Citrus Sinensis ID: 032404

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-
Protein Sequence
MAPKAEKKPAEEKKTPVAEKAPAEKKPKAGKKLPKEAAAGDKKKKRTKKSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHccccHHHHHHHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccHHHccccccccccccccccccccccccHHHHHHHHHHHccccEEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEcHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mapkaekkpaeekktpvaekapaekkpkagkklpkeaaagdkkkkrTKKSIETYKIYIFKVLKQvhpdigissKAMGIMNSFINDIFEKLAQESSRLarynkkptitsrEIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS
Flexible Loop (DISEMBL)
mapkaekkpaeekktpvaekapaekkpkagkklpkeaaagdkkkkrtkksiETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLArynkkptitsreiqTAVRLVLPGElakhavsegtkavtkftss
Low Complexity Region (SEG)
MapkaekkpaeekktpvaekapaekkpkagkklpkeaaaGDkkkkrtkkSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS
Disordered region (IsUnstruct)
**************************************************IETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQ****LARY****TITSREIQTAVRLVLPGELA*****************
Disordered Region (DISOPRED)
********************************************************YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKF***
Disordered Region (DISEMBL)
************************************************KSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHA**************
Disordered Region (DISPRO)
***************************************************ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVT**T**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAPKAEKKPAEEKKTPVAEKAPAEKKPKAGKKLPKEAAAGDKKKKRTKKSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	141	2.2.26 [Sep-21-2011]
P93354	146	Histone H2B OS=Nicotiana	N/A	no	1.0	0.965	0.863	1e-64
O65819	137	Histone H2B.3 (Fragment)	N/A	no	0.957	0.985	0.948	8e-64
Q1S9I9	148	Probable histone H2B.1 OS	N/A	no	1.0	0.952	0.912	2e-63
Q1SWQ1	148	Probable histone H2B.2 OS	N/A	no	1.0	0.952	0.898	3e-62
O23629	150	Histone H2B.6 OS=Arabidop	yes	no	1.0	0.94	0.873	3e-61
O49118	145	Histone H2B OS=Capsicum a	N/A	no	0.978	0.951	0.871	5e-60
Q9SI96	151	Histone H2B.3 OS=Arabidop	no	no	1.0	0.933	0.867	9e-60
Q9LQQ4	148	Histone H2B.1 OS=Arabidop	no	no	0.992	0.945	0.865	1e-59
O22582	147	Histone H2B OS=Gossypium	N/A	no	0.886	0.850	0.960	2e-59
P40283	150	Histone H2B.11 OS=Arabido	yes	no	0.936	0.88	0.911	7e-59

>sp|P93354|H2B_TOBAC Histone H2B OS=Nicotiana tabacum GN=HIS2B PE=2 SV=3

 Score =  244 bits (623), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 126/146 (86%), Positives = 137/146 (93%), Gaps = 5/146 (3%)

Query: 1   MAPKAEKKPAEEK----KTPVAEKAPAEKKPKAGKKLPKEA-AAGDKKKKRTKKSIETYK 55
           MAP+A+KKPAE+K    KTPVAEKAPAEKKP+AGKKLP++A AAGDKKKKR + S+ETYK
Sbjct: 1   MAPRADKKPAEKKPGAEKTPVAEKAPAEKKPRAGKKLPRDAGAAGDKKKKRAEMSVETYK 60

Query: 56  IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAV 115
           IYIF+VLK VHPDIGISSKAMGIMNSFINDIFEKLA+ESSRLA YNKKPTI+SREIQTAV
Sbjct: 61  IYIFRVLKHVHPDIGISSKAMGIMNSFINDIFEKLARESSRLAGYNKKPTISSREIQTAV 120

Query: 116 RLVLPGELAKHAVSEGTKAVTKFTSS 141
           RLVLPGELAKHAVSEGTKAVTKFTSS
Sbjct: 121 RLVLPGELAKHAVSEGTKAVTKFTSS 146

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.
Nicotiana tabacum (taxid: 4097)

>sp|O65819|H2B3_SOLLC Histone H2B.3 (Fragment) OS=Solanum lycopersicum GN=H2B-3 PE=2 SV=1

 Score =  241 bits (616), Expect = 8e-64,   Method: Compositional matrix adjust.
 Identities = 130/137 (94%), Positives = 135/137 (98%), Gaps = 2/137 (1%)

Query: 5   AEKKPAEEKKTPVAEKAPAEKKPKAGKKLPKEAAAGDKKKKRTKKSIETYKIYIFKVLKQ 64
           AEKKPAE  KTPVAEKAPAEKKPKAGKKLPK+AAAGDKKKKR+KK++ETYKIYIFKVLKQ
Sbjct: 3   AEKKPAE--KTPVAEKAPAEKKPKAGKKLPKDAAAGDKKKKRSKKAVETYKIYIFKVLKQ 60

Query: 65  VHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELA 124
           VHPDIGISSKAMGIMNSFINDIFEKLAQE+SRLARYNKKPTITSREIQTAVRLVLPGELA
Sbjct: 61  VHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPGELA 120

Query: 125 KHAVSEGTKAVTKFTSS 141
           KHAVSEGTKAVTKFTSS
Sbjct: 121 KHAVSEGTKAVTKFTSS 137

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.

Solanum lycopersicum (taxid: 4081)

>sp|Q1S9I9|H2B1_MEDTR Probable histone H2B.1 OS=Medicago truncatula PE=3 SV=3

 Score =  240 bits (613), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 135/148 (91%), Positives = 140/148 (94%), Gaps = 7/148 (4%)

Query: 1   MAPK-----AEKKPAEEKKTPVAEKAPAEKKPKAGKKLPKE--AAAGDKKKKRTKKSIET 53
           MAPK     AEKKPAEEKK+ VAEKAPAEKKPKAGKKLPKE  +AAG+KKKKR+KKS+ET
Sbjct: 1   MAPKGEKKPAEKKPAEEKKSTVAEKAPAEKKPKAGKKLPKEGGSAAGEKKKKRSKKSVET 60

Query: 54  YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT 113
           YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT
Sbjct: 61  YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT 120

Query: 114 AVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           AVRLVLPGELAKHAVSEGTKAVTKFTSS
Sbjct: 121 AVRLVLPGELAKHAVSEGTKAVTKFTSS 148

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.

Medicago truncatula (taxid: 3880)

>sp|Q1SWQ1|H2B2_MEDTR Probable histone H2B.2 OS=Medicago truncatula PE=3 SV=3

 Score =  236 bits (602), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 133/148 (89%), Positives = 138/148 (93%), Gaps = 7/148 (4%)

Query: 1   MAPK-----AEKKPAEEKKTPVAEKAPAEKKPKAGKKLPKE--AAAGDKKKKRTKKSIET 53
           MAPK     AEKKPAEEKK+ VAEKAPAEKKPKAGKKLPKE  +AAG+KKKKR+KKS+ET
Sbjct: 1   MAPKGEKKPAEKKPAEEKKSTVAEKAPAEKKPKAGKKLPKEGGSAAGEKKKKRSKKSVET 60

Query: 54  YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT 113
           YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKL QESSRLARYNKKPTITSREIQT
Sbjct: 61  YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLTQESSRLARYNKKPTITSREIQT 120

Query: 114 AVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           AVRLVLPGELAKH VSEGTKAVTKFTSS
Sbjct: 121 AVRLVLPGELAKHDVSEGTKAVTKFTSS 148

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.

Medicago truncatula (taxid: 3880)

>sp|O23629|H2B6_ARATH Histone H2B.6 OS=Arabidopsis thaliana GN=H2B PE=1 SV=3

 Score =  233 bits (593), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 131/150 (87%), Positives = 136/150 (90%), Gaps = 9/150 (6%)

Query: 1   MAPKAEKKPAEEK---KTPV-----AEKAPAEKKPKAGKKLPKEAAAG-DKKKKRTKKSI 51
           MAP+AEKKPAE+K   + PV     AEKAPAEKKPKAGKKLPKEA AG DKKKK  KKS+
Sbjct: 1   MAPRAEKKPAEKKPAAEKPVEEKSKAEKAPAEKKPKAGKKLPKEAGAGGDKKKKMKKKSV 60

Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLA ESS+LARYNKKPTITSREI
Sbjct: 61  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLASESSKLARYNKKPTITSREI 120

Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           QTAVRLVLPGELAKHAVSEGTKAVTKFTSS
Sbjct: 121 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 150

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)

>sp|O49118|H2B_CAPAN Histone H2B OS=Capsicum annuum GN=HIS2B PE=2 SV=3

 Score =  229 bits (583), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 129/148 (87%), Positives = 132/148 (89%), Gaps = 10/148 (6%)

Query: 1   MAPKA-------EKKPAEEKKTPVAEKAPAEKKPKAGKKLPKEAAAGDKKKKRTKKSIET 53
           MAPKA       EKKP EEKK   AE+ PAEKKPKAGKKLPK+A   DKKKKR KKSIET
Sbjct: 1   MAPKAAAGKKPAEKKPVEEKK---AEEVPAEKKPKAGKKLPKDAGRPDKKKKRAKKSIET 57

Query: 54  YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT 113
           YKIYIFKVLKQVHPDIGISSK+MGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT
Sbjct: 58  YKIYIFKVLKQVHPDIGISSKSMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT 117

Query: 114 AVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           AVRLVLPGELAKHAVSEGTKAVTKFTSS
Sbjct: 118 AVRLVLPGELAKHAVSEGTKAVTKFTSS 145

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.

Capsicum annuum (taxid: 4072)

>sp|Q9SI96|H2B3_ARATH Histone H2B.3 OS=Arabidopsis thaliana GN=At2g28720 PE=1 SV=3

 Score =  228 bits (581), Expect = 9e-60,   Method: Compositional matrix adjust.
 Identities = 131/151 (86%), Positives = 135/151 (89%), Gaps = 10/151 (6%)

Query: 1   MAPKAEKKPAEEK---KTP-----VAEKAPAEKKPKAGKKLPKEAAAG--DKKKKRTKKS 50
           MAPKA KKPAE+K   K P     VAEKAPAEKKPKAGKKLPKEA  G  +KKKKR KKS
Sbjct: 1   MAPKAGKKPAEKKPAEKAPAEEEKVAEKAPAEKKPKAGKKLPKEAVTGGVEKKKKRVKKS 60

Query: 51  IETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSRE 110
            ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQE+S+LARYNKKPTITSRE
Sbjct: 61  TETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASKLARYNKKPTITSRE 120

Query: 111 IQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           IQTAVRLVLPGELAKHAVSEGTKAVTKFTSS
Sbjct: 121 IQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 151

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)

>sp|Q9LQQ4|H2B1_ARATH Histone H2B.1 OS=Arabidopsis thaliana GN=At1g07790 PE=1 SV=3

 Score =  228 bits (580), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 129/149 (86%), Positives = 137/149 (91%), Gaps = 9/149 (6%)

Query: 1   MAPKAEKKPAEEK---KTPV-----AEKAPAEKKPKAGKKLPKEAAAGDKKKKRTKKSIE 52
           MAP+AEKKPAE+K   + PV     AEKAPAEKKPKAGKKLP + A GDKKKKR+KK++E
Sbjct: 1   MAPRAEKKPAEKKTAAERPVEENKAAEKAPAEKKPKAGKKLPPKEA-GDKKKKRSKKNVE 59

Query: 53  TYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQ 112
           TYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESS+LARYNKKPTITSREIQ
Sbjct: 60  TYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSKLARYNKKPTITSREIQ 119

Query: 113 TAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           TAVRLVLPGELAKHAVSEGTKAVTKFTSS
Sbjct: 120 TAVRLVLPGELAKHAVSEGTKAVTKFTSS 148

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)

>sp|O22582|H2B_GOSHI Histone H2B OS=Gossypium hirsutum GN=HIS2B PE=2 SV=3

 Score =  226 bits (577), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 122/127 (96%), Positives = 124/127 (97%), Gaps = 2/127 (1%)

Query: 17  VAEKAPAEKKPKAGKKLPKE--AAAGDKKKKRTKKSIETYKIYIFKVLKQVHPDIGISSK 74
           VAEKAPAEKKPKAGKKLPKE  AAAGDKKKKR KKS+ETYKIYIFKVLKQVHPDIGISSK
Sbjct: 21  VAEKAPAEKKPKAGKKLPKEGGAAAGDKKKKRVKKSVETYKIYIFKVLKQVHPDIGISSK 80

Query: 75  AMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKA 134
           AMGIMNSFINDIFEKLAQE+SRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKA
Sbjct: 81  AMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKA 140

Query: 135 VTKFTSS 141
           VTKFTSS
Sbjct: 141 VTKFTSS 147

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.

Gossypium hirsutum (taxid: 3635)

>sp|P40283|H2B11_ARATH Histone H2B.11 OS=Arabidopsis thaliana GN=At5g59910 PE=1 SV=5

 Score =  225 bits (573), Expect = 7e-59,   Method: Compositional matrix adjust.
 Identities = 123/135 (91%), Positives = 126/135 (93%), Gaps = 3/135 (2%)

Query: 8   KPAEEKKTPVAEKAPAEKKPKAGKKLPKEAAAG-DKKKKRTKKSIETYKIYIFKVLKQVH 66
           KP EEK    AEKAPAEKKPKAGKKLPKEA AG DKKKK  KKS+ETYKIYIFKVLKQVH
Sbjct: 18  KPVEEKSK--AEKAPAEKKPKAGKKLPKEAGAGGDKKKKMKKKSVETYKIYIFKVLKQVH 75

Query: 67  PDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKH 126
           PDIGISSKAMGIMNSFINDIFEKLAQE+S+LARYNKKPTITSREIQTAVRLVLPGELAKH
Sbjct: 76  PDIGISSKAMGIMNSFINDIFEKLAQEASKLARYNKKPTITSREIQTAVRLVLPGELAKH 135

Query: 127 AVSEGTKAVTKFTSS 141
           AVSEGTKAVTKFTSS
Sbjct: 136 AVSEGTKAVTKFTSS 150

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	141
357472693	147	Histone H2B [Medicago truncatula] gi|355	0.992	0.952	0.905	9e-65
7387729	146	RecName: Full=Histone H2B gi|1848210|emb	1.0	0.965	0.863	8e-63
357472685	148	Histone H2B [Medicago truncatula] gi|357	1.0	0.952	0.912	2e-62
75278464	137	RecName: Full=Histone H2B.3; AltName: Fu	0.957	0.985	0.948	6e-62
217071596	148	unknown [Medicago truncatula] gi|3885169	1.0	0.952	0.905	9e-62
357473451	148	Histone H2B [Medicago truncatula] gi|108	1.0	0.952	0.912	1e-61
224065198	148	histone 2 [Populus trichocarpa] gi|11848	1.0	0.952	0.905	3e-61
449450686	152	PREDICTED: probable histone H2B.1-like [	1.0	0.927	0.888	5e-61
357473279	290	Histone H2B [Medicago truncatula] gi|355	0.985	0.479	0.910	1e-60
108860773	148	RecName: Full=Probable histone H2B.2	1.0	0.952	0.898	2e-60

>gi|357472693|ref|XP_003606631.1| Histone H2B [Medicago truncatula] gi|355507686|gb|AES88828.1| Histone H2B [Medicago truncatula]

 Score =  251 bits (640), Expect = 9e-65,   Method: Compositional matrix adjust.
 Identities = 134/148 (90%), Positives = 139/148 (93%), Gaps = 8/148 (5%)

Query: 1   MAPK-----AEKKPAEEKKTPVAEKAPAEKKPKAGKKLPKE--AAAGDKKKKRTKKSIET 53
           MAPK     AEKKPAEEKK+ VAEKAPAEKKPKAGKKLPKE  +AAGDKKK R+KK++ET
Sbjct: 1   MAPKGEKKPAEKKPAEEKKSTVAEKAPAEKKPKAGKKLPKEGGSAAGDKKK-RSKKNVET 59

Query: 54  YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT 113
           YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT
Sbjct: 60  YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT 119

Query: 114 AVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           AVRLVLPGELAKHAVSEGTKAVTKFTSS
Sbjct: 120 AVRLVLPGELAKHAVSEGTKAVTKFTSS 147

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|7387729|sp|P93354.3|H2B_TOBAC RecName: Full=Histone H2B gi|1848210|emb|CAA72091.1| histone H2B1 [Nicotiana tabacum]

 Score =  244 bits (623), Expect = 8e-63,   Method: Compositional matrix adjust.
 Identities = 126/146 (86%), Positives = 137/146 (93%), Gaps = 5/146 (3%)

Query: 1   MAPKAEKKPAEEK----KTPVAEKAPAEKKPKAGKKLPKEA-AAGDKKKKRTKKSIETYK 55
           MAP+A+KKPAE+K    KTPVAEKAPAEKKP+AGKKLP++A AAGDKKKKR + S+ETYK
Sbjct: 1   MAPRADKKPAEKKPGAEKTPVAEKAPAEKKPRAGKKLPRDAGAAGDKKKKRAEMSVETYK 60

Query: 56  IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAV 115
           IYIF+VLK VHPDIGISSKAMGIMNSFINDIFEKLA+ESSRLA YNKKPTI+SREIQTAV
Sbjct: 61  IYIFRVLKHVHPDIGISSKAMGIMNSFINDIFEKLARESSRLAGYNKKPTISSREIQTAV 120

Query: 116 RLVLPGELAKHAVSEGTKAVTKFTSS 141
           RLVLPGELAKHAVSEGTKAVTKFTSS
Sbjct: 121 RLVLPGELAKHAVSEGTKAVTKFTSS 146

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357472685|ref|XP_003606627.1| Histone H2B [Medicago truncatula] gi|357472689|ref|XP_003606629.1| Histone H2B [Medicago truncatula] gi|355507682|gb|AES88824.1| Histone H2B [Medicago truncatula] gi|355507684|gb|AES88826.1| Histone H2B [Medicago truncatula] gi|388495180|gb|AFK35656.1| unknown [Medicago truncatula]

 Score =  243 bits (620), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 135/148 (91%), Positives = 140/148 (94%), Gaps = 7/148 (4%)

Query: 1   MAPK-----AEKKPAEEKKTPVAEKAPAEKKPKAGKKLPKE--AAAGDKKKKRTKKSIET 53
           MAPK     AEKKPAEEKK+ VAEKAPAEKKPKAGKKLPKE  +AAGDKKKKR+KK++ET
Sbjct: 1   MAPKGEKKPAEKKPAEEKKSTVAEKAPAEKKPKAGKKLPKEGGSAAGDKKKKRSKKNVET 60

Query: 54  YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT 113
           YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT
Sbjct: 61  YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT 120

Query: 114 AVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           AVRLVLPGELAKHAVSEGTKAVTKFTSS
Sbjct: 121 AVRLVLPGELAKHAVSEGTKAVTKFTSS 148

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|75278464|sp|O65819.1|H2B3_SOLLC RecName: Full=Histone H2B.3; AltName: Full=LeH2B-3 gi|3021485|emb|CAA12231.1| histone H2B-3 [Solanum lycopersicum]

 Score =  241 bits (616), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 130/137 (94%), Positives = 135/137 (98%), Gaps = 2/137 (1%)

Query: 5   AEKKPAEEKKTPVAEKAPAEKKPKAGKKLPKEAAAGDKKKKRTKKSIETYKIYIFKVLKQ 64
           AEKKPAE  KTPVAEKAPAEKKPKAGKKLPK+AAAGDKKKKR+KK++ETYKIYIFKVLKQ
Sbjct: 3   AEKKPAE--KTPVAEKAPAEKKPKAGKKLPKDAAAGDKKKKRSKKAVETYKIYIFKVLKQ 60

Query: 65  VHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELA 124
           VHPDIGISSKAMGIMNSFINDIFEKLAQE+SRLARYNKKPTITSREIQTAVRLVLPGELA
Sbjct: 61  VHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPGELA 120

Query: 125 KHAVSEGTKAVTKFTSS 141
           KHAVSEGTKAVTKFTSS
Sbjct: 121 KHAVSEGTKAVTKFTSS 137

Source: Solanum lycopersicum

Species: Solanum lycopersicum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217071596|gb|ACJ84158.1| unknown [Medicago truncatula] gi|388516999|gb|AFK46561.1| unknown [Medicago truncatula]

 Score =  241 bits (614), Expect = 9e-62,   Method: Compositional matrix adjust.
 Identities = 134/148 (90%), Positives = 140/148 (94%), Gaps = 7/148 (4%)

Query: 1   MAPK-----AEKKPAEEKKTPVAEKAPAEKKPKAGKKLPKE--AAAGDKKKKRTKKSIET 53
           MAPK     AEKKPAEEKK+ VAEKAPAEKKPKAGKKLPKE  +AAG+KKKKR+KK++ET
Sbjct: 1   MAPKGEKKPAEKKPAEEKKSTVAEKAPAEKKPKAGKKLPKEGGSAAGEKKKKRSKKNVET 60

Query: 54  YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT 113
           YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT
Sbjct: 61  YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT 120

Query: 114 AVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           AVRLVLPGELAKHAVSEGTKAVTKFTSS
Sbjct: 121 AVRLVLPGELAKHAVSEGTKAVTKFTSS 148

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357473451|ref|XP_003607010.1| Histone H2B [Medicago truncatula] gi|108860772|sp|Q1S9I9.3|H2B1_MEDTR RecName: Full=Probable histone H2B.1 gi|355508065|gb|AES89207.1| Histone H2B [Medicago truncatula] gi|388510538|gb|AFK43335.1| unknown [Medicago truncatula]

 Score =  240 bits (613), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 135/148 (91%), Positives = 140/148 (94%), Gaps = 7/148 (4%)

Query: 1   MAPK-----AEKKPAEEKKTPVAEKAPAEKKPKAGKKLPKE--AAAGDKKKKRTKKSIET 53
           MAPK     AEKKPAEEKK+ VAEKAPAEKKPKAGKKLPKE  +AAG+KKKKR+KKS+ET
Sbjct: 1   MAPKGEKKPAEKKPAEEKKSTVAEKAPAEKKPKAGKKLPKEGGSAAGEKKKKRSKKSVET 60

Query: 54  YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT 113
           YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT
Sbjct: 61  YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT 120

Query: 114 AVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           AVRLVLPGELAKHAVSEGTKAVTKFTSS
Sbjct: 121 AVRLVLPGELAKHAVSEGTKAVTKFTSS 148

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224065198|ref|XP_002301712.1| histone 2 [Populus trichocarpa] gi|118489629|gb|ABK96616.1| unknown [Populus trichocarpa x Populus deltoides] gi|222843438|gb|EEE80985.1| histone 2 [Populus trichocarpa]

 Score =  239 bits (610), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 134/148 (90%), Positives = 136/148 (91%), Gaps = 7/148 (4%)

Query: 1   MAPKAEKKPAE----EKKTPVAEKAPAEKKPKAGKKLPKE---AAAGDKKKKRTKKSIET 53
           MAP+AEKKPAE    E+K  VAEKAPAEKKPKAGKKLPKE   A AGDKKKKR KKS ET
Sbjct: 1   MAPRAEKKPAEKKPAEEKKTVAEKAPAEKKPKAGKKLPKEGGAAVAGDKKKKRVKKSTET 60

Query: 54  YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT 113
           YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT
Sbjct: 61  YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT 120

Query: 114 AVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           AVRLVLPGELAKHAVSEGTKAVTKFTSS
Sbjct: 121 AVRLVLPGELAKHAVSEGTKAVTKFTSS 148

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449450686|ref|XP_004143093.1| PREDICTED: probable histone H2B.1-like [Cucumis sativus] gi|449508145|ref|XP_004163232.1| PREDICTED: probable histone H2B.1-like [Cucumis sativus]

 Score =  238 bits (608), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 135/152 (88%), Positives = 139/152 (91%), Gaps = 11/152 (7%)

Query: 1   MAPKAEKKPAE---------EKKTPVAEKAPAEKKPKAGKKLPKE--AAAGDKKKKRTKK 49
           MAPKA+KKPAE         E+K  VAEKAPAEKKPKAGKKLPKE  AAAGDKKKKRTKK
Sbjct: 1   MAPKADKKPAEKKPASEKPAEEKKTVAEKAPAEKKPKAGKKLPKEGGAAAGDKKKKRTKK 60

Query: 50  SIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSR 109
           S+ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESS+LARYNKKPTITSR
Sbjct: 61  SVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSKLARYNKKPTITSR 120

Query: 110 EIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           EIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS
Sbjct: 121 EIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 152

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357473279|ref|XP_003606924.1| Histone H2B [Medicago truncatula] gi|355507979|gb|AES89121.1| Histone H2B [Medicago truncatula]

 Score =  237 bits (605), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 133/146 (91%), Positives = 138/146 (94%), Gaps = 7/146 (4%)

Query: 1   MAPK-----AEKKPAEEKKTPVAEKAPAEKKPKAGKKLPKE--AAAGDKKKKRTKKSIET 53
           MAPK     AEKKPAEEKK+ VAEKAPAEKKPKAGKKLPKE  +AAG+KKKKR+KKS+ET
Sbjct: 1   MAPKGEKKPAEKKPAEEKKSTVAEKAPAEKKPKAGKKLPKEGGSAAGEKKKKRSKKSVET 60

Query: 54  YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT 113
           YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT
Sbjct: 61  YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT 120

Query: 114 AVRLVLPGELAKHAVSEGTKAVTKFT 139
           AVRLVLPGELAKHAVSEGTKAVTKFT
Sbjct: 121 AVRLVLPGELAKHAVSEGTKAVTKFT 146

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|108860773|sp|Q1SWQ1.3|H2B2_MEDTR RecName: Full=Probable histone H2B.2

 Score =  236 bits (602), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 133/148 (89%), Positives = 138/148 (93%), Gaps = 7/148 (4%)

Query: 1   MAPK-----AEKKPAEEKKTPVAEKAPAEKKPKAGKKLPKE--AAAGDKKKKRTKKSIET 53
           MAPK     AEKKPAEEKK+ VAEKAPAEKKPKAGKKLPKE  +AAG+KKKKR+KKS+ET
Sbjct: 1   MAPKGEKKPAEKKPAEEKKSTVAEKAPAEKKPKAGKKLPKEGGSAAGEKKKKRSKKSVET 60

Query: 54  YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT 113
           YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKL QESSRLARYNKKPTITSREIQT
Sbjct: 61  YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLTQESSRLARYNKKPTITSREIQT 120

Query: 114 AVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           AVRLVLPGELAKH VSEGTKAVTKFTSS
Sbjct: 121 AVRLVLPGELAKHDVSEGTKAVTKFTSS 148

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	141
TAIR|locus:2026494	148	HTB1 [Arabidopsis thaliana (ta	0.723	0.689	0.892	1.5e-42
TAIR|locus:2168093	150	HTB4 [Arabidopsis thaliana (ta	0.723	0.68	0.892	1.9e-42
TAIR|locus:2077182	150	HTB9 [Arabidopsis thaliana (ta	0.723	0.68	0.892	3.2e-42
TAIR|locus:2077152	145	HTB11 [Arabidopsis thaliana (t	0.723	0.703	0.892	3.2e-42
TAIR|locus:2181823	132	AT5G02570 [Arabidopsis thalian	0.652	0.696	0.978	8.4e-42
TAIR|locus:2172691	145	HTB2 "histone B2" [Arabidopsis	0.723	0.703	0.882	8.4e-42
TAIR|locus:2084096	138	AT3G53650 [Arabidopsis thalian	0.652	0.666	0.967	1.1e-41
TAIR|locus:2054553	151	AT2G28720 [Arabidopsis thalian	0.652	0.609	0.967	1.4e-41
TAIR|locus:2049857	138	AT2G37470 [Arabidopsis thalian	0.645	0.659	0.956	2.2e-41
TAIR|locus:2074959	126	AT3G09480 [Arabidopsis thalian	0.652	0.730	0.934	4.2e-40

TAIR|locus:2026494 HTB1 [Arabidopsis thaliana (taxid:3702)]

 Score = 450 (163.5 bits), Expect = 1.5e-42, P = 1.5e-42
 Identities = 91/102 (89%), Positives = 94/102 (92%)

Query:    40 GDXXXXXXXXSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLAR 99
             GD        ++ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESS+LAR
Sbjct:    47 GDKKKKRSKKNVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSKLAR 106

Query:   100 YNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
             YNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS
Sbjct:   107 YNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 148

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:0009507 "chloroplast" evidence=IDA

TAIR|locus:2168093 HTB4 [Arabidopsis thaliana (taxid:3702)]

 Score = 449 (163.1 bits), Expect = 1.9e-42, P = 1.9e-42
 Identities = 91/102 (89%), Positives = 94/102 (92%)

Query:    40 GDXXXXXXXXSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLAR 99
             GD        S+ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQE+S+LAR
Sbjct:    49 GDKKKKMKKKSVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASKLAR 108

Query:   100 YNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
             YNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS
Sbjct:   109 YNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 150

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:0009534 "chloroplast thylakoid" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009062 "fatty acid catabolic process" evidence=RCA

TAIR|locus:2077182 HTB9 [Arabidopsis thaliana (taxid:3702)]

 Score = 447 (162.4 bits), Expect = 3.2e-42, P = 3.2e-42
 Identities = 91/102 (89%), Positives = 93/102 (91%)

Query:    40 GDXXXXXXXXSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLAR 99
             GD        S+ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLA ESS+LAR
Sbjct:    49 GDKKKKMKKKSVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLASESSKLAR 108

Query:   100 YNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
             YNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS
Sbjct:   109 YNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 150

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:0009534 "chloroplast thylakoid" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0007020 "microtubule nucleation" evidence=RCA

TAIR|locus:2077152 HTB11 [Arabidopsis thaliana (taxid:3702)]

 Score = 447 (162.4 bits), Expect = 3.2e-42, P = 3.2e-42
 Identities = 91/102 (89%), Positives = 93/102 (91%)

Query:    40 GDXXXXXXXXSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLAR 99
             GD        S+ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLA ESS+LAR
Sbjct:    44 GDKKKKMKKKSVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLASESSKLAR 103

Query:   100 YNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
             YNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS
Sbjct:   104 YNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 145

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:0009506 "plasmodesma" evidence=IDA

TAIR|locus:2181823 AT5G02570 [Arabidopsis thaliana (taxid:3702)]

 Score = 443 (161.0 bits), Expect = 8.4e-42, P = 8.4e-42
 Identities = 90/92 (97%), Positives = 90/92 (97%)

Query:    50 SIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSR 109
             S ETYKIYIFKVLKQVHPDIGIS KAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSR
Sbjct:    41 STETYKIYIFKVLKQVHPDIGISGKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSR 100

Query:   110 EIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
             EIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS
Sbjct:   101 EIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 132

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:0048610 "cellular process involved in reproduction" evidence=RCA

GO:0048868 "pollen tube development" evidence=RCA

TAIR|locus:2172691 HTB2 "histone B2" [Arabidopsis thaliana (taxid:3702)]

 Score = 443 (161.0 bits), Expect = 8.4e-42, P = 8.4e-42
 Identities = 90/102 (88%), Positives = 93/102 (91%)

Query:    40 GDXXXXXXXXSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLAR 99
             GD        ++ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLA ESS+LAR
Sbjct:    44 GDKKKKRSKKNVETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAGESSKLAR 103

Query:   100 YNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
             YNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS
Sbjct:   104 YNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 145

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:0005515 "protein binding" evidence=IPI

GO:0008283 "cell proliferation" evidence=RCA

TAIR|locus:2084096 AT3G53650 [Arabidopsis thaliana (taxid:3702)]

 Score = 442 (160.7 bits), Expect = 1.1e-41, P = 1.1e-41
 Identities = 89/92 (96%), Positives = 91/92 (98%)

Query:    50 SIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSR 109
             +IETYKIYIFKVLKQVHPDIGIS KAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSR
Sbjct:    47 NIETYKIYIFKVLKQVHPDIGISGKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSR 106

Query:   110 EIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
             EIQTAVRLVLPGEL+KHAVSEGTKAVTKFTSS
Sbjct:   107 EIQTAVRLVLPGELSKHAVSEGTKAVTKFTSS 138

GO:0000786 "nucleosome" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006334 "nucleosome assembly" evidence=IEA

TAIR|locus:2054553 AT2G28720 [Arabidopsis thaliana (taxid:3702)]

 Score = 441 (160.3 bits), Expect = 1.4e-41, P = 1.4e-41
 Identities = 89/92 (96%), Positives = 91/92 (98%)

Query:    50 SIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSR 109
             S ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQE+S+LARYNKKPTITSR
Sbjct:    60 STETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASKLARYNKKPTITSR 119

Query:   110 EIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
             EIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS
Sbjct:   120 EIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 151

GO:0000786 "nucleosome" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006334 "nucleosome assembly" evidence=IEA

TAIR|locus:2049857 AT2G37470 [Arabidopsis thaliana (taxid:3702)]

 Score = 439 (159.6 bits), Expect = 2.2e-41, P = 2.2e-41
 Identities = 87/91 (95%), Positives = 90/91 (98%)

Query:    50 SIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSR 109
             S+ETYKIYIFKVLKQVHPD+GIS KAMGIMNSFINDIFEKLAQESS+LARYNKKPTITSR
Sbjct:    48 SVETYKIYIFKVLKQVHPDVGISGKAMGIMNSFINDIFEKLAQESSKLARYNKKPTITSR 107

Query:   110 EIQTAVRLVLPGELAKHAVSEGTKAVTKFTS 140
             EIQTAVRLVLPGELAKHAVSEGTKAVTKFTS
Sbjct:   108 EIQTAVRLVLPGELAKHAVSEGTKAVTKFTS 138

GO:0000786 "nucleosome" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006334 "nucleosome assembly" evidence=IEA

TAIR|locus:2074959 AT3G09480 [Arabidopsis thaliana (taxid:3702)]

 Score = 427 (155.4 bits), Expect = 4.2e-40, P = 4.2e-40
 Identities = 86/92 (93%), Positives = 88/92 (95%)

Query:    50 SIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSR 109
             S ETYKIY+FKVLKQVHPDIGIS KAMGIMNSFIND FEK+A ESSRLARYNKKPTITSR
Sbjct:    35 STETYKIYLFKVLKQVHPDIGISGKAMGIMNSFINDTFEKIALESSRLARYNKKPTITSR 94

Query:   110 EIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
             EIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS
Sbjct:    95 EIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 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

---

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)
Q6ZBP3	H2B2_ORYSJ	No assigned EC number	0.7709	0.8794	0.8266	no	no
Q9LFF6	H2B8_ARATH	No assigned EC number	0.8521	0.9716	0.9927	no	no
Q59VP1	H2B2_CANAL	No assigned EC number	0.6737	0.9078	0.9846	N/A	no
A2WKS8	H2B7_ORYSI	No assigned EC number	0.7804	0.8297	0.7647	N/A	no
P40283	H2B11_ARATH	No assigned EC number	0.9111	0.9361	0.88	yes	no
Q9FFC0	H2B10_ARATH	No assigned EC number	0.8601	0.9787	0.9517	no	no
P93354	H2B_TOBAC	No assigned EC number	0.8630	1.0	0.9657	N/A	no
P30755	H2B1_MAIZE	No assigned EC number	0.8425	0.8723	0.8145	N/A	no
Q2U5A9	H2B_ASPOR	No assigned EC number	0.7042	0.9787	0.9787	yes	no
Q43261	H2B3_MAIZE	No assigned EC number	0.8230	0.8794	0.8104	N/A	no
O65819	H2B3_SOLLC	No assigned EC number	0.9489	0.9574	0.9854	N/A	no
O65818	H2B2_SOLLC	No assigned EC number	0.9145	0.8156	0.8214	N/A	no
P69070	H2B_SALTR	No assigned EC number	0.7377	0.8368	0.9516	N/A	no
Q9LQQ4	H2B1_ARATH	No assigned EC number	0.8657	0.9929	0.9459	no	no
P27807	H2B1_WHEAT	No assigned EC number	0.776	0.8510	0.7894	N/A	no
Q9LZ45	H2B9_ARATH	No assigned EC number	0.8321	0.9219	0.9848	no	no
Q9SI96	H2B3_ARATH	No assigned EC number	0.8675	1.0	0.9337	no	no
O23629	H2B6_ARATH	No assigned EC number	0.8733	1.0	0.94	yes	no
Q9SF55	H2B5_ARATH	No assigned EC number	0.8412	0.8794	0.9841	no	no
O49118	H2B_CAPAN	No assigned EC number	0.8716	0.9787	0.9517	N/A	no
A2WKT1	H2B6_ORYSI	No assigned EC number	0.7967	0.8297	0.7647	N/A	no
Q943L2	H2B11_ORYSJ	No assigned EC number	0.9456	0.6524	0.6618	no	no
A2QY49	H2B_ASPNC	No assigned EC number	0.6971	0.9787	0.9787	yes	no
A2WWU2	H2B11_ORYSI	No assigned EC number	0.9456	0.6524	0.6618	N/A	no
A2WKP3	H2B3_ORYSI	No assigned EC number	0.7967	0.8297	0.7647	N/A	no
A2WKP5	H2B4_ORYSI	No assigned EC number	0.8048	0.8297	0.7647	N/A	no
Q9ZUS0	H2B4_ARATH	No assigned EC number	0.8439	0.9716	0.9927	no	no
A3AGM4	H2B1_ORYSJ	No assigned EC number	0.8244	0.8794	0.8157	yes	no
A2YWI3	H2B2_ORYSI	No assigned EC number	0.7709	0.8794	0.8266	N/A	no
O22582	H2B_GOSHI	No assigned EC number	0.9606	0.8865	0.8503	N/A	no
Q9LZT0	H2B7_ARATH	No assigned EC number	0.944	0.8794	0.8551	yes	no
Q1SWQ1	H2B2_MEDTR	No assigned EC number	0.8986	1.0	0.9527	N/A	no
A5DWF0	H2B_LODEL	No assigned EC number	0.6666	0.9148	0.9847	N/A	no
Q6CMV8	H2B2_KLULA	No assigned EC number	0.6666	0.9148	0.9772	yes	no
Q1E5N0	H2B_COCIM	No assigned EC number	0.6971	0.9645	0.9784	N/A	no
O65821	H2B1_SOLLC	No assigned EC number	0.8689	0.9787	0.9718	N/A	no
Q43215	H2B4_WHEAT	No assigned EC number	0.7692	0.9432	0.9851	N/A	no
A2WKS5	H2B8_ORYSI	No assigned EC number	0.7967	0.8297	0.7647	N/A	no
Q43216	H2B5_WHEAT	No assigned EC number	0.8297	0.9645	1.0	N/A	no
A2WKS3	H2B10_ORYSI	No assigned EC number	0.8048	0.8297	0.7647	N/A	no
Q1SU99	H2B3_MEDTR	No assigned EC number	0.9519	0.7375	0.7536	N/A	no
P05621	H2B2_WHEAT	No assigned EC number	0.7567	0.9645	0.9066	N/A	no
Q1S9I9	H2B1_MEDTR	No assigned EC number	0.9121	1.0	0.9527	N/A	no
P48989	H2B1_CANAL	No assigned EC number	0.6737	0.9078	0.9846	N/A	no
A2XF66	H2B1_ORYSI	No assigned EC number	0.8244	0.8794	0.8157	N/A	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:
	HTB903	histone 2; 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 (By similarity) (148 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.III.2578.1	hypothetical protein (82 aa)							•		0.502
	HTR913	RecName- Full=Histone H3; (136 aa)							•		0.502
	HTR908	RecName- Full=Histone H3; (137 aa)							•		0.502
	grail3.0011011101	RecName- Full=Histone H3; (137 aa)							•		0.502
	HTR904	histone H3 (129 aa)							•		0.502
	fgenesh4_pg.C_LG_II000927	hypothetical protein (309 aa)							•		0.502
	HTR905	histone H4 (70 aa)							•		0.502
	HTR901	RecName- Full=Histone H3; (137 aa)							•		0.502
	gw1.13136.3.1	hypothetical protein (60 aa)							•		0.502
	grail3.2024000101	hypothetical protein (140 aa)							•		0.502

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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	141
smart00427	97	smart00427, H2B, Histone H2B	9e-51
PLN00158	116	PLN00158, PLN00158, histone H2B; Provisional	1e-42
PTZ00463	117	PTZ00463, PTZ00463, histone H2B; Provisional	1e-35
pfam00125	75	pfam00125, Histone, Core histone H2A/H2B/H3/H4	7e-23

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

 Score =  156 bits (396), Expect = 9e-51
 Identities = 77/97 (79%), Positives = 88/97 (90%)

Query: 44  KKRTKKSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKK 103
           KKR KK  ETY IYI+KVLKQVHPD GISS+AM IMNSF+NDIFE++A E+S+LARYNKK
Sbjct: 1   KKRVKKRKETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKK 60

Query: 104 PTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTS 140
            T++SREIQTAVRL+LPGELAKHAVSEGTKAVTK +S
Sbjct: 61  STLSSREIQTAVRLILPGELAKHAVSEGTKAVTKASS 97

Length = 97

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

 Score =  136 bits (344), Expect = 1e-42
 Identities = 88/114 (77%), Positives = 97/114 (85%)

Query: 28  KAGKKLPKEAAAGDKKKKRTKKSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIF 87
           K   K P + AA   KKK +K   ETYKIYI+KVLKQVHPD GISSKAM IMNSFINDIF
Sbjct: 3   KTPSKKPAKKAAKGAKKKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIF 62

Query: 88  EKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           EK+A E+ +LARYNKKPT+TSREIQTAVRL+LPGELAKHAVSEGTKAVTKFTS+
Sbjct: 63  EKIATEAGKLARYNKKPTVTSREIQTAVRLILPGELAKHAVSEGTKAVTKFTSA 116

Length = 116

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

 Score =  119 bits (298), Expect = 1e-35
 Identities = 76/113 (67%), Positives = 89/113 (78%)

Query: 28  KAGKKLPKEAAAGDKKKKRTKKSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIF 87
           K   K  K A   D KKKR K   ++Y +YIFKVLKQVHPD GIS K+M IMNSF+ D F
Sbjct: 4   KKPAKAKKAATGPDGKKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTF 63

Query: 88  EKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTS 140
           EK+A E+SRL +Y ++ T++SREIQTA+RLVLPGELAKHAVSEGTKAVTKFTS
Sbjct: 64  EKIATEASRLCKYTRRDTLSSREIQTAIRLVLPGELAKHAVSEGTKAVTKFTS 116

Length = 117

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

 Score = 84.9 bits (211), Expect = 7e-23
 Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 4/75 (5%)

Query: 48  KKSIETYKIYIFKVLKQVHPD----IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKK 103
              +   K+   +V++++       + ISSKA   +   + D+ E++ +++  LAR+ K+
Sbjct: 1   SSRLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKR 60

Query: 104 PTITSREIQTAVRLV 118
            TIT R+IQ AVRL 
Sbjct: 61  KTITPRDIQLAVRLD 75

Length = 75

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	141
PLN00158	116	histone H2B; Provisional	100.0
PTZ00463	117	histone H2B; Provisional	100.0
smart00427	89	H2B Histone H2B.	100.0
KOG1744	127	consensus Histone H2B [Chromatin structure and dyn	100.0
PF00125	75	Histone: Core histone H2A/H2B/H3/H4 histone h2a si	99.61
cd07981	72	TAF12 TATA Binding Protein (TBP) Associated Factor	98.49
COG2036	91	HHT1 Histones H3 and H4 [Chromatin structure and d	98.3
PF00808	65	CBFD_NFYB_HMF: Histone-like transcription factor (	98.26
smart00803	65	TAF TATA box binding protein associated factor. TA	97.86
cd00074	115	H2A Histone 2A; H2A is a subunit of the nucleosome	97.78
PLN00035	103	histone H4; Provisional	97.77
cd00076	85	H4 Histone H4, one of the four histones, along wit	97.71
PF03847	68	TFIID_20kDa: Transcription initiation factor TFIID	97.7
PTZ00015	102	histone H4; Provisional	97.67
smart00428	105	H3 Histone H3.	97.51
cd07979	117	TAF9 TATA Binding Protein (TBP) Associated Factor	97.32
smart00417	74	H4 Histone H4.	97.25
KOG0869	168	consensus CCAAT-binding factor, subunit A (HAP3) [	96.84
PLN00156	139	histone H2AX; Provisional	96.57
KOG0871	156	consensus Class 2 transcription repressor NC2, bet	96.51
KOG1142	258	consensus Transcription initiation factor TFIID, s	96.46
smart00414	106	H2A Histone 2A.	96.38
PF02969	66	TAF: TATA box binding protein associated factor (T	96.3
PLN00157	132	histone H2A; Provisional	96.29
PTZ00017	134	histone H2A; Provisional	96.25
cd08050	343	TAF6 TATA Binding Protein (TBP) Associated Factor	96.23
PLN00153	129	histone H2A; Provisional	96.05
smart00576	77	BTP Bromodomain transcription factors and PHD doma	95.77
PTZ00252	134	histone H2A; Provisional	95.5
PLN00154	136	histone H2A; Provisional	95.4
COG5262	132	HTA1 Histone H2A [Chromatin structure and dynamics	95.36
PLN00121	136	histone H3; Provisional	95.19
PF15510	102	CENP-W: Centromere kinetochore component W	95.01
PTZ00018	136	histone H3; Provisional	94.94
KOG0870	172	consensus DNA polymerase epsilon, subunit D [Trans	94.69
PF15630	76	CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C	94.52
KOG1756	131	consensus Histone 2A [Chromatin structure and dyna	93.77
PLN00161	135	histone H3; Provisional	93.33
PLN00160	97	histone H3; Provisional	92.04
PF15511	414	CENP-T: Centromere kinetochore component CENP-T; P	91.95
PF07524	77	Bromo_TP: Bromodomain associated; InterPro: IPR006	91.92
PF02291	129	TFIID-31kDa: Transcription initiation factor IID,	89.86
KOG2549	576	consensus Transcription initiation factor TFIID, s	88.84
PF02269	93	TFIID-18kDa: Transcription initiation factor IID,	86.96
cd08048	85	TAF11 TATA Binding Protein (TBP) Associated Factor	85.36
cd07978	92	TAF13 The TATA Binding Protein (TBP) Associated Fa	85.15
KOG3334	148	consensus Transcription initiation factor TFIID, s	82.92

>PLN00158 histone H2B; Provisional

Probab=100.00  E-value=1.8e-55  Score=330.16  Aligned_cols=99  Identities=84%  Similarity=1.164  Sum_probs=95.4

Q ss_pred             ccccccccchhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchH
Q 032404           43 KKKRTKKSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGE  122 (141)
Q Consensus        43 ~kk~~k~r~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGE  122 (141)
                      +++++++|.|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+|+|||+||||+|||||||||
T Consensus        18 ~kk~~~kr~esy~~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLvLpgE   97 (116)
T PLN00158         18 KKKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLILPGE   97 (116)
T ss_pred             cccccccccccHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHhccHH
Confidence            45567778999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhHHHhhhhhhhcccCC
Q 032404          123 LAKHAVSEGTKAVTKFTSS  141 (141)
Q Consensus       123 LaKhAvseGtkAV~ky~ss  141 (141)
                      |+||||+||++||++|+++
T Consensus        98 LaKhAvsEGtkAv~k~~~~  116 (116)
T PLN00158         98 LAKHAVSEGTKAVTKFTSA  116 (116)
T ss_pred             HHHHHHHHHHHHHHHhhcC
Confidence            9999999999999999985

>PTZ00463 histone H2B; Provisional

Probab=100.00  E-value=5.6e-55  Score=327.77  Aligned_cols=98  Identities=72%  Similarity=1.067  Sum_probs=94.7

Q ss_pred             ccccccccchhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchH
Q 032404           43 KKKRTKKSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGE  122 (141)
Q Consensus        43 ~kk~~k~r~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGE  122 (141)
                      +++++++|.|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+++|||+||||||||||||||
T Consensus        19 ~kk~~~kr~esy~~YI~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLlLpGE   98 (117)
T PTZ00463         19 KKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLVLPGE   98 (117)
T ss_pred             cccccccccchHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhcccHH
Confidence            45667778999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhHHHhhhhhhhcccC
Q 032404          123 LAKHAVSEGTKAVTKFTS  140 (141)
Q Consensus       123 LaKhAvseGtkAV~ky~s  140 (141)
                      |+||||+|||+||++|++
T Consensus        99 LaKhAvsEGtkAv~k~~~  116 (117)
T PTZ00463         99 LAKHAVSEGTKAVTKFTS  116 (117)
T ss_pred             HHHhhhhHHHHHHHHhhc
Confidence            999999999999999986

>smart00427 H2B Histone H2B

Probab=100.00  E-value=1.1e-52  Score=302.98  Aligned_cols=89  Identities=82%  Similarity=1.187  Sum_probs=87.8

Q ss_pred             hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHHHhHHHhh
Q 032404           52 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEG  131 (141)
Q Consensus        52 esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELaKhAvseG  131 (141)
                      |+|++||||||||||||+|||++||+||||||||||||||.||++|++||+|+|||+||||+||||+|||||+||||+||
T Consensus         1 esy~~Yi~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~LpgeLakhAvsEg   80 (89)
T smart00427        1 ETYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVSEG   80 (89)
T ss_pred             CcHHHHHHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHHccHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhcccC
Q 032404          132 TKAVTKFTS  140 (141)
Q Consensus       132 tkAV~ky~s  140 (141)
                      ||||+||++
T Consensus        81 tkAv~k~~~   89 (89)
T smart00427       81 TKAVTKYSS   89 (89)
T ss_pred             HHHHHhhcC
Confidence            999999985

>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]

Probab=100.00  E-value=1.1e-46  Score=286.35  Aligned_cols=99  Identities=75%  Similarity=1.106  Sum_probs=95.9

Q ss_pred             ccccccccchhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchH
Q 032404           43 KKKRTKKSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGE  122 (141)
Q Consensus        43 ~kk~~k~r~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGE  122 (141)
                      +|++..++.++|+.||||||||||||+|||+++|.|||||||||||+||.||++|++||+|+||++||||+||||+||||
T Consensus        28 gk~~~~~~~e~~s~yv~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLllPge  107 (127)
T KOG1744|consen   28 GKKRSTRRKESYSEYVYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLLLPGE  107 (127)
T ss_pred             cccCcccccCceeeehhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHhCchH
Confidence            46677888999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhHHHhhhhhhhcccCC
Q 032404          123 LAKHAVSEGTKAVTKFTSS  141 (141)
Q Consensus       123 LaKhAvseGtkAV~ky~ss  141 (141)
                      |++||++||++||++|+++
T Consensus       108 l~khA~seGtkav~ky~~s  126 (127)
T KOG1744|consen  108 LAKHAVSEGTKAVTKYTSS  126 (127)
T ss_pred             HhhhhhcccchhheeeccC
Confidence            9999999999999999875

>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=99.61  E-value=8.5e-16  Score=103.84  Aligned_cols=68  Identities=31%  Similarity=0.417  Sum_probs=65.2

Q ss_pred             cchhHHHHHHHHhhhhcCC----CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           50 SIETYKIYIFKVLKQVHPD----IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        50 r~esy~~YIyKVLKQVhpd----~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      +...+..||+|++++++++    ..||++||.+|+++++|+|.+|.++|..++.+++|.||+++|||.|+|+
T Consensus         3 ~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~   74 (75)
T PF00125_consen    3 RRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRI   74 (75)
T ss_dssp             SHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHH
T ss_pred             ccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhc
Confidence            4567899999999999999    8999999999999999999999999999999999999999999999986

Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....

>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=98.49  E-value=1e-06  Score=60.59  Aligned_cols=61  Identities=16%  Similarity=0.373  Sum_probs=58.0

Q ss_pred             HHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           58 IFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        58 IyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      +...++++.|+..++..+...|-.+++|+.+.|+.+|..||.+.++.||..+|||-+++-.
T Consensus         7 l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~   67 (72)
T cd07981           7 LQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERN   67 (72)
T ss_pred             HHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            6678999999999999999999999999999999999999999999999999999998754

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

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

Probab=98.30  E-value=2.3e-06  Score=62.30  Aligned_cols=63  Identities=19%  Similarity=0.380  Sum_probs=59.3

Q ss_pred             HHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCch
Q 032404           58 IFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPG  121 (141)
Q Consensus        58 IyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPG  121 (141)
                      |-|++|++.++ .||..|...|+..+..+++.|+.+|+.+|.+.+|+||+.+||+-|.+.+...
T Consensus        25 v~Ri~r~~~~~-Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~   87 (91)
T COG2036          25 VRRILRKAGAE-RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRR   87 (91)
T ss_pred             HHHHHHHHhHH-HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhccc
Confidence            78889998888 9999999999999999999999999999999999999999999999987653

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

Probab=98.26  E-value=4.6e-06  Score=55.39  Aligned_cols=58  Identities=26%  Similarity=0.458  Sum_probs=52.6

Q ss_pred             HHHHHhhhhcCC-CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHH
Q 032404           57 YIFKVLKQVHPD-IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAV  115 (141)
Q Consensus        57 YIyKVLKQVhpd-~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAV  115 (141)
                      -|.|++|+. || ..||.+|...|......+.+.|+.+|...+..++|+||+.+||..||
T Consensus         7 ~vkri~k~~-~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av   65 (65)
T PF00808_consen    7 RVKRIMKSD-PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV   65 (65)
T ss_dssp             HHHHHHHHT-STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred             HHHHHhccC-CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence            488999999 76 56999999999999999999999999999999999999999999986

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

>smart00803 TAF TATA box binding protein associated factor

Probab=97.86  E-value=7.3e-05  Score=50.88  Aligned_cols=59  Identities=22%  Similarity=0.317  Sum_probs=52.4

Q ss_pred             HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      .|.+++++..= ..||..+..-|-..+.+..+.|+.+|..++++.+|+|||..||..|++
T Consensus         7 ~i~ria~~~Gi-~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk   65 (65)
T smart00803        7 TIKDVAESLGI-GNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR   65 (65)
T ss_pred             HHHHHHHHCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence            47778877643 378999999999999999999999999999999999999999988864

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.

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

Probab=97.78  E-value=8.2e-05  Score=56.03  Aligned_cols=65  Identities=25%  Similarity=0.277  Sum_probs=58.7

Q ss_pred             hhHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           52 ETYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        52 esy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      -.|.. =|+|.|++-.--..||..|..-|...+.++...|.+.|...++.+++++||.|+|+.|++
T Consensus        19 L~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~   84 (115)
T cd00074          19 LQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVR   84 (115)
T ss_pred             ccCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHh
Confidence            34544 599999986666899999999999999999999999999999999999999999999998

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.

>PLN00035 histone H4; Provisional

Probab=97.77  E-value=0.00015  Score=54.05  Aligned_cols=60  Identities=12%  Similarity=0.145  Sum_probs=54.7

Q ss_pred             HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      -|.|+++.-- -..||..+..-|...++++++.|+.+|..++.+.+|+||+..||..|++.
T Consensus        34 ~IrRLARr~G-vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr   93 (103)
T PLN00035         34 AIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR   93 (103)
T ss_pred             HHHHHHHHcC-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence            4788888764 46899999999999999999999999999999999999999999999874

>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=97.71  E-value=0.00021  Score=51.37  Aligned_cols=60  Identities=13%  Similarity=0.191  Sum_probs=53.7

Q ss_pred             HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      -|.|+++.-- -..||..+..-+...++.+++.|+.+|..++.+.+|+||+..||..|++.
T Consensus        18 ~I~RLarr~G-vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr   77 (85)
T cd00076          18 AIRRLARRGG-VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKR   77 (85)
T ss_pred             HHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence            5778887653 46899999999999999999999999999999999999999999998873

>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=97.70  E-value=0.00018  Score=49.62  Aligned_cols=59  Identities=17%  Similarity=0.383  Sum_probs=48.9

Q ss_pred             HHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           58 IFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        58 IyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      +...++||-|+..+...+..+|-.+.+|+.+.+..-|++||++.+-.||..+|||...+
T Consensus         5 l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Le   63 (68)
T PF03847_consen    5 LQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLE   63 (68)
T ss_dssp             HHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHH
T ss_pred             HHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHH
Confidence            66789999999999999999999999999999999999999999999999999998764

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

>PTZ00015 histone H4; Provisional

Probab=97.67  E-value=0.00025  Score=52.72  Aligned_cols=61  Identities=15%  Similarity=0.239  Sum_probs=54.3

Q ss_pred             HHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           56 IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        56 ~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      .-|.|+++.- --..||..+..-+..+++++++.|+.+|..++.|.+|+||+..||..|++.
T Consensus        34 ~~IrRLarr~-GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr   94 (102)
T PTZ00015         34 GAIRRLARRG-GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKR   94 (102)
T ss_pred             HHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHh
Confidence            4588888764 236899999999999999999999999999999999999999999998864

>smart00428 H3 Histone H3

Probab=97.51  E-value=0.00068  Score=50.52  Aligned_cols=68  Identities=19%  Similarity=0.262  Sum_probs=62.5

Q ss_pred             chhHHHHHHHHhhhhcC--CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           51 IETYKIYIFKVLKQVHP--DIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        51 ~esy~~YIyKVLKQVhp--d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      +-.|+..|..+..+..+  |..+++.|+.-|.....+.+-.+.++|..++.+.+|.||..+|||-|.||-
T Consensus        32 k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~rir  101 (105)
T smart00428       32 KAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRIR  101 (105)
T ss_pred             cccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHHh
Confidence            45788888888888888  899999999999999999999999999999999999999999999998863

>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=97.32  E-value=0.0018  Score=48.44  Aligned_cols=65  Identities=11%  Similarity=0.149  Sum_probs=57.8

Q ss_pred             HHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCc
Q 032404           55 KIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLP  120 (141)
Q Consensus        55 ~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLP  120 (141)
                      ...|.++||... ...++..+...|..|+....+.|+.+|..++.+.+|+||+..||..|+...+.
T Consensus         4 ~~~v~~iLk~~G-v~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~   68 (117)
T cd07979           4 ARVIAAILKSMG-ITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD   68 (117)
T ss_pred             HHHHHHHHHHCC-CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc
Confidence            356888998752 35779999999999999999999999999999999999999999999988774

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

>smart00417 H4 Histone H4

Probab=97.25  E-value=0.0008  Score=47.34  Aligned_cols=56  Identities=11%  Similarity=0.166  Sum_probs=48.7

Q ss_pred             HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHH
Q 032404           57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT  113 (141)
Q Consensus        57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqt  113 (141)
                      -|.|+++.- ---.||..+..-+..+++++++.|+.+|..++.+.+|+|++..||..
T Consensus        18 ~IrRLaRr~-GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~   73 (74)
T smart00417       18 AIRRLARRG-GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY   73 (74)
T ss_pred             HHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence            477887764 22578999999999999999999999999999999999999999853

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

Probab=96.84  E-value=0.0047  Score=49.52  Aligned_cols=61  Identities=18%  Similarity=0.306  Sum_probs=56.2

Q ss_pred             HHHHhhhhcCC-CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           58 IFKVLKQVHPD-IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        58 IyKVLKQVhpd-~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      |-|+.|+.-|. ..||.+|-..|.-.|..+.-=|..||+..++..+|+||+..||..|+--|
T Consensus        38 V~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tL   99 (168)
T KOG0869|consen   38 VSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTL   99 (168)
T ss_pred             HHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHc
Confidence            78899988776 68999999999999999999999999999999999999999999998643

>PLN00156 histone H2AX; Provisional

Probab=96.57  E-value=0.0075  Score=47.18  Aligned_cols=70  Identities=26%  Similarity=0.276  Sum_probs=60.5

Q ss_pred             hHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHH
Q 032404           53 TYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELA  124 (141)
Q Consensus        53 sy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELa  124 (141)
                      .|.. -|+|.|+.-+--..|+..|.--|-..+.++...|-+-|..-++.+++.-|+.|.||.||+  -..||.
T Consensus        29 ~FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr--nDeEL~   99 (139)
T PLN00156         29 QFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR--NDEELS   99 (139)
T ss_pred             ccchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc--CcHHHH
Confidence            4654 699999998777899999999999999999999999999999999999999999999998  334443

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

Probab=96.51  E-value=0.013  Score=46.66  Aligned_cols=66  Identities=18%  Similarity=0.318  Sum_probs=59.6

Q ss_pred             HHHHHhhhhcC-CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchH
Q 032404           57 YIFKVLKQVHP-DIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGE  122 (141)
Q Consensus        57 YIyKVLKQVhp-d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGE  122 (141)
                      -|.|++|.+-| |..+..+|..+++..--.+..-|+.||.+++....|+||....|+.|..-|==||
T Consensus        17 tv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~e   83 (156)
T KOG0871|consen   17 TVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGE   83 (156)
T ss_pred             HHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHH
Confidence            48899999999 9999999999998888889999999999999999999999999999998654343

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

Probab=96.46  E-value=0.0045  Score=52.63  Aligned_cols=67  Identities=18%  Similarity=0.336  Sum_probs=60.0

Q ss_pred             HHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH----hhCchH
Q 032404           56 IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR----LVLPGE  122 (141)
Q Consensus        56 ~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr----LlLPGE  122 (141)
                      .-+...++||.+++.|..+.-++|-.+..|+.+.|..-+++||++.+..||-.|||+..+.    +-|||.
T Consensus       158 ~kl~dLvqqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm~iPgf  228 (258)
T KOG1142|consen  158 RKLDDLVQQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNMEIPGF  228 (258)
T ss_pred             cchhHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccccccCCCc
Confidence            3488899999999999999999999999999999999999999999999999999998764    345554

>smart00414 H2A Histone 2A

Probab=96.38  E-value=0.0095  Score=44.27  Aligned_cols=70  Identities=23%  Similarity=0.292  Sum_probs=57.2

Q ss_pred             hHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHH
Q 032404           53 TYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELA  124 (141)
Q Consensus        53 sy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELa  124 (141)
                      .|.. .|+|.|+.-.--..|+.-|.--|-..+..+...|-+-|..-++.+++.-||.|+||.|++-  -.||.
T Consensus         9 ~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n--D~EL~   79 (106)
T smart00414        9 QFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN--DEELN   79 (106)
T ss_pred             cCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC--CHHHH
Confidence            3443 6999999877677999999888888888888888888888889999999999999999983  44443

>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=96.30  E-value=0.018  Score=39.58  Aligned_cols=47  Identities=21%  Similarity=0.374  Sum_probs=38.7

Q ss_pred             CcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           70 GISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        70 gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      .++.++-..|-.=++.-+..|..+|.+++++.+|.+||..||..|.|
T Consensus        20 ~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr   66 (66)
T PF02969_consen   20 NLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR   66 (66)
T ss_dssp             -B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence            45788888888888888999999999999999999999999999876

TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.

>PLN00157 histone H2A; Provisional

Probab=96.29  E-value=0.0077  Score=46.72  Aligned_cols=65  Identities=25%  Similarity=0.266  Sum_probs=58.2

Q ss_pred             hhHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           52 ETYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        52 esy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      -.|.. -|+|.|++-+-...|+..|.--|-..+..+...|-+-|..-++.+++.-|+.|.||.|++
T Consensus        25 L~FPVgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~   90 (132)
T PLN00157         25 LQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR   90 (132)
T ss_pred             cccchHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence            45554 699999998777899999999999999999999999999999999999999999999998

>PTZ00017 histone H2A; Provisional

Probab=96.25  E-value=0.0093  Score=46.34  Aligned_cols=65  Identities=22%  Similarity=0.270  Sum_probs=56.8

Q ss_pred             hhHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           52 ETYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        52 esy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      -.|.. -|+|.|++-+.-..|+..|.--|-..+..++..|-+-|..-++.+++.-||.|.||.|++
T Consensus        26 L~FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~   91 (134)
T PTZ00017         26 LQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR   91 (134)
T ss_pred             cccchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence            34554 699999987777799999988888888888888888899999999999999999999998

>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=96.23  E-value=0.015  Score=50.16  Aligned_cols=49  Identities=18%  Similarity=0.379  Sum_probs=46.6

Q ss_pred             CcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           70 GISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        70 gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      .+|.+|...|..-+.+....|+.||.+++++.+|+||+..||..|++..
T Consensus        16 ~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~   64 (343)
T cd08050          16 SLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLR   64 (343)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHh
Confidence            6799999999999999999999999999999999999999999999863

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

>PLN00153 histone H2A; Provisional

Probab=96.05  E-value=0.013  Score=45.21  Aligned_cols=71  Identities=25%  Similarity=0.256  Sum_probs=60.6

Q ss_pred             hhHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHH
Q 032404           52 ETYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELA  124 (141)
Q Consensus        52 esy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELa  124 (141)
                      -.|.. -|+|.|++-+.-..|+..|.--|-..+..+...|-+-|..-++.|++.-|+.|.||.||+  -..||.
T Consensus        23 L~FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~--nDeEL~   94 (129)
T PLN00153         23 LQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR--NDEELG   94 (129)
T ss_pred             cccchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc--CcHHHH
Confidence            45554 699999987777899999999999999999999999999999999999999999999998  334443

>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins

Probab=95.77  E-value=0.088  Score=36.24  Aligned_cols=60  Identities=8%  Similarity=0.155  Sum_probs=48.7

Q ss_pred             HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      .|-++|+..-= -+++..|++.|-.++.+.+..|+.++..++.+.+|.+.+..||..|+.-
T Consensus        11 ~Vaqil~~~Gf-~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~   70 (77)
T smart00576       11 AVAQILESAGF-DSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALEN   70 (77)
T ss_pred             HHHHHHHHcCc-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence            34444544311 3568889999999999999999999999999999999999999988764

subdomain of archael histone-like transcription factors

>PTZ00252 histone H2A; Provisional

Probab=95.50  E-value=0.038  Score=43.03  Aligned_cols=66  Identities=18%  Similarity=0.184  Sum_probs=55.2

Q ss_pred             chhHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhh--cCCCCcChHHHHHHHH
Q 032404           51 IETYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARY--NKKPTITSREIQTAVR  116 (141)
Q Consensus        51 ~esy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~--nkk~TltsreIqtAVr  116 (141)
                      .-.|.. -|+|.|++-+-...|+.-|.--|-..+..++..|-+-|..-++-  |++.-|+.|.||.||+
T Consensus        23 GL~FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr   91 (134)
T PTZ00252         23 GLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR   91 (134)
T ss_pred             CccCchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence            345654 69999999888889999999888888888888888888877743  8889999999999998

>PLN00154 histone H2A; Provisional

Probab=95.40  E-value=0.044  Score=42.76  Aligned_cols=71  Identities=20%  Similarity=0.213  Sum_probs=56.9

Q ss_pred             hHHH-HHHHHhhhhc-CCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHHH
Q 032404           53 TYKI-YIFKVLKQVH-PDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAK  125 (141)
Q Consensus        53 sy~~-YIyKVLKQVh-pd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELaK  125 (141)
                      .|-. -|.|.||+-. -...|+..|.--|-..+..+.-.|-+-|..-++.+++.-||.|.||.|++  =-.||.+
T Consensus        38 ~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr--nDeEL~~  110 (136)
T PLN00154         38 QFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR--GDEELDT  110 (136)
T ss_pred             cCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc--CcHHHHH
Confidence            4544 6999999975 45689998988888888888888888888888999999999999999998  3345443

>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]

Probab=95.36  E-value=0.037  Score=42.76  Aligned_cols=67  Identities=25%  Similarity=0.290  Sum_probs=58.3

Q ss_pred             HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHHH
Q 032404           57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAK  125 (141)
Q Consensus        57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELaK  125 (141)
                      -|.|+||.-.-.+.|+++|.--+.-.+..+.-.|.+-|..-++-++++-|+.|.||-|+|  =..||-+
T Consensus        31 rvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr--nD~EL~~   97 (132)
T COG5262          31 RVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR--NDEELNK   97 (132)
T ss_pred             HHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc--CcHHHHH
Confidence            599999977777999999999888899999999999999999999999999999999998  3445433

>PLN00121 histone H3; Provisional

Probab=95.19  E-value=0.1  Score=40.67  Aligned_cols=66  Identities=18%  Similarity=0.241  Sum_probs=55.7

Q ss_pred             hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           52 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        52 esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      -.|...|..|.....++..+.+.|+.-|..-..+.+-.+-+++.-.+.+.+|-||..+|||-+.||
T Consensus        66 ~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ri  131 (136)
T PLN00121         66 LPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI  131 (136)
T ss_pred             ccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHHh
Confidence            457777777777777889999999998887777777777778899999999999999999999875

>PF15510 CENP-W: Centromere kinetochore component W

Probab=95.01  E-value=0.041  Score=40.88  Aligned_cols=65  Identities=23%  Similarity=0.369  Sum_probs=53.3

Q ss_pred             HHHHHHHHhhhhcCCCCc--chHHH--------------HHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           54 YKIYIFKVLKQVHPDIGI--SSKAM--------------GIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        54 y~~YIyKVLKQVhpd~gI--SskAm--------------~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      -..++.||+|+--|.+.+  +.+.|              --||-++  +..|+|+||---+.-||+.||....|+.|.+.
T Consensus        18 PrgfLkrv~Kr~KphlRl~~~~Dllv~~~~f~~~~~~~~vhLncLL--FvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaKv   95 (102)
T PF15510_consen   18 PRGFLKRVFKRQKPHLRLETSGDLLVRFCPFSGWQWGGEVHLNCLL--FVHRLAEEARTNACENKCGTIKKEHVLAAAKV   95 (102)
T ss_pred             chHHHHHHHHhcCCceeecccccHHHhhcccccccccceeehhHHH--HHHHHHHHHHHHHHHHhhccccHHHHHHHHHH
Confidence            346789999998888766  44445              3456665  67899999999999999999999999999998


Q ss_pred             hCc
Q 032404          118 VLP  120 (141)
Q Consensus       118 lLP  120 (141)
                      +|-
T Consensus        96 iLK   98 (102)
T PF15510_consen   96 ILK   98 (102)
T ss_pred             HHH
Confidence            874

>PTZ00018 histone H3; Provisional

Probab=94.94  E-value=0.13  Score=40.11  Aligned_cols=66  Identities=18%  Similarity=0.241  Sum_probs=55.4

Q ss_pred             hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           52 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        52 esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      -.|...|..|..+..++..+.+.|+.-|..-..+.+-.+-+++.-.+.+.+|-||..+|||-|.||
T Consensus        66 ~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ri  131 (136)
T PTZ00018         66 LPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI  131 (136)
T ss_pred             ccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHHh
Confidence            356777777777777889999999998887777777777778899999999999999999999875

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

Probab=94.69  E-value=0.19  Score=40.63  Aligned_cols=63  Identities=22%  Similarity=0.299  Sum_probs=49.9

Q ss_pred             HHHHHHhhhhcCC--CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           56 IYIFKVLKQVHPD--IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        56 ~YIyKVLKQVhpd--~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      .-|-|+.|.+-|+  .+||.+|...|-.-..=+..-+..-|..+|+-++|+||+..||-.|.+-+
T Consensus        14 AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Ei   78 (172)
T KOG0870|consen   14 AIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEI   78 (172)
T ss_pred             HHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHh
Confidence            4577888888776  58999998877665444445566667779999999999999999999865

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

Probab=94.52  E-value=0.14  Score=35.97  Aligned_cols=59  Identities=15%  Similarity=0.330  Sum_probs=47.9

Q ss_pred             HHHHhhhh--cCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           58 IFKVLKQV--HPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        58 IyKVLKQV--hpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      |-++..++  ..+..+|.+.++-|..++.+..+.++.+---++++.+|+||+..|+.-.+|
T Consensus        11 v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~R   71 (76)
T PF15630_consen   11 VGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLAR   71 (76)
T ss_dssp             HHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTT
T ss_pred             HHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhh
Confidence            45566666  456788999999999999999999999999999999999999999875544

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

Probab=93.77  E-value=0.18  Score=39.27  Aligned_cols=67  Identities=25%  Similarity=0.298  Sum_probs=54.6

Q ss_pred             HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHHH
Q 032404           57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAK  125 (141)
Q Consensus        57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELaK  125 (141)
                      -|.|+||.-..-..||..|-..|.-.+..+--.|.+-|..-++-|++.-|++|.||-|++  =..||.+
T Consensus        32 ri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~--NDeEL~~   98 (131)
T KOG1756|consen   32 RIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR--NDEELNK   98 (131)
T ss_pred             HHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh--CcHHHHH
Confidence            699999997777899999988777777777777777777778899999999999999998  3344443

>PLN00161 histone H3; Provisional

Probab=93.33  E-value=0.54  Score=36.72  Aligned_cols=66  Identities=15%  Similarity=0.208  Sum_probs=52.3

Q ss_pred             hhHHHHHHHHhhhhcC-CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           52 ETYKIYIFKVLKQVHP-DIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        52 esy~~YIyKVLKQVhp-d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      -.|+..|..|..+..+ |+.+.+.|+.-|..-..+.+-.+-+++.-.+.+.+|-||..+|||-|.||
T Consensus        59 lPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~ri  125 (135)
T PLN00161         59 LPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRI  125 (135)
T ss_pred             ccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHh
Confidence            3566666666655544 68899999888877776666666678888999999999999999999875

>PLN00160 histone H3; Provisional

Probab=92.04  E-value=1.1  Score=33.18  Aligned_cols=66  Identities=15%  Similarity=0.148  Sum_probs=50.5

Q ss_pred             hhHHHHHHHHhhhhcC-CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           52 ETYKIYIFKVLKQVHP-DIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        52 esy~~YIyKVLKQVhp-d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      -.|+.-+..+.-.... +..+.+.|+.-|..-..+.+-.+-+++.-.+.+.+|-||..+|||-|.|+
T Consensus        25 ~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~ri   91 (97)
T PLN00160         25 LPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARRI   91 (97)
T ss_pred             ccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHHh
Confidence            4566666666554433 37889999888877666666666668888899999999999999999874

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

Probab=91.95  E-value=0.45  Score=42.27  Aligned_cols=54  Identities=19%  Similarity=0.282  Sum_probs=41.7

Q ss_pred             HHHHHhhhhc-----CCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHH
Q 032404           57 YIFKVLKQVH-----PDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSRE  110 (141)
Q Consensus        57 YIyKVLKQVh-----pd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~Tltsre  110 (141)
                      +|.+++....     -.+.||.+||..+....+.+||.|+..=.-.+.+.+|+||...|
T Consensus       356 ~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD  414 (414)
T PF15511_consen  356 VVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD  414 (414)
T ss_dssp             HHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred             HHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence            5555555543     45899999999999999999999999999999999999998765

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

Probab=91.92  E-value=1.7  Score=29.45  Aligned_cols=48  Identities=13%  Similarity=0.269  Sum_probs=44.4

Q ss_pred             CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           69 IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        69 ~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      .+++..|+++|..++.+.+..|+..+...+....|...+..||..|..
T Consensus        22 ~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~   69 (77)
T PF07524_consen   22 DSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALE   69 (77)
T ss_pred             cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence            467899999999999999999999999999999999999999998875

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 [, ].

>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=89.86  E-value=1.1  Score=34.43  Aligned_cols=60  Identities=17%  Similarity=0.303  Sum_probs=44.4

Q ss_pred             HHHHHHhhhhcCCCCcc---hHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032404           56 IYIFKVLKQVHPDIGIS---SKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVL  119 (141)
Q Consensus        56 ~YIyKVLKQVhpd~gIS---skAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlL  119 (141)
                      ..|.-+|+.    +||+   .+....|-.|+.-..-.|-.+|..++.+.++.+|+..||+.|+..-+
T Consensus        16 ~~i~~iL~~----~Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~   78 (129)
T PF02291_consen   16 RVIHLILKS----MGVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRL   78 (129)
T ss_dssp             HHHHHHHHH----TT---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT-
T ss_pred             HHHHHHHHH----cCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHH
Confidence            456666654    5664   56667777777777788889999999999999999999999998654

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

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

Probab=88.84  E-value=1.6  Score=41.02  Aligned_cols=50  Identities=12%  Similarity=0.271  Sum_probs=45.7

Q ss_pred             CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           69 IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        69 ~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      ..|+.++-.+|---|..=.+.|+.+|+++.++.+|.+||..||.-|.|.+
T Consensus        27 ~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~   76 (576)
T KOG2549|consen   27 TNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSL   76 (576)
T ss_pred             cccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhc
Confidence            44678999999888999999999999999999999999999999999864

>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=86.96  E-value=0.9  Score=32.63  Aligned_cols=47  Identities=13%  Similarity=0.244  Sum_probs=23.6

Q ss_pred             CcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           70 GISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        70 gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      --+.++..+|..+|.+-.-.+..+|..++....+..|+..||..++|
T Consensus        19 ~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR   65 (93)
T PF02269_consen   19 EPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLR   65 (93)
T ss_dssp             S--HHHHHHHHHHHHHHHHHHHHHHHC--------------------
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHh
Confidence            45678999999999999999999999999999999999999999887

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

>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=85.36  E-value=7.2  Score=27.85  Aligned_cols=60  Identities=12%  Similarity=0.196  Sum_probs=49.8

Q ss_pred             HHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCC---CCcChHHHHHHHHhh
Q 032404           58 IFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKK---PTITSREIQTAVRLV  118 (141)
Q Consensus        58 IyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk---~TltsreIqtAVrLl  118 (141)
                      |.|++.++-. .+++..-..+|..+-.-+.-.|.++|..+..-...   ..|.++.|..|.|.+
T Consensus        22 iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl   84 (85)
T cd08048          22 IKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL   84 (85)
T ss_pred             HHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence            7777777754 78888888888888888888999999998877554   899999999999976

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

>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=85.15  E-value=4  Score=29.44  Aligned_cols=51  Identities=8%  Similarity=0.281  Sum_probs=42.3

Q ss_pred             cCCC-CcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           66 HPDI-GISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        66 hpd~-gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      +-|. .-..++..+|..+|.+..-.|..+|..++. .++.-++..||..++|-
T Consensus        15 ~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~   66 (92)
T cd07978          15 FGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRK   66 (92)
T ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhc
Confidence            3443 346789999999999999999999999998 55556699999999873

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

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

Probab=82.92  E-value=5  Score=31.88  Aligned_cols=59  Identities=19%  Similarity=0.356  Sum_probs=42.5

Q ss_pred             HHHHHhhhhcCCCCcch---HHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032404           57 YIFKVLKQVHPDIGISS---KAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVL  119 (141)
Q Consensus        57 YIyKVLKQVhpd~gISs---kAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlL  119 (141)
                      -|.-+|+    ++||..   +-++.|=.|..--.-.|-..|.-++.+.++.||+..||+.|+....
T Consensus        18 ~i~~iL~----s~GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~   79 (148)
T KOG3334|consen   18 VIASILK----SLGIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRV   79 (148)
T ss_pred             HHHHHHH----HcCccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHh
Confidence            3444554    467754   3344444454555567889999999999999999999999998653

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	141
1u35_D	126	Crystal Structure Of The Nucleosome Core Particle C		6e-41
2hio_B	125	Histone Octamer (Chicken), Chromosomal Protein Leng		8e-41
1eqz_B	126	X-Ray Structure Of The Nucleosome Core Particle At		8e-41
3a6n_D	129	The Nucleosome Containing A Testis-Specific Histone		1e-40
2cv5_D	126	Crystal Structure Of Human Nucleosome Core Particle		2e-40
2xql_B	90	Fitting Of The H2a-H2b Histones In The Electron Mic		3e-40
2pyo_D	122	Drosophila Nucleosome Core Length = 122		3e-40
3c9k_B	125	Model Of Histone Octamer Tubular Crystals Length =		4e-40
2f8n_H	123	2.9 Angstrom X-Ray Structure Of Hybrid Macroh2a Nuc		9e-40
1s32_D	122	Molecular Recognition Of The Nucleosomal 'supergroo		1e-39
1aoi_D	99	Complex Between Nucleosome Core Particle (H3,H4,H2a		1e-39
3c1b_D	125	The Effect Of H3 K79 Dimethylation And H4 K20 Trime		1e-39
1zla_D	125	X-Ray Structure Of A Kaposi's Sarcoma Herpesvirus L		1e-39
2nqb_D	123	Drosophila Nucleosome Structure Length = 123		1e-39
3kwq_D	93	Structural Characterization Of H3k56q Nucleosomes A		1e-39
1p34_D	125	Crystallographic Studies Of Nucleosome Core Particl		1e-39
1kx3_D	125	X-Ray Structure Of The Nucleosome Core Particle, Nc		1e-39
1f66_D	126	2.6 A Crystal Structure Of A Nucleosome Core Partic		1e-39
3an2_D	129	The Structure Of The Centromeric Nucleosome Contain		6e-39
1hio_B	90	Histone Octamer (Chicken), Chromosomal Protein, Alp		5e-38
1id3_D	130	Crystal Structure Of The Yeast Nucleosome Core Part		4e-37
2jss_A	192	Nmr Structure Of Chaperone Chz1 Complexed With Hist		3e-35

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

Iteration: 1
 Score =  162 bits (410), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 74/90 (82%), Positives = 85/90 (94%)
Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           E+Y IY++KVLKQVHPD GISSKAMGIMNSF+NDIFE++A E+SRLA YNK+ TITSRE+
Sbjct: 36  ESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIASEASRLAHYNKRSTITSREV 95
Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           QTAVRL+LPGELAKHAVSEGTKAVTK+TSS
Sbjct: 96  QTAVRLLLPGELAKHAVSEGTKAVTKYTSS 125

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

Iteration: 1
 Score =  162 bits (409), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 75/90 (83%), Positives = 85/90 (94%)
Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           E+Y IY++KVLKQVHPD GISSKAMGIMNSF+NDIFE++A E+SRLA YNK+ TITSREI
Sbjct: 35  ESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREI 94
Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           QTAVRL+LPGELAKHAVSEGTKAVTK+TSS
Sbjct: 95  QTAVRLLLPGELAKHAVSEGTKAVTKYTSS 124

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

Iteration: 1
 Score =  162 bits (409), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 75/90 (83%), Positives = 85/90 (94%)
Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           E+Y IY++KVLKQVHPD GISSKAMGIMNSF+NDIFE++A E+SRLA YNK+ TITSREI
Sbjct: 36  ESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREI 95
Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           QTAVRL+LPGELAKHAVSEGTKAVTK+TSS
Sbjct: 96  QTAVRLLLPGELAKHAVSEGTKAVTKYTSS 125

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

Iteration: 1
 Score =  161 bits (407), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 74/90 (82%), Positives = 85/90 (94%)
Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           E+Y IY++KVLKQVHPD GISSKAMGIMNSF+NDIFE++A E+SRLA YNK+ TITSREI
Sbjct: 39  ESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREI 98
Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           QTAVRL+LPGELAKHAVSEGTKAVTK+TS+
Sbjct: 99  QTAVRLLLPGELAKHAVSEGTKAVTKYTSA 128

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

Iteration: 1
 Score =  160 bits (405), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 73/90 (81%), Positives = 85/90 (94%)
Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           E+Y +Y++KVLKQVHPD GISSKAMGIMNSF+NDIFE++A E+SRLA YNK+ TITSREI
Sbjct: 36  ESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREI 95
Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           QTAVRL+LPGELAKHAVSEGTKAVTK+TS+
Sbjct: 96  QTAVRLLLPGELAKHAVSEGTKAVTKYTSA 125

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

Iteration: 1
 Score =  160 bits (404), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 74/89 (83%), Positives = 84/89 (94%)
Query: 53  TYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQ 112
           +Y IY++KVLKQVHPD GISSKAMGIMNSF+NDIFE++A E+SRLA YNK+ TITSREIQ
Sbjct: 1   SYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQ 60
Query: 113 TAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           TAVRL+LPGELAKHAVSEGTKAVTK+TSS
Sbjct: 61  TAVRLLLPGELAKHAVSEGTKAVTKYTSS 89

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

Iteration: 1
 Score =  160 bits (404), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 75/90 (83%), Positives = 84/90 (93%)
Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           E+Y IYI+KVLKQVHPD GISSKAM IMNSF+NDIFE++A E+SRLA YNK+ TITSREI
Sbjct: 32  ESYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREI 91
Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           QTAVRL+LPGELAKHAVSEGTKAVTK+TSS
Sbjct: 92  QTAVRLLLPGELAKHAVSEGTKAVTKYTSS 121

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

Iteration: 1
 Score =  159 bits (403), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 74/90 (82%), Positives = 84/90 (93%)
Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           E+Y IY++KVLKQVHPD GISSKAM IMNSF+NDIFE++A E+SRLA YNK+ TITSREI
Sbjct: 35  ESYSIYVYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAGEASRLAHYNKRSTITSREI 94
Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           QTAVRL+LPGELAKHAVSEGTKAVTK+TSS
Sbjct: 95  QTAVRLLLPGELAKHAVSEGTKAVTKYTSS 124

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

Iteration: 1
 Score =  158 bits (400), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 72/90 (80%), Positives = 84/90 (93%)
Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           E+Y IY++KVLKQVHPD GISSKAM IMNSF+ND+FE++A E+SRLA YNK+ TITSREI
Sbjct: 33  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 92
Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           QTAVRL+LPGELAKHAVSEGTKAVTK+TS+
Sbjct: 93  QTAVRLLLPGELAKHAVSEGTKAVTKYTSA 122

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

Iteration: 1
 Score =  158 bits (399), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 72/90 (80%), Positives = 84/90 (93%)
Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           E+Y IY++KVLKQVHPD GISSKAM IMNSF+ND+FE++A E+SRLA YNK+ TITSREI
Sbjct: 32  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 91
Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           QTAVRL+LPGELAKHAVSEGTKAVTK+TS+
Sbjct: 92  QTAVRLLLPGELAKHAVSEGTKAVTKYTSA 121

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

Iteration: 1
 Score =  158 bits (399), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 72/90 (80%), Positives = 84/90 (93%)
Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           E+Y IY++KVLKQVHPD GISSKAM IMNSF+ND+FE++A E+SRLA YNK+ TITSREI
Sbjct: 9   ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 68
Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           QTAVRL+LPGELAKHAVSEGTKAVTK+TS+
Sbjct: 69  QTAVRLLLPGELAKHAVSEGTKAVTKYTSA 98

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

Iteration: 1
 Score =  158 bits (399), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 72/90 (80%), Positives = 84/90 (93%)
Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           E+Y IY++KVLKQVHPD GISSKAM IMNSF+ND+FE++A E+SRLA YNK+ TITSREI
Sbjct: 35  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 94
Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           QTAVRL+LPGELAKHAVSEGTKAVTK+TS+
Sbjct: 95  QTAVRLLLPGELAKHAVSEGTKAVTKYTSA 124

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

Iteration: 1
 Score =  158 bits (399), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 72/90 (80%), Positives = 84/90 (93%)
Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           E+Y IY++KVLKQVHPD GISSKAM IMNSF+ND+FE++A E+SRLA YNK+ TITSREI
Sbjct: 35  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 94
Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           QTAVRL+LPGELAKHAVSEGTKAVTK+TS+
Sbjct: 95  QTAVRLLLPGELAKHAVSEGTKAVTKYTSA 124

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

Iteration: 1
 Score =  158 bits (399), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 74/90 (82%), Positives = 83/90 (92%)
Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           E+Y IYI+ VLKQVHPD GISSKAM IMNSF+NDIFE++A E+SRLA YNK+ TITSREI
Sbjct: 33  ESYAIYIYTVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREI 92
Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           QTAVRL+LPGELAKHAVSEGTKAVTK+TSS
Sbjct: 93  QTAVRLLLPGELAKHAVSEGTKAVTKYTSS 122

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

Iteration: 1
 Score =  158 bits (399), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 72/90 (80%), Positives = 84/90 (93%)
Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           E+Y IY++KVLKQVHPD GISSKAM IMNSF+ND+FE++A E+SRLA YNK+ TITSREI
Sbjct: 3   ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 62
Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           QTAVRL+LPGELAKHAVSEGTKAVTK+TS+
Sbjct: 63  QTAVRLLLPGELAKHAVSEGTKAVTKYTSA 92

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

Iteration: 1
 Score =  157 bits (398), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 72/90 (80%), Positives = 84/90 (93%)
Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           E+Y IY++KVLKQVHPD GISSKAM IMNSF+ND+FE++A E+SRLA YNK+ TITSREI
Sbjct: 35  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 94
Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           QTAVRL+LPGELAKHAVSEGTKAVTK+TS+
Sbjct: 95  QTAVRLLLPGELAKHAVSEGTKAVTKYTSA 124

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

Iteration: 1
 Score =  157 bits (398), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 72/90 (80%), Positives = 84/90 (93%)
Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           E+Y IY++KVLKQVHPD GISSKAM IMNSF+ND+FE++A E+SRLA YNK+ TITSREI
Sbjct: 35  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 94
Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           QTAVRL+LPGELAKHAVSEGTKAVTK+TS+
Sbjct: 95  QTAVRLLLPGELAKHAVSEGTKAVTKYTSA 124

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

Iteration: 1
 Score =  157 bits (398), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 72/90 (80%), Positives = 84/90 (93%)
Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           E+Y IY++KVLKQVHPD GISSKAM IMNSF+ND+FE++A E+SRLA YNK+ TITSREI
Sbjct: 36  ESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREI 95
Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           QTAVRL+LPGELAKHAVSEGTKAVTK+TS+
Sbjct: 96  QTAVRLLLPGELAKHAVSEGTKAVTKYTSA 125

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

Iteration: 1
 Score =  155 bits (393), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 72/90 (80%), Positives = 83/90 (92%)
Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           E+Y IY++KVLKQVHPD GISSKA GI NSF+NDIFE++A E+SRLA YNK+ TITSREI
Sbjct: 39  ESYSIYVYKVLKQVHPDTGISSKAXGIXNSFVNDIFERIAGEASRLAHYNKRSTITSREI 98
Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           QTAVRL+LPGELAKHAVSEGTKAVTK+TS+
Sbjct: 99  QTAVRLLLPGELAKHAVSEGTKAVTKYTSA 128

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

Iteration: 1
 Score =  152 bits (385), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 72/89 (80%), Positives = 81/89 (91%)
Query: 53  TYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQ 112
           +Y IY++KVLKQVHPD GISSKAMG MNSF+NDIFE++A  +SRLA YNK+ TITSREIQ
Sbjct: 1   SYSIYVYKVLKQVHPDTGISSKAMGSMNSFVNDIFERIAGLASRLAHYNKRSTITSREIQ 60
Query: 113 TAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           TAVRL+LPGELAKHAVSEGTKAVTK TSS
Sbjct: 61  TAVRLLLPGELAKHAVSEGTKAVTKHTSS 89

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

Iteration: 1
 Score =  149 bits (377), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 67/90 (74%), Positives = 81/90 (90%)
Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           ETY  YI+KVLKQ HPD GIS K+M I+NSF+NDIFE++A E+S+LA YNKK TI++REI
Sbjct: 38  ETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREI 97
Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           QTAVRL+LPGELAKHAVSEGT+AVTK++SS
Sbjct: 98  QTAVRLILPGELAKHAVSEGTRAVTKYSSS 127

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

Iteration: 1
 Score =  143 bits (361), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 65/87 (74%), Positives = 78/87 (89%)
Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           ETY  YI+KVLKQ HPD GIS K+M I+NSF+NDIFE++A E+S+LA YNKK TI++REI
Sbjct: 3   ETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREI 62
Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKF 138
           QTAVRL+LPGELAKHAVSEGT+AVTK+
Sbjct: 63  QTAVRLILPGELAKHAVSEGTRAVTKY 89

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	141
2nqb_D	123	Histone H2B; nucleosome, NCP, chromatin, structura	1e-35
1tzy_B	126	Histone H2B; histone-fold, tetramer-dimer-dimer, D	5e-34
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	2e-28
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-07

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

 Score =  118 bits (296), Expect = 1e-35
 Identities = 84/121 (69%), Positives = 96/121 (79%), Gaps = 1/121 (0%)

Query: 22  PAEKKPKAGKKLPKEAAAGDK-KKKRTKKSIETYKIYIFKVLKQVHPDIGISSKAMGIMN 80
           P +   KA KK  K      K  KK+ +K  E+Y IYI+ VLKQVHPD GISSKAM IMN
Sbjct: 2   PPKTSGKAAKKAGKAQKNITKTDKKKKRKRKESYAIYIYTVLKQVHPDTGISSKAMSIMN 61

Query: 81  SFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTKFTS 140
           SF+NDIFE++A E+SRLA YNK+ TITSREIQTAVRL+LPGELAKHAVSEGTKAVTK+TS
Sbjct: 62  SFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 121

Query: 141 S 141
           S
Sbjct: 122 S 122

>1tzy_B Histone H2B; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1eqz_B 1hq3_B 2aro_B 2hio_B 3c9k_B 3azg_D 3a6n_D 3an2_D 3av1_D 3av2_D 3ayw_D 3aze_D 3azf_D 3afa_D 3azh_D 3azi_D 3azj_D 3azk_D 3azl_D 3azm_D ... Length = 126

 Score =  114 bits (286), Expect = 5e-34
 Identities = 85/124 (68%), Positives = 96/124 (77%)

Query: 18  AEKAPAEKKPKAGKKLPKEAAAGDKKKKRTKKSIETYKIYIFKVLKQVHPDIGISSKAMG 77
            E A +   PK G K           KKR K   E+Y IY++KVLKQVHPD GISSKAMG
Sbjct: 2   PEPAKSAPAPKKGSKKAVTKTQKKGDKKRKKSRKESYSIYVYKVLKQVHPDTGISSKAMG 61

Query: 78  IMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTK 137
           IMNSF+NDIFE++A E+SRLA YNK+ TITSREIQTAVRL+LPGELAKHAVSEGTKAVTK
Sbjct: 62  IMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK 121

Query: 138 FTSS 141
           +TSS
Sbjct: 122 YTSS 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 =  102 bits (254), Expect = 2e-28
 Identities = 65/88 (73%), Positives = 79/88 (89%)

Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           ETY  YI+KVLKQ HPD GIS K+M I+NSF+NDIFE++A E+S+LA YNKK TI++REI
Sbjct: 3   ETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREI 62

Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFT 139
           QTAVRL+LPGELAKHAVSEGT+AVTK++
Sbjct: 63  QTAVRLILPGELAKHAVSEGTRAVTKYS 90

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

 Score = 46.0 bits (108), Expect = 8e-07
 Identities = 23/139 (16%), Positives = 44/139 (31%), Gaps = 49/139 (35%)

Query: 31  KKLPKEAAAG---------------------------DKKKKRTKKSI------ETYKIY 57
           + LP+E                               DK     + S+      E  K++
Sbjct: 316 QDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMF 375

Query: 58  ----IFKVLKQVHPDIGISSKAMGIM-----NSFINDIFEKLAQESSRLARYNKKPTITS 108
               +F       P   I +  + ++      S +  +  KL + S  + +  K+ TI+ 
Sbjct: 376 DRLSVFP------PSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSL-VEKQPKESTISI 428

Query: 109 REIQTAVRLVLPGELAKHA 127
             I   +++ L  E A H 
Sbjct: 429 PSIYLELKVKLENEYALHR 447

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	141
2nqb_D	123	Histone H2B; nucleosome, NCP, chromatin, structura	100.0
1tzy_B	126	Histone H2B; histone-fold, tetramer-dimer-dimer, D	100.0
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	100.0
3b0c_W	76	CENP-W, centromere protein W; histone fold, DNA bi	99.68
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	99.11
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	98.89
2yfw_B	103	Histone H4, H4; cell cycle, kinetochore, centromer	98.4
1tzy_D	103	Histone H4-VI; histone-fold, tetramer-dimer-dimer,	98.38
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	98.35
1id3_B	102	Histone H4; nucleosome core particle, chromatin, p	98.16
1n1j_A	93	NF-YB; histone-like PAIR, DNA binding protein; 1.6	98.16
2hue_C	84	Histone H4; mini beta sheet, elongated beta sandwh	98.06
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	98.03
1jfi_B	179	DR1 protein, transcription regulator NC2 beta chai	98.02
2byk_B	128	Chrac-14; nucleosome sliding, histone fold, DNA-bi	97.96
2nqb_C	123	Histone H2A; nucleosome, NCP, chromatin, structura	97.92
2f8n_G	120	Core histone macro-H2A.1; nucleosome, NCP, macroh2	97.9
1tzy_A	129	Histone H2A-IV; histone-fold, tetramer-dimer-dimer	97.87
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	97.87
1id3_C	131	Histone H2A.1; nucleosome core particle, chromatin	97.85
1taf_B	70	TFIID TBP associated factor 62; transcription init	97.83
2f8n_K	149	Histone H2A type 1; nucleosome, NCP, macroh2A, his	97.79
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	97.76
1f66_C	128	Histone H2A.Z; nucleosome, chromatin, histone vari	97.69
4g92_C	119	HAPE; transcription factor, nucleosome, minor groo	97.67
1h3o_B	76	Transcription initiation factor TFIID 20/15 kDa su	97.59
1taf_A	68	TFIID TBP associated factor 42; transcription init	97.59
2hue_B	77	Histone H3; mini beta sheet, elongated beta sandwh	97.58
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	97.5
4dra_A	113	Centromere protein S; DNA binding complex, DNA dam	97.46
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	97.42
3v9r_A	90	MHF1, uncharacterized protein YOL086W-A; histone f	97.36
3b0b_B	107	CENP-S, centromere protein S; histone fold, DNA bi	97.34
3nqj_A	82	Histone H3-like centromeric protein A; alpha helix	97.3
1tzy_C	136	Histone H3; histone-fold, tetramer-dimer-dimer, DN	97.27
2yfv_A	100	Histone H3-like centromeric protein CSE4; cell cyc	97.2
3ksy_A	1049	SOS-1, SON of sevenless homolog 1; RAS, RAS activa	97.15
3vh5_A	140	CENP-S; histone fold, chromosome segregation, DNA	97.07
2ly8_A	121	Budding yeast chaperone SCM3; centromere protein,	97.02
3nqu_A	140	Histone H3-like centromeric protein A; alpha helix	96.89
3r45_A	156	Histone H3-like centromeric protein A; histone fol	96.86
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	96.84
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	96.38
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	90.35
3b0b_C	81	CENP-X, centromere protein X; histone fold, DNA bi	88.53
1bh9_B	89	TAFII28; histone fold, tata binding protein, trans	88.43
4dra_E	84	Centromere protein X; DNA binding complex, DNA dam	88.2
3ksy_A	1049	SOS-1, SON of sevenless homolog 1; RAS, RAS activa	86.0

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

Probab=100.00  E-value=2.4e-55  Score=331.38  Aligned_cols=99  Identities=78%  Similarity=1.103  Sum_probs=92.5

Q ss_pred             ccccccccchhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchH
Q 032404           43 KKKRTKKSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGE  122 (141)
Q Consensus        43 ~kk~~k~r~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGE  122 (141)
                      +++++++|.|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+|+|||+||||+|||||||||
T Consensus        24 ~~k~~~~~~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtAvrLlLpGE  103 (123)
T 2nqb_D           24 DKKKKRKRKESYAIYIYTVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGE  103 (123)
T ss_dssp             -----CCCCCCSHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHHHSCHH
T ss_pred             CCCCCccccchHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHHHhCcHH
Confidence            45566788999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhHHHhhhhhhhcccCC
Q 032404          123 LAKHAVSEGTKAVTKFTSS  141 (141)
Q Consensus       123 LaKhAvseGtkAV~ky~ss  141 (141)
                      |+||||+|||+||++|+++
T Consensus       104 LaKhAvseGtkAV~ky~ss  122 (123)
T 2nqb_D          104 LAKHAVSEGTKAVTKYTSS  122 (123)
T ss_dssp             HHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHhcccCC
Confidence            9999999999999999875

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

Probab=100.00  E-value=3.2e-55  Score=331.83  Aligned_cols=99  Identities=80%  Similarity=1.128  Sum_probs=91.0

Q ss_pred             ccccccccchhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchH
Q 032404           43 KKKRTKKSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGE  122 (141)
Q Consensus        43 ~kk~~k~r~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGE  122 (141)
                      +++++++|.++|++||||||||||||+|||++||+||||||||||||||.||++|++||+|+|||+||||+|||||||||
T Consensus        27 ~~k~~~~~~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtAvrLlLpGE  106 (126)
T 1tzy_B           27 DKKRKKSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGE  106 (126)
T ss_dssp             -------CCCCCHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHSCHH
T ss_pred             CCCccccccccHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcHH
Confidence            45667788999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhHHHhhhhhhhcccCC
Q 032404          123 LAKHAVSEGTKAVTKFTSS  141 (141)
Q Consensus       123 LaKhAvseGtkAV~ky~ss  141 (141)
                      |+||||+|||+||++|+++
T Consensus       107 LaKhAvseGtkAV~ky~ss  125 (126)
T 1tzy_B          107 LAKHAVSEGTKAVTKYTSS  125 (126)
T ss_dssp             HHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHhcccCC
Confidence            9999999999999999875

>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=1.2e-39  Score=258.40  Aligned_cols=91  Identities=73%  Similarity=1.083  Sum_probs=88.7

Q ss_pred             cchhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHHHhHHH
Q 032404           50 SIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVS  129 (141)
Q Consensus        50 r~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELaKhAvs  129 (141)
                      |+++|++||||||||||||++||++||++||+|++|||+||+.||++|++||+|+|||+||||+||||+|||||+|||++
T Consensus         1 ~~~~~~~yi~kvLkqv~p~~~iS~~Am~~m~s~v~di~~rIa~eA~~L~~~~~r~Tit~~eIq~Avrl~lpgeLak~Av~   80 (192)
T 2jss_A            1 RKETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVS   80 (192)
T ss_dssp             CCSTTHHHHHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCSCCHHHHHHHHHHHSCSHHHHHHHH
T ss_pred             CcchHHHHHHHHHcccCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhcCHHHHHHHHH
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhcccC
Q 032404          130 EGTKAVTKFTS  140 (141)
Q Consensus       130 eGtkAV~ky~s  140 (141)
                      ||++||++|++
T Consensus        81 eG~kAv~k~~~   91 (192)
T 2jss_A           81 EGTRAVTKYSS   91 (192)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHhhcc
Confidence            99999999953

>3b0c_W CENP-W, centromere protein W; histone fold, DNA binding, DNA binding protein; HET: CIT; 2.20A {Gallus gallus} PDB: 3b0d_W* 3vh5_W 3vh6_W

Probab=99.68  E-value=6.7e-17  Score=111.00  Aligned_cols=66  Identities=18%  Similarity=0.237  Sum_probs=63.2

Q ss_pred             HHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCc
Q 032404           55 KIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLP  120 (141)
Q Consensus        55 ~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLP  120 (141)
                      ..+|+|++||+|||.+||.+|+.+|+.+++++++.|+.||..++++++|+||+.+||+.|++.+|-
T Consensus         7 ~A~V~rI~K~~~p~~~is~~A~~~i~~~~~~Fi~~la~eA~~~a~~~~rKTI~~~dI~~A~~~ll~   72 (76)
T 3b0c_W            7 RGTLRKIIKKHKPHLRLAANTDLLVHLSFLLFLHRLAEEARTNAFENKSKIIKPEHTIAAAKVILK   72 (76)
T ss_dssp             HHHHHHHHHHHCTTCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSBCHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHhCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHH
Confidence            357999999999999999999999999999999999999999999999999999999999998873

>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=99.11  E-value=1.6e-10  Score=76.79  Aligned_cols=61  Identities=21%  Similarity=0.309  Sum_probs=58.3

Q ss_pred             HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      =|.|++|++ ++..||+.|+..|...+.++++.|+.+|..++.+++|+||+.+|||.|++.|
T Consensus         7 ~v~Ri~k~~-~~~ris~~A~~~l~~a~e~fi~~l~~~A~~~a~~~kRkTI~~~Di~~A~~~l   67 (68)
T 1b67_A            7 PIGRIIKNA-GAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARKMF   67 (68)
T ss_dssp             HHHHHHHHT-TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHGGGG
T ss_pred             HHHHHHhcC-CcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhc
Confidence            378999999 8899999999999999999999999999999999999999999999999865

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

Probab=98.89  E-value=2.8e-09  Score=82.52  Aligned_cols=63  Identities=21%  Similarity=0.346  Sum_probs=61.1

Q ss_pred             HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCc
Q 032404           57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLP  120 (141)
Q Consensus        57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLP  120 (141)
                      =|.|++|+. ....||+.|...|..++.++.+.|+.+|..++++++|+||+.+||+.|++..||
T Consensus        87 ~V~Ri~k~~-g~~RVS~~A~~~l~~~le~f~~~I~~~A~~~a~ha~RKTIt~eDV~~Al~~~~~  149 (154)
T 1f1e_A           87 TVRRILKRA-GIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITYSMP  149 (154)
T ss_dssp             HHHHHHHHT-TCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHSG
T ss_pred             HHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhcCC
Confidence            389999998 778999999999999999999999999999999999999999999999999999

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

Probab=98.40  E-value=6.8e-07  Score=64.30  Aligned_cols=62  Identities=15%  Similarity=0.162  Sum_probs=58.4

Q ss_pred             HHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           56 IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        56 ~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      -.|.|+++..-. ..||..+..-|..++.++++.|+.+|..++++++|+|||.+||+.|++-+
T Consensus        33 ~~I~Rlar~~G~-~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktvt~~DV~~Alr~~   94 (103)
T 2yfw_B           33 PAIRRLARRGGV-KRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQ   94 (103)
T ss_dssp             HHHHHHHHHTTC-CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCc-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHc
Confidence            469999999876 68999999999999999999999999999999999999999999999965

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

Probab=98.38  E-value=7.8e-07  Score=63.91  Aligned_cols=63  Identities=14%  Similarity=0.147  Sum_probs=58.8

Q ss_pred             HHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           55 KIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        55 ~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      .-.|.|+++..-. ..||..+..-|..++.++++.|+.+|..++++++|+|||.+||+.|++-+
T Consensus        32 ~~~I~Rlar~~G~-~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktIt~~DV~~Alr~~   94 (103)
T 1tzy_D           32 KPAIRRLARRGGV-KRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ   94 (103)
T ss_dssp             HHHHHHHHHHTTC-CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCc-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHc
Confidence            3479999999876 68999999999999999999999999999999999999999999999965

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

Probab=98.35  E-value=1.2e-06  Score=58.48  Aligned_cols=59  Identities=14%  Similarity=0.330  Sum_probs=55.4

Q ss_pred             HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      -|.|++|+. ....||..+..-|..++.++++.|+.+|..++.+.+|+||+.+||+.|++
T Consensus        11 ~v~Rl~r~~-g~~ris~~a~~~l~e~~~~~~~~v~~dA~~~a~hakRkTI~~~DV~lA~~   69 (70)
T 1ku5_A           11 PVDRLIRKA-GAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIK   69 (70)
T ss_dssp             HHHHHHHHT-TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHT
T ss_pred             HHHHHHHHc-CcceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence            588999987 46899999999999999999999999999999999999999999999975

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

Probab=98.16  E-value=4.7e-06  Score=60.07  Aligned_cols=63  Identities=17%  Similarity=0.185  Sum_probs=57.9

Q ss_pred             HHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           55 KIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        55 ~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      .-.|.|+++..-. ..||..+...|..++.++++.|+.||..++++.+|+|||..||..|++.+
T Consensus        31 ~~~I~Rlar~~Gv-~rIS~da~~~l~~~le~fi~~I~~dA~~~a~HakRKTVt~~DV~~ALkr~   93 (102)
T 1id3_B           31 KPAIRRLARRGGV-KRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQ   93 (102)
T ss_dssp             HHHHHHHHHHTTC-CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCc-hhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHc
Confidence            3479999998754 78999999999999999999999999999999999999999999999854

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

Probab=98.16  E-value=8.5e-06  Score=57.04  Aligned_cols=60  Identities=18%  Similarity=0.299  Sum_probs=56.8

Q ss_pred             HHHHHhhhhcCC-CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           57 YIFKVLKQVHPD-IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        57 YIyKVLKQVhpd-~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      -|.|+.|+.-|| ..||.+|...|......+...|+.+|...+...+|+||+..||+.|++
T Consensus        13 ~i~ri~K~~~~~~~~is~dA~~~l~~a~e~Fi~~l~~~A~~~a~~~kRkTI~~~Dv~~Al~   73 (93)
T 1n1j_A           13 NVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMS   73 (93)
T ss_dssp             HHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHH
T ss_pred             HHHHHHHHhCCccceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHH
Confidence            488999999775 789999999999999999999999999999999999999999999998

>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=98.06  E-value=6.5e-06  Score=57.10  Aligned_cols=62  Identities=13%  Similarity=0.132  Sum_probs=56.8

Q ss_pred             HHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           56 IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        56 ~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      -.|.|+.+..-. ..||..+...|..++...++.|+.+|..++++.+|+|||..||..|++-+
T Consensus        14 ~~I~Riar~~Gv-~rIs~da~~~l~~~l~~~~~~I~~dA~~~a~ha~RKTvt~~DV~~Alk~~   75 (84)
T 2hue_C           14 PAIRRLARRGGV-KRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ   75 (84)
T ss_dssp             HHHHHHHHHTTC-CEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTT
T ss_pred             HHHHHHHHHcCc-hhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHc
Confidence            358899998754 78999999999999999999999999999999999999999999998754

>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=98.03  E-value=1.4e-05  Score=58.44  Aligned_cols=61  Identities=10%  Similarity=0.219  Sum_probs=56.8

Q ss_pred             HHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           56 IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        56 ~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      ..|.|+.+.. ....||..+...|..++.++++.|+.+|..++++.+|+||+..||..|++-
T Consensus        11 a~I~Ri~r~~-g~~rIS~~a~~~l~e~l~~f~~~v~~da~~~A~HA~RKTV~~eDV~lalrr   71 (111)
T 3b0c_T           11 SLIKQIFSHY-VKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAGRKTVEMADVELLMRR   71 (111)
T ss_dssp             HHHHHHHHHH-HCSCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             HHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHH
Confidence            4688888877 679999999999999999999999999999999999999999999999884

>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=98.02  E-value=2.1e-05  Score=62.18  Aligned_cols=63  Identities=16%  Similarity=0.327  Sum_probs=59.2

Q ss_pred             HHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           56 IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        56 ~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      .=|.|++|++-|+..||.+|...|...+..+..-|+.+|..++...+|+||+..||..|+.-+
T Consensus        19 A~V~RImK~alp~~rISkDA~~al~ec~~eFI~~LtseA~e~a~~~~RKTI~~eDVl~Al~~L   81 (179)
T 1jfi_B           19 AAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALESL   81 (179)
T ss_dssp             HHHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhc
Confidence            458999999999999999999999999999999999999999999999999999999998743

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

Probab=97.96  E-value=2.9e-05  Score=57.93  Aligned_cols=62  Identities=19%  Similarity=0.249  Sum_probs=57.7

Q ss_pred             HHHHHhhhhcCC-CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           57 YIFKVLKQVHPD-IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        57 YIyKVLKQVhpd-~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      -|.|++|++-|| ..||..|...|.....-+...|+.+|..++...+|+||+..||..|+.-+
T Consensus        14 ~I~rImK~~~pd~~~iS~dA~~~l~ka~e~FI~~lt~~A~~~a~~~kRKTI~~~Dv~~Al~~l   76 (128)
T 2byk_B           14 VIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTEL   76 (128)
T ss_dssp             HHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHT
T ss_pred             HHHHHHHHhCcccceECHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHc
Confidence            389999998875 78999999999999999999999999999999999999999999999864

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

Probab=97.92  E-value=3e-05  Score=57.67  Aligned_cols=64  Identities=20%  Similarity=0.256  Sum_probs=58.7

Q ss_pred             hHH-HHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           53 TYK-IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        53 sy~-~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      .|. ..|+|+|++..--..||..|...|...+..+...|.+.|...++.+++.+|+.|+||.|++
T Consensus        23 ~fPV~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hi~lAI~   87 (123)
T 2nqb_C           23 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR   87 (123)
T ss_dssp             SSCHHHHHHHHHHTTSCSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             eccHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHHHHHh
Confidence            354 3899999998555699999999999999999999999999999999999999999999999

>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=97.90  E-value=3.4e-05  Score=57.19  Aligned_cols=64  Identities=25%  Similarity=0.334  Sum_probs=58.9

Q ss_pred             hHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           53 TYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        53 sy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      .|.. .|+|+|++..--..||..|-..|...+..+...|.+.|...++.+++.+|+.|+||.||+
T Consensus        22 qfPV~ri~R~Lk~~~~a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~~rItp~hi~lAI~   86 (120)
T 2f8n_G           22 IFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILLAVA   86 (120)
T ss_dssp             SSCHHHHHHHHHHHSSSCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             cCChHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHHHHh
Confidence            3544 799999998766789999999999999999999999999999999999999999999999

>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=97.87  E-value=3.9e-05  Score=57.58  Aligned_cols=64  Identities=19%  Similarity=0.298  Sum_probs=58.6

Q ss_pred             hHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           53 TYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        53 sy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      .|.. .|+|+|++..--..||..|...|...+..+...|.+.|...++.+++.+|+.|+||.|++
T Consensus        25 qfPV~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hi~lAI~   89 (129)
T 1tzy_A           25 QFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIR   89 (129)
T ss_dssp             SSCHHHHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             eccHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEcHHHHHHHHh
Confidence            3544 799999997555699999999999999999999999999999999999999999999999

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

Probab=97.87  E-value=3.9e-05  Score=59.24  Aligned_cols=61  Identities=15%  Similarity=0.217  Sum_probs=57.8

Q ss_pred             HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      -|-|++|+.-|+..||..|-.-|...+..+.+-|+.+|..++.+.+|+||+..||..|+.-
T Consensus         9 ~V~Riik~~lg~~rVS~dA~~~l~~~l~~f~~~i~~~A~~~a~ha~RKTv~a~DV~~a~~~   69 (154)
T 1f1e_A            9 AIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADV   69 (154)
T ss_dssp             HHHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHH
T ss_pred             HHHHHHHhcCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHh
Confidence            3789999998999999999999999999999999999999999999999999999999944

>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=97.85  E-value=3.5e-05  Score=57.97  Aligned_cols=64  Identities=23%  Similarity=0.330  Sum_probs=58.6

Q ss_pred             hHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           53 TYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        53 sy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      .|.. .|+|+|++..--..||..|...|...+..+...|.+.|...++.+++.+|+.|+||.||+
T Consensus        25 qfPV~rI~R~Lk~~~~a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hI~lAI~   89 (131)
T 1id3_C           25 TFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRHLQLAIR   89 (131)
T ss_dssp             SSCHHHHHHHHHTTCSCSEECSSHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             ecCHHHHHHHHHccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHHHHh
Confidence            4544 899999997555699999999999999999999999999999999999999999999999

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

Probab=97.83  E-value=7.4e-05  Score=50.97  Aligned_cols=60  Identities=10%  Similarity=0.231  Sum_probs=53.4

Q ss_pred             HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      .|.++.+++.= ..+|.++-..|-.-+.+....|+.||.+++++.+|+|||..||..|+++
T Consensus        11 ~v~~iaes~Gi-~~lsddaa~~LA~dvEyr~~eI~qeA~kfmrHakRk~Lt~~DI~~Alk~   70 (70)
T 1taf_B           11 SMKVIAESIGV-GSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLKV   70 (70)
T ss_dssp             HHHHHHHHTTC-CCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC-
T ss_pred             HHHHHHHHCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHcC
Confidence            47777777643 4789999999999999999999999999999999999999999999874

>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=97.79  E-value=5.2e-05  Score=58.36  Aligned_cols=64  Identities=19%  Similarity=0.303  Sum_probs=58.7

Q ss_pred             hHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           53 TYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        53 sy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      .|.. .|+|+||+..--..|+..|...|...+.++...|.+.|...++.+++.+|+.|+||.||+
T Consensus        44 qFPVgrI~R~LK~~~~a~RVs~~A~VyLAAVLEYL~aEILelAgn~A~~~krkrItprhI~lAI~  108 (149)
T 2f8n_K           44 QFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIR  108 (149)
T ss_dssp             SSCHHHHHHHHHHTTSCSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             eccHHHHHHHHHccccccccCcCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHh
Confidence            3544 799999998655699999999999999999999999999999999999999999999999

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

Probab=97.76  E-value=7.7e-05  Score=52.81  Aligned_cols=60  Identities=22%  Similarity=0.169  Sum_probs=54.8

Q ss_pred             HHHHHhhhhcCC-CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           57 YIFKVLKQVHPD-IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        57 YIyKVLKQVhpd-~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      =|.|++|.- || ..||..|.-.|.-.+..+...|+.+|...++.++|+||+.+||+.||+-
T Consensus        24 rIkrImK~~-~~~~~is~eA~~~laka~E~Fi~~l~~~A~~~a~~~krktI~~~di~~Av~~   84 (97)
T 1n1j_B           24 RIKKIMKLD-EDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITK   84 (97)
T ss_dssp             HHHHHHTTS-TTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTT
T ss_pred             HHHHHHccC-ccccccChHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHHhc
Confidence            489999986 77 5699999999999999999999999999999999999999999999863

>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=97.69  E-value=9.2e-05  Score=55.44  Aligned_cols=64  Identities=17%  Similarity=0.216  Sum_probs=57.9

Q ss_pred             hHHH-HHHHHhhhhcC-CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           53 TYKI-YIFKVLKQVHP-DIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        53 sy~~-YIyKVLKQVhp-d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      .|-. .|+|+|+...- ...||..|...|...+..+...|.+.|...++.+++.+|+.|+||-||+
T Consensus        27 qfPV~ri~R~Lk~~~~a~~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItprhi~lAI~   92 (128)
T 1f66_C           27 QFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR   92 (128)
T ss_dssp             SSCHHHHHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHH
T ss_pred             cCChHHHHHHHHHcccchhhccccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEcHHHHHHHHh
Confidence            4544 79999999864 3589999999999999999999999999999999999999999999998

>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=97.67  E-value=9.7e-05  Score=54.26  Aligned_cols=59  Identities=25%  Similarity=0.226  Sum_probs=53.9

Q ss_pred             HHHHHhhhhcCC-CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           57 YIFKVLKQVHPD-IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        57 YIyKVLKQVhpd-~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      =|.|++|.. || ..||..|.-+|.-.+.-+...|+.+|...++.++|+||+.+||+.||+
T Consensus        46 RIkrImK~d-~~~~~is~eA~v~la~a~E~Fi~~L~~~A~~~a~~~krktI~~~di~~Av~  105 (119)
T 4g92_C           46 RIKKVMKAD-PEVKMISAEAPILFAKGCDVFITELTMRAWIHAEDNKRRTLQRSDIAAALS  105 (119)
T ss_dssp             HHHHHHHTS-TTCCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHT
T ss_pred             HHHHHHhhC-CccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccCHHHHHHHHh
Confidence            499999976 55 678999999999888889999999999999999999999999999996

>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=97.59  E-value=0.00037  Score=48.25  Aligned_cols=60  Identities=17%  Similarity=0.369  Sum_probs=56.1

Q ss_pred             HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      -+...++||-|...+...+..+|-.+.+|+.+.+.+.|++||++.+-.||..+|||....
T Consensus        10 ~L~~Lv~~idp~~~ld~~vee~ll~lADdFV~~V~~~ac~lAKhR~s~~le~kDvql~Le   69 (76)
T 1h3o_B           10 KLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLE   69 (76)
T ss_dssp             HHHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHH
T ss_pred             HHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHHH
Confidence            367889999999999999999999999999999999999999999999999999998665

>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=97.59  E-value=0.00044  Score=46.83  Aligned_cols=63  Identities=16%  Similarity=0.250  Sum_probs=56.0

Q ss_pred             HHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032404           56 IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVL  119 (141)
Q Consensus        56 ~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlL  119 (141)
                      ..|.++||...- ..+|..+...|-.|+......|+.+|..++.+.+|+||+..||+.|++..+
T Consensus         5 ~~i~~iLk~~G~-~~~~~~v~~~L~e~~~ry~~~il~dA~~~a~HAgrktv~~eDVkLAi~~~~   67 (68)
T 1taf_A            5 QVIMSILKELNV-QEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLATEVTL   67 (68)
T ss_dssp             HHHHHHHHHTTC-CCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTC
T ss_pred             HHHHHHHHHCCC-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhcc
Confidence            468889988533 477999999999999999999999999999999999999999999998654

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

Probab=97.58  E-value=0.00036  Score=48.37  Aligned_cols=66  Identities=18%  Similarity=0.244  Sum_probs=58.1

Q ss_pred             hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           52 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        52 esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      -.|...|..+..+..+|..+++.|+..|.....+..-.+.+++..++.+.+|.||..+|||-|.|+
T Consensus         7 ~PF~RLVRei~~~~~~~~R~q~~Al~aLQea~Eaylv~lfeda~l~A~HAkRvTi~~kDiqLa~ri   72 (77)
T 2hue_B            7 LPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRI   72 (77)
T ss_dssp             HHHHHHHHHHHHTTCSSCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHcCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHhhHHHHHHH
Confidence            346666666666667789999999999999999999999999999999999999999999999986

>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=97.50  E-value=0.00011  Score=52.27  Aligned_cols=59  Identities=12%  Similarity=0.255  Sum_probs=51.2

Q ss_pred             HHHHHhhhhcCC-CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           57 YIFKVLKQVHPD-IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        57 YIyKVLKQVhpd-~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      =|.|++|. .|| ..||..|.-.|.-....+.+.|+.+|...++.++|+||+.+||+.||+
T Consensus        16 RIkrimK~-~~~~~~vs~~A~v~la~a~E~Fi~el~~~A~~~a~~~krktI~~~di~~av~   75 (98)
T 1jfi_A           16 RIKKIMQT-DEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQCIE   75 (98)
T ss_dssp             HHHHHHTT-STTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC---CBCHHHHHTTCC
T ss_pred             HHHHHHHc-CccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHh
Confidence            48999997 566 679999999999999999999999999999999999999999999986

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

Probab=97.46  E-value=0.0002  Score=53.02  Aligned_cols=61  Identities=16%  Similarity=0.251  Sum_probs=54.9

Q ss_pred             HHHHHhhhhcC--CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           57 YIFKVLKQVHP--DIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        57 YIyKVLKQVhp--d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      -|.|+++++-.  ++.+|.+++.-|..++.+.++.|+.++..++++.+|+||+..||..++|-
T Consensus        32 ~V~rIvke~gaer~~~vS~~ai~aL~El~~~~~~~ia~Dl~~fAkHAgRkTI~~eDV~La~Rr   94 (113)
T 4dra_A           32 TVGCLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARR   94 (113)
T ss_dssp             HHHHHHHHHHHHHTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHcCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHh
Confidence            46778877743  57899999999999999999999999999999999999999999999873

>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=97.42  E-value=0.00039  Score=54.63  Aligned_cols=71  Identities=23%  Similarity=0.254  Sum_probs=60.8

Q ss_pred             hHHH-HHHHHhhhhcC-CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHHH
Q 032404           53 TYKI-YIFKVLKQVHP-DIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAK  125 (141)
Q Consensus        53 sy~~-YIyKVLKQVhp-d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELaK  125 (141)
                      .|.. .|+|.||+..- ...|+..|...|...+..+...|.+.|...++.+++.+|++++||.|++  -..||..
T Consensus       105 ~fPv~ri~R~lk~~~~a~~Rv~~~A~vyLaavLEyl~~eIlelA~n~a~~~~~~~I~p~~i~lAi~--nD~eL~~  177 (192)
T 2jss_A          105 QFPVGRIKRYLKRHATGRTRVGSKAAIYLTAVLEYLTAEVLELAGNAAKDLKVKRITPRHLQLAIR--GDDELDS  177 (192)
T ss_dssp             CSCHHHHHHHHHHTTCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCHHHHHHHHH--TSHHHHH
T ss_pred             cCCHHHHHHHHHhcCccccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHh--ccHHHHH
Confidence            4543 79999999744 3589999999999999999999999999999999999999999999999  3445543

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

Probab=97.36  E-value=0.00056  Score=48.63  Aligned_cols=60  Identities=13%  Similarity=0.192  Sum_probs=52.8

Q ss_pred             HHHHhhhhcC--CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           58 IFKVLKQVHP--DIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        58 IyKVLKQVhp--d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      |-++..++-+  +..+|..++.-|..++.+.++.|+.++..++++.+|+||+..||..++|-
T Consensus        18 V~ki~~e~~~~~g~~vs~~~i~aL~e~~~~~~~~ia~Dl~~fA~HAgRkTI~~eDV~L~~Rr   79 (90)
T 3v9r_A           18 VEERLQQVLSSEDIKYTPRFINSLLELAYLQLGEMGSDLQAFARHAGRGVVNKSDLMLYLRK   79 (90)
T ss_dssp             HHHHHHHHSCSSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTT
T ss_pred             HHHHHHHHHHhcCceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHh
Confidence            5566666644  36689999999999999999999999999999999999999999998873

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

Probab=97.34  E-value=0.00035  Score=51.07  Aligned_cols=62  Identities=19%  Similarity=0.208  Sum_probs=55.1

Q ss_pred             HHHHHHhhhhcC--CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           56 IYIFKVLKQVHP--DIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        56 ~YIyKVLKQVhp--d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      ..|-|+++++--  +..+|.+++..|..|+.+.++.|+.++..++++.+|+||+..||..|+|-
T Consensus        23 ~~V~rI~~~~g~~~~~~vs~~~i~aL~E~~~~~~~~ia~Da~~fA~HAgRkTI~~eDV~La~Rr   86 (107)
T 3b0b_B           23 YTTGCLCQDVAEDKGVLFSKQTVAAISEITFRQCENFARDLEMFARHAKRSTITSEDVKLLARR   86 (107)
T ss_dssp             HHHHHHHHHHHHHHTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTT
T ss_pred             HHHHHHHHHHhhhcCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcCcCCHHHHHHHHHh
Confidence            346677777643  57899999999999999999999999999999999999999999999884

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

Probab=97.30  E-value=0.0014  Score=45.84  Aligned_cols=67  Identities=12%  Similarity=0.145  Sum_probs=56.6

Q ss_pred             hhHHHHHHHHhhhhc--CCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           52 ETYKIYIFKVLKQVH--PDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        52 esy~~YIyKVLKQVh--pd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      -.|...|..+-.+..  .|..+++.|+..|-.-..+..-.+.+++..++.+.+|.||..+|||-|.|+-
T Consensus         7 lPF~RLVREI~~~~~~~~~~R~q~~Al~aLQea~E~ylv~Lfeda~lcAiHAkRvTi~~kDiqLa~rir   75 (82)
T 3nqj_A            7 LPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIR   75 (82)
T ss_dssp             HHHHHHHHHHHHHHHSSCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHhccCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHHHHHHHHHc
Confidence            345555665655554  4689999999999999999999999999999999999999999999999973

>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=97.27  E-value=0.0012  Score=50.20  Aligned_cols=65  Identities=18%  Similarity=0.259  Sum_probs=56.3

Q ss_pred             hHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           53 TYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        53 sy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      -|...|..+..+..+|..+++.|+..|.....+.+-.|.+++..++.+.+|.||..+|||-|.|+
T Consensus        67 PF~RLVREI~~~~~~~~R~q~~Al~aLQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa~ri  131 (136)
T 1tzy_C           67 PFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI  131 (136)
T ss_dssp             HHHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhhhhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHhHHHHHHH
Confidence            34555555555556899999999999999999999999999999999999999999999999986

>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=97.20  E-value=0.0013  Score=47.45  Aligned_cols=66  Identities=20%  Similarity=0.199  Sum_probs=55.7

Q ss_pred             hhHHHHHHHHhhhhcC---CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           52 ETYKIYIFKVLKQVHP---DIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        52 esy~~YIyKVLKQVhp---d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      -.|...|..+..+..+   |..+++.|+..|.....+.+-.+.+++..++.+.+|.||..+|||-|.|+
T Consensus        31 ~PF~RLVREI~~~~~~~~~~~R~q~~Al~ALQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa~ri   99 (100)
T 2yfv_A           31 MPFARLVKEVTDQFTTESEPLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARRI   99 (100)
T ss_dssp             HHHHHHHHHHHHTTC-----CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHC
T ss_pred             ccHHHHHHHHHHHhccccchhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHHHh
Confidence            4566666666666555   78999999999999999999999999999999999999999999999885

>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=97.15  E-value=0.0015  Score=61.65  Aligned_cols=75  Identities=20%  Similarity=0.321  Sum_probs=66.7

Q ss_pred             chhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHHHhHHHh
Q 032404           51 IETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSE  130 (141)
Q Consensus        51 ~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELaKhAvse  130 (141)
                      ..-|-.-|+|||.||||+++|..+|+.-+++++-.++-.|+.          ....|..|++..|.-.||+.|.++|+.+
T Consensus        20 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~   89 (1049)
T 3ksy_A           20 RGLLVPALKKVQGQVHPTLESNDDALQYVEELILQLLNMLCQ----------AQPRSASDVEERVQKSFPHPIDKWAIAD   89 (1049)
T ss_dssp             SSSSHHHHHHHHHHHCTTSBCCHHHHHHHHHHHHHHHHHHHH----------TCCCSHHHHHHHHHHHSCTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCCCccHhHHHHHHHHHHHHHHHHhc----------CCCccHHHHHHHHHHhCCCchHHHHHHH
Confidence            456888899999999999999999999999999888877764          4688999999999999999999999999


Q ss_pred             hhhhh
Q 032404          131 GTKAV  135 (141)
Q Consensus       131 GtkAV  135 (141)
                      +-.++
T Consensus        90 ~~~~~   94 (1049)
T 3ksy_A           90 AQSAI   94 (1049)
T ss_dssp             HHHHH
T ss_pred             HHHhh
Confidence            86664

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

Probab=97.07  E-value=0.00081  Score=51.46  Aligned_cols=60  Identities=20%  Similarity=0.235  Sum_probs=52.8

Q ss_pred             HHHHhhhhc--CCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           58 IFKVLKQVH--PDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        58 IyKVLKQVh--pd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      |-|+.+++-  .++.+|.+++..|..|+.+.++.|+.++..++++.+|+||+..||..++|-
T Consensus        25 VgkIvee~~~~~~~~vS~~ai~aL~El~~~~~e~ia~DLe~FAkHAGRKTI~~eDVkLa~Rr   86 (140)
T 3vh5_A           25 TGALAQDVAEDKGVLFSKQTVAAISEITFRQAENFARDLEMFARHAKRSTITSEDVKLLARR   86 (140)
T ss_dssp             HHHHHHHHHHHHTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTT
T ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHh
Confidence            445555552  357899999999999999999999999999999999999999999999884

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

Probab=97.02  E-value=0.0013  Score=49.11  Aligned_cols=49  Identities=18%  Similarity=0.247  Sum_probs=46.3

Q ss_pred             CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           69 IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        69 ~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      -.||..+..-+...++++++.|+.+|..++.+.+|+|||..||.-|++.
T Consensus        63 kRIS~~iy~e~r~vl~~~l~~i~rdav~yaehA~RKTVta~DV~~Alkr  111 (121)
T 2ly8_A           63 KRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKR  111 (121)
T ss_dssp             SCCSSCHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCBCHHHHHHHHHH
T ss_pred             cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHh
Confidence            4789999999999999999999999999999999999999999999874

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

Probab=96.89  E-value=0.0041  Score=47.49  Aligned_cols=65  Identities=12%  Similarity=0.163  Sum_probs=53.2

Q ss_pred             HHHHHHHHhhhhc--CCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           54 YKIYIFKVLKQVH--PDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        54 y~~YIyKVLKQVh--pd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      |...|..+-.+..  .|..+++.|+..|-....+.+-.|.++|..++.+.+|.||..+|||-|.|+-
T Consensus        67 F~RLVREI~~~~~~~~~~Rfq~~Al~ALQEAaEayLv~LFEdanlcAiHAkRVTIm~kDiqLArrir  133 (140)
T 3nqu_A           67 FSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIR  133 (140)
T ss_dssp             HHHHHHHHHHHHHTTCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcccccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHHHHhc
Confidence            4444444443333  3688999999999998899889998999999999999999999999999974

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

Probab=96.86  E-value=0.0039  Score=48.46  Aligned_cols=61  Identities=13%  Similarity=0.209  Sum_probs=51.8

Q ss_pred             HHHHhhhhc------CCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           58 IFKVLKQVH------PDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        58 IyKVLKQVh------pd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      |-|+++++-      .|..+++.|+..|-....+++-.|.++|..++.+.+|.||..+|||-|.||-
T Consensus        83 F~RLVREIa~~~~~~~~lRfqs~Al~ALQEAaEayLV~LFEdanLcAiHAkRVTIm~kDIqLArrIr  149 (156)
T 3r45_A           83 FSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIR  149 (156)
T ss_dssp             HHHHHHHHHHTTTTTCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHHHHHc
Confidence            344555543      3678999999999998889888998999999999999999999999999973

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

Probab=96.84  E-value=0.0023  Score=48.40  Aligned_cols=59  Identities=12%  Similarity=0.096  Sum_probs=49.0

Q ss_pred             HHHHHhhhhcCC-CCcchHHHHHHHHHHHHHHHHHHHHHhHHh-hhcCCCCcChHHHHHHHH
Q 032404           57 YIFKVLKQVHPD-IGISSKAMGIMNSFINDIFEKLAQESSRLA-RYNKKPTITSREIQTAVR  116 (141)
Q Consensus        57 YIyKVLKQVhpd-~gISskAm~ImnSfvnDiferIA~EAs~La-~~nkk~TltsreIqtAVr  116 (141)
                      =|.|++|.- || ..||..|.-+|.-.+.-+...|+.+|...+ +.++|+||+.++|..||+
T Consensus        24 RIKrIMK~d-pdv~~Is~eA~vliakA~ElFI~~Lt~~A~~~a~~~~kRKtI~~~Dl~~AV~   84 (140)
T 2byk_A           24 RVRTIMKSS-MDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVN   84 (140)
T ss_dssp             -----CCSS-SSCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHH
T ss_pred             HHHHHHhcC-cccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccCHHHHHHHHh
Confidence            488999886 77 568999998888888888889999999999 999999999999999997

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

Probab=96.38  E-value=0.0081  Score=49.30  Aligned_cols=50  Identities=18%  Similarity=0.232  Sum_probs=47.3

Q ss_pred             CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           69 IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        69 ~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      -.||..+..-+...+.++++.|+.+|..++.+.+|+|+|..||.-|++..
T Consensus       177 kRIS~~iyeelr~vLe~fle~IirdAv~yaeHA~RKTVta~DV~~ALKr~  226 (235)
T 2l5a_A          177 KRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQ  226 (235)
T ss_dssp             CTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHhc
Confidence            46899999999999999999999999999999999999999999999854

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

Probab=90.35  E-value=0.82  Score=37.42  Aligned_cols=68  Identities=21%  Similarity=0.213  Sum_probs=52.7

Q ss_pred             cchhHHHHHHHHhhhhcC---CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           50 SIETYKIYIFKVLKQVHP---DIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        50 r~esy~~YIyKVLKQVhp---d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      ++-.|+..+..+..+..+   |+.+.+.|+.-|..-..+.+-.+=+.+.-.+.+.+|-||..+|||-|-|+
T Consensus        13 ~KlPFqRLVREIaq~~~~~~~~lRfqs~Al~ALQEAaEayLV~LFEd~nLcaiHAkRVTim~kDiqLarri   83 (235)
T 2l5a_A           13 SKIPFARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMKKDMQLARRI   83 (235)
T ss_dssp             SCCHHHHHHHHHHHTSCGGGTTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTSGGGTTHHHHHHTS
T ss_pred             cCccHHHHHHHHHHHhccCCccceecHHHHHHHHHHHHHHHHHHHhhhHHHHhcccccccchhhHHHHHHH
Confidence            456788888888877665   78999999877765444444444456777788999999999999999986

>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=88.53  E-value=2  Score=29.60  Aligned_cols=58  Identities=9%  Similarity=0.195  Sum_probs=40.7

Q ss_pred             HHHHHHhhhhcC--CCCcchHHHHHHH----HHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           56 IYIFKVLKQVHP--DIGISSKAMGIMN----SFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        56 ~YIyKVLKQVhp--d~gISskAm~Imn----SfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      .-|.|+|++.+.  .+.|++.|+..+.    -||+.-+.|-+.+|    .-.....|...+++.-.-+
T Consensus        12 ~lI~ril~~~f~~~ktrI~~dAl~l~aeyl~iFV~EAv~RA~~~a----~~e~~~~le~~~LEki~pq   75 (81)
T 3b0b_C           12 ETVERLLRLHFRDGRTRVNGDALLLMAELLKVFVREAAARAARQA----QAEDLEKVDIEHVEKVLPQ   75 (81)
T ss_dssp             HHHHHHHHHHCCSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHH----HHTTCSEECHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccCcccccHHHHHHHHHHHHHHHHHHHHHHHHHH----HhCCCCeecHHHHHHHHHH
Confidence            358899999877  5999999988754    45555555555554    4456678999998874433

>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=88.43  E-value=3.2  Score=28.89  Aligned_cols=61  Identities=13%  Similarity=0.263  Sum_probs=50.8

Q ss_pred             HHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhc-CCCCcChHHHHHHHHhhC
Q 032404           58 IFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYN-KKPTITSREIQTAVRLVL  119 (141)
Q Consensus        58 IyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~n-kk~TltsreIqtAVrLlL  119 (141)
                      |.|+..++. +.++|....-+|..+-.-+.-.|.++|..+.... ....|..+.|+.|+|.+-
T Consensus        22 vKrl~~~~~-~~~v~~~v~i~v~glaKvfVgelVE~A~~V~~~~~~~~Pl~P~HireA~rrl~   83 (89)
T 1bh9_B           22 IKRLIQSIT-GTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLK   83 (89)
T ss_dssp             HHHHHHHHH-SSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHc-CCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHH
Confidence            777777775 7899998888888888888889999999887654 455999999999999764

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

Probab=88.20  E-value=2.6  Score=29.36  Aligned_cols=63  Identities=11%  Similarity=0.170  Sum_probs=41.3

Q ss_pred             HHHHHHhhhhc--CCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           56 IYIFKVLKQVH--PDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        56 ~YIyKVLKQVh--pd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      --|.|+|++-+  .++.||..|+.++.-+++=+.......|...+.-....+|+..+++.-.-+|
T Consensus        16 ~li~ril~~~F~~~kTkIs~dAl~l~aeyl~iFV~EAv~RA~~~a~~e~~~~le~e~LEki~pQL   80 (84)
T 4dra_E           16 ELVSRLLHLHFKDDKTKVSGDALQLMVELLKVFVVEAAVRGVRQAQAEDALRVDVDQLEKVLPQL   80 (84)
T ss_dssp             HHHHHHHHTTCSSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHH
Confidence            35899999876  4599999998886555533333333333334444566789999988754433

>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=86.00  E-value=2.1  Score=40.43  Aligned_cols=65  Identities=17%  Similarity=0.173  Sum_probs=52.0

Q ss_pred             hhHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           52 ETYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        52 esy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      -.|-. -|+|.||..+- -.|+..|.--|...+..+.-.|-+-|..-++.+++..|+.|+||.|++-
T Consensus       103 l~~pv~~~~~~l~~~~~-~r~~~~~~~y~~avleyl~~~~l~la~~~~~~~~~~~i~p~~~~~ai~~  168 (1049)
T 3ksy_A          103 LSLPVEKIHPLLKEVLG-YKIDHQVSVYIVAVLEYISADILKLVGNYVRNIRHYEITKQDIKVAMCA  168 (1049)
T ss_dssp             CSSCHHHHHHHHHHHHC-SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCBCCHHHHHHHHHH
T ss_pred             ccccHHHHHHHhhcccc-cccCCCCcchhHHHHHHHHHHHHHHHHHHHHHcCCceecCccccccccC
Confidence            34543 68899965554 5899999888888887777777777888888999999999999999963

---

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	141
d1tzyb_	92	a.22.1.1 (B:) Histone H2B {Chicken (Gallus gallus)	3e-51
d1q9ca_	172	a.22.1.3 (A:) Histone domain of Son of sevenless p	1e-20
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	6e-17
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	0.003

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

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

 Score =  155 bits (394), Expect = 3e-51
 Identities = 75/90 (83%), Positives = 85/90 (94%)

Query: 52  ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREI 111
           E+Y IY++KVLKQVHPD GISSKAMGIMNSF+NDIFE++A E+SRLA YNK+ TITSREI
Sbjct: 3   ESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREI 62

Query: 112 QTAVRLVLPGELAKHAVSEGTKAVTKFTSS 141
           QTAVRL+LPGELAKHAVSEGTKAVTK+TSS
Sbjct: 63  QTAVRLLLPGELAKHAVSEGTKAVTKYTSS 92

>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 = 80.6 bits (199), Expect = 1e-20
 Identities = 16/95 (16%), Positives = 36/95 (37%), Gaps = 10/95 (10%)

Query: 43  KKKRTKKSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNK 102
            ++   K        + KV  QVHP +  +  A+  +   I  +   L           +
Sbjct: 7   SEENAPKWRGLLVPALKKVQGQVHPTLESNDDALQYVEELILQLLNMLC----------Q 56

Query: 103 KPTITSREIQTAVRLVLPGELAKHAVSEGTKAVTK 137
               ++ +++  V+   P  + K A+++   A+ K
Sbjct: 57  AQPRSASDVEERVQKSFPHPIDKWAIADAQSAIEK 91

>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 = 70.2 bits (172), Expect = 6e-17
 Identities = 10/80 (12%), Positives = 32/80 (40%)

Query: 58  IFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL 117
           I ++ +Q   +  +S  A   +  F+  + E +A  +  +   + K T+    ++    +
Sbjct: 7   IERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADV 66

Query: 118 VLPGELAKHAVSEGTKAVTK 137
           ++   +  +      +A  +
Sbjct: 67  LMVEGVEDYDGELFGRATVR 86

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

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

 Score = 33.6 bits (77), Expect = 0.003
 Identities = 14/55 (25%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 71  ISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLP--GEL 123
            SS A+ + N  I    E+L ++++  A  + + T+   +++ A+   +P  GEL
Sbjct: 97  ASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITYSMPKGGEL 151

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	141
d1tzyb_	92	Histone H2B {Chicken (Gallus gallus), erythrocytes	100.0
d1q9ca_	172	Histone domain of Son of sevenless protein {Human	99.75
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	99.73
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	98.89
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	98.51
d1ku5a_	66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	98.28
d1n1ja_	87	Nuclear transcription factor Y subunit beta (Nf-Yb	98.05
d2bykb1	89	Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax	97.91
d1jfib_	135	Negative cofactor 2, NC2, beta chain {Human (Homo	97.9
d1jfia_	66	Negative cofactor 2, NC2, alpha chain {Human (Homo	97.87
d2huec1	82	Histone H4 {African clawed frog (Xenopus laevis) [	97.76
d1n1jb_	78	Nuclear transcription factor Y subunit gamma (Nf-Y	97.61
d1q9ca_	172	Histone domain of Son of sevenless protein {Human	97.47
d1tzyc_	95	Histone H3 {Chicken (Gallus gallus), erythrocytes	97.38
d1h3ob_	74	TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom	97.34
d1u35c1	106	macro-H2A.1, histone domain {Human (Homo sapiens)	96.93
d1tzya_	106	Histone H2A {Chicken (Gallus gallus), erythrocytes	96.83
d1f66c_	103	Histone H2A {Human (Homo sapiens), variant H2A.Z [	96.46
d1tafb_	70	TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta	96.21
d2byka1	72	Chrac-16 {Fruit fly (Drosophila melanogaster) [Tax	94.03
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	93.29
d1tafa_	68	TAF(II)42 {Fruit fly (Drosophila melanogaster) [Ta	88.3
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	85.78

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

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

Probab=100.00  E-value=2.7e-54  Score=310.08  Aligned_cols=92  Identities=82%  Similarity=1.160  Sum_probs=90.5

Q ss_pred             cchhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHHHhHHH
Q 032404           50 SIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVS  129 (141)
Q Consensus        50 r~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELaKhAvs  129 (141)
                      |+|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+|+|||+||||+||||+|||||+||||+
T Consensus         1 R~esy~~Yi~kVLKqVhp~~giS~kam~imnsfvndiferIa~EA~~La~~~kr~TitsreIqtAvrL~LPgeLaKhAvs   80 (92)
T d1tzyb_           1 RKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVS   80 (92)
T ss_dssp             CCCCCHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHSCHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHHCcHHHHHHHHH
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhcccCC
Q 032404          130 EGTKAVTKFTSS  141 (141)
Q Consensus       130 eGtkAV~ky~ss  141 (141)
                      ||+|||++|++|
T Consensus        81 eGtkAv~ky~ss   92 (92)
T d1tzyb_          81 EGTKAVTKYTSS   92 (92)
T ss_dssp             HHHHHHHHHHHC
T ss_pred             HHHHHHHHhccC
Confidence            999999999986

>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=99.75  E-value=8.2e-19  Score=136.36  Aligned_cols=78  Identities=19%  Similarity=0.303  Sum_probs=71.9

Q ss_pred             chhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHHHhHHHh
Q 032404           51 IETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSE  130 (141)
Q Consensus        51 ~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELaKhAvse  130 (141)
                      +..|-.||+|||+||||+++|+++|+.+||+|+++||++|+          ...+.|.+|||.+|+++|||+|.+||+++
T Consensus        15 ~g~f~~~i~KVl~qvhP~l~i~~~Al~~i~~~i~~ll~~L~----------~~~p~sv~dVe~~v~~~fp~~i~~~ai~~   84 (172)
T d1q9ca_          15 RGLLVPALKKVQGQVHPTLESNDDALQYVEELILQLLNMLC----------QAQPRSASDVEERVQKSFPHPIDKWAIAD   84 (172)
T ss_dssp             TTSSHHHHHHHHHHHCSSSBCCHHHHHHHHHHHHHHHHHHH----------TTCCCSTTHHHHHHHHSSCTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHHHHHHHHH----------ccCCccHHHHHHHHHHhCCchHHHHHHHH
Confidence            46899999999999999999999999999999999999996          35799999999999999999999999999


Q ss_pred             hhhhhhcc
Q 032404          131 GTKAVTKF  138 (141)
Q Consensus       131 GtkAV~ky  138 (141)
                      +..++...
T Consensus        85 a~~~~~sr   92 (172)
T d1q9ca_          85 AQSAIEKR   92 (172)
T ss_dssp             HHHHHC--
T ss_pred             HHHHHhcc
Confidence            99987653

>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=99.73  E-value=1.5e-18  Score=130.67  Aligned_cols=71  Identities=13%  Similarity=0.192  Sum_probs=69.0

Q ss_pred             HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHHHhH
Q 032404           57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHA  127 (141)
Q Consensus        57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELaKhA  127 (141)
                      -|+|||||+||+.+||.+||.+|++|++|+|++|+.||..|+.+++|+||+.+|||.|++++++|++.+|+
T Consensus         6 ~I~rilk~~~~~~ris~da~~~l~~~~~~~~~~Ia~eA~~l~~~~~rKTi~~edi~~a~~~~~~~~~~~~~   76 (151)
T d1f1ea_           6 AIERIFRQGIGERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADVLMVEGVEDYD   76 (151)
T ss_dssp             HHHHHHHTTSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHHHTCTTSTTCC
T ss_pred             HHHHHHHHhCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhcccccccccc
Confidence            48999999999999999999999999999999999999999999999999999999999999999998874

>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=1.4e-09  Score=80.92  Aligned_cols=68  Identities=24%  Similarity=0.400  Sum_probs=63.5

Q ss_pred             HHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCc--hHH
Q 032404           55 KIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLP--GEL  123 (141)
Q Consensus        55 ~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLP--GEL  123 (141)
                      ..+|.|++|.. -...||++|...|...+.+++..|+.+|...+.+++|+||+.+||+.||+..+|  |||
T Consensus        82 ~a~IkRi~k~~-g~~ris~dA~~~l~~~~E~fi~~l~~~A~~~a~~~kRkTI~~~DI~~Av~~~~~~~~~~  151 (151)
T d1f1ea_          82 RATVRRILKRA-GIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITYSMPKGGEL  151 (151)
T ss_dssp             HHHHHHHHHHT-TCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHSGGGGCC
T ss_pred             HHHHHHHHHcC-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHcCCCcCCC
Confidence            45999999964 356899999999999999999999999999999999999999999999999999  886

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

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

Probab=98.51  E-value=2.8e-07  Score=59.54  Aligned_cols=62  Identities=21%  Similarity=0.304  Sum_probs=56.9

Q ss_pred             HHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           56 IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        56 ~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      ..|.|+.|...+ ..||.++...|...+..++..|+.+|...+.+.+|+||+.+||..|++.+
T Consensus         7 a~I~ri~k~~~~-~ris~ea~~~l~~~~e~fi~~l~~~a~~~a~~~kRkTi~~~DV~~Alk~~   68 (68)
T d1htaa_           7 APIGRIIKNAGA-ERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARKMF   68 (68)
T ss_dssp             HHHHHHHHHTTC-SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHTC
T ss_pred             HHHHHHHHHCCc-chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHhC
Confidence            458899999855 57999999999999999999999999999999999999999999999853

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

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

Probab=98.28  E-value=9.7e-07  Score=56.78  Aligned_cols=60  Identities=13%  Similarity=0.324  Sum_probs=55.7

Q ss_pred             HHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           56 IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        56 ~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      ..|.|+.|...+ ..||.+|...|......+++.|+.+|...+.+.+|+||+..||..|++
T Consensus         6 a~I~rI~k~~~~-~ris~ea~~~l~~a~e~Fi~~l~~~a~~~a~~~~RKTI~~~Dv~~Al~   65 (66)
T d1ku5a_           6 APVDRLIRKAGA-ERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIK   65 (66)
T ss_dssp             HHHHHHHHHTTC-SEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHT
T ss_pred             HHHHHHHHhCcc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHh
Confidence            458899998755 689999999999999999999999999999999999999999999975

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

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Nuclear transcription factor Y subunit beta (Nf-Yb3)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.05  E-value=9.8e-06  Score=54.52  Aligned_cols=63  Identities=17%  Similarity=0.265  Sum_probs=57.7

Q ss_pred             HHHHHhhhhcCC-CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032404           57 YIFKVLKQVHPD-IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVL  119 (141)
Q Consensus        57 YIyKVLKQVhpd-~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlL  119 (141)
                      =|.|+.|+.-|| ..||.+|...|......+...|+.+|...+..++|+||+..||..|+.-+=
T Consensus         7 ~v~ri~K~~~p~~~~is~ea~~~i~~a~e~Fi~~lt~~A~~~a~~~~rKTI~~~dv~~Al~~~~   70 (87)
T d1n1ja_           7 NVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLG   70 (87)
T ss_dssp             HHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTT
T ss_pred             HHHHHHHHhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHcC
Confidence            378999998776 679999999999999999999999999999999999999999999998653

>d2bykb1 a.22.1.3 (B:11-99) Chrac-14 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Chrac-14
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=97.91  E-value=2.4e-05  Score=52.83  Aligned_cols=61  Identities=20%  Similarity=0.259  Sum_probs=56.0

Q ss_pred             HHHHhhhhcCC-CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           58 IFKVLKQVHPD-IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        58 IyKVLKQVhpd-~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      |.|+.|+.-|+ ..||.+|...|.....-+...|+.+|...+..++|+||+..||..|+.-+
T Consensus         5 i~ri~K~~~p~~~~iskeA~~~i~~aae~FI~~lt~~A~~~a~~~~rKtI~~~dv~~Al~~~   66 (89)
T d2bykb1           5 IGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTEL   66 (89)
T ss_dssp             HHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHT
T ss_pred             HHHHHHHhCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHC
Confidence            78899988665 78999999999999999999999999999999999999999999999854

>d1jfib_ a.22.1.3 (B:) Negative cofactor 2, NC2, beta chain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Negative cofactor 2, NC2, beta chain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.90  E-value=2.6e-05  Score=56.48  Aligned_cols=62  Identities=16%  Similarity=0.337  Sum_probs=58.6

Q ss_pred             HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      =|.|+.|..-|+..||.+|..+|.....-+...|+.+|...+...+|+||+..||..|+.-+
T Consensus         9 ~I~kI~K~~~~~~~is~dA~~~i~~a~~~Fi~~lt~~A~~~a~~~~RkTi~~~Dv~~Al~~~   70 (135)
T d1jfib_           9 AINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALESL   70 (135)
T ss_dssp             HHHHHHHHHSTTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             HHHHHHhhCCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHc
Confidence            38899999999999999999999999999999999999999999999999999999999864

>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=97.87  E-value=1e-05  Score=51.94  Aligned_cols=59  Identities=12%  Similarity=0.200  Sum_probs=50.2

Q ss_pred             HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHH
Q 032404           57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAV  115 (141)
Q Consensus        57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAV  115 (141)
                      =|.|++|.......||.+|...|......+...|+.+|...++.++|+||+.+||..||
T Consensus         7 rVkkimk~~~~~~~is~~A~~~~~~a~E~Fi~~l~~~A~~~a~~~krktI~~~dl~~ai   65 (66)
T d1jfia_           7 RIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQCI   65 (66)
T ss_dssp             HHHHHHTTSTTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC---CBCHHHHHTTC
T ss_pred             HHHHHHhcCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHh
Confidence            37899998744468999999999999999999999999999999999999999998875

>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=97.76  E-value=1.3e-05  Score=54.12  Aligned_cols=60  Identities=13%  Similarity=0.153  Sum_probs=52.7

Q ss_pred             HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      -|.|+.+..- -..||..+...+...+++.++.|+.+|..++.+.+|+|||..||..|++-
T Consensus        14 ~i~Riar~~G-v~ris~d~~~~l~~~l~~~l~~i~~~a~~~~~hakRKTvt~~DV~~Alkr   73 (82)
T d2huec1          14 AIRRLARRGG-VKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKR   73 (82)
T ss_dssp             HHHHHHHHTT-CCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTT
T ss_pred             HHHHHHHHcC-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHh
Confidence            4667776642 24689999999999999999999999999999999999999999999873

>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=97.61  E-value=9e-05  Score=48.41  Aligned_cols=59  Identities=22%  Similarity=0.200  Sum_probs=53.6

Q ss_pred             HHHHhhhhcCC-CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           58 IFKVLKQVHPD-IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        58 IyKVLKQVhpd-~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      |.|++|. .|| ..||++|..+|.--..-+...|+.+|...++.++|+||+.+||..||+-
T Consensus         6 VkrImK~-~~~~~~is~ea~~~i~~a~E~Fi~~l~~~A~~~a~~~~rkti~~~dl~~av~~   65 (78)
T d1n1jb_           6 IKKIMKL-DEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITK   65 (78)
T ss_dssp             HHHHHTT-STTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTT
T ss_pred             HHHHHhc-CCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHhc
Confidence            7788886 566 6789999999999999999999999999999999999999999999874

>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=97.47  E-value=0.00016  Score=54.90  Aligned_cols=63  Identities=17%  Similarity=0.220  Sum_probs=57.4

Q ss_pred             hHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           53 TYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        53 sy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      .|-. .|+|+||+.+ ...||+.|.--|-..+.++...|...|...++.+++++||.+||+-|++
T Consensus        99 ~fPV~rv~rlLk~~~-a~RVs~~A~vyLaavLEyl~aeILelAgn~a~~~krkrItp~dI~lAi~  162 (172)
T d1q9ca_          99 SLPVEKIHPLLKEVL-GYKIDHQVSVYIVAVLEYISADILKLAGNYVRNIRHYEITKQDIKVAMC  162 (172)
T ss_dssp             CCCHHHHHHHHHHHH-SSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSBCCHHHHHHHHH
T ss_pred             eecHHHHHHHHHhcc-ccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCceecHHHHHHHHh
Confidence            4443 6899999986 5689999999999999999999999999999999999999999999998

>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=97.38  E-value=0.00042  Score=47.98  Aligned_cols=68  Identities=18%  Similarity=0.214  Sum_probs=62.8

Q ss_pred             chhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404           51 IETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV  118 (141)
Q Consensus        51 ~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl  118 (141)
                      +-.|...|..|.....+|+.+++.|+..|-..+.+.+-.+-++|..++.+.+|-||+.+|||-|.||-
T Consensus        24 k~pF~RLVRei~~~~~~~~r~~~~Al~aLQea~E~yLv~lfeda~~~a~HakRvTl~~kD~~Larrir   91 (95)
T d1tzyc_          24 KLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR   91 (95)
T ss_dssp             HHHHHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHhcCCCCEeeHHHHHHHHHHHHHHHHHHHHHhHHHHHhcCCCcCCHHHHHHHHHHh
Confidence            56799999999999999999999999999998888888888899999999999999999999999863

>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=97.34  E-value=0.00062  Score=45.37  Aligned_cols=60  Identities=17%  Similarity=0.369  Sum_probs=55.3

Q ss_pred             HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      -+...++||-|+..+...+-.+|-.+..|+.+.+..-|++||++.+-.||..+|||.-..
T Consensus         8 ~L~eLv~~idp~~~ld~~vee~ll~iADdFV~~V~~~ac~lAKhR~s~~le~kDvql~Le   67 (74)
T d1h3ob_           8 KLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLE   67 (74)
T ss_dssp             HHHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCcHHHHHHHHH
Confidence            367789999999999999999999999999999999999999999999999999997654

>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=96.93  E-value=0.0012  Score=46.58  Aligned_cols=60  Identities=27%  Similarity=0.318  Sum_probs=55.6

Q ss_pred             HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      -|+|.|++-+-...|++.|---|...+..+...|-+-|...++.+++.-|+.|+||-|+|
T Consensus        16 ri~r~Lk~~~~~~rv~~~apVylaAVLEYL~aEILELAgn~a~~~k~~rItprhi~lair   75 (106)
T d1u35c1          16 RMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILLAVA   75 (106)
T ss_dssp             HHHHHHHHHSTTSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             HHHHHHhCCCCccccCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCeeecchhhhccc
Confidence            589999998778899999999999999999999999999999999999999999999997

>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=96.83  E-value=0.0017  Score=45.64  Aligned_cols=60  Identities=20%  Similarity=0.276  Sum_probs=53.1

Q ss_pred             HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      .|+|.||+-+-...|++.|---|-..+..+...|-+-|.+-++.+++.-||.|+||-|||
T Consensus        17 rv~r~Lk~~~~~~rv~~~apVylaAVLEYLtaEiLELAgn~a~~~k~~rItPrhi~lAir   76 (106)
T d1tzya_          17 RVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIR   76 (106)
T ss_dssp             HHHHHHHHTTSSSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             HHHHHHHcCccccccCCCchHHHHHHHHHHHHHHHHHhhHHHHhcCCceecchhhhhccc
Confidence            699999997666789999988888888888888888888888999999999999999997

>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=96.46  E-value=0.0048  Score=42.90  Aligned_cols=67  Identities=19%  Similarity=0.177  Sum_probs=55.8

Q ss_pred             HHHHHhhhhcCC-CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHHH
Q 032404           57 YIFKVLKQVHPD-IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAK  125 (141)
Q Consensus        57 YIyKVLKQVhpd-~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELaK  125 (141)
                      -|+|.|+..+-- ..|+..|---|...+.++...|-+-|..-++.+++..||.|+||-|++  =-.||.+
T Consensus        16 rv~r~L~~~~~~~~rv~~~A~VyLaAvLEYL~aEILelagn~a~~~~~~rItpr~l~lai~--nD~EL~~   83 (103)
T d1f66c_          16 RIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR--GDEELDS   83 (103)
T ss_dssp             HHHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHH--HSHHHHH
T ss_pred             HHHHHHhccCccceecCCCceeeHHHHHHHHHHHHHHHhhhhhccCCCCeeechhhhcccc--CcHHHHH
Confidence            488999987654 459999988899998888888888888889999999999999999998  2345544

>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=96.21  E-value=0.01  Score=39.03  Aligned_cols=48  Identities=13%  Similarity=0.328  Sum_probs=40.7

Q ss_pred             CcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404           70 GISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        70 gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL  117 (141)
                      .++.++-..|-.=|..=...|..||.+++++.||.+||..||..|.|+
T Consensus        23 ~l~de~a~~LA~DveYRl~eiiQeA~KFMrhskR~~Ltt~Did~ALkv   70 (70)
T d1tafb_          23 SLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLKV   70 (70)
T ss_dssp             CBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC-
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcCcHHHHHHHHcC
Confidence            456777777777777778889999999999999999999999999875

>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=94.03  E-value=0.09  Score=33.57  Aligned_cols=53  Identities=13%  Similarity=0.139  Sum_probs=40.7

Q ss_pred             hcCCCC-cchHHHHHHHHHHHHHHHHHHHHHhHHh-hhcCCCCcChHHHHHHHHh
Q 032404           65 VHPDIG-ISSKAMGIMNSFINDIFEKLAQESSRLA-RYNKKPTITSREIQTAVRL  117 (141)
Q Consensus        65 Vhpd~g-ISskAm~ImnSfvnDiferIA~EAs~La-~~nkk~TltsreIqtAVrL  117 (141)
                      -.||.+ ||..|.-++.--..-+.+.++.+|...+ ..++++||+..||-.||..
T Consensus         3 ~d~dv~~is~ea~~lvskAtElFi~~L~~~a~~~a~~~~~~ktl~~~dl~~aV~~   57 (72)
T d2byka1           3 SSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNK   57 (72)
T ss_dssp             SSSSCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHHT
T ss_pred             CCHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCccccHHHHHHHHcc
Confidence            356754 5888877776666666688999998777 4567789999999999863

>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=93.29  E-value=0.36  Score=33.73  Aligned_cols=70  Identities=13%  Similarity=0.144  Sum_probs=51.1

Q ss_pred             hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHH------------HHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032404           52 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFI------------NDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVL  119 (141)
Q Consensus        52 esy~~YIyKVLKQVhpd~gISskAm~ImnSfv------------nDiferIA~EAs~La~~nkk~TltsreIqtAVrLlL  119 (141)
                      +....++.+.++..+.+..++.+++..+....            -.....+..+|..+|..+.+.+|+.+||+.|.+-||
T Consensus       195 ~e~~~il~~r~~~~~~~~~~~~~~l~~ia~~~~~~~~~~~~~G~~R~a~~ll~~a~~~A~~~~~~~I~~edv~~A~~~~~  274 (276)
T d1fnna2         195 DQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPEDVRKSSKEVL  274 (276)
T ss_dssp             HHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHhcccccccHHHHHHHHHHhhhhhhhhhcCCCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHh
Confidence            33455677778888888889988877664432            012234556788899999999999999999998776


Q ss_pred             ch
Q 032404          120 PG  121 (141)
Q Consensus       120 PG  121 (141)
                      =|
T Consensus       275 ~g  276 (276)
T d1fnna2         275 FG  276 (276)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=88.30  E-value=0.8  Score=29.32  Aligned_cols=53  Identities=13%  Similarity=0.270  Sum_probs=37.1

Q ss_pred             CCCCcch---HHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032404           67 PDIGISS---KAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVL  119 (141)
Q Consensus        67 pd~gISs---kAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlL  119 (141)
                      .++||+.   +-...|=.|..--.-.|-.+|.-.+.+.++.+|+..||+.|+..-|
T Consensus        12 ~~~GV~~yeprV~~qlLef~yRYtt~VL~DA~vys~HA~k~~id~dDVkLAi~~r~   67 (68)
T d1tafa_          12 KELNVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLATEVTL   67 (68)
T ss_dssp             HHTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTC
T ss_pred             HHcCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhcc
Confidence            3467753   3333333444444445677899999999999999999999987543

>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=85.78  E-value=2.8  Score=29.06  Aligned_cols=60  Identities=7%  Similarity=0.066  Sum_probs=43.7

Q ss_pred             HHHHHHhhhhcCCCCcchHHHHHHHHHH----------HHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404           56 IYIFKVLKQVHPDIGISSKAMGIMNSFI----------NDIFEKLAQESSRLARYNKKPTITSREIQTAVR  116 (141)
Q Consensus        56 ~YIyKVLKQVhpd~gISskAm~ImnSfv----------nDiferIA~EAs~La~~nkk~TltsreIqtAVr  116 (141)
                      .++...+++.+.+..++.++...+-..+          ++.+ .+..+|..+|....+.+||..+|+.|+.
T Consensus       216 ~Il~~r~~~~~~~~~~~~~al~~ia~~~~~~~~~~gd~R~ai-~~l~~a~~~A~~~~~~~It~~~V~~A~~  285 (287)
T d1w5sa2         216 TILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRAI-VALKMACEMAEAMGRDSLSEDLVRKAVS  285 (287)
T ss_dssp             HHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGGTSCCCHHHHH-HHHHHHHHHHHHTTCSSCCHHHHHHHHH
T ss_pred             HHHhhhHHHhhccCCCCHHHHHHHHHHHhccccCCCCHHHHH-HHHHHHHHHHHHcCCCCCCHHHHHHHHh
Confidence            3445555666777889988877665443          1221 4667888999999999999999999985