS KAGLQFPVGRIARFLKAGKYA+RVGAGAPVYLSAVLEYL
Sbjct: 7   SGTTKGGRGKPKATKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYL 66

Query: 64  AAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPR 123
           AAEVLELAGNAARDNKK RIVPRHIQLAVRNDEELSKLLG+VTIANGGVLPNIHQNLLP 
Sbjct: 67  AAEVLELAGNAARDNKKTRIVPRHIQLAVRNDEELSKLLGSVTIANGGVLPNIHQNLLPS 126

Query: 124 KMGKGREDIGSASQEF 139
           K+GK + DIGSASQEF
Sbjct: 127 KVGKNKGDIGSASQEF 142

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	139
TAIR|locus:2199486	142	GAMMA-H2AX "gamma histone vari	0.992	0.971	0.753	2.2e-50
TAIR|locus:2036054	142	H2AXA [Arabidopsis thaliana (t	0.992	0.971	0.746	4.6e-50
TAIR|locus:2172119	130	RAT5 "RESISTANT TO AGROBACTERI	0.920	0.984	0.669	2.1e-38
TAIR|locus:2131704	131	HTA2 "histone H2A 2" [Arabidop	0.863	0.916	0.685	1.9e-37
TAIR|locus:2026032	132	HTA10 "histone H2A 10" [Arabid	0.906	0.954	0.651	1e-36
TAIR|locus:2083430	132	HTA13 "histone H2A 13" [Arabid	0.906	0.954	0.666	1e-36
CGD|CAL0000204	132	HTA1 [Candida albicans (taxid:	0.913	0.962	0.598	3.1e-35
UNIPROTKB|Q59SU5	132	HTA1 "Histone H2A.1" [Candida	0.913	0.962	0.598	3.1e-35
CGD|CAL0001183	131	HTA2 [Candida albicans (taxid:	0.906	0.961	0.590	2.2e-34
ASPGD|ASPL0000038151	132	H2A.X [Emericella nidulans (ta	0.892	0.939	0.592	7.4e-34

TAIR|locus:2199486 GAMMA-H2AX "gamma histone variant H2AX" [Arabidopsis thaliana (taxid:3702)]

 Score = 524 (189.5 bits), Expect = 2.2e-50, P = 2.2e-50
 Identities = 104/138 (75%), Positives = 113/138 (81%)

Query:     2 SSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXX 61
             + +G+TKGGRGKPK+TKS+SRS KAGLQFPVGRIARFLKAGKYA+RVGAGAP        
Sbjct:     5 AGSGTTKGGRGKPKATKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLE 64

Query:    62 XXXXXXXXXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLL 121
                       GNAARDNKK RIVPRHIQLAVRNDEELSKLLG+VTIANGGVLPNIHQ LL
Sbjct:    65 YLAAEVLELAGNAARDNKKTRIVPRHIQLAVRNDEELSKLLGSVTIANGGVLPNIHQTLL 124

Query:   122 PRKMGKGREDIGSASQEF 139
             P K+GK + DIGSASQEF
Sbjct:   125 PSKVGKNKGDIGSASQEF 142

GO:0000786 "nucleosome" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IEA;IDA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0005730 "nucleolus" evidence=IDA

GO:0001510 "RNA methylation" evidence=RCA

GO:0008283 "cell proliferation" evidence=RCA

TAIR|locus:2036054 H2AXA [Arabidopsis thaliana (taxid:3702)]

 Score = 521 (188.5 bits), Expect = 4.6e-50, P = 4.6e-50
 Identities = 103/138 (74%), Positives = 113/138 (81%)

Query:     2 SSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXX 61
             + +G+TKGGRGKPK+TKS+SRS KAGLQFPVGRIARFLK+GKYA+RVGAGAP        
Sbjct:     5 AGSGTTKGGRGKPKATKSVSRSSKAGLQFPVGRIARFLKSGKYAERVGAGAPVYLSAVLE 64

Query:    62 XXXXXXXXXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLL 121
                       GNAARDNKK RIVPRHIQLAVRNDEELSKLLG+VTIANGGVLPNIHQ LL
Sbjct:    65 YLAAEVLELAGNAARDNKKTRIVPRHIQLAVRNDEELSKLLGSVTIANGGVLPNIHQTLL 124

Query:   122 PRKMGKGREDIGSASQEF 139
             P K+GK + DIGSASQEF
Sbjct:   125 PSKVGKNKGDIGSASQEF 142

GO:0000786 "nucleosome" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IEA;IDA

GO:0006334 "nucleosome assembly" evidence=IEA

TAIR|locus:2172119 RAT5 "RESISTANT TO AGROBACTERIUM TRANSFORMATION 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 411 (149.7 bits), Expect = 2.1e-38, P = 2.1e-38
 Identities = 89/133 (66%), Positives = 95/133 (71%)

Query:     1 MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXX 60
             M+  G T G  G  K+T   SRS KAGLQFPVGRIARFLKAGKYA+RVGAGAP       
Sbjct:     1 MAGRGKTLGSGGAKKAT---SRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLAAVL 57

Query:    61 XXXXXXXXXXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNL 120
                        GNAARDNKK RIVPRHIQLAVRNDEELSKLLG VTIANGGV+PNIH  L
Sbjct:    58 EYLAAEVLELAGNAARDNKKTRIVPRHIQLAVRNDEELSKLLGDVTIANGGVMPNIHNLL 117

Query:   121 LPRKMG--KGRED 131
             LP+K G  K +ED
Sbjct:   118 LPKKAGASKPQED 130

GO:0000786 "nucleosome" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0005730 "nucleolus" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0009294 "DNA mediated transformation" evidence=IMP

GO:0009611 "response to wounding" evidence=IEP

GO:0009617 "response to bacterium" evidence=IEP

TAIR|locus:2131704 HTA2 "histone H2A 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 402 (146.6 bits), Expect = 1.9e-37, P = 1.9e-37
 Identities = 85/124 (68%), Positives = 90/124 (72%)

Query:    10 GRGKPKST----KSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXX 65
             GRGK   +    KS SRS KAGLQFPVGRIARFLKAGKYA+RVGAGAP            
Sbjct:     3 GRGKQLGSGAAKKSTSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLAAVLEYLAA 62

Query:    66 XXXXXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKM 125
                   GNAARDNKK RIVPRHIQLAVRNDEELSKLLG VTIANGGV+PNIH  LLP+K 
Sbjct:    63 EVLELAGNAARDNKKTRIVPRHIQLAVRNDEELSKLLGDVTIANGGVMPNIHNLLLPKKA 122

Query:   126 GKGR 129
             G  +
Sbjct:   123 GSSK 126

GO:0000786 "nucleosome" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IEA;IDA

GO:0006334 "nucleosome assembly" evidence=IEA

TAIR|locus:2026032 HTA10 "histone H2A 10" [Arabidopsis thaliana (taxid:3702)]

 Score = 395 (144.1 bits), Expect = 1.0e-36, P = 1.0e-36
 Identities = 84/129 (65%), Positives = 91/129 (70%)

Query:     1 MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXX 60
             M+  G T G  G  K  K+ +RS KAGLQFPVGRIARFLK GKYA+RVGAGAP       
Sbjct:     1 MAGRGKTLGS-GSAK--KATTRSSKAGLQFPVGRIARFLKKGKYAERVGAGAPVYLAAVL 57

Query:    61 XXXXXXXXXXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNL 120
                        GNAARDNKK RIVPRHIQLAVRNDEELSKLLG VTIANGGV+PNIH  L
Sbjct:    58 EYLAAEVLELAGNAARDNKKTRIVPRHIQLAVRNDEELSKLLGDVTIANGGVMPNIHNLL 117

Query:   121 LPRKMGKGR 129
             LP+K G  +
Sbjct:   118 LPKKTGASK 126

GO:0000786 "nucleosome" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0005730 "nucleolus" evidence=IDA

GO:0005618 "cell wall" evidence=IDA

TAIR|locus:2083430 HTA13 "histone H2A 13" [Arabidopsis thaliana (taxid:3702)]

 Score = 395 (144.1 bits), Expect = 1.0e-36, P = 1.0e-36
 Identities = 86/129 (66%), Positives = 90/129 (69%)

Query:     1 MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXX 60
             M+  G T G  G  K  KS SRS KAGLQFPVGRIARFLK GKYA RVGAGAP       
Sbjct:     1 MAGRGKTLGS-GVAK--KSTSRSSKAGLQFPVGRIARFLKNGKYATRVGAGAPVYLAAVL 57

Query:    61 XXXXXXXXXXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNL 120
                        GNAARDNKK RIVPRHIQLAVRNDEELSKLLG VTIANGGV+PNIH  L
Sbjct:    58 EYLAAEVLELAGNAARDNKKTRIVPRHIQLAVRNDEELSKLLGDVTIANGGVMPNIHSLL 117

Query:   121 LPRKMGKGR 129
             LP+K G  +
Sbjct:   118 LPKKAGASK 126

GO:0000786 "nucleosome" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0008283 "cell proliferation" evidence=RCA

CGD|CAL0000204 HTA1 [Candida albicans (taxid:5476)]

 Score = 381 (139.2 bits), Expect = 3.1e-35, P = 3.1e-35
 Identities = 79/132 (59%), Positives = 93/132 (70%)

Query:     9 GGRGKPKSTK--SISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXXX 66
             GG+GK  +++  S SRS KAGL FPVGR+ R L+ G YA R+G+GAP             
Sbjct:     3 GGKGKAGTSEKASTSRSAKAGLTFPVGRVHRLLRKGNYAQRIGSGAPVYLTSVLEYLAAE 62

Query:    67 XXXXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMG 126
                  GNAARDNKK+RI+PRH+QLA+RNDEEL+KLLG VTIA GGVLPNIHQNLLP+K G
Sbjct:    63 ILELAGNAARDNKKSRIIPRHLQLAIRNDEELNKLLGDVTIAQGGVLPNIHQNLLPKKSG 122

Query:   127 KGREDIGSASQE 138
             KG      ASQE
Sbjct:   123 KGGV---KASQE 131

GO:0003677 "DNA binding" evidence=IDA

GO:0005634 "nucleus" evidence=IEA

GO:0042770 "signal transduction in response to DNA damage" evidence=IEA

GO:0006975 "DNA damage induced protein phosphorylation" evidence=IEA

GO:0034501 "protein localization to kinetochore" evidence=IEA

UNIPROTKB|Q59SU5 HTA1 "Histone H2A.1" [Candida albicans SC5314 (taxid:237561)]

 Score = 381 (139.2 bits), Expect = 3.1e-35, P = 3.1e-35
 Identities = 79/132 (59%), Positives = 93/132 (70%)

Query:     9 GGRGKPKSTK--SISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXXX 66
             GG+GK  +++  S SRS KAGL FPVGR+ R L+ G YA R+G+GAP             
Sbjct:     3 GGKGKAGTSEKASTSRSAKAGLTFPVGRVHRLLRKGNYAQRIGSGAPVYLTSVLEYLAAE 62

Query:    67 XXXXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMG 126
                  GNAARDNKK+RI+PRH+QLA+RNDEEL+KLLG VTIA GGVLPNIHQNLLP+K G
Sbjct:    63 ILELAGNAARDNKKSRIIPRHLQLAIRNDEELNKLLGDVTIAQGGVLPNIHQNLLPKKSG 122

Query:   127 KGREDIGSASQE 138
             KG      ASQE
Sbjct:   123 KGGV---KASQE 131

GO:0003677 "DNA binding" evidence=IDA

CGD|CAL0001183 HTA2 [Candida albicans (taxid:5476)]

 Score = 373 (136.4 bits), Expect = 2.2e-34, P = 2.2e-34
 Identities = 78/132 (59%), Positives = 92/132 (69%)

Query:     9 GGRGKPKSTK--SISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXXX 66
             GG+GK  S++  S SRS KAGL FPVGR+ R L+ G YA R+G+GAP             
Sbjct:     3 GGKGKAGSSEKASTSRSAKAGLTFPVGRVHRLLRKGNYAQRIGSGAPVYLTSVLEYLAAE 62

Query:    67 XXXXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMG 126
                  GNAARDNKK+RI+PRH+QLA+RNDEEL+KLLG VTIA GGVLPNIHQ+LLP K  
Sbjct:    63 ILELAGNAARDNKKSRIIPRHLQLAIRNDEELNKLLGDVTIAQGGVLPNIHQSLLPAKKA 122

Query:   127 KGREDIGSASQE 138
             K     G+ASQE
Sbjct:   123 KA----GAASQE 130

GO:0031298 "replication fork protection complex" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

ASPGD|ASPL0000038151 H2A.X [Emericella nidulans (taxid:162425)]

 Score = 368 (134.6 bits), Expect = 7.4e-34, P = 7.4e-34
 Identities = 77/130 (59%), Positives = 90/130 (69%)

Query:     9 GGR--GKPKSTKSI-SRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXX 65
             GG+  GK   +K+  SRS KAGL FPVGR+ R L+ G YA RVGAGAP            
Sbjct:     3 GGKSGGKASGSKNAQSRSSKAGLAFPVGRVHRLLRKGNYAQRVGAGAPVYLAAVLEYLAA 62

Query:    66 XXXXXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKM 125
                   GNAARDNKK RI+PRH+QLA+RNDEEL+KLLG VTIA GGVLPNIHQNLLP+K 
Sbjct:    63 EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGHVTIAQGGVLPNIHQNLLPKKT 122

Query:   126 ---GKGREDI 132
                GKG +++
Sbjct:   123 PKAGKGSQEL 132

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006975 "DNA damage induced protein phosphorylation" evidence=IEA

GO:0034501 "protein localization to kinetochore" evidence=IEA

GO:0042770 "signal transduction in response to DNA damage" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0000786 "nucleosome" evidence=IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0031298 "replication fork protection complex" evidence=IEA

GO:0031618 "nuclear centromeric heterochromatin" 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)
Q5G578	H2A_MAGO7	No assigned EC number	0.8130	0.7697	0.7867	N/A	no
Q6BKW8	H2A1_DEBHA	No assigned EC number	0.7142	0.9064	0.9692	yes	no
P40282	H2A_PLAFA	No assigned EC number	0.6940	0.9424	0.9924	yes	no
Q875B8	H2A_PODAS	No assigned EC number	0.7563	0.8417	0.8666	yes	no
A5DWF1	H2A1_LODEL	No assigned EC number	0.6917	0.9064	0.9692	N/A	no
A3LXE7	H2A2_PICST	No assigned EC number	0.7067	0.9136	0.9694	yes	no
O65759	H2AX_CICAR	No assigned EC number	0.8848	1.0	1.0	N/A	no
Q6CK59	H2A_KLULA	No assigned EC number	0.6865	0.9280	0.9923	yes	no
P35061	H2A_ACRFO	No assigned EC number	0.7457	0.8489	0.944	N/A	no
P35063	H2AX_PICAB	No assigned EC number	0.8848	0.9928	1.0	N/A	no
A2XLI0	H2AXA_ORYSI	No assigned EC number	0.8661	0.9064	0.9197	N/A	no
P0C953	H2A_ASPNC	No assigned EC number	0.7563	0.8417	0.8731	yes	no
Q2QPG9	H2AXB_ORYSJ	No assigned EC number	0.8916	0.8633	0.8695	yes	no
Q757L4	H2A2_ASHGO	No assigned EC number	0.6791	0.9352	0.9923	yes	no
A2YVE5	H2A3_ORYSI	No assigned EC number	0.8376	0.8129	0.8432	N/A	no
P04735	H2A1_PSAMI	No assigned EC number	0.7627	0.8489	0.944	N/A	no
A3LZZ0	H2A1_PICST	No assigned EC number	0.7142	0.9136	0.9694	yes	no
Q2HH37	H2A_CHAGB	No assigned EC number	0.8130	0.7697	0.7985	N/A	no
O04848	H2AXA_ARATH	No assigned EC number	0.8897	0.9784	0.9577	yes	no
Q43208	H2A4_WHEAT	No assigned EC number	0.8942	0.7482	0.7703	N/A	no
Q9LHQ5	H2A2_ARATH	No assigned EC number	0.8347	0.8417	0.8863	no	no
Q6ZL42	H2A2_ORYSJ	No assigned EC number	0.8376	0.8129	0.8370	no	no
A2ZK26	H2A8_ORYSI	No assigned EC number	0.8532	0.7841	0.8074	N/A	no
A5DBG4	H2A1_PICGU	No assigned EC number	0.6992	0.9064	0.9692	N/A	no
A2ZK29	H2A7_ORYSI	No assigned EC number	0.8623	0.7841	0.8074	N/A	no
P16865	H2A3_VOLCA	No assigned EC number	0.7967	0.8705	0.9379	N/A	no
Q4HTT1	H2A_GIBZE	No assigned EC number	0.8130	0.7697	0.7985	yes	no
Q9S9K7	H2AXB_ARATH	No assigned EC number	0.8802	1.0	0.9788	yes	no
Q8X132	H2A_NEUCR	No assigned EC number	0.7647	0.8345	0.8656	N/A	no
Q9LD28	H2A6_ARATH	No assigned EC number	0.7969	0.9208	0.9846	no	no
P16866	H2A4_VOLCA	No assigned EC number	0.7967	0.8705	0.9379	N/A	no
O74268	H2A_BOTFB	No assigned EC number	0.8037	0.7697	0.7867	N/A	no
Q59SU5	H2A1_CANAL	No assigned EC number	0.7067	0.9208	0.9696	N/A	no
P0C952	H2A_ASPNG	No assigned EC number	0.7563	0.8417	0.8731	yes	no
A2YMC5	H2A1_ORYSI	No assigned EC number	0.8623	0.7841	0.8074	N/A	no
A2YMC6	H2A2_ORYSI	No assigned EC number	0.8376	0.8129	0.8370	N/A	no
Q8LLP5	H2AXA_ORYSJ	No assigned EC number	0.8661	0.9064	0.9197	no	no
Q43312	H2A7_WHEAT	No assigned EC number	0.8264	0.8417	0.8731	N/A	no
A2ZL69	H2AXB_ORYSI	No assigned EC number	0.8916	0.8633	0.8695	N/A	no
Q9C681	H2A1_ARATH	No assigned EC number	0.8181	0.8417	0.8863	no	no
Q74ZL4	H2A1_ASHGO	No assigned EC number	0.6716	0.9352	0.9923	yes	no
A5DJJ2	H2A2_PICGU	No assigned EC number	0.7520	0.8417	0.9	N/A	no
Q9HGX4	H2A_AGABI	No assigned EC number	0.7317	0.8776	0.8776	N/A	no
Q84NJ4	H2A3_ORYSJ	No assigned EC number	0.8376	0.8129	0.8432	no	no
P50567	H2A_CHLRE	No assigned EC number	0.7967	0.8705	0.9379	N/A	no
O81826	H2A3_ARATH	No assigned EC number	0.8225	0.8633	0.9160	no	no
Q6BRG3	H2A2_DEBHA	No assigned EC number	0.7067	0.9136	0.9694	yes	no
P08844	H2A_EMENI	No assigned EC number	0.7563	0.8273	0.8712	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00006109001	RecName- Full=Histone H2A; (139 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00024423001	RecName- Full=Histone H4;; Core component of nucleosome. Nucleosomes wrap and compact DNA into [...] (103 aa)				•			•		0.483
	GSVIVG00036813001	RecName- Full=Histone H3.3;; Variant histone H3 which replaces conventional H3 in a wide range [...] (136 aa)							•		0.483
	GSVIVG00034895001	RecName- Full=Histone H3; (136 aa)							•		0.483
	GSVIVG00027005001	RecName- Full=Histone H3; (156 aa)							•		0.483
	GSVIVG00024652001	RecName- Full=Histone H3; (136 aa)							•		0.483
	GSVIVG00013065001	RecName- Full=Histone H3.3;; Variant histone H3 which replaces conventional H3 in a wide range [...] (136 aa)							•		0.483

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	139
PLN00156	139	PLN00156, PLN00156, histone H2AX; Provisional	1e-81
PLN00157	132	PLN00157, PLN00157, histone H2A; Provisional	4e-69
PTZ00017	134	PTZ00017, PTZ00017, histone H2A; Provisional	7e-69
cd00074	115	cd00074, H2A, Histone 2A; H2A is a subunit of the	1e-62
smart00414	106	smart00414, H2A, Histone 2A	4e-61
PLN00153	129	PLN00153, PLN00153, histone H2A; Provisional	1e-55
COG5262	132	COG5262, HTA1, Histone H2A [Chromatin structure an	1e-51
PLN00154	136	PLN00154, PLN00154, histone H2A; Provisional	3e-38
PTZ00252	134	PTZ00252, PTZ00252, histone H2A; Provisional	4e-28
pfam00125	75	pfam00125, Histone, Core histone H2A/H2B/H3/H4	9e-25
PLN00155	58	PLN00155, PLN00155, histone H2A; Provisional	5e-19
COG5247	113	COG5247, BUR6, Class 2 transcription repressor NC2	5e-07
COG2036	91	COG2036, HHT1, Histones H3 and H4 [Chromatin struc	0.003
pfam00808	65	pfam00808, CBFD_NFYB_HMF, Histone-like transcripti	0.004

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

 Score =  236 bits (602), Expect = 1e-81
 Identities = 123/138 (89%), Positives = 133/138 (96%)

Query: 2   SSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLE 61
           + +G+TKGGRGKPK+TKS+SRS KAGLQFPVGRIARFLKAGKYA+RVGAGAPVYLSAVLE
Sbjct: 2   AGSGTTKGGRGKPKATKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLE 61

Query: 62  YLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLL 121
           YLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLG+VTIA GGVLPNIHQ LL
Sbjct: 62  YLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGSVTIAAGGVLPNIHQTLL 121

Query: 122 PRKMGKGREDIGSASQEF 139
           P+K+GKG+ DIGSASQEF
Sbjct: 122 PKKVGKGKGDIGSASQEF 139

Length = 139

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

 Score =  204 bits (520), Expect = 4e-69
 Identities = 105/128 (82%), Positives = 110/128 (85%), Gaps = 3/128 (2%)

Query: 1   MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVL 60
           MS  G  KGG G  K+T   SRS KAGLQFPVGRIAR+LKAGKYA RVGAGAPVYL+AVL
Sbjct: 1   MSGRGKRKGGGGGKKAT---SRSAKAGLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVL 57

Query: 61  EYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNL 120
           EYLAAEVLELAGNAARDNKK+RIVPRHIQLAVRNDEELSKLLG VTIA GGVLPNIH  L
Sbjct: 58  EYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRNDEELSKLLGGVTIAAGGVLPNIHSVL 117

Query: 121 LPRKMGKG 128
           LP+K GK 
Sbjct: 118 LPKKSGKS 125

Length = 132

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

 Score =  203 bits (518), Expect = 7e-69
 Identities = 90/121 (74%), Positives = 101/121 (83%)

Query: 4   AGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYL 63
            G  K G GK    K +SRS KAGLQFPVGR+ R+LK G+YA RVGAGAPVYL+AVLEYL
Sbjct: 2   GGKGKTGGGKAGKKKPVSRSAKAGLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYL 61

Query: 64  AAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPR 123
            AEVLELAGNAA+DNKK RI PRHIQLA+RNDEEL+KLL  VTIA+GGVLPNIH+ LLP+
Sbjct: 62  TAEVLELAGNAAKDNKKKRITPRHIQLAIRNDEELNKLLAGVTIASGGVLPNIHKVLLPK 121

Query: 124 K 124
           K
Sbjct: 122 K 122

Length = 134

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

 Score =  187 bits (476), Expect = 1e-62
 Identities = 91/115 (79%), Positives = 101/115 (87%), Gaps = 1/115 (0%)

Query: 10  GRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLE 69
           G GK KS K  SRS +AGLQFPVGRI R+LK G+YA+RVGAGAPVYL+AVLEYL AEVLE
Sbjct: 2   GGGKKKSKK-RSRSARAGLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLE 60

Query: 70  LAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRK 124
           LAGNAARDNKK RI PRH+QLAVRNDEEL+KLL  VTIA+GGVLPNIH+ LLP+K
Sbjct: 61  LAGNAARDNKKKRITPRHLQLAVRNDEELNKLLKGVTIASGGVLPNIHKVLLPKK 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|197711 smart00414, H2A, Histone 2A

 Score =  182 bits (465), Expect = 4e-61
 Identities = 84/106 (79%), Positives = 92/106 (86%)

Query: 21  SRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKK 80
           SRS +AGLQFPVGRI R L+ G YA RVGAGAPVYL+AVLEYL AEVLELAGNAARDNKK
Sbjct: 1   SRSARAGLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKK 60

Query: 81  NRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMG 126
            RI PRH+QLA+RNDEEL+KLL  VTIA GGVLPNIH+ LLP+K G
Sbjct: 61  RRITPRHLQLAIRNDEELNKLLKGVTIAQGGVLPNIHKVLLPKKTG 106

Length = 106

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

 Score =  169 bits (430), Expect = 1e-55
 Identities = 98/124 (79%), Positives = 108/124 (87%), Gaps = 2/124 (1%)

Query: 10  GRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLE 69
           G+GK    K++SRS KAGLQFPVGRIAR+LK GKYA+R+GAGAPVYL+AVLEYL AEVLE
Sbjct: 5   GKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLE 64

Query: 70  LAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKM--GK 127
           LAGNAARDNKKNRIVPRHIQLA+RNDEEL KLLG VTIA+GGVLPNIH  LLP+K   GK
Sbjct: 65  LAGNAARDNKKNRIVPRHIQLAIRNDEELGKLLGEVTIASGGVLPNIHAVLLPKKTKGGK 124

Query: 128 GRED 131
           G E 
Sbjct: 125 GEET 128

Length = 129

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

 Score =  160 bits (405), Expect = 1e-51
 Identities = 88/132 (66%), Positives = 99/132 (75%), Gaps = 5/132 (3%)

Query: 8   KGGRGKPKSTKSI-SRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAE 66
            G  GK    +   SRS KAGL FPVGR+ R LK G Y  R+GAGAPVYL+AVLEYLAAE
Sbjct: 4   GGKGGKAADARVSQSRSAKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAE 63

Query: 67  VLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMG 126
           +LELAGNAARDNKK RI+PRH+QLA+RNDEEL+KLLG VTIA GGVLPNI+  LLP+   
Sbjct: 64  ILELAGNAARDNKKKRIIPRHLQLAIRNDEELNKLLGDVTIAQGGVLPNINPGLLPKSSK 123

Query: 127 KGREDIGSASQE 138
           KG       SQE
Sbjct: 124 KG----SKRSQE 131

Length = 132

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

 Score =  126 bits (317), Expect = 3e-38
 Identities = 67/123 (54%), Positives = 83/123 (67%), Gaps = 2/123 (1%)

Query: 6   STKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYAD-RVGAGAPVYLSAVLEYLA 64
           +    +      K  SRS +AGLQFPVGRI R LK    A  RVGA A VY +A+LEYL 
Sbjct: 15  TAAAAKKDKDKKKPTSRSSRAGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLT 74

Query: 65  AEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRK 124
           AEVLELAGNA++D K  RI PRH+QLA+R DEEL  L+   TIA GGV+P+IH++L+ + 
Sbjct: 75  AEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLI-KGTIAGGGVIPHIHKSLINKS 133

Query: 125 MGK 127
             K
Sbjct: 134 TKK 136

Length = 136

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

 Score =  100 bits (250), Expect = 4e-28
 Identities = 54/116 (46%), Positives = 75/116 (64%), Gaps = 2/116 (1%)

Query: 13  KPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAG 72
           K  S     RS KAGL FPVGR+   L+ G+YA R+GA   VY++AVLEYL AE+LEL+ 
Sbjct: 9   KKASKSGSGRSAKAGLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSV 68

Query: 73  NAARDN--KKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMG 126
            AA     K  R+ PR + LAVR+D++L  LL  VT++ GGV+P++++ L  +   
Sbjct: 69  KAAAQQAKKPKRLTPRTVTLAVRHDDDLGSLLKNVTLSRGGVMPSLNKALAKKHKS 124

Length = 134

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

 Score = 89.9 bits (224), Expect = 9e-25
 Identities = 36/75 (48%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 22 RSHKAGLQFPVGRIARFLKAGKYAD-RVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKK 80
           S    L+ P  R+ R LK G YA+ R+ + APV L   LE L  E+LE AG  AR  K+
Sbjct: 1  SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKR 60

Query: 81 NRIVPRHIQLAVRND 95
            I PR IQLAVR D
Sbjct: 61 KTITPRDIQLAVRLD 75

Length = 75

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

 Score = 74.7 bits (183), Expect = 5e-19
 Identities = 41/54 (75%), Positives = 48/54 (88%)

Query: 10 GRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYL 63
          G+GK    K++SRS KAGLQFPVGRIAR+LK GKYA+R+GAGAPVYL+AVLEYL
Sbjct: 5  GKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYL 58

Length = 58

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

 Score = 45.3 bits (107), Expect = 5e-07
 Identities = 20/82 (24%), Positives = 36/82 (43%)

Query: 29  QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHI 88
           +FP+ R+ + ++  +   +VG   PV  S  LE    E++ L+   AR     R+    +
Sbjct: 23  RFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFL 82

Query: 89  QLAVRNDEELSKLLGTVTIANG 110
           + A  +DE+   L       N 
Sbjct: 83  KRATESDEKFDFLKNMEQFKNR 104

Length = 113

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

 Score = 34.6 bits (80), Expect = 0.003
 Identities = 28/85 (32%), Positives = 37/85 (43%), Gaps = 5/85 (5%)

Query: 10 GRGKPKSTKSISRSHKAGLQF-PVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVL 68
          G    K  +   RS    L   PV RI R  KAG  A+RV + A   L   LE    E+ 
Sbjct: 2  GAVGLKEIRRYQRSTDLLLPKAPVRRILR--KAG--AERVSSSAIEELQEALEEYLEEIA 57

Query: 69 ELAGNAARDNKKNRIVPRHIQLAVR 93
          E A   A   K+  +    I+LA++
Sbjct: 58 EDAVELAEHAKRKTVKAEDIKLALK 82

Length = 91

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

 Score = 33.7 bits (78), Expect = 0.004
 Identities = 16/63 (25%), Positives = 28/63 (44%)

Query: 30 FPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQ 89
           P+ R+ R +K+   A R+   A   ++  +E     +   A    +  K+  I   HI+
Sbjct: 3  LPIARVKRIMKSDPDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAEHIK 62

Query: 90 LAV 92
          LAV
Sbjct: 63 LAV 65

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	139
PLN00156	139	histone H2AX; Provisional	100.0
PLN00153	129	histone H2A; Provisional	100.0
PTZ00017	134	histone H2A; Provisional	100.0
PTZ00252	134	histone H2A; Provisional	100.0
PLN00157	132	histone H2A; Provisional	100.0
KOG1756	131	consensus Histone 2A [Chromatin structure and dyna	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	131	consensus Histone 2A [Chromatin structure and dyna	100.0
PLN00155	58	histone H2A; Provisional	99.86
COG5247	113	BUR6 Class 2 transcription repressor NC2, alpha su	99.62
PF00125	75	Histone: Core histone H2A/H2B/H3/H4 histone h2a si	99.55
PLN00035	103	histone H4; Provisional	99.4
KOG1659	224	consensus Class 2 transcription repressor NC2, alp	99.37
PTZ00015	102	histone H4; Provisional	99.26
PF00808	65	CBFD_NFYB_HMF: Histone-like transcription factor (	99.2
smart00803	65	TAF TATA box binding protein associated factor. TA	98.98
COG2036	91	HHT1 Histones H3 and H4 [Chromatin structure and d	98.98
cd00076	85	H4 Histone H4, one of the four histones, along wit	98.85
COG5208	286	HAP5 CCAAT-binding factor, subunit C [Transcriptio	98.74
smart00417	74	H4 Histone H4.	98.73
KOG1657	236	consensus CCAAT-binding factor, subunit C (HAP5) [	98.57
cd07981	72	TAF12 TATA Binding Protein (TBP) Associated Factor	98.25
cd07979	117	TAF9 TATA Binding Protein (TBP) Associated Factor	98.07
KOG3467	103	consensus Histone H4 [Chromatin structure and dyna	97.98
PF02969	66	TAF: TATA box binding protein associated factor (T	97.77
cd08048	85	TAF11 TATA Binding Protein (TBP) Associated Factor	97.69
PLN00158	116	histone H2B; Provisional	97.64
smart00576	77	BTP Bromodomain transcription factors and PHD doma	97.63
cd08050	343	TAF6 TATA Binding Protein (TBP) Associated Factor	97.62
smart00428	105	H3 Histone H3.	97.44
PF04719	90	TAFII28: hTAFII28-like protein conserved region; I	97.1
KOG3219	195	consensus Transcription initiation factor TFIID, s	97.0
KOG0869	168	consensus CCAAT-binding factor, subunit A (HAP3) [	96.81
smart00427	89	H2B Histone H2B.	96.73
PTZ00463	117	histone H2B; Provisional	96.43
PF15511	414	CENP-T: Centromere kinetochore component CENP-T; P	96.42
KOG0871	156	consensus Class 2 transcription repressor NC2, bet	96.22
PF09415	72	CENP-X: CENP-S associating Centromere protein X; I	96.16
PF03847	68	TFIID_20kDa: Transcription initiation factor TFIID	96.11
PF15630	76	CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C	95.92
KOG1658	162	consensus DNA polymerase epsilon, subunit C [Repli	95.67
PF02291	129	TFIID-31kDa: Transcription initiation factor IID,	95.4
PLN00160	97	histone H3; Provisional	95.37
PTZ00018	136	histone H3; Provisional	95.31
PF07524	77	Bromo_TP: Bromodomain associated; InterPro: IPR006	95.27
PLN00121	136	histone H3; Provisional	95.02
KOG0870	172	consensus DNA polymerase epsilon, subunit D [Trans	94.99
PLN00161	135	histone H3; Provisional	94.98
KOG1744	127	consensus Histone H2B [Chromatin structure and dyn	94.47
KOG1142	258	consensus Transcription initiation factor TFIID, s	94.21
PLN00163	59	histone H4; Provisional	93.21
PF02269	93	TFIID-18kDa: Transcription initiation factor IID,	93.04
cd07978	92	TAF13 The TATA Binding Protein (TBP) Associated Fa	93.02
KOG1745	137	consensus Histones H3 and H4 [Chromatin structure	91.48
COG5094	145	TAF9 Transcription initiation factor TFIID, subuni	90.98
KOG3334	148	consensus Transcription initiation factor TFIID, s	84.32
COG5150	148	Class 2 transcription repressor NC2, beta subunit	82.2
COG5251	199	TAF40 Transcription initiation factor TFIID, subun	81.78

>PLN00156 histone H2AX; Provisional

Probab=100.00  E-value=1.2e-51  Score=307.44  Aligned_cols=138  Identities=89%  Similarity=1.307  Sum_probs=127.4

Q ss_pred             CCCCCCCCCCCCCCCCCCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCC
Q 032523            2 SSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKN   81 (139)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~k   81 (139)
                      +|.|.+++||||+++++..|+|+||+|+|||+||+|+|++.+|+.||+++|||||+||||||++||||+|+|.|++++++
T Consensus         2 ~~~~~~~~~~g~~~~~k~~srS~rAgL~FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~   81 (139)
T PLN00156          2 AGSGTTKGGRGKPKATKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKN   81 (139)
T ss_pred             CCCCCCCCCCCcccccCCcCcccccCcccchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence            35677899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccchhhHHHhhhCcHHHHhhhcCceecCCccCCcccccccccccCCCCccCCccCCCC
Q 032523           82 RIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGKGREDIGSASQEF  139 (139)
Q Consensus        82 rItP~hI~~AI~nD~EL~~L~~~~~Ia~ggv~P~i~~~l~~~k~~~~~~~~~~~~~~~  139 (139)
                      +|+|+||++||+||+||+.||+++||++|||+|+||++|+++|.++++.+...++|++
T Consensus        82 RItPrHi~lAIrnDeEL~~Ll~~vTIa~GGV~P~i~~~l~~kk~~~~~~~~~~~~~~~  139 (139)
T PLN00156         82 RIVPRHIQLAVRNDEELSKLLGSVTIAAGGVLPNIHQTLLPKKVGKGKGDIGSASQEF  139 (139)
T ss_pred             cCcHHHHHhhccCcHHHHHHHCCCccCCCccCCCccHhhccccccccccccccccCCC
Confidence            9999999999999999999999999999999999999999999865533333446653

>PLN00153 histone H2A; Provisional

Probab=100.00  E-value=2.2e-49  Score=292.54  Aligned_cols=123  Identities=79%  Similarity=1.190  Sum_probs=115.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 032523            1 MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKK   80 (139)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~   80 (139)
                      |||+|  +   |+..+++..|+|+||||+|||+||+|+|++++|+.||+++|+|||+||||||++||||+|+|.|+++++
T Consensus         1 m~g~~--~---~~~~~~k~~srS~ragL~FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk   75 (129)
T PLN00153          1 MAGRG--K---GKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKK   75 (129)
T ss_pred             CCCCC--C---CCccccCccCcccccCcccchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            88877  2   334456789999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccchhhHHHhhhCcHHHHhhhcCceecCCccCCcccccccccccCCC
Q 032523           81 NRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGKG  128 (139)
Q Consensus        81 krItP~hI~~AI~nD~EL~~L~~~~~Ia~ggv~P~i~~~l~~~k~~~~  128 (139)
                      ++|+|+||++||+||+||+.||+++||++|||+|+||++|+++|.+++
T Consensus        76 ~RItPrHi~lAI~nDeEL~~Ll~~vTIa~GGV~P~i~~~l~~kk~~~~  123 (129)
T PLN00153         76 NRIVPRHIQLAIRNDEELGKLLGEVTIASGGVLPNIHAVLLPKKTKGG  123 (129)
T ss_pred             CccChHHHHhhccCcHHHHHHHCCCccCCCccCCCcchhhcCcccCCC
Confidence            999999999999999999999999999999999999999999987555

>PTZ00017 histone H2A; Provisional

Probab=100.00  E-value=8.2e-49  Score=291.27  Aligned_cols=126  Identities=71%  Similarity=1.074  Sum_probs=116.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 032523            1 MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKK   80 (139)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~   80 (139)
                      |||.| ++ +.|++.+++..|+|+||||+|||+||+|||++++|+.||+++|+|||+||||||++||||+|+|.|+++++
T Consensus         1 ~~~~~-~~-~~~~~~~~k~~srS~ragL~FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk   78 (134)
T PTZ00017          1 KGGKG-KT-GGGKAGKKKPVSRSAKAGLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKK   78 (134)
T ss_pred             CCCCC-cC-CCCcccCcCcccccccCCcccchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            56665 33 23344467899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccchhhHHHhhhCcHHHHhhhcCceecCCccCCcccccccccccCCC
Q 032523           81 NRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGKG  128 (139)
Q Consensus        81 krItP~hI~~AI~nD~EL~~L~~~~~Ia~ggv~P~i~~~l~~~k~~~~  128 (139)
                      ++|+|+||++||+||+||+.||+++||++|||+|+||++|+++|.+++
T Consensus        79 ~RItPrHi~lAI~nDeEL~~Ll~~vtIa~GGV~P~i~~~l~~k~~~~~  126 (134)
T PTZ00017         79 KRITPRHIQLAIRNDEELNKLLAGVTIASGGVLPNIHKVLLPKKSKPK  126 (134)
T ss_pred             CeecHHHHHhhccCcHHHHHHHcCCcccCCccCCCccHhhccCCCCcc
Confidence            999999999999999999999999999999999999999999998666

>PTZ00252 histone H2A; Provisional

Probab=100.00  E-value=1.1e-48  Score=289.64  Aligned_cols=131  Identities=46%  Similarity=0.763  Sum_probs=116.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhh--c
Q 032523            1 MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARD--N   78 (139)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~--~   78 (139)
                      |+ ++  .++| ++.++...++|+||||+|||+||+|||++++|+.||+++|+|||+||||||++||||+|+|.|++  +
T Consensus         1 ~~-~~--~~~~-~~~~~~~~~rS~rAGL~FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~   76 (134)
T PTZ00252          1 MA-TP--KQAK-KKASKSGSGRSAKAGLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAK   76 (134)
T ss_pred             CC-Cc--cchh-hcccccccccccccCccCchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence            44 55  5555 44444444599999999999999999999999999999999999999999999999999999966  6


Q ss_pred             CCCccchhhHHHhhhCcHHHHhhhcCceecCCccCCccccccccc-ccCCCCccCCccCCCC
Q 032523           79 KKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPR-KMGKGREDIGSASQEF  139 (139)
Q Consensus        79 ~~krItP~hI~~AI~nD~EL~~L~~~~~Ia~ggv~P~i~~~l~~~-k~~~~~~~~~~~~~~~  139 (139)
                      ++++|+|+||++||+||+|||.||+++||++|||+|+||++|+++ +.++|    ++|+|++
T Consensus        77 kk~RItPrHi~lAIrNDeEL~~Ll~~vTIa~GGVlP~i~~~l~~k~~~~~~----~~~~~~~  134 (134)
T PTZ00252         77 KPKRLTPRTVTLAVRHDDDLGSLLKNVTLSRGGVMPSLNKALAKKHKSGKK----AKATPSA  134 (134)
T ss_pred             CcccccHHHHHhhccChHHHHHHHcCCccCCCccCCCccHhhccccccCCC----CCCCCCC
Confidence            778999999999999999999999999999999999999999999 55555    6688874

>PLN00157 histone H2A; Provisional

Probab=100.00  E-value=1.2e-48  Score=289.55  Aligned_cols=125  Identities=81%  Similarity=1.154  Sum_probs=115.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 032523            1 MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKK   80 (139)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~   80 (139)
                      |||+| ++.  |++.+++..|+|+||||+|||+||+|+|++++|+.||+++|+|||+||||||++||||+|+|.|++.++
T Consensus         1 ms~~g-~~~--~~~~~~k~~srS~ragL~FPVgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk   77 (132)
T PLN00157          1 MSGRG-KRK--GGGGGKKATSRSAKAGLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKK   77 (132)
T ss_pred             CCCCC-CCC--CCccCcCCcCcccccCcccchHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            89887 321  233566899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccchhhHHHhhhCcHHHHhhhcCceecCCccCCcccccccccccCCC
Q 032523           81 NRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGKG  128 (139)
Q Consensus        81 krItP~hI~~AI~nD~EL~~L~~~~~Ia~ggv~P~i~~~l~~~k~~~~  128 (139)
                      ++|+|+||++||+||+||+.||+++||++|||+|+||++|+++|.+++
T Consensus        78 ~RItPrHi~lAI~nDeEL~~Ll~~vtIa~GGV~P~i~~~ll~kk~~~~  125 (132)
T PLN00157         78 SRIVPRHIQLAVRNDEELSKLLGGVTIAAGGVLPNIHSVLLPKKSGKS  125 (132)
T ss_pred             ccccHHHHhhcccCcHHHHHHHcCceecCCccCCCcchhhcCCCCCCC
Confidence            999999999999999999999999999999999999999999987544

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

Probab=100.00  E-value=9.4e-47  Score=276.45  Aligned_cols=126  Identities=73%  Similarity=1.147  Sum_probs=120.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 032523            1 MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKK   80 (139)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~   80 (139)
                      |||++  ++||++..++...|+|.|++|||||++|+|+|++.+|..||+.+|||||+||||||++||||+|+|+|+++++
T Consensus         1 ~s~~~--k~gk~~~~~~~~~srs~~agl~fPvgri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk   78 (131)
T KOG1756|consen    1 MSGRG--KGGKAKPRAKAKSSRSSRAGLQFPVGRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKK   78 (131)
T ss_pred             CCccC--CCCcccchhhhhcchhhhcccccCHHHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCc
Confidence            77777  8888777778999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccchhhHHHhhhCcHHHHhhhcCceecCCccCCcccccccccccCCC
Q 032523           81 NRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGKG  128 (139)
Q Consensus        81 krItP~hI~~AI~nD~EL~~L~~~~~Ia~ggv~P~i~~~l~~~k~~~~  128 (139)
                      .+|+|+||++||+||+||.+|+++|+|++|||+|+||+.|+++|+.+.
T Consensus        79 ~ri~PrH~~lAI~NDeEL~~lL~~vtIa~GGvlPnI~~~lLpKk~~~~  126 (131)
T KOG1756|consen   79 TRITPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAILLPKKTGKH  126 (131)
T ss_pred             cccChHHHHHHHhCcHHHHHHhccceeccCCcccccchhhcccccccC
Confidence            999999999999999999999999999999999999999999998664

>PLN00154 histone H2A; Provisional

Probab=100.00  E-value=6.3e-46  Score=275.73  Aligned_cols=112  Identities=59%  Similarity=0.870  Sum_probs=106.1

Q ss_pred             CCCCCcCcccccCcccchHHHHHHHHhCC-CccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           15 KSTKSISRSHKAGLQFPVGRIARFLKAGK-YADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        15 ~~~~~~s~ssragL~fPvsri~R~Lk~~~-~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      .+++..|||+|++|+|||+||+|+|+++. +.+||+.+|+|||+||||||++||||||+|.|+++++++|+|+||++||+
T Consensus        24 ~~~k~~srS~rAgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr  103 (136)
T PLN00154         24 DKKKPTSRSSRAGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR  103 (136)
T ss_pred             CCcCCcCcccccCccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence            45689999999999999999999999986 46899999999999999999999999999999999999999999999999


Q ss_pred             CcHHHHhhhcCceecCCccCCcccccccccccCC
Q 032523           94 NDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGK  127 (139)
Q Consensus        94 nD~EL~~L~~~~~Ia~ggv~P~i~~~l~~~k~~~  127 (139)
                      ||+||++||+ +||++|||+|+||++|+++|.+|
T Consensus       104 nDeEL~~Ll~-~TIa~GGVlP~i~~~l~~k~~~~  136 (136)
T PLN00154        104 GDEELDTLIK-GTIAGGGVIPHIHKSLINKSTKK  136 (136)
T ss_pred             CcHHHHHHhc-CCccCCccCCCcchhhcccccCC
Confidence            9999999997 69999999999999999988654

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

Probab=100.00  E-value=1.7e-45  Score=268.10  Aligned_cols=110  Identities=79%  Similarity=1.184  Sum_probs=106.7

Q ss_pred             CCCCCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhC
Q 032523           15 KSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN   94 (139)
Q Consensus        15 ~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~n   94 (139)
                      .+++.+|+|+|+||+|||+||+|||+++.+++||+++|+|||+||||||++||||+|+|.|++.++++|+|+||++||+|
T Consensus         6 ~~~~~~s~s~ragL~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n   85 (115)
T cd00074           6 KKSKKRSRSARAGLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN   85 (115)
T ss_pred             cCcCccccccccCccCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence            56678899999999999999999999988999999999999999999999999999999999999999999999999999


Q ss_pred             cHHHHhhhcCceecCCccCCcccccccccc
Q 032523           95 DEELSKLLGTVTIANGGVLPNIHQNLLPRK  124 (139)
Q Consensus        95 D~EL~~L~~~~~Ia~ggv~P~i~~~l~~~k  124 (139)
                      |+|||+||+++||++|||+|+||++|+++|
T Consensus        86 D~EL~~L~~~vtI~~ggv~p~i~~~l~~~~  115 (115)
T cd00074          86 DEELNKLLKGVTIASGGVLPNIHKVLLPKK  115 (115)
T ss_pred             cHHHHHHHcCCcccCCccCCCcchhhcCCC
Confidence            999999999999999999999999999875

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=5.3e-45  Score=262.28  Aligned_cols=105  Identities=79%  Similarity=1.190  Sum_probs=102.9

Q ss_pred             CcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHHHh
Q 032523           21 SRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSK  100 (139)
Q Consensus        21 s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL~~  100 (139)
                      |+|+|+||+|||+||+|||++++++.||+++|+|||+||||||++||||+|+|.|++.++++|+|+||++||+||+|||+
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             hhcCceecCCccCCccccccccccc
Q 032523          101 LLGTVTIANGGVLPNIHQNLLPRKM  125 (139)
Q Consensus       101 L~~~~~Ia~ggv~P~i~~~l~~~k~  125 (139)
                      ||+++||++|||+|+||++|+++|.
T Consensus        81 L~~~vti~~ggv~p~i~~~l~~~~~  105 (106)
T smart00414       81 LLKGVTIAQGGVLPNIHKVLLPKKT  105 (106)
T ss_pred             HHcCcccCCCccCCCcchhhcccCC
Confidence            9999999999999999999999874

>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]

Probab=100.00  E-value=1.8e-44  Score=261.64  Aligned_cols=121  Identities=71%  Similarity=1.070  Sum_probs=114.3

Q ss_pred             CCCCCCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           14 PKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        14 ~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      +..+-..|+|.+++|+|||+||+|+|+.+++..||+.+|+||++||||||++||||+|+|.|++.++++|+|+||++||+
T Consensus        11 a~~r~~~s~sa~agl~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr   90 (132)
T COG5262          11 ADARVSQSRSAKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR   90 (132)
T ss_pred             ccchhccchhhhcCccccHHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence            34456789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcHHHHhhhcCceecCCccCCcccccccccccCCCCccCCccCCC
Q 032523           94 NDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGKGREDIGSASQE  138 (139)
Q Consensus        94 nD~EL~~L~~~~~Ia~ggv~P~i~~~l~~~k~~~~~~~~~~~~~~  138 (139)
                      ||+||++|+++|+|++|||+|+||+.|+++.++|.    ++.+|+
T Consensus        91 nD~EL~~l~~~~tIa~GGvlp~I~~~ll~k~skK~----sk~~~~  131 (132)
T COG5262          91 NDEELNKLLGDVTIAQGGVLPNINPGLLPKSSKKG----SKRSQE  131 (132)
T ss_pred             CcHHHHHHhhhheeecCCcccccChhhhhhhhccC----Cccccc
Confidence            99999999999999999999999999999998887    666665

>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]

Probab=100.00  E-value=6.6e-39  Score=231.24  Aligned_cols=112  Identities=60%  Similarity=0.908  Sum_probs=105.5

Q ss_pred             CCCCcCcccccCcccchHHHHHHHHhCCCcc-ccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhC
Q 032523           16 STKSISRSHKAGLQFPVGRIARFLKAGKYAD-RVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN   94 (139)
Q Consensus        16 ~~~~~s~ssragL~fPvsri~R~Lk~~~~~~-RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~n   94 (139)
                      +.+.+|+|.|+||||||+||+|.|+....+. ||+..++||++++||||++|+||||+|.+++.+.+||||+|+++||+.
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            3588999999999999999999999886664 999999999999999999999999999999999999999999999999


Q ss_pred             cHHHHhhhcCceecCCccCCcccccccccccCCC
Q 032523           95 DEELSKLLGTVTIANGGVLPNIHQNLLPRKMGKG  128 (139)
Q Consensus        95 D~EL~~L~~~~~Ia~ggv~P~i~~~l~~~k~~~~  128 (139)
                      |+|||.|++ .+|+.|||+||||++|+.++.+++
T Consensus        97 DeELDtLIk-~TiagGgViPhihk~l~~k~~~~~  129 (131)
T KOG1757|consen   97 DEELDTLIK-ATIAGGGVIPHIHKSLINKKGKKK  129 (131)
T ss_pred             cHHHHHHHH-HhhccCccccchHHHHhccccccC
Confidence            999999995 589999999999999999887765

>PLN00155 histone H2A; Provisional

Probab=99.86  E-value=4.3e-22  Score=128.74  Aligned_cols=58  Identities=72%  Similarity=1.202  Sum_probs=51.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHH
Q 032523            1 MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYL   63 (139)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL   63 (139)
                      |||+|     ||++.+++.+|+|+|++|||||+||+|+|++++++.||+.+|||||+||||||
T Consensus         1 msg~g-----~g~~~~~k~~srS~rAgL~FPVgri~r~Lr~g~~a~Rvga~apVYlAAVLEYL   58 (58)
T PLN00155          1 MAGRG-----KGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYL   58 (58)
T ss_pred             CCCCC-----CCCccccCccCcccccccccchHHHHHHHhcCChhhcccCCcHHHHHHHHHhC
Confidence            88766     23445567899999999999999999999999999999999999999999997

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

Probab=99.62  E-value=1.7e-15  Score=107.92  Aligned_cols=101  Identities=24%  Similarity=0.391  Sum_probs=87.1

Q ss_pred             CCCCCCCCCCCCCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchh
Q 032523            7 TKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPR   86 (139)
Q Consensus         7 ~~~~~~~~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~   86 (139)
                      .-||-|-.++.+...   +-..+||++|++++|+.+++..+|+..+||.....||+|+++|+.++++.|+..+.+|||.+
T Consensus         4 Pv~N~~t~~k~n~~~---~~ktrFP~ar~KkIMQ~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e   80 (113)
T COG5247           4 PVGNMGTMPKQNSQK---KKKTRFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSE   80 (113)
T ss_pred             CCCCCCCCCCCchhh---hhhhcCCHHHHHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHH
Confidence            345555555444333   66788999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHhhhCcHHHHhhhcCceecCC
Q 032523           87 HIQLAVRNDEELSKLLGTVTIANG  110 (139)
Q Consensus        87 hI~~AI~nD~EL~~L~~~~~Ia~g  110 (139)
                      ||..|+.+|+.|++|-.-+.+-.+
T Consensus        81 ~lk~a~~sdekFdFL~~~~~~~~~  104 (113)
T COG5247          81 FLKRATESDEKFDFLKNMEQFKNR  104 (113)
T ss_pred             HHHHHHhhhHHHHHHHHHHHhcCC
Confidence            999999999999999865555444

>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=99.55  E-value=7.1e-15  Score=98.12  Aligned_cols=73  Identities=44%  Similarity=0.614  Sum_probs=68.1

Q ss_pred             ccccCcccchHHHHHHHHhCCCcc-ccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCc
Q 032523           23 SHKAGLQFPVGRIARFLKAGKYAD-RVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRND   95 (139)
Q Consensus        23 ssragL~fPvsri~R~Lk~~~~~~-RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD   95 (139)
                      +.+..+.||+.|+.+-+....+.. ||+.+|.+||.+++||++.+|+++|++.|.+.++++|+|+||+.|++.|
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            566788999999999999887775 9999999999999999999999999999999999999999999999875

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=99.40  E-value=5.3e-13  Score=95.69  Aligned_cols=89  Identities=21%  Similarity=0.334  Sum_probs=79.2

Q ss_pred             CCCCCCCCC----CCCCCCCCCCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHh
Q 032523            1 MSSAGSTKG----GRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAAR   76 (139)
Q Consensus         1 ~~~~~~~~~----~~~~~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~   76 (139)
                      |||.|  ++    ||||.+|..++.+.+-++  +|.+.|.|+++.. .+.|||+++-..|..+||.++.+|+..|..+|.
T Consensus         1 m~~~~--k~~~g~g~~g~kr~~k~~~d~i~~--ipk~~IrRLARr~-GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~   75 (103)
T PLN00035          1 MSGRG--KGGKGLGKGGAKRHRKVLRDNIQG--ITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTE   75 (103)
T ss_pred             CCCCC--CCCCCCCCCcchHHHHHHHhhhcc--CCHHHHHHHHHHc-CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            88888  44    455667777777777777  8888999999998 899999999999999999999999999999999


Q ss_pred             hcCCCccchhhHHHhhhC
Q 032523           77 DNKKNRIVPRHIQLAVRN   94 (139)
Q Consensus        77 ~~~~krItP~hI~~AI~n   94 (139)
                      +.++++|+.+||.+|++.
T Consensus        76 HA~RKTV~~~DV~~Alkr   93 (103)
T PLN00035         76 HARRKTVTAMDVVYALKR   93 (103)
T ss_pred             hcCCCcCcHHHHHHHHHH
Confidence            999999999999999864

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

Probab=99.37  E-value=9.5e-13  Score=104.45  Aligned_cols=82  Identities=22%  Similarity=0.356  Sum_probs=76.9

Q ss_pred             cccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHHHhh
Q 032523           22 RSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKL  101 (139)
Q Consensus        22 ~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL~~L  101 (139)
                      +-.+-...||++||+++||.+++..+|...+||.+...||.|+.+|+..++.+++..+.++++++||..||.+|+.|+||
T Consensus         6 ~~~~~~trfp~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFL   85 (224)
T KOG1659|consen    6 SFKKYKTRFPPARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFL   85 (224)
T ss_pred             hhhhhhccCCHHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHH
Confidence            34455677999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hc
Q 032523          102 LG  103 (139)
Q Consensus       102 ~~  103 (139)
                      -.
T Consensus        86 k~   87 (224)
T KOG1659|consen   86 KE   87 (224)
T ss_pred             HH
Confidence            74

>PTZ00015 histone H4; Provisional

Probab=99.26  E-value=1.8e-11  Score=87.72  Aligned_cols=89  Identities=21%  Similarity=0.343  Sum_probs=75.8

Q ss_pred             CCCCCCCCCC-----CCCCCCCCCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHH
Q 032523            1 MSSAGSTKGG-----RGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAA   75 (139)
Q Consensus         1 ~~~~~~~~~~-----~~~~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A   75 (139)
                      ||++|  ++|     +|++++..+..+.+-.+  +|.+.|.|+++.. .+.|||+++-..+..+||.++.+|+..|..+|
T Consensus         1 ~~~~~--k~~~~~~~~g~~kr~rk~~r~~i~g--I~k~~IrRLarr~-GvkRIS~d~y~e~r~vle~~l~~I~rdav~~a   75 (102)
T PTZ00015          1 MSGMG--KGKKSLGAKGGQKRQKKVLRDNIRG--ITKGAIRRLARRG-GVKRISGDIYEEVRGVLKAFLENVVRDSTAYT   75 (102)
T ss_pred             CCCcc--cCCCccccccchhhHHHHHhhcccC--CCHHHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            77777  333     55556666666666666  6677899999988 99999999999999999999999999999999


Q ss_pred             hhcCCCccchhhHHHhhhC
Q 032523           76 RDNKKNRIVPRHIQLAVRN   94 (139)
Q Consensus        76 ~~~~~krItP~hI~~AI~n   94 (139)
                      .+.++++|+.+||.+|++.
T Consensus        76 eHA~RKTVt~~DV~~AlKr   94 (102)
T PTZ00015         76 EYARRKTVTAMDVVYALKR   94 (102)
T ss_pred             HhcCCCcccHHHHHHHHHh
Confidence            9999999999999999853

>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=99.20  E-value=6.1e-11  Score=77.52  Aligned_cols=64  Identities=22%  Similarity=0.283  Sum_probs=58.2

Q ss_pred             ccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhh
Q 032523           29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAV   92 (139)
Q Consensus        29 ~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI   92 (139)
                      .||+++|+|+|+......+|+.+|..+|+.+.|.|+.+|...|...|...++++|+++||..|+
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            5999999999999977789999999999999999999999999999999999999999999885

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

>smart00803 TAF TATA box binding protein associated factor

Probab=98.98  E-value=2e-09  Score=71.20  Aligned_cols=64  Identities=20%  Similarity=0.232  Sum_probs=61.0

Q ss_pred             ccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        29 ~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      .+|.+.|.|+.+.. +..||++++...|+..+||.+.+|+..|.+.+++.+|++++++||+.|++
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            48999999999988 89999999999999999999999999999999999999999999999864

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

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

Probab=98.98  E-value=5.6e-10  Score=78.52  Aligned_cols=68  Identities=28%  Similarity=0.355  Sum_probs=63.4

Q ss_pred             ccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           25 KAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        25 ragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      ...+-||+..|.|+|++. ...||+.+|...|..++|-++.+|.+.|...|.+.+|++|+++||++|+.
T Consensus        15 ~~~~~Lp~apv~Ri~r~~-~~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~   82 (91)
T COG2036          15 STDLLLPKAPVRRILRKA-GAERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALK   82 (91)
T ss_pred             hhhhhcCchHHHHHHHHH-hHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHH
Confidence            345669999999999998 77799999999999999999999999999999999999999999999985

>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution

Probab=98.85  E-value=6.6e-09  Score=72.25  Aligned_cols=72  Identities=18%  Similarity=0.268  Sum_probs=64.6

Q ss_pred             cCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhC
Q 032523           20 ISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN   94 (139)
Q Consensus        20 ~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~n   94 (139)
                      +-+.+-+|  +|.+.|.|+.+.. ++.|||.++-..+..+||.++.+|+..|..++.+.++++|+++||.+|++.
T Consensus         6 ~~~~~~~g--i~k~~I~RLarr~-GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr   77 (85)
T cd00076           6 VLRDNIKG--ITKPAIRRLARRG-GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKR   77 (85)
T ss_pred             HHHHhhcc--CCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence            33444455  7888999999998 899999999999999999999999999999999999999999999999864

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

Probab=98.74  E-value=2.3e-08  Score=80.35  Aligned_cols=75  Identities=25%  Similarity=0.376  Sum_probs=72.7

Q ss_pred             cccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHHHhhh
Q 032523           28 LQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLL  102 (139)
Q Consensus        28 L~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL~~L~  102 (139)
                      +.+|++||+++|+.+++..-|++.||+.++.+.|-|++|+...|+-.|..++|+++.-.||..|+...+-|++|+
T Consensus       108 h~LPlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLi  182 (286)
T COG5208         108 HNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLI  182 (286)
T ss_pred             ccCcHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHh
Confidence            459999999999999999999999999999999999999999999999999999999999999999999999999

>smart00417 H4 Histone H4

Probab=98.73  E-value=2.7e-08  Score=67.57  Aligned_cols=61  Identities=15%  Similarity=0.139  Sum_probs=57.6

Q ss_pred             cchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHh
Q 032523           30 FPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLA   91 (139)
Q Consensus        30 fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~A   91 (139)
                      +|.+.|.|+++.. ++.|||+++-..+..+||.++.+|+..|..+|.+.++++|+.+||..|
T Consensus        14 I~k~~IrRLaRr~-GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a   74 (74)
T smart00417       14 ITKPAIRRLARRG-GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA   74 (74)
T ss_pred             CCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence            7788899999998 999999999999999999999999999999999999999999998653

>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]

Probab=98.57  E-value=4.7e-08  Score=79.21  Aligned_cols=84  Identities=21%  Similarity=0.276  Sum_probs=77.3

Q ss_pred             cccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHHHhh
Q 032523           22 RSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKL  101 (139)
Q Consensus        22 ~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL~~L  101 (139)
                      ...=....||++||+++|+.+.....|+.+|||.++.++|+|+.|+-..++..+..++++.+.-.||..++.++.-|++|
T Consensus        67 ~~d~~~~~lPlaRiKkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL  146 (236)
T KOG1657|consen   67 QLDFKNHILPLARIKKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFL  146 (236)
T ss_pred             ccchhhccCcHhhccccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccce
Confidence            33444678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCc
Q 032523          102 LGTV  105 (139)
Q Consensus       102 ~~~~  105 (139)
                      ...+
T Consensus       147 ~Div  150 (236)
T KOG1657|consen  147 RDIV  150 (236)
T ss_pred             eccc
Confidence            9543

>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=98.25  E-value=5.3e-06  Score=55.61  Aligned_cols=66  Identities=15%  Similarity=0.256  Sum_probs=60.1

Q ss_pred             cchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCc
Q 032523           30 FPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRND   95 (139)
Q Consensus        30 fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD   95 (139)
                      ++-..+..++++-....|++.+|...|..++|-|+.+|++.|...|++.++++|.++||+++++.+
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            445678888888866789999999999999999999999999999999999999999999999765

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

>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=98.07  E-value=1.3e-05  Score=58.55  Aligned_cols=61  Identities=20%  Similarity=0.112  Sum_probs=57.2

Q ss_pred             HHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhC
Q 032523           33 GRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN   94 (139)
Q Consensus        33 sri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~n   94 (139)
                      --|+++|++. ++.+++..++..|...++-++.+|+..|...|++.++++|+.+||++||..
T Consensus         5 ~~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~   65 (117)
T cd07979           5 RVIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQS   65 (117)
T ss_pred             HHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence            3588999987 888999999999999999999999999999999999999999999999974

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

>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]

Probab=97.98  E-value=1.5e-05  Score=55.87  Aligned_cols=90  Identities=21%  Similarity=0.312  Sum_probs=77.0

Q ss_pred             CCCCC--CCCCCCCCCCCCCCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 032523            1 MSSAG--STKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDN   78 (139)
Q Consensus         1 ~~~~~--~~~~~~~~~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~   78 (139)
                      ||+.|  .|..+||+++|..+.-+.+-.+++-|.  |.|+-+.. ...||+...-.....++.-++.+++-.|...+.+.
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            66554  234458899999988888888988887  88888877 88999998888899999999999999999999999


Q ss_pred             CCCccchhhHHHhhh
Q 032523           79 KKNRIVPRHIQLAVR   93 (139)
Q Consensus        79 ~~krItP~hI~~AI~   93 (139)
                      ++++||..|+-.+.+
T Consensus        78 KRKTvT~~dvv~~LK   92 (103)
T KOG3467|consen   78 KRKTVTAMDVVYALK   92 (103)
T ss_pred             hhceeeHHHHHHHHH
Confidence            999999999987765

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

Probab=97.77  E-value=0.00014  Score=48.38  Aligned_cols=64  Identities=19%  Similarity=0.234  Sum_probs=49.5

Q ss_pred             ccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        29 ~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      .||..-|+.+-..- +...+++++.-.|+.=+||-+.||+..|.+..++.+|+++|++||+.|++
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            47777777766655 67789999999999999999999999999999999999999999999874

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.

>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=97.69  E-value=0.00023  Score=49.44  Aligned_cols=63  Identities=21%  Similarity=0.391  Sum_probs=56.2

Q ss_pred             cchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcC---CCccchhhHHHhhh
Q 032523           30 FPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNK---KNRIVPRHIQLAVR   93 (139)
Q Consensus        30 fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~---~krItP~hI~~AI~   93 (139)
                      ||-..++|++... ....|+.+..+.|+++-..|+.||+|.|...-...+   ...|.|.||+.|.+
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            8888899999977 668999999999999999999999999998876644   47899999999875

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

>PLN00158 histone H2B; Provisional

Probab=97.64  E-value=0.00029  Score=51.61  Aligned_cols=61  Identities=28%  Similarity=0.291  Sum_probs=54.9

Q ss_pred             HHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           33 GRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        33 sri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      ..|++.|++..-..-|+..+.-.|...+..++.-|...|...++-+++.+|++++|+.|++
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            4699999988666789999998899999999999999999999999999999999999987

>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins

Probab=97.63  E-value=0.00023  Score=48.02  Aligned_cols=59  Identities=20%  Similarity=0.155  Sum_probs=54.1

Q ss_pred             HHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhC
Q 032523           35 IARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN   94 (139)
Q Consensus        35 i~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~n   94 (139)
                      |.++|+.. +..+++.+|...|+.++|-++.+|.+.+-+.|.+.+|+..++.||.+|+.+
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            45677776 889999999999999999999999999999999999999999999999854

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=97.62  E-value=0.00017  Score=61.10  Aligned_cols=60  Identities=18%  Similarity=0.263  Sum_probs=54.1

Q ss_pred             HHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           33 GRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        33 sri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      .-|+-+.+.. +..|++++|...|+..+||.+.+|++.|.+.+++.+|++++++||+.|++
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            3455555554 88899999999999999999999999999999999999999999999987

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

>smart00428 H3 Histone H3

Probab=97.44  E-value=0.00033  Score=50.54  Aligned_cols=68  Identities=24%  Similarity=0.225  Sum_probs=57.7

Q ss_pred             cCcccchHHHHHHHHhC----CC--ccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           26 AGLQFPVGRIARFLKAG----KY--ADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        26 agL~fPvsri~R~Lk~~----~~--~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      ..|.+|-..+.|+.++-    ..  ..|++.+|...|-.+.|.++.++++.|...|.+.++.+|+|+|+++|.+
T Consensus        26 t~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~r   99 (105)
T smart00428       26 TDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARR   99 (105)
T ss_pred             cccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHH
Confidence            45667777777776543    11  3499999999999999999999999999999999999999999999854

>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=97.10  E-value=0.0016  Score=45.81  Aligned_cols=64  Identities=16%  Similarity=0.268  Sum_probs=48.0

Q ss_pred             cchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcC-CCccchhhHHHhhh
Q 032523           30 FPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNK-KNRIVPRHIQLAVR   93 (139)
Q Consensus        30 fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~-~krItP~hI~~AI~   93 (139)
                      ||-+.|++++...-...-|+....+.++++--.|+.||+|.|.......+ ...|.|.||+.|.+
T Consensus        24 ~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~r   88 (90)
T PF04719_consen   24 FNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYR   88 (90)
T ss_dssp             --HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHH
T ss_pred             CCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHH
Confidence            88899999999873338999999999999999999999999998876533 45899999998864

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

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

Probab=97.00  E-value=0.001  Score=52.65  Aligned_cols=65  Identities=20%  Similarity=0.346  Sum_probs=55.9

Q ss_pred             cccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhc-CCCccchhhHHHhhh
Q 032523           28 LQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDN-KKNRIVPRHIQLAVR   93 (139)
Q Consensus        28 L~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~-~~krItP~hI~~AI~   93 (139)
                      .-||-+.|+++|..-.... |+..+.++++++-.-|+-||+|+|..+.... ....+.|.||+.|.+
T Consensus       111 s~f~Ka~iKkL~~~itg~~-v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~r  176 (195)
T KOG3219|consen  111 SAFPKAQIKKLMSSITGQS-VSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYR  176 (195)
T ss_pred             hcCCHHHHHHHHHHHhCCc-cCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHH
Confidence            3499999999999884444 9999999999999999999999998887553 356799999999975

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

Probab=96.81  E-value=0.0046  Score=47.62  Aligned_cols=65  Identities=15%  Similarity=0.222  Sum_probs=58.6

Q ss_pred             ccchHHHHHHHHhCCCc-cccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           29 QFPVGRIARFLKAGKYA-DRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        29 ~fPvsri~R~Lk~~~~~-~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      -+|++-|-|+|++.-.. .+|+.+|...+--++-.|++=|.-.|...|...+|++|+.+||-+|+.
T Consensus        32 ~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~   97 (168)
T KOG0869|consen   32 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMS   97 (168)
T ss_pred             hccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHH
Confidence            38999999999988333 399999999999999899999999999999999999999999999986

>smart00427 H2B Histone H2B

Probab=96.73  E-value=0.007  Score=42.49  Aligned_cols=60  Identities=27%  Similarity=0.280  Sum_probs=54.0

Q ss_pred             HHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           34 RIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        34 ri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      .|+|.|++..-..-|+..|.-.+...+..++.-|...|...++.+++.+|++++|+.|++
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            588999988666689999998899999999999999999999999999999999999986

>PTZ00463 histone H2B; Provisional

Probab=96.43  E-value=0.013  Score=42.95  Aligned_cols=61  Identities=16%  Similarity=0.164  Sum_probs=53.7

Q ss_pred             HHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           33 GRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        33 sri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      -.|++.|++..-..-|+..|.-.|...+.-++..|...|.+.|+-+++.+|++++|+.|++
T Consensus        32 ~YI~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvr   92 (117)
T PTZ00463         32 LYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIR   92 (117)
T ss_pred             HHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHh
Confidence            3699999988666789998988888888888888888899999989999999999999987

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

Probab=96.42  E-value=0.0062  Score=52.96  Aligned_cols=72  Identities=11%  Similarity=0.099  Sum_probs=45.8

Q ss_pred             CCCCcCcccccCcccchHHHHHHHHhC----CCc-cccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhh
Q 032523           16 STKSISRSHKAGLQFPVGRIARFLKAG----KYA-DRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRH   87 (139)
Q Consensus        16 ~~~~~s~ssragL~fPvsri~R~Lk~~----~~~-~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~h   87 (139)
                      ++++.|+-......+|-+.|++++...    .|+ .+|+.+|--.|..++|||...|-+=-.-+|.|.|||+|.+.|
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            567777777778889999999988654    344 399999999999999999999999999999999999999875

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

Probab=96.22  E-value=0.02  Score=43.73  Aligned_cols=70  Identities=19%  Similarity=0.217  Sum_probs=60.8

Q ss_pred             ccCcccchHHHHHHHHhCCC-ccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhC
Q 032523           25 KAGLQFPVGRIARFLKAGKY-ADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN   94 (139)
Q Consensus        25 ragL~fPvsri~R~Lk~~~~-~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~n   94 (139)
                      .-.+.+|-+-|..++++.-. ..||..++-..|-.+.=||+.-|--.|..+|....+++|.|+|+-.|..|
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            45788999999999998844 35999999988888877888888889999999999999999999999875

>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=96.16  E-value=0.027  Score=37.93  Aligned_cols=61  Identities=18%  Similarity=0.202  Sum_probs=48.4

Q ss_pred             chHHHHHHHHhCC--CccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCc-cchhhHHHh
Q 032523           31 PVGRIARFLKAGK--YADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNR-IVPRHIQLA   91 (139)
Q Consensus        31 Pvsri~R~Lk~~~--~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~kr-ItP~hI~~A   91 (139)
                      |-.-|.|+|+...  ..-||+.+|...++..|+-|+.|-+-+|...|...+... |..+||+..
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            4456888998542  234999999999999999999999999999999998888 999999863

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

>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=96.11  E-value=0.022  Score=37.94  Aligned_cols=63  Identities=13%  Similarity=0.261  Sum_probs=50.3

Q ss_pred             HHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCc
Q 032523           33 GRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRND   95 (139)
Q Consensus        33 sri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD   95 (139)
                      .++..++++-.....+..++...|..+.+-|+.+++..|...|++.+..++.+.||+..+..+
T Consensus         3 ~~l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler~   65 (68)
T PF03847_consen    3 RKLQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLERN   65 (68)
T ss_dssp             HHHHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHhh
Confidence            357778888767779999999999999999999999999999999999999999999887654

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

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

Probab=95.92  E-value=0.059  Score=36.64  Aligned_cols=48  Identities=21%  Similarity=0.337  Sum_probs=36.2

Q ss_pred             chHHHHHHHHHHHHHHHHHHHH---HHHhhcCCCccchhhHHHhhhCcHHH
Q 032523           51 GAPVYLSAVLEYLAAEVLELAG---NAARDNKKNRIVPRHIQLAVRNDEEL   98 (139)
Q Consensus        51 ~A~vyLaAvLEyL~~EILelAg---~~A~~~~~krItP~hI~~AI~nD~EL   98 (139)
                      -++-|++++.|.....+-.++.   ..|++.||++|+++|+.+..+.++.|
T Consensus        26 ~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rrn~~L   76 (76)
T PF15630_consen   26 VSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARRNPSL   76 (76)
T ss_dssp             E-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT-HHH
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhcCCCC
Confidence            4778888888888777776663   34799999999999999999999876

>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]

Probab=95.67  E-value=0.011  Score=45.40  Aligned_cols=77  Identities=19%  Similarity=0.226  Sum_probs=68.5

Q ss_pred             CcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHHHhhhc
Q 032523           27 GLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLG  103 (139)
Q Consensus        27 gL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL~~L~~  103 (139)
                      -+++|++||+.+++.+....-....+...++...|.++.+|-..++..+....++++.-+++..||..-+||.+|-.
T Consensus        57 l~rLpL~rik~vvkl~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~de~~fle~  133 (162)
T KOG1658|consen   57 LSRLPLARIKQVVKLDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAVDEFAFLEG  133 (162)
T ss_pred             hhhccHHHHHhhccCCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccchHHHHHHhh
Confidence            36799999999999886666666677777899999999999999999999999999999999999999999998884

>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=95.40  E-value=0.077  Score=39.50  Aligned_cols=60  Identities=20%  Similarity=0.104  Sum_probs=41.5

Q ss_pred             HHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           33 GRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        33 sri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      --|+-+|++. +.......++.-|--..--++.+||+-|..+|.+.++..|+..||++||.
T Consensus        16 ~~i~~iL~~~-Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~   75 (129)
T PF02291_consen   16 RVIHLILKSM-GVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQ   75 (129)
T ss_dssp             HHHHHHHHHT-T---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHH
T ss_pred             HHHHHHHHHc-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHH
Confidence            4577788877 44433444444444444446899999999999999999999999999998

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

>PLN00160 histone H3; Provisional

Probab=95.37  E-value=0.037  Score=39.40  Aligned_cols=68  Identities=25%  Similarity=0.217  Sum_probs=57.2

Q ss_pred             cCcccchHHHHHHHHhCC-----CccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           26 AGLQFPVGRIARFLKAGK-----YADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        26 agL~fPvsri~R~Lk~~~-----~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      ..|.+|-..+.|+.++-.     ...|...+|...|--+-|.++-.++|-+...|.+.++-+|.|.|++++.+
T Consensus        18 t~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~r   90 (97)
T PLN00160         18 TDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARR   90 (97)
T ss_pred             hhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHH
Confidence            356777777777776541     23599999999999999999999999999999999999999999998854

>PTZ00018 histone H3; Provisional

Probab=95.31  E-value=0.035  Score=41.78  Aligned_cols=66  Identities=24%  Similarity=0.205  Sum_probs=56.8

Q ss_pred             CcccchHHHHHHHHhC----CCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhh
Q 032523           27 GLQFPVGRIARFLKAG----KYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAV   92 (139)
Q Consensus        27 gL~fPvsri~R~Lk~~----~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI   92 (139)
                      .|.||-..|.|++++-    ....|+..+|...|--+-|.++-.++|.+...|.+.++-+|.|.|++++.
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            5667777788877654    12349999999999999999999999999999999999999999999884

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

Probab=95.27  E-value=0.093  Score=34.94  Aligned_cols=58  Identities=19%  Similarity=0.162  Sum_probs=51.0

Q ss_pred             HHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           35 IARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        35 i~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      |..+++.. +...++..|...|+.+++.++.+|...+-.+|.+.+|...++.|+..|+.
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            34456554 77899999999999999999999999999999999999999999998874

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 [, ].

>PLN00121 histone H3; Provisional

Probab=95.02  E-value=0.032  Score=41.99  Aligned_cols=67  Identities=25%  Similarity=0.225  Sum_probs=57.1

Q ss_pred             CcccchHHHHHHHHhC----CCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           27 GLQFPVGRIARFLKAG----KYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        27 gL~fPvsri~R~Lk~~----~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      .|.||-..|.|++++-    ....|+..+|...|--+-|.++-.++|.+.-.|.+.++-+|.+.|++++.+
T Consensus        60 ~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r  130 (136)
T PLN00121         60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR  130 (136)
T ss_pred             ccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHH
Confidence            5667777788777653    123499999999999999999999999999999999999999999998843

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

Probab=94.99  E-value=0.1  Score=40.58  Aligned_cols=66  Identities=17%  Similarity=0.283  Sum_probs=58.4

Q ss_pred             CcccchHHHHHHHHhCCCcc---ccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           27 GLQFPVGRIARFLKAGKYAD---RVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        27 gL~fPvsri~R~Lk~~~~~~---RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      -|-||.+-|-|++++. ..+   -|+.+|-..|+..---|+..++--|...|+++++++|++.|+-.|+.
T Consensus         8 dl~lP~AiI~rlvke~-l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~   76 (172)
T KOG0870|consen    8 DLNLPNAIITRLVKEV-LPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALD   76 (172)
T ss_pred             HhhccHHHHHHHHHHh-CccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHH
Confidence            4679999999999876 443   58889999999999999999999999999999999999999998885

>PLN00161 histone H3; Provisional

Probab=94.98  E-value=0.064  Score=40.35  Aligned_cols=68  Identities=25%  Similarity=0.197  Sum_probs=56.8

Q ss_pred             cCcccchHHHHHHHHhC----C-CccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           26 AGLQFPVGRIARFLKAG----K-YADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        26 agL~fPvsri~R~Lk~~----~-~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      .+|.+|-..|.|++++-    . ...|+..+|...|--+-|.++-.++|-+.-.|.+.++-+|.|.|++++.+
T Consensus        52 t~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~r  124 (135)
T PLN00161         52 TELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARR  124 (135)
T ss_pred             cccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHH
Confidence            35667777777777653    1 13599999999999999999999999999999999999999999998854

>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]

Probab=94.47  E-value=0.19  Score=37.41  Aligned_cols=68  Identities=25%  Similarity=0.219  Sum_probs=52.0

Q ss_pred             ccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           23 SHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        23 ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      ...-...++|   .|.|++..-.--|+..+.-.+.+.+--++..|+..|+..|+-.++.+|+.++|+.|++
T Consensus        34 ~~~e~~s~yv---~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~r  101 (127)
T KOG1744|consen   34 RRKESYSEYV---YKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVR  101 (127)
T ss_pred             cccCceeeeh---hhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHH
Confidence            3334445554   4466665333458888888888888888899999999999999999999999999885

>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=94.21  E-value=0.083  Score=43.57  Aligned_cols=68  Identities=10%  Similarity=0.187  Sum_probs=61.6

Q ss_pred             ccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcH
Q 032523           29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDE   96 (139)
Q Consensus        29 ~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~   96 (139)
                      .+-.-++..+|++-.....+.+++-.+|.-+.+-|+..|+..+...|++.+..+|..+||++.++++.
T Consensus       154 il~k~kl~dLvqqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~  221 (258)
T KOG1142|consen  154 ILSKRKLDDLVQQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNF  221 (258)
T ss_pred             cccccchhHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccc
Confidence            35556788999988677799999999999999999999999999999999999999999999998873

>PLN00163 histone H4; Provisional

Probab=93.21  E-value=0.039  Score=35.91  Aligned_cols=46  Identities=33%  Similarity=0.585  Sum_probs=35.7

Q ss_pred             CCCCCCCCC----CCCCCCCCCCcCcccccCcccchHHHHHHHHhCCCccccCCc
Q 032523            1 MSSAGSTKG----GRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAG   51 (139)
Q Consensus         1 ~~~~~~~~~----~~~~~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~   51 (139)
                      |+|.|  ++    |||++++..++.+.+-.+++-|.  |.|+-+.. ...|||..
T Consensus         1 m~g~g--kggkglGkggaKRhrk~lrd~i~gItKpa--IrRLARRg-GVKRIs~~   50 (59)
T PLN00163          1 MSGRG--KGGKGLGKGGAKRHRKVLRDNIQGITKPA--IRRLARRG-GVKRISGL   50 (59)
T ss_pred             CCCCC--CCCCccCCccchhHHHHHHHhhcccchHH--HHHHHHhc-Cceeecch
Confidence            78777  44    45677788877787778877776  99988887 88999974

>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=93.04  E-value=0.11  Score=36.39  Aligned_cols=63  Identities=10%  Similarity=0.062  Sum_probs=18.2

Q ss_pred             HHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHHH
Q 032523           37 RFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELS   99 (139)
Q Consensus        37 R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL~   99 (139)
                      .+|---.+...-..++..++-.++--.+.+++..|.+.|...|+++|+.+|+..++++|+.--
T Consensus         9 ~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D~~Kl   71 (93)
T PF02269_consen    9 QMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKDPKKL   71 (93)
T ss_dssp             HHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC--------------------------
T ss_pred             HHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcCHHHH
Confidence            344333333444444555555555555567777777888888889999999999999997543

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=93.02  E-value=0.66  Score=32.47  Aligned_cols=63  Identities=11%  Similarity=0.125  Sum_probs=40.4

Q ss_pred             HHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHH
Q 032523           35 IARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEEL   98 (139)
Q Consensus        35 i~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL   98 (139)
                      |..+|---.+...-...+..+|-.++--++.+++-.|...|. .++.+|+++|+.-+|++|+.-
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            555565443433333344444544444444666667777776 567788999999999999753

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

>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]

Probab=91.48  E-value=0.2  Score=37.72  Aligned_cols=61  Identities=26%  Similarity=0.228  Sum_probs=50.3

Q ss_pred             HHHHHHHH----hCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           33 GRIARFLK----AGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        33 sri~R~Lk----~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      .++.|+.+    +-...-|+.++|...|--..|.++-.++|-+.-.|.+.++-+|.|.||++|.+
T Consensus        67 ~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArr  131 (137)
T KOG1745|consen   67 LPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR  131 (137)
T ss_pred             CcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhh
Confidence            34455554    33333499999999999999999999999999999999999999999999865

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

Probab=90.98  E-value=2.1  Score=32.03  Aligned_cols=62  Identities=19%  Similarity=0.193  Sum_probs=46.8

Q ss_pred             HHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccch---hhHHHhhhCc
Q 032523           33 GRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVP---RHIQLAVRND   95 (139)
Q Consensus        33 sri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP---~hI~~AI~nD   95 (139)
                      --|+-+|..- ..+--+..+++-|-..---.+.++|+-|.-+|++.|+..|++   +|+++|+..-
T Consensus        18 rlihliL~Sl-gi~~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~   82 (145)
T COG5094          18 RLIHLILRSL-GIEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATK   82 (145)
T ss_pred             hHHHHHHHhc-CchhhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHH
Confidence            3466666644 555555667776665556678999999999999999988888   9999999753

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

Probab=84.32  E-value=4.8  Score=30.72  Aligned_cols=56  Identities=27%  Similarity=0.342  Sum_probs=43.1

Q ss_pred             HHHHHHhCCCccccCCchHHHHHHHHHH---HHHHHHHHHHHHHhhcCCCccchhhHHHhhhC
Q 032523           35 IARFLKAGKYADRVGAGAPVYLSAVLEY---LAAEVLELAGNAARDNKKNRIVPRHIQLAVRN   94 (139)
Q Consensus        35 i~R~Lk~~~~~~RVs~~A~vyLaAvLEy---L~~EILelAg~~A~~~~~krItP~hI~~AI~n   94 (139)
                      |+-+|++.    =|.+.-+-.+.-.||+   .+..||+-|.-++.+.++..|..+|+++||..
T Consensus        19 i~~iL~s~----GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~   77 (148)
T KOG3334|consen   19 IASILKSL----GIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQM   77 (148)
T ss_pred             HHHHHHHc----CccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHH
Confidence            66677765    3444445555566665   56889999999999999999999999999974

>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]

Probab=82.20  E-value=6.3  Score=29.62  Aligned_cols=67  Identities=15%  Similarity=0.277  Sum_probs=46.4

Q ss_pred             CcccchHHHHHHHHhCCCcc--ccCC-chHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCc
Q 032523           27 GLQFPVGRIARFLKAGKYAD--RVGA-GAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRND   95 (139)
Q Consensus        27 gL~fPvsri~R~Lk~~~~~~--RVs~-~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD   95 (139)
                      .+.+|-+-|..++.+- .-.  -+.. .--+++-+++||+. -+--.|..+|.+..+++|.++|+-.|..|=
T Consensus         9 e~sLPKATVqKMvS~i-Lp~dl~ftKearei~in~cieFi~-~lsseAne~ce~EaKKTIa~EHviKALenL   78 (148)
T COG5150           9 ENSLPKATVQKMVSSI-LPKDLVFTKEAREIFINACIEFIN-MLSSEANEACEEEAKKTIAYEHVIKALENL   78 (148)
T ss_pred             cccCcHHHHHHHHHHh-ccccccccHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhccccHHHHHHHHHhc
Confidence            5678888888877654 211  2333 34567888888764 334446677777888999999999998753

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

Probab=81.78  E-value=2.5  Score=33.28  Aligned_cols=65  Identities=17%  Similarity=0.244  Sum_probs=52.8

Q ss_pred             ccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhh-cCCCccchhhHHHhhhC
Q 032523           29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARD-NKKNRIVPRHIQLAVRN   94 (139)
Q Consensus        29 ~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~-~~~krItP~hI~~AI~n   94 (139)
                      -||-..|+.+.-.. ...-|+....++|.++-.-|+.||+|+|..+-.. .-.....|.|++.|++-
T Consensus       115 ~lnKt~VKKlastV-~nQtVspNi~I~l~g~~KVfvGEiIElA~~Vq~~w~~sgpl~p~h~reayr~  180 (199)
T COG5251         115 SLNKTQVKKLASTV-ANQTVSPNIRIFLQGVGKVFVGEIIELAMIVQNKWLTSGPLIPFHKREAYRY  180 (199)
T ss_pred             CCCHHHHHHHHHHH-hccccCCCeeeeeechhHHHHHHHHHHHHHHHHHhcccCCCChHHHHHHHHH
Confidence            37788888877765 7778999999999999999999999999765433 33456899999999863

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	139
1id3_C	131	Crystal Structure Of The Yeast Nucleosome Core Part		2e-34
3c1b_C	129	The Effect Of H3 K79 Dimethylation And H4 K20 Trime		2e-33
1m18_C	129	Ligand Binding Alters The Structure And Dynamics Of		2e-33
1zbb_C	129	Structure Of The 4_601_167 Tetranucleosome Length =		2e-33
2hio_A	128	Histone Octamer (Chicken), Chromosomal Protein Leng		2e-33
1eqz_A	129	X-Ray Structure Of The Nucleosome Core Particle At		2e-33
1s32_C	119	Molecular Recognition Of The Nucleosomal 'supergroo		3e-33
1aoi_C	116	Complex Between Nucleosome Core Particle (H3,H4,H2a		6e-33
3a6n_C	133	The Nucleosome Containing A Testis-Specific Histone		7e-33
1kx3_C	128	X-Ray Structure Of The Nucleosome Core Particle, Nc		1e-32
2cv5_C	130	Crystal Structure Of Human Nucleosome Core Particle		1e-32
2nqb_C	123	Drosophila Nucleosome Structure Length = 123		1e-32
3kwq_C	107	Structural Characterization Of H3k56q Nucleosomes A		2e-32
2f8n_K	149	2.9 Angstrom X-Ray Structure Of Hybrid Macroh2a Nuc		2e-32
1zla_C	129	X-Ray Structure Of A Kaposi's Sarcoma Herpesvirus L		2e-32
2pyo_C	120	Drosophila Nucleosome Core Length = 120		3e-32
1hio_A	95	Histone Octamer (Chicken), Chromosomal Protein, Alp		3e-29
1u35_C	120	Crystal Structure Of The Nucleosome Core Particle C		7e-27
2xql_A	91	Fitting Of The H2a-H2b Histones In The Electron Mic		9e-27
1f66_C	128	2.6 A Crystal Structure Of A Nucleosome Core Partic		3e-21
2jss_A	192	Nmr Structure Of Chaperone Chz1 Complexed With Hist		5e-16

>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 =  140 bits (354), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 71/119 (59%), Positives = 82/119 (68%), Gaps = 4/119 (3%)
Query: 21  SRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKK 80
           SRS KAGL FPVGR+ R L+ G YA R+G+GAP                  GNAARDNKK
Sbjct: 17  SRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKK 76
Query: 81  NRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGKGREDIGSASQEF 139
            RI+PRH+QLA+RND+EL+KLLG VTIA GGVLPNIHQNLLP+K  K  +    ASQE 
Sbjct: 77  TRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPKKSAKATK----ASQEL 131

>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 =  137 bits (346), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 70/119 (58%), Positives = 82/119 (68%)
Query: 6   STKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXX 65
           S +G +G     K+ +RS +AGLQFPVGR+ R L+ G YA+RVGAGAP            
Sbjct: 1   SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA 60
Query: 66  XXXXXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRK 124
                 GNAARDNKK RI+PRH+QLAVRNDEEL+KLLG VTIA GGVLPNI   LLP+K
Sbjct: 61  EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK 119

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

Iteration: 1
 Score =  137 bits (345), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 70/119 (58%), Positives = 82/119 (68%)
Query: 6   STKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXX 65
           S +G +G     K+ +RS +AGLQFPVGR+ R L+ G YA+RVGAGAP            
Sbjct: 1   SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA 60
Query: 66  XXXXXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRK 124
                 GNAARDNKK RI+PRH+QLAVRNDEEL+KLLG VTIA GGVLPNI   LLP+K
Sbjct: 61  EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK 119

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

Iteration: 1
 Score =  137 bits (345), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 70/119 (58%), Positives = 82/119 (68%)
Query: 6   STKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXX 65
           S +G +G     K+ +RS +AGLQFPVGR+ R L+ G YA+RVGAGAP            
Sbjct: 1   SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA 60
Query: 66  XXXXXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRK 124
                 GNAARDNKK RI+PRH+QLAVRNDEEL+KLLG VTIA GGVLPNI   LLP+K
Sbjct: 61  EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK 119

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

Iteration: 1
 Score =  137 bits (345), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 70/119 (58%), Positives = 82/119 (68%)
Query: 6   STKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXX 65
           S +G +G     K+ SRS +AGLQFPVGR+ R L+ G YA+RVGAGAP            
Sbjct: 1   SGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA 60
Query: 66  XXXXXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRK 124
                 GNAARDNKK RI+PRH+QLA+RNDEEL+KLLG VTIA GGVLPNI   LLP+K
Sbjct: 61  EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKK 119

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

Iteration: 1
 Score =  137 bits (345), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 70/119 (58%), Positives = 82/119 (68%)
Query: 6   STKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXX 65
           S +G +G     K+ SRS +AGLQFPVGR+ R L+ G YA+RVGAGAP            
Sbjct: 2   SGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA 61
Query: 66  XXXXXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRK 124
                 GNAARDNKK RI+PRH+QLA+RNDEEL+KLLG VTIA GGVLPNI   LLP+K
Sbjct: 62  EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKK 120

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

Iteration: 1
 Score =  137 bits (344), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 70/119 (58%), Positives = 82/119 (68%)
Query: 6   STKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXX 65
           S +G +G     K+ +RS +AGLQFPVGR+ R L+ G YA+RVGAGAP            
Sbjct: 1   SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA 60
Query: 66  XXXXXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRK 124
                 GNAARDNKK RI+PRH+QLAVRNDEEL+KLLG VTIA GGVLPNI   LLP+K
Sbjct: 61  EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK 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 =  135 bits (341), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 69/116 (59%), Positives = 80/116 (68%)
Query: 9   GGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXXXXX 68
           G +G     K+ +RS +AGLQFPVGR+ R L+ G YA+RVGAGAP               
Sbjct: 1   GKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEIL 60
Query: 69  XXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRK 124
              GNAARDNKK RI+PRH+QLAVRNDEEL+KLLG VTIA GGVLPNI   LLP+K
Sbjct: 61  ELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK 116

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

Iteration: 1
 Score =  135 bits (340), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 71/123 (57%), Positives = 83/123 (67%), Gaps = 3/123 (2%)
Query: 5   GSTKGGRGKP---KSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXX 61
           GS   GRGK       K+ +RS +AGLQFPVGR+ R L+ G Y++RVGAGAP        
Sbjct: 1   GSHMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLE 60
Query: 62  XXXXXXXXXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLL 121
                     GNAARDNKK RI+PRH+QLA+RNDEEL+KLLG VTIA GGVLPNI   LL
Sbjct: 61  YLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLL 120
Query: 122 PRK 124
           P+K
Sbjct: 121 PKK 123

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

Iteration: 1
 Score =  134 bits (338), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 69/117 (58%), Positives = 80/117 (68%)
Query: 6   STKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXX 65
           S +G +G     K+ +RS +AGLQFPVGR+ R L+ G YA+RVGAGAP            
Sbjct: 1   SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA 60
Query: 66  XXXXXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLP 122
                 GNAARDNKK RI+PRH+QLAVRNDEEL+KLLG VTIA GGVLPNI   LLP
Sbjct: 61  EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLP 117

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

Iteration: 1
 Score =  134 bits (338), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 68/119 (57%), Positives = 82/119 (68%)
Query: 6   STKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXX 65
           S +G +G     K+ +RS +AGLQFPVGR+ R L+ G Y++RVGAGAP            
Sbjct: 2   SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTA 61
Query: 66  XXXXXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRK 124
                 GNAARDNKK RI+PRH+QLA+RNDEEL+KLLG VTIA GGVLPNI   LLP+K
Sbjct: 62  EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK 120

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

Iteration: 1
 Score =  134 bits (337), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 67/107 (62%), Positives = 76/107 (71%)
Query: 21  SRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKK 80
           SRS++AGLQFPVGRI R L+ G YA+RVGAGAP                  GNAARDNKK
Sbjct: 15  SRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKK 74
Query: 81  NRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGK 127
            RI+PRH+QLA+RNDEEL+KLL  VTIA GGVLPNI   LLP+K  K
Sbjct: 75  TRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTEK 121

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

Iteration: 1
 Score =  134 bits (337), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 66/104 (63%), Positives = 75/104 (72%)
Query: 21  SRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKK 80
           +RS +AGLQFPVGR+ R L+ G YA+RVGAGAP                  GNAARDNKK
Sbjct: 3   TRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKK 62
Query: 81  NRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRK 124
            RI+PRH+QLAVRNDEEL+KLLG VTIA GGVLPNI   LLP+K
Sbjct: 63  TRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK 106

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

Iteration: 1
 Score =  134 bits (337), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 68/119 (57%), Positives = 82/119 (68%)
Query: 6   STKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXX 65
           S +G +G     K+ +RS +AGLQFPVGR+ R L+ G Y++RVGAGAP            
Sbjct: 21  SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTA 80
Query: 66  XXXXXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRK 124
                 GNAARDNKK RI+PRH+QLA+RNDEEL+KLLG VTIA GGVLPNI   LLP+K
Sbjct: 81  EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK 139

>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 =  134 bits (336), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 68/119 (57%), Positives = 80/119 (67%)
Query: 6   STKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXX 65
           S +G +G     K+ +RS +AGLQFPVGR+ R L+ G YA+RVGAGAP            
Sbjct: 1   SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA 60
Query: 66  XXXXXXGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRK 124
                 GN  RDNKK RI+PRH+QLAVRNDEEL+KLLG VTIA GGVLPNI   LLP+K
Sbjct: 61  EILELAGNWERDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK 119

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

Iteration: 1
 Score =  133 bits (335), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 66/104 (63%), Positives = 75/104 (72%)
Query: 21  SRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKK 80
           SRS++AGLQFPVGRI R L+ G YA+RVGAGAP                  GNAARDNKK
Sbjct: 15  SRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKK 74
Query: 81  NRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRK 124
            RI+PRH+QLA+RNDEEL+KLL  VTIA GGVLPNI   LLP+K
Sbjct: 75  TRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKK 118

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

Iteration: 1
 Score =  123 bits (308), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 60/94 (63%), Positives = 68/94 (72%)
Query: 21  SRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKK 80
           SRS +AGLQFPVGR+ R L+ G YA+RVGAGAP                  GNAARDNKK
Sbjct: 2   SRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKK 61
Query: 81  NRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLP 114
            RI+PRH+QLA+RNDEEL+KLLG VTIA GGVLP
Sbjct: 62  TRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLP 95

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

Iteration: 1
 Score =  115 bits (289), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 64/115 (55%), Positives = 75/115 (65%), Gaps = 1/115 (0%)
Query: 12  GKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXXXXXXXX 71
           GK KSTK+ SRS KAG+ FPVGR+ R++K G    R+G GAP                  
Sbjct: 6   GKKKSTKT-SRSAKAGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELA 64
Query: 72  GNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMG 126
            NAARDNKK R+ PRHI LAV NDEEL++LL  VTIA+GGVLPNIH  LL +K G
Sbjct: 65  VNAARDNKKGRVTPRHILLAVANDEELNQLLKGVTIASGGVLPNIHPELLAKKRG 119

>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 =  115 bits (288), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 56/90 (62%), Positives = 64/90 (71%)
Query: 21  SRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKK 80
           SRS +AGLQFPVGR+ R L+ G YA+RVGAGAP                  GNAARDNKK
Sbjct: 2   SRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKK 61
Query: 81  NRIVPRHIQLAVRNDEELSKLLGTVTIANG 110
            RI+PRH+QLA+RNDEEL+KLLG VTIA G
Sbjct: 62  TRIIPRHLQLAIRNDEELNKLLGKVTIAQG 91

>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 = 97.1 bits (240), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 56/114 (49%), Positives = 72/114 (63%), Gaps = 3/114 (2%)
Query: 12  GKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYAD-RVGAGAPXXXXXXXXXXXXXXXXX 70
           GK K TK++SRS +AGLQFPVGRI R LK+   +  RVGA A                  
Sbjct: 11  GKAK-TKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLEL 69
Query: 71  XGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRK 124
            GNA++D K  RI PRH+QLA+R DEEL  L+   TIA GGV+P+IH++L+ +K
Sbjct: 70  AGNASKDLKVKRITPRHLQLAIRGDEELDSLI-KATIAGGGVIPHIHKSLIGKK 122

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

Iteration: 1
 Score = 79.7 bits (195), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 46/95 (48%), Positives = 57/95 (60%), Gaps = 6/95 (6%)
Query: 25  KAGLQFPVGRIARFLK---AGKYADRVGAGAPXXXXXXXXXXXXXXXXXXGNAARDNKKN 81
           +AGLQFPVGRI R+LK    G+   RVG+ A                   GNAA+D K  
Sbjct: 101 RAGLQFPVGRIKRYLKRHATGR--TRVGSKAAIYLTAVLEYLTAEVLELAGNAAKDLKVK 158
Query: 82  RIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNI 116
           RI PRH+QLA+R D+EL  L+   TIA+GGVLP+I
Sbjct: 159 RITPRHLQLAIRGDDELDSLIRA-TIASGGVLPHI 192
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	139
1tzy_A	129	Histone H2A-IV; histone-fold, tetramer-dimer-dimer	3e-45
2f8n_G	120	Core histone macro-H2A.1; nucleosome, NCP, macroh2	6e-45
2f8n_K	149	Histone H2A type 1; nucleosome, NCP, macroh2A, his	7e-45
1id3_C	131	Histone H2A.1; nucleosome core particle, chromatin	4e-44
2nqb_C	123	Histone H2A; nucleosome, NCP, chromatin, structura	3e-43
1f66_C	128	Histone H2A.Z; nucleosome, chromatin, histone vari	6e-38
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	1e-27
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	3e-23
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	2e-11
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	4e-08
3ksy_A	1049	SOS-1, SON of sevenless homolog 1; RAS, RAS activa	4e-07
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 =  143 bits (360), Expect = 3e-45
 Identities = 85/122 (69%), Positives = 99/122 (81%)

Query: 6   STKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAA 65
           S +G +G     K+ SRS +AGLQFPVGR+ R L+ G YA+RVGAGAPVYL+AVLEYL A
Sbjct: 2   SGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA 61

Query: 66  EVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKM 125
           E+LELAGNAARDNKK RI+PRH+QLA+RNDEEL+KLLG VTIA GGVLPNI   LLP+K 
Sbjct: 62  EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKT 121

Query: 126 GK 127
             
Sbjct: 122 DS 123

>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 =  141 bits (357), Expect = 6e-45
 Identities = 75/117 (64%), Positives = 89/117 (76%)

Query: 10  GRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLE 69
            RG  K +   SRS KAG+ FPVGR+ R++K G    R+G GAPVY++AVLEYL AE+LE
Sbjct: 3   SRGGKKKSTKTSRSAKAGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILE 62

Query: 70  LAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMG 126
           LA NAARDNKK R+ PRHI LAV NDEEL++LL  VTIA+GGVLPNIH  LL +K G
Sbjct: 63  LAVNAARDNKKGRVTPRHILLAVANDEELNQLLKGVTIASGGVLPNIHPELLAKKRG 119

>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 =  142 bits (359), Expect = 7e-45
 Identities = 83/122 (68%), Positives = 99/122 (81%)

Query: 6   STKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAA 65
           S +G +G     K+ +RS +AGLQFPVGR+ R L+ G Y++RVGAGAPVYL+AVLEYL A
Sbjct: 21  SGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTA 80

Query: 66  EVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKM 125
           E+LELAGNAARDNKK RI+PRH+QLA+RNDEEL+KLLG VTIA GGVLPNI   LLP+K 
Sbjct: 81  EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKT 140

Query: 126 GK 127
             
Sbjct: 141 ES 142

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

 Score =  140 bits (353), Expect = 4e-44
 Identities = 91/134 (67%), Positives = 105/134 (78%), Gaps = 4/134 (2%)

Query: 6   STKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAA 65
             KGG+    +  S SRS KAGL FPVGR+ R L+ G YA R+G+GAPVYL+AVLEYLAA
Sbjct: 2   GGKGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAA 61

Query: 66  EVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKM 125
           E+LELAGNAARDNKK RI+PRH+QLA+RND+EL+KLLG VTIA GGVLPNIHQNLLP+K 
Sbjct: 62  EILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPKKS 121

Query: 126 GKGREDIGSASQEF 139
            K       ASQE 
Sbjct: 122 AKA----TKASQEL 131

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

 Score =  138 bits (347), Expect = 3e-43
 Identities = 86/118 (72%), Positives = 99/118 (83%)

Query: 10  GRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLE 69
           G+G     K+ SRS++AGLQFPVGRI R L+ G YA+RVGAGAPVYL+AV+EYLAAEVLE
Sbjct: 4   GKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLE 63

Query: 70  LAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGK 127
           LAGNAARDNKK RI+PRH+QLA+RNDEEL+KLL  VTIA GGVLPNI   LLP+K  K
Sbjct: 64  LAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTEK 121

>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 =  124 bits (312), Expect = 6e-38
 Identities = 71/128 (55%), Positives = 92/128 (71%), Gaps = 4/128 (3%)

Query: 1   MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADR-VGAGAPVYLSAV 59
           M+   + K   GK K TK++SRS +AGLQFPVGRI R LK+   +   VGA A VY +A+
Sbjct: 1   MAGGKAGKDS-GKAK-TKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAI 58

Query: 60  LEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQN 119
           LEYL AEVLELAGNA++D K  RI PRH+QLA+R DEEL  L+   TIA GGV+P+IH++
Sbjct: 59  LEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIK-ATIAGGGVIPHIHKS 117

Query: 120 LLPRKMGK 127
           L+ +K  +
Sbjct: 118 LIGKKGQQ 125

>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 = 99.9 bits (247), Expect = 1e-27
 Identities = 64/111 (57%), Positives = 79/111 (71%), Gaps = 2/111 (1%)

Query: 7   TKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADR-VGAGAPVYLSAVLEYLAA 65
           T+       ST++ S S +AGLQFPVGRI R+LK        VG+ A +YL+AVLEYL A
Sbjct: 83  TRAVTKYSSSTQAQSSSARAGLQFPVGRIKRYLKRHATGRTRVGSKAAIYLTAVLEYLTA 142

Query: 66  EVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNI 116
           EVLELAGNAA+D K  RI PRH+QLA+R D+EL  L+   TIA+GGVLP+I
Sbjct: 143 EVLELAGNAAKDLKVKRITPRHLQLAIRGDDELDSLIR-ATIASGGVLPHI 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 = 86.1 bits (213), Expect = 3e-23
 Identities = 16/80 (20%), Positives = 34/80 (42%)

Query: 21  SRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKK 80
           S+  K   +FP  RI + ++  +   +V A  PV +S  LE     +L+ A    +    
Sbjct: 3   SKKKKYNARFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNA 62

Query: 81  NRIVPRHIQLAVRNDEELSK 100
             +   H++  +  + + + 
Sbjct: 63  KTMTTSHLKQCIELEGDPAA 82

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

 Score = 55.7 bits (134), Expect = 2e-11
 Identities = 17/77 (22%), Positives = 33/77 (42%)

Query: 29  QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHI 88
           + P+ RI + +K  +    + A APV  +   +    E+   A     DNK+  +    I
Sbjct: 19  ELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDI 78

Query: 89  QLAVRNDEELSKLLGTV 105
            +A+   ++   L+  V
Sbjct: 79  AMAITKFDQFDFLIDIV 95

>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 = 48.2 bits (114), Expect = 4e-08
 Identities = 16/95 (16%), Positives = 32/95 (33%), Gaps = 1/95 (1%)

Query: 12  GKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELA 71
           G+P+S   + R   A    P+ R+   +K+      +       ++   E     +   A
Sbjct: 2   GEPRSQPPVERPPTAETFLPLSRVRTIMKSSMDTGLITNEVLFLMTKCTELFVRHLAGAA 61

Query: 72  GNAARDNKKNRIV-PRHIQLAVRNDEELSKLLGTV 105
                  +    +   H+   V  ++ L  LL  V
Sbjct: 62  YTEEFGQRPGEALKYEHLSQVVNKNKNLEFLLQIV 96

>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 = 47.1 bits (111), Expect = 4e-07
 Identities = 25/81 (30%), Positives = 43/81 (53%), Gaps = 1/81 (1%)

Query: 22  RSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKN 81
           R  +  L  PV +I   LK      ++     VY+ AVLEY++A++L+L GN  R+ +  
Sbjct: 97  RKRRNPLSLPVEKIHPLLKE-VLGYKIDHQVSVYIVAVLEYISADILKLVGNYVRNIRHY 155

Query: 82  RIVPRHIQLAVRNDEELSKLL 102
            I  + I++A+  D+ L  + 
Sbjct: 156 EITKQDIKVAMCADKVLMDMF 176

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

 Score = 37.4 bits (87), Expect = 1e-04
 Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 4/64 (6%)

Query: 31 PVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQL 90
          PV R+ R  KAG  A+RV   A   L+  LE  A E+ + A   AR   +  +    I+L
Sbjct: 11 PVDRLIR--KAG--AERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKL 66

Query: 91 AVRN 94
          A+++
Sbjct: 67 AIKS 70

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	139
1id3_C	131	Histone H2A.1; nucleosome core particle, chromatin	100.0
1tzy_A	129	Histone H2A-IV; histone-fold, tetramer-dimer-dimer	100.0
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
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	99.9
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	99.9
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	99.81
4g92_C	119	HAPE; transcription factor, nucleosome, minor groo	99.79
1tzy_D	103	Histone H4-VI; histone-fold, tetramer-dimer-dimer,	99.78
2yfw_B	103	Histone H4, H4; cell cycle, kinetochore, centromer	99.77
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	99.73
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	99.45
1id3_B	102	Histone H4; nucleosome core particle, chromatin, p	99.41
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	99.29
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	99.28
1n1j_A	93	NF-YB; histone-like PAIR, DNA binding protein; 1.6	99.09
3b0c_W	76	CENP-W, centromere protein W; histone fold, DNA bi	98.96
2hue_C	84	Histone H4; mini beta sheet, elongated beta sandwh	98.95
2byk_B	128	Chrac-14; nucleosome sliding, histone fold, DNA-bi	98.94
1taf_B	70	TFIID TBP associated factor 62; transcription init	98.9
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	98.82
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	98.62
1taf_A	68	TFIID TBP associated factor 42; transcription init	98.57
1jfi_B	179	DR1 protein, transcription regulator NC2 beta chai	98.51
3v9r_A	90	MHF1, uncharacterized protein YOL086W-A; histone f	98.34
2hue_B	77	Histone H3; mini beta sheet, elongated beta sandwh	98.22
4dra_A	113	Centromere protein S; DNA binding complex, DNA dam	98.22
3nqj_A	82	Histone H3-like centromeric protein A; alpha helix	98.21
3b0b_B	107	CENP-S, centromere protein S; histone fold, DNA bi	98.16
2yfv_A	100	Histone H3-like centromeric protein CSE4; cell cyc	98.02
3vh5_A	140	CENP-S; histone fold, chromosome segregation, DNA	98.01
3r45_A	156	Histone H3-like centromeric protein A; histone fol	98.0
3nqu_A	140	Histone H3-like centromeric protein A; alpha helix	98.0
1tzy_B	126	Histone H2B; histone-fold, tetramer-dimer-dimer, D	97.96
1tzy_C	136	Histone H3; histone-fold, tetramer-dimer-dimer, DN	97.91
2ly8_A	121	Budding yeast chaperone SCM3; centromere protein,	97.87
2nqb_D	123	Histone H2B; nucleosome, NCP, chromatin, structura	97.74
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	97.71
1bh9_B	89	TAFII28; histone fold, tata binding protein, trans	97.32
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	97.22
4dra_E	84	Centromere protein X; DNA binding complex, DNA dam	96.9
3b0b_C	81	CENP-X, centromere protein X; histone fold, DNA bi	96.74
1h3o_B	76	Transcription initiation factor TFIID 20/15 kDa su	95.96
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	93.45
1wwi_A	148	Hypothetical protein TTHA1479; structural genomics	89.52
1k6k_A	143	ATP-dependent CLP protease ATP-binding subunit CLP	88.08
1khy_A	148	CLPB protein; alpha helix, chaperone; 1.95A {Esche	83.72
3v9r_B	88	MHF2, uncharacterized protein YDL160C-A; histone f	83.43
3fes_A	145	ATP-dependent CLP endopeptidase; alpha-helical bun	81.99
2y1q_A	150	CLPC N-domain, negative regulator of genetic compe	81.69
1r4v_A	171	Hypothetical protein AQ_328; structural genomics,	81.2
3fh2_A	146	Probable ATP-dependent protease (heat shock prote;	80.52

>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=4.2e-48  Score=286.42  Aligned_cols=128  Identities=71%  Similarity=1.112  Sum_probs=107.5

Q ss_pred             CCCCCCCCCCCCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhh
Q 032523            8 KGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRH   87 (139)
Q Consensus         8 ~~~~~~~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~h   87 (139)
                      ++|||+.++++.+|+|+|++|+|||+||+|||+++++++||+++|+|||+||||||++||||+|+|+|+++++++|+|+|
T Consensus         4 ~~~~~~~~~~~~~srS~ragLqfPV~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~h   83 (131)
T 1id3_C            4 KGGKAGSAAKASQSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRH   83 (131)
T ss_dssp             ------------CCTTGGGTCSSCHHHHHHHHHTTCSCSEECSSHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHH
T ss_pred             CCCCCCCCCCCCCCccccCCeecCHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHH
Confidence            56777777889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhCcHHHHhhhcCceecCCccCCcccccccccccCCCCccCCccCCCC
Q 032523           88 IQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGKGREDIGSASQEF  139 (139)
Q Consensus        88 I~~AI~nD~EL~~L~~~~~Ia~ggv~P~i~~~l~~~k~~~~~~~~~~~~~~~  139 (139)
                      |++||+||+|||+||+++||++|||+|+||++|++++.+++    ..++|++
T Consensus        84 I~lAI~nDeEL~~Ll~~vtIa~ggvlP~i~~~l~~k~~~~~----~~~~~~~  131 (131)
T 1id3_C           84 LQLAIRNDDELNKLLGNVTIAQGGVLPNIHQNLLPKKSAKA----TKASQEL  131 (131)
T ss_dssp             HHHHHHTCHHHHHHTTTEEETTCCCCCCCCGGGSCCSCCSC----C------
T ss_pred             HHHHHhccHHHHHHhcCceecCCccCCCccHHHcCcccccc----ccccccC
Confidence            99999999999999999999999999999999999998766    2556653

>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=6.1e-48  Score=284.88  Aligned_cols=124  Identities=70%  Similarity=1.114  Sum_probs=105.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 032523            1 MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKK   80 (139)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~   80 (139)
                      |||.| +++||   ++++.+|+|+|++|+|||+||+|||+++++++||+++|+|||+||||||++||||+|+|.|+++++
T Consensus         1 m~~~~-~~~~~---~~~~~~srS~ragLqfPV~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~   76 (129)
T 1tzy_A            1 MSGRG-KQGGK---ARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKK   76 (129)
T ss_dssp             -----------------CCCCHHHHHTCSSCHHHHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCC-CCCCC---CCCCCCCccccCceeccHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            88877 43444   677889999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccchhhHHHhhhCcHHHHhhhcCceecCCccCCcccccccccccCCC
Q 032523           81 NRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGKG  128 (139)
Q Consensus        81 krItP~hI~~AI~nD~EL~~L~~~~~Ia~ggv~P~i~~~l~~~k~~~~  128 (139)
                      ++|+|+||++||+||+|||+||+++||++|||+|+||++|+++|.+++
T Consensus        77 krItp~hi~lAI~nDeEL~~L~~~vtIa~ggvlP~i~~~l~~k~~~~~  124 (129)
T 1tzy_A           77 TRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTDSH  124 (129)
T ss_dssp             SEECHHHHHHHHHTSHHHHHHTTTEEETTCCCCCCCCGGGSCC-----
T ss_pred             CeEcHHHHHHHHhccHHHHHHhCCCeecCCCcCCCCCHHHcCcccccc
Confidence            999999999999999999999999999999999999999999987655

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

Probab=100.00  E-value=5e-47  Score=278.01  Aligned_cols=118  Identities=72%  Similarity=1.094  Sum_probs=105.1

Q ss_pred             CCCCCCCCCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHH
Q 032523           11 RGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQL   90 (139)
Q Consensus        11 ~~~~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~   90 (139)
                      ||+.++++.+|+|+|++|+|||+||+|||+++++++||+++|+|||+||||||++||||+|+|.|++.++++|+|+||++
T Consensus         5 ~~~~~~~~~~s~s~ragL~fPV~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hi~l   84 (123)
T 2nqb_C            5 KGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQL   84 (123)
T ss_dssp             --------CCCHHHHHTCSSCHHHHHHHHHHTTSCSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHH
T ss_pred             CCCCCCCCCCCccccCCeeccHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHHH
Confidence            45557778999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhCcHHHHhhhcCceecCCccCCcccccccccccCCC
Q 032523           91 AVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGKG  128 (139)
Q Consensus        91 AI~nD~EL~~L~~~~~Ia~ggv~P~i~~~l~~~k~~~~  128 (139)
                      ||+||+|||+||+++||++|||+|+||++|+++|.+++
T Consensus        85 AI~nDeEL~~Ll~~vtia~ggvlp~i~~~l~~k~~~~~  122 (123)
T 2nqb_C           85 AIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTEKK  122 (123)
T ss_dssp             HHHTSHHHHHHTTTEEETTCCCCCCCCGGGSSCC----
T ss_pred             HHhccHHHHHHhcCceeCCCCcCCCccHHHcCcccccC
Confidence            99999999999999999999999999999999987654

>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=5.9e-47  Score=276.62  Aligned_cols=113  Identities=65%  Similarity=0.979  Sum_probs=106.3

Q ss_pred             CCCCCCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           14 PKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        14 ~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      +++++.+|+|+|++|+|||+||+|||++++|++||+++|+|||+||||||++||||+|+|.|+++++++|+|+||++||+
T Consensus         7 ~~~~~~~srs~ragLqfPV~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~~rItp~hi~lAI~   86 (120)
T 2f8n_G            7 KKKSTKTSRSAKAGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILLAVA   86 (120)
T ss_dssp             ---CCCCCHHHHHTCSSCHHHHHHHHHHHSSSCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             CCCcCCcCcccccCccCChHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHHHHh
Confidence            35667899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcHHHHhhhcCceecCCccCCcccccccccccC
Q 032523           94 NDEELSKLLGTVTIANGGVLPNIHQNLLPRKMG  126 (139)
Q Consensus        94 nD~EL~~L~~~~~Ia~ggv~P~i~~~l~~~k~~  126 (139)
                      ||+|||+||+++||++|||+|+||++|+++|.+
T Consensus        87 nDeEL~~Ll~~vtia~ggv~p~i~~~l~~k~~~  119 (120)
T 2f8n_G           87 NDEELNQLLKGVTIASGGVLPNIHPELLAKKRG  119 (120)
T ss_dssp             TSHHHHHHTTTEEETTCCCCCCCCGGGSCCC--
T ss_pred             cCHHHHHHhCCceECCCCcCCCcCHHHcCCccC
Confidence            999999999999999999999999999998753

>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=9.3e-47  Score=284.17  Aligned_cols=124  Identities=68%  Similarity=1.076  Sum_probs=104.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 032523            1 MSSAGSTKGGRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKK   80 (139)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~   80 (139)
                      |||.| +.+   +.++++.+|+|+|++|+|||+||+|||++++|++||+++|+|||+||||||++||||+|+|.|++.++
T Consensus        20 ~~~~~-~~~---~~~~~k~~srS~ragLqFPVgrI~R~LK~~~~a~RVs~~A~VyLAAVLEYL~aEILelAgn~A~~~kr   95 (149)
T 2f8n_K           20 MSGRG-KQG---GKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKK   95 (149)
T ss_dssp             ------------------CCCHHHHHTCSSCHHHHHHHHHHTTSCSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             cccCC-CCC---CCCCCCCCCccccCCeeccHHHHHHHHHccccccccCcCcHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            67666 322   33677889999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CccchhhHHHhhhCcHHHHhhhcCceecCCccCCcccccccccccCCC
Q 032523           81 NRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGKG  128 (139)
Q Consensus        81 krItP~hI~~AI~nD~EL~~L~~~~~Ia~ggv~P~i~~~l~~~k~~~~  128 (139)
                      ++|+|+||++||+||+|||+||++++|++|||+|+||++|++++.+++
T Consensus        96 krItprhI~lAI~nDeEL~~Ll~~vtIa~gGVlP~i~~~l~~k~~~~~  143 (149)
T 2f8n_K           96 TRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESH  143 (149)
T ss_dssp             SEECHHHHHHHHHHSHHHHHHTTTEEETTCCCCCCCCGGGSCC-----
T ss_pred             CcCcHHHHHHHHhccHHHHHHhcCceEcCCCCCCCccHHHcCcccccc
Confidence            999999999999999999999999999999999999999999998766

>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=1.1e-45  Score=272.42  Aligned_cols=120  Identities=58%  Similarity=0.883  Sum_probs=99.5

Q ss_pred             CCCCC-CCCCCCCcCcccccCcccchHHHHHHHHhCCCc-cccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccch
Q 032523            8 KGGRG-KPKSTKSISRSHKAGLQFPVGRIARFLKAGKYA-DRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVP   85 (139)
Q Consensus         8 ~~~~~-~~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~-~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP   85 (139)
                      +++|+ +..+++.+|+|+|++|+|||+||+|||+++.++ +||+++|+|||+||||||++||||+|+|.|++.++++|+|
T Consensus         5 ~~~~~~~~~~~~~~srS~ragLqfPV~ri~R~Lk~~~~a~~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp   84 (128)
T 1f66_C            5 KAGKDSGKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITP   84 (128)
T ss_dssp             ------------CCCHHHHHTCSSCHHHHHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECH
T ss_pred             CCCCCCCCcCCCCcCccccCCccCChHHHHHHHHHcccchhhccccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEcH
Confidence            44542 334568899999999999999999999999887 5999999999999999999999999999999999999999


Q ss_pred             hhHHHhhhCcHHHHhhhcCceecCCccCCcccccccccccCCC
Q 032523           86 RHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRKMGKG  128 (139)
Q Consensus        86 ~hI~~AI~nD~EL~~L~~~~~Ia~ggv~P~i~~~l~~~k~~~~  128 (139)
                      +||++||+||+|||+||+ +||++|||+|+||++|+++|.+++
T Consensus        85 rhi~lAI~nDeEL~~Ll~-~tia~ggv~P~i~~~l~~k~~~~~  126 (128)
T 1f66_C           85 RHLQLAIRGDEELDSLIK-ATIAGGGVIPHIHKSLIGKKGQQK  126 (128)
T ss_dssp             HHHHHHHHHSHHHHHHCC-SEETTCCCCCCCCGGGC-------
T ss_pred             HHHHHHHhccHHHhhhhc-ceecCCccCCCCCHHhcCcccccC
Confidence            999999999999999995 599999999999999999987654

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

Probab=100.00  E-value=5.3e-36  Score=233.44  Aligned_cols=98  Identities=63%  Similarity=0.970  Sum_probs=94.4

Q ss_pred             CCcCcccccCcccchHHHHHHHHhCCCc-cccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcH
Q 032523           18 KSISRSHKAGLQFPVGRIARFLKAGKYA-DRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDE   96 (139)
Q Consensus        18 ~~~s~ssragL~fPvsri~R~Lk~~~~~-~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~   96 (139)
                      +.+|+|+|+||+|||+||+|||++++++ +||+++|+|||+||||||++||+|+|+|.|++.++++|+|+||++||+||+
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            5679999999999999999999999887 699999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhhcCceecCCccCCcc
Q 032523           97 ELSKLLGTVTIANGGVLPNI  116 (139)
Q Consensus        97 EL~~L~~~~~Ia~ggv~P~i  116 (139)
                      |||+||+ ++|++|||+|+|
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            9999996 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=99.90  E-value=1.1e-24  Score=202.25  Aligned_cols=101  Identities=25%  Similarity=0.411  Sum_probs=81.5

Q ss_pred             CcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHH
Q 032523           19 SISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEEL   98 (139)
Q Consensus        19 ~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL   98 (139)
                      ..++|+||||+|||+||+|+| ++.|++||+.+|||||+||||||++||||+|||+|++.++.+|+|+||++||+||+||
T Consensus        94 ~~~~~~~~~l~~pv~~~~~~l-~~~~~~r~~~~~~~y~~avleyl~~~~l~la~~~~~~~~~~~i~p~~~~~ai~~d~eL  172 (1049)
T 3ksy_A           94 IEKRKRRNPLSLPVEKIHPLL-KEVLGYKIDHQVSVYIVAVLEYISADILKLVGNYVRNIRHYEITKQDIKVAMCADKVL  172 (1049)
T ss_dssp             HTTCCCSSSCSSCHHHHHHHH-HHHHCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCBCCHHHHHHHHHHCSSH
T ss_pred             hhcccccCCccccHHHHHHHh-hcccccccCCCCcchhHHHHHHHHHHHHHHHHHHHHHcCCceecCccccccccCCHHH
Confidence            468999999999999999999 7789999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhcCceecCCccCCccccccc
Q 032523           99 SKLLGTVTIANGGVLPNIHQNLL  121 (139)
Q Consensus        99 ~~L~~~~~Ia~ggv~P~i~~~l~  121 (139)
                      ..||++. ...+|++|+......
T Consensus       173 ~~l~~~d-ee~~~~lp~~~~~~~  194 (1049)
T 3ksy_A          173 MDMFHQD-VEDINILSLTDEEPS  194 (1049)
T ss_dssp             HHHCC------------------
T ss_pred             HHHHhhc-cccccCCCCccccCc
Confidence            9999764 456778887665433

>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=99.90  E-value=3.3e-24  Score=151.03  Aligned_cols=81  Identities=19%  Similarity=0.356  Sum_probs=62.4

Q ss_pred             cccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHHHhh
Q 032523           22 RSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKL  101 (139)
Q Consensus        22 ~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL~~L  101 (139)
                      ++.+++++||++||+|+|+.+.+..||+.+|++|+++++|||+.||+++|++.|.+.++++|+|+||..||++|++|++|
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            57789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             h
Q 032523          102 L  102 (139)
Q Consensus       102 ~  102 (139)
                      +
T Consensus        84 ~   84 (98)
T 1jfi_A           84 K   84 (98)
T ss_dssp             -
T ss_pred             H
Confidence            9

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

Probab=99.81  E-value=4.2e-20  Score=129.66  Aligned_cols=79  Identities=20%  Similarity=0.303  Sum_probs=71.9

Q ss_pred             cccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHHHhhh
Q 032523           24 HKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLL  102 (139)
Q Consensus        24 sragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL~~L~  102 (139)
                      .-.+++||++||+|+|+.+.+..||+.+|++|+++++|||+.+|++.|++.|.+.++++|+++||..||++|++|++|.
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            3457889999999999999888999999999999999999999999999999999999999999999999999999998

>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=99.79  E-value=2.1e-19  Score=130.40  Aligned_cols=76  Identities=24%  Similarity=0.309  Sum_probs=73.4

Q ss_pred             CcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHHHhhh
Q 032523           27 GLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLL  102 (139)
Q Consensus        27 gL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL~~L~  102 (139)
                      ..+||++||+|+|+.+.+..+|+.+|++|+++++|||+.+|+++|++.|...++++|+|+||..||.+|++|++|.
T Consensus        39 ~~~lPvaRIkrImK~d~~~~~is~eA~v~la~a~E~Fi~~L~~~A~~~a~~~krktI~~~di~~Av~~~e~~dFL~  114 (119)
T 4g92_C           39 IHQLPLARIKKVMKADPEVKMISAEAPILFAKGCDVFITELTMRAWIHAEDNKRRTLQRSDIAAALSKSDMFDFLI  114 (119)
T ss_dssp             CCSSCHHHHHHHHHTSTTCCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTCGGGGGGT
T ss_pred             cCCCCHHHHHHHHhhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccCHHHHHHHHhcCchhhHHH
Confidence            4569999999999999899999999999999999999999999999999999999999999999999999999987

>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=99.78  E-value=4.8e-19  Score=125.51  Aligned_cols=90  Identities=22%  Similarity=0.334  Sum_probs=71.0

Q ss_pred             CCCCCCCCCC----CCCCCCCCCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHh
Q 032523            1 MSSAGSTKGG----RGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAAR   76 (139)
Q Consensus         1 ~~~~~~~~~~----~~~~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~   76 (139)
                      |||.|  ++|    ||+++++.++++++..+  ||++.|+|+++.. ...||+.++..+|+.+|||++.+|++.|.+.|+
T Consensus         1 m~g~g--k~~kg~~~~~~kr~~k~~r~~~~g--ip~~~I~Rlar~~-G~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~   75 (103)
T 1tzy_D            1 MSGRG--KGGKGLGKGGAKRHRKVLRDNIQG--ITKPAIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTE   75 (103)
T ss_dssp             ----------------------CCCCCGGGG--SCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCC--CCCCCCCCCCccccccchhhhccc--CCHHHHHHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            88876  344    45667888899999999  9999999999998 568999999999999999999999999999999


Q ss_pred             hcCCCccchhhHHHhhhCc
Q 032523           77 DNKKNRIVPRHIQLAVRND   95 (139)
Q Consensus        77 ~~~~krItP~hI~~AI~nD   95 (139)
                      +.++++|+++||.+|+++.
T Consensus        76 hakRktIt~~DV~~Alr~~   94 (103)
T 1tzy_D           76 HAKRKTVTAMDVVYALKRQ   94 (103)
T ss_dssp             HTTCSEECHHHHHHHHHHT
T ss_pred             HcCCCcCCHHHHHHHHHHc
Confidence            9999999999999999865

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

Probab=99.77  E-value=5e-19  Score=125.52  Aligned_cols=91  Identities=23%  Similarity=0.332  Sum_probs=63.0

Q ss_pred             CCCCCCCCCCC----CCCCCCCCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHh
Q 032523            1 MSSAGSTKGGR----GKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAAR   76 (139)
Q Consensus         1 ~~~~~~~~~~~----~~~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~   76 (139)
                      |||.|  ++||    |+.+++.++++++.++  ||++.|+|+++.. ...||+.++.++|+.+|||++.+|++.|.+.|+
T Consensus         1 m~~~g--k~gkg~~~~~~kr~~~~~r~~~~g--ip~~~I~Rlar~~-G~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~   75 (103)
T 2yfw_B            1 MSGRG--KGGKGLGKGGAKRHRKILRDNIQG--ITKPAIRRLARRG-GVKRISGLIYEEVRNVLKTFLESVIRDAVTYTE   75 (103)
T ss_dssp             ---------------------------------CCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCC--CCCCCCCCCCccchhhhhhhhhcc--CCHHHHHHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            88886  3554    4667888899999999  9999999999998 568999999999999999999999999999999


Q ss_pred             hcCCCccchhhHHHhhhCcH
Q 032523           77 DNKKNRIVPRHIQLAVRNDE   96 (139)
Q Consensus        77 ~~~~krItP~hI~~AI~nD~   96 (139)
                      +.++++|+++||.+|+++..
T Consensus        76 hakRktvt~~DV~~Alr~~g   95 (103)
T 2yfw_B           76 HAKRKTVTSLDVVYALKRQG   95 (103)
T ss_dssp             HTTCSEECHHHHHHHHHHHC
T ss_pred             HcCCCcCcHHHHHHHHHHcC
Confidence            99999999999999998654

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

Probab=99.73  E-value=1.8e-18  Score=128.81  Aligned_cols=85  Identities=14%  Similarity=0.211  Sum_probs=62.8

Q ss_pred             CCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHH-hhcCCCccchhhHHHhhhCcH
Q 032523           18 KSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAA-RDNKKNRIVPRHIQLAVRNDE   96 (139)
Q Consensus        18 ~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A-~~~~~krItP~hI~~AI~nD~   96 (139)
                      +..+++.+..++||++||+|+|+.+.+..+|+.+|+++++.++|||+.+|++.|++.| ...++++|++.||..||.+++
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            3578888999999999999999999999999999999999999999999999999999 999999999999999999999


Q ss_pred             HHHhhh
Q 032523           97 ELSKLL  102 (139)
Q Consensus        97 EL~~L~  102 (139)
                      +|+||.
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=99.45  E-value=1.3e-13  Score=104.00  Aligned_cols=71  Identities=17%  Similarity=0.200  Sum_probs=68.3

Q ss_pred             cccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCc
Q 032523           24 HKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRND   95 (139)
Q Consensus        24 sragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD   95 (139)
                      .+.++.||++.|.|+|++. +..|||++|.++|+.+||||+.+|+..|.+.|.+.+|++|+++||.+|++++
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            4788999999999999999 8999999999999999999999999999999999999999999999999875

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

Probab=99.41  E-value=6.8e-13  Score=93.84  Aligned_cols=83  Identities=19%  Similarity=0.282  Sum_probs=66.3

Q ss_pred             CCCCCCCCCCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHH
Q 032523           10 GRGKPKSTKSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQ   89 (139)
Q Consensus        10 ~~~~~~~~~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~   89 (139)
                      ||||++|..++.+.+..+  +|.+.|.|+++.. ...|||.++...|..+|||++.+|+..|...|++.+|++|+++||.
T Consensus        11 ~~~g~kr~~k~~r~~i~~--ip~~~I~Rlar~~-Gv~rIS~da~~~l~~~le~fi~~I~~dA~~~a~HakRKTVt~~DV~   87 (102)
T 1id3_B           11 GKGGAKRHRKILRDNIQG--ITKPAIRRLARRG-GVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVV   87 (102)
T ss_dssp             -------------CCGGG--SCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHH
T ss_pred             CCCccchHHHHHHhccCC--CCHHHHHHHHHHc-CchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHH
Confidence            466888888888888887  8999999999987 7899999999999999999999999999999999999999999999


Q ss_pred             HhhhCc
Q 032523           90 LAVRND   95 (139)
Q Consensus        90 ~AI~nD   95 (139)
                      +|++..
T Consensus        88 ~ALkr~   93 (102)
T 1id3_B           88 YALKRQ   93 (102)
T ss_dssp             HHHHHT
T ss_pred             HHHHHc
Confidence            999854

>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=99.29  E-value=8.9e-12  Score=81.41  Aligned_cols=64  Identities=30%  Similarity=0.437  Sum_probs=61.6

Q ss_pred             ccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        29 ~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      .||.++|.|+|++. +..||+.+|...|..++|+|+.+|.+.|...|.+.+|++|+|+||.+|++
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            48999999999999 77899999999999999999999999999999999999999999999986

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

Probab=99.28  E-value=9.3e-12  Score=81.98  Aligned_cols=65  Identities=26%  Similarity=0.405  Sum_probs=62.4

Q ss_pred             ccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhC
Q 032523           29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN   94 (139)
Q Consensus        29 ~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~n   94 (139)
                      .||++.|.|++++. +..||+.++...|..++|+++.+|++.|...|.+.+|++|+++||.+|+++
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            58999999999987 788999999999999999999999999999999999999999999999875

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

Probab=99.09  E-value=2.4e-10  Score=78.92  Aligned_cols=67  Identities=15%  Similarity=0.283  Sum_probs=63.0

Q ss_pred             CcccchHHHHHHHHhC-CCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           27 GLQFPVGRIARFLKAG-KYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        27 gL~fPvsri~R~Lk~~-~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      .+.||.++|.|+|++. ....||+.+|...|..+.|.|+.+|...|...|.+.+|++|+++||..|++
T Consensus         6 d~~LP~a~i~ri~K~~~~~~~~is~dA~~~l~~a~e~Fi~~l~~~A~~~a~~~kRkTI~~~Dv~~Al~   73 (93)
T 1n1j_A            6 DIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMS   73 (93)
T ss_dssp             -CCCCHHHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHH
T ss_pred             cccCChhHHHHHHHHhCCccceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHH
Confidence            5789999999999998 445799999999999999999999999999999999999999999999997

>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=98.96  E-value=2.1e-09  Score=71.85  Aligned_cols=65  Identities=23%  Similarity=0.290  Sum_probs=61.0

Q ss_pred             ccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        29 ~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      .||.+.|.|+|++.-...+|+.+|...|..++|.|+.+|...|...|.+.++++|+++||..|++
T Consensus         4 ~LP~A~V~rI~K~~~p~~~is~~A~~~i~~~~~~Fi~~la~eA~~~a~~~~rKTI~~~dI~~A~~   68 (76)
T 3b0c_W            4 TVPRGTLRKIIKKHKPHLRLAANTDLLVHLSFLLFLHRLAEEARTNAFENKSKIIKPEHTIAAAK   68 (76)
T ss_dssp             CCCHHHHHHHHHHHCTTCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSBCHHHHHHHHH
T ss_pred             cccccHHHHHHHHhCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence            59999999999976456799999999999999999999999999999999999999999999985

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

Probab=98.95  E-value=2.9e-09  Score=72.50  Aligned_cols=71  Identities=17%  Similarity=0.215  Sum_probs=65.0

Q ss_pred             cccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCc
Q 032523           22 RSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRND   95 (139)
Q Consensus        22 ~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD   95 (139)
                      +.+..+  +|.+.|.|+++.. +..|||.++...|..++||++.+|+..|...+.+.+|++|+++||.+|++..
T Consensus         5 r~~~~~--ip~~~I~Riar~~-Gv~rIs~da~~~l~~~l~~~~~~I~~dA~~~a~ha~RKTvt~~DV~~Alk~~   75 (84)
T 2hue_C            5 RDNIQG--ITKPAIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ   75 (84)
T ss_dssp             GGGCCS--SCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTT
T ss_pred             cccCCC--CCHHHHHHHHHHc-CchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHc
Confidence            344445  8999999999988 8899999999999999999999999999999999999999999999999865

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

Probab=98.94  E-value=9e-10  Score=80.60  Aligned_cols=75  Identities=17%  Similarity=0.147  Sum_probs=64.2

Q ss_pred             CcccchHHHHHHHHh-CCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHHHhh
Q 032523           27 GLQFPVGRIARFLKA-GKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKL  101 (139)
Q Consensus        27 gL~fPvsri~R~Lk~-~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL~~L  101 (139)
                      .+.||+++|.|+|++ .....+|+.+|...|+.++|.|+.+|...|...|.+.+|++|+++||..|+...+-+++|
T Consensus         7 d~~LP~A~I~rImK~~~pd~~~iS~dA~~~l~ka~e~FI~~lt~~A~~~a~~~kRKTI~~~Dv~~Al~~l~f~~fl   82 (128)
T 2byk_B            7 DLNLPNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFESFV   82 (128)
T ss_dssp             ----CCSHHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCTTTH
T ss_pred             cccCCHHHHHHHHHHhCcccceECHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHcCcHHHH
Confidence            467999999999996 445789999999999999999999999999999999999999999999999876544443

>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=98.90  E-value=5.2e-09  Score=69.37  Aligned_cols=65  Identities=9%  Similarity=0.126  Sum_probs=62.1

Q ss_pred             cccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           28 LQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        28 L~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      -.||++.|+++.+.. +..+|++++...|+.-+||-+.||++.|.+.+++.+|++++.+||+.|++
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            469999999999988 88999999999999999999999999999999999999999999999975

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

Probab=98.82  E-value=8.2e-09  Score=77.74  Aligned_cols=64  Identities=17%  Similarity=0.255  Sum_probs=61.3

Q ss_pred             ccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhh
Q 032523           29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAV   92 (139)
Q Consensus        29 ~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI   92 (139)
                      -||.+.|.|+|++.-+..|||.+|...|+.++|.|+.+|...|.+.|.+.+|++|+++||..|+
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            4899999999999856699999999999999999999999999999999999999999999998

>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=98.62  E-value=2.9e-08  Score=70.89  Aligned_cols=71  Identities=8%  Similarity=0.033  Sum_probs=62.1

Q ss_pred             CcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHH
Q 032523           27 GLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEEL   98 (139)
Q Consensus        27 gL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL   98 (139)
                      .+.||.+-|.|+++.. ...|||.++...|..+++.++.+|...|...|++.+|++|+++||.+|++.+..+
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            3568999999999998 7889999999999999999999999999999999999999999999999865543

>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=98.57  E-value=2.2e-07  Score=61.16  Aligned_cols=61  Identities=18%  Similarity=0.066  Sum_probs=57.7

Q ss_pred             HHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhC
Q 032523           33 GRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN   94 (139)
Q Consensus        33 sri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~n   94 (139)
                      -.|.++|++. ++.+++..++..|.-.+|-++.+|+..|..+|.+.|+++|+.+||++||..
T Consensus         5 ~~i~~iLk~~-G~~~~~~~v~~~L~e~~~ry~~~il~dA~~~a~HAgrktv~~eDVkLAi~~   65 (68)
T 1taf_A            5 QVIMSILKEL-NVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLATEV   65 (68)
T ss_dssp             HHHHHHHHHT-TCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             HHHHHHHHHC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHh
Confidence            3588999987 899999999999999999999999999999999999999999999999974

>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=2.5e-07  Score=71.18  Aligned_cols=78  Identities=17%  Similarity=0.216  Sum_probs=67.5

Q ss_pred             cccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHHHhhh
Q 032523           24 HKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLL  102 (139)
Q Consensus        24 sragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL~~L~  102 (139)
                      .-..+.||++.|.|+|++.--..||+.+|...|..+++-|+..|...|...|.+.+|++|+++||..|+. +-+|..++
T Consensus        10 ~~eD~~LP~A~V~RImK~alp~~rISkDA~~al~ec~~eFI~~LtseA~e~a~~~~RKTI~~eDVl~Al~-~LgF~~fv   87 (179)
T 1jfi_B           10 NDDDLTIPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALE-SLGFGSYI   87 (179)
T ss_dssp             --CCCCCCHHHHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHH-HHTTGGGH
T ss_pred             chhhhhcCHHHHHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH-hcChHHHH
Confidence            3446789999999999988225799999999999999999999999999999999999999999999997 55555444

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

Probab=98.34  E-value=1.3e-06  Score=60.29  Aligned_cols=79  Identities=14%  Similarity=0.021  Sum_probs=65.9

Q ss_pred             ccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHHHhhhcC
Q 032523           25 KAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGT  104 (139)
Q Consensus        25 ragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL~~L~~~  104 (139)
                      |+.|.+-|++|-.=.-+ .....|+.++...|+.+++..+.+|.+-+...|++.||++|+++||.++++.++.|..++.+
T Consensus        11 Kaal~~~V~ki~~e~~~-~~g~~vs~~~i~aL~e~~~~~~~~ia~Dl~~fA~HAgRkTI~~eDV~L~~Rrn~~L~~~l~~   89 (90)
T 3v9r_A           11 KARLWIRVEERLQQVLS-SEDIKYTPRFINSLLELAYLQLGEMGSDLQAFARHAGRGVVNKSDLMLYLRKQPDLQERVTQ   89 (90)
T ss_dssp             HHHHHHHHHHHHHHHSC-SSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTCHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHHHH-hcCceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhChHHHHHhhc
Confidence            45566777776654421 12347999999999999999999999999999999999999999999999999999998754

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

Probab=98.22  E-value=4.1e-06  Score=56.31  Aligned_cols=66  Identities=24%  Similarity=0.205  Sum_probs=59.0

Q ss_pred             cccchHHHHHHHHhC----CCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           28 LQFPVGRIARFLKAG----KYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        28 L~fPvsri~R~Lk~~----~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      |.+|...+.|++++-    ....|++++|...|.-+.|.++-+++|-+...|.+.++.+|+|+||++|.+
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            567888888888765    234699999999999999999999999999999999999999999999975

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

Probab=98.22  E-value=2.1e-06  Score=61.59  Aligned_cols=75  Identities=19%  Similarity=0.214  Sum_probs=63.7

Q ss_pred             ccCcccchHHHHHHHHhCCCccc---cCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHHHhh
Q 032523           25 KAGLQFPVGRIARFLKAGKYADR---VGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKL  101 (139)
Q Consensus        25 ragL~fPvsri~R~Lk~~~~~~R---Vs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL~~L  101 (139)
                      ++.|.+.|++|-+   +. ...|   |+.++...|+.+++.++.+|.+-+...|++.||++|+++||.++++.++.|..+
T Consensus        26 Kaal~y~V~rIvk---e~-gaer~~~vS~~ai~aL~El~~~~~~~ia~Dl~~fAkHAgRkTI~~eDV~La~Rr~~~L~~~  101 (113)
T 4dra_A           26 KAAVHYTVGCLCE---EV-ALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARRSNSLLKY  101 (113)
T ss_dssp             HHHHHHHHHHHHH---HH-HHHHTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTCHHHHHH
T ss_pred             HHHHHHHHHHHHH---HH-HHHcCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHhCHHHHHH
Confidence            4556677666544   33 3334   999999999999999999999999999999999999999999999999999887


Q ss_pred             hc
Q 032523          102 LG  103 (139)
Q Consensus       102 ~~  103 (139)
                      +.
T Consensus       102 l~  103 (113)
T 4dra_A          102 IT  103 (113)
T ss_dssp             HH
T ss_pred             HH
Confidence            75

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

Probab=98.21  E-value=3.4e-06  Score=57.36  Aligned_cols=66  Identities=20%  Similarity=0.103  Sum_probs=59.4

Q ss_pred             cccchHHHHHHHHhCC------CccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           28 LQFPVGRIARFLKAGK------YADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        28 L~fPvsri~R~Lk~~~------~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      |-+|...+.|++++-.      ...|++++|...|.-+.|.++-+++|-+...|.+.++.+|.|.||++|.+
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            4578888888888653      35699999999999999999999999999999999999999999999875

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

Probab=98.16  E-value=2.7e-06  Score=60.45  Aligned_cols=78  Identities=14%  Similarity=0.167  Sum_probs=63.9

Q ss_pred             ccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHHHhhhc
Q 032523           25 KAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLG  103 (139)
Q Consensus        25 ragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL~~L~~  103 (139)
                      |+.|.+-|++|-+-.-.. ...|++.++...|+.+++.++.+|..-+...|++.||++|+++||.++++.++.|...+.
T Consensus        18 Kaal~~~V~rI~~~~g~~-~~~~vs~~~i~aL~E~~~~~~~~ia~Da~~fA~HAgRkTI~~eDV~La~Rrn~~l~~~l~   95 (107)
T 3b0b_B           18 RAAVHYTTGCLCQDVAED-KGVLFSKQTVAAISEITFRQCENFARDLEMFARHAKRSTITSEDVKLLARRSNSLLKYIT   95 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHH-HTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhh-cCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcCcCCHHHHHHHHHhCHHHHHHHH
Confidence            445666666655422211 235999999999999999999999999999999999999999999999999999877664

>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=98.02  E-value=1e-05  Score=56.82  Aligned_cols=68  Identities=25%  Similarity=0.163  Sum_probs=58.0

Q ss_pred             cCcccchHHHHHHHHhCC-------CccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           26 AGLQFPVGRIARFLKAGK-------YADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        26 agL~fPvsri~R~Lk~~~-------~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      .+|.+|...|.|++++-.       ...|++++|...|.-+.|.++-+++|-+...|.+.++.+|+|.||++|.+
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            578899999999998763       15699999999999999999999999999999999999999999999864

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

Probab=98.01  E-value=8.2e-06  Score=60.44  Aligned_cols=79  Identities=16%  Similarity=0.188  Sum_probs=66.2

Q ss_pred             ccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHHHhhhcC
Q 032523           25 KAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGT  104 (139)
Q Consensus        25 ragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL~~L~~~  104 (139)
                      ++.|.+-|++|-.=.-.. ....|+.++...|+.+++.++.+|..-+...|+|.||++|+++||.++++.++.|..++.+
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            456677777766433222 2347999999999999999999999999999999999999999999999999999888863

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

Probab=98.00  E-value=8.8e-06  Score=61.24  Aligned_cols=73  Identities=18%  Similarity=0.060  Sum_probs=63.2

Q ss_pred             ccCcccchHHHHHHHHhCC------CccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHH
Q 032523           25 KAGLQFPVGRIARFLKAGK------YADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEE   97 (139)
Q Consensus        25 ragL~fPvsri~R~Lk~~~------~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~E   97 (139)
                      -.+|.||...|.|++++-.      ...|++.+|...|.-+.|.++-+|+|-+...|.+.++.+|+|.||++|.+--.|
T Consensus        73 SteLLIpKlPF~RLVREIa~~~~~~~~lRfqs~Al~ALQEAaEayLV~LFEdanLcAiHAkRVTIm~kDIqLArrIrg~  151 (156)
T 3r45_A           73 STHLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIRGL  151 (156)
T ss_dssp             --CCCSCHHHHHHHHHHHHHTTTTTCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSEECHHHHHHHHHHHHH
T ss_pred             ccccccccccHHHHHHHHHHHhccCccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHHHHHccc
Confidence            3568899999999998753      256999999999999999999999999999999999999999999999864333

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

Probab=98.00  E-value=1e-05  Score=59.92  Aligned_cols=70  Identities=19%  Similarity=0.081  Sum_probs=61.8

Q ss_pred             ccCcccchHHHHHHHHhCC------CccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhC
Q 032523           25 KAGLQFPVGRIARFLKAGK------YADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN   94 (139)
Q Consensus        25 ragL~fPvsri~R~Lk~~~------~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~n   94 (139)
                      -.+|.+|...|.|++++-.      ...|++++|...|.-+.|.++-+++|-+...|.+.++.+|+|.||++|.+-
T Consensus        57 st~LLIpKlPF~RLVREI~~~~~~~~~~Rfq~~Al~ALQEAaEayLv~LFEdanlcAiHAkRVTIm~kDiqLArri  132 (140)
T 3nqu_A           57 STHLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRI  132 (140)
T ss_dssp             --CCCSCTTHHHHHHHHHHHHHHTTCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             ccccccccccHHHHHHHHHHHhcccccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHHHHh
Confidence            3568899999999998753      357999999999999999999999999999999999999999999999763

>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=97.96  E-value=2e-05  Score=57.40  Aligned_cols=71  Identities=23%  Similarity=0.242  Sum_probs=61.7

Q ss_pred             CcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh--CcHHH
Q 032523           27 GLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR--NDEEL   98 (139)
Q Consensus        27 gL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~--nD~EL   98 (139)
                      .-.|.+ .|+++|++..-...|+..|...|...++.++..|...|...|+.+++++|++++|+.|++  -..||
T Consensus        35 ~esy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtAvrLlLpGEL  107 (126)
T 1tzy_B           35 KESYSI-YVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGEL  107 (126)
T ss_dssp             CCCCHH-HHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHSCHHH
T ss_pred             cccHHH-HHHHHHHHhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcHHH
Confidence            345666 799999988555589999999999999999999999999999999999999999999986  33444

>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=97.91  E-value=3e-05  Score=57.21  Aligned_cols=68  Identities=25%  Similarity=0.219  Sum_probs=61.2

Q ss_pred             cCcccchHHHHHHHHhC----CCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           26 AGLQFPVGRIARFLKAG----KYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        26 agL~fPvsri~R~Lk~~----~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      .+|.||...|.|++++-    ....|++++|...|.-+.|.++-+++|.+...|.+.++.+|.|.||++|.+
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            46779999999998765    134699999999999999999999999999999999999999999999975

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

Probab=97.87  E-value=3.4e-05  Score=55.84  Aligned_cols=52  Identities=13%  Similarity=0.160  Sum_probs=49.0

Q ss_pred             CCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhC
Q 032523           43 KYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN   94 (139)
Q Consensus        43 ~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~n   94 (139)
                      .++.|||+++-..+..+||.++.+|+..|..++.+.+|++|+..||..|++.
T Consensus        60 gGvkRIS~~iy~e~r~vl~~~l~~i~rdav~yaehA~RKTVta~DV~~Alkr  111 (121)
T 2ly8_A           60 RGSKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKR  111 (121)
T ss_dssp             CCSSCCSSCHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCBCHHHHHHHHHH
T ss_pred             cCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHh
Confidence            3677999999999999999999999999999999999999999999999863

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

Probab=97.74  E-value=6.2e-05  Score=54.60  Aligned_cols=69  Identities=25%  Similarity=0.236  Sum_probs=60.1

Q ss_pred             ccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh--CcHHH
Q 032523           29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR--NDEEL   98 (139)
Q Consensus        29 ~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~--nD~EL   98 (139)
                      .|. -.|+++|++..-...|+..|...|...++.++..|...|.+.|+.+++++|++++|+.|++  -..||
T Consensus        34 sy~-~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtAvrLlLpGEL  104 (123)
T 2nqb_D           34 SYA-IYIYTVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGEL  104 (123)
T ss_dssp             CSH-HHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHHHSCHHH
T ss_pred             hHH-HHHHHHHHHhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHHHhCcHHH
Confidence            354 5799999988555699999999999999999999999999999999999999999999986  33444

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

Probab=97.71  E-value=3e-05  Score=61.74  Aligned_cols=59  Identities=14%  Similarity=0.115  Sum_probs=53.9

Q ss_pred             HHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCc
Q 032523           36 ARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRND   95 (139)
Q Consensus        36 ~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD   95 (139)
                      .|+.+.+ ++.|||.++...+..+||.++.+|+..|..+|.+.++++|++.||.+|++.-
T Consensus       168 ~RlaRrg-GVkRIS~~iyeelr~vLe~fle~IirdAv~yaeHA~RKTVta~DV~~ALKr~  226 (235)
T 2l5a_A          168 EEDGDKG-GVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQ  226 (235)
T ss_dssp             CTTSCCT-TCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHH
T ss_pred             HHHhhcC-CchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHhc
Confidence            3666665 8899999999999999999999999999999999999999999999998743

>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=97.32  E-value=0.00061  Score=46.69  Aligned_cols=64  Identities=23%  Similarity=0.364  Sum_probs=55.9

Q ss_pred             ccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhc-CCCccchhhHHHhhh
Q 032523           29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDN-KKNRIVPRHIQLAVR   93 (139)
Q Consensus        29 ~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~-~~krItP~hI~~AI~   93 (139)
                      .||-..|+|++..- ....|+.+..+.|+++--.|+.||+|.|....... ....|.|.||+.|.+
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            47888899999876 67799999999999999999999999999988664 456899999999975

>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=97.22  E-value=0.00073  Score=51.97  Aligned_cols=61  Identities=26%  Similarity=0.258  Sum_probs=56.2

Q ss_pred             HHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           33 GRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        33 sri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      ..|+|+|++..-...|+.+|..+|...+..++..|...|.+.+..+++++||+++|+.|++
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            3689999988555789999999999999999999999999999999999999999999997

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

Probab=96.90  E-value=0.0046  Score=41.95  Aligned_cols=67  Identities=16%  Similarity=0.161  Sum_probs=56.8

Q ss_pred             ccCcccchHHHHHHHHhCC--CccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHh
Q 032523           25 KAGLQFPVGRIARFLKAGK--YADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLA   91 (139)
Q Consensus        25 ragL~fPvsri~R~Lk~~~--~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~A   91 (139)
                      .++..||..-|.|+|+..-  ...||+.+|...++..|+-|+.|-+-+|...|...+...|..+||+..
T Consensus         8 ~~~~~i~~~li~ril~~~F~~~kTkIs~dAl~l~aeyl~iFV~EAv~RA~~~a~~e~~~~le~e~LEki   76 (84)
T 4dra_E            8 GAGSGFRKELVSRLLHLHFKDDKTKVSGDALQLMVELLKVFVVEAAVRGVRQAQAEDALRVDVDQLEKV   76 (84)
T ss_dssp             ---CCCCHHHHHHHHHTTCSSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHhcCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHH
Confidence            3466899999999999652  223999999999999999999999999999998888889999999864

>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=96.74  E-value=0.0049  Score=41.48  Aligned_cols=65  Identities=17%  Similarity=0.229  Sum_probs=56.9

Q ss_pred             CcccchHHHHHHHHhCCC--ccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHh
Q 032523           27 GLQFPVGRIARFLKAGKY--ADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLA   91 (139)
Q Consensus        27 gL~fPvsri~R~Lk~~~~--~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~A   91 (139)
                      ...||-.-|.|+|+..-.  ..||+.+|...++..|+-|+.|-+.+|...|...+...|..+||+..
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            457999999999997522  34999999999999999999999999999998888889999999873

>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=95.96  E-value=0.026  Score=37.54  Aligned_cols=68  Identities=12%  Similarity=0.221  Sum_probs=61.5

Q ss_pred             cccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCc
Q 032523           28 LQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRND   95 (139)
Q Consensus        28 L~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD   95 (139)
                      -.|+-.++..++++-.....+..++-..|..+.+-|+..+++.|...|++.+..++.+.||++....+
T Consensus         4 ~vl~k~~L~~Lv~~idp~~~ld~~vee~ll~lADdFV~~V~~~ac~lAKhR~s~~le~kDvql~Ler~   71 (76)
T 1h3o_B            4 MVLTKKKLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLERQ   71 (76)
T ss_dssp             CSSCHHHHHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHHH
T ss_pred             ccccHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHhh
Confidence            35678889999998877789999999999999999999999999999999999999999999887643

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

Probab=93.45  E-value=0.11  Score=41.22  Aligned_cols=66  Identities=24%  Similarity=0.134  Sum_probs=53.7

Q ss_pred             CcccchHHHHHHHHhC----CC---ccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhh
Q 032523           27 GLQFPVGRIARFLKAG----KY---ADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAV   92 (139)
Q Consensus        27 gL~fPvsri~R~Lk~~----~~---~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI   92 (139)
                      .|.+|-.++.|++++-    ..   ..|..++|...|--+-|.++-.++|-+.-.|.+.++-+|.|.|+++|-
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            4666766777766543    11   348999999999999999999999999999999999999999999984

>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=89.52  E-value=1.1  Score=33.25  Aligned_cols=61  Identities=16%  Similarity=0.205  Sum_probs=51.9

Q ss_pred             ccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHH
Q 032523           29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQL   90 (139)
Q Consensus        29 ~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~   90 (139)
                      .+++.+++|+++.. ..--|..+-.--+..++|--+.+++..|..-|+.++|..|.|.||-.
T Consensus         2 vm~~~~~e~lFR~a-a~LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~n~RdvI~~~DLPI   62 (148)
T 1wwi_A            2 LMKVAEFERLFRQA-AGLDVDKNDLKRVSDFLRNKLYDLLAVAERNAKYNGRDLIFEPDLPI   62 (148)
T ss_dssp             CSCHHHHHHHHHHH-HCCCCCGGGHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECGGGSCC
T ss_pred             cCCHHHHHHHHHHH-hccCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeeccccCCc
Confidence            47889999999987 44466676677788888999999999999999999999999999753

>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=88.08  E-value=0.56  Score=32.58  Aligned_cols=40  Identities=20%  Similarity=0.251  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHHHhhhc
Q 032523           64 AAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLG  103 (139)
Q Consensus        64 ~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL~~L~~  103 (139)
                      +.++|+.|.+.|...+...|+|+||-+++-.+++...++.
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            4688999999999999999999999999988877666664

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

Probab=83.72  E-value=1.1  Score=31.17  Aligned_cols=33  Identities=27%  Similarity=0.201  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHhhcCCCccchhhHHHhhhCcH
Q 032523           64 AAEVLELAGNAARDNKKNRIVPRHIQLAVRNDE   96 (139)
Q Consensus        64 ~~EILelAg~~A~~~~~krItP~hI~~AI~nD~   96 (139)
                      +.++|+.|...|...+...|+|+||-+++-.++
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            467899999999999999999999999997665

>3v9r_B MHF2, uncharacterized protein YDL160C-A; histone fold, fanconi anemia, DNA repair, DNA BI protein; 2.40A {Saccharomyces cerevisiae}

Probab=83.43  E-value=4.7  Score=27.27  Aligned_cols=48  Identities=8%  Similarity=0.137  Sum_probs=39.5

Q ss_pred             cchHHHHHHHHhCCCc--cccCCchHHHHHHHHHHHHHHHHHHHHHHHhh
Q 032523           30 FPVGRIARFLKAGKYA--DRVGAGAPVYLSAVLEYLAAEVLELAGNAARD   77 (139)
Q Consensus        30 fPvsri~R~Lk~~~~~--~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~   77 (139)
                      +|..-+.|+|+..-..  -||+.+|...++..++-|+.|-+-+|......
T Consensus         2 ip~~llaRIL~~~F~~~kTrIt~da~~lv~kY~diFVrEAv~Rs~e~ke~   51 (88)
T 3v9r_B            2 LSKEALIKILSQNEGGNDMKIADEVVPMIQKYLDIFIDEAVLRSLQSHKD   51 (88)
T ss_dssp             CCSHHHHHHHTTTSCSSCCEECTTTHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHhCCCCceecHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            6778899999855222  39999999999999999999999999765544

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

Probab=81.99  E-value=0.82  Score=32.26  Aligned_cols=40  Identities=28%  Similarity=0.350  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHHHhhcCCCccchhhHHHhhhCcH--HHHhhhc
Q 032523           64 AAEVLELAGNAARDNKKNRIVPRHIQLAVRNDE--ELSKLLG  103 (139)
Q Consensus        64 ~~EILelAg~~A~~~~~krItP~hI~~AI~nD~--EL~~L~~  103 (139)
                      +.++|+.|.+.|...+...|+|+||-+|+-.++  ....++.
T Consensus        12 a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~~~~~iL~   53 (145)
T 3fes_A           12 AKKAIDLAFESAKSLGHNIVGSEHILLGLLREEEGIAAKVLS   53 (145)
T ss_dssp             HHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHCSSHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCCccHHHHHHHHHhCCCChHHHHHH
Confidence            468899999999999999999999999998654  3455553

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

Probab=81.69  E-value=1  Score=31.42  Aligned_cols=40  Identities=35%  Similarity=0.353  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHH--HHhhhc
Q 032523           64 AAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEE--LSKLLG  103 (139)
Q Consensus        64 ~~EILelAg~~A~~~~~krItP~hI~~AI~nD~E--L~~L~~  103 (139)
                      +.++|+.|.+.|...+...|+|+||-+++-.+++  ...++.
T Consensus        10 ~~~al~~A~~~A~~~~h~~i~~eHlLlaLl~~~~~~~~~iL~   51 (150)
T 2y1q_A           10 AQKVLALAQEEALRLGHNNIGTEHILLGLVREGEGIAAKALQ   51 (150)
T ss_dssp             HHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHCSSHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCCccHHHHHHHHHhCCCCHHHHHHH
Confidence            4678899999999999999999999999976543  444443

>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=81.20  E-value=1.4  Score=33.28  Aligned_cols=61  Identities=10%  Similarity=0.079  Sum_probs=52.4

Q ss_pred             ccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHH
Q 032523           29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQL   90 (139)
Q Consensus        29 ~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~   90 (139)
                      .+++.+++|+++.. ..--|..+-.--+..++|--+.++|..|..-|+.++|..|.|.||-+
T Consensus        26 vmg~~kferlFR~a-agLDvdK~d~kr~~d~V~~Kl~DLl~va~~~Ak~NgRDvI~~~DLPI   86 (171)
T 1r4v_A           26 PKGFDKLDHYFRTE-LDIDLTDETIELLLNSVKAAFGKLFYGAEQRARWNGRDFIALADLNI   86 (171)
T ss_dssp             CTTHHHHHHHHHHH-HCCCCCHHHHHHHHHHHHHHHHHTTTTHHHHHHHTTCSEECGGGSCC
T ss_pred             cCChHHHHHHHHHH-hccCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeeccccCCc
Confidence            78999999999987 44466676667788888989999999999999999999999999753

>3fh2_A Probable ATP-dependent protease (heat shock prote; struct genomics, PSI2, MCSG, protein structure initiative; 1.60A {Corynebacterium glutamicum}

Probab=80.52  E-value=1.7  Score=30.56  Aligned_cols=40  Identities=33%  Similarity=0.311  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHHHhhcCCCccchhhHHHhhhCc--HHHHhhhc
Q 032523           64 AAEVLELAGNAARDNKKNRIVPRHIQLAVRND--EELSKLLG  103 (139)
Q Consensus        64 ~~EILelAg~~A~~~~~krItP~hI~~AI~nD--~EL~~L~~  103 (139)
                      +.++|+.|.+.|...+...|+|+||-+|+-.|  .....++.
T Consensus        11 ~~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~~~~~iL~   52 (146)
T 3fh2_A           11 ARRVIVLAQEEARMLNHNYIGTEHILLGLIHEGEGVAAKALE   52 (146)
T ss_dssp             HHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHCCSHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCCchHHHHHHHHHhCCCChHHHHHH
Confidence            46789999999999999999999999999765  44555554

---

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	139
d1u35c1	106	a.22.1.1 (C:814-919) macro-H2A.1, histone domain {	6e-56
d1tzya_	106	a.22.1.1 (A:) Histone H2A {Chicken (Gallus gallus)	2e-55
d1f66c_	103	a.22.1.1 (C:) Histone H2A {Human (Homo sapiens), v	2e-47
d1q9ca_	172	a.22.1.3 (A:) Histone domain of Son of sevenless p	1e-40
d1jfia_	66	a.22.1.3 (A:) Negative cofactor 2, NC2, alpha chai	2e-22
d1n1jb_	78	a.22.1.3 (B:) Nuclear transcription factor Y subun	2e-21
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	1e-12
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	3e-09
d1htaa_	68	a.22.1.2 (A:) Archaeal histone {Archaeon Methanoth	7e-05
d1ku5a_	66	a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococc	3e-04
d1n1ja_	87	a.22.1.3 (A:) Nuclear transcription factor Y subun	0.002

>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 =  168 bits (426), Expect = 6e-56
 Identities = 71/104 (68%), Positives = 84/104 (80%)

Query: 21  SRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKK 80
           SRS KAG+ FPVGR+ R++K G    R+G GAPVY++AVLEYL AE+LELA NAARDNKK
Sbjct: 3   SRSAKAGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKK 62

Query: 81  NRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPRK 124
            R+ PRHI LAV NDEEL++LL  VTIA+GGVLPNIH  LL +K
Sbjct: 63  GRVTPRHILLAVANDEELNQLLKGVTIASGGVLPNIHPELLAKK 106

>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 =  166 bits (423), Expect = 2e-55
 Identities = 81/106 (76%), Positives = 93/106 (87%)

Query: 18  KSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARD 77
           K+ SRS +AGLQFPVGR+ R L+ G YA+RVGAGAPVYL+AVLEYL AE+LELAGNAARD
Sbjct: 1   KAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARD 60

Query: 78  NKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLLPR 123
           NKK RI+PRH+QLA+RNDEEL+KLLG VTIA GGVLPNI   LLP+
Sbjct: 61  NKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPK 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 =  146 bits (369), Expect = 2e-47
 Identities = 64/104 (61%), Positives = 81/104 (77%), Gaps = 2/104 (1%)

Query: 19  SISRSHKAGLQFPVGRIARFLKAGKYAD-RVGAGAPVYLSAVLEYLAAEVLELAGNAARD 77
           ++SRS +AGLQFPVGRI R LK+   +  RVGA A VY +A+LEYL AEVLELAGNA++D
Sbjct: 1   AVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKD 60

Query: 78  NKKNRIVPRHIQLAVRNDEELSKLLGTVTIANGGVLPNIHQNLL 121
            K  RI PRH+QLA+R DEEL  L+   TIA GGV+P+IH++L+
Sbjct: 61  LKVKRITPRHLQLAIRGDEELDSLIK-ATIAGGGVIPHIHKSLI 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 =  131 bits (331), Expect = 1e-40
 Identities = 26/82 (31%), Positives = 44/82 (53%), Gaps = 1/82 (1%)

Query: 21  SRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKK 80
            R  +  L  PV +I   LK      ++     VY+ AVLEY++A++L+LAGN  R+ + 
Sbjct: 91  KRKRRNPLSLPVEKIHPLLKEV-LGYKIDHQVSVYIVAVLEYISADILKLAGNYVRNIRH 149

Query: 81  NRIVPRHIQLAVRNDEELSKLL 102
             I  + I++A+  D+ L  + 
Sbjct: 150 YEITKQDIKVAMCADKVLMDMF 171

>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 = 82.1 bits (203), Expect = 2e-22
 Identities = 14/64 (21%), Positives = 28/64 (43%)

Query: 29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHI 88
          +FP  RI + ++  +   +V A  PV +S  LE     +L+ A    +      +   H+
Sbjct: 2  RFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHL 61

Query: 89 QLAV 92
          +  +
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 = 79.5 bits (196), Expect = 2e-21
 Identities = 17/75 (22%), Positives = 32/75 (42%)

Query: 31  PVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQL 90
           P+ RI + +K  +    + A APV  +   +    E+   A     DNK+  +    I +
Sbjct: 2   PLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAM 61

Query: 91  AVRNDEELSKLLGTV 105
           A+   ++   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 = 59.0 bits (143), Expect = 1e-12
 Identities = 12/73 (16%), Positives = 26/73 (35%), Gaps = 1/73 (1%)

Query: 22  RSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKN 81
                G  F    + R LK     +R  + A    + ++     E+ E A   A ++ + 
Sbjct: 72  VEDYDGELFGRATVRRILKRAG-IERASSDAVDLYNKLICRATEELGEKAAEYADEDGRK 130

Query: 82  RIVPRHIQLAVRN 94
            +    ++ A+  
Sbjct: 131 TVQGEDVEKAITY 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 = 50.2 bits (120), Expect = 3e-09
 Identities = 11/65 (16%), Positives = 23/65 (35%)

Query: 29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHI 88
          + P   I R  + G    R+   A   +   +  +A  V   A +    + K  ++  H+
Sbjct: 1  ELPKAAIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHL 60

Query: 89 QLAVR 93
          +    
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 = 36.6 bits (85), Expect = 7e-05
 Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHI 88
          + P+  I R +K    A+RV   A + L+ VLE +  E+   A   A+   +  I    I
Sbjct: 3  ELPIAPIGRIIKNAG-AERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDI 61

Query: 89 QLAVR 93
          +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 = 34.7 bits (80), Expect = 3e-04
 Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 1/66 (1%)

Query: 29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHI 88
          + P+  + R ++    A+RV   A   L+  LE  A E+ + A   AR   +  +    I
Sbjct: 2  ELPIAPVDRLIRKAG-AERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDI 60

Query: 89 QLAVRN 94
          +LA+++
Sbjct: 61 KLAIKS 66

>d1n1ja_ a.22.1.3 (A:) Nuclear transcription factor Y subunit beta (Nf-Yb3) {Human (Homo sapiens) [TaxId: 9606]} Length = 87

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]

 Score = 33.3 bits (76), Expect = 0.002
 Identities = 12/73 (16%), Positives = 24/73 (32%), Gaps = 1/73 (1%)

Query: 28 LQFPVGRIARFLK-AGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPR 86
          +  P+  +AR +K A     ++   A   +   +    + +   A       K+  I   
Sbjct: 1  IYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGE 60

Query: 87 HIQLAVRNDEELS 99
           I  A+      S
Sbjct: 61 DILFAMSTLGFDS 73

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	139
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	99.95
d1jfia_	66	Negative cofactor 2, NC2, alpha chain {Human (Homo	99.69
d1n1jb_	78	Nuclear transcription factor Y subunit gamma (Nf-Y	99.61
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	99.42
d1ku5a_	66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	99.29
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	99.28
d1n1ja_	87	Nuclear transcription factor Y subunit beta (Nf-Yb	99.18
d1jfib_	135	Negative cofactor 2, NC2, beta chain {Human (Homo	98.96
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	98.89
d2byka1	72	Chrac-16 {Fruit fly (Drosophila melanogaster) [Tax	98.81
d2huec1	82	Histone H4 {African clawed frog (Xenopus laevis) [	98.7
d2bykb1	89	Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax	98.66
d1tzyc_	95	Histone H3 {Chicken (Gallus gallus), erythrocytes	97.33
d1tafb_	70	TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta	97.32
d1tzyb_	92	Histone H2B {Chicken (Gallus gallus), erythrocytes	97.26
d1bh9b_	89	TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]}	97.26
d1tafa_	68	TAF(II)42 {Fruit fly (Drosophila melanogaster) [Ta	95.98
d1h3ob_	74	TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom	95.54
d1k6ka_	142	N-terminal, ClpS-binding domain of ClpA, an Hsp100	91.43
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	90.0
d1wwia1	148	Hypothetical protein TTHA1479 {Thermus thermophilu	89.54
d1khya_	139	N-terminal domain of ClpB (heat shock protein F84.	87.87
d1qvra1	145	N-terminal domain of ClpB (heat shock protein F84.	87.68
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	84.04

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

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

Probab=100.00  E-value=2.8e-46  Score=265.86  Aligned_cols=106  Identities=76%  Similarity=1.203  Sum_probs=103.7

Q ss_pred             CCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHH
Q 032523           18 KSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEE   97 (139)
Q Consensus        18 ~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~E   97 (139)
                      +.+|||+||||+|||+||+|+|++++|++||+.+|||||+||||||++||||+|||+|+++++++|+|+||++||+||+|
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            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhcCceecCCccCCccccccccc
Q 032523           98 LSKLLGTVTIANGGVLPNIHQNLLPR  123 (139)
Q Consensus        98 L~~L~~~~~Ia~ggv~P~i~~~l~~~  123 (139)
                      |+.||+++||++|||+|+||++|+||
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=2.2e-46  Score=266.41  Aligned_cols=106  Identities=67%  Similarity=1.014  Sum_probs=103.7

Q ss_pred             CcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHH
Q 032523           19 SISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEEL   98 (139)
Q Consensus        19 ~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL   98 (139)
                      +.|||+||||+|||+||+|+|++++|++||+.+|||||+||||||++||||+|+|+|+++++++|+|+||++||+||+||
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            36899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhhcCceecCCccCCcccccccccc
Q 032523           99 SKLLGTVTIANGGVLPNIHQNLLPRK  124 (139)
Q Consensus        99 ~~L~~~~~Ia~ggv~P~i~~~l~~~k  124 (139)
                      ++||+++||++|||+|+||++|++||
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=7.2e-44  Score=252.49  Aligned_cols=102  Identities=63%  Similarity=0.988  Sum_probs=98.5

Q ss_pred             CcCcccccCcccchHHHHHHHHhCCCcc-ccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHH
Q 032523           19 SISRSHKAGLQFPVGRIARFLKAGKYAD-RVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEE   97 (139)
Q Consensus        19 ~~s~ssragL~fPvsri~R~Lk~~~~~~-RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~E   97 (139)
                      .+|||+||||+|||+||+|||++.+++. ||+++|||||+||||||++||||+|+|.|+++++++|||+||++||+||+|
T Consensus         1 ~~Srs~rAgL~FpVgrv~r~L~~~~~~~~rv~~~A~VyLaAvLEYL~aEILelagn~a~~~~~~rItpr~l~lai~nD~E   80 (103)
T d1f66c_           1 AVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEE   80 (103)
T ss_dssp             CCCHHHHHTCSSCHHHHHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHHSHH
T ss_pred             CCCccccCCcccChHHHHHHHhccCccceecCCCceeeHHHHHHHHHHHHHHHhhhhhccCCCCeeechhhhccccCcHH
Confidence            3799999999999999999999999986 699999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhcCceecCCccCCccccccc
Q 032523           98 LSKLLGTVTIANGGVLPNIHQNLL  121 (139)
Q Consensus        98 L~~L~~~~~Ia~ggv~P~i~~~l~  121 (139)
                      ||.|| ++||++|||+|+||++|+
T Consensus        81 L~~L~-~vti~~GGv~p~I~~~Ll  103 (103)
T d1f66c_          81 LDSLI-KATIAGGGVIPHIHKSLI  103 (103)
T ss_dssp             HHHHC-CSEETTCCCCCCCCGGGC
T ss_pred             HHHHh-CeEeeCCeecccccHhhC
Confidence            99999 599999999999999986

>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=99.95  E-value=2.6e-29  Score=191.18  Aligned_cols=85  Identities=31%  Similarity=0.504  Sum_probs=74.1

Q ss_pred             CCcCcccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHH
Q 032523           18 KSISRSHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEE   97 (139)
Q Consensus        18 ~~~s~ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~E   97 (139)
                      .-.|+|+|+||+|||++|+|+|++. +++||+++|+|||+||||||++||||+|+|+|++.++++|+|+||++||+||+|
T Consensus        88 ~~~srs~ragL~fPV~rv~rlLk~~-~a~RVs~~A~vyLaavLEyl~aeILelAgn~a~~~krkrItp~dI~lAi~nD~e  166 (172)
T d1q9ca_          88 AIEKRKRRNPLSLPVEKIHPLLKEV-LGYKIDHQVSVYIVAVLEYISADILKLAGNYVRNIRHYEITKQDIKVAMCADKV  166 (172)
T ss_dssp             HHC--------CCCHHHHHHHHHHH-HSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSBCCHHHHHHHHHTCHH
T ss_pred             HHhccccccCceecHHHHHHHHHhc-cccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCceecHHHHHHHHhCCHH
Confidence            3468999999999999999999997 999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhc
Q 032523           98 LSKLLG  103 (139)
Q Consensus        98 L~~L~~  103 (139)
                      |+.||+
T Consensus       167 L~~Lf~  172 (172)
T d1q9ca_         167 LMDMFH  172 (172)
T ss_dssp             HHHHCC
T ss_pred             HHHhhC
Confidence            999984

>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=99.69  E-value=2.4e-17  Score=106.49  Aligned_cols=65  Identities=22%  Similarity=0.451  Sum_probs=59.9

Q ss_pred             ccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        29 ~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      +||++||+|+|+.+.+..+|+.+|+++|+.++|||+.+|++.|++.|...++++|+++||..||+
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            69999999999999899999999999999999999999999999999999999999999999874

>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=99.61  E-value=1.2e-15  Score=100.88  Aligned_cols=73  Identities=22%  Similarity=0.358  Sum_probs=70.8

Q ss_pred             cchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHHHhhh
Q 032523           30 FPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLL  102 (139)
Q Consensus        30 fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL~~L~  102 (139)
                      +|+++|+|+|+.+....+|+.+|+++++.++|+|+.++.+.|++.|...++++|+++||..||+++++|++|.
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            6999999999988888999999999999999999999999999999999999999999999999999999986

>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=99.42  E-value=1.6e-13  Score=101.00  Aligned_cols=71  Identities=17%  Similarity=0.198  Sum_probs=67.1

Q ss_pred             ccccCcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhC
Q 032523           23 SHKAGLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN   94 (139)
Q Consensus        23 ssragL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~n   94 (139)
                      +.+.++.||+++|+|+|++. +..||+.+|.++|+.++|||+.+|++.|.+.|.+.+|++|+|+||.+|+..
T Consensus        73 ~~~~~~~fp~a~IkRi~k~~-g~~ris~dA~~~l~~~~E~fi~~l~~~A~~~a~~~kRkTI~~~DI~~Av~~  143 (151)
T d1f1ea_          73 EDYDGELFGRATVRRILKRA-GIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITY  143 (151)
T ss_dssp             TTCCSCCCCHHHHHHHHHHT-TCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             cccccCccCHHHHHHHHHcC-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHH
Confidence            45679999999999999976 788999999999999999999999999999999999999999999999964

>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=99.29  E-value=4.2e-12  Score=81.18  Aligned_cols=65  Identities=26%  Similarity=0.405  Sum_probs=62.0

Q ss_pred             ccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhC
Q 032523           29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN   94 (139)
Q Consensus        29 ~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~n   94 (139)
                      ++|.++|.|+|+.+ ...||+.+|...|..++|+|+.+|++.|...|.+.+|++|+++||..|+++
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            58999999999998 667999999999999999999999999999999999999999999999875

>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=5.5e-12  Score=80.92  Aligned_cols=63  Identities=30%  Similarity=0.435  Sum_probs=60.9

Q ss_pred             cchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           30 FPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        30 fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      +|.++|.|+++.+ +..||+.++...|+.++|+|+.+|++.|...|.+.+|++|+++||..|++
T Consensus         4 LP~a~I~ri~k~~-~~~ris~ea~~~l~~~~e~fi~~l~~~a~~~a~~~kRkTi~~~DV~~Alk   66 (68)
T d1htaa_           4 LPIAPIGRIIKNA-GAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARK   66 (68)
T ss_dssp             SCHHHHHHHHHHT-TCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHH
T ss_pred             CcHHHHHHHHHHC-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHH
Confidence            8999999999997 77899999999999999999999999999999999999999999999986

>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=99.18  E-value=2.1e-11  Score=81.80  Aligned_cols=74  Identities=15%  Similarity=0.209  Sum_probs=67.2

Q ss_pred             cccchHHHHHHHHhC-CCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHHHhh
Q 032523           28 LQFPVGRIARFLKAG-KYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKL  101 (139)
Q Consensus        28 L~fPvsri~R~Lk~~-~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL~~L  101 (139)
                      |.||.++|.|+|++. ....+|+.+|...++.+.|.|+.+|...|.+.|...+|++|+++||..|+.+.+-++++
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            579999999999965 56789999999999999999999999999999999999999999999999987655443

>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=98.96  E-value=5.4e-10  Score=80.48  Aligned_cols=71  Identities=18%  Similarity=0.184  Sum_probs=65.8

Q ss_pred             CcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHH
Q 032523           27 GLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEE   97 (139)
Q Consensus        27 gL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~E   97 (139)
                      .|.||.++|.|+|+..-...+|+.+|...|+.+.|.|+.+|...|...|...+|++|++.||..|+.+-+-
T Consensus         2 dl~LP~a~I~kI~K~~~~~~~is~dA~~~i~~a~~~Fi~~lt~~A~~~a~~~~RkTi~~~Dv~~Al~~~~f   72 (135)
T d1jfib_           2 DLTIPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALESLGF   72 (135)
T ss_dssp             CCCCCHHHHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHTT
T ss_pred             cccccHHHHHHHHhhCCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHcCc
Confidence            37899999999999986677999999999999999999999999999999999999999999999986443

>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=98.89  E-value=1.6e-09  Score=79.13  Aligned_cols=65  Identities=17%  Similarity=0.249  Sum_probs=61.9

Q ss_pred             ccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        29 ~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      .||++.|.|+|++.....||+.+|...|..++++++..|...|.+.|.+.++++|+|+||+.++.
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            38999999999987678899999999999999999999999999999999999999999999985

>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=98.81  E-value=2.2e-09  Score=69.68  Aligned_cols=64  Identities=13%  Similarity=0.135  Sum_probs=57.9

Q ss_pred             HHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhh-cCCCccchhhHHHhhhCcHHHHhhh
Q 032523           39 LKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARD-NKKNRIVPRHIQLAVRNDEELSKLL  102 (139)
Q Consensus        39 Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~-~~~krItP~hI~~AI~nD~EL~~L~  102 (139)
                      ||.+.+...|+.+|++.++.++|.|+.++.+.|++.+.. .++++|++.||..||.+++.|+||-
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            456778889999999999999999999999999988854 5568999999999999999999997

>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=98.70  E-value=3e-08  Score=65.72  Aligned_cols=65  Identities=15%  Similarity=0.180  Sum_probs=61.6

Q ss_pred             cchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCc
Q 032523           30 FPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRND   95 (139)
Q Consensus        30 fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD   95 (139)
                      +|-+-|.|+++.. +..||++++...|+.++||++.+|+..|...+.+.+|++|+++||.+|++..
T Consensus        10 I~k~~i~Riar~~-Gv~ris~d~~~~l~~~l~~~l~~i~~~a~~~~~hakRKTvt~~DV~~Alkr~   74 (82)
T d2huec1          10 ITKPAIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ   74 (82)
T ss_dssp             SCHHHHHHHHHHT-TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTT
T ss_pred             cCHHHHHHHHHHc-CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHhc
Confidence            6777899999987 8999999999999999999999999999999999999999999999999865

>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=98.66  E-value=2.4e-08  Score=66.78  Aligned_cols=69  Identities=16%  Similarity=0.191  Sum_probs=61.9

Q ss_pred             chHHHHHHHHhC-CCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHHHh
Q 032523           31 PVGRIARFLKAG-KYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSK  100 (139)
Q Consensus        31 Pvsri~R~Lk~~-~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL~~  100 (139)
                      |.++|.|+|++. ....+|+.+|...++.+.|.|+.+|...|...|...++++|+++||..|+.+- +|+.
T Consensus         1 P~a~i~ri~K~~~p~~~~iskeA~~~i~~aae~FI~~lt~~A~~~a~~~~rKtI~~~dv~~Al~~~-~f~~   70 (89)
T d2bykb1           1 PNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTEL-DFES   70 (89)
T ss_dssp             CCSHHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHT-TCTT
T ss_pred             CccHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHC-CcHH
Confidence            789999999964 46679999999999999999999999999999999999999999999999743 3443

>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=97.33  E-value=0.00037  Score=46.74  Aligned_cols=69  Identities=25%  Similarity=0.217  Sum_probs=60.4

Q ss_pred             ccCcccchHHHHHHHHhC----CCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           25 KAGLQFPVGRIARFLKAG----KYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        25 ragL~fPvsri~R~Lk~~----~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      -..|.+|-..+.|++++-    ....|+..+|...|-.+.|.++-++++-|...|.+.++-+|+|.|+++|.+
T Consensus        17 st~lLIpk~pF~RLVRei~~~~~~~~r~~~~Al~aLQea~E~yLv~lfeda~~~a~HakRvTl~~kD~~Larr   89 (95)
T d1tzyc_          17 STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR   89 (95)
T ss_dssp             CCSCCSCHHHHHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             CcccccccccHHHHHHHHHHhcCCCCEeeHHHHHHHHHHHHHHHHHHHHHhHHHHHhcCCCcCCHHHHHHHHH
Confidence            346888999999988754    223499999999999999999999999999999999999999999998854

>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=97.32  E-value=0.00065  Score=43.18  Aligned_cols=66  Identities=11%  Similarity=0.158  Sum_probs=59.8

Q ss_pred             CcccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           27 GLQFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        27 gL~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      +-.||..-|+-+-..- +...+++++.-.|+-=+||=+.||++.|.+.-++.+|+++|.+||..|.+
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            4568988898777655 78899999999999999999999999999999999999999999999874

>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=97.26  E-value=0.00034  Score=46.69  Aligned_cols=60  Identities=23%  Similarity=0.242  Sum_probs=56.5

Q ss_pred             HHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           34 RIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        34 ri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      .|+|.|++..-...|+..|.-.|...+..+...|...|...|+.+++.+|+.++|+.|++
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            589999998777799999999999999999999999999999999999999999999997

>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=97.26  E-value=0.00038  Score=46.19  Aligned_cols=63  Identities=24%  Similarity=0.358  Sum_probs=56.2

Q ss_pred             cchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcC-CCccchhhHHHhhh
Q 032523           30 FPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNK-KNRIVPRHIQLAVR   93 (139)
Q Consensus        30 fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~-~krItP~hI~~AI~   93 (139)
                      ||-+.|+|+|+.- ....|+....+.++++---|+.||+|.|.......+ ...|.|+||+.|.+
T Consensus        17 ~~K~~vkrl~~~~-~g~sv~~~v~i~v~giaKvFvGEiVE~A~~V~~~~~e~~PL~P~HireA~r   80 (89)
T d1bh9b_          17 FPKAAIKRLIQSI-TGTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVR   80 (89)
T ss_dssp             CCHHHHHHHHHHH-HSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH-cCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCcHHHHHHHH
Confidence            8999999999987 678999999999999999999999999998876543 45799999999976

>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=95.98  E-value=0.019  Score=35.90  Aligned_cols=59  Identities=19%  Similarity=0.085  Sum_probs=42.2

Q ss_pred             HHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhC
Q 032523           35 IARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN   94 (139)
Q Consensus        35 i~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~n   94 (139)
                      |+-+|++. +..-.....+.-|--..--.+.+||+-|.-++.+.+++.|+..|+++||..
T Consensus         7 i~~iL~~~-GV~~yeprV~~qlLef~yRYtt~VL~DA~vys~HA~k~~id~dDVkLAi~~   65 (68)
T d1tafa_           7 IMSILKEL-NVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLATEV   65 (68)
T ss_dssp             HHHHHHHT-TCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             HHHHHHHc-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHh
Confidence            56677766 433333333443333334467899999999999999999999999999963

>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=95.54  E-value=0.025  Score=35.86  Aligned_cols=67  Identities=12%  Similarity=0.210  Sum_probs=60.1

Q ss_pred             ccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHHhhhCc
Q 032523           29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRND   95 (139)
Q Consensus        29 ~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~AI~nD   95 (139)
                      .|.-.++..++++-.....+..++-..|.-+.+-|+..+++.|...|++.+..+|.+.||++....+
T Consensus         3 il~K~~L~eLv~~idp~~~ld~~vee~ll~iADdFV~~V~~~ac~lAKhR~s~~le~kDvql~LeR~   69 (74)
T d1h3ob_           3 VLTKKKLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLERQ   69 (74)
T ss_dssp             SSCHHHHHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCcHHHHHHHHHhh
Confidence            3556778888988877789999999999999999999999999999999999999999999887654

>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=91.43  E-value=0.11  Score=34.63  Aligned_cols=39  Identities=21%  Similarity=0.264  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHHHHhhh
Q 032523           64 AAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLL  102 (139)
Q Consensus        64 ~~EILelAg~~A~~~~~krItP~hI~~AI~nD~EL~~L~  102 (139)
                      +.++|..|.+.|...+...|+|+||-+|+-+|++...++
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            367789999999999999999999999999998865555

>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=90.00  E-value=0.23  Score=35.11  Aligned_cols=31  Identities=16%  Similarity=0.219  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHhhcCCCccchhhHHHhhhCc
Q 032523           65 AEVLELAGNAARDNKKNRIVPRHIQLAVRND   95 (139)
Q Consensus        65 ~EILelAg~~A~~~~~krItP~hI~~AI~nD   95 (139)
                      -+++..|...|...++..|+++|++.|+..|
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            3577888888988899999999999999754

>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=89.54  E-value=0.49  Score=33.26  Aligned_cols=61  Identities=16%  Similarity=0.205  Sum_probs=51.8

Q ss_pred             ccchHHHHHHHHhCCCccccCCchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccchhhHHH
Q 032523           29 QFPVGRIARFLKAGKYADRVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQL   90 (139)
Q Consensus        29 ~fPvsri~R~Lk~~~~~~RVs~~A~vyLaAvLEyL~~EILelAg~~A~~~~~krItP~hI~~   90 (139)
                      ..|++++++++++. ..--|..+-.--+..+++-=+.++|..|..-|+.++|..|.|.||-.
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            46899999999987 44466666677788888999999999999999999999999999754

>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=87.87  E-value=0.24  Score=32.62  Aligned_cols=40  Identities=30%  Similarity=0.245  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHH--HHhhhc
Q 032523           64 AAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEE--LSKLLG  103 (139)
Q Consensus        64 ~~EILelAg~~A~~~~~krItP~hI~~AI~nD~E--L~~L~~  103 (139)
                      +.+++..|-..|...+...|+|+||-+|+-+|++  +..++.
T Consensus         7 ~~~~l~~A~~~A~~~~h~~v~~eHlL~all~~~~~~~~~iL~   48 (139)
T d1khya_           7 FQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLT   48 (139)
T ss_dssp             HHHHHHHHHHHHHHTTCSSBCHHHHHHHHHTCTTCSHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCcccHHHHHHHHHhCcccHHHHHHH
Confidence            4688999999999999999999999999987654  445553

>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=87.68  E-value=0.25  Score=33.52  Aligned_cols=41  Identities=29%  Similarity=0.235  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHHhhcCCCccchhhHHHhhhCcHH--HHhhhcC
Q 032523           64 AAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEE--LSKLLGT  104 (139)
Q Consensus        64 ~~EILelAg~~A~~~~~krItP~hI~~AI~nD~E--L~~L~~~  104 (139)
                      +.++|+.|-+.|...+...|+|.||-+|+-+|++  +..++..
T Consensus         7 a~~~l~~A~~~A~~~~~~~i~~~HlL~all~~~~~~~~~iL~~   49 (145)
T d1qvra1           7 AREALAQAQVLAQRMKHQAIDLPHLWAVLLKDERSLAWRLLEK   49 (145)
T ss_dssp             HHHHHHHHHHHHHHTTCSEECHHHHHHHHCCSSSSHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCCcccHHHHHHHHHcCCcchHHHHHHH
Confidence            4689999999999999999999999999987664  6676653

>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=84.04  E-value=0.86  Score=31.74  Aligned_cols=29  Identities=21%  Similarity=0.416  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHHhhcCCCccchhhHHHhhh
Q 032523           65 AEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
Q Consensus        65 ~EILelAg~~A~~~~~krItP~hI~~AI~   93 (139)
                      .++++.|...|...++.+|+++||+.|..
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            45778888999999999999999999875