Citrus Sinensis ID: 038014

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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
MVDSAGHNLESYDNSYNFTVGASSGTDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRELEGERANQNKAGNNNNG
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccHHHHccHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccHHHHcHccHHHHHHHHHHccccccEEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEcHHHHHHHHHHcccHHHHHHHHHHHHHHHcHHccccccccccccccc
Coil and Loop (DISEMBL)
mvdsaghnlesydnsynftvgassgtdqdgvikeqdrllpianvgrimkqilppnakISKEAKETMQECVSEFISFVtgeasdkchkekrktvngdDICWALATLGFDNYADQLKRYLHRYRELEgeranqnkagnnnng
Flexible Loop (DISEMBL)
mvdsaghnlesydNSYNFTVGASSGTDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISfvtgeasdkchkekrktvngdDICWALATLGFDNYADQLKRYLHRYRElegeranqnkagnnnng
Low Complexity Region (SEG)
MVDSAGHNLESYDNSYNFTVGASSGTDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRELEGERanqnkagnnnng
Disordered region (IsUnstruct)
*******************************IKEQDRLLPIANVGRIMKQILP*************QECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYR******************
Disordered Region (DISOPRED)
*************************************LLPIANVGRIMKQILP*****SKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYL**********************
Disordered Region (DISEMBL)
********LESYDNSYNFTVGASSGTDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRELEGERANQNKAGNNNNG
Disordered Region (DISPRO)
*****************************GVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYREL****************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MVDSAGHNLESYDNSYNFTVGASSGTDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGxxxxxxxxxxxxxxxxxxxxxxxxxxxxGNNNNG
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	140	2.2.26 [Sep-21-2011]
O82248	160	Nuclear transcription fac	yes	no	0.75	0.656	0.838	5e-49
O04027	139	Nuclear transcription fac	no	no	0.771	0.776	0.715	5e-42
Q9SLG0	141	Nuclear transcription fac	no	no	0.842	0.836	0.644	6e-42
Q9FGJ3	190	Nuclear transcription fac	no	no	0.692	0.510	0.762	9e-41
Q67XJ2	176	Nuclear transcription fac	no	no	0.764	0.607	0.672	4e-40
Q9SIT9	215	Nuclear transcription fac	no	no	0.721	0.469	0.732	8e-40
O23310	161	Nuclear transcription fac	no	no	0.764	0.664	0.672	9e-40
Q8VYK4	173	Nuclear transcription fac	no	no	0.764	0.618	0.654	1e-38
Q60EQ4	185	Nuclear transcription fac	no	no	0.764	0.578	0.635	2e-38
Q5QMG3	178	Nuclear transcription fac	no	no	0.828	0.651	0.603	4e-38

>sp|O82248|NFYB5_ARATH Nuclear transcription factor Y subunit B-5 OS=Arabidopsis thaliana GN=NFYB5 PE=2 SV=1

 Score =  192 bits (488), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 88/105 (83%), Positives = 96/105 (91%)

Query: 31  VIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKR 90
           ++KEQDRLLPIANVGRIMK ILP NAK+SKEAKETMQECVSEFISFVTGEASDKCHKEKR
Sbjct: 48  MVKEQDRLLPIANVGRIMKNILPANAKVSKEAKETMQECVSEFISFVTGEASDKCHKEKR 107

Query: 91  KTVNGDDICWALATLGFDNYADQLKRYLHRYRELEGERANQNKAG 135
           KTVNGDDICWA+A LGFD+YA QLK+YLHRYR LEGE+ N +  G
Sbjct: 108 KTVNGDDICWAMANLGFDDYAAQLKKYLHRYRVLEGEKPNHHGKG 152

Component of the NF-Y/HAP transcription factor complex. The NF-Y complex stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.
Arabidopsis thaliana (taxid: 3702)

>sp|O04027|NFYB4_ARATH Nuclear transcription factor Y subunit B-4 OS=Arabidopsis thaliana GN=NFYB4 PE=1 SV=1

 Score =  169 bits (428), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 78/109 (71%), Positives = 94/109 (86%), Gaps = 1/109 (0%)

Query: 32  IKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRK 91
           + ++DRLLPIANVGR+MKQILP NAKISKEAK+T+QEC +EFISFVT EAS+KCH+E RK
Sbjct: 1   MTDEDRLLPIANVGRLMKQILPSNAKISKEAKQTVQECATEFISFVTCEASEKCHRENRK 60

Query: 92  TVNGDDICWALATLGFDNYADQLKRYLHRYRELEGERANQNKAGNNNNG 140
           TVNGDDI WAL+TLG DNYAD + R+LH+YRE E ER   NK G+N++G
Sbjct: 61  TVNGDDIWWALSTLGLDNYADAVGRHLHKYREAERERTEHNK-GSNDSG 108

Component of the NF-Y/HAP transcription factor complex. The NF-Y complex stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SLG0|NFYB1_ARATH Nuclear transcription factor Y subunit B-1 OS=Arabidopsis thaliana GN=NFYB1 PE=1 SV=2

 Score =  169 bits (427), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 76/118 (64%), Positives = 94/118 (79%)

Query: 22  ASSGTDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEA 81
           A  G +  G ++EQDR LPIAN+ RIMK+ LPPN KI K+AK+T+QECVSEFISF+T EA
Sbjct: 9   AGDGGESGGSVREQDRYLPIANISRIMKKALPPNGKIGKDAKDTVQECVSEFISFITSEA 68

Query: 82  SDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRELEGERANQNKAGNNNN 139
           SDKC KEKRKTVNGDD+ WA+ATLGF++Y + LK YL RYRELEG+     K+G+ +N
Sbjct: 69  SDKCQKEKRKTVNGDDLLWAMATLGFEDYLEPLKIYLARYRELEGDNKGSGKSGDGSN 126

Component of the NF-Y/HAP transcription factor complex. The NF-Y complex stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FGJ3|NFYB2_ARATH Nuclear transcription factor Y subunit B-2 OS=Arabidopsis thaliana GN=NFYB2 PE=2 SV=1

 Score =  165 bits (417), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 74/97 (76%), Positives = 85/97 (87%)

Query: 33  KEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKT 92
           +EQDR LPIANV RIMK+ LP NAKISK+AKETMQECVSEFISFVTGEASDKC KEKRKT
Sbjct: 26  REQDRFLPIANVSRIMKKALPANAKISKDAKETMQECVSEFISFVTGEASDKCQKEKRKT 85

Query: 93  VNGDDICWALATLGFDNYADQLKRYLHRYRELEGERA 129
           +NGDD+ WA+ TLGF++Y + LK YL R+RE+EGER 
Sbjct: 86  INGDDLLWAMTTLGFEDYVEPLKVYLQRFREIEGERT 122

Component of the NF-Y/HAP transcription factor complex. The NF-Y complex stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.

Arabidopsis thaliana (taxid: 3702)

>sp|Q67XJ2|NFYBA_ARATH Nuclear transcription factor Y subunit B-10 OS=Arabidopsis thaliana GN=NFYB10 PE=2 SV=1

 Score =  162 bits (411), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 72/107 (67%), Positives = 88/107 (82%)

Query: 32  IKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRK 91
           ++EQDR LPIAN+ RIMK+ LP N KI+K+AKETMQECVSEFISFVT EASDKC +EKRK
Sbjct: 27  VREQDRFLPIANISRIMKRGLPLNGKIAKDAKETMQECVSEFISFVTSEASDKCQREKRK 86

Query: 92  TVNGDDICWALATLGFDNYADQLKRYLHRYRELEGERANQNKAGNNN 138
           T+NGDD+ WA+ATLGF++Y D LK YL RYRE+EG+     K G ++
Sbjct: 87  TINGDDLLWAMATLGFEDYIDPLKVYLMRYREMEGDTKGSGKGGESS 133

Component of the NF-Y/HAP transcription factor complex. The NF-Y complex stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SIT9|NFYB7_ARATH Nuclear transcription factor Y subunit B-7 OS=Arabidopsis thaliana GN=NFYB7 PE=2 SV=1

 Score =  162 bits (409), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 74/101 (73%), Positives = 86/101 (85%)

Query: 33  KEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKT 92
           KEQDR LPIANVGRIMK++LP N KISK+AKET+QECVSEFISFVTGEASDKC +EKRKT
Sbjct: 35  KEQDRFLPIANVGRIMKKVLPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKT 94

Query: 93  VNGDDICWALATLGFDNYADQLKRYLHRYRELEGERANQNK 133
           +NGDDI WA+ TLGF++Y   LK YL +YR+ EGE+ N  K
Sbjct: 95  INGDDIIWAITTLGFEDYVAPLKVYLCKYRDTEGEKVNSPK 135

Component of the NF-Y/HAP transcription factor complex. The NF-Y complex stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.

Arabidopsis thaliana (taxid: 3702)

>sp|O23310|NFYB3_ARATH Nuclear transcription factor Y subunit B-3 OS=Arabidopsis thaliana GN=NFYB3 PE=2 SV=1

 Score =  161 bits (408), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 74/110 (67%), Positives = 90/110 (81%), Gaps = 3/110 (2%)

Query: 24  SGTDQDG---VIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGE 80
           SG  +DG     +EQDR LPIANV RIMK+ LP NAKISK+AKET+QECVSEFISF+TGE
Sbjct: 8   SGGHKDGGNASTREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFITGE 67

Query: 81  ASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRELEGERAN 130
           ASDKC +EKRKT+NGDD+ WA+ TLGF++Y + LK YL +YRE+EGE+  
Sbjct: 68  ASDKCQREKRKTINGDDLLWAMTTLGFEDYVEPLKVYLQKYREVEGEKTT 117

Component of the NF-Y/HAP transcription factor complex. The NF-Y complex stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8VYK4|NFYB8_ARATH Nuclear transcription factor Y subunit B-8 OS=Arabidopsis thaliana GN=NFYB8 PE=2 SV=1

 Score =  157 bits (398), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 70/107 (65%), Positives = 87/107 (81%)

Query: 32  IKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRK 91
           ++EQDR LPIAN+ RIMK+ LP N KI+K+AKE +QECVSEFISFVT EASDKC +EKRK
Sbjct: 28  VREQDRFLPIANISRIMKRGLPANGKIAKDAKEIVQECVSEFISFVTSEASDKCQREKRK 87

Query: 92  TVNGDDICWALATLGFDNYADQLKRYLHRYRELEGERANQNKAGNNN 138
           T+NGDD+ WA+ATLGF++Y + LK YL RYRE+EG+     K G+ N
Sbjct: 88  TINGDDLLWAMATLGFEDYMEPLKVYLMRYREMEGDTKGSAKGGDPN 134

Component of the NF-Y/HAP transcription factor complex. The NF-Y complex stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.

Arabidopsis thaliana (taxid: 3702)

>sp|Q60EQ4|NFYB3_ORYSJ Nuclear transcription factor Y subunit B-3 OS=Oryza sativa subsp. japonica GN=NFYB3 PE=1 SV=2

 Score =  157 bits (397), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 68/107 (63%), Positives = 89/107 (83%)

Query: 32  IKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRK 91
           ++EQDR LPIAN+ RIMK+ +P N KI+K+AKET+QECVSEFISF+T EASDKC +EKRK
Sbjct: 36  VREQDRFLPIANISRIMKKAIPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRK 95

Query: 92  TVNGDDICWALATLGFDNYADQLKRYLHRYRELEGERANQNKAGNNN 138
           T+NGDD+ WA+ATLGF++Y + LK YL +YRE+EG+     KAG+ +
Sbjct: 96  TINGDDLLWAMATLGFEDYIEPLKVYLQKYREMEGDSKLTAKAGDGS 142

Component of the NF-Y/HAP transcription factor complex. The NF-Y complex stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters. May regulate the expression of photosynthetic genes, and may be involved in chloroplast and amyloplast development.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q5QMG3|NFYB2_ORYSJ Nuclear transcription factor Y subunit B-2 OS=Oryza sativa subsp. japonica GN=NFYB2 PE=2 SV=1

 Score =  156 bits (394), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 70/116 (60%), Positives = 91/116 (78%)

Query: 23  SSGTDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEAS 82
           S    + G ++EQDR LPIAN+ RIMK+ +P N KI+K+AKET+QECVSEFISFVT EAS
Sbjct: 23  SGSPPRSGGVREQDRFLPIANISRIMKKAVPANGKIAKDAKETLQECVSEFISFVTSEAS 82

Query: 83  DKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRELEGERANQNKAGNNN 138
           DKC KEKRKT+NG+D+ +A+ TLGF+ Y D LK YLH+YRE+ G+    +KAG+ +
Sbjct: 83  DKCQKEKRKTINGEDLLFAMGTLGFEEYVDPLKIYLHKYREVIGDSKLSSKAGDGS 138

Component of the NF-Y/HAP transcription factor complex. The NF-Y complex stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters. May regulate the expression of photosynthetic genes, and may be involved in chloroplast and amyloplast development.

Oryza sativa subsp. japonica (taxid: 39947)

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	140
147853040	175	hypothetical protein VITISV_021316 [Viti	0.985	0.788	0.8	5e-59
356500286	147	PREDICTED: nuclear transcription factor	0.942	0.897	0.833	3e-58
356536735	145	PREDICTED: nuclear transcription factor	0.971	0.937	0.801	1e-57
388498174	175	unknown [Lotus japonicus]	0.942	0.754	0.727	5e-51
255551711	158	ccaat-binding transcription factor subun	0.842	0.746	0.789	4e-49
224123212	150	predicted protein [Populus trichocarpa]	0.857	0.8	0.766	4e-49
297736862	138	unnamed protein product [Vitis vinifera]	0.821	0.833	0.837	8e-49
359477283	325	PREDICTED: uncharacterized protein LOC10	0.828	0.356	0.830	9e-49
297828501	152	hypothetical protein ARALYDRAFT_483964 [	0.728	0.671	0.872	6e-48
224131188	98	predicted protein [Populus trichocarpa]	0.7	1.0	0.908	9e-48

>gi|147853040|emb|CAN82321.1| hypothetical protein VITISV_021316 [Vitis vinifera]

 Score =  232 bits (591), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 112/140 (80%), Positives = 123/140 (87%), Gaps = 2/140 (1%)

Query: 1   MVDSAGHNLE-SYDNSYNFTVGASSGTDQDGVIKEQDRLLPIANVGRIMKQILPPNAKIS 59
           MVD  G N +  YD+ YN+  G SS + +DG+IKEQDRLLPIANVGRIMKQILPPNAKIS
Sbjct: 1   MVDDIGTNABRDYDHKYNY-AGGSSVSAEDGIIKEQDRLLPIANVGRIMKQILPPNAKIS 59

Query: 60  KEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLH 119
           KEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWAL TLGFD+YA+ LKRYLH
Sbjct: 60  KEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALGTLGFDDYAEPLKRYLH 119

Query: 120 RYRELEGERANQNKAGNNNN 139
           RYRELEGE+ANQ+KA   N+
Sbjct: 120 RYRELEGEKANQSKASEEND 139

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356500286|ref|XP_003518964.1| PREDICTED: nuclear transcription factor Y subunit B-5-like [Glycine max]

 Score =  229 bits (584), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 110/132 (83%), Positives = 115/132 (87%)

Query: 6   GHNLESYDNSYNFTVGASSGTDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKET 65
           G  LE     YNFT  AS  + QD VIKEQDRLLPIANVGRIMKQILPPNAKISKEAKET
Sbjct: 7   GKVLEREGFKYNFTAAASDTSAQDEVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKET 66

Query: 66  MQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRELE 125
           MQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD+Y++ LKRYLH+YRE E
Sbjct: 67  MQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDDYSEPLKRYLHKYREFE 126

Query: 126 GERANQNKAGNN 137
           GERANQNK  NN
Sbjct: 127 GERANQNKGNNN 138

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356536735|ref|XP_003536891.1| PREDICTED: nuclear transcription factor Y subunit B-5-like [Glycine max]

 Score =  227 bits (578), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 109/136 (80%), Positives = 118/136 (86%)

Query: 1   MVDSAGHNLESYDNSYNFTVGASSGTDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISK 60
           M D+ G  L+     YNFT  AS  + QDGVIKEQDRLLPIANVGRIMKQILPPNAKISK
Sbjct: 1   MGDNIGKVLDREGFKYNFTASASGTSAQDGVIKEQDRLLPIANVGRIMKQILPPNAKISK 60

Query: 61  EAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHR 120
           EAKETMQE VSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD+Y++ LKRYL++
Sbjct: 61  EAKETMQESVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDDYSEPLKRYLYK 120

Query: 121 YRELEGERANQNKAGN 136
           YRE+EGERANQNK  N
Sbjct: 121 YREMEGERANQNKGSN 136

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388498174|gb|AFK37153.1| unknown [Lotus japonicus]

 Score =  205 bits (522), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 99/136 (72%), Positives = 117/136 (86%), Gaps = 4/136 (2%)

Query: 6   GHNLESYDNSYNFTVGASSGTDQDGVI-KEQDRLLPIANVGRIMKQILPPNAKISKEAKE 64
           G    +++ +YNF+    +  ++DG+I +EQDRLLPIANVGRIMKQILP NAKISKEAKE
Sbjct: 2   GEREAAFNINYNFS---DNTAEEDGIIIREQDRLLPIANVGRIMKQILPSNAKISKEAKE 58

Query: 65  TMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYREL 124
           TMQECVSEF+SFVTGEASDKCHKEKRKTVNGDD+CWAL TLGFD+YAD LKRYL++YREL
Sbjct: 59  TMQECVSEFVSFVTGEASDKCHKEKRKTVNGDDVCWALGTLGFDDYADPLKRYLNKYREL 118

Query: 125 EGERANQNKAGNNNNG 140
           +G RANQNK  N+ +G
Sbjct: 119 DGGRANQNKGNNSGDG 134

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255551711|ref|XP_002516901.1| ccaat-binding transcription factor subunit A, putative [Ricinus communis] gi|223543989|gb|EEF45515.1| ccaat-binding transcription factor subunit A, putative [Ricinus communis]

 Score =  199 bits (505), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 94/119 (78%), Positives = 107/119 (89%), Gaps = 1/119 (0%)

Query: 20  VGASSGTDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTG 79
           VGAS G++++G  K QDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVT 
Sbjct: 28  VGAS-GSNEEGGTKGQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTS 86

Query: 80  EASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRELEGERANQNKAGNNN 138
           EAS+KC KE+RKTVNGDD+CWA+  LGFD+YA  L+RYL RYRELEG+RANQ+KA N+N
Sbjct: 87  EASEKCRKERRKTVNGDDVCWAMGALGFDDYAGPLRRYLQRYRELEGDRANQDKARNSN 145

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224123212|ref|XP_002330366.1| predicted protein [Populus trichocarpa] gi|222871570|gb|EEF08701.1| predicted protein [Populus trichocarpa]

 Score =  199 bits (505), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 92/120 (76%), Positives = 102/120 (85%)

Query: 20  VGASSGTDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTG 79
           VGA + +D  GV  EQDRLLPIANVGRIMKQILP NAKISKEAKETMQEC SEFISFVTG
Sbjct: 5   VGAGASSDDGGVKLEQDRLLPIANVGRIMKQILPANAKISKEAKETMQECASEFISFVTG 64

Query: 80  EASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRELEGERANQNKAGNNNN 139
           EAS+KC KE+RKTVNGDD+CWA+  LGFD+YA  L+RYL RYRE+EG+RANQ K  N NN
Sbjct: 65  EASEKCRKERRKTVNGDDVCWAMGALGFDDYAGPLRRYLQRYREIEGDRANQEKPANANN 124

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297736862|emb|CBI26063.3| unnamed protein product [Vitis vinifera]

 Score =  197 bits (502), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 98/117 (83%), Positives = 103/117 (88%), Gaps = 2/117 (1%)

Query: 21  GASSGTDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGE 80
           GAS+ TD DG IKEQDRLLPIANV RIMKQ LP NAKISKEAKETMQECVSEFISFVTGE
Sbjct: 6   GASASTD-DGSIKEQDRLLPIANVSRIMKQTLPTNAKISKEAKETMQECVSEFISFVTGE 64

Query: 81  ASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRELEGERA-NQNKAGN 136
           AS+KC KE+RKTVNGDDICWALA LGFD+YA  LKRYL RYRELEG+R  NQ KAGN
Sbjct: 65  ASEKCKKERRKTVNGDDICWALAALGFDDYAGPLKRYLQRYRELEGDRVLNQEKAGN 121

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359477283|ref|XP_002275948.2| PREDICTED: uncharacterized protein LOC100256274 [Vitis vinifera]

 Score =  197 bits (502), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 98/118 (83%), Positives = 103/118 (87%), Gaps = 2/118 (1%)

Query: 21  GASSGTDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGE 80
           GAS+ TD DG IKEQDRLLPIANV RIMKQ LP NAKISKEAKETMQECVSEFISFVTGE
Sbjct: 6   GASASTD-DGSIKEQDRLLPIANVSRIMKQTLPTNAKISKEAKETMQECVSEFISFVTGE 64

Query: 81  ASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRELEGERA-NQNKAGNN 137
           AS+KC KE+RKTVNGDDICWALA LGFD+YA  LKRYL RYRELEG+R  NQ KAGN 
Sbjct: 65  ASEKCKKERRKTVNGDDICWALAALGFDDYAGPLKRYLQRYRELEGDRVLNQEKAGNT 122

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297828501|ref|XP_002882133.1| hypothetical protein ARALYDRAFT_483964 [Arabidopsis lyrata subsp. lyrata] gi|297327972|gb|EFH58392.1| hypothetical protein ARALYDRAFT_483964 [Arabidopsis lyrata subsp. lyrata]

 Score =  195 bits (495), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 89/102 (87%), Positives = 96/102 (94%)

Query: 31  VIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKR 90
           +IKEQDRLLPIANVGRIMK ILPPNAK+SKEAKETMQECVSEFISFVTGEASDKCHKEKR
Sbjct: 40  MIKEQDRLLPIANVGRIMKNILPPNAKVSKEAKETMQECVSEFISFVTGEASDKCHKEKR 99

Query: 91  KTVNGDDICWALATLGFDNYADQLKRYLHRYRELEGERANQN 132
           KTVNGDDICWA+A LGFD+YA QLK+YLHRYR LEGE+ N +
Sbjct: 100 KTVNGDDICWAMANLGFDDYATQLKKYLHRYRVLEGEKPNHH 141

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224131188|ref|XP_002321022.1| predicted protein [Populus trichocarpa] gi|222861795|gb|EEE99337.1| predicted protein [Populus trichocarpa]

 Score =  194 bits (493), Expect = 9e-48,   Method: Compositional matrix adjust.
 Identities = 89/98 (90%), Positives = 97/98 (98%)

Query: 33  KEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKT 92
           KEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKT
Sbjct: 1   KEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKT 60

Query: 93  VNGDDICWALATLGFDNYADQLKRYLHRYRELEGERAN 130
           VNGDDICWALA+LGFD+Y++ LKRYL++YRE+EGERA+
Sbjct: 61  VNGDDICWALASLGFDDYSEPLKRYLYKYREVEGERAS 98

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	140
TAIR|locus:2043293	160	NF-YB5 ""nuclear factor Y, sub	0.728	0.637	0.843	6.4e-44
TAIR|locus:2168983	190	NF-YB2 ""nuclear factor Y, sub	0.771	0.568	0.696	5.5e-38
TAIR|locus:2129885	161	NF-YB3 ""nuclear factor Y, sub	0.75	0.652	0.685	1.7e-36
TAIR|locus:2036064	139	NF-YB4 ""nuclear factor Y, sub	0.678	0.683	0.768	2.1e-36
TAIR|locus:2054095	215	NF-YB7 ""nuclear factor Y, sub	0.685	0.446	0.75	5.7e-36
TAIR|locus:2083941	176	NF-YB10 ""nuclear factor Y, su	0.742	0.590	0.691	1.9e-35
TAIR|locus:2061789	173	NF-YB8 ""nuclear factor Y, sub	0.742	0.601	0.663	3.6e-34
TAIR|locus:2169028	234	NF-YB6 ""nuclear factor Y, sub	0.757	0.452	0.594	2e-33
CGD|CAL0000086	105	HAP31 [Candida albicans (taxid	0.685	0.914	0.687	1.3e-31
UNIPROTKB|Q5A6N7	105	HAP31 "Potential histone-like	0.685	0.914	0.687	1.3e-31

TAIR|locus:2043293 NF-YB5 ""nuclear factor Y, subunit B5"" [Arabidopsis thaliana (taxid:3702)]

 Score = 463 (168.0 bits), Expect = 6.4e-44, P = 6.4e-44
 Identities = 86/102 (84%), Positives = 95/102 (93%)

Query:    27 DQDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCH 86
             ++  ++KEQDRLLPIANVGRIMK ILP NAK+SKEAKETMQECVSEFISFVTGEASDKCH
Sbjct:    44 EESMMVKEQDRLLPIANVGRIMKNILPANAKVSKEAKETMQECVSEFISFVTGEASDKCH 103

Query:    87 KEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRELEGER 128
             KEKRKTVNGDDICWA+A LGFD+YA QLK+YLHRYR LEGE+
Sbjct:   104 KEKRKTVNGDDICWAMANLGFDDYAAQLKKYLHRYRVLEGEK 145

GO:0003677 "DNA binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

TAIR|locus:2168983 NF-YB2 ""nuclear factor Y, subunit B2"" [Arabidopsis thaliana (taxid:3702)]

 Score = 407 (148.3 bits), Expect = 5.5e-38, P = 5.5e-38
 Identities = 78/112 (69%), Positives = 92/112 (82%)

Query:    21 GASSGTDQDGVI----KEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISF 76
             G  +G +Q+G      +EQDR LPIANV RIMK+ LP NAKISK+AKETMQECVSEFISF
Sbjct:    10 GGQNGNNQNGQSSLSPREQDRFLPIANVSRIMKKALPANAKISKDAKETMQECVSEFISF 69

Query:    77 VTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRELEGER 128
             VTGEASDKC KEKRKT+NGDD+ WA+ TLGF++Y + LK YL R+RE+EGER
Sbjct:    70 VTGEASDKCQKEKRKTINGDDLLWAMTTLGFEDYVEPLKVYLQRFREIEGER 121

GO:0003677 "DNA binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

TAIR|locus:2129885 NF-YB3 ""nuclear factor Y, subunit B3"" [Arabidopsis thaliana (taxid:3702)]

 Score = 393 (143.4 bits), Expect = 1.7e-36, P = 1.7e-36
 Identities = 74/108 (68%), Positives = 90/108 (83%)

Query:    24 SGTDQDG---VIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGE 80
             SG  +DG     +EQDR LPIANV RIMK+ LP NAKISK+AKET+QECVSEFISF+TGE
Sbjct:     8 SGGHKDGGNASTREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFITGE 67

Query:    81 ASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRELEGER 128
             ASDKC +EKRKT+NGDD+ WA+ TLGF++Y + LK YL +YRE+EGE+
Sbjct:    68 ASDKCQREKRKTINGDDLLWAMTTLGFEDYVEPLKVYLQKYREVEGEK 115

GO:0003677 "DNA binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

TAIR|locus:2036064 NF-YB4 ""nuclear factor Y, subunit B4"" [Arabidopsis thaliana (taxid:3702)]

 Score = 392 (143.0 bits), Expect = 2.1e-36, P = 2.1e-36
 Identities = 73/95 (76%), Positives = 85/95 (89%)

Query:    34 EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTV 93
             ++DRLLPIANVGR+MKQILP NAKISKEAK+T+QEC +EFISFVT EAS+KCH+E RKTV
Sbjct:     3 DEDRLLPIANVGRLMKQILPSNAKISKEAKQTVQECATEFISFVTCEASEKCHRENRKTV 62

Query:    94 NGDDICWALATLGFDNYADQLKRYLHRYRELEGER 128
             NGDDI WAL+TLG DNYAD + R+LH+YRE E ER
Sbjct:    63 NGDDIWWALSTLGLDNYADAVGRHLHKYREAERER 97

GO:0003677 "DNA binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA;TAS

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2054095 NF-YB7 ""nuclear factor Y, subunit B7"" [Arabidopsis thaliana (taxid:3702)]

 Score = 388 (141.6 bits), Expect = 5.7e-36, P = 5.7e-36
 Identities = 72/96 (75%), Positives = 84/96 (87%)

Query:    33 KEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKT 92
             KEQDR LPIANVGRIMK++LP N KISK+AKET+QECVSEFISFVTGEASDKC +EKRKT
Sbjct:    35 KEQDRFLPIANVGRIMKKVLPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKT 94

Query:    93 VNGDDICWALATLGFDNYADQLKRYLHRYRELEGER 128
             +NGDDI WA+ TLGF++Y   LK YL +YR+ EGE+
Sbjct:    95 INGDDIIWAITTLGFEDYVAPLKVYLCKYRDTEGEK 130

GO:0003677 "DNA binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

TAIR|locus:2083941 NF-YB10 ""nuclear factor Y, subunit B10"" [Arabidopsis thaliana (taxid:3702)]

 Score = 383 (139.9 bits), Expect = 1.9e-35, P = 1.9e-35
 Identities = 74/107 (69%), Positives = 88/107 (82%)

Query:    24 SGTDQDGV---IKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGE 80
             SG DQ      ++EQDR LPIAN+ RIMK+ LP N KI+K+AKETMQECVSEFISFVT E
Sbjct:    16 SGGDQSPRSLNVREQDRFLPIANISRIMKRGLPLNGKIAKDAKETMQECVSEFISFVTSE 75

Query:    81 ASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRELEGE 127
             ASDKC +EKRKT+NGDD+ WA+ATLGF++Y D LK YL RYRE+EG+
Sbjct:    76 ASDKCQREKRKTINGDDLLWAMATLGFEDYIDPLKVYLMRYREMEGD 122

GO:0003677 "DNA binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

TAIR|locus:2061789 NF-YB8 ""nuclear factor Y, subunit B8"" [Arabidopsis thaliana (taxid:3702)]

 Score = 371 (135.7 bits), Expect = 3.6e-34, P = 3.6e-34
 Identities = 71/107 (66%), Positives = 87/107 (81%)

Query:    24 SGTDQDGV---IKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGE 80
             SG DQ      ++EQDR LPIAN+ RIMK+ LP N KI+K+AKE +QECVSEFISFVT E
Sbjct:    17 SGGDQSPRSLHVREQDRFLPIANISRIMKRGLPANGKIAKDAKEIVQECVSEFISFVTSE 76

Query:    81 ASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRELEGE 127
             ASDKC +EKRKT+NGDD+ WA+ATLGF++Y + LK YL RYRE+EG+
Sbjct:    77 ASDKCQREKRKTINGDDLLWAMATLGFEDYMEPLKVYLMRYREMEGD 123

GO:0003677 "DNA binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

TAIR|locus:2169028 NF-YB6 ""nuclear factor Y, subunit B6"" [Arabidopsis thaliana (taxid:3702)]

 Score = 364 (133.2 bits), Expect = 2.0e-33, P = 2.0e-33
 Identities = 63/106 (59%), Positives = 90/106 (84%)

Query:    23 SSGTDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEAS 82
             S+G +++  ++EQDR +PIANV RIM++ILP +AKIS ++KET+QECVSE+ISF+TGEA+
Sbjct:    47 SNGGEEECTVREQDRFMPIANVIRIMRRILPAHAKISDDSKETIQECVSEYISFITGEAN 106

Query:    83 DKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRELEGER 128
             ++C +E+RKT+  +D+ WA++ LGFD+Y + L  YLHRYRELEGER
Sbjct:   107 ERCQREQRKTITAEDVLWAMSKLGFDDYIEPLTLYLHRYRELEGER 152

GO:0003677 "DNA binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA;TAS

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

GO:0009738 "abscisic acid mediated signaling pathway" evidence=IMP

GO:0033613 "activating transcription factor binding" evidence=IPI

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IDA

CGD|CAL0000086 HAP31 [Candida albicans (taxid:5476)]

 Score = 347 (127.2 bits), Expect = 1.3e-31, P = 1.3e-31
 Identities = 66/96 (68%), Positives = 80/96 (83%)

Query:    28 QDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHK 87
             +D  ++EQDR LPIANV RIMK  LPP AK+SK+AKE MQECVSEFISF+T EASDKC K
Sbjct:     7 RDIELREQDRWLPIANVARIMKNTLPPTAKVSKDAKECMQECVSEFISFITSEASDKCLK 66

Query:    88 EKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRE 123
             EKRKT+NG+DI +++  LGF+NYA+ LK YL +YRE
Sbjct:    67 EKRKTINGEDILYSMYDLGFENYAEVLKIYLAKYRE 102

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=NAS

GO:0071280 "cellular response to copper ion" evidence=IMP

GO:0035690 "cellular response to drug" evidence=IMP

GO:0016602 "CCAAT-binding factor complex" evidence=IEA

GO:0043457 "regulation of cellular respiration" evidence=IEA

GO:0000436 "carbon catabolite activation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0000978 "RNA polymerase II core promoter proximal region sequence-specific DNA binding" evidence=IEA

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=IEA

UNIPROTKB|Q5A6N7 HAP31 "Potential histone-like transcription factor" [Candida albicans SC5314 (taxid:237561)]

 Score = 347 (127.2 bits), Expect = 1.3e-31, P = 1.3e-31
 Identities = 66/96 (68%), Positives = 80/96 (83%)

Query:    28 QDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHK 87
             +D  ++EQDR LPIANV RIMK  LPP AK+SK+AKE MQECVSEFISF+T EASDKC K
Sbjct:     7 RDIELREQDRWLPIANVARIMKNTLPPTAKVSKDAKECMQECVSEFISFITSEASDKCLK 66

Query:    88 EKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRE 123
             EKRKT+NG+DI +++  LGF+NYA+ LK YL +YRE
Sbjct:    67 EKRKTINGEDILYSMYDLGFENYAEVLKIYLAKYRE 102

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=NAS

GO:0035690 "cellular response to drug" evidence=IMP

GO:0071280 "cellular response to copper ion" evidence=IMP

---

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)
P36611	HAP3_SCHPO	No assigned EC number	0.6559	0.6642	0.8017	yes	no
O82248	NFYB5_ARATH	No assigned EC number	0.8380	0.75	0.6562	yes	no
P13434	HAP3_YEAST	No assigned EC number	0.6153	0.7357	0.7152	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00023559001 SubName- Full=Chromosome chr7 scaffold_31, whole genome shotgun sequence; (186 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	140
pfam00808	65	pfam00808, CBFD_NFYB_HMF, Histone-like transcripti	9e-30
COG2036	91	COG2036, HHT1, Histones H3 and H4 [Chromatin struc	4e-24
COG5150	148	COG5150, COG5150, Class 2 transcription repressor	1e-13
pfam00125	75	pfam00125, Histone, Core histone H2A/H2B/H3/H4	4e-04

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

 Score =  102 bits (256), Expect = 9e-30
 Identities = 34/66 (51%), Positives = 44/66 (66%), Gaps = 1/66 (1%)

Query: 37  RLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGD 96
             LPIA V RIMK   P   +IS++AKE + ECV EFI F+  EA++ C KEKRKT+N +
Sbjct: 1   AELPIARVKRIMKSD-PDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAE 59

Query: 97  DICWAL 102
            I  A+
Sbjct: 60  HIKLAV 65

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

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

 Score = 88.5 bits (220), Expect = 4e-24
 Identities = 29/92 (31%), Positives = 45/92 (48%), Gaps = 2/92 (2%)

Query: 21  GASSGTDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGE 80
           GA    +     +  D LLP A V RI+++      ++S  A E +QE + E++  +  +
Sbjct: 2   GAVGLKEIRRYQRSTDLLLPKAPVRRILRKAGAE--RVSSSAIEELQEALEEYLEEIAED 59

Query: 81  ASDKCHKEKRKTVNGDDICWALATLGFDNYAD 112
           A +     KRKTV  +DI  AL  LG   Y +
Sbjct: 60  AVELAEHAKRKTVKAEDIKLALKRLGRRIYGE 91

Length = 91

>gnl|CDD|227479 COG5150, COG5150, Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]

 Score = 63.1 bits (153), Expect = 1e-13
 Identities = 26/85 (30%), Positives = 45/85 (52%)

Query: 39  LPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDI 98
           LP A V +++  ILP +   +KEA+E       EFI+ ++ EA++ C +E +KT+  + +
Sbjct: 12  LPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHV 71

Query: 99  CWALATLGFDNYADQLKRYLHRYRE 123
             AL  L F+ Y +        Y+ 
Sbjct: 72  IKALENLEFEEYIESCMEEHENYKS 96

Length = 148

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

 Score = 36.4 bits (85), Expect = 4e-04
 Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 3/70 (4%)

Query: 36  DRLLPIANVGRIMKQI---LPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKT 92
             L+      R+++++        +IS +A   +QE + + +  +  +A       KRKT
Sbjct: 3   RLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKRKT 62

Query: 93  VNGDDICWAL 102
           +   DI  A+
Sbjct: 63  ITPRDIQLAV 72

Length = 75

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	140
KOG0869	168	consensus CCAAT-binding factor, subunit A (HAP3) [	99.98
KOG0871	156	consensus Class 2 transcription repressor NC2, bet	99.94
KOG0870	172	consensus DNA polymerase epsilon, subunit D [Trans	99.93
COG5150	148	Class 2 transcription repressor NC2, beta subunit	99.86
PF00808	65	CBFD_NFYB_HMF: Histone-like transcription factor (	99.76
COG2036	91	HHT1 Histones H3 and H4 [Chromatin structure and d	99.75
cd00076	85	H4 Histone H4, one of the four histones, along wit	99.51
PLN00035	103	histone H4; Provisional	99.47
PTZ00015	102	histone H4; Provisional	99.42
smart00417	74	H4 Histone H4.	99.29
smart00803	65	TAF TATA box binding protein associated factor. TA	99.26
smart00428	105	H3 Histone H3.	99.25
cd07981	72	TAF12 TATA Binding Protein (TBP) Associated Factor	99.06
PLN00160	97	histone H3; Provisional	99.05
PF00125	75	Histone: Core histone H2A/H2B/H3/H4 histone h2a si	99.04
PLN00161	135	histone H3; Provisional	99.02
PLN00121	136	histone H3; Provisional	99.01
COG5208	286	HAP5 CCAAT-binding factor, subunit C [Transcriptio	99.0
PTZ00018	136	histone H3; Provisional	98.97
KOG3467	103	consensus Histone H4 [Chromatin structure and dyna	98.81
smart00576	77	BTP Bromodomain transcription factors and PHD doma	98.67
KOG1745	137	consensus Histones H3 and H4 [Chromatin structure	98.66
KOG1657	236	consensus CCAAT-binding factor, subunit C (HAP5) [	98.59
cd00074	115	H2A Histone 2A; H2A is a subunit of the nucleosome	98.52
cd07979	117	TAF9 TATA Binding Protein (TBP) Associated Factor	98.51
PF15511	414	CENP-T: Centromere kinetochore component CENP-T; P	98.46
KOG1659	224	consensus Class 2 transcription repressor NC2, alp	98.24
cd08050	343	TAF6 TATA Binding Protein (TBP) Associated Factor	98.23
PF15630	76	CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C	98.09
COG5247	113	BUR6 Class 2 transcription repressor NC2, alpha su	98.01
PF07524	77	Bromo_TP: Bromodomain associated; InterPro: IPR006	97.98
COG5262	132	HTA1 Histone H2A [Chromatin structure and dynamics	97.91
PF03847	68	TFIID_20kDa: Transcription initiation factor TFIID	97.91
cd08048	85	TAF11 TATA Binding Protein (TBP) Associated Factor	97.84
PF02969	66	TAF: TATA box binding protein associated factor (T	97.8
smart00427	89	H2B Histone H2B.	97.78
PF09415	72	CENP-X: CENP-S associating Centromere protein X; I	97.65
PLN00158	116	histone H2B; Provisional	97.55
PF04719	90	TAFII28: hTAFII28-like protein conserved region; I	97.53
PTZ00463	117	histone H2B; Provisional	97.5
smart00414	106	H2A Histone 2A.	97.4
PLN00154	136	histone H2A; Provisional	97.28
PTZ00017	134	histone H2A; Provisional	97.11
KOG1142	258	consensus Transcription initiation factor TFIID, s	97.01
PLN00153	129	histone H2A; Provisional	96.93
PF02291	129	TFIID-31kDa: Transcription initiation factor IID,	96.92
KOG1756	131	consensus Histone 2A [Chromatin structure and dyna	96.92
PLN00156	139	histone H2AX; Provisional	96.92
KOG1658	162	consensus DNA polymerase epsilon, subunit C [Repli	96.86
PLN00157	132	histone H2A; Provisional	96.79
PF02269	93	TFIID-18kDa: Transcription initiation factor IID,	96.76
KOG1744	127	consensus Histone H2B [Chromatin structure and dyn	96.44
PF15510	102	CENP-W: Centromere kinetochore component W	96.43
KOG3219	195	consensus Transcription initiation factor TFIID, s	96.39
PTZ00252	134	histone H2A; Provisional	95.85
cd07978	92	TAF13 The TATA Binding Protein (TBP) Associated Fa	95.55
KOG3423	176	consensus Transcription initiation factor TFIID, s	95.15
KOG4336	323	consensus TBP-associated transcription factor Prod	94.57
KOG2549	576	consensus Transcription initiation factor TFIID, s	94.5
KOG3334	148	consensus Transcription initiation factor TFIID, s	92.2
KOG2389	353	consensus Predicted bromodomain transcription fact	89.91
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	89.62
PRK00411	394	cdc6 cell division control protein 6; Reviewed	89.18
COG5095	450	TAF6 Transcription initiation factor TFIID, subuni	85.78
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	85.6
PF03540	51	TFIID_30kDa: Transcription initiation factor TFIID	85.24
KOG1757	131	consensus Histone 2A [Chromatin structure and dyna	84.67
cd08045	212	TAF4 TATA Binding Protein (TBP) Associated Factor	83.96
PF13654	509	AAA_32: AAA domain; PDB: 3K1J_B.	83.16
COG5162	197	Transcription initiation factor TFIID, subunit TAF	81.77

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

Probab=99.98  E-value=2e-32  Score=209.98  Aligned_cols=111  Identities=68%  Similarity=1.111  Sum_probs=105.5

Q ss_pred             CCCCCCccccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           25 GTDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        25 ~~~~~~~~~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      .|+.....+++|..||+|+|.||||..||.+.+|+|||++.+|+|+.+||.+|+++|.+.|.+++||||+++||+|||..
T Consensus        19 ~~~~~~~~reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~t   98 (168)
T KOG0869|consen   19 SPQSSLSLREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMST   98 (168)
T ss_pred             CCccccccchhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHH
Confidence            56666789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCchhHHHHHHHHHHHHHHHHHHhhhhccC
Q 038014          105 LGFDNYADQLKRYLHRYRELEGERANQNKAG  135 (140)
Q Consensus       105 lgf~~y~~~l~~~l~~~re~~~~kk~q~k~~  135 (140)
                      |||++|+++|+.+|..||+++.++....+.+
T Consensus        99 LGFe~Y~eplkiyL~kYRe~e~e~~~~~~~~  129 (168)
T KOG0869|consen   99 LGFENYAEPLKIYLQKYRELEGERGRSGKGG  129 (168)
T ss_pred             cCcHhHHHHHHHHHHHHHHHhhhcccccccC
Confidence            9999999999999999999998887766655

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

Probab=99.94  E-value=1.4e-26  Score=176.25  Aligned_cols=95  Identities=33%  Similarity=0.662  Sum_probs=92.0

Q ss_pred             cccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHHH
Q 038014           34 EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQ  113 (140)
Q Consensus        34 ~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~~  113 (140)
                      .+++.||+|+|.+|||+.||.++||.+||+++|..||.+||+.|+++|+++|....||||.++||++||+.|||.+|++.
T Consensus         8 dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eYiee   87 (156)
T KOG0871|consen    8 DDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEYIEE   87 (156)
T ss_pred             cccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHHHHH
Confidence            48899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHH
Q 038014          114 LKRYLHRYRELEGER  128 (140)
Q Consensus       114 l~~~l~~~re~~~~k  128 (140)
                      +.+.+++|+...+.+
T Consensus        88 ~~~vl~~~K~~~~~~  102 (156)
T KOG0871|consen   88 AEEVLENCKEEAKKR  102 (156)
T ss_pred             HHHHHHHHHHHHHHh
Confidence            999999999987754

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

Probab=99.93  E-value=5.7e-26  Score=175.54  Aligned_cols=106  Identities=27%  Similarity=0.449  Sum_probs=99.8

Q ss_pred             CccccccccCchhHHHHHHhhhCCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014           30 GVIKEQDRLLPIANVGRIMKQILPPN-AKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD  108 (140)
Q Consensus        30 ~~~~~~d~~LP~A~V~RI~K~~lp~~-~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~  108 (140)
                      ...+++|+.||+|+|.||+|++||.. +.|++||+.+|+++|++|++||++.|++.|+.++||||+++||+.||++|+|.
T Consensus         2 e~eri~dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs   81 (172)
T KOG0870|consen    2 EDERIEDLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFS   81 (172)
T ss_pred             cchhHHHhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchH
Confidence            35678999999999999999999987 89999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHHHHHhhhhccC
Q 038014          109 NYADQLKRYLHRYRELEGERANQNKAG  135 (140)
Q Consensus       109 ~y~~~l~~~l~~~re~~~~kk~q~k~~  135 (140)
                      .|.++|+..|+.|+...+.||..+...
T Consensus        82 ~f~~plk~~Le~yk~~~k~Kk~~~~~~  108 (172)
T KOG0870|consen   82 SFVNPLKSALEAYKKAVKQKKLAKANK  108 (172)
T ss_pred             HHhhHHHHHHHHHHHHHHHHHHhcccc
Confidence            999999999999999999888665543

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

Probab=99.86  E-value=1.3e-21  Score=146.42  Aligned_cols=96  Identities=27%  Similarity=0.533  Sum_probs=92.5

Q ss_pred             ccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHH
Q 038014           33 KEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYAD  112 (140)
Q Consensus        33 ~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~  112 (140)
                      ..+++.||+|+|++.+-+.||.+..+.+||++.+..||.+||+.|+++|++.|..+.+|||.++||++||+.|||.+|++
T Consensus         6 ~dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi~   85 (148)
T COG5150           6 NDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIE   85 (148)
T ss_pred             ccccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHHH
Confidence            34788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHH
Q 038014          113 QLKRYLHRYRELEGER  128 (140)
Q Consensus       113 ~l~~~l~~~re~~~~k  128 (140)
                      .+.+.+.+|+..++.|
T Consensus        86 ~~~e~~~n~k~~qK~k  101 (148)
T COG5150          86 SCMEEHENYKSYQKQK  101 (148)
T ss_pred             HHHHHHHHHHHHHhhc
Confidence            9999999999988765

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

Probab=99.76  E-value=1.7e-18  Score=114.49  Aligned_cols=64  Identities=39%  Similarity=0.618  Sum_probs=59.2

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHH
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWAL  102 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~AL  102 (140)
                      .||.+.|+||||.. |+..+||+||..+|++|+++|+.+|+.+|++.|.+.+||||+++||..||
T Consensus         2 ~lP~a~vkri~k~~-~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av   65 (65)
T PF00808_consen    2 SLPLARVKRIMKSD-PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV   65 (65)
T ss_dssp             SS-HHHHHHHHHHT-STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred             CCChHHHHHHhccC-CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence            69999999999999 88889999999999999999999999999999999999999999999986

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 ....

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

Probab=99.75  E-value=1.8e-18  Score=122.89  Aligned_cols=80  Identities=34%  Similarity=0.474  Sum_probs=74.4

Q ss_pred             CCccccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014           29 DGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD  108 (140)
Q Consensus        29 ~~~~~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~  108 (140)
                      .+..+..+..||+++|.||||++.++  |||.+|.++|++++++|+..|+..|+++|.|+|||||+++||..|++.+||.
T Consensus        10 r~~~~~~~~~Lp~apv~Ri~r~~~~~--Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~   87 (91)
T COG2036          10 RRYQRSTDLLLPKAPVRRILRKAGAE--RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRR   87 (91)
T ss_pred             HhhhhhhhhhcCchHHHHHHHHHhHH--HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhccc
Confidence            34556788999999999999999654  9999999999999999999999999999999999999999999999999998


Q ss_pred             hh
Q 038014          109 NY  110 (140)
Q Consensus       109 ~y  110 (140)
                      .|
T Consensus        88 ~~   89 (91)
T COG2036          88 IY   89 (91)
T ss_pred             cc
Confidence            65

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

Probab=99.51  E-value=7.1e-14  Score=98.27  Aligned_cols=71  Identities=21%  Similarity=0.291  Sum_probs=67.3

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchh
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNY  110 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y  110 (140)
                      .||+++|.||+|..  +..|||.|+.+.+.++.++|+..|..+|..+|+|++||||+++||..||++.|-.-|
T Consensus        13 gi~k~~I~RLarr~--GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~y   83 (85)
T cd00076          13 GITKPAIRRLARRG--GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY   83 (85)
T ss_pred             cCCHHHHHHHHHHc--CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCcc
Confidence            59999999999999  778999999999999999999999999999999999999999999999999986544

>PLN00035 histone H4; Provisional

Probab=99.47  E-value=2e-13  Score=99.03  Aligned_cols=72  Identities=21%  Similarity=0.213  Sum_probs=67.2

Q ss_pred             cccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCch
Q 038014           36 DRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDN  109 (140)
Q Consensus        36 d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~  109 (140)
                      ...||+++|.||++..  +..|||.|+.+++.+..++|+..|+.+|..+|+|++||||+++||..||+.+|-.-
T Consensus        27 i~~ipk~~IrRLARr~--GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~l   98 (103)
T PLN00035         27 IQGITKPAIRRLARRG--GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTL   98 (103)
T ss_pred             hccCCHHHHHHHHHHc--CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCcC
Confidence            3469999999999999  77899999999999999999999999999999999999999999999999987543

>PTZ00015 histone H4; Provisional

Probab=99.42  E-value=6.6e-13  Score=96.19  Aligned_cols=74  Identities=22%  Similarity=0.302  Sum_probs=68.6

Q ss_pred             ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchh
Q 038014           35 QDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNY  110 (140)
Q Consensus        35 ~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y  110 (140)
                      ..-.||+++|.||+|..  +..|||.|+.+.+.++.++|+..|+.+|..+|+|++||||+++||..||+..|-.-|
T Consensus        27 ~i~gI~k~~IrRLarr~--GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~y  100 (102)
T PTZ00015         27 NIRGITKGAIRRLARRG--GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTLY  100 (102)
T ss_pred             cccCCCHHHHHHHHHHc--CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCCC
Confidence            34469999999999999  778999999999999999999999999999999999999999999999999886543

>smart00417 H4 Histone H4

Probab=99.29  E-value=6e-12  Score=86.49  Aligned_cols=62  Identities=18%  Similarity=0.266  Sum_probs=59.0

Q ss_pred             ccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHH
Q 038014           37 RLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICW  100 (140)
Q Consensus        37 ~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~  100 (140)
                      -.||+++|.||+|..  +.-|||.++.+.+.+..++|+..|+.+|..+|+|+|||||+++||..
T Consensus        12 ~gI~k~~IrRLaRr~--GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~   73 (74)
T smart00417       12 QGITKPAIRRLARRG--GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY   73 (74)
T ss_pred             cCCCHHHHHHHHHHc--CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence            369999999999999  77799999999999999999999999999999999999999999974

>smart00803 TAF TATA box binding protein associated factor

Probab=99.26  E-value=2e-11  Score=81.73  Aligned_cols=64  Identities=27%  Similarity=0.264  Sum_probs=61.1

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA  103 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe  103 (140)
                      .||+++|+||++..  +-.+||.|+..+|.+-++.|+..|..+|..+++|.|||||+++||..||+
T Consensus         2 ~~p~~~i~ria~~~--Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk   65 (65)
T smart00803        2 WLPKETIKDVAESL--GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR   65 (65)
T ss_pred             CCCHHHHHHHHHHC--CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence            58999999999999  66789999999999999999999999999999999999999999999984

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.

>smart00428 H3 Histone H3

Probab=99.25  E-value=1.7e-11  Score=89.25  Aligned_cols=72  Identities=21%  Similarity=0.235  Sum_probs=66.1

Q ss_pred             ccccccCchhHHHHHHhhhCCC-----CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           33 KEQDRLLPIANVGRIMKQILPP-----NAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        33 ~~~d~~LP~A~V~RI~K~~lp~-----~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      +..++.+|+.++.|++++..++     +.+++.+|..+||+++|.|+..+...|+.+|.|+||+||+++|+..|..-
T Consensus        24 kst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~ri  100 (105)
T smart00428       24 KSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRI  100 (105)
T ss_pred             cCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHH
Confidence            5678899999999999998643     68999999999999999999999999999999999999999999888643

>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=99.06  E-value=9.7e-10  Score=74.56  Aligned_cols=66  Identities=20%  Similarity=0.322  Sum_probs=61.8

Q ss_pred             CchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014           39 LPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL  105 (140)
Q Consensus        39 LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l  105 (140)
                      +++..+..++|+.-| ..+++.||.++|++.++.|+..++..|..+|+|.||+||.++||..+|++.
T Consensus         2 ~~k~~l~~lv~~id~-~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~   67 (72)
T cd07981           2 LTKRKLQELLKEIDP-REQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERN   67 (72)
T ss_pred             CcHHHHHHHHHhhCC-CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            678899999999965 589999999999999999999999999999999999999999999999863

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

>PLN00160 histone H3; Provisional

Probab=99.05  E-value=5.6e-10  Score=80.32  Aligned_cols=71  Identities=18%  Similarity=0.143  Sum_probs=65.3

Q ss_pred             ccccccCchhHHHHHHhhhCC----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014           33 KEQDRLLPIANVGRIMKQILP----PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA  103 (140)
Q Consensus        33 ~~~d~~LP~A~V~RI~K~~lp----~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe  103 (140)
                      +..++.||++++.|++++..+    ++.+++.+|..+||+++|.|+..+...++.+|.|+||.||++.|+..+..
T Consensus        16 kst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~r   90 (97)
T PLN00160         16 KSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARR   90 (97)
T ss_pred             cchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHH
Confidence            457889999999999999853    35899999999999999999999999999999999999999999988764

>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=99.04  E-value=5.7e-10  Score=74.79  Aligned_cols=68  Identities=28%  Similarity=0.374  Sum_probs=62.6

Q ss_pred             cccCchhHHHHHHhhhCCC---CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014           36 DRLLPIANVGRIMKQILPP---NAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA  103 (140)
Q Consensus        36 d~~LP~A~V~RI~K~~lp~---~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe  103 (140)
                      ...+|+.+|.|++|+..++   ..+||++|...|+.+++.|+..|...|..+|.+.||+||+++||..|++
T Consensus         3 ~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r   73 (75)
T PF00125_consen    3 RRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVR   73 (75)
T ss_dssp             SHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHH
T ss_pred             ccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHh
Confidence            4578999999999998653   2699999999999999999999999999999999999999999999985

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 ....

>PLN00161 histone H3; Provisional

Probab=99.02  E-value=1.2e-09  Score=82.73  Aligned_cols=71  Identities=20%  Similarity=0.232  Sum_probs=65.4

Q ss_pred             ccccccCchhHHHHHHhhhC----CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014           33 KEQDRLLPIANVGRIMKQIL----PPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA  103 (140)
Q Consensus        33 ~~~d~~LP~A~V~RI~K~~l----p~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe  103 (140)
                      +..++.||+.++.||+++..    +.+++++.+|..+||+++|.|+..|..+++-+|.|+||.||.+.|+..+..
T Consensus        50 kst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~r  124 (135)
T PLN00161         50 KSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARR  124 (135)
T ss_pred             cccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHH
Confidence            56788999999999999985    346899999999999999999999999999999999999999999988864

>PLN00121 histone H3; Provisional

Probab=99.01  E-value=6.7e-10  Score=84.19  Aligned_cols=71  Identities=18%  Similarity=0.209  Sum_probs=65.3

Q ss_pred             ccccccCchhHHHHHHhhhCCC---CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014           33 KEQDRLLPIANVGRIMKQILPP---NAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA  103 (140)
Q Consensus        33 ~~~d~~LP~A~V~RI~K~~lp~---~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe  103 (140)
                      +..++.||+.++.||+++...+   +++++.+|..+||+++|.|+..|..+++.+|.|++|.||++.|+..+..
T Consensus        57 kst~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r  130 (136)
T PLN00121         57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR  130 (136)
T ss_pred             cccccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHH
Confidence            4468899999999999998643   6899999999999999999999999999999999999999999988763

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

Probab=99.00  E-value=2.8e-10  Score=92.53  Aligned_cols=79  Identities=27%  Similarity=0.286  Sum_probs=72.2

Q ss_pred             cccccccCchhHHHHHHhhhCCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchh
Q 038014           32 IKEQDRLLPIANVGRIMKQILPPNA-KISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNY  110 (140)
Q Consensus        32 ~~~~d~~LP~A~V~RI~K~~lp~~~-rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y  110 (140)
                      +-..++.||.|+|+|+||-.  +++ .||.||..++.+.++.||..|+..|.-.|++.+|+|+.-.||-.|+++.++.+|
T Consensus       103 ~~~k~h~LPlARIkkvMKtd--edVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDF  180 (286)
T COG5208         103 ILLKDHNLPLARIKKVMKTD--EDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDF  180 (286)
T ss_pred             HHHHhccCcHHHHHHHHhcc--cchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhH
Confidence            44467789999999999998  666 499999999999999999999999999999999999999999999999988877


Q ss_pred             HH
Q 038014          111 AD  112 (140)
Q Consensus       111 ~~  112 (140)
                      .-
T Consensus       181 Li  182 (286)
T COG5208         181 LI  182 (286)
T ss_pred             Hh
Confidence            53

>PTZ00018 histone H3; Provisional

Probab=98.97  E-value=1.7e-09  Score=81.93  Aligned_cols=71  Identities=18%  Similarity=0.213  Sum_probs=65.2

Q ss_pred             ccccccCchhHHHHHHhhhCC---CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014           33 KEQDRLLPIANVGRIMKQILP---PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA  103 (140)
Q Consensus        33 ~~~d~~LP~A~V~RI~K~~lp---~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe  103 (140)
                      +..++.||+.++.||+++...   .+++++.+|..+||+++|.|+..|..+++.+|.|++|.||++.|+..+..
T Consensus        57 kst~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r  130 (136)
T PTZ00018         57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR  130 (136)
T ss_pred             ccchhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHH
Confidence            446889999999999999853   46899999999999999999999999999999999999999999988764

>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]

Probab=98.81  E-value=1.4e-08  Score=72.07  Aligned_cols=69  Identities=23%  Similarity=0.254  Sum_probs=64.7

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD  108 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~  108 (140)
                      .+.+.+|+||.+..  +.-||+.-.-+.+..++.+|+..+...|..+++|++||||++.||+.+|+++|.-
T Consensus        29 gitKpaIRRlARr~--GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~   97 (103)
T KOG3467|consen   29 GITKPAIRRLARRG--GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT   97 (103)
T ss_pred             ccchHHHHHHHHhc--CcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence            47799999999999  6678999999999999999999999999999999999999999999999998754

>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins

Probab=98.67  E-value=1.4e-07  Score=64.51  Aligned_cols=66  Identities=21%  Similarity=0.263  Sum_probs=60.1

Q ss_pred             hhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014           41 IANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD  108 (140)
Q Consensus        41 ~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~  108 (140)
                      +-.|.+|++..  +--+++.+|.+.|.+.++.|+..|+..+..+|+++||++++..||..||+++|+.
T Consensus         9 ~~~Vaqil~~~--Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~   74 (77)
T smart00576        9 RIAVAQILESA--GFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS   74 (77)
T ss_pred             HHHHHHHHHHc--CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence            44677888887  4458999999999999999999999999999999999999999999999999974

subdomain of archael histone-like transcription factors

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

Probab=98.66  E-value=1.4e-08  Score=76.95  Aligned_cols=75  Identities=20%  Similarity=0.228  Sum_probs=66.7

Q ss_pred             cccccccCchhHHHHHHhhhC---CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcC
Q 038014           32 IKEQDRLLPIANVGRIMKQIL---PPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLG  106 (140)
Q Consensus        32 ~~~~d~~LP~A~V~RI~K~~l---p~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lg  106 (140)
                      .+..|+.|++.+..|++++..   -.+.++...|+.+||++++.|+..|...++-+|.|+||.||.+.|+..|..-.|
T Consensus        57 QkstdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg  134 (137)
T KOG1745|consen   57 QKSTDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG  134 (137)
T ss_pred             HhhhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhccc
Confidence            346788999999999999553   347899999999999999999999999999999999999999999998876443

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

Probab=98.59  E-value=4.6e-08  Score=80.09  Aligned_cols=87  Identities=24%  Similarity=0.294  Sum_probs=73.2

Q ss_pred             ccccccCchhHHHHHHhhhCCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc---CCc
Q 038014           33 KEQDRLLPIANVGRIMKQILPPNA-KISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL---GFD  108 (140)
Q Consensus        33 ~~~d~~LP~A~V~RI~K~~lp~~~-rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l---gf~  108 (140)
                      ......||+++|++|||..  +++ .|+.||...+.+||+.||..|+..+...+...+|+|+...|+-.++..-   +|.
T Consensus        69 d~~~~~lPlaRiKkimK~d--edv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL  146 (236)
T KOG1657|consen   69 DFKNHILPLARIKKIMKSD--EDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFL  146 (236)
T ss_pred             chhhccCcHhhcccccccc--ccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccce
Confidence            3344579999999999999  555 6999999999999999999999999999999999999999999999874   444


Q ss_pred             hhHHHHHHHHHHH
Q 038014          109 NYADQLKRYLHRY  121 (140)
Q Consensus       109 ~y~~~l~~~l~~~  121 (140)
                      -.+-+-+...+.|
T Consensus       147 ~DivP~~~~~~~~  159 (236)
T KOG1657|consen  147 RDIVPRKILAEKY  159 (236)
T ss_pred             eccccchhccccc
Confidence            4444556656555

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

Probab=98.52  E-value=3e-07  Score=67.94  Aligned_cols=70  Identities=13%  Similarity=0.178  Sum_probs=63.8

Q ss_pred             cccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           34 EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        34 ~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      -..+.||.++|.|+||+.- ...||+.+|...|..+.|-+...|...|...|++.+|++|+++||..|+..
T Consensus        16 ragL~fPV~ri~R~Lk~~~-~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n   85 (115)
T cd00074          16 RAGLQFPVGRIHRYLKKGR-YAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN   85 (115)
T ss_pred             ccCccCcHHHHHHHHHcCc-cccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence            3578999999999999852 247999999999999999999999999999999999999999999999874

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.

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

Probab=98.51  E-value=4.1e-07  Score=67.13  Aligned_cols=78  Identities=12%  Similarity=0.177  Sum_probs=66.0

Q ss_pred             hHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHH-HHHHHHHH
Q 038014           42 ANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYAD-QLKRYLHR  120 (140)
Q Consensus        42 A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~-~l~~~l~~  120 (140)
                      ..|.+|+|..  +..+++.+++..|.+.+..++..|..+|..+|+|+||+||+++||..|++..+-..|.+ +-+++|-+
T Consensus         5 ~~v~~iLk~~--Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l~~   82 (117)
T cd07979           5 RVIAAILKSM--GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFLLE   82 (117)
T ss_pred             HHHHHHHHHC--CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHHHH
Confidence            3578888887  56799999999999999999999999999999999999999999999999766544544 35666544


Q ss_pred             H
Q 038014          121 Y  121 (140)
Q Consensus       121 ~  121 (140)
                      .
T Consensus        83 ~   83 (117)
T cd07979          83 L   83 (117)
T ss_pred             H
Confidence            3

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

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

Probab=98.46  E-value=2.5e-07  Score=80.71  Aligned_cols=64  Identities=22%  Similarity=0.294  Sum_probs=48.2

Q ss_pred             cccccCchhHHHHHHhhhCC----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCccc
Q 038014           34 EQDRLLPIANVGRIMKQILP----PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDD   97 (140)
Q Consensus        34 ~~d~~LP~A~V~RI~K~~lp----~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eD   97 (140)
                      +..-.||.+.|+|++.....    .+++|++||..+|.+|..+|...|+..-..+|.|+|||||..+|
T Consensus       347 i~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD  414 (414)
T PF15511_consen  347 IPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD  414 (414)
T ss_dssp             -----S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred             CCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence            34446999999999877743    46899999999999999999999999999999999999998876

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

Probab=98.24  E-value=3.8e-06  Score=67.99  Aligned_cols=88  Identities=11%  Similarity=0.170  Sum_probs=75.3

Q ss_pred             cccccCchhHHHHHHhhhCCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHH
Q 038014           34 EQDRLLPIANVGRIMKQILPPN-AKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYAD  112 (140)
Q Consensus        34 ~~d~~LP~A~V~RI~K~~lp~~-~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~  112 (140)
                      ---..||.++|+|||...  .+ .+|+.-....+.++.+.|+..|...+.+++...+-|||+++|+..+++.-.-.+|..
T Consensus         9 ~~~trfp~aRiKKIMQ~d--EdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk   86 (224)
T KOG1659|consen    9 KYKTRFPPARIKKIMQSD--EDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLK   86 (224)
T ss_pred             hhhccCCHHHHHHHHhhh--hhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHH
Confidence            334579999999999988  55 489999999999999999999999999999999999999999999999887777777


Q ss_pred             HHHHHHHHHHH
Q 038014          113 QLKRYLHRYRE  123 (140)
Q Consensus       113 ~l~~~l~~~re  123 (140)
                      .+-..+..+..
T Consensus        87 ~~v~~vpd~~~   97 (224)
T KOG1659|consen   87 EVVEKVPDRQQ   97 (224)
T ss_pred             HHHHhcCCCcc
Confidence            65555443333

>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=98.23  E-value=4.4e-06  Score=71.18  Aligned_cols=67  Identities=19%  Similarity=0.237  Sum_probs=60.9

Q ss_pred             chhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014           40 PIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD  108 (140)
Q Consensus        40 P~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~  108 (140)
                      |..+|+-|++..  +-.++++||..+|.+.++.++..|+.+|...++|.||||++++||-.||+.++.+
T Consensus         1 ~~~~i~~ia~~~--Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~e   67 (343)
T cd08050           1 PQESIKLIAESL--GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVE   67 (343)
T ss_pred             ChhHHHHHHHHc--CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCC
Confidence            567788888888  5559999999999999999999999999999999999999999999999976554

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

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

Probab=98.09  E-value=1.2e-05  Score=55.51  Aligned_cols=62  Identities=18%  Similarity=0.230  Sum_probs=52.5

Q ss_pred             HHHHHHhhhC-CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           43 NVGRIMKQIL-PPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        43 ~V~RI~K~~l-p~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      +|.+|+.+.. +.++.+++.+..+|.+.+-.++..++.+---.|+|+||+||+.+||+...++
T Consensus        10 ~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rr   72 (76)
T PF15630_consen   10 TVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARR   72 (76)
T ss_dssp             HHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT
T ss_pred             HHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhc
Confidence            5778888874 5578999999999999999999999999999999999999999999977653

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

Probab=98.01  E-value=1.6e-05  Score=57.87  Aligned_cols=79  Identities=14%  Similarity=0.261  Sum_probs=68.7

Q ss_pred             ccCchhHHHHHHhhhCCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHHHHH
Q 038014           37 RLLPIANVGRIMKQILPPN-AKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLK  115 (140)
Q Consensus        37 ~~LP~A~V~RI~K~~lp~~-~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~~l~  115 (140)
                      ..+|.|.|+|||...  .+ .+|+.-......++.+.|+..|.....+.|+..+-|.|+.+++..|.+.-+=.+|...+.
T Consensus        22 trFP~ar~KkIMQ~d--eDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~~   99 (113)
T COG5247          22 TRFPIARLKKIMQLD--EDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNME   99 (113)
T ss_pred             hcCCHHHHHHHHHhh--hhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHHH
Confidence            469999999999988  44 489999999999999999999999999999999999999999999998765555655544


Q ss_pred             HH
Q 038014          116 RY  117 (140)
Q Consensus       116 ~~  117 (140)
                      .+
T Consensus       100 ~~  101 (113)
T COG5247         100 QF  101 (113)
T ss_pred             Hh
Confidence            43

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

Probab=97.98  E-value=5.4e-05  Score=51.26  Aligned_cols=65  Identities=20%  Similarity=0.265  Sum_probs=57.0

Q ss_pred             hHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014           42 ANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD  108 (140)
Q Consensus        42 A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~  108 (140)
                      -.|.+|++..  +=-.++..|.+.|...+..|+..|+..+..+|.+.||...+..||..||+++|+.
T Consensus        10 ~~va~il~~~--GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~   74 (77)
T PF07524_consen   10 RSVAQILKHA--GFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS   74 (77)
T ss_pred             HHHHHHHHHc--CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence            3455566665  2237999999999999999999999999999999999999999999999999984

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 [, ].

>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]

Probab=97.91  E-value=2.7e-05  Score=58.13  Aligned_cols=77  Identities=13%  Similarity=0.172  Sum_probs=65.9

Q ss_pred             CCCCCccccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014           26 TDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA  103 (140)
Q Consensus        26 ~~~~~~~~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe  103 (140)
                      -..++......+.+|...|+||||.. ...+||+++|...+.-|.+-.+..+..-|-..|+..|+|.|++.|+..|+.
T Consensus        14 r~~~s~sa~agl~fpvgrvkr~lk~~-~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr   90 (132)
T COG5262          14 RVSQSRSAKAGLIFPVGRVKRLLKKG-NYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR   90 (132)
T ss_pred             hhccchhhhcCccccHHHHHHHHHcC-ccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence            34455555567889999999999954 346899999999999999888888888899999999999999999999986

>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=97.91  E-value=5.8e-05  Score=50.98  Aligned_cols=63  Identities=24%  Similarity=0.325  Sum_probs=51.7

Q ss_pred             hhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           41 IANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        41 ~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      +..+..++++.=| +..+..++.++|.+.+..||..+++.|...|+|.|-.||...||...|++
T Consensus         2 K~~l~~Lv~~iDp-~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler   64 (68)
T PF03847_consen    2 KRKLQELVKQIDP-NEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLER   64 (68)
T ss_dssp             HHHHHHHHHCC-S-S----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH
T ss_pred             hHHHHHHHHHcCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHh
Confidence            4567888999844 78999999999999999999999999999999999999999999999875

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

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

Probab=97.84  E-value=0.00011  Score=51.65  Aligned_cols=66  Identities=15%  Similarity=0.188  Sum_probs=60.9

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC---CccCcccHHHHHHhc
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKR---KTVNGDDICWALATL  105 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kR---KTI~~eDVl~ALe~l  105 (140)
                      .||++.|+|||...++  ..++.+...+|.-.+.+|+-.|...|.++..+.+.   ..|.++||..|...|
T Consensus        16 ~f~k~~iKr~~~~~~~--~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl   84 (85)
T cd08048          16 SFPKAAIKRLIQSVTG--QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL   84 (85)
T ss_pred             hccHHHHHHHHHHHcC--CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence            4999999999999965  78999999999999999999999999999888776   789999999999876

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

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

Probab=97.80  E-value=0.00014  Score=48.92  Aligned_cols=64  Identities=25%  Similarity=0.257  Sum_probs=51.3

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA  103 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe  103 (140)
                      .+|..+|+-+....  +-..++.|+...|.+-++--|..|..+|....+|.+|++++++||-.||+
T Consensus         3 ~~~~esvk~iAes~--Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr   66 (66)
T PF02969_consen    3 VFSQESVKDIAESL--GISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR   66 (66)
T ss_dssp             ---HHHHHHHHHHT--T---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred             cCCHHHHHHHHHHc--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence            47888998888887  44589999999999999999999999999999999999999999999985

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.

>smart00427 H2B Histone H2B

Probab=97.78  E-value=0.00013  Score=51.90  Aligned_cols=62  Identities=24%  Similarity=0.373  Sum_probs=57.6

Q ss_pred             HHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014           43 NVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL  105 (140)
Q Consensus        43 ~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l  105 (140)
                      -|.|++|++-| +..||..+...+.--+..+...|+.+|...+.-.+|+||+..+|..|.+-+
T Consensus         6 Yi~kvLKqVhp-d~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~   67 (89)
T smart00427        6 YIYKVLKQVHP-DTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI   67 (89)
T ss_pred             HHHHHHHHhCC-CccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence            58999999987 679999999999999999999999999999999999999999999998654

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

Probab=97.65  E-value=6.8e-05  Score=51.19  Aligned_cols=65  Identities=18%  Similarity=0.278  Sum_probs=54.2

Q ss_pred             chhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCc-cCcccHHHHHHh
Q 038014           40 PIANVGRIMKQILP-PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKT-VNGDDICWALAT  104 (140)
Q Consensus        40 P~A~V~RI~K~~lp-~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKT-I~~eDVl~ALe~  104 (140)
                      |+.+|.||++.... +..+|++||..++.+-...|+..-...|...++..|..+ |..+|+-+.+-.
T Consensus         1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~pq   67 (72)
T PF09415_consen    1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILPQ   67 (72)
T ss_dssp             -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCHC
T ss_pred             ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence            88999999998774 467999999999999999999999999999999999998 999999876543

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

>PLN00158 histone H2B; Provisional

Probab=97.55  E-value=0.0004  Score=51.51  Aligned_cols=67  Identities=21%  Similarity=0.279  Sum_probs=60.5

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL  105 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l  105 (140)
                      +--..-|.|++|++-| +..||..+...+.-....+..-|+.+|...|.-.+|+||+..+|..|++-+
T Consensus        27 esy~~YI~kVLKQVhP-d~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv   93 (116)
T PLN00158         27 ETYKIYIYKVLKQVHP-DTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI   93 (116)
T ss_pred             ccHHHHHHHHHHHhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence            4455679999999987 678999999999999999999999999999999999999999999998654

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

Probab=97.53  E-value=0.0004  Score=49.36  Aligned_cols=67  Identities=18%  Similarity=0.218  Sum_probs=51.4

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC-ccCcccHHHHHHhc
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRK-TVNGDDICWALATL  105 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRK-TI~~eDVl~ALe~l  105 (140)
                      .||++.|+|||...++ +..|+.....++.-.+..|+-.|...|.+++...+.. .|.+.|+..|.++|
T Consensus        23 ~~~k~~ikkli~~~~~-~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rrL   90 (90)
T PF04719_consen   23 SFNKAAIKKLINQVLG-NQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRRL   90 (90)
T ss_dssp             ---HHHHHHHHHHHHS--S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHcC-CCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHhC
Confidence            5999999999999985 5799999999999999999999999999998866543 79999999998765

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

>PTZ00463 histone H2B; Provisional

Probab=97.50  E-value=0.00051  Score=51.00  Aligned_cols=63  Identities=22%  Similarity=0.379  Sum_probs=57.7

Q ss_pred             hHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014           42 ANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL  105 (140)
Q Consensus        42 A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l  105 (140)
                      .-|.|++|++-| +..||..+...|+-.......-|+.+|...|.-.+|.||+..+|..|++-+
T Consensus        32 ~YI~KVLKqVhP-d~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl   94 (117)
T PTZ00463         32 LYIFKVLKQVHP-DTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV   94 (117)
T ss_pred             HHHHHHHHhhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence            349999999987 678999999999999999999999999999999999999999999998644

>smart00414 H2A Histone 2A

Probab=97.40  E-value=0.00051  Score=50.07  Aligned_cols=69  Identities=10%  Similarity=0.198  Sum_probs=61.3

Q ss_pred             ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           35 QDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        35 ~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      ..+.||.+.|.|+||+.-. ..||+..|...|.-+.|-+...|...|...|...+++.|+++|+..|+..
T Consensus         6 agL~fPVgRi~r~Lk~~~~-~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n   74 (106)
T smart00414        6 AGLQFPVGRIHRLLRKGTY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN   74 (106)
T ss_pred             CCccCchHHHHHHHHcCcc-ccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence            4678999999999998732 45999999999999999888888888999999999999999999999864

>PLN00154 histone H2A; Provisional

Probab=97.28  E-value=0.00074  Score=51.37  Aligned_cols=71  Identities=14%  Similarity=0.171  Sum_probs=61.1

Q ss_pred             cccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           34 EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        34 ~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      -..+.||.++|.|++|+...-..||+..|...|.-..|=+...|...|-..|...+++.|++.||..|+..
T Consensus        34 rAgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn  104 (136)
T PLN00154         34 RAGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG  104 (136)
T ss_pred             ccCccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence            34788999999999999843356999999999998888777777778888899999999999999999853

>PTZ00017 histone H2A; Provisional

Probab=97.11  E-value=0.0011  Score=50.43  Aligned_cols=69  Identities=16%  Similarity=0.192  Sum_probs=61.7

Q ss_pred             cccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014           34 EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA  103 (140)
Q Consensus        34 ~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe  103 (140)
                      -..+.||.+.|.|+||+.-. ..||+..|...|.-+.|-+...|...|...|...+++-|+++||..|+.
T Consensus        23 ragL~FPVgRi~R~Lk~g~~-a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~   91 (134)
T PTZ00017         23 KAGLQFPVGRVHRYLKKGRY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR   91 (134)
T ss_pred             cCCcccchHHHHHHHhccch-hccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence            35788999999999998632 3599999999999999999999999999999999999999999999985

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

Probab=97.01  E-value=0.002  Score=53.54  Aligned_cols=76  Identities=17%  Similarity=0.323  Sum_probs=66.3

Q ss_pred             ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh---cCCchhH
Q 038014           35 QDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT---LGFDNYA  111 (140)
Q Consensus        35 ~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~---lgf~~y~  111 (140)
                      ....|-+-.+.-+++.+- .+..|-+|+.+.|.+.|..||..|+..|...|+|.+..||-+.||...||+   +.|..|.
T Consensus       151 ~~~il~k~kl~dLvqqId-~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm~iPgf~  229 (258)
T KOG1142|consen  151 NNPILSKRKLDDLVQQID-GTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNMEIPGFS  229 (258)
T ss_pred             CCccccccchhHHHHhhc-CcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccccccCCCcc
Confidence            444678888999999993 367899999999999999999999999999999999999999999999996   5555443

>PLN00153 histone H2A; Provisional

Probab=96.93  E-value=0.0034  Score=47.39  Aligned_cols=74  Identities=14%  Similarity=0.155  Sum_probs=63.1

Q ss_pred             CccccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           30 GVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        30 ~~~~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      +-..-..+.||.+.|.|++|+.-. ..||+..|...|.-+.|-....|...|-..|...+++-|+++||..|+..
T Consensus        16 srS~ragL~FpVgRi~R~Lr~g~~-a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n   89 (129)
T PLN00153         16 SRSAKAGLQFPVGRIARYLKKGKY-AERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRN   89 (129)
T ss_pred             CcccccCcccchHHHHHHHhcCch-hhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccC
Confidence            333445789999999999998633 45999999999999988888888888888999999999999999999853

>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=96.92  E-value=0.0041  Score=46.83  Aligned_cols=82  Identities=18%  Similarity=0.223  Sum_probs=48.4

Q ss_pred             cCchh--HHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH-hcCCchhHHHH
Q 038014           38 LLPIA--NVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA-TLGFDNYADQL  114 (140)
Q Consensus        38 ~LP~A--~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe-~lgf~~y~~~l  114 (140)
                      .+|+.  .|.-|+|+.  +-......++..|.+.+-.|+..|..+|..+|.|+||++|+.+||..|++ ++++.-..++-
T Consensus        10 ~~PrDa~~i~~iL~~~--Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~ppp   87 (129)
T PF02291_consen   10 SLPRDARVIHLILKSM--GVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQPPP   87 (129)
T ss_dssp             ---HHHHHHHHHHHHT--T---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT----------
T ss_pred             cCChHHHHHHHHHHHc--CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccCCCC
Confidence            45552  345555665  44468888999999999999999999999999999999999999999999 56777777777


Q ss_pred             HHHHHHH
Q 038014          115 KRYLHRY  121 (140)
Q Consensus       115 ~~~l~~~  121 (140)
                      +++|-+.
T Consensus        88 re~llel   94 (129)
T PF02291_consen   88 REFLLEL   94 (129)
T ss_dssp             -------
T ss_pred             hHHHHHH
Confidence            7776544

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

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

Probab=96.92  E-value=0.0024  Score=48.21  Aligned_cols=71  Identities=8%  Similarity=0.173  Sum_probs=57.8

Q ss_pred             cccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014           32 IKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA  103 (140)
Q Consensus        32 ~~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe  103 (140)
                      ..-..+.+|...|.|++|+. ....||+.+|...+.-+.+-....+...|-..++..++..|++.||..|+.
T Consensus        21 s~~agl~fPvgri~r~Lr~~-~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~   91 (131)
T KOG1756|consen   21 SSRAGLQFPVGRIHRLLRKG-RYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR   91 (131)
T ss_pred             hhhcccccCHHHHHHHHHcc-chhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence            34467789999999999994 235799999999999776666666666666677888999999999999986

>PLN00156 histone H2AX; Provisional

Probab=96.92  E-value=0.0036  Score=47.84  Aligned_cols=70  Identities=13%  Similarity=0.172  Sum_probs=60.3

Q ss_pred             ccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014           33 KEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA  103 (140)
Q Consensus        33 ~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe  103 (140)
                      .-..+.||.++|.|++|+.-- ..||+..|...|.-+.|=....|...|-..|...+++.|+++||..|+.
T Consensus        24 ~rAgL~FPVgRi~R~Lk~g~y-a~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr   93 (139)
T PLN00156         24 SKAGLQFPVGRIARFLKAGKY-AERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR   93 (139)
T ss_pred             cccCcccchHHHHHHHhcCCh-hhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence            345788999999999998732 3599999999999988877777888888888999999999999999985

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

Probab=96.86  E-value=0.00069  Score=52.62  Aligned_cols=69  Identities=23%  Similarity=0.302  Sum_probs=60.7

Q ss_pred             ccccCchhHHHHHHhhhCCCCcc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014           35 QDRLLPIANVGRIMKQILPPNAK-ISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL  105 (140)
Q Consensus        35 ~d~~LP~A~V~RI~K~~lp~~~r-IskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l  105 (140)
                      .-..||.++|+.+||..  ++++ ...+++.++.++++.||..|...+...+...+|||+.-.|+-.|++.-
T Consensus        56 ~l~rLpL~rik~vvkl~--pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~  125 (162)
T KOG1658|consen   56 SLSRLPLARIKQVVKLD--PDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAV  125 (162)
T ss_pred             hhhhccHHHHHhhccCC--cchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccch
Confidence            34579999999999977  6776 667889999999999999999999999999999999999888877653

>PLN00157 histone H2A; Provisional

Probab=96.79  E-value=0.0026  Score=48.17  Aligned_cols=71  Identities=13%  Similarity=0.159  Sum_probs=61.6

Q ss_pred             ccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           33 KEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        33 ~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      .-..+.||...|.|++|+.-- ..||+..|...|.-+.|-....|...|-..|...+++-|+++||..|+..
T Consensus        21 ~ragL~FPVgRi~R~Lk~g~~-a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n   91 (132)
T PLN00157         21 AKAGLQFPVGRIARYLKAGKY-ATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRN   91 (132)
T ss_pred             cccCcccchHHHHHHHhcCch-hhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccC
Confidence            345789999999999999632 46999999999999888888888888888999999999999999999853

>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=96.76  E-value=0.0018  Score=45.85  Aligned_cols=60  Identities=17%  Similarity=0.261  Sum_probs=29.4

Q ss_pred             HHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           44 VGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        44 V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      |..+|-.- ++...-..|++.+|-+.+..||..+...|..+|...|+++|+.+|++-+|+.
T Consensus         7 I~~mMy~f-GD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~   66 (93)
T PF02269_consen    7 IRQMMYGF-GDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK   66 (93)
T ss_dssp             CHHHHHCT-TS-SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred             HHHHHHHc-CCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence            34445444 3445788999999999999999999999999999999999999999999985

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

>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]

Probab=96.44  E-value=0.013  Score=44.24  Aligned_cols=63  Identities=29%  Similarity=0.380  Sum_probs=56.9

Q ss_pred             hHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014           42 ANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL  105 (140)
Q Consensus        42 A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l  105 (140)
                      ..|.|++|++-|+ .-|+..+...+.--.-.++..|+.+|...+.-.||.||+..++..|++-+
T Consensus        41 ~yv~kvlk~Vhpd-~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl  103 (127)
T KOG1744|consen   41 EYVYKVLKQVHPD-LGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL  103 (127)
T ss_pred             eehhhhhhcccCC-CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence            3477799999885 77999999999999999999999999999999999999999999988643

>PF15510 CENP-W: Centromere kinetochore component W

Probab=96.43  E-value=0.0056  Score=43.99  Aligned_cols=66  Identities=15%  Similarity=0.190  Sum_probs=54.1

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKET--------------MQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA  103 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~a--------------l~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe  103 (140)
                      .-|++.++|++|..-| ..|+....-.+              +.--|-.|++-|+.+|...|-.++-.||..+||+.|-+
T Consensus        16 kaPrgfLkrv~Kr~Kp-hlRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaK   94 (102)
T PF15510_consen   16 KAPRGFLKRVFKRQKP-HLRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAAAK   94 (102)
T ss_pred             hCchHHHHHHHHhcCC-ceeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHH
Confidence            5799999999998755 56655544444              55668899999999999999999999999999998865


Q ss_pred             h
Q 038014          104 T  104 (140)
Q Consensus       104 ~  104 (140)
                      .
T Consensus        95 v   95 (102)
T PF15510_consen   95 V   95 (102)
T ss_pred             H
Confidence            3

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

Probab=96.39  E-value=0.0039  Score=50.00  Aligned_cols=70  Identities=20%  Similarity=0.220  Sum_probs=61.2

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC-ccCcccHHHHHHhcCCch
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRK-TVNGDDICWALATLGFDN  109 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRK-TI~~eDVl~ALe~lgf~~  109 (140)
                      .||++.|+|||....+.  .|+.-+..++.-.+.+|+-.|..+|.++|..-+.. .|.+.||-.|..+|+...
T Consensus       112 ~f~Ka~iKkL~~~itg~--~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~qg  182 (195)
T KOG3219|consen  112 AFPKAQIKKLMSSITGQ--SVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQG  182 (195)
T ss_pred             cCCHHHHHHHHHHHhCC--ccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhcC
Confidence            59999999999999653  39999999999999999999999999999877753 599999999998876543

>PTZ00252 histone H2A; Provisional

Probab=95.85  E-value=0.026  Score=42.92  Aligned_cols=69  Identities=12%  Similarity=0.198  Sum_probs=52.8

Q ss_pred             cccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh--CCCCccCcccHHHHHH
Q 038014           34 EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHK--EKRKTVNGDDICWALA  103 (140)
Q Consensus        34 ~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~--~kRKTI~~eDVl~ALe  103 (140)
                      -..+.||.+.|.|++|+.-- ..||+..|...|.-+.|=....|...|...|..  .+++-|+++||..|+.
T Consensus        21 rAGL~FPVgRi~R~Lr~g~y-a~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr   91 (134)
T PTZ00252         21 KAGLIFPVGRVGSLLRRGQY-ARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR   91 (134)
T ss_pred             ccCccCchHHHHHHHHcCCc-ccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence            35789999999999998743 459999999888876655555555555555543  5678899999999985

>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=95.55  E-value=0.28  Score=34.77  Aligned_cols=60  Identities=17%  Similarity=0.276  Sum_probs=48.5

Q ss_pred             HHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           43 NVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        43 ~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      -|+.+|-.- ++.-.-..|.+.+|-+.+..||..++..|.+.|. .+|.-++.+|++-+|+.
T Consensus         7 ei~~mmy~~-GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~   66 (92)
T cd07978           7 EIRQMMYGF-GDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRK   66 (92)
T ss_pred             HHHHHHHHc-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhc
Confidence            466666665 3334678899999999999999999999999998 44445699999999964

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

>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=95.15  E-value=0.11  Score=40.93  Aligned_cols=69  Identities=19%  Similarity=0.246  Sum_probs=57.0

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC--------------CCccCcccHHHHHH
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEK--------------RKTVNGDDICWALA  103 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~k--------------RKTI~~eDVl~ALe  103 (140)
                      .||-+.+.-.++.+  +-.....-.+-+|+-++..||..|+..|.+.|+-.+              |-|++-+|+-.||+
T Consensus        86 ~IPDavt~~yL~~a--Gf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL~  163 (176)
T KOG3423|consen   86 TIPDAVTDHYLKKA--GFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPALA  163 (176)
T ss_pred             CCcHHHHHHHHHhc--CCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHHH
Confidence            48888888888888  333455667788999999999999999999997443              55899999999999


Q ss_pred             hcCCc
Q 038014          104 TLGFD  108 (140)
Q Consensus       104 ~lgf~  108 (140)
                      +-|..
T Consensus       164 EyGin  168 (176)
T KOG3423|consen  164 EYGIN  168 (176)
T ss_pred             HhCcc
Confidence            98875

>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]

Probab=94.57  E-value=0.23  Score=42.58  Aligned_cols=75  Identities=20%  Similarity=0.298  Sum_probs=62.4

Q ss_pred             HHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHHHHHHHHHHH
Q 038014           43 NVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRY  121 (140)
Q Consensus        43 ~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~~l~~~l~~~  121 (140)
                      .|.-|.+..  +=--|++-|++.|.+....+|..++..+.-+|.++||...+..||...|-+||+.  ++.|..+++.+
T Consensus        10 VV~~Ll~~~--gfd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~~   84 (323)
T KOG4336|consen   10 VVSNLLKTK--GFDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQKQ   84 (323)
T ss_pred             HHHHHHHHh--CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHhc
Confidence            444455555  2235999999999999999999999999999999999999999999999999998  56666666544

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

Probab=94.50  E-value=0.15  Score=46.64  Aligned_cols=66  Identities=23%  Similarity=0.267  Sum_probs=58.0

Q ss_pred             chhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCC
Q 038014           40 PIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGF  107 (140)
Q Consensus        40 P~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf  107 (140)
                      |.-.++-+++..  +-..|+.|+..+|.+-++.=|..++.+|.+.-.|.+|.+++.+||..||+-+..
T Consensus        13 ~~Es~k~vAEsl--Gi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nV   78 (576)
T KOG2549|consen   13 PKESVKVVAESL--GITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNV   78 (576)
T ss_pred             cHHHHHHHHHHh--CccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhccc
Confidence            466777777766  456799999999999999999999999999999999999999999999996543

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

Probab=92.20  E-value=0.72  Score=35.62  Aligned_cols=74  Identities=14%  Similarity=0.229  Sum_probs=55.6

Q ss_pred             HHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHH-HHHHHHH
Q 038014           44 VGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYAD-QLKRYLH  119 (140)
Q Consensus        44 V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~-~l~~~l~  119 (140)
                      |.-|+|+.  +---...-...-|.+.+-.++..|...|.-++.|+++.||.++||..|++-..-..|.+ +=+++|-
T Consensus        19 i~~iL~s~--GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~pPpRe~lL   93 (148)
T KOG3334|consen   19 IASILKSL--GIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTPPPPREFLL   93 (148)
T ss_pred             HHHHHHHc--CccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCCCCchHHHH
Confidence            34444444  22245666777788889999999999999999999999999999999999766666655 4444443

>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]

Probab=89.91  E-value=0.88  Score=39.58  Aligned_cols=69  Identities=20%  Similarity=0.225  Sum_probs=59.9

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD  108 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~  108 (140)
                      .|-+..|..|+...  +--....-|...|+.-+..||..|+..|..++...||.-.+..||+.||+.|+..
T Consensus        29 sla~~avaQIcqsl--g~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s   97 (353)
T KOG2389|consen   29 SLARVAVAQICQSL--GYSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSAS   97 (353)
T ss_pred             HHHHHHHHHHHHhc--CCcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhh
Confidence            46777888888887  3335666699999999999999999999999999999999999999999987654

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=89.62  E-value=1.3  Score=35.10  Aligned_cols=69  Identities=13%  Similarity=0.241  Sum_probs=54.3

Q ss_pred             CchhHHHHHHhhhCC-----CCccccHHHHHHHHHHHHH---HHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCC
Q 038014           39 LPIANVGRIMKQILP-----PNAKISKEAKETMQECVSE---FISFVTGEASDKCHKEKRKTVNGDDICWALATLGF  107 (140)
Q Consensus        39 LP~A~V~RI~K~~lp-----~~~rIskdA~~al~~aa~~---Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf  107 (140)
                      |....+..++...+.     ....++.++...|.+.+.=   .|..++..+...+-..+.++|+.++|..++.++.|
T Consensus       192 l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~~  268 (269)
T TIGR03015       192 LDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEIDF  268 (269)
T ss_pred             CCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhhc
Confidence            444556666554431     2346999999999988774   79999999999988899999999999999998864

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=89.18  E-value=1.7  Score=36.50  Aligned_cols=70  Identities=11%  Similarity=0.106  Sum_probs=51.5

Q ss_pred             hhHHHHHHhhhCCC---CccccHHHHHHHHHHH------HHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchh
Q 038014           41 IANVGRIMKQILPP---NAKISKEAKETMQECV------SEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNY  110 (140)
Q Consensus        41 ~A~V~RI~K~~lp~---~~rIskdA~~al~~aa------~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y  110 (140)
                      ...+..|++..+..   ...++.++.+.+.+.+      -..+..+...|...|...++.+|+.+||..|++++....+
T Consensus       209 ~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~~~  287 (394)
T PRK00411        209 ADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVHL  287 (394)
T ss_pred             HHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHH
Confidence            45566666654421   2358899988888777      3455667788888999999999999999999998854443

>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=85.78  E-value=3.2  Score=36.35  Aligned_cols=66  Identities=23%  Similarity=0.248  Sum_probs=56.4

Q ss_pred             hhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014           41 IANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD  108 (140)
Q Consensus        41 ~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~  108 (140)
                      +.+|+-++..-  +-..|..|+..+|..-.+--|+.+..+|...-.|.+|..++-+||-.||+.++.+
T Consensus         8 ~et~KdvAesl--Gi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVe   73 (450)
T COG5095           8 KETLKDVAESL--GISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVE   73 (450)
T ss_pred             HHHHHHHHHHc--CCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCC
Confidence            44555555544  3457999999999999999999999999999999999999999999999987654

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=85.60  E-value=4  Score=33.84  Aligned_cols=75  Identities=9%  Similarity=0.061  Sum_probs=51.2

Q ss_pred             hhHHHHHHhhhCC---CCccccHHHHHHHHHHHH------HHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhH
Q 038014           41 IANVGRIMKQILP---PNAKISKEAKETMQECVS------EFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYA  111 (140)
Q Consensus        41 ~A~V~RI~K~~lp---~~~rIskdA~~al~~aa~------~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~  111 (140)
                      ...+..|++..+.   ....++.++...+.+.+.      ..+..+...|...|...++.+|+.+||..|+..+....+.
T Consensus       201 ~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~~~~~~  280 (365)
T TIGR02928       201 AEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIEKDRLL  280 (365)
T ss_pred             HHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHH
Confidence            3446667765542   123588888777665442      3455566678888888899999999999999988655554


Q ss_pred             HHHH
Q 038014          112 DQLK  115 (140)
Q Consensus       112 ~~l~  115 (140)
                      ..+.
T Consensus       281 ~~i~  284 (365)
T TIGR02928       281 ELIR  284 (365)
T ss_pred             HHHH
Confidence            4333

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors

Probab=85.24  E-value=6  Score=25.37  Aligned_cols=48  Identities=15%  Similarity=0.188  Sum_probs=37.3

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHK   87 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~   87 (140)
                      .+|-+.+.-+++.+  +--.-..-..-+++-++..||..++..|.++|+-
T Consensus         2 ~IPD~v~~~yL~~~--G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~   49 (51)
T PF03540_consen    2 TIPDEVTDYYLERS--GFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI   49 (51)
T ss_pred             CCCHHHHHHHHHHC--CCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            47888888999888  2222334456688889999999999999999874

The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus

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

Probab=84.67  E-value=1.4  Score=32.97  Aligned_cols=67  Identities=13%  Similarity=0.243  Sum_probs=51.0

Q ss_pred             ccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhC----CCCccCcccHHHHHH
Q 038014           33 KEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKE----KRKTVNGDDICWALA  103 (140)
Q Consensus        33 ~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~----kRKTI~~eDVl~ALe  103 (140)
                      ....+.||..+|.|.+|.......|+..-+....    ...+.||+.+-.+.|..+    +-|.|++.|+..|++
T Consensus        25 ~raGlqFpVgRihr~LK~r~t~h~rVGataavy~----aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR   95 (131)
T KOG1757|consen   25 ARAGLQFPVGRIHRHLKTRTTSHGRVGATAAVYS----AAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR   95 (131)
T ss_pred             HhcccccchHHHHHHHHHhcccccccchHHHHHH----HHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence            3456789999999999999777778876665433    335678888888877554    457899999988875

>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

Probab=83.96  E-value=11  Score=29.95  Aligned_cols=78  Identities=8%  Similarity=0.095  Sum_probs=58.9

Q ss_pred             ccccCchhHHHHHHhhhCCC-Cc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhC------CCCccCcccHHHHHHhcC
Q 038014           35 QDRLLPIANVGRIMKQILPP-NA-KISKEAKETMQECVSEFISFVTGEASDKCHKE------KRKTVNGDDICWALATLG  106 (140)
Q Consensus        35 ~d~~LP~A~V~RI~K~~lp~-~~-rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~------kRKTI~~eDVl~ALe~lg  106 (140)
                      ....|....+.+.|...+.. +. .|+.|.+.+|+.||+.++..|.......|+|-      ..+++...||..-|..|+
T Consensus        41 ~~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l~  120 (212)
T cd08045          41 DPSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFLE  120 (212)
T ss_pred             hhhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHHH
Confidence            44567777777777666532 22 79999999999999999999999999999865      446677889988777665


Q ss_pred             CchhHH
Q 038014          107 FDNYAD  112 (140)
Q Consensus       107 f~~y~~  112 (140)
                      --+-..
T Consensus       121 ~~ek~e  126 (212)
T cd08045         121 QLEREE  126 (212)
T ss_pred             HHHHHH
Confidence            444333

The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) 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 eukaryote. 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 hypotheses are

>PF13654 AAA_32: AAA domain; PDB: 3K1J_B

Probab=83.16  E-value=5.5  Score=36.09  Aligned_cols=60  Identities=15%  Similarity=0.176  Sum_probs=41.5

Q ss_pred             HHHHHhhhCCCCccccHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014           44 VGRIMKQILPPNAKISKEAKETMQECVSE-----------FISFVTGEASDKCHKEKRKTVNGDDICWALATL  105 (140)
Q Consensus        44 V~RI~K~~lp~~~rIskdA~~al~~aa~~-----------Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l  105 (140)
                      |.+++++.  +-..++.+|+..|-+.+..           -|..|..+|+.+|...+++.|+++||..|++.-
T Consensus       436 i~~~~~~~--~L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r  506 (509)
T PF13654_consen  436 IASICQKE--GLPPFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEER  506 (509)
T ss_dssp             HHHHHHHH--SS--BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred             HHHHHHhC--CCCCCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence            44444444  2225777777777766543           567788899999999999999999999999864

>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]

Probab=81.77  E-value=9.6  Score=30.32  Aligned_cols=68  Identities=15%  Similarity=0.189  Sum_probs=48.7

Q ss_pred             CchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh-------------------------------
Q 038014           39 LPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHK-------------------------------   87 (140)
Q Consensus        39 LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~-------------------------------   87 (140)
                      ||-+.+.=.+-.+  +-.....-.+.+|.-.+..||..|+-.|.++.+-                               
T Consensus        89 iPd~v~DYyl~k~--Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~~~~~~  166 (197)
T COG5162          89 IPDSVTDYYLEKA--GFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIGSSGRR  166 (197)
T ss_pred             ccHHHHHHHHHhc--CceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhcccccccccccc
Confidence            4555554444444  2234556677888999999999999999887641                               


Q ss_pred             --CCCCccCcccHHHHHHhcCCc
Q 038014           88 --EKRKTVNGDDICWALATLGFD  108 (140)
Q Consensus        88 --~kRKTI~~eDVl~ALe~lgf~  108 (140)
                        .++.+++..|+-.||++.|+.
T Consensus       167 ~dr~K~vltv~DLs~Al~EyGin  189 (197)
T COG5162         167 GDRKKPVLTVVDLSKALEEYGIN  189 (197)
T ss_pred             cccCCceeeehHHHHHHHHhccc
Confidence              145678999999999998764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	140
4g91_B	92	Ccaat-Binding Complex From Aspergillus Nidulans Len		6e-36
4awl_B	94	The Nf-y Transcription Factor Is Structurally And F		3e-32
1n1j_A	93	Crystal Structure Of The Nf-YbNF-Yc Histone Pair Le		4e-32
1jfi_B	179	Crystal Structure Of The Nc2-Tbp-Dna Ternary Comple		2e-12
2byk_B	128	Histone Fold Heterodimer Of The Chromatin Accessibi		8e-11

>pdb|4G91|B Chain B, Ccaat-Binding Complex From Aspergillus Nidulans Length = 92

Iteration: 1
 Score =  145 bits (367), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 67/92 (72%), Positives = 79/92 (85%)
Query: 32  IKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRK 91
           +KEQDR LPIANV RIMK  LP NAKI+KEAKE MQECVSEFISF+T EAS+KC +EKRK
Sbjct: 1   MKEQDRWLPIANVARIMKLALPENAKIAKEAKECMQECVSEFISFITSEASEKCQQEKRK 60
Query: 92  TVNGDDICWALATLGFDNYADQLKRYLHRYRE 123
           TVNG+DI +A+ +LGF+NYA+ LK YL +YRE
Sbjct: 61  TVNGEDILFAMTSLGFENYAEALKIYLSKYRE 92

>pdb|4AWL|B Chain B, The Nf-y Transcription Factor Is Structurally And Functionally A Sequence Specific Histone Length = 94

Iteration: 1
 Score =  133 bits (334), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 58/92 (63%), Positives = 76/92 (82%)
Query: 32  IKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRK 91
            +EQD  LPIANV RIMK  +P   KI+K+AKE +QECVSEFISF+T EAS++CH+EKRK
Sbjct: 3   FREQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRK 62
Query: 92  TVNGDDICWALATLGFDNYADQLKRYLHRYRE 123
           T+NG+DI +A++TLGFD+Y + LK YL ++RE
Sbjct: 63  TINGEDILFAMSTLGFDSYVEPLKLYLQKFRE 94

>pdb|1N1J|A Chain A, Crystal Structure Of The Nf-YbNF-Yc Histone Pair Length = 93

Iteration: 1
 Score =  133 bits (334), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 58/92 (63%), Positives = 76/92 (82%)
Query: 32  IKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRK 91
            +EQD  LPIANV RIMK  +P   KI+K+AKE +QECVSEFISF+T EAS++CH+EKRK
Sbjct: 2   FREQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRK 61
Query: 92  TVNGDDICWALATLGFDNYADQLKRYLHRYRE 123
           T+NG+DI +A++TLGFD+Y + LK YL ++RE
Sbjct: 62  TINGEDILFAMSTLGFDSYVEPLKLYLQKFRE 93

>pdb|1JFI|B Chain B, Crystal Structure Of The Nc2-Tbp-Dna Ternary Complex Length = 179

Iteration: 1
 Score = 67.4 bits (163), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 33/109 (30%), Positives = 65/109 (59%), Gaps = 8/109 (7%)
Query: 20  VGASSGTDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTG 79
           + +SSG D D  I       P A + +++K+ LP N +++ +A+E +  C +EFI  ++ 
Sbjct: 4   MASSSGNDDDLTI-------PRAAINKMIKETLP-NVRVANDARELVVNCCTEFIHLISS 55
Query: 80  EASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRELEGER 128
           EA++ C+K ++KT++ + +  AL +LGF +Y  ++K  L   + +  +R
Sbjct: 56  EANEICNKSEKKTISPEHVIQALESLGFGSYISEVKEVLQECKTVALKR 104

>pdb|2BYK|B Chain B, Histone Fold Heterodimer Of The Chromatin Accessibility Complex Length = 128

Iteration: 1
 Score = 62.4 bits (150), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 32/88 (36%), Positives = 49/88 (55%)
Query: 35  QDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVN 94
           +D  LP A +GR++K+ LP +A +SKEA+  +    S F  FVT  ++   HK+  KT+ 
Sbjct: 6   EDLNLPNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTIT 65
Query: 95  GDDICWALATLGFDNYADQLKRYLHRYR 122
             DI   L  L F+++   L + L  YR
Sbjct: 66  AKDILQTLTELDFESFVPSLTQDLEVYR 93

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	140
2byk_B	128	Chrac-14; nucleosome sliding, histone fold, DNA-bi	1e-47
1n1j_A	93	NF-YB; histone-like PAIR, DNA binding protein; 1.6	5e-47
1jfi_B	179	DR1 protein, transcription regulator NC2 beta chai	5e-42
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	1e-25
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	5e-24
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	2e-12
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	7e-11
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	7e-07
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	3e-05
2yfw_B	103	Histone H4, H4; cell cycle, kinetochore, centromer	3e-04

>2byk_B Chrac-14; nucleosome sliding, histone fold, DNA-binding protein; 2.4A {Drosophila melanogaster} SCOP: a.22.1.3 PDB: 2bym_B Length = 128

 Score =  148 bits (376), Expect = 1e-47
 Identities = 35/110 (31%), Positives = 59/110 (53%)

Query: 31  VIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKR 90
           V + +D  LP A +GR++K+ LP +A +SKEA+  +    S F  FVT  ++   HK+  
Sbjct: 2   VERIEDLNLPNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNH 61

Query: 91  KTVNGDDICWALATLGFDNYADQLKRYLHRYRELEGERANQNKAGNNNNG 140
           KT+   DI   L  L F+++   L + L  YR++  E+     +  ++N 
Sbjct: 62  KTITAKDILQTLTELDFESFVPSLTQDLEVYRKVVKEKKESKASKKDSNT 111

>1n1j_A NF-YB; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3 Length = 93

 Score =  146 bits (369), Expect = 5e-47
 Identities = 58/91 (63%), Positives = 76/91 (83%)

Query: 33  KEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKT 92
           +EQD  LPIANV RIMK  +P   KI+K+AKE +QECVSEFISF+T EAS++CH+EKRKT
Sbjct: 3   REQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKT 62

Query: 93  VNGDDICWALATLGFDNYADQLKRYLHRYRE 123
           +NG+DI +A++TLGFD+Y + LK YL ++RE
Sbjct: 63  INGEDILFAMSTLGFDSYVEPLKLYLQKFRE 93

>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 Length = 179

 Score =  136 bits (343), Expect = 5e-42
 Identities = 29/107 (27%), Positives = 62/107 (57%), Gaps = 1/107 (0%)

Query: 33  KEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKT 92
            + D  +P A + +++K+ LP N +++ +A+E +  C +EFI  ++ EA++ C+K ++KT
Sbjct: 10  NDDDLTIPRAAINKMIKETLP-NVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKT 68

Query: 93  VNGDDICWALATLGFDNYADQLKRYLHRYRELEGERANQNKAGNNNN 139
           ++ + +  AL +LGF +Y  ++K  L   + +  +R   +    N  
Sbjct: 69  ISPEHVIQALESLGFGSYISEVKEVLQECKTVALKRRKASSRLENLG 115

>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 Length = 68

 Score = 91.2 bits (227), Expect = 1e-25
 Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 2/67 (2%)

Query: 39  LPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDI 98
           LPIA +GRI+K       ++S +A+  + + + E    +  EA        RKT+  +DI
Sbjct: 3   LPIAPIGRIIKNAGAE--RVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDI 60

Query: 99  CWALATL 105
             A    
Sbjct: 61  ELARKMF 67

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

 Score = 87.1 bits (216), Expect = 5e-24
 Identities = 18/66 (27%), Positives = 36/66 (54%), Gaps = 2/66 (3%)

Query: 39  LPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDI 98
           LPIA V R++++      ++S++A + + E + E+   +  +A +      RKTV  +DI
Sbjct: 7   LPIAPVDRLIRKAGAE--RVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDI 64

Query: 99  CWALAT 104
             A+ +
Sbjct: 65  KLAIKS 70

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

 Score = 58.4 bits (141), Expect = 2e-12
 Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 1/71 (1%)

Query: 34  EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTV 93
            + + LP+A + +IMK        IS EA     +    FI+ +T  A       KR+T+
Sbjct: 15  FRVQELPLARIKKIMKLD-EDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTL 73

Query: 94  NGDDICWALAT 104
             +DI  A+  
Sbjct: 74  QRNDIAMAITK 84

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

 Score = 55.5 bits (133), Expect = 7e-11
 Identities = 19/125 (15%), Positives = 46/125 (36%), Gaps = 5/125 (4%)

Query: 20  VGASSGTDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTG 79
           +G              +  LP++ V  IMK        I+ E    M +C   F+  + G
Sbjct: 1   MGEPRSQPPVERPPTAETFLPLSRVRTIMKS-SMDTGLITNEVLFLMTKCTELFVRHLAG 59

Query: 80  EA-SDKCHKEKRKTVNGDDICWALA---TLGFDNYADQLKRYLHRYRELEGERANQNKAG 135
            A +++  +   + +  + +   +     L F       K  +H+++E+     +     
Sbjct: 60  AAYTEEFGQRPGEALKYEHLSQVVNKNKNLEFLLQIVPQKIRVHQFQEMLRLNRSAGSDD 119

Query: 136 NNNNG 140
           ++++ 
Sbjct: 120 DDDDD 124

>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 Length = 111

 Score = 44.2 bits (104), Expect = 7e-07
 Identities = 14/102 (13%), Positives = 36/102 (35%), Gaps = 4/102 (3%)

Query: 39  LPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDI 98
           +  + + +I    +     ++++A + +++C   +   ++ +         RKTV   D+
Sbjct: 8   IASSLIKQIFSHYV--KTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAGRKTVEMADV 65

Query: 99  CWALATLGFDNYADQLKRYLHRY--RELEGERANQNKAGNNN 138
              +   G       L   + R+   E          +GN  
Sbjct: 66  ELLMRRQGLVTDKMPLHVLVERHLPLEYRKLLIPIAVSGNKV 107

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

 Score = 39.5 bits (92), Expect = 3e-05
 Identities = 10/72 (13%), Positives = 25/72 (34%), Gaps = 1/72 (1%)

Query: 33  KEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKT 92
           K+ +   P A + +IM+       K++      +   +  F+  +  +A         KT
Sbjct: 6   KKYNARFPPARIKKIMQTD-EEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKT 64

Query: 93  VNGDDICWALAT 104
           +    +   +  
Sbjct: 65  MTTSHLKQCIEL 76

>2yfw_B Histone H4, H4; cell cycle, kinetochore, centromere, histone chaperone, BUDD; 2.60A {Kluyveromyces lactis nrrl y-1140} Length = 103

 Score = 36.9 bits (85), Expect = 3e-04
 Identities = 15/50 (30%), Positives = 23/50 (46%)

Query: 57  KISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLG 106
           +IS    E ++  +  F+  V  +A       KRKTV   D+ +AL   G
Sbjct: 46  RISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQG 95

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	140
1jfi_B	179	DR1 protein, transcription regulator NC2 beta chai	99.96
2byk_B	128	Chrac-14; nucleosome sliding, histone fold, DNA-bi	99.96
1n1j_A	93	NF-YB; histone-like PAIR, DNA binding protein; 1.6	99.96
3b0c_W	76	CENP-W, centromere protein W; histone fold, DNA bi	99.84
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	99.82
1b67_A	68	Protein (histone HMFA); DNA binding protein; 1.48A	99.8
3b0c_T	111	CENP-T, centromere protein T; histone fold, DNA bi	99.8
2byk_A	140	Chrac-16; nucleosome sliding, histone fold, DNA-bi	99.71
1f1e_A	154	Histone fold protein; archaeal histone protein, DN	99.71
2hue_C	84	Histone H4; mini beta sheet, elongated beta sandwh	99.7
1id3_B	102	Histone H4; nucleosome core particle, chromatin, p	99.69
1ku5_A	70	HPHA, archaeal histon; histone fold, DNA binding p	99.67
1n1j_B	97	NF-YC; histone-like PAIR, DNA binding protein; 1.6	99.66
4g92_C	119	HAPE; transcription factor, nucleosome, minor groo	99.65
1tzy_D	103	Histone H4-VI; histone-fold, tetramer-dimer-dimer,	99.64
2yfw_B	103	Histone H4, H4; cell cycle, kinetochore, centromer	99.62
1jfi_A	98	Transcription regulator NC2 alpha chain; histone,	99.44
2hue_B	77	Histone H3; mini beta sheet, elongated beta sandwh	99.44
2yfv_A	100	Histone H3-like centromeric protein CSE4; cell cyc	99.35
3nqj_A	82	Histone H3-like centromeric protein A; alpha helix	99.33
1tzy_C	136	Histone H3; histone-fold, tetramer-dimer-dimer, DN	99.28
3r45_A	156	Histone H3-like centromeric protein A; histone fol	99.26
3nqu_A	140	Histone H3-like centromeric protein A; alpha helix	99.26
1taf_B	70	TFIID TBP associated factor 62; transcription init	99.08
2ly8_A	121	Budding yeast chaperone SCM3; centromere protein,	99.07
3vh5_A	140	CENP-S; histone fold, chromosome segregation, DNA	99.0
4dra_A	113	Centromere protein S; DNA binding complex, DNA dam	98.92
3v9r_A	90	MHF1, uncharacterized protein YOL086W-A; histone f	98.9
3b0b_B	107	CENP-S, centromere protein S; histone fold, DNA bi	98.9
1taf_A	68	TFIID TBP associated factor 42; transcription init	98.86
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	98.77
2nqb_C	123	Histone H2A; nucleosome, NCP, chromatin, structura	98.64
2l5a_A	235	Histone H3-like centromeric protein CSE4, protein	98.63
2f8n_G	120	Core histone macro-H2A.1; nucleosome, NCP, macroh2	98.62
1tzy_A	129	Histone H2A-IV; histone-fold, tetramer-dimer-dimer	98.62
1id3_C	131	Histone H2A.1; nucleosome core particle, chromatin	98.6
1f66_C	128	Histone H2A.Z; nucleosome, chromatin, histone vari	98.6
2f8n_K	149	Histone H2A type 1; nucleosome, NCP, macroh2A, his	98.53
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	98.39
2nqb_D	123	Histone H2B; nucleosome, NCP, chromatin, structura	98.3
1tzy_B	126	Histone H2B; histone-fold, tetramer-dimer-dimer, D	98.27
4dra_E	84	Centromere protein X; DNA binding complex, DNA dam	98.14
1h3o_B	76	Transcription initiation factor TFIID 20/15 kDa su	98.03
3b0b_C	81	CENP-X, centromere protein X; histone fold, DNA bi	98.01
2jss_A	192	Chimera of histone H2B.1 and histone H2A.Z; histon	97.94
1bh9_B	89	TAFII28; histone fold, tata binding protein, trans	97.69
3v9r_B	88	MHF2, uncharacterized protein YDL160C-A; histone f	96.79
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	91.65
3ksy_A	1049	SOS-1, SON of sevenless homolog 1; RAS, RAS activa	90.46
1r4v_A	171	Hypothetical protein AQ_328; structural genomics,	90.29
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	85.88
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	84.71
1wwi_A	148	Hypothetical protein TTHA1479; structural genomics	84.08
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	82.18
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	80.73
3kw6_A	78	26S protease regulatory subunit 8; structural geno	80.26

>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=99.96  E-value=1e-29  Score=198.27  Aligned_cols=100  Identities=28%  Similarity=0.618  Sum_probs=93.7

Q ss_pred             cccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhH
Q 038014           32 IKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYA  111 (140)
Q Consensus        32 ~~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~  111 (140)
                      ...+|+.||+++|.||||++|| +++||+||+++|++||++||+||+++|++.|.+++||||+++||++||++|||++|+
T Consensus         9 ~~~eD~~LP~A~V~RImK~alp-~~rISkDA~~al~ec~~eFI~~LtseA~e~a~~~~RKTI~~eDVl~Al~~LgF~~fv   87 (179)
T 1jfi_B            9 GNDDDLTIPRAAINKMIKETLP-NVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALESLGFGSYI   87 (179)
T ss_dssp             ---CCCCCCHHHHHHHHHHHST-TCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHTTGGGH
T ss_pred             CchhhhhcCHHHHHHHHHHhCC-ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhcChHHHH
Confidence            5678999999999999999999 899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhhhh
Q 038014          112 DQLKRYLHRYRELEGERANQN  132 (140)
Q Consensus       112 ~~l~~~l~~~re~~~~kk~q~  132 (140)
                      ++|+.+|+.||+..+.|+.++
T Consensus        88 ~~lk~~L~~yre~~~~kkr~~  108 (179)
T 1jfi_B           88 SEVKEVLQECKTVALKRRKAS  108 (179)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCcccc
Confidence            999999999999998876543

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

Probab=99.96  E-value=9.5e-30  Score=189.08  Aligned_cols=103  Identities=32%  Similarity=0.535  Sum_probs=88.2

Q ss_pred             ccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHH
Q 038014           33 KEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYAD  112 (140)
Q Consensus        33 ~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~  112 (140)
                      +++|+.||+|+|.||||.++|+..+||+||+.+|++||++||+||++.|++.|.+.+||||+++||+.||+.+||.+|++
T Consensus         4 ~~~d~~LP~A~I~rImK~~~pd~~~iS~dA~~~l~ka~e~FI~~lt~~A~~~a~~~kRKTI~~~Dv~~Al~~l~f~~fl~   83 (128)
T 2byk_B            4 RIEDLNLPNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFESFVP   83 (128)
T ss_dssp             -------CCSHHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCTTTHH
T ss_pred             ccccccCCHHHHHHHHHHhCcccceECHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHcCcHHHHH
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhhhhccC
Q 038014          113 QLKRYLHRYRELEGERANQNKAG  135 (140)
Q Consensus       113 ~l~~~l~~~re~~~~kk~q~k~~  135 (140)
                      +|+.+|+.||+.++.|+..++..
T Consensus        84 ~lk~~l~~yr~~~~~kk~~~~~~  106 (128)
T 2byk_B           84 SLTQDLEVYRKVVKEKKESKASK  106 (128)
T ss_dssp             HHHHHHHHHHHHHTTC-------
T ss_pred             HHHHHHHHHHHHHHhhhhhhhcc
Confidence            99999999999999888765443

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

Probab=99.96  E-value=4.4e-29  Score=175.42  Aligned_cols=92  Identities=63%  Similarity=1.072  Sum_probs=85.8

Q ss_pred             cccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhH
Q 038014           32 IKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYA  111 (140)
Q Consensus        32 ~~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~  111 (140)
                      ++++|+.||+++|+||||+++|++.+||+||+.+|++|+++||.+|+.+|+++|.++|||||+++||..|++++||.+|+
T Consensus         2 ~~~~d~~LP~a~i~ri~K~~~~~~~~is~dA~~~l~~a~e~Fi~~l~~~A~~~a~~~kRkTI~~~Dv~~Al~~l~F~~~i   81 (93)
T 1n1j_A            2 FREQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYV   81 (93)
T ss_dssp             -----CCCCHHHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTTCGGGH
T ss_pred             CCcccccCChhHHHHHHHHhCCccceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHcCcHhhH
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 038014          112 DQLKRYLHRYRE  123 (140)
Q Consensus       112 ~~l~~~l~~~re  123 (140)
                      ++++.+|++||+
T Consensus        82 ~~~~~~l~~~r~   93 (93)
T 1n1j_A           82 EPLKLYLQKFRE   93 (93)
T ss_dssp             HHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhC
Confidence            999999999984

>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=99.84  E-value=2.4e-21  Score=131.66  Aligned_cols=68  Identities=16%  Similarity=0.272  Sum_probs=64.7

Q ss_pred             ccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014           37 RLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL  105 (140)
Q Consensus        37 ~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l  105 (140)
                      ..||+|+|.||||+++| +++||+||.++|++|+++|+++|+++|++.|.+++||||+++||+.|++.+
T Consensus         3 ~~LP~A~V~rI~K~~~p-~~~is~~A~~~i~~~~~~Fi~~la~eA~~~a~~~~rKTI~~~dI~~A~~~l   70 (76)
T 3b0c_W            3 RTVPRGTLRKIIKKHKP-HLRLAANTDLLVHLSFLLFLHRLAEEARTNAFENKSKIIKPEHTIAAAKVI   70 (76)
T ss_dssp             -CCCHHHHHHHHHHHCT-TCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSBCHHHHHHHHHHH
T ss_pred             CcccccHHHHHHHHhCC-CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            47999999999999998 689999999999999999999999999999999999999999999999764

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

Probab=99.82  E-value=1.1e-20  Score=144.29  Aligned_cols=75  Identities=23%  Similarity=0.314  Sum_probs=71.5

Q ss_pred             ccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHH
Q 038014           37 RLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYAD  112 (140)
Q Consensus        37 ~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~  112 (140)
                      ..||+++|.||||++||. .|||+||.++|++|+++|+.+|+++|+++|.|+|||||+++||++||..|||++|..
T Consensus         3 ~~LP~a~V~Riik~~lg~-~rVS~dA~~~l~~~l~~f~~~i~~~A~~~a~ha~RKTv~a~DV~~a~~~lg~~~v~d   77 (154)
T 1f1e_A            3 VELPKAAIERIFRQGIGE-RRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADVLMVEGVED   77 (154)
T ss_dssp             -CCCHHHHHHHHHTTSTT-CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHHHTCTTSTT
T ss_pred             ccCCccHHHHHHHhcCCc-cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhcccccCCc
Confidence            379999999999999985 999999999999999999999999999999999999999999999999999998754

>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=99.80  E-value=8.1e-20  Score=121.08  Aligned_cols=66  Identities=29%  Similarity=0.431  Sum_probs=63.8

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL  105 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l  105 (140)
                      .||+++|+||||+.  ++.+||+||+.+|++|+++|+.+|+.+|+.+|.++|||||+++||..|++.|
T Consensus         2 ~lP~a~v~Ri~k~~--~~~ris~~A~~~l~~a~e~fi~~l~~~A~~~a~~~kRkTI~~~Di~~A~~~l   67 (68)
T 1b67_A            2 ELPIAPIGRIIKNA--GAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARKMF   67 (68)
T ss_dssp             CSCHHHHHHHHHHT--TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHGGGG
T ss_pred             CCCccHHHHHHhcC--CcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhc
Confidence            59999999999999  6899999999999999999999999999999999999999999999999876

>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=99.80  E-value=1.1e-19  Score=132.00  Aligned_cols=91  Identities=13%  Similarity=0.242  Sum_probs=80.4

Q ss_pred             cccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHHH
Q 038014           34 EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQ  113 (140)
Q Consensus        34 ~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~~  113 (140)
                      .+|..||++.|+||+|..  +..+||+++..+|.+|+++|+..++.+|..+|+|+|||||+++||+.||+++|+..|..+
T Consensus         3 ~~d~~lP~a~I~Ri~r~~--g~~rIS~~a~~~l~e~l~~f~~~v~~da~~~A~HA~RKTV~~eDV~lalrr~g~~~~~~~   80 (111)
T 3b0c_T            3 TREPEIASSLIKQIFSHY--VKTPVTRDAYKIVEKCSERYFKQISSDLEAYSQHAGRKTVEMADVELLMRRQGLVTDKMP   80 (111)
T ss_dssp             -------CHHHHHHHHHH--HCSCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTTSSBTTBC
T ss_pred             CCCCCCCHHHHHHHHHHC--CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHCCCcccccc
Confidence            367899999999999999  789999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHH--HHHHH
Q 038014          114 LKRYLHRY--RELEG  126 (140)
Q Consensus       114 l~~~l~~~--re~~~  126 (140)
                      +...++.|  +|+.+
T Consensus        81 l~~l~~~~lp~E~~~   95 (111)
T 3b0c_T           81 LHVLVERHLPLEYRK   95 (111)
T ss_dssp             HHHHHHHHSCHHHHH
T ss_pred             HHHHHHHhCcHHHHH
Confidence            99999999  55444

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

Probab=99.71  E-value=1.7e-18  Score=130.25  Aligned_cols=97  Identities=18%  Similarity=0.245  Sum_probs=61.8

Q ss_pred             cccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHH-HhCCCCccCcccHHHHHHhc---CCch
Q 038014           34 EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKC-HKEKRKTVNGDDICWALATL---GFDN  109 (140)
Q Consensus        34 ~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a-~~~kRKTI~~eDVl~ALe~l---gf~~  109 (140)
                      ..++.||.++|+||||.. |+..+||++|..+|++|++.||.+|+..|+..| ...+||||+++||..|+...   +|..
T Consensus        15 ~~~~~LPlaRIKrIMK~d-pdv~~Is~eA~vliakA~ElFI~~Lt~~A~~~a~~~~kRKtI~~~Dl~~AV~~~e~~dFL~   93 (140)
T 2byk_A           15 TAETFLPLSRVRTIMKSS-MDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEFLL   93 (140)
T ss_dssp             --------------CCSS-SSCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHHTCSTTGGGT
T ss_pred             ccCCCCCHHHHHHHHhcC-cccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccCHHHHHHHHhcCchhhhHh
Confidence            467899999999999998 777899999999999999999999999999999 99999999999999999865   5555


Q ss_pred             hHHHHHHHHHHHHHHHHHHhhh
Q 038014          110 YADQLKRYLHRYRELEGERANQ  131 (140)
Q Consensus       110 y~~~l~~~l~~~re~~~~kk~q  131 (140)
                      ++-|.+..+.+|+++.+.++++
T Consensus        94 divP~ki~l~~~~~~~~~~~~~  115 (140)
T 2byk_A           94 QIVPQKIRVHQFQEMLRLNRSA  115 (140)
T ss_dssp             TTSCSCC---------------
T ss_pred             ccccchhhHHHHHHHHHhcccc
Confidence            4558899999999988876544

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

Probab=99.71  E-value=1.7e-17  Score=126.61  Aligned_cols=74  Identities=24%  Similarity=0.324  Sum_probs=70.4

Q ss_pred             CCccccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           29 DGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        29 ~~~~~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      .++...+++.||+++|.||||+.  +..|||+||.+++++|+++|+.+|+.+|.++|.|+|||||+++||++||+.
T Consensus        73 ~~v~d~~~l~lP~a~V~Ri~k~~--g~~RVS~~A~~~l~~~le~f~~~I~~~A~~~a~ha~RKTIt~eDV~~Al~~  146 (154)
T 1f1e_A           73 EGVEDYDGELFGRATVRRILKRA--GIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITY  146 (154)
T ss_dssp             TTSTTCCSCCCCHHHHHHHHHHT--TCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             ccCCccccccCCccHHHHHHHHc--CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHh
Confidence            45677899999999999999999  688999999999999999999999999999999999999999999999985

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

Probab=99.70  E-value=2.2e-17  Score=114.18  Aligned_cols=78  Identities=23%  Similarity=0.288  Sum_probs=72.1

Q ss_pred             ccccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchh
Q 038014           31 VIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNY  110 (140)
Q Consensus        31 ~~~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y  110 (140)
                      +.+.....||+++|+||+|..  +..+||+|+.+++.+++++|+..++.+|..+|+|+|||||+++||..||+.+|++-|
T Consensus         3 ~~r~~~~~ip~~~I~Riar~~--Gv~rIs~da~~~l~~~l~~~~~~I~~dA~~~a~ha~RKTvt~~DV~~Alk~~g~~lY   80 (84)
T 2hue_C            3 VLRDNIQGITKPAIRRLARRG--GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY   80 (84)
T ss_dssp             CGGGGCCSSCHHHHHHHHHHT--TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTTCEEEE
T ss_pred             cccccCCCCCHHHHHHHHHHc--CchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHcCCCCC
Confidence            345566789999999999998  567999999999999999999999999999999999999999999999999998765

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

Probab=99.69  E-value=5e-17  Score=116.31  Aligned_cols=81  Identities=20%  Similarity=0.288  Sum_probs=71.1

Q ss_pred             CCCccccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCC
Q 038014           28 QDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGF  107 (140)
Q Consensus        28 ~~~~~~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf  107 (140)
                      ...+.+.....||+++|+||++..  +..+||.|+.++|.+++++|+..|+.+|.++|+|++||||+++||..||+.+|+
T Consensus        18 ~~k~~r~~i~~ip~~~I~Rlar~~--Gv~rIS~da~~~l~~~le~fi~~I~~dA~~~a~HakRKTVt~~DV~~ALkr~g~   95 (102)
T 1id3_B           18 HRKILRDNIQGITKPAIRRLARRG--GVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGR   95 (102)
T ss_dssp             ------CCGGGSCHHHHHHHHHHT--TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTTC
T ss_pred             HHHHHHhccCCCCHHHHHHHHHHc--CchhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHcCC
Confidence            334556677789999999999998  567999999999999999999999999999999999999999999999999998


Q ss_pred             chh
Q 038014          108 DNY  110 (140)
Q Consensus       108 ~~y  110 (140)
                      .-|
T Consensus        96 ~lY   98 (102)
T 1id3_B           96 TLY   98 (102)
T ss_dssp             CEE
T ss_pred             CCC
Confidence            765

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

Probab=99.67  E-value=1.3e-16  Score=106.35  Aligned_cols=64  Identities=28%  Similarity=0.431  Sum_probs=61.9

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA  103 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe  103 (140)
                      .||+++|.||+|+.  +..+||+++..+|+++++.|+..|+.+|+.+|.|+|||||+++||..|++
T Consensus         6 ~lp~a~v~Rl~r~~--g~~ris~~a~~~l~e~~~~~~~~v~~dA~~~a~hakRkTI~~~DV~lA~~   69 (70)
T 1ku5_A            6 ELPIAPVDRLIRKA--GAERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIK   69 (70)
T ss_dssp             CSCHHHHHHHHHHT--TCSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHT
T ss_pred             cCChHHHHHHHHHc--CcceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence            79999999999998  67899999999999999999999999999999999999999999999985

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

Probab=99.66  E-value=1.6e-16  Score=112.33  Aligned_cols=80  Identities=25%  Similarity=0.241  Sum_probs=68.6

Q ss_pred             cccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhH
Q 038014           32 IKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYA  111 (140)
Q Consensus        32 ~~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~  111 (140)
                      ....++.||.++|+||||.. |+..+||+||..++++|++.|+.+|+..|...|.+.|||||+++||..|++..++.+|.
T Consensus        13 ~~~~~~~lP~arIkrImK~~-~~~~~is~eA~~~laka~E~Fi~~l~~~A~~~a~~~krktI~~~di~~Av~~~e~~~FL   91 (97)
T 1n1j_B           13 KDFRVQELPLARIKKIMKLD-EDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFL   91 (97)
T ss_dssp             -------CCHHHHHHHHTTS-TTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTCGGGGGG
T ss_pred             CCcCCCcCCHHHHHHHHccC-ccccccChHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHHhcCcHHHHH
Confidence            34456789999999999999 65579999999999999999999999999999999999999999999999998887775


Q ss_pred             H
Q 038014          112 D  112 (140)
Q Consensus       112 ~  112 (140)
                      .
T Consensus        92 ~   92 (97)
T 1n1j_B           92 I   92 (97)
T ss_dssp             T
T ss_pred             H
Confidence            3

>4g92_C HAPE; transcription factor, nucleosome, minor groove binding, CCAA complex, histone fold motif, specific binding to the ccaat- nucleus; HET: DNA; 1.80A {Aspergillus nidulans} PDB: 4g91_C*

Probab=99.65  E-value=2.6e-16  Score=115.13  Aligned_cols=77  Identities=27%  Similarity=0.302  Sum_probs=69.9

Q ss_pred             cccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhH
Q 038014           34 EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYA  111 (140)
Q Consensus        34 ~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~  111 (140)
                      .....||.++|+||||.. |+..+||+||..++++|++.||.+|+..|...|...+||||+++||..|++..+..+|.
T Consensus        37 ~k~~~lPvaRIkrImK~d-~~~~~is~eA~v~la~a~E~Fi~~L~~~A~~~a~~~krktI~~~di~~Av~~~e~~dFL  113 (119)
T 4g92_C           37 YKIHQLPLARIKKVMKAD-PEVKMISAEAPILFAKGCDVFITELTMRAWIHAEDNKRRTLQRSDIAAALSKSDMFDFL  113 (119)
T ss_dssp             SSCCSSCHHHHHHHHHTS-TTCCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTCGGGGGG
T ss_pred             cccCCCCHHHHHHHHhhC-CccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccCHHHHHHHHhcCchhhHH
Confidence            346679999999999987 77789999999999999999999999999999999999999999999999876655553

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

Probab=99.64  E-value=5.4e-16  Score=110.77  Aligned_cols=79  Identities=23%  Similarity=0.280  Sum_probs=72.4

Q ss_pred             CccccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCch
Q 038014           30 GVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDN  109 (140)
Q Consensus        30 ~~~~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~  109 (140)
                      .+.+.....||+++|.||++..  +..+||.|+.+.|.++++.|+..|+.+|..+|+|++||||+++||..||+.+|++.
T Consensus        21 k~~r~~~~gip~~~I~Rlar~~--G~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktIt~~DV~~Alr~~g~~l   98 (103)
T 1tzy_D           21 KVLRDNIQGITKPAIRRLARRG--GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTL   98 (103)
T ss_dssp             CCCCCGGGGSCHHHHHHHHHHT--TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTTCEE
T ss_pred             cchhhhcccCCHHHHHHHHHHc--CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHcCCCC
Confidence            3456667779999999999999  44699999999999999999999999999999999999999999999999999875


Q ss_pred             h
Q 038014          110 Y  110 (140)
Q Consensus       110 y  110 (140)
                      |
T Consensus        99 Y   99 (103)
T 1tzy_D           99 Y   99 (103)
T ss_dssp             E
T ss_pred             c
Confidence            5

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

Probab=99.62  E-value=6.7e-16  Score=110.38  Aligned_cols=78  Identities=22%  Similarity=0.308  Sum_probs=64.2

Q ss_pred             ccccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchh
Q 038014           31 VIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNY  110 (140)
Q Consensus        31 ~~~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y  110 (140)
                      +.+.....||+++|.||++..  +..+||.|+.+.|.++++.|+..|+.+|..+|+|++||||+++||..||+.+|++.|
T Consensus        22 ~~r~~~~gip~~~I~Rlar~~--G~~rIs~~a~~~l~~vle~~~~~V~~dA~~~a~hakRktvt~~DV~~Alr~~g~~lY   99 (103)
T 2yfw_B           22 ILRDNIQGITKPAIRRLARRG--GVKRISGLIYEEVRNVLKTFLESVIRDAVTYTEHAKRKTVTSLDVVYALKRQGRTLY   99 (103)
T ss_dssp             --------CCHHHHHHHHHHT--TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHC----
T ss_pred             hhhhhhccCCHHHHHHHHHHc--CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHcCCCCc
Confidence            345566679999999999998  446999999999999999999999999999999999999999999999999998655

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

Probab=99.44  E-value=6.4e-14  Score=99.24  Aligned_cols=77  Identities=13%  Similarity=0.157  Sum_probs=59.8

Q ss_pred             ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHH
Q 038014           35 QDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYAD  112 (140)
Q Consensus        35 ~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~  112 (140)
                      ..+.||.++|+||||.. |+..+||.+|..++.+++|.|+.+|+..|...|.+.|||||+++||..|++.-+..+|..
T Consensus         8 ~~~~fPvaRIkrimK~~-~~~~~vs~~A~v~la~a~E~Fi~el~~~A~~~a~~~krktI~~~di~~av~~~e~l~FL~   84 (98)
T 1jfi_A            8 YNARFPPARIKKIMQTD-EEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQCIELEGDPAANK   84 (98)
T ss_dssp             --CCCCHHHHHHHHTTS-TTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC---CBCHHHHHTTCC---------
T ss_pred             cCCCCChHHHHHHHHcC-ccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHhcCchhhHHH
Confidence            45789999999999987 445699999999999999999999999999999999999999999999998765555544

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

Probab=99.44  E-value=2.4e-13  Score=93.06  Aligned_cols=71  Identities=18%  Similarity=0.208  Sum_probs=65.2

Q ss_pred             cccCchhHHHHHHhhhCC---CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcC
Q 038014           36 DRLLPIANVGRIMKQILP---PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLG  106 (140)
Q Consensus        36 d~~LP~A~V~RI~K~~lp---~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lg  106 (140)
                      ++.||++++.||+|+..+   ++.|++.+|..+||+++|.|+..|..+++.+|.|+||+||+++||..|.+--|
T Consensus         1 ~lli~k~PF~RLVRei~~~~~~~~R~q~~Al~aLQea~Eaylv~lfeda~l~A~HAkRvTi~~kDiqLa~rirg   74 (77)
T 2hue_B            1 MALIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRG   74 (77)
T ss_dssp             -CCSCHHHHHHHHHHHHHTTCSSCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHTT
T ss_pred             CCccccchHHHHHHHHHHHcCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHhhHHHHHHHhC
Confidence            478999999999999943   57899999999999999999999999999999999999999999999987554

>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=99.35  E-value=1.4e-12  Score=93.16  Aligned_cols=72  Identities=17%  Similarity=0.168  Sum_probs=60.4

Q ss_pred             cccccccCchhHHHHHHhhhCCC------CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014           32 IKEQDRLLPIANVGRIMKQILPP------NAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA  103 (140)
Q Consensus        32 ~~~~d~~LP~A~V~RI~K~~lp~------~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe  103 (140)
                      .+..++.||++++.||+|+...+      +.|++.+|..+||+++|.|+..|..+|+.+|.|+||+||++.||..|..
T Consensus        21 Qkst~llIpk~PF~RLVREI~~~~~~~~~~~R~q~~Al~ALQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa~r   98 (100)
T 2yfv_A           21 QRSTDLLISRMPFARLVKEVTDQFTTESEPLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARR   98 (100)
T ss_dssp             -------CCHHHHHHHHHHHHHTTC-----CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             cccchhhhccccHHHHHHHHHHHhccccchhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHHH
Confidence            35688999999999999999632      6899999999999999999999999999999999999999999998863

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

Probab=99.33  E-value=3.3e-12  Score=88.33  Aligned_cols=70  Identities=19%  Similarity=0.152  Sum_probs=63.9

Q ss_pred             ccCchhHHHHHHhhhCC-----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcC
Q 038014           37 RLLPIANVGRIMKQILP-----PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLG  106 (140)
Q Consensus        37 ~~LP~A~V~RI~K~~lp-----~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lg  106 (140)
                      +.||++++.||+|+...     .+.|++.+|..+||+++|.|+..|..+|+.+|.|+||+||+++|+..|..--|
T Consensus         2 lLI~klPF~RLVREI~~~~~~~~~~R~q~~Al~aLQea~E~ylv~Lfeda~lcAiHAkRvTi~~kDiqLa~rirg   76 (82)
T 3nqj_A            2 LLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIRG   76 (82)
T ss_dssp             CSSCHHHHHHHHHHHHHHHHSSCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHC
T ss_pred             CCcccccHHHHHHHHHHHhccCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHHHHHHHHHcc
Confidence            57999999999999862     26799999999999999999999999999999999999999999999876444

>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=99.28  E-value=6.2e-12  Score=94.16  Aligned_cols=74  Identities=19%  Similarity=0.220  Sum_probs=67.8

Q ss_pred             ccccccCchhHHHHHHhhhCC---CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcC
Q 038014           33 KEQDRLLPIANVGRIMKQILP---PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLG  106 (140)
Q Consensus        33 ~~~d~~LP~A~V~RI~K~~lp---~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lg  106 (140)
                      +..++.||++++.||+|+...   ++.+++.+|+.+||+++|.|+..|+.+++.+|.|+||+||++.||..|..--|
T Consensus        57 kst~lLIpk~PF~RLVREI~~~~~~~~R~q~~Al~aLQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa~rirg  133 (136)
T 1tzy_C           57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG  133 (136)
T ss_dssp             HCCSCCSCHHHHHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHT
T ss_pred             cchhhhhccchHHHHHHHHHHHhhhhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHhHHHHHHHhC
Confidence            457889999999999999943   57899999999999999999999999999999999999999999999986544

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

Probab=99.26  E-value=6.5e-12  Score=95.81  Aligned_cols=72  Identities=18%  Similarity=0.145  Sum_probs=64.4

Q ss_pred             ccccccCchhHHHHHHhhhCC-----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           33 KEQDRLLPIANVGRIMKQILP-----PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        33 ~~~d~~LP~A~V~RI~K~~lp-----~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      +..++.||++++.||+|+...     .+.+++.+|+.+||+++|.|+..|+.+|+.+|.|+||+||+++||..|+.-
T Consensus        72 kSteLLIpKlPF~RLVREIa~~~~~~~~lRfqs~Al~ALQEAaEayLV~LFEdanLcAiHAkRVTIm~kDIqLArrI  148 (156)
T 3r45_A           72 KSTHLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRI  148 (156)
T ss_dssp             ---CCCSCHHHHHHHHHHHHHTTTTTCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSEECHHHHHHHHHH
T ss_pred             cccccccccccHHHHHHHHHHHhccCccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHHHHH
Confidence            568899999999999999963     257999999999999999999999999999999999999999999998754

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

Probab=99.26  E-value=1.1e-11  Score=93.30  Aligned_cols=75  Identities=19%  Similarity=0.167  Sum_probs=65.9

Q ss_pred             ccccccCchhHHHHHHhhhCC-----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCC
Q 038014           33 KEQDRLLPIANVGRIMKQILP-----PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGF  107 (140)
Q Consensus        33 ~~~d~~LP~A~V~RI~K~~lp-----~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf  107 (140)
                      +..++.||++++.||+|+...     .+.+++.+|+.+||+++|.|+..|+.+|+.+|.|+||+||+++||..|+.--|.
T Consensus        56 kst~LLIpKlPF~RLVREI~~~~~~~~~~Rfq~~Al~ALQEAaEayLv~LFEdanlcAiHAkRVTIm~kDiqLArrirg~  135 (140)
T 3nqu_A           56 KSTHLLIRKLPFSRLAREICVKFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLTLHAGRVTLFPKDVQLARRIRGL  135 (140)
T ss_dssp             ---CCCSCTTHHHHHHHHHHHHHHTTCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHC-
T ss_pred             cccccccccccHHHHHHHHHHHhcccccceecHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcccccHHHHHHHHHhccc
Confidence            568899999999999999852     268999999999999999999999999999999999999999999999875553

>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=99.08  E-value=4.1e-10  Score=75.66  Aligned_cols=65  Identities=20%  Similarity=0.221  Sum_probs=61.7

Q ss_pred             ccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014           37 RLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA  103 (140)
Q Consensus        37 ~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe  103 (140)
                      ..||.++|.+|++..  +-.++|.|+...|.+-++..+..|+.+|...++|.||||++++||-.||+
T Consensus         5 s~lp~~~v~~iaes~--Gi~~lsddaa~~LA~dvEyr~~eI~qeA~kfmrHakRk~Lt~~DI~~Alk   69 (70)
T 1taf_B            5 SSISAESMKVIAESI--GVGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLK   69 (70)
T ss_dssp             CCCCHHHHHHHHHHT--TCCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC
T ss_pred             ccCCHHHHHHHHHHC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHc
Confidence            479999999999999  55699999999999999999999999999999999999999999999985

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

Probab=99.07  E-value=2.9e-10  Score=83.60  Aligned_cols=73  Identities=22%  Similarity=0.315  Sum_probs=55.5

Q ss_pred             cCchhHHHHHHhhhC---CC---CccccHHHHHHHHHHHHHHHHHHHH--------------------------------
Q 038014           38 LLPIANVGRIMKQIL---PP---NAKISKEAKETMQECVSEFISFVTG--------------------------------   79 (140)
Q Consensus        38 ~LP~A~V~RI~K~~l---p~---~~rIskdA~~al~~aa~~Fi~~Las--------------------------------   79 (140)
                      .||+.++.|++|+..   ..   +.|++.+|..+||+++|.|+..|..                                
T Consensus         1 LI~klPF~RLVREI~~~~~~~~~~lRfq~~Al~ALQeAsEayLV~lFEd~nlcaiHA~~gGvkRIS~~iy~e~r~vl~~~   80 (121)
T 2ly8_A            1 LISKIPFARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEHTNLLALHLVPRGSKRISGLIYEEVRAVLKSF   80 (121)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTCCSSCCBCHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCCSSCCSSCHHHHHHHHHHHH
T ss_pred             CCCccchHHHHHHHHHHhcCCCCCccccHHHHHHHHHHHHHHHHHHHHHHhHHHHcCCccCccchhHHHHHHHHHHHHHH
Confidence            368888888887753   11   4677777777777777776666554                                


Q ss_pred             ------HHHHHHHhCCCCccCcccHHHHHHhcCCchh
Q 038014           80 ------EASDKCHKEKRKTVNGDDICWALATLGFDNY  110 (140)
Q Consensus        80 ------~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y  110 (140)
                            +|..+++|+|||||+++||..||+..|-.-|
T Consensus        81 l~~i~rdav~yaehA~RKTVta~DV~~Alkr~G~~ly  117 (121)
T 2ly8_A           81 LESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLY  117 (121)
T ss_dssp             HHHHHHHHHHHHHHTTCCCBCHHHHHHHHHHTTCGGG
T ss_pred             HHHHHHHHHHHHHhcCCCcCcHHHHHHHHHhCCCcCC
Confidence                  4778888999999999999999999886544

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

Probab=99.00  E-value=4.4e-10  Score=84.44  Aligned_cols=63  Identities=13%  Similarity=0.147  Sum_probs=57.4

Q ss_pred             HHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014           43 NVGRIMKQILP-PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL  105 (140)
Q Consensus        43 ~V~RI~K~~lp-~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l  105 (140)
                      +|.||+++... .++.||.+++.+|.+.+..|+..|+.++...|+|+|||||+++||..++++.
T Consensus        24 ~VgkIvee~~~~~~~~vS~~ai~aL~El~~~~~e~ia~DLe~FAkHAGRKTI~~eDVkLa~Rrn   87 (140)
T 3vh5_A           24 TTGALAQDVAEDKGVLFSKQTVAAISEITFRQAENFARDLEMFARHAKRSTITSEDVKLLARRS   87 (140)
T ss_dssp             HHHHHHHHHHHHHTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHhcCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhC
Confidence            57788887743 3688999999999999999999999999999999999999999999999875

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

Probab=98.92  E-value=2.1e-09  Score=78.15  Aligned_cols=75  Identities=17%  Similarity=0.223  Sum_probs=64.1

Q ss_pred             HHHHHHhhhCCC-CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHHHHHHHHHHH
Q 038014           43 NVGRIMKQILPP-NAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRY  121 (140)
Q Consensus        43 ~V~RI~K~~lp~-~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~~l~~~l~~~  121 (140)
                      +|.||+++.... ++.+|++++.+|.+.+..|+..|+.++...|+|+|||||+++||..++++.      +.|...|..|
T Consensus        32 ~V~rIvke~gaer~~~vS~~ai~aL~El~~~~~~~ia~Dl~~fAkHAgRkTI~~eDV~La~Rr~------~~L~~~l~~~  105 (113)
T 4dra_A           32 TVGCLCEEVALDKEMQFSKQTIAAISELTFRQCENFAKDLEMFARHAKRTTINTEDVKLLARRS------NSLLKYITDK  105 (113)
T ss_dssp             HHHHHHHHHHHHHTCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTC------HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHhC------HHHHHHHHHH
Confidence            688999988432 567999999999999999999999999999999999999999999999874      4555555555


Q ss_pred             HH
Q 038014          122 RE  123 (140)
Q Consensus       122 re  123 (140)
                      .+
T Consensus       106 ~~  107 (113)
T 4dra_A          106 SE  107 (113)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

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

Probab=98.90  E-value=3e-09  Score=74.52  Aligned_cols=63  Identities=16%  Similarity=0.153  Sum_probs=58.5

Q ss_pred             HHHHHHhhhCCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014           43 NVGRIMKQILPPN-AKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL  105 (140)
Q Consensus        43 ~V~RI~K~~lp~~-~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l  105 (140)
                      +|.+|+.+.++.. +.+|.+++.+|.+.+..++..|+.++...|+|+|||||+++||..++++.
T Consensus        17 ~V~ki~~e~~~~~g~~vs~~~i~aL~e~~~~~~~~ia~Dl~~fA~HAgRkTI~~eDV~L~~Rrn   80 (90)
T 3v9r_A           17 RVEERLQQVLSSEDIKYTPRFINSLLELAYLQLGEMGSDLQAFARHAGRGVVNKSDLMLYLRKQ   80 (90)
T ss_dssp             HHHHHHHHHSCSSCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHhcCceeCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhC
Confidence            5789999998754 88999999999999999999999999999999999999999999998763

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

Probab=98.90  E-value=3.2e-09  Score=76.53  Aligned_cols=75  Identities=13%  Similarity=0.199  Sum_probs=62.8

Q ss_pred             HHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHHHHHHHHHHH
Q 038014           43 NVGRIMKQILP-PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRY  121 (140)
Q Consensus        43 ~V~RI~K~~lp-~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~~l~~~l~~~  121 (140)
                      +|.||+++... .+.++|.+++.+|.+.+..|+..|+.+|...|+|+|||||+.+||..++++.      +.|...+..|
T Consensus        24 ~V~rI~~~~g~~~~~~vs~~~i~aL~E~~~~~~~~ia~Da~~fA~HAgRkTI~~eDV~La~Rrn------~~l~~~l~~~   97 (107)
T 3b0b_B           24 TTGCLCQDVAEDKGVLFSKQTVAAISEITFRQCENFARDLEMFARHAKRSTITSEDVKLLARRS------NSLLKYITQK   97 (107)
T ss_dssp             HHHHHHHHHHHHHTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTC------HHHHHHHHHH
T ss_pred             HHHHHHHHHhhhcCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcCcCCHHHHHHHHHhC------HHHHHHHHHH
Confidence            48899988832 2479999999999999999999999999999999999999999999999874      3444444444


Q ss_pred             HH
Q 038014          122 RE  123 (140)
Q Consensus       122 re  123 (140)
                      .+
T Consensus        98 ~~   99 (107)
T 3b0b_B           98 SD   99 (107)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

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

Probab=98.86  E-value=9.5e-09  Score=68.57  Aligned_cols=61  Identities=15%  Similarity=0.240  Sum_probs=57.1

Q ss_pred             hHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           42 ANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        42 A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      -.|.||+|..  +--+++.++...|.+.+..++..|+.+|..+|+|+|||||+++||..|++.
T Consensus         5 ~~i~~iLk~~--G~~~~~~~v~~~L~e~~~ry~~~il~dA~~~a~HAgrktv~~eDVkLAi~~   65 (68)
T 1taf_A            5 QVIMSILKEL--NVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLATEV   65 (68)
T ss_dssp             HHHHHHHHHT--TCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             HHHHHHHHHC--CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHh
Confidence            3689999998  666999999999999999999999999999999999999999999999874

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

Probab=98.77  E-value=1e-08  Score=82.57  Aligned_cols=72  Identities=17%  Similarity=0.182  Sum_probs=63.8

Q ss_pred             ccccCchhHHHHHHhhhCCC------CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcC
Q 038014           35 QDRLLPIANVGRIMKQILPP------NAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLG  106 (140)
Q Consensus        35 ~d~~LP~A~V~RI~K~~lp~------~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lg  106 (140)
                      .-+.||+.++.||+|+..++      +.|++.+|..+||+++|.|+..|...++-+|.|++|.||++.|+..|..--|
T Consensus         8 ~~~lI~KlPFqRLVREIaq~~~~~~~~lRfqs~Al~ALQEAaEayLV~LFEd~nLcaiHAkRVTim~kDiqLarrirg   85 (235)
T 2l5a_A            8 KKLLISKIPFARLVKEVTDEFTTKDQDLRWQSMAIMALQEASEAYLVGLLEHTNLLALHAKRITIMKKDMQLARRIRG   85 (235)
T ss_dssp             ---CCSCCHHHHHHHHHHHTSCGGGTTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTSGGGTTHHHHHHTSSC
T ss_pred             ccccccCccHHHHHHHHHHHhccCCccceecHHHHHHHHHHHHHHHHHHHhhhHHHHhcccccccchhhHHHHHHHhh
Confidence            45789999999999998643      6799999999999999999999999999999999999999999999976544

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

Probab=98.64  E-value=8.2e-08  Score=70.49  Aligned_cols=70  Identities=10%  Similarity=0.161  Sum_probs=64.1

Q ss_pred             cccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           34 EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        34 ~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      -..+.||.+.|.|+||+.-. ..||+.+|...|..+.|-|...|...|...|.+.+|++|+++||..|+..
T Consensus        19 ragL~fPV~ri~R~Lk~~~~-a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hi~lAI~n   88 (123)
T 2nqb_C           19 RAGLQFPVGRIHRLLRKGNY-AERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN   88 (123)
T ss_dssp             HHTCSSCHHHHHHHHHHTTS-CSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT
T ss_pred             cCCeeccHHHHHHHHHcccc-ccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHHHHHhc
Confidence            45789999999999999832 34999999999999999999999999999999999999999999999873

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

Probab=98.63  E-value=1.7e-08  Score=81.35  Aligned_cols=61  Identities=23%  Similarity=0.222  Sum_probs=56.5

Q ss_pred             HHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcC
Q 038014           44 VGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLG  106 (140)
Q Consensus        44 V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lg  106 (140)
                      +.||+|..  +..|||.++.+.+....+.|+..|+.+|..+|+|++||||+++||..||+.+|
T Consensus       167 ~~RlaRrg--GVkRIS~~iyeelr~vLe~fle~IirdAv~yaeHA~RKTVta~DV~~ALKr~g  227 (235)
T 2l5a_A          167 DEEDGDKG--GVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQG  227 (235)
T ss_dssp             CCTTSCCT--TCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHH
T ss_pred             HHHHhhcC--CchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHhcC
Confidence            44778877  66799999999999999999999999999999999999999999999999865

>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=98.62  E-value=1e-07  Score=69.74  Aligned_cols=70  Identities=19%  Similarity=0.230  Sum_probs=64.2

Q ss_pred             cccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           34 EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        34 ~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      -..+.||.+.|.|+||+.-- ..||+.+|...|..+.|-|...|...|...|++.+|++|+++||..|+..
T Consensus        18 ragLqfPV~ri~R~Lk~~~~-a~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~~rItp~hi~lAI~n   87 (120)
T 2f8n_G           18 KAGVIFPVGRMLRYIKKGHP-KYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILLAVAN   87 (120)
T ss_dssp             HHTCSSCHHHHHHHHHHHSS-SCEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT
T ss_pred             ccCccCChHHHHHHHHcCcc-ccccccchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHHHHhc
Confidence            46789999999999999821 45999999999999999999999999999999999999999999999873

>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=98.62  E-value=1e-07  Score=70.49  Aligned_cols=70  Identities=10%  Similarity=0.163  Sum_probs=64.2

Q ss_pred             cccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           34 EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        34 ~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      -..+.||.+.|.|+||+.-. ..||+.+|...|..+.|-|...|...|...|.+.+|++|+++||..|+..
T Consensus        21 ragLqfPV~rI~R~Lk~~~~-a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hi~lAI~n   90 (129)
T 1tzy_A           21 RAGLQFPVGRVHRLLRKGNY-AERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRN   90 (129)
T ss_dssp             HHTCSSCHHHHHHHHHHTTS-SSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT
T ss_pred             cCceeccHHHHHHHHHcccc-ccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEcHHHHHHHHhc
Confidence            46789999999999999732 34999999999999999999999999999999999999999999999873

>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=98.60  E-value=9.7e-08  Score=70.83  Aligned_cols=72  Identities=11%  Similarity=0.159  Sum_probs=65.0

Q ss_pred             cccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           32 IKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        32 ~~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      ..-..+.||.+.|.|+||+.-. ..||+.+|...|..+.|-|+..|...|...|++.+|++|+++||..|+..
T Consensus        19 S~ragLqfPV~rI~R~Lk~~~~-a~RVs~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItp~hI~lAI~n   90 (131)
T 1id3_C           19 SAKAGLTFPVGRVHRLLRRGNY-AQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRHLQLAIRN   90 (131)
T ss_dssp             TGGGTCSSCHHHHHHHHHTTCS-CSEECSSHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT
T ss_pred             cccCCeecCHHHHHHHHHcccc-ccccchhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCceEcHHHHHHHHhc
Confidence            3446789999999999999732 34999999999999999999999999999999999999999999999873

>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=98.60  E-value=1.2e-07  Score=70.04  Aligned_cols=71  Identities=13%  Similarity=0.138  Sum_probs=64.3

Q ss_pred             cccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           34 EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        34 ~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      -..+.||.++|.|+||+.-.-..||+.+|...|..+.|-|...|...|...|++.+|++|+++||..|+..
T Consensus        23 ragLqfPV~ri~R~Lk~~~~a~~RV~~~A~VyLaAvLEyL~aEIlelAgn~A~~~k~krItprhi~lAI~n   93 (128)
T 1f66_C           23 RAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG   93 (128)
T ss_dssp             HHTCSSCHHHHHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHH
T ss_pred             cCCccCChHHHHHHHHHcccchhhccccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEcHHHHHHHHhc
Confidence            46789999999999999832235999999999999999999999999999999999999999999999874

>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=98.53  E-value=2.2e-07  Score=70.37  Aligned_cols=70  Identities=10%  Similarity=0.169  Sum_probs=64.0

Q ss_pred             cccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           34 EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        34 ~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      -..+.||.+.|.|+||+.-. ..||+.+|...|..++|-|+..|...|...|++.+|++|+++||..|+..
T Consensus        40 ragLqFPVgrI~R~LK~~~~-a~RVs~~A~VyLAAVLEYL~aEILelAgn~A~~~krkrItprhI~lAI~n  109 (149)
T 2f8n_K           40 RAGLQFPVGRVHRLLRKGNY-SERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRN  109 (149)
T ss_dssp             HHTCSSCHHHHHHHHHHTTS-CSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             cCCeeccHHHHHHHHHcccc-ccccCcCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHhc
Confidence            35788999999999999832 34999999999999999999999999999999999999999999999873

>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=98.39  E-value=6.1e-07  Score=69.94  Aligned_cols=71  Identities=13%  Similarity=0.173  Sum_probs=64.3

Q ss_pred             cccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           34 EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        34 ~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      -..+.||.+.|.|+||+.-....||+.+|...|..+.+-++..|...|...|++.||++|+++||..|+..
T Consensus       101 ragl~fPv~ri~R~lk~~~~a~~Rv~~~A~vyLaavLEyl~~eIlelA~n~a~~~~~~~I~p~~i~lAi~n  171 (192)
T 2jss_A          101 RAGLQFPVGRIKRYLKRHATGRTRVGSKAAIYLTAVLEYLTAEVLELAGNAAKDLKVKRITPRHLQLAIRG  171 (192)
T ss_dssp             HSSCCSCHHHHHHHHHHTTCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCHHHHHHHHHT
T ss_pred             cCCCcCCHHHHHHHHHhcCccccccccChHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhc
Confidence            45789999999999999822135999999999999999999999999999999999999999999999873

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

Probab=98.30  E-value=1.8e-06  Score=63.52  Aligned_cols=63  Identities=29%  Similarity=0.393  Sum_probs=59.2

Q ss_pred             hHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014           42 ANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL  105 (140)
Q Consensus        42 A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l  105 (140)
                      ..|.|++|++-| +..||.+|...|...+..+...|+.+|...+...+|+||+.+||..|++-+
T Consensus        37 ~YIyKVLKQVhp-d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtAvrLl   99 (123)
T 2nqb_D           37 IYIYTVLKQVHP-DTGISSKAMSIMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLL   99 (123)
T ss_dssp             HHHHHHHHHHCT-TCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCC-CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHHHh
Confidence            579999999976 689999999999999999999999999999999999999999999999754

>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=98.27  E-value=2.3e-06  Score=63.14  Aligned_cols=67  Identities=30%  Similarity=0.362  Sum_probs=60.6

Q ss_pred             hhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014           41 IANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD  108 (140)
Q Consensus        41 ~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~  108 (140)
                      ...|.|++|++-| +..||.+|...|...+..+...|+.+|...+...+|+||+..||..|++-+==+
T Consensus        39 ~~YIyKVLKQVhp-d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkr~TitsreIqtAvrLlLpG  105 (126)
T 1tzy_B           39 SIYVYKVLKQVHP-DTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPG  105 (126)
T ss_dssp             HHHHHHHHHHHCT-TCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHSCH
T ss_pred             HHHHHHHHHHhCC-CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcH
Confidence            3479999999976 689999999999999999999999999999999999999999999999755333

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

Probab=98.14  E-value=1.3e-05  Score=55.40  Aligned_cols=70  Identities=19%  Similarity=0.188  Sum_probs=62.9

Q ss_pred             cccCchhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014           36 DRLLPIANVGRIMKQILP-PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL  105 (140)
Q Consensus        36 d~~LP~A~V~RI~K~~lp-~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l  105 (140)
                      +..+|...|.||++..+. +..||++||..++.+-...|+......|...++..+..+|..+|+-+.+-.|
T Consensus        10 ~~~i~~~li~ril~~~F~~~kTkIs~dAl~l~aeyl~iFV~EAv~RA~~~a~~e~~~~le~e~LEki~pQL   80 (84)
T 4dra_E           10 GSGFRKELVSRLLHLHFKDDKTKVSGDALQLMVELLKVFVVEAAVRGVRQAQAEDALRVDVDQLEKVLPQL   80 (84)
T ss_dssp             -CCCCHHHHHHHHHTTCSSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHhcCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHH
Confidence            458999999999998886 4689999999999999999999999999999999999999999998877543

>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=98.03  E-value=2.6e-05  Score=52.88  Aligned_cols=66  Identities=18%  Similarity=0.352  Sum_probs=62.1

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      -|++..+..++++.=| ...+..|+-++|.+.|..||..+++.|...|+|-|-.||...||...|++
T Consensus         5 vl~k~~L~~Lv~~idp-~~~ld~~vee~ll~lADdFV~~V~~~ac~lAKhR~s~~le~kDvql~Ler   70 (76)
T 1h3o_B            5 VLTKKKLQDLVREVDP-NEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLER   70 (76)
T ss_dssp             SSCHHHHHHHHHHHCS-SCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHH
T ss_pred             cccHHHHHHHHHhcCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHh
Confidence            4799999999999954 67999999999999999999999999999999999999999999999885

>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=98.01  E-value=2.8e-05  Score=53.29  Aligned_cols=71  Identities=15%  Similarity=0.223  Sum_probs=62.8

Q ss_pred             ccccCchhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014           35 QDRLLPIANVGRIMKQILP-PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL  105 (140)
Q Consensus        35 ~d~~LP~A~V~RI~K~~lp-~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l  105 (140)
                      .+-.+|...|.||++.... +..||++||..++.+-...|+......|...++..|-..|..+|+-+.+-.|
T Consensus         5 ~~~~~~~~lI~ril~~~f~~~ktrI~~dAl~l~aeyl~iFV~EAv~RA~~~a~~e~~~~le~~~LEki~pqL   76 (81)
T 3b0b_C            5 REGGFRKETVERLLRLHFRDGRTRVNGDALLLMAELLKVFVREAAARAARQAQAEDLEKVDIEHVEKVLPQL   76 (81)
T ss_dssp             --CCCCHHHHHHHHHHHCCSTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHHHHhccCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeecHHHHHHHHHHH
Confidence            3558999999999999986 4679999999999999999999999999999999999999999998876543

>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=97.94  E-value=2.7e-05  Score=60.58  Aligned_cols=63  Identities=21%  Similarity=0.337  Sum_probs=58.7

Q ss_pred             hHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014           42 ANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL  105 (140)
Q Consensus        42 A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l  105 (140)
                      ..|.|++|++-| +..||.+|...|...+..++..|+.+|...+...+|+||+..||..|++-+
T Consensus         7 ~yi~kvLkqv~p-~~~iS~~Am~~m~s~v~di~~rIa~eA~~L~~~~~r~Tit~~eIq~Avrl~   69 (192)
T 2jss_A            7 SYIYKVLKQTHP-DTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLI   69 (192)
T ss_dssp             HHHHHHHHHHCS-SCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCSCCHHHHHHHHHHH
T ss_pred             HHHHHHHcccCC-CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHh
Confidence            468999999976 688999999999999999999999999999999999999999999999743

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

Probab=97.69  E-value=0.00015  Score=50.31  Aligned_cols=67  Identities=22%  Similarity=0.287  Sum_probs=60.5

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CCccCcccHHHHHHhcC
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEK-RKTVNGDDICWALATLG  106 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~k-RKTI~~eDVl~ALe~lg  106 (140)
                      .||++.|+|||...+  +..++.+...+|.-.+.+|+-.|...|.++..+.+ +..|.+.||..|.++|.
T Consensus        16 ~f~k~~vKrl~~~~~--~~~v~~~v~i~v~glaKvfVgelVE~A~~V~~~~~~~~Pl~P~HireA~rrl~   83 (89)
T 1bh9_B           16 AFPKAAIKRLIQSIT--GTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLK   83 (89)
T ss_dssp             CCCHHHHHHHHHHHH--SSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHc--CCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHHHH
Confidence            699999999999996  56899999999999999999999999999998776 44799999999988764

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

Probab=96.79  E-value=0.0028  Score=43.95  Aligned_cols=49  Identities=18%  Similarity=0.158  Sum_probs=42.5

Q ss_pred             CchhHHHHHHhhhCCC-CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 038014           39 LPIANVGRIMKQILPP-NAKISKEAKETMQECVSEFISFVTGEASDKCHK   87 (140)
Q Consensus        39 LP~A~V~RI~K~~lp~-~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~   87 (140)
                      ||+.+|.||++..+.+ +.||++||..++++-..+|+..-...|.+..+.
T Consensus         2 ip~~llaRIL~~~F~~~kTrIt~da~~lv~kY~diFVrEAv~Rs~e~ke~   51 (88)
T 3v9r_B            2 LSKEALIKILSQNEGGNDMKIADEVVPMIQKYLDIFIDEAVLRSLQSHKD   51 (88)
T ss_dssp             CCSHHHHHHHTTTSCSSCCEECTTTHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHhCCCCceecHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            8999999999988753 689999999999999999999888888766544

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=91.65  E-value=0.46  Score=37.68  Aligned_cols=80  Identities=19%  Similarity=0.210  Sum_probs=56.2

Q ss_pred             CchhHHHHHHhhhCC-CCccccHHHHHHHHHHHH----HHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh-cCCchhHH
Q 038014           39 LPIANVGRIMKQILP-PNAKISKEAKETMQECVS----EFISFVTGEASDKCHKEKRKTVNGDDICWALAT-LGFDNYAD  112 (140)
Q Consensus        39 LP~A~V~RI~K~~lp-~~~rIskdA~~al~~aa~----~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~-lgf~~y~~  112 (140)
                      ++...+..|++..+. .+..++.++...|.+.+.    ..+..+...|...|...++.+|+.+||..+++. ++...-..
T Consensus       259 ~~~~e~~~il~~~~~~~~~~~~~~~l~~l~~~~~~G~~r~~~~ll~~a~~~A~~~~~~~It~~~v~~a~~~~~~~~~~~~  338 (368)
T 3uk6_A          259 YSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSLFLDESRSTQ  338 (368)
T ss_dssp             CCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHSBCHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHhcCHHHHHH
Confidence            455667777775543 246799999999988775    356667778888888899999999999999986 44443333


Q ss_pred             HHHHHH
Q 038014          113 QLKRYL  118 (140)
Q Consensus       113 ~l~~~l  118 (140)
                      .+++..
T Consensus       339 ~~~~~~  344 (368)
T 3uk6_A          339 YMKEYQ  344 (368)
T ss_dssp             HHC---
T ss_pred             HHHHhh
Confidence            343333

>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=90.46  E-value=0.92  Score=42.56  Aligned_cols=69  Identities=13%  Similarity=0.205  Sum_probs=56.6

Q ss_pred             cccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           34 EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        34 ~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      -..+.+|.++|.|++|...  ..||+..|...+.-..+-....+...|...|+..+++.|++.||..|+..
T Consensus       100 ~~~l~~pv~~~~~~l~~~~--~~r~~~~~~~y~~avleyl~~~~l~la~~~~~~~~~~~i~p~~~~~ai~~  168 (1049)
T 3ksy_A          100 RNPLSLPVEKIHPLLKEVL--GYKIDHQVSVYIVAVLEYISADILKLVGNYVRNIRHYEITKQDIKVAMCA  168 (1049)
T ss_dssp             SSSCSSCHHHHHHHHHHHH--CSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCBCCHHHHHHHHHH
T ss_pred             cCCccccHHHHHHHhhccc--ccccCCCCcchhHHHHHHHHHHHHHHHHHHHHHcCCceecCccccccccC
Confidence            3578899999999996664  35999999988887766666666667778888899999999999998864

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

Probab=90.29  E-value=0.36  Score=37.03  Aligned_cols=79  Identities=14%  Similarity=0.140  Sum_probs=56.8

Q ss_pred             CcccccCCCCCCCCCCccccccc--cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCc
Q 038014           15 SYNFTVGASSGTDQDGVIKEQDR--LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKT   92 (140)
Q Consensus        15 ~~~~~~~~~~~~~~~~~~~~~d~--~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKT   92 (140)
                      .|||.--.|   +.-.-.+++..  .+|.+.+.|+.|.+  .+.-|.++-..-+...++.=+..|.-.|...|+.+||-+
T Consensus         4 ~~~~~~~~~---~~~~~~~~~~Mm~vmg~~kferlFR~a--agLDvdK~d~kr~~d~V~~Kl~DLl~va~~~Ak~NgRDv   78 (171)
T 1r4v_A            4 KYNFGKVSS---QHKNYSKIETMLRPKGFDKLDHYFRTE--LDIDLTDETIELLLNSVKAAFGKLFYGAEQRARWNGRDF   78 (171)
T ss_dssp             --------------------CCTTSCTTHHHHHHHHHHH--HCCCCCHHHHHHHHHHHHHHHHHTTTTHHHHHHHTTCSE
T ss_pred             ccccccchh---hhccHHHHHHHHhcCChHHHHHHHHHH--hccCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCe
Confidence            466655444   34455566777  88999999999999  457788999999999999999999999999999999999


Q ss_pred             cCcccH
Q 038014           93 VNGDDI   98 (140)
Q Consensus        93 I~~eDV   98 (140)
                      |...|+
T Consensus        79 I~~~DL   84 (171)
T 1r4v_A           79 IALADL   84 (171)
T ss_dssp             ECGGGS
T ss_pred             eccccC
Confidence            999885

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=85.88  E-value=3.3  Score=32.46  Aligned_cols=75  Identities=8%  Similarity=0.075  Sum_probs=54.9

Q ss_pred             CchhHHHHHHhhhCCC---CccccHHHHHHHHHHH------------HHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014           39 LPIANVGRIMKQILPP---NAKISKEAKETMQECV------------SEFISFVTGEASDKCHKEKRKTVNGDDICWALA  103 (140)
Q Consensus        39 LP~A~V~RI~K~~lp~---~~rIskdA~~al~~aa------------~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe  103 (140)
                      ++...+..+++..+..   ...++.++...+.+.+            -.++..+...|...|...++.+|+.+||..++.
T Consensus       193 l~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~l~~a~~~a~~~~~~~i~~~~v~~~~~  272 (389)
T 1fnn_A          193 YTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPEDVRKSSK  272 (389)
T ss_dssp             CBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHHHHHHHHHHhCCCCcCHHHHHHHHH
Confidence            3446677777665432   3478999999888887            345667777888888888999999999999998


Q ss_pred             hcCCchhHHH
Q 038014          104 TLGFDNYADQ  113 (140)
Q Consensus       104 ~lgf~~y~~~  113 (140)
                      ......+...
T Consensus       273 ~~~~~~~~~~  282 (389)
T 1fnn_A          273 EVLFGISEEV  282 (389)
T ss_dssp             HHSCCCCHHH
T ss_pred             HHhhhhHHHH
Confidence            8765544333

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=84.71  E-value=2.1  Score=33.42  Aligned_cols=66  Identities=8%  Similarity=0.056  Sum_probs=51.7

Q ss_pred             hhHHHHHHhhhCC---CCccccHHHHHHHHHHHH------HHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcC
Q 038014           41 IANVGRIMKQILP---PNAKISKEAKETMQECVS------EFISFVTGEASDKCHKEKRKTVNGDDICWALATLG  106 (140)
Q Consensus        41 ~A~V~RI~K~~lp---~~~rIskdA~~al~~aa~------~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lg  106 (140)
                      ...+..|++..+.   ....++.++...+.+.+.      ..+..+...|...|...++.+|+.+||..+++.+.
T Consensus       203 ~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~~l~~a~~~a~~~~~~~i~~~~v~~a~~~~~  277 (387)
T 2v1u_A          203 APQLRDILETRAEEAFNPGVLDPDVVPLCAALAAREHGDARRALDLLRVAGEIAERRREERVRREHVYSARAEIE  277 (387)
T ss_dssp             HHHHHHHHHHHHHHHBCTTTBCSSHHHHHHHHHHSSSCCHHHHHHHHHHHHHHHHHTTCSCBCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHh
Confidence            5667777765542   245789999998888776      56667777888888888999999999999998764

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

Probab=84.08  E-value=2.2  Score=31.89  Aligned_cols=59  Identities=14%  Similarity=0.240  Sum_probs=53.2

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccH
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDI   98 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDV   98 (140)
                      -+|.+.+.|+.|.+  .+.-|.|+-..-++..++.=+..|.-.|...|+.+||-+|...|+
T Consensus         2 vm~~~~~e~lFR~a--a~LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~n~RdvI~~~DL   60 (148)
T 1wwi_A            2 LMKVAEFERLFRQA--AGLDVDKNDLKRVSDFLRNKLYDLLAVAERNAKYNGRDLIFEPDL   60 (148)
T ss_dssp             CSCHHHHHHHHHHH--HCCCCCGGGHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECGGGS
T ss_pred             cCCHHHHHHHHHHH--hccCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeeccccC
Confidence            46788999999999  457788888899999999999999999999999999999999885

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=82.18  E-value=2.9  Score=34.94  Aligned_cols=66  Identities=12%  Similarity=0.075  Sum_probs=49.3

Q ss_pred             CchhHHHHHHhhhCC-CCccccHHHHHHHHHHH-H---HHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           39 LPIANVGRIMKQILP-PNAKISKEAKETMQECV-S---EFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        39 LP~A~V~RI~K~~lp-~~~rIskdA~~al~~aa-~---~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      ++...+..+++..+. .+..++.++...+.+.+ .   .....|...|...|...|+..|+.+||..++.-
T Consensus       366 ~~~~e~~~iL~~~~~~~~~~~~~~~~~~i~~~a~~g~~r~a~~ll~~a~~~A~~~~~~~v~~~~v~~~~~~  436 (456)
T 2c9o_A          366 YTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLLTPANLLAKINGKDSIEKEHVEEISEL  436 (456)
T ss_dssp             CCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHHHSCHHHHHHTHHHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHccCCCHHHHHHHHHHHHHHHhhcCCCccCHHHHHHHHHH
Confidence            445566666665432 24578999988888766 2   356667778888999999999999999999865

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=80.73  E-value=5.4  Score=30.97  Aligned_cols=72  Identities=7%  Similarity=0.025  Sum_probs=52.4

Q ss_pred             CchhHHHHHHhhhCC---CCccccHHHHHHHHHHHH------HHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCch
Q 038014           39 LPIANVGRIMKQILP---PNAKISKEAKETMQECVS------EFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDN  109 (140)
Q Consensus        39 LP~A~V~RI~K~~lp---~~~rIskdA~~al~~aa~------~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~  109 (140)
                      |+...+..+++..+.   ....++.++...+.+.+.      ..+..+...|...+...++.+|+.+||..|++++....
T Consensus       197 l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~ll~~a~~~a~~~~~~~i~~~~v~~a~~~~~~~~  276 (386)
T 2qby_A          197 YNAEELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDLLRVSGEIAERMKDTKVKEEYVYMAKEEIERDR  276 (386)
T ss_dssp             CCHHHHHHHHHHHHHHHBCSSCSCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHHhhch
Confidence            445667777765432   135789999888887765      34555777888888888999999999999998765443


Q ss_pred             h
Q 038014          110 Y  110 (140)
Q Consensus       110 y  110 (140)
                      +
T Consensus       277 ~  277 (386)
T 2qby_A          277 V  277 (386)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Homo sapiens}

Probab=80.26  E-value=1.5  Score=27.91  Aligned_cols=32  Identities=28%  Similarity=0.285  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014           74 ISFVTGEASDKCHKEKRKTVNGDDICWALATL  105 (140)
Q Consensus        74 i~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l  105 (140)
                      |..|..+|...|...++..|+.+|+..||++.
T Consensus        42 i~~l~~eA~~~a~~~~~~~i~~~d~~~Al~~v   73 (78)
T 3kw6_A           42 VKGVCTEAGMYALRERRVHVTQEDFEMAVAKV   73 (78)
T ss_dssp             HHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Confidence            66677778888888899999999999999863

---

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	140
d2bykb1	89	a.22.1.3 (B:11-99) Chrac-14 {Fruit fly (Drosophila	5e-39
d1n1ja_	87	a.22.1.3 (A:) Nuclear transcription factor Y subun	3e-36
d1jfib_	135	a.22.1.3 (B:) Negative cofactor 2, NC2, beta chain	3e-35
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	1e-21
d1f1ea_	151	a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy	3e-15
d1htaa_	68	a.22.1.2 (A:) Archaeal histone {Archaeon Methanoth	4e-21
d1ku5a_	66	a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococc	5e-21
d1jfia_	66	a.22.1.3 (A:) Negative cofactor 2, NC2, alpha chai	6e-19
d1n1jb_	78	a.22.1.3 (B:) Nuclear transcription factor Y subun	2e-18
d2huec1	82	a.22.1.1 (C:20-101) Histone H4 {African clawed fro	1e-09

>d2bykb1 a.22.1.3 (B:11-99) Chrac-14 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 89

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]

 Score =  124 bits (314), Expect = 5e-39
 Identities = 31/89 (34%), Positives = 50/89 (56%)

Query: 40  PIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDIC 99
           P A +GR++K+ LP +A +SKEA+  +    S F  FVT  ++   HK+  KT+   DI 
Sbjct: 1   PNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDIL 60

Query: 100 WALATLGFDNYADQLKRYLHRYRELEGER 128
             L  L F+++   L + L  YR++  E+
Sbjct: 61  QTLTELDFESFVPSLTQDLEVYRKVVKEK 89

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

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

 Score =  117 bits (295), Expect = 3e-36
 Identities = 55/86 (63%), Positives = 72/86 (83%)

Query: 38  LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDD 97
            LPIANV RIMK  +P   KI+K+AKE +QECVSEFISF+T EAS++CH+EKRKT+NG+D
Sbjct: 2   YLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGED 61

Query: 98  ICWALATLGFDNYADQLKRYLHRYRE 123
           I +A++TLGFD+Y + LK YL ++RE
Sbjct: 62  ILFAMSTLGFDSYVEPLKLYLQKFRE 87

>d1jfib_ a.22.1.3 (B:) Negative cofactor 2, NC2, beta chain {Human (Homo sapiens) [TaxId: 9606]} Length = 135

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]

 Score =  116 bits (293), Expect = 3e-35
 Identities = 29/105 (27%), Positives = 61/105 (58%), Gaps = 1/105 (0%)

Query: 36  DRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNG 95
           D  +P A + +++K+ LP N +++ +A+E +  C +EFI  ++ EA++ C+K ++KT++ 
Sbjct: 2   DLTIPRAAINKMIKETLP-NVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISP 60

Query: 96  DDICWALATLGFDNYADQLKRYLHRYRELEGERANQNKAGNNNNG 140
           + +  AL +LGF +Y  ++K  L   + +  +R   +    N   
Sbjct: 61  EHVIQALESLGFGSYISEVKEVLQECKTVALKRRKASSRLENLGI 105

>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 = 82.1 bits (203), Expect = 1e-21
 Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 1/68 (1%)

Query: 39  LPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDI 98
           LP A + RI +Q +    ++S++AK+T+ + V     +V   A        +KT+  + +
Sbjct: 2   LPKAAIERIFRQGIG-ERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHL 60

Query: 99  CWALATLG 106
                 L 
Sbjct: 61  KALADVLM 68

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

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

 Score = 65.6 bits (160), Expect = 3e-15
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 2/73 (2%)

Query: 30  GVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEK 89
           GV      L   A V RI+K+      + S +A +   + +      +  +A++   ++ 
Sbjct: 71  GVEDYDGELFGRATVRRILKRAGI--ERASSDAVDLYNKLICRATEELGEKAAEYADEDG 128

Query: 90  RKTVNGDDICWAL 102
           RKTV G+D+  A+
Sbjct: 129 RKTVQGEDVEKAI 141

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

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

 Score = 78.6 bits (194), Expect = 4e-21
 Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 2/67 (2%)

Query: 39  LPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDI 98
           LPIA +GRI+K       ++S +A+  + + + E    +  EA        RKT+  +DI
Sbjct: 4   LPIAPIGRIIKNAGAE--RVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDI 61

Query: 99  CWALATL 105
             A    
Sbjct: 62  ELARKMF 68

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

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

 Score = 78.3 bits (193), Expect = 5e-21
 Identities = 18/66 (27%), Positives = 36/66 (54%), Gaps = 2/66 (3%)

Query: 39  LPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDI 98
           LPIA V R++++      ++S++A + + E + E+   +  +A +      RKTV  +DI
Sbjct: 3   LPIAPVDRLIRKAGAE--RVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDI 60

Query: 99  CWALAT 104
             A+ +
Sbjct: 61  KLAIKS 66

>d1jfia_ a.22.1.3 (A:) Negative cofactor 2, NC2, alpha chain {Human (Homo sapiens) [TaxId: 9606]} Length = 66

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

 Score = 73.2 bits (180), Expect = 6e-19
 Identities = 9/64 (14%), Positives = 22/64 (34%), Gaps = 1/64 (1%)

Query: 39  LPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDI 98
            P A + +IM+       K++      +   +  F+  +  +A         KT+    +
Sbjct: 3   FPPARIKKIMQT-DEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHL 61

Query: 99  CWAL 102
              +
Sbjct: 62  KQCI 65

>d1n1jb_ a.22.1.3 (B:) Nuclear transcription factor Y subunit gamma (Nf-Yc2) {Human (Homo sapiens) [TaxId: 9606]} Length = 78

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

 Score = 72.2 bits (177), Expect = 2e-18
 Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 39  LPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDI 98
           LP+A + +IMK        IS EA     +    FI+ +T  A       KR+T+  +DI
Sbjct: 1   LPLARIKKIMKL-DEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDI 59

Query: 99  CWALAT 104
             A+  
Sbjct: 60  AMAITK 65

>d2huec1 a.22.1.1 (C:20-101) Histone H4 {African clawed frog (Xenopus laevis) [TaxId: 8355]} Length = 82

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]

 Score = 49.8 bits (119), Expect = 1e-09
 Identities = 17/76 (22%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 31  VIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKR 90
           V+++  + +    + R+ ++      +IS    E  +  +  F+  V  +A       KR
Sbjct: 2   VLRDNIQGITKPAIRRLARRG--GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKR 59

Query: 91  KTVNGDDICWALATLG 106
           KTV   D+ +AL   G
Sbjct: 60  KTVTAMDVVYALKRQG 75

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	140
d1jfib_	135	Negative cofactor 2, NC2, beta chain {Human (Homo	99.95
d2bykb1	89	Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax	99.95
d1n1ja_	87	Nuclear transcription factor Y subunit beta (Nf-Yb	99.94
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	99.78
d1ku5a_	66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	99.77
d1n1jb_	78	Nuclear transcription factor Y subunit gamma (Nf-Y	99.73
d1jfia_	66	Negative cofactor 2, NC2, alpha chain {Human (Homo	99.64
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	99.59
d1f1ea_	151	Archaeal histone {Archaeon Methanopyrus kandleri [	99.54
d2huec1	82	Histone H4 {African clawed frog (Xenopus laevis) [	99.41
d1tzyc_	95	Histone H3 {Chicken (Gallus gallus), erythrocytes	99.19
d2byka1	72	Chrac-16 {Fruit fly (Drosophila melanogaster) [Tax	98.8
d1q9ca_	172	Histone domain of Son of sevenless protein {Human	98.54
d1tzyb_	92	Histone H2B {Chicken (Gallus gallus), erythrocytes	97.97
d1h3ob_	74	TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom	97.77
d1tafb_	70	TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta	97.73
d1bh9b_	89	TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]}	97.62
d1f66c_	103	Histone H2A {Human (Homo sapiens), variant H2A.Z [	97.58
d1u35c1	106	macro-H2A.1, histone domain {Human (Homo sapiens)	97.38
d1tzya_	106	Histone H2A {Chicken (Gallus gallus), erythrocytes	97.09
d1tafa_	68	TAF(II)42 {Fruit fly (Drosophila melanogaster) [Ta	96.92
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	95.49
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	94.74
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	87.4
d1wwia1	148	Hypothetical protein TTHA1479 {Thermus thermophilu	85.93

>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=99.95  E-value=3e-28  Score=180.25  Aligned_cols=99  Identities=28%  Similarity=0.626  Sum_probs=93.8

Q ss_pred             ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHHHH
Q 038014           35 QDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQL  114 (140)
Q Consensus        35 ~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~~l  114 (140)
                      +|+.||+|+|.||||..+| +++||+||+.+|++||++||.||++.|++.|...+||||+++||++||+.+||.+|+++|
T Consensus         1 ddl~LP~a~I~kI~K~~~~-~~~is~dA~~~i~~a~~~Fi~~lt~~A~~~a~~~~RkTi~~~Dv~~Al~~~~f~~f~~~l   79 (135)
T d1jfib_           1 DDLTIPRAAINKMIKETLP-NVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALESLGFGSYISEV   79 (135)
T ss_dssp             CCCCCCHHHHHHHHHHHST-TCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHTTGGGHHHH
T ss_pred             CcccccHHHHHHHHhhCCc-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHcCcHHHHHHH
Confidence            5899999999999999987 789999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhhcc
Q 038014          115 KRYLHRYRELEGERANQNKA  134 (140)
Q Consensus       115 ~~~l~~~re~~~~kk~q~k~  134 (140)
                      +..+..|++..+.||..++.
T Consensus        80 ~~~l~~~ke~~~~kk~~~~~   99 (135)
T d1jfib_          80 KEVLQECKTVALKRRKASSR   99 (135)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhhccc
Confidence            99999999999888655443

>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=99.95  E-value=6.3e-28  Score=166.93  Aligned_cols=89  Identities=35%  Similarity=0.596  Sum_probs=86.7

Q ss_pred             chhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHHHHHHHHH
Q 038014           40 PIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLH  119 (140)
Q Consensus        40 P~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~~l~~~l~  119 (140)
                      |+|+|+||||+.+|++++||+||+.+|++|+++||.||+++|++.|...+||||+++||+.||+++||++|+++|+.+|+
T Consensus         1 P~a~i~ri~K~~~p~~~~iskeA~~~i~~aae~FI~~lt~~A~~~a~~~~rKtI~~~dv~~Al~~~~f~~~~~~l~~~l~   80 (89)
T d2bykb1           1 PNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFESFVPSLTQDLE   80 (89)
T ss_dssp             CCSHHHHHHHHHSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCTTTHHHHHHHHH
T ss_pred             CccHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHCCcHHHHHHHHHHHH
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHH
Q 038014          120 RYRELEGER  128 (140)
Q Consensus       120 ~~re~~~~k  128 (140)
                      .||+.++.|
T Consensus        81 ~~~e~~~~k   89 (89)
T d2bykb1          81 VYRKVVKEK   89 (89)
T ss_dssp             HHHHHHTTC
T ss_pred             HHHHHHccC
Confidence            999988753

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

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

Probab=99.94  E-value=3.1e-27  Score=162.67  Aligned_cols=87  Identities=63%  Similarity=1.078  Sum_probs=85.0

Q ss_pred             ccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHHHHHH
Q 038014           37 RLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKR  116 (140)
Q Consensus        37 ~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~~l~~  116 (140)
                      +.||+|+|+||||+.+|++.+||+||+.++++|+++||.+|+++|++.|...+||||+++||+.|++++||.+|.++|+.
T Consensus         1 l~LP~a~v~ri~K~~~p~~~~is~ea~~~i~~a~e~Fi~~lt~~A~~~a~~~~rKTI~~~dv~~Al~~~~~~~fl~~l~~   80 (87)
T d1n1ja_           1 IYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYVEPLKL   80 (87)
T ss_dssp             CCCCHHHHHHHHHHTSCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTTCGGGHHHHHH
T ss_pred             CCCcHhHHHHHHHHhCCccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHcCcHhHHHHHHH
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHH
Q 038014          117 YLHRYRE  123 (140)
Q Consensus       117 ~l~~~re  123 (140)
                      ++++||+
T Consensus        81 ~~~~~ke   87 (87)
T d1n1ja_          81 YLQKFRE   87 (87)
T ss_dssp             HHHHHHC
T ss_pred             HHHHhcC
Confidence            9999985

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

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

Probab=99.78  E-value=2.7e-19  Score=117.05  Aligned_cols=66  Identities=29%  Similarity=0.431  Sum_probs=62.7

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL  105 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l  105 (140)
                      .||+++|+||||..  +..+||+|+..+|++|+++|+.+|+.+|+++|.++|||||+++||..||+.+
T Consensus         3 eLP~a~I~ri~k~~--~~~ris~ea~~~l~~~~e~fi~~l~~~a~~~a~~~kRkTi~~~DV~~Alk~~   68 (68)
T d1htaa_           3 ELPIAPIGRIIKNA--GAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARKMF   68 (68)
T ss_dssp             CSCHHHHHHHHHHT--TCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHTC
T ss_pred             cCcHHHHHHHHHHC--CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHhC
Confidence            49999999999998  4568999999999999999999999999999999999999999999999874

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

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

Probab=99.77  E-value=2.5e-19  Score=116.84  Aligned_cols=64  Identities=28%  Similarity=0.419  Sum_probs=61.3

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA  103 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe  103 (140)
                      .||+++|+||||...+  .+||+||..+|++|+++||.+|+..|+++|.+.|||||+++||..||+
T Consensus         2 ~LP~a~I~rI~k~~~~--~ris~ea~~~l~~a~e~Fi~~l~~~a~~~a~~~~RKTI~~~Dv~~Al~   65 (66)
T d1ku5a_           2 ELPIAPVDRLIRKAGA--ERVSEQAAKVLAEYLEEYAIEIAKKAVEFARHAGRKTVKVEDIKLAIK   65 (66)
T ss_dssp             CSCHHHHHHHHHHTTC--SEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHT
T ss_pred             CCCHHHHHHHHHhCcc--cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHh
Confidence            6999999999999954  699999999999999999999999999999999999999999999986

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

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

Probab=99.73  E-value=2.6e-18  Score=114.98  Aligned_cols=72  Identities=28%  Similarity=0.322  Sum_probs=67.9

Q ss_pred             CchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhH
Q 038014           39 LPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYA  111 (140)
Q Consensus        39 LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~  111 (140)
                      ||.++|+||||. .|+..+||+||+.++++|+++||.+|+..|.+.|...+||||+++||..|++..+..+|.
T Consensus         1 LP~srVkrImK~-~~~~~~is~ea~~~i~~a~E~Fi~~l~~~A~~~a~~~~rkti~~~dl~~av~~~~~~~FL   72 (78)
T d1n1jb_           1 LPLARIKKIMKL-DEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFL   72 (78)
T ss_dssp             CCHHHHHHHHTT-STTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHTTCGGGGGG
T ss_pred             CCHHHHHHHHhc-CCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHhcCChhHHH
Confidence            899999999996 477889999999999999999999999999999999999999999999999998877774

>d1jfia_ a.22.1.3 (A:) Negative cofactor 2, NC2, alpha chain {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=99.64  E-value=6.8e-17  Score=105.26  Aligned_cols=64  Identities=14%  Similarity=0.214  Sum_probs=57.9

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHH
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWAL  102 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~AL  102 (140)
                      .||.++|+||||.. |+..+||+||+.+|++|++.|+.+|+..|.+.|...+||||+++||..|+
T Consensus         2 ~fP~srVkkimk~~-~~~~~is~~A~~~~~~a~E~Fi~~l~~~A~~~a~~~krktI~~~dl~~ai   65 (66)
T d1jfia_           2 RFPPARIKKIMQTD-EEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQCI   65 (66)
T ss_dssp             CCCHHHHHHHHTTS-TTCCCBCTTHHHHHHHHHHHHHHHHHHHHHHHHHTC---CBCHHHHHTTC
T ss_pred             CCChHHHHHHHhcC-CccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHh
Confidence            48999999999998 77789999999999999999999999999999999999999999998775

>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=99.59  E-value=1.1e-15  Score=113.67  Aligned_cols=68  Identities=24%  Similarity=0.329  Sum_probs=65.2

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcC
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLG  106 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lg  106 (140)
                      +||+|+|.||||+.+| +.+||+||.+.|+.|+++|+++|+++|+.+|.++|||||+++||..|++.+|
T Consensus         1 ~lP~a~I~rilk~~~~-~~ris~da~~~l~~~~~~~~~~Ia~eA~~l~~~~~rKTi~~edi~~a~~~~~   68 (151)
T d1f1ea_           1 ELPKAAIERIFRQGIG-ERRLSQDAKDTIYDFVPTMAEYVANAAKSVLDASGKKTLMEEHLKALADVLM   68 (151)
T ss_dssp             CCCHHHHHHHHHTTST-TCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHHHT
T ss_pred             CCCccHHHHHHHHhCC-ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHhcc
Confidence            5999999999999987 5699999999999999999999999999999999999999999999998877

>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=99.54  E-value=6.9e-15  Score=109.36  Aligned_cols=74  Identities=24%  Similarity=0.324  Sum_probs=68.4

Q ss_pred             CCccccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           29 DGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        29 ~~~~~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      +.+.+.+++.||+++|+||||..  +..|||+||..+|+++++.|+..|+..|+.+|.+.|||||+++||..||..
T Consensus        70 ~~~~~~~~~~fp~a~IkRi~k~~--g~~ris~dA~~~l~~~~E~fi~~l~~~A~~~a~~~kRkTI~~~DI~~Av~~  143 (151)
T d1f1ea_          70 EGVEDYDGELFGRATVRRILKRA--GIERASSDAVDLYNKLICRATEELGEKAAEYADEDGRKTVQGEDVEKAITY  143 (151)
T ss_dssp             TTSTTCCSCCCCHHHHHHHHHHT--TCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH
T ss_pred             ccccccccCccCHHHHHHHHHcC--CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHH
Confidence            44456678899999999999987  678999999999999999999999999999999999999999999999975

>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=99.41  E-value=1.8e-13  Score=92.69  Aligned_cols=69  Identities=23%  Similarity=0.261  Sum_probs=65.5

Q ss_pred             ccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCC
Q 038014           37 RLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGF  107 (140)
Q Consensus        37 ~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf  107 (140)
                      ..+|++.|+||++.+  +..+||+|+.++|.++.+.|+..++.+|...|+|++||||+++||..||+++|-
T Consensus         8 ~gI~k~~i~Riar~~--Gv~ris~d~~~~l~~~l~~~l~~i~~~a~~~~~hakRKTvt~~DV~~Alkr~g~   76 (82)
T d2huec1           8 QGITKPAIRRLARRG--GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR   76 (82)
T ss_dssp             CSSCHHHHHHHHHHT--TCCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTTTCE
T ss_pred             cCcCHHHHHHHHHHc--CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHhcCC
Confidence            369999999999999  677999999999999999999999999999999999999999999999998764

>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=99.19  E-value=2.4e-11  Score=84.37  Aligned_cols=73  Identities=18%  Similarity=0.191  Sum_probs=66.7

Q ss_pred             ccccccCchhHHHHHHhhhC---CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014           33 KEQDRLLPIANVGRIMKQIL---PPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL  105 (140)
Q Consensus        33 ~~~d~~LP~A~V~RI~K~~l---p~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l  105 (140)
                      +..++.||++++.|++|+..   .++++++.+|..+||+++|.|+..|...|+.+|.|.||.||++.|+..|..-.
T Consensus        16 kst~lLIpk~pF~RLVRei~~~~~~~~r~~~~Al~aLQea~E~yLv~lfeda~~~a~HakRvTl~~kD~~Larrir   91 (95)
T d1tzyc_          16 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR   91 (95)
T ss_dssp             HCCSCCSCHHHHHHHHHHHHHHHCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             CCcccccccccHHHHHHHHHHhcCCCCEeeHHHHHHHHHHHHHHHHHHHHHhHHHHHhcCCCcCCHHHHHHHHHHh
Confidence            35788999999999999985   34789999999999999999999999999999999999999999999887543

>d2byka1 a.22.1.3 (A:29-100) Chrac-16 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: Chrac-16
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=98.80  E-value=3.5e-09  Score=69.43  Aligned_cols=59  Identities=12%  Similarity=0.169  Sum_probs=50.8

Q ss_pred             CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHH-hCCCCccCcccHHHHHHhcCCchhH
Q 038014           53 PPNAKISKEAKETMQECVSEFISFVTGEASDKCH-KEKRKTVNGDDICWALATLGFDNYA  111 (140)
Q Consensus        53 p~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~-~~kRKTI~~eDVl~ALe~lgf~~y~  111 (140)
                      |+...||.||..++++|+|.||.+|+..|...+. ..+||||+++||..|++.-+--+|.
T Consensus         5 ~dv~~is~ea~~lvskAtElFi~~L~~~a~~~a~~~~~~ktl~~~dl~~aV~~~~~f~FL   64 (72)
T d2byka1           5 MDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEFL   64 (72)
T ss_dssp             SSCSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSCEECHHHHHHHHHTCSTTGGG
T ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCccccHHHHHHHHccCchhhHH
Confidence            4456899999999999999999999999998885 4566999999999999987655554

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

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

Probab=98.54  E-value=7.4e-08  Score=72.64  Aligned_cols=68  Identities=13%  Similarity=0.186  Sum_probs=61.9

Q ss_pred             ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           35 QDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        35 ~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      ..+.||.+.|.|++|+.  ...|||.+|...|...++-+...|...|...|++.||+||+++||..|+..
T Consensus        96 agL~fPV~rv~rlLk~~--~a~RVs~~A~vyLaavLEyl~aeILelAgn~a~~~krkrItp~dI~lAi~n  163 (172)
T d1q9ca_          96 NPLSLPVEKIHPLLKEV--LGYKIDHQVSVYIVAVLEYISADILKLAGNYVRNIRHYEITKQDIKVAMCA  163 (172)
T ss_dssp             ---CCCHHHHHHHHHHH--HSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSBCCHHHHHHHHHT
T ss_pred             cCceecHHHHHHHHHhc--cccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCceecHHHHHHHHhC
Confidence            56889999999999998  357999999999999999999999999999999999999999999999864

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

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

Probab=97.97  E-value=1.1e-05  Score=54.84  Aligned_cols=62  Identities=32%  Similarity=0.448  Sum_probs=58.3

Q ss_pred             HHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014           43 NVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL  105 (140)
Q Consensus        43 ~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l  105 (140)
                      -|.|++|++-| +..||..|...|+.-+......|+.+|...|.-.+|+||+..+|..|+.-+
T Consensus         8 Yi~kVLKqVhp-~~giS~kam~imnsfvndiferIa~EA~~La~~~kr~TitsreIqtAvrL~   69 (92)
T d1tzyb_           8 YVYKVLKQVHP-DTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLL   69 (92)
T ss_dssp             HHHHHHHHHCT-TCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHH
T ss_pred             HHHHHHHhhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHH
Confidence            58999999987 789999999999999999999999999999999999999999999999744

>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=97.77  E-value=6.7e-05  Score=49.05  Aligned_cols=66  Identities=18%  Similarity=0.352  Sum_probs=60.9

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      -|-+..+..++++.=| ...+..|+-+.+.+.|..||..++..|...|++.|-.||...||...|++
T Consensus         3 il~K~~L~eLv~~idp-~~~ld~~vee~ll~iADdFV~~V~~~ac~lAKhR~s~~le~kDvql~LeR   68 (74)
T d1h3ob_           3 VLTKKKLQDLVREVDP-NEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDVQLHLER   68 (74)
T ss_dssp             SSCHHHHHHHHHHHCS-SCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCEECHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCcHHHHHHHHHh
Confidence            3678889999999954 67899999999999999999999999999999999999999999999875

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

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

Probab=97.73  E-value=7.6e-05  Score=48.32  Aligned_cols=64  Identities=20%  Similarity=0.226  Sum_probs=59.3

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA  103 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe  103 (140)
                      .+|..+|+-|+...  +-..++.|+...|.+-++-=|..+..+|....+|.+|++++.+||-.||+
T Consensus         6 ~~~~esik~iAeS~--Gi~~l~de~a~~LA~DveYRl~eiiQeA~KFMrhskR~~Ltt~Did~ALk   69 (70)
T d1tafb_           6 SISAESMKVIAESI--GVGSLSDDAAKELAEDVSIKLKRIVQDAAKFMNHAKRQKLSVRDIDMSLK   69 (70)
T ss_dssp             CCCHHHHHHHHHHT--TCCCBCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHC
T ss_pred             cCCHHHHHHHHHHc--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcCcHHHHHHHHc
Confidence            58999998888888  45579999999999999999999999999999999999999999999985

>d1bh9b_ a.22.1.3 (B:) TAF(II)28 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)28
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.62  E-value=0.0001  Score=49.66  Aligned_cols=68  Identities=22%  Similarity=0.270  Sum_probs=60.2

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-CccCcccHHHHHHhcCC
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKR-KTVNGDDICWALATLGF  107 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kR-KTI~~eDVl~ALe~lgf  107 (140)
                      .||++.|+|||...++  ..|+.....++.-.+.+|+-.|-..|.+++...+- ..|.++||..|..+|.-
T Consensus        16 ~~~K~~vkrl~~~~~g--~sv~~~v~i~v~giaKvFvGEiVE~A~~V~~~~~e~~PL~P~HireA~rrl~~   84 (89)
T d1bh9b_          16 AFPKAAIKRLIQSITG--TSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLKS   84 (89)
T ss_dssp             CCCHHHHHHHHHHHHS--SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSCCHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHHcC--CCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHH
Confidence            4999999999999974  68999999999999999999999999999876654 47999999999887643

>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=97.58  E-value=0.00013  Score=50.31  Aligned_cols=70  Identities=13%  Similarity=0.138  Sum_probs=60.6

Q ss_pred             ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           35 QDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        35 ~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      ..+.||.+.|.|++|+.--...||+..|...|.-+.|-....+...|...|...+++.|+++||..|+..
T Consensus         8 AgL~FpVgrv~r~L~~~~~~~~rv~~~A~VyLaAvLEYL~aEILelagn~a~~~~~~rItpr~l~lai~n   77 (103)
T d1f66c_           8 AGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG   77 (103)
T ss_dssp             HTCSSCHHHHHHHHHHTSCSSCEECTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSEECHHHHHHHHHH
T ss_pred             CCcccChHHHHHHHhccCccceecCCCceeeHHHHHHHHHHHHHHHhhhhhccCCCCeeechhhhccccC
Confidence            4678999999999998743345799999999999888878888888888899999999999999999874

>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=97.38  E-value=0.00032  Score=48.52  Aligned_cols=68  Identities=19%  Similarity=0.229  Sum_probs=59.7

Q ss_pred             ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014           35 QDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA  103 (140)
Q Consensus        35 ~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe  103 (140)
                      ..+.||.+.|.|++|+.-. ..||+..|...+.-+.|-....+...|-..|...+++.|+++||..|+.
T Consensus         8 agL~FpV~ri~r~Lk~~~~-~~rv~~~apVylaAVLEYL~aEILELAgn~a~~~k~~rItprhi~lair   75 (106)
T d1u35c1           8 AGVIFPVGRMLRYIKKGHP-KYRIGVGAPVYMAAVLEYLTAEILELAVNAARDNKKGRVTPRHILLAVA   75 (106)
T ss_dssp             HTCSSCHHHHHHHHHHHST-TSEECTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHH
T ss_pred             CCcccCHHHHHHHHhCCCC-ccccCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCeeecchhhhccc
Confidence            4678999999999999732 5699999999999888877778888888899999999999999999985

>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=97.09  E-value=0.001  Score=45.83  Aligned_cols=69  Identities=10%  Similarity=0.163  Sum_probs=57.0

Q ss_pred             ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           35 QDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        35 ~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      ..+.||.+.|.|++|+.-- ..||+..|...+.-..|=....+...|-..|...+++.|+++|+..|+..
T Consensus         9 AgL~FpV~rv~r~Lk~~~~-~~rv~~~apVylaAVLEYLtaEiLELAgn~a~~~k~~rItPrhi~lAirn   77 (106)
T d1tzya_           9 AGLQFPVGRVHRLLRKGNY-AERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRN   77 (106)
T ss_dssp             HTCSSCHHHHHHHHHHTTS-SSEECTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHT
T ss_pred             CCccCChHHHHHHHHcCcc-ccccCCCchHHHHHHHHHHHHHHHHHhhHHHHhcCCceecchhhhhcccC
Confidence            5678999999999999632 45999999988887666666666666777889999999999999999863

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

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

Probab=96.92  E-value=0.0024  Score=40.79  Aligned_cols=59  Identities=15%  Similarity=0.249  Sum_probs=50.8

Q ss_pred             HHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014           43 NVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA  103 (140)
Q Consensus        43 ~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe  103 (140)
                      .|.-|+|+.  +-.....-....|.+.+-.++..+..+|.-++.|+||++|+++||..|++
T Consensus         6 ~i~~iL~~~--GV~~yeprV~~qlLef~yRYtt~VL~DA~vys~HA~k~~id~dDVkLAi~   64 (68)
T d1tafa_           6 VIMSILKEL--NVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLATE   64 (68)
T ss_dssp             HHHHHHHHT--TCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHH
T ss_pred             HHHHHHHHc--CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHH
Confidence            355566666  44567888889999999999999999999999999999999999999986

>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=95.49  E-value=0.032  Score=39.79  Aligned_cols=54  Identities=9%  Similarity=0.135  Sum_probs=41.9

Q ss_pred             CccccHHHHHHHHHHHH------------HHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014           55 NAKISKEAKETMQECVS------------EFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD  108 (140)
Q Consensus        55 ~~rIskdA~~al~~aa~------------~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~  108 (140)
                      ...++.++.+.|.+-+.            .-+..+...|...|...++++|+.+||..|++++-|+
T Consensus       211 ~~~~~~~~l~~ia~~~~~~~~~~~~~G~~R~a~~ll~~a~~~A~~~~~~~I~~edv~~A~~~~~~g  276 (276)
T d1fnna2         211 EGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPEDVRKSSKEVLFG  276 (276)
T ss_dssp             TTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHSCC
T ss_pred             cccccHHHHHHHHHHhhhhhhhhhcCCCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHhCC
Confidence            45688998887766431            1234455678899999999999999999999998774

>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=94.74  E-value=0.07  Score=38.13  Aligned_cols=50  Identities=10%  Similarity=0.048  Sum_probs=39.3

Q ss_pred             CccccHHHHHHHHHHHH---------HHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014           55 NAKISKEAKETMQECVS---------EFISFVTGEASDKCHKEKRKTVNGDDICWALAT  104 (140)
Q Consensus        55 ~~rIskdA~~al~~aa~---------~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~  104 (140)
                      ...++.++.+.+.+-+.         .-+..+...|...|..+++.+|+.+||.+|+++
T Consensus       228 ~~~~~~~al~~ia~~~~~~~~~~gd~R~ai~~l~~a~~~A~~~~~~~It~~~V~~A~~e  286 (287)
T d1w5sa2         228 DTVWEPRHLELISDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSE  286 (287)
T ss_dssp             TTSCCHHHHHHHHHHHCGGGTSCCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHhccccCCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhc
Confidence            34688999888876542         134456677889999999999999999999875

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

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: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=87.40  E-value=0.68  Score=32.83  Aligned_cols=70  Identities=14%  Similarity=0.125  Sum_probs=52.0

Q ss_pred             chhHHHHHHhhhCC-CCccccHHHHHHHHHHHH---HHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCch
Q 038014           40 PIANVGRIMKQILP-PNAKISKEAKETMQECVS---EFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDN  109 (140)
Q Consensus        40 P~A~V~RI~K~~lp-~~~rIskdA~~al~~aa~---~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~  109 (140)
                      +...+.++++..+. .++.++.++...|.+.+.   .....+...+...+...+...|+.+++.++|..|+.++
T Consensus       166 ~~~~~~~i~~~~~~~~~i~~~~~~l~~ia~~s~gd~R~a~~~l~~~~~~a~~~~~~~It~~~~~~~l~~l~~De  239 (239)
T d1ixsb2         166 TPEELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRLFRRVRDFAQVAGEEVITRERALEALAALGLDE  239 (239)
T ss_dssp             CHHHHHHHHHHHHGGGCCCBCHHHHHHHHHHTTSSHHHHHHHHHHHHHHHTTSCCSCBCHHHHHHHHHHHTCCT
T ss_pred             ChhhhhHHHHHHHHHhCCccchHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhhhCcCC
Confidence            34445555554442 367899999999988775   44445556677788888999999999999999998764

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

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

Probab=85.93  E-value=0.82  Score=32.46  Aligned_cols=59  Identities=14%  Similarity=0.240  Sum_probs=53.7

Q ss_pred             cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccH
Q 038014           38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDI   98 (140)
Q Consensus        38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDV   98 (140)
                      .+|.+.+.|+.|.+  .+.-|.++-..-+...++.=+..|.-.|.+.|+.+||-+|...|+
T Consensus         2 ~m~~~k~e~~FR~a--a~LdvdK~d~~r~~d~V~~Kl~DLllva~~~A~~n~RdvI~~~DL   60 (148)
T d1wwia1           2 LMKVAEFERLFRQA--AGLDVDKNDLKRVSDFLRNKLYDLLAVAERNAKYNGRDLIFEPDL   60 (148)
T ss_dssp             CSCHHHHHHHHHHH--HCCCCCGGGHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECGGGS
T ss_pred             CCcHHHHHHHHHHH--hccCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeeccccC
Confidence            47889999999999  457788999999999999999999999999999999999999885