Citrus Sinensis ID: 029524

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190--
Protein Sequence
MATEGEAVTEQQPAAEEPEKVVTEKKAKAAKEKKPKAPKEKKPKQSKTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKLSEAAAGKTKKEIKTKAKAPRKTRSVTAAAKIKAESAAAAPPPPKKAKKSAAAKPKQPKSIKSPAAKKAKKAAAQ
Secondary Structure (PSIPRED)
cccccccccccccccccccccHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHccccccccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHcccEEEEcccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHcccEEEEEccEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mategeavteqqpaaeepeKVVTEKKAKAAkekkpkapkekkpkqsktpshppyFQMITEALMALqdksgsspYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKLSEAAAGKTKKEIKtkakaprktrSVTAAAKIKaesaaaappppkkakksaaakpkqpksikspAAKKAKKAAAQ
Flexible Loop (DISEMBL)
mategeavteqqpaaeepekvvTEKKakaakekkpkapkekkpkqsktpshpPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKlseaaagktkkeiktkakaprktrsvtAAAKIkaesaaaappppkkakksaaakpkqpksikspaakkakkaaaq
Low Complexity Region (SEG)
MATEGEAVTEQQpaaeepekvvtekkakaakekkpkapkekkpkQSKTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKLSeaaagktkkeiktkakaPRKTRSVTaaakikaesaaaappppkkakksaaakpkqpksikspaakkakkaaaQ
Disordered region (IsUnstruct)
*********************************************************IT****************IAKY********LPANFRKILAVQLKHFAAKGNLIKIRASYKL**************************************************************************
Disordered Region (DISOPRED)
******************************************************FQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRA******************************************************************************
Disordered Region (DISEMBL)
**************************************************HPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKLS*************************************************************************
Disordered Region (DISPRO)
*************************************************SHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKLS*************************************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MATEGEAVTEQQPAAEEPEKVVTEKKAKAAKEKKPKAPKEKKPKQSKTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKLSEAAAGKTKKEIKTKAKAPRKTRSVTAAAKIKAESAAAAPPPPKKAKKSAAAKPKQPKSIKSPAAKKAKKAAAQ
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	192	2.2.26 [Sep-21-2011]
P40267	202	Histone H1 OS=Solanum pen	N/A	no	0.843	0.801	0.588	8e-42
P27806	238	Histone H1 OS=Triticum ae	N/A	no	0.437	0.352	0.534	2e-19
P23444	246	Histone H1 OS=Zea mays PE	N/A	no	0.385	0.300	0.554	4e-19
P26569	273	Histone H1.2 OS=Arabidops	no	no	0.427	0.300	0.469	3e-16
P37218	287	Histone H1 OS=Solanum lyc	N/A	no	0.385	0.257	0.533	9e-15
Q08865	241	Histone H1-II OS=Volvox c	N/A	no	0.453	0.360	0.466	1e-14
Q9M5W4	229	Histone H1 OS=Euphorbia e	N/A	no	0.395	0.331	0.506	3e-14
P08283	265	Histone H1 OS=Pisum sativ	N/A	no	0.359	0.260	0.557	5e-13
Q08864	261	Histone H1-I OS=Volvox ca	N/A	no	0.453	0.333	0.431	6e-13
P26568	274	Histone H1.1 OS=Arabidops	no	no	0.390	0.273	0.5	3e-11

>sp|P40267|H1_SOLPN Histone H1 OS=Solanum pennellii PE=2 SV=1

 Score =  169 bits (429), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 103/175 (58%), Positives = 121/175 (69%), Gaps = 13/175 (7%)

Query: 30  AKEKKPKAPKEKKPKQSKTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELP 89
           A +KKP+APKEKKPK +K  +HPPYFQMI EAL+AL +K GSSPYA+AKYME+KHKDELP
Sbjct: 28  ATDKKPRAPKEKKPKSAKAVTHPPYFQMIKEALLALNEKGGSSPYAVAKYMEDKHKDELP 87

Query: 90  ANFRKILAVQLKHFAAKGNLIKIRASYKLSEAAAGKTKKEIKTKA-------KAPRKTRS 142
           ANFRKIL +QLK+ AAKG LIKI+ASYKLSEA   +T  +  TK        K PR TR+
Sbjct: 88  ANFRKILGLQLKNSAAKGKLIKIKASYKLSEAGKKETTTKTSTKKLPKADSKKKPRSTRA 147

Query: 143 VTAAAK------IKAESAAAAPPPPKKAKKSAAAKPKQPKSIKSPAAKKAKKAAA 191
              AAK          +        K+ +KS  AK KQPKSIKSPAAK+AKK A 
Sbjct: 148 TATAAKKTEVPKKAKATPKPKKVGAKRTRKSTPAKAKQPKSIKSPAAKRAKKIAV 202

Histones H1 are necessary for the condensation of nucleosome chains into higher order structures.
Solanum pennellii (taxid: 28526)

>sp|P27806|H1_WHEAT Histone H1 OS=Triticum aestivum PE=2 SV=2

 Score = 95.1 bits (235), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 46/86 (53%), Positives = 63/86 (73%), Gaps = 2/86 (2%)

Query: 38  PKEKKPKQSKTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILA 97
           P  KKP+   TP+HP Y +M++EA+ AL+++SGSS  AI K++E+KHK  LPANFRKIL 
Sbjct: 44  PGPKKPRV--TPAHPSYAEMVSEAIAALKERSGSSTIAIGKFIEDKHKAHLPANFRKILL 101

Query: 98  VQLKHFAAKGNLIKIRASYKLSEAAA 123
            Q+K   A G L K++ SYKL++A A
Sbjct: 102 TQIKKLVAAGKLTKVKGSYKLAKAPA 127

Histones H1 are necessary for the condensation of nucleosome chains into higher order structures.

Triticum aestivum (taxid: 4565)

>sp|P23444|H1_MAIZE Histone H1 OS=Zea mays PE=2 SV=2

 Score = 94.4 bits (233), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 41/74 (55%), Positives = 59/74 (79%)

Query: 48  TPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKG 107
           +P+H PY +M++EA+ +L++++GSS YAIAK++E+KHK +LP NFRK+L VQLK   A G
Sbjct: 47  SPTHLPYAEMVSEAITSLKERTGSSSYAIAKFVEDKHKAKLPPNFRKLLNVQLKKLVAGG 106

Query: 108 NLIKIRASYKLSEA 121
            L K++ SYKLS A
Sbjct: 107 KLTKVKNSYKLSSA 120

Histones H1 are necessary for the condensation of nucleosome chains into higher order structures.

Zea mays (taxid: 4577)

>sp|P26569|H12_ARATH Histone H1.2 OS=Arabidopsis thaliana GN=At2g30620 PE=1 SV=1

 Score = 84.7 bits (208), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 39/83 (46%), Positives = 57/83 (68%), Gaps = 1/83 (1%)

Query: 44  KQSKTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHF 103
           K+  T SHP Y +MI +A++ L++++GSS YAI K++EEKHK  LP  FRK+L V LK  
Sbjct: 55  KKKTTSSHPTYEEMIKDAIVTLKERTGSSQYAIQKFIEEKHKS-LPPTFRKLLLVNLKRL 113

Query: 104 AAKGNLIKIRASYKLSEAAAGKT 126
            A   L+K++AS+K+  A +  T
Sbjct: 114 VASEKLVKVKASFKIPSARSAAT 136

Histones H1 are necessary for the condensation of nucleosome chains into higher order structures.

Arabidopsis thaliana (taxid: 3702)

>sp|P37218|H1_SOLLC Histone H1 OS=Solanum lycopersicum PE=3 SV=1

 Score = 80.1 bits (196), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 40/75 (53%), Positives = 59/75 (78%), Gaps = 1/75 (1%)

Query: 44  KQSKTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHF 103
           K+S TP+HPPYF+MI +A++ L++++GSS +AI K++EEK K  LP+NF+K+L  QLK F
Sbjct: 49  KRSATPTHPPYFEMIKDAIVTLKERTGSSQHAITKFIEEKQKS-LPSNFKKLLLTQLKKF 107

Query: 104 AAKGNLIKIRASYKL 118
            A   L+K++ SYKL
Sbjct: 108 VASEKLVKVKNSYKL 122

Histones H1 are necessary for the condensation of nucleosome chains into higher order structures.

Solanum lycopersicum (taxid: 4081)

>sp|Q08865|H12_VOLCA Histone H1-II OS=Volvox carteri GN=H1-II PE=2 SV=3

 Score = 79.3 bits (194), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 42/90 (46%), Positives = 63/90 (70%), Gaps = 3/90 (3%)

Query: 33  KKPKAPKEKKPKQSKTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKH-KDELPAN 91
           K PKA  +KKPK +  P+HPPY QM+T+A+++L+++ GSS  A+ K++E K+ KD     
Sbjct: 9   KAPKAKTQKKPKTA--PTHPPYIQMVTDAILSLKERDGSSLPALKKFIEAKYGKDIHDKK 66

Query: 92  FRKILAVQLKHFAAKGNLIKIRASYKLSEA 121
           F K L++ LK F   G L+K++ SYKLS+A
Sbjct: 67  FPKTLSLALKTFVKNGKLVKVKNSYKLSDA 96

Histones H1 are necessary for the condensation of nucleosome chains into higher order structures.

Volvox carteri (taxid: 3067)

>sp|Q9M5W4|H1_EUPES Histone H1 OS=Euphorbia esula PE=2 SV=1

 Score = 78.6 bits (192), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 58/77 (75%), Gaps = 1/77 (1%)

Query: 41  KKPKQSKTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQL 100
           KKPK   T SHP +F+MI++A+  L++++GSS YAI K++E+KHK +LP+NFRK+L   L
Sbjct: 41  KKPKSKGTSSHPSFFEMISDAISTLKERTGSSQYAINKFVEDKHK-QLPSNFRKLLLFHL 99

Query: 101 KHFAAKGNLIKIRASYK 117
           K   A G L+K++ S+K
Sbjct: 100 KKLVASGKLVKVKNSFK 116

Histones H1 are necessary for the condensation of nucleosome chains into higher order structures.

Euphorbia esula (taxid: 3993)

>sp|P08283|H1_PEA Histone H1 OS=Pisum sativum PE=2 SV=1

 Score = 73.9 bits (180), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 39/70 (55%), Positives = 55/70 (78%), Gaps = 1/70 (1%)

Query: 50  SHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNL 109
           SHP Y +MI +A+++L++K+GSS YAIAK++EEK K +LPANF+K+L   LK   A G L
Sbjct: 61  SHPTYEEMIKDAIVSLKEKNGSSQYAIAKFIEEKQK-QLPANFKKLLLQNLKKNVASGKL 119

Query: 110 IKIRASYKLS 119
           IK++ S+KLS
Sbjct: 120 IKVKGSFKLS 129

Histones H1 are necessary for the condensation of nucleosome chains into higher order structures.

Pisum sativum (taxid: 3888)

>sp|Q08864|H11_VOLCA Histone H1-I OS=Volvox carteri GN=H1-I PE=2 SV=3

 Score = 73.9 bits (180), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 38/88 (43%), Positives = 57/88 (64%), Gaps = 1/88 (1%)

Query: 50  SHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKH-KDELPANFRKILAVQLKHFAAKGN 108
           +HPPY +M+ +A+  L++++GSS  A+ K++E K+ KD    NF K L+  +K F   G 
Sbjct: 58  THPPYIEMVKDAITTLKERNGSSLPALKKFIENKYGKDIHDKNFAKTLSQVVKTFVKGGK 117

Query: 109 LIKIRASYKLSEAAAGKTKKEIKTKAKA 136
           L+K++ S+KLSEA   K KK    KAKA
Sbjct: 118 LVKVKGSFKLSEALKAKAKKSTPKKAKA 145

Histones H1 are necessary for the condensation of nucleosome chains into higher order structures.

Volvox carteri (taxid: 3067)

>sp|P26568|H11_ARATH Histone H1.1 OS=Arabidopsis thaliana GN=At1g06760 PE=2 SV=1

 Score = 68.6 bits (166), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 38/76 (50%), Positives = 55/76 (72%), Gaps = 1/76 (1%)

Query: 43  PKQSKTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKH 102
           PK+    SHP Y +MI +A++ L++++GSS YAI K++EEK K ELP  FRK+L + LK 
Sbjct: 54  PKKRTVSSHPTYEEMIKDAIVTLKERTGSSQYAIQKFIEEKRK-ELPPTFRKLLLLNLKR 112

Query: 103 FAAKGNLIKIRASYKL 118
             A G L+K++AS+KL
Sbjct: 113 LVASGKLVKVKASFKL 128

Histones H1 are necessary for the condensation of nucleosome chains into higher order structures.

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	192
7595978	202	histone H1 variant [Solanum chilense]	0.921	0.876	0.587	2e-42
350606427	207	H1 histone-like protein [Solanum lycoper	0.927	0.859	0.554	7e-42
23506611	206	histone H1D [Nicotiana tabacum]	0.796	0.742	0.634	5e-41
27529850	206	stress-inducible H1 histone-like protein	0.796	0.742	0.628	1e-40
449434184	197	PREDICTED: histone H1-like isoform 3 [Cu	0.968	0.944	0.559	1e-40
729668	202	RecName: Full=Histone H1 gi|436823|gb|AA	0.843	0.801	0.588	4e-40
224133758	202	histone H1 [Populus trichocarpa] gi|2228	0.942	0.896	0.604	2e-39
449434180	207	PREDICTED: histone H1-like isoform 1 [Cu	0.906	0.840	0.573	1e-38
5726575	206	histone H1C [Nicotiana tabacum]	0.885	0.825	0.550	3e-37
189473427	207	histone H1-like protein [Camellia sinens	0.614	0.570	0.672	2e-33

>gi|7595978|gb|AAF64525.1|AF253416_1 histone H1 variant [Solanum chilense]

 Score =  177 bits (450), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 118/201 (58%), Positives = 134/201 (66%), Gaps = 24/201 (11%)

Query: 3   TEGEAVTEQQPAAEEPEKVVTEKKAKAAKEKKPKAPKEKKPKQSKTPSHPPYFQMITEAL 62
           TE   V EQ PA E           KA KEKKP+APKEKKPK +K  +HPPYFQMI EAL
Sbjct: 12  TEASKVKEQAPATE-----------KAVKEKKPRAPKEKKPKSAKAVTHPPYFQMIKEAL 60

Query: 63  MALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKLSEAA 122
           +AL +K GSSPYA+AKYME+KHKDELPANFRKIL +QLK+ AAKG LIKI+ASYKLSEA 
Sbjct: 61  LALNEKGGSSPYAVAKYMEDKHKDELPANFRKILGLQLKNSAAKGKLIKIKASYKLSEAG 120

Query: 123 ----AGKTKKEIKTKAKAPRKTRSV--TAAAKIKAESAAAAPPPP-------KKAKKSAA 169
                 KT  +   KA + +KTRS   TA A  K E    A   P       K+ +KS  
Sbjct: 121 KKETTTKTSTKKLLKADSKKKTRSTRATATAAKKTEVPKKAKATPKPKKVGAKRTRKSTP 180

Query: 170 AKPKQPKSIKSPAAKKAKKAA 190
           AK KQPKSIKSPAAK+AKK A
Sbjct: 181 AKAKQPKSIKSPAAKRAKKIA 201

Source: Solanum chilense

Species: Solanum chilense

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|350606427|ref|NP_001234389.1| H1 histone-like protein [Solanum lycopersicum] gi|825521|emb|CAA77867.1| H1 histone-like protein [Solanum lycopersicum]

 Score =  175 bits (444), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 112/202 (55%), Positives = 131/202 (64%), Gaps = 24/202 (11%)

Query: 3   TEGEAVTEQQPAAEEPEKVVTEKKAKAAKEKKPKAPKEKKPKQSKTPSHPPYFQMITEAL 62
           TE   V EQ  A E           KA KEKKP+APKEKKPK +K  +HPPYFQMI EAL
Sbjct: 17  TEASKVKEQASATE-----------KAVKEKKPRAPKEKKPKSAKAVTHPPYFQMIKEAL 65

Query: 63  MALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKLSEAA 122
           ++L +K GSSPYA+AKYME+KHKDELPANFRKIL +QLK+ AAKG LIKI+ASYKLSEA 
Sbjct: 66  LSLNEKGGSSPYAVAKYMEDKHKDELPANFRKILGLQLKNSAAKGKLIKIKASYKLSEAG 125

Query: 123 AGKTKKEIKTKA-------KAPRKTRSVTAAAK------IKAESAAAAPPPPKKAKKSAA 169
             +T  +  TK        K PR TR+ + AAK          +        K+ +KS  
Sbjct: 126 KKETTTKTSTKKLPKADSKKKPRSTRATSTAAKKTEVPKKAKATPKPKKVGAKRTRKSTP 185

Query: 170 AKPKQPKSIKSPAAKKAKKAAA 191
           AK KQPKSIKSPAAK+AKK A 
Sbjct: 186 AKAKQPKSIKSPAAKRAKKIAV 207

Source: Solanum lycopersicum

Species: Solanum lycopersicum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|23506611|gb|AAN37904.1| histone H1D [Nicotiana tabacum]

 Score =  172 bits (437), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 106/167 (63%), Positives = 119/167 (71%), Gaps = 14/167 (8%)

Query: 28  KAAKEKKPKAPKEKKPKQSKTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDE 87
           K+ KEKKP+AP+EKKPK +KT +HPPYFQMI EAL+AL +K GSSPYAIAKYME+KHKDE
Sbjct: 31  KSVKEKKPRAPREKKPKSAKTVTHPPYFQMIKEALLALNEKGGSSPYAIAKYMEDKHKDE 90

Query: 88  LPANFRKILAVQLKHFAAKGNLIKIRASYKLS-----EAAAGKTKKEIKTKA-KAPRKTR 141
           LPANFRKIL +QLK+ AAKG L+KI+ASYKLS     E     TKK  K    K PR TR
Sbjct: 91  LPANFRKILGLQLKNSAAKGKLMKIKASYKLSVAGKKERTTASTKKVPKADTKKKPRSTR 150

Query: 142 SVTAAAKIKAESAAAAPPPP-------KKAKKSAAAKPKQPKSIKSP 181
           S TA AK K E A  A P         KK +KS  AK KQPKSIKSP
Sbjct: 151 STTATAK-KTEVAKKAKPTQKPKKVGAKKIRKSTPAKAKQPKSIKSP 196

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|27529850|dbj|BAC53940.1| stress-inducible H1 histone-like protein [Nicotiana tabacum]

 Score =  171 bits (434), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 105/167 (62%), Positives = 118/167 (70%), Gaps = 14/167 (8%)

Query: 28  KAAKEKKPKAPKEKKPKQSKTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDE 87
           K+ KEKKP+AP+EKKPK +KT +HPPYFQMI EAL+AL +K GSSPYAIAKYME+KHKDE
Sbjct: 31  KSVKEKKPRAPREKKPKSAKTVTHPPYFQMIKEALLALNEKGGSSPYAIAKYMEDKHKDE 90

Query: 88  LPANFRKILAVQLKHFAAKGNLIKIRASYKLS-----EAAAGKTKKEIKTKA-KAPRKTR 141
           LPANFRKIL +QLK+ AAKG L+KI+ASYKLS     E     TKK  K    K PR TR
Sbjct: 91  LPANFRKILGLQLKNSAAKGKLMKIKASYKLSVAGKKERTTASTKKVPKADTKKKPRSTR 150

Query: 142 SVTAAAKIKAESAAAAPPPP-------KKAKKSAAAKPKQPKSIKSP 181
           S TA AK K E    A P         KK +KS  AK KQPKSIKSP
Sbjct: 151 STTATAK-KTEVTKKAKPTQKPKKVGAKKIRKSTPAKAKQPKSIKSP 196

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449434184|ref|XP_004134876.1| PREDICTED: histone H1-like isoform 3 [Cucumis sativus] gi|449491384|ref|XP_004158879.1| PREDICTED: histone H1-like isoform 3 [Cucumis sativus]

 Score =  171 bits (433), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 113/202 (55%), Positives = 133/202 (65%), Gaps = 16/202 (7%)

Query: 1   MATEGEAVTEQQPAAEEPEKVVTEKKAKAAKEKKPKAPKEKKPKQSKTPSHPPYFQMITE 60
           M++ GEA   + PA EEP++V      K  KEKKP+A +EKKP+QSK  SHPPYFQMI E
Sbjct: 1   MSSTGEAAEVKVPATEEPKEV-----EKPVKEKKPRATREKKPRQSKVASHPPYFQMINE 55

Query: 61  ALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKLSE 120
           A+ +L +K+GSSPYAIAKYMEEKHK  LPANFRKILA+QLK+  AKG L KI+ASYKLSE
Sbjct: 56  AISSLNEKNGSSPYAIAKYMEEKHKAVLPANFRKILALQLKNSTAKGKLTKIKASYKLSE 115

Query: 121 AAAGKTKKEIKT-KAKAPRKTRSVTAAAK-------IKAE---SAAAAPPPPKKAKKSAA 169
               K     K  KA A +KT+              +K E   S A      KK K+S  
Sbjct: 116 TGKKKDMNATKVAKANAEKKTKQARTTRTTGRKRKAVKTEEAVSKAVKKVVAKKPKRSTP 175

Query: 170 AKPKQPKSIKSPAAKKAKKAAA 191
           AKPKQPKSIKSPAAK+AKKA  
Sbjct: 176 AKPKQPKSIKSPAAKRAKKAVV 197

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|729668|sp|P40267.1|H1_SOLPN RecName: Full=Histone H1 gi|436823|gb|AAB03076.1| histone H1 [Solanum pennellii]

 Score =  169 bits (429), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 103/175 (58%), Positives = 121/175 (69%), Gaps = 13/175 (7%)

Query: 30  AKEKKPKAPKEKKPKQSKTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELP 89
           A +KKP+APKEKKPK +K  +HPPYFQMI EAL+AL +K GSSPYA+AKYME+KHKDELP
Sbjct: 28  ATDKKPRAPKEKKPKSAKAVTHPPYFQMIKEALLALNEKGGSSPYAVAKYMEDKHKDELP 87

Query: 90  ANFRKILAVQLKHFAAKGNLIKIRASYKLSEAAAGKTKKEIKTKA-------KAPRKTRS 142
           ANFRKIL +QLK+ AAKG LIKI+ASYKLSEA   +T  +  TK        K PR TR+
Sbjct: 88  ANFRKILGLQLKNSAAKGKLIKIKASYKLSEAGKKETTTKTSTKKLPKADSKKKPRSTRA 147

Query: 143 VTAAAK------IKAESAAAAPPPPKKAKKSAAAKPKQPKSIKSPAAKKAKKAAA 191
              AAK          +        K+ +KS  AK KQPKSIKSPAAK+AKK A 
Sbjct: 148 TATAAKKTEVPKKAKATPKPKKVGAKRTRKSTPAKAKQPKSIKSPAAKRAKKIAV 202

Source: Solanum pennellii

Species: Solanum pennellii

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224133758|ref|XP_002327673.1| histone H1 [Populus trichocarpa] gi|222836758|gb|EEE75151.1| histone H1 [Populus trichocarpa]

 Score =  167 bits (424), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 127/210 (60%), Positives = 142/210 (67%), Gaps = 29/210 (13%)

Query: 1   MATEGEA-----VTEQQPAAEEPEKVVTEKKAKAAKEKKPKAPKEKKPKQSK--TPSHPP 53
           M T  EA     V EQ PA EEP+  V EK     KEKKP+ P+EKKP+Q K    +HPP
Sbjct: 1   MTTSKEAETEAPVVEQPPATEEPK--VEEK---PLKEKKPRTPREKKPRQPKPKAVAHPP 55

Query: 54  YFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR 113
           YFQMI EA++AL +KSGSSPYAIAKYMEEKHK  LPANF+KIL +QLK+ AA+G LIKIR
Sbjct: 56  YFQMIKEAILALNEKSGSSPYAIAKYMEEKHKAVLPANFKKILGLQLKNSAARGKLIKIR 115

Query: 114 ASYKLSEAA------AGKTKKEI----KTKAKAP--RKTRSVTAAAKIKAESAAAAPPPP 161
           ASYKLSEA        GK  K      KTK   P  RKTRSV      KA++ A      
Sbjct: 116 ASYKLSEAGKKEKSTTGKVSKGSSAVKKTKEVKPSMRKTRSVN-----KADAGAKKVVGA 170

Query: 162 KKAKKSAAAKPKQPKSIKSPAAKKAKKAAA 191
           KKAKKSAAAKPKQPKSIKSPAAK+AKK  A
Sbjct: 171 KKAKKSAAAKPKQPKSIKSPAAKRAKKVTA 200

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449434180|ref|XP_004134874.1| PREDICTED: histone H1-like isoform 1 [Cucumis sativus] gi|449434182|ref|XP_004134875.1| PREDICTED: histone H1-like isoform 2 [Cucumis sativus] gi|449491377|ref|XP_004158877.1| PREDICTED: histone H1-like isoform 1 [Cucumis sativus] gi|449491381|ref|XP_004158878.1| PREDICTED: histone H1-like isoform 2 [Cucumis sativus]

 Score =  165 bits (417), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 109/190 (57%), Positives = 126/190 (66%), Gaps = 16/190 (8%)

Query: 13  PAAEEPEKVVTEKKAKAAKEKKPKAPKEKKPKQSKTPSHPPYFQMITEALMALQDKSGSS 72
           PA EEP++V      K  KEKKP+A +EKKP+QSK  SHPPYFQMI EA+ +L +K+GSS
Sbjct: 23  PATEEPKEV-----EKPVKEKKPRATREKKPRQSKVASHPPYFQMINEAISSLNEKNGSS 77

Query: 73  PYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKLSEAAAGKTKKEIKT 132
           PYAIAKYMEEKHK  LPANFRKILA+QLK+  AKG L KI+ASYKLSE    K     K 
Sbjct: 78  PYAIAKYMEEKHKAVLPANFRKILALQLKNSTAKGKLTKIKASYKLSETGKKKDMNATKV 137

Query: 133 -KAKAPRKTRSVTAAAK-------IKAE---SAAAAPPPPKKAKKSAAAKPKQPKSIKSP 181
            KA A +KT+              +K E   S A      KK K+S  AKPKQPKSIKSP
Sbjct: 138 AKANAEKKTKQARTTRTTGRKRKAVKTEEAVSKAVKKVVAKKPKRSTPAKPKQPKSIKSP 197

Query: 182 AAKKAKKAAA 191
           AAK+AKKA  
Sbjct: 198 AAKRAKKAVV 207

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|5726575|gb|AAD48472.1|AF170089_1 histone H1C [Nicotiana tabacum]

 Score =  160 bits (404), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 114/207 (55%), Positives = 132/207 (63%), Gaps = 37/207 (17%)

Query: 1   MATEGEAVTEQQPAAEEP--EKVVTEKKA----KAAKEKKPKAPKEKKPKQSKTPSHPPY 54
           M+  GE    + PA E+P  E    E +     K+ KEKKP+AP+EKKPK +KT +HPPY
Sbjct: 1   MSATGEV---ENPAVEQPPAEAPTAENQPPATKKSVKEKKPRAPREKKPKSAKTVTHPPY 57

Query: 55  FQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRA 114
           FQMI EAL+AL +K GSSPYAIAKY E+KHKDELPANFRKIL +QLK+ AAKG L+KI+A
Sbjct: 58  FQMIKEALLALNEKGGSSPYAIAKYTEDKHKDELPANFRKILGLQLKNSAAKGKLMKIKA 117

Query: 115 SYKLSEAA-----AGKTKKEIKTKA-KAPRKTRSVTAAAKIKAESAAAAPPPPKKAKKS- 167
           SYKLSEA         TKK  K  + K PR TRS TA AK K E        PKKAK + 
Sbjct: 118 SYKLSEAGKKERITASTKKVPKADSKKKPRSTRSATATAK-KTEV-------PKKAKLTQ 169

Query: 168 -------------AAAKPKQPKSIKSP 181
                        A AK KQPKSIKSP
Sbjct: 170 KPKKVGAKKAKKSAPAKAKQPKSIKSP 196

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|189473427|gb|ACD99685.1| histone H1-like protein [Camellia sinensis]

 Score =  147 bits (371), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 84/125 (67%), Positives = 95/125 (76%), Gaps = 7/125 (5%)

Query: 28  KAAKEKKPKAPKEKKPKQSKTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDE 87
           K  KEKKP+ PKEKKP+  K  SHPPYFQMI EAL+AL +KSGSSPYAIAKYMEE+HK  
Sbjct: 30  KPVKEKKPRVPKEKKPRAPKIASHPPYFQMIKEALLALNEKSGSSPYAIAKYMEEEHKPV 89

Query: 88  LPANFRKILAVQLKHFAAKGNLIKIRASYKLSEAAAGKTKKEIKTKA----KAPRKTRSV 143
           LP NFRKIL +QLK+ AAKG LIKI+ASYKLSE  AGK K    TKA    K P++ RS 
Sbjct: 90  LPENFRKILGLQLKNSAAKGKLIKIKASYKLSE--AGK-KDNGTTKAPMAEKKPKQARST 146

Query: 144 TAAAK 148
           T AA+
Sbjct: 147 TTAAR 151

Source: Camellia sinensis

Species: Camellia sinensis

Genus: Camellia

Family: Theaceae

Order: Ericales

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	192
TAIR|locus:2060984	167	HIS1-3 "histone H1-3" [Arabido	0.380	0.437	0.712	3.8e-23
TAIR|locus:2033118	274	AT1G06760 [Arabidopsis thalian	0.489	0.343	0.410	4.7e-16
TAIR|locus:2064332	273	AT2G30620 [Arabidopsis thalian	0.364	0.256	0.507	4.2e-15
DICTYBASE|DDB_G0285319	180	H1 "transcriptional repressor"	0.364	0.388	0.436	8.4e-10
TAIR|locus:2038573	479	HON5 "high mobility group A5"	0.359	0.144	0.385	8.2e-07
TAIR|locus:2030275	287	AT1G72740 [Arabidopsis thalian	0.348	0.233	0.4	8.8e-07
TAIR|locus:2006862	204	HMGA "high mobility group A" [	0.364	0.343	0.369	1.6e-06
TAIR|locus:2020193	197	AT1G54260 [Arabidopsis thalian	0.333	0.324	0.348	3.1e-06
TAIR|locus:2007878	296	AT1G17520 [Arabidopsis thalian	0.307	0.199	0.426	3.3e-06
TAIR|locus:2158611	299	TRB2 "AT5G67580" [Arabidopsis	0.322	0.207	0.375	7.3e-06

TAIR|locus:2060984 HIS1-3 "histone H1-3" [Arabidopsis thaliana (taxid:3702)]

 Score = 267 (99.0 bits), Expect = 3.8e-23, P = 3.8e-23
 Identities = 52/73 (71%), Positives = 62/73 (84%)

Query:    47 KTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAK 106
             KT +HPPYFQMI EALM L++K+GSSPYAIAK +EEKHK  LP +FRK L++QLK+  AK
Sbjct:    20 KTTTHPPYFQMIKEALMVLKEKNGSSPYAIAKKIEEKHKSLLPESFRKTLSLQLKNSVAK 79

Query:   107 GNLIKIRASYKLS 119
             G L+KIRASYKLS
Sbjct:    80 GKLVKIRASYKLS 92

GO:0000786 "nucleosome" evidence=IEA;ISS

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

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006334 "nucleosome assembly" evidence=IEA;ISS

GO:0009414 "response to water deprivation" evidence=IEP

GO:0031492 "nucleosomal DNA binding" evidence=ISS

TAIR|locus:2033118 AT1G06760 [Arabidopsis thaliana (taxid:3702)]

 Score = 200 (75.5 bits), Expect = 4.7e-16, P = 4.7e-16
 Identities = 39/95 (41%), Positives = 56/95 (58%)

Query:    50 SHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNL 109
             SHP Y +MI +A++ L++++GSS YAI K++EEK K ELP  FRK+L + LK   A G L
Sbjct:    61 SHPTYEEMIKDAIVTLKERTGSSQYAIQKFIEEKRK-ELPPTFRKLLLLNLKRLVASGKL 119

Query:   110 IKIRASYKLSXXXXXXXXXXXXXXXXXPRKTRSVT 144
             +K++AS+KL                  P K +  T
Sbjct:   120 VKVKASFKLPSASAKASSPKAAAEKSAPAKKKPAT 154

GO:0000786 "nucleosome" evidence=IEA;ISS

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

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006334 "nucleosome assembly" evidence=IEA;ISS

TAIR|locus:2064332 AT2G30620 [Arabidopsis thaliana (taxid:3702)]

 Score = 191 (72.3 bits), Expect = 4.2e-15, P = 4.2e-15
 Identities = 36/71 (50%), Positives = 52/71 (73%)

Query:    48 TPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKG 107
             T SHP Y +MI +A++ L++++GSS YAI K++EEKHK  LP  FRK+L V LK   A  
Sbjct:    59 TSSHPTYEEMIKDAIVTLKERTGSSQYAIQKFIEEKHKS-LPPTFRKLLLVNLKRLVASE 117

Query:   108 NLIKIRASYKL 118
              L+K++AS+K+
Sbjct:   118 KLVKVKASFKI 128

GO:0000786 "nucleosome" evidence=IEA;ISS

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

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

GO:0006334 "nucleosome assembly" evidence=IEA;ISS

GO:0005730 "nucleolus" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

DICTYBASE|DDB_G0285319 H1 "transcriptional repressor" [Dictyostelium discoideum (taxid:44689)]

 Score = 141 (54.7 bits), Expect = 8.4e-10, P = 8.4e-10
 Identities = 31/71 (43%), Positives = 44/71 (61%)

Query:    49 PSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGN 108
             P+HP Y  MI+ A+   +D++GSS  AI KY+E  + +  P  F+  L + LK   AKG 
Sbjct:    22 PNHPTYQVMISTAIAHYKDRTGSSQPAIIKYIEANY-NVAPDTFKTQLKLALKRLVAKGT 80

Query:   109 LIKIRASYKLS 119
             L  ++ASYKLS
Sbjct:    81 LTMVKASYKLS 91

GO:0005516 "calmodulin binding" evidence=IEA;IDA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000786 "nucleosome" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

TAIR|locus:2038573 HON5 "high mobility group A5" [Arabidopsis thaliana (taxid:3702)]

 Score = 122 (48.0 bits), Expect = 8.2e-07, P = 8.2e-07
 Identities = 27/70 (38%), Positives = 39/70 (55%)

Query:    50 SHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNL 109
             SHPPY  MI  A+ AL +  GSS  AI++Y+E  +   +P     +L   LK     G L
Sbjct:    74 SHPPYSDMICTAIAALNEPDGSSKQAISRYIERIYTG-IPTAHGALLTHHLKTLKTSGIL 132

Query:   110 IKIRASYKLS 119
             + ++ SYKL+
Sbjct:   133 VMVKKSYKLA 142

GO:0000786 "nucleosome" evidence=IEA;ISS

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

GO:0005634 "nucleus" evidence=IEA;ISS

GO:0006334 "nucleosome assembly" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0009294 "DNA mediated transformation" evidence=IMP

TAIR|locus:2030275 AT1G72740 [Arabidopsis thaliana (taxid:3702)]

 Score = 118 (46.6 bits), Expect = 8.8e-07, P = 8.8e-07
 Identities = 28/70 (40%), Positives = 45/70 (64%)

Query:    48 TPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKG 107
             T + P Y  +I EAL AL D +GS   +I  ++E +H  E+P NFR+IL+ +L+  AA+ 
Sbjct:   117 TKNAPRYDGVIFEALSALADGNGSDVSSIYHFIEPRH--EVPPNFRRILSTRLRRLAAQS 174

Query:   108 NLIKIRASYK 117
              L K+ +++K
Sbjct:   175 KLEKV-STFK 183

GO:0000786 "nucleosome" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0006334 "nucleosome assembly" evidence=IEA

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

TAIR|locus:2006862 HMGA "high mobility group A" [Arabidopsis thaliana (taxid:3702)]

 Score = 112 (44.5 bits), Expect = 1.6e-06, P = 1.6e-06
 Identities = 27/73 (36%), Positives = 41/73 (56%)

Query:    46 SKTPSH--PPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHF 103
             S+ PS   PPY QMI EA+ +L DK+G +   IAK++E   +  LP +   +L+  L   
Sbjct:    16 SELPSFSLPPYPQMIMEAIESLNDKNGCNKTTIAKHIESTQQT-LPPSHMTLLSYHLNQM 74

Query:   104 AAKGNLIKIRASY 116
                G LI ++ +Y
Sbjct:    75 KKTGQLIMVKNNY 87

GO:0000785 "chromatin" evidence=IEA

GO:0000786 "nucleosome" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA;ISS

GO:0006334 "nucleosome assembly" evidence=IEA

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

GO:0009507 "chloroplast" evidence=ISM

GO:0001708 "cell fate specification" evidence=RCA

GO:0008283 "cell proliferation" evidence=RCA

TAIR|locus:2020193 AT1G54260 [Arabidopsis thaliana (taxid:3702)]

 Score = 109 (43.4 bits), Expect = 3.1e-06, P = 3.1e-06
 Identities = 23/66 (34%), Positives = 41/66 (62%)

Query:    54 YFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR 113
             Y  M+ EA+  + D++GS+   I +++E +H  E+P NF+K+L+  L    ++  L K+R
Sbjct:     7 YDAMVFEAVSTINDENGSNLKEILRFIEGQH--EVPQNFKKLLSYSLGILVSQDKLKKVR 64

Query:   114 ASYKLS 119
               YK+S
Sbjct:    65 NRYKIS 70

GO:0000786 "nucleosome" evidence=IEA;ISS

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

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006334 "nucleosome assembly" evidence=IEA;ISS

TAIR|locus:2007878 AT1G17520 [Arabidopsis thaliana (taxid:3702)]

 Score = 113 (44.8 bits), Expect = 3.3e-06, P = 3.3e-06
 Identities = 26/61 (42%), Positives = 39/61 (63%)

Query:    52 PPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIK 111
             P Y  MI EAL  L D +GS   AI  ++E++   E+P NFR++L+ +L+  AA+G L K
Sbjct:   128 PRYDGMIFEALSNLTDANGSDVSAIFNFIEQRQ--EVPPNFRRMLSSRLRRLAAQGKLEK 185

Query:   112 I 112
             +
Sbjct:   186 V 186

GO:0000786 "nucleosome" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006334 "nucleosome assembly" evidence=IEA

GO:0009651 "response to salt stress" evidence=IEP

GO:0009723 "response to ethylene stimulus" evidence=IEP

GO:0009733 "response to auxin stimulus" evidence=IEP

GO:0009751 "response to salicylic acid stimulus" evidence=IEP

GO:0009753 "response to jasmonic acid stimulus" evidence=IEP

GO:0046686 "response to cadmium ion" evidence=IEP

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA

TAIR|locus:2158611 TRB2 "AT5G67580" [Arabidopsis thaliana (taxid:3702)]

 Score = 110 (43.8 bits), Expect = 7.3e-06, P = 7.3e-06
 Identities = 24/64 (37%), Positives = 40/64 (62%)

Query:    56 QMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRAS 115
             ++I EA+  L++  GS   +I  Y+EE  K   P N ++ +AV+LKH ++ G L+KI+  
Sbjct:   127 KIIFEAITNLRELRGSDRTSIFLYIEENFKT--PPNMKRHVAVRLKHLSSNGTLVKIKHK 184

Query:   116 YKLS 119
             Y+ S
Sbjct:   185 YRFS 188

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0006334 "nucleosome assembly" evidence=IEA

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

GO:0003691 "double-stranded telomeric DNA binding" evidence=IDA

GO:0042803 "protein homodimerization activity" evidence=IPI

GO:0043047 "single-stranded telomeric DNA binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0009651 "response to salt stress" evidence=IEP

GO:0009723 "response to ethylene stimulus" evidence=IEP

GO:0009733 "response to auxin stimulus" evidence=IEP

GO:0009737 "response to abscisic acid stimulus" evidence=IEP

GO:0009739 "response to gibberellin stimulus" evidence=IEP

GO:0009751 "response to salicylic acid stimulus" evidence=IEP

GO:0009753 "response to jasmonic acid stimulus" evidence=IEP

GO:0046686 "response to cadmium ion" evidence=IEP

GO:0042162 "telomeric DNA binding" evidence=IDA

---

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)
P40267	H1_SOLPN	No assigned EC number	0.5885	0.8437	0.8019	N/A	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: HON906 histone H1 (202 aa) (Populus trichocarpa)

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	192
smart00526	66	smart00526, H15, Domain in histone families 1 and	7e-14
cd00073	88	cd00073, H15, linker histone 1 and histone 5 domai	1e-11
pfam00538	77	pfam00538, Linker_histone, linker histone H1 and H	8e-10
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	2e-05
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	8e-04
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	0.001
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	0.001
PRK12270	1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	0.003

>gnl|CDD|197772 smart00526, H15, Domain in histone families 1 and 5

 Score = 63.0 bits (154), Expect = 7e-14
 Identities = 33/67 (49%), Positives = 46/67 (68%), Gaps = 1/67 (1%)

Query: 48  TPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKG 107
            PSHPPY +MI EA+ AL+++ GSS  AI KY+E  +K  LP NFRK+L + LK   A G
Sbjct: 1   PPSHPPYSEMIVEAISALKERKGSSLQAIKKYIEANYK-VLPNNFRKLLKLALKRLVASG 59

Query: 108 NLIKIRA 114
            L++++ 
Sbjct: 60  KLVQVKG 66

Length = 66

>gnl|CDD|238028 cd00073, H15, linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber

 Score = 57.6 bits (140), Expect = 1e-11
 Identities = 39/89 (43%), Positives = 55/89 (61%), Gaps = 6/89 (6%)

Query: 48  TPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKG 107
            PSHPPY +M+TEA+ AL+++ GSS  AI KY+E K+K     NF K+L + LK   AKG
Sbjct: 1   PPSHPPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKV-DDENFNKLLKLALKKGVAKG 59

Query: 108 NLIKIR-----ASYKLSEAAAGKTKKEIK 131
            L++++      S+KLS+    K K   K
Sbjct: 60  KLVQVKGTGASGSFKLSKKKKKKKKPAKK 88

Length = 88

>gnl|CDD|215982 pfam00538, Linker_histone, linker histone H1 and H5 family

 Score = 52.8 bits (127), Expect = 8e-10
 Identities = 29/77 (37%), Positives = 47/77 (61%), Gaps = 6/77 (7%)

Query: 50  SHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPA-NFRKILAVQLKHFAAKGN 108
           SHPPY +MI  A+ AL+++ GSS  AI KY+E  +K ++ A N   +L + LK     G 
Sbjct: 1   SHPPYSEMIVAAIAALKERKGSSVQAIKKYIEANYKVDINASNLAPLLKLALKKGVKSGK 60

Query: 109 LIKIR-----ASYKLSE 120
           L++++      S+KL++
Sbjct: 61  LVQVKGTGASGSFKLAK 77

Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures Histone H1 is replaced by histone H5 in some cell types. Length = 77

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 43.7 bits (104), Expect = 2e-05
 Identities = 20/62 (32%), Positives = 23/62 (37%)

Query: 131 KTKAKAPRKTRSVTAAAKIKAESAAAAPPPPKKAKKSAAAKPKQPKSIKSPAAKKAKKAA 190
              A A     S  AAA      AA AP PP  A  +A  KP    +  +  A     AA
Sbjct: 45  TAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAA 104

Query: 191 AQ 192
           A 
Sbjct: 105 AA 106

Length = 1228

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 39.1 bits (92), Expect = 8e-04
 Identities = 21/72 (29%), Positives = 25/72 (34%)

Query: 119 SEAAAGKTKKEIKTKAKAPRKTRSVTAAAKIKAESAAAAPPPPKKAKKSAAAKPKQPKSI 178
             AAA          A AP        A    A +A AAPP P  A  +AAA    P + 
Sbjct: 44  PTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAA 103

Query: 179 KSPAAKKAKKAA 190
            + A   A    
Sbjct: 104 AAAAPAAAAVED 115

Length = 1228

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 38.7 bits (91), Expect = 0.001
 Identities = 18/74 (24%), Positives = 24/74 (32%)

Query: 119 SEAAAGKTKKEIKTKAKAPRKTRSVTAAAKIKAESAAAAPPPPKKAKKSAAAKPKQPKSI 178
           + A            +       +   AA   A  AAAAP  P K   +AAA        
Sbjct: 41  TAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPP 100

Query: 179 KSPAAKKAKKAAAQ 192
            + AA     AA +
Sbjct: 101 AAAAAAAPAAAAVE 114

Length = 1228

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 38.7 bits (91), Expect = 0.001
 Identities = 17/74 (22%), Positives = 24/74 (32%)

Query: 119 SEAAAGKTKKEIKTKAKAPRKTRSVTAAAKIKAESAAAAPPPPKKAKKSAAAKPKQPKSI 178
           + AAA          A    K  +  A A   A + AA P P   A  +AA       + 
Sbjct: 45  TAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAA 104

Query: 179 KSPAAKKAKKAAAQ 192
            +  A  A +    
Sbjct: 105 AAAPAAAAVEDEVT 118

Length = 1228

>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed

 Score = 37.6 bits (88), Expect = 0.003
 Identities = 17/73 (23%), Positives = 24/73 (32%)

Query: 119 SEAAAGKTKKEIKTKAKAPRKTRSVTAAAKIKAESAAAAPPPPKKAKKSAAAKPKQPKSI 178
           + A+A       K  A       +  A A     +AAAA      A  +AAA      + 
Sbjct: 53  AAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAAAPAAAA 112

Query: 179 KSPAAKKAKKAAA 191
                   + AAA
Sbjct: 113 VEDEVTPLRGAAA 125

Length = 1228

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	192
PF00538	77	Linker_histone: linker histone H1 and H5 family; I	99.91
cd00073	88	H15 linker histone 1 and histone 5 domains; the ba	99.9
smart00526	66	H15 Domain in histone families 1 and 5.	99.89
KOG4012	243	consensus Histone H1 [Chromatin structure and dyna	99.81
PF10264	80	Stork_head: Winged helix Storkhead-box1 domain; In	96.08
PF14338	92	Mrr_N: Mrr N-terminal domain	95.78
PF00250	96	Fork_head: Fork head domain; InterPro: IPR001766 T	94.83
cd00059	78	FH Forkhead (FH), also known as a "winged helix".	94.18
smart00339	89	FH FORKHEAD. FORKHEAD, also known as a "winged hel	92.4
PF08672	60	APC2: Anaphase promoting complex (APC) subunit 2;	86.82
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	84.84
PF05066	72	HARE-HTH: HB1, ASXL, restriction endonuclease HTH	84.46
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	80.67

>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication)

Probab=99.91  E-value=1.9e-24  Score=156.42  Aligned_cols=71  Identities=46%  Similarity=0.709  Sum_probs=66.1

Q ss_pred             CCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCch-hHHHHHHHHHHHHHhcCceEecC-----CceecCc
Q 029524           50 SHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPA-NFRKILAVQLKHFAAKGNLIKIR-----ASYKLSE  120 (192)
Q Consensus        50 sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~-nf~~lLk~aLKk~Ve~G~LVqvK-----GSFKLs~  120 (192)
                      +||+|.+||.|||.+|+||+|||+++|.+||+++|+++++. +|+.+|+.+|+++|++|.|+|++     |||+|+.
T Consensus         1 shP~y~~mI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~~~kg~G~sgsfkl~k   77 (77)
T PF00538_consen    1 SHPPYSDMILEAIKALKERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVEKGKLVQVKGKGASGSFKLSK   77 (77)
T ss_dssp             -SSCHHHHHHHHHHHCCSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHHCTSEEECSCSTTSSEEEESS
T ss_pred             CCCCHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHHCCcEEeecccCCccceecCC
Confidence            69999999999999999999999999999999999865554 89999999999999999999999     8999973

Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.

>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber

Probab=99.90  E-value=7.7e-24  Score=157.23  Aligned_cols=70  Identities=51%  Similarity=0.784  Sum_probs=66.7

Q ss_pred             CCCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC-----CceecC
Q 029524           49 PSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR-----ASYKLS  119 (192)
Q Consensus        49 ~sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK-----GSFKLs  119 (192)
                      ++||+|.+||.|||.+|+||+|||+++|.+||+++|+. +..+|+.+|+.+|+++|++|.|+|++     |+|+|+
T Consensus         2 ~~hP~y~~MI~eAI~~l~er~GsS~~aI~kyI~~~y~~-~~~~~~~~l~~aLkk~v~~G~l~~~kG~g~~gsfkl~   76 (88)
T cd00073           2 PSHPPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKV-DDENFNKLLKLALKKGVAKGKLVQVKGTGASGSFKLS   76 (88)
T ss_pred             CCCCCHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCCc-chHHHHHHHHHHHHHHHHCCCeEeecCCCCccceEeC
Confidence            58999999999999999999999999999999999995 34889999999999999999999999     899997

>smart00526 H15 Domain in histone families 1 and 5

Probab=99.89  E-value=2.5e-23  Score=146.14  Aligned_cols=65  Identities=51%  Similarity=0.861  Sum_probs=62.2

Q ss_pred             CCCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCC
Q 029524           49 PSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRA  114 (192)
Q Consensus        49 ~sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKG  114 (192)
                      .+||+|.+||.|||.+|+||+|||+++|.+||+++|++ ++.+|+.+|+.+|+++|++|.|+|++|
T Consensus         2 ~~hP~~~~mI~eAI~~l~er~GsS~~aI~kyi~~~~~~-~~~~~~~~l~~~Lk~~v~~G~l~q~kg   66 (66)
T smart00526        2 PSHPPYSEMITEAISALKERKGSSLQAIKKYIEANYKV-LPNNFRSLLKLALKKLVASGKLVQVKG   66 (66)
T ss_pred             CCCCCHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCC-ChHHHHHHHHHHHHHHHhcCceeecCC
Confidence            58999999999999999999999999999999999985 678999999999999999999999987

>KOG4012 consensus Histone H1 [Chromatin structure and dynamics]

Probab=99.81  E-value=4e-20  Score=160.91  Aligned_cols=80  Identities=39%  Similarity=0.571  Sum_probs=71.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCC-----cee
Q 029524           43 PKQSKTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRA-----SYK  117 (192)
Q Consensus        43 ~~~~k~~sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKG-----SFK  117 (192)
                      +.......||+|.+||.|||..|+||+|+|+.+|.+||.+||..++-.+|+.+|+++|++||.+|.|+|++|     ||+
T Consensus        36 ~~~k~~a~~P~~~~mi~eAi~a~keR~GsS~aAikK~i~~~Y~g~~v~k~n~~lk~alK~~v~~g~l~QtkG~GAsGsFk  115 (243)
T KOG4012|consen   36 PKVKKKAAHPPYSEMITEAISALKERKGSSLAAIKKYIAANYPGDDVEKNNSRLKLALKKGVSKGVLVQTKGTGASGSFK  115 (243)
T ss_pred             cccccccCCCcHHHHHHHHHHHhhhcccchHHHHHHHHhhcCccchhhhhhHHHHHHHHhhhccCceeeeccCCcccccc
Confidence            344567899999999999999999999999999999999999654457899999999999999999999984     999


Q ss_pred             cCccc
Q 029524          118 LSEAA  122 (192)
Q Consensus       118 Ls~~~  122 (192)
                      |....
T Consensus       116 ~~KK~  120 (243)
T KOG4012|consen  116 LAKKA  120 (243)
T ss_pred             ccccc
Confidence            87655

>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []

Probab=96.08  E-value=0.032  Score=41.94  Aligned_cols=67  Identities=7%  Similarity=0.129  Sum_probs=56.3

Q ss_pred             CCHHHHHHHHHHHcCC-CCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCCceecC
Q 029524           52 PPYFQMITEALMALQD-KSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKLS  119 (192)
Q Consensus        52 P~Y~eMI~EAI~aLke-R~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKGSFKLs  119 (192)
                      -+..|.|..+|.+|+. ...++..+|..||...|+. +..--...|..+|-.|+..|+|-.+.+-|.|.
T Consensus        10 iPL~EvlC~~I~dln~~~~~at~E~l~~~L~~~yp~-i~~Ps~e~l~~~L~~Li~erkIY~tg~GYfiv   77 (80)
T PF10264_consen   10 IPLPEVLCWVISDLNAAGQPATQETLREHLRKHYPG-IAIPSQEVLYNTLGTLIKERKIYHTGEGYFIV   77 (80)
T ss_pred             eeHHHHHHHHHHHHhccCCcchHHHHHHHHHHhCCC-CCCCCHHHHHHHHHHHHHcCceeeCCCceEee
Confidence            3688999999999995 7779999999999999995 43223568999999999999999988666554

This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.

>PF14338 Mrr_N: Mrr N-terminal domain

Probab=95.78  E-value=0.035  Score=41.04  Aligned_cols=72  Identities=18%  Similarity=0.294  Sum_probs=60.3

Q ss_pred             CHHHHHHHHHHHcCC-CCCCcHHHHHHHHHHhCCCC-------Cc-----hhHHHHHHHHHHHHHhcCceEecC-Cceec
Q 029524           53 PYFQMITEALMALQD-KSGSSPYAIAKYMEEKHKDE-------LP-----ANFRKILAVQLKHFAAKGNLIKIR-ASYKL  118 (192)
Q Consensus        53 ~Y~eMI~EAI~aLke-R~GSS~~AIkKYIe~~Y~~~-------lp-----~nf~~lLk~aLKk~Ve~G~LVqvK-GSFKL  118 (192)
                      +|.+|+.-.|..|.| ....++..|..+|.++++..       ++     ..|...+.=++..|...|.|..++ |.|+|
T Consensus         1 ~~~~~~~piL~~L~~~g~~~~~~ei~~~v~~~~~ls~e~~~~~~~sg~~~~~~~~ri~Wa~~~L~~aGli~~~~rG~~~i   80 (92)
T PF14338_consen    1 TYDELMPPILEALKDLGGSASRKEIYERVAERFGLSDEERNERLPSGQGYSRFKNRIRWARSYLKKAGLIERPKRGIWRI   80 (92)
T ss_pred             CHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHhCCCHHHHHHHcccCCcchhHHHhHHHHHHHHHHCCCccCCCCCceEE
Confidence            588999999999999 77799999999999988632       11     147888999999999999999965 89999


Q ss_pred             Cccccc
Q 029524          119 SEAAAG  124 (192)
Q Consensus       119 s~~~Kk  124 (192)
                      .+.+.+
T Consensus        81 T~~G~~   86 (92)
T PF14338_consen   81 TEKGRK   86 (92)
T ss_pred             CHhHHH
Confidence            988764

>PF00250 Fork_head: Fork head domain; InterPro: IPR001766 The fork head protein of Drosophila melanogaster, a transcription factor that promotes terminal rather than segmental development, contains neither homeodomains nor zinc-fingers characteristic of other transcription factors []

Probab=94.83  E-value=0.048  Score=41.47  Aligned_cols=58  Identities=14%  Similarity=0.261  Sum_probs=42.5

Q ss_pred             CCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC--CCchhHHHHHHHHHHHHHhcCceEecC
Q 029524           52 PPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD--ELPANFRKILAVQLKHFAAKGNLIKIR  113 (192)
Q Consensus        52 P~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~--~lp~nf~~lLk~aLKk~Ve~G~LVqvK  113 (192)
                      -+|..||..||.. ...++.+..-|..||+.+|+.  ..+..+..-|++.|.   .+.-|+++.
T Consensus         4 ~sY~~LI~~Ai~~-sp~~~Ltl~eIy~~i~~~~pyyr~~~~~WknSIRHnLS---~~~~F~kv~   63 (96)
T PF00250_consen    4 YSYATLIAMAILS-SPDKRLTLSEIYEWIEENFPYYRDASKGWKNSIRHNLS---LNKCFVKVP   63 (96)
T ss_dssp             S-HHHHHHHHHHT-STTSEBEHHHHHHHHHHHCGHHHCTHCHHHHHHHHHHH---HSTTEEEES
T ss_pred             CcHHHHHHHHHHh-CCCCCccHHHHHHHHHHhhccccccchhhhhHHhhhcc---ccceeeecC
Confidence            4699999999998 445569999999999999973  123456666777663   346777764

Instead, it contains a distinct type of DNA-binding region, containing around 100 amino acids, which has since been identified in a number of transcription factors (including D. melanogaster FD1-5, mammalian HNF-3, human HTLF, Saccharomyces cerevisiae HCM1, etc.). This is referred to as the fork head domain but is also known as a 'winged helix' [, , ]. The fork head domain binds B-DNA as a monomer [], but shows no similarity to previously identified DNA-binding motifs. Although the domain is found in several different transcription factors, a common function is their involvement in early developmental decisions of cell fates during embryogenesis [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2UZK_A 2K86_A 1JXS_A 2C6Y_A 2A3S_A 2D2W_A 2KIU_A 1VTN_C 2A07_J 2AS5_F ....

>cd00059 FH Forkhead (FH), also known as a "winged helix"

Probab=94.18  E-value=0.083  Score=38.97  Aligned_cols=34  Identities=15%  Similarity=0.176  Sum_probs=29.9

Q ss_pred             CCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC
Q 029524           52 PPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD   86 (192)
Q Consensus        52 P~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~   86 (192)
                      -+|..||..||.+.. ..+.+..-|-.||+++|+.
T Consensus         4 ~sY~~LI~~Ai~~sp-~~~lTL~eIy~~I~~~~py   37 (78)
T cd00059           4 YSYSALIAMAIQSSP-EKRLTLSEIYKWISDNFPY   37 (78)
T ss_pred             CCHHHHHHHHHHhCC-CCCeeHHHHHHHHHHhCCc
Confidence            479999999999965 5569999999999999974

FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix.

>smart00339 FH FORKHEAD

Probab=92.40  E-value=0.23  Score=37.35  Aligned_cols=33  Identities=18%  Similarity=0.312  Sum_probs=29.2

Q ss_pred             CHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC
Q 029524           53 PYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD   86 (192)
Q Consensus        53 ~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~   86 (192)
                      +|..||..||.+. ...+.+..-|-.||+++|+.
T Consensus         5 sY~~lI~~ai~~s-p~~~ltl~~Iy~~I~~~~py   37 (89)
T smart00339        5 SYIALIAMAILSS-PDKRLTLSEIYKWIEDNFPY   37 (89)
T ss_pred             CHHHHHHHHHHhC-CCCCeeHHHHHHHHHHhCch
Confidence            5999999999995 45579999999999999974

FORKHEAD, also known as a "winged helix"

>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase

Probab=86.82  E-value=0.84  Score=32.18  Aligned_cols=26  Identities=31%  Similarity=0.319  Sum_probs=22.2

Q ss_pred             HHHHHHHHHHHHhcCceEecCCceec
Q 029524           93 RKILAVQLKHFAAKGNLIKIRASYKL  118 (192)
Q Consensus        93 ~~lLk~aLKk~Ve~G~LVqvKGSFKL  118 (192)
                      ...|...|.++|+.|+|+.+.|+|||
T Consensus        35 ~~eL~~fL~~lv~e~~L~~~~G~YkL   60 (60)
T PF08672_consen   35 LEELQEFLDRLVEEGKLECSGGSYKL   60 (60)
T ss_dssp             HHHHHHHHHHHHHTTSEE--TTEEEE
T ss_pred             HHHHHHHHHHHHHCCcEEecCCEEeC
Confidence            56799999999999999999999997

The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.

>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A)

Probab=84.84  E-value=1.8  Score=32.16  Aligned_cols=54  Identities=11%  Similarity=0.177  Sum_probs=40.8

Q ss_pred             CCCCHHHHHHHHHHH-cCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEec
Q 029524           50 SHPPYFQMITEALMA-LQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKI  112 (192)
Q Consensus        50 sHP~Y~eMI~EAI~a-LkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqv  112 (192)
                      ..-+..++|++.|.. .....|+++..|...+  .+.       ..-|+.+|..|+..|.|--+
T Consensus        44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l--~~~-------~~~v~~al~~L~~eG~IYsT   98 (102)
T PF08784_consen   44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQL--GMS-------ENEVRKALDFLSNEGHIYST   98 (102)
T ss_dssp             -S-HHHHHHHHHHHC----TTTEEHHHHHHHS--TS--------HHHHHHHHHHHHHTTSEEES
T ss_pred             CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHh--CcC-------HHHHHHHHHHHHhCCeEecc
Confidence            356678999999999 7778999999999888  443       33699999999999998643

RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.

>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2

Probab=84.46  E-value=3.8  Score=28.68  Aligned_cols=63  Identities=13%  Similarity=0.119  Sum_probs=37.2

Q ss_pred             CHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCC-chh----HHHHHHHHHHHHHhcCceEec-CCceecC
Q 029524           53 PYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDEL-PAN----FRKILAVQLKHFAAKGNLIKI-RASYKLS  119 (192)
Q Consensus        53 ~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~l-p~n----f~~lLk~aLKk~Ve~G~LVqv-KGSFKLs  119 (192)
                      +|.+++.+.|.+.+  ...+..-|...|.+...... ...    ....|...++  -.+|.|+++ .|.|-|.
T Consensus         2 t~~eaa~~vL~~~~--~pm~~~eI~~~i~~~~~~~~~~k~p~~~i~a~ly~~~~--~~d~~F~~vg~~~~~L~   70 (72)
T PF05066_consen    2 TFKEAAYEVLEEAG--RPMTFKEIWEEIQERGLYKKSGKTPEATIAAQLYTDIK--NEDSRFVKVGPGRWGLR   70 (72)
T ss_dssp             -HHHHHHHHHHHH---S-EEHHHHHHHHHHHHTS---GGGGGHHHH-HHHHHHH---T-SS-EESSSSEEE-G
T ss_pred             CHHHHHHHHHHhcC--CCcCHHHHHHHHHHhCCCCcccCCHHHHHHHHHHHHcc--cCCCCEEEeCCCcEEee
Confidence            45666666666665  67999999999998875421 122    2334445555  488999999 5888764

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.

>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A

Probab=80.67  E-value=1.6  Score=31.38  Aligned_cols=60  Identities=28%  Similarity=0.377  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCCceecCccccc
Q 029524           55 FQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKLSEAAAG  124 (192)
Q Consensus        55 ~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKGSFKLs~~~Kk  124 (192)
                      .++|.+=+..|. .+|.+..-|.      |..+|+   -..+...|..|++.|-|....+.|.|.+.+.+
T Consensus         5 ~~Ii~~IL~~l~-~~~~~~t~i~------~~~~L~---~~~~~~yL~~L~~~gLI~~~~~~Y~lTekG~~   64 (77)
T PF14947_consen    5 LEIIFDILKILS-KGGAKKTEIM------YKANLN---YSTLKKYLKELEEKGLIKKKDGKYRLTEKGKE   64 (77)
T ss_dssp             THHHHHHHHHH--TT-B-HHHHH------TTST-----HHHHHHHHHHHHHTTSEEEETTEEEE-HHHHH
T ss_pred             HHHHHHHHHHHH-cCCCCHHHHH------HHhCcC---HHHHHHHHHHHHHCcCeeCCCCEEEECccHHH
Confidence            466777777776 6667766555      222232   34688999999999999888899999988764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	192
1uhm_A	78	Histone H1, histone HHO1P; winged helix-turn-helix	4e-11
2rqp_A	88	Heterochromatin protein 1-binding protein 3; histo	5e-09
1ghc_A	75	GH1; chromosomal protein; NMR {Gallus gallus} SCOP	1e-08
1uss_A	88	Histone H1; DNA binding protein, linker histone, D	2e-08
1ust_A	93	Histone H1; DNA binding protein, linker histone, D	2e-08
1hst_A	90	Histone H5; chromosomal protein; 2.60A {Gallus gal	5e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04

>1uhm_A Histone H1, histone HHO1P; winged helix-turn-helix, linker histone, riken structural genomics/proteomics initiative, RSGI; NMR {Saccharomyces cerevisiae} SCOP: a.4.5.13 Length = 78

 Score = 55.9 bits (135), Expect = 4e-11
 Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 4/76 (5%)

Query: 49  PSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHK-DELPANFRKILAVQLKHFAAKG 107
            S   Y ++I E L AL+++ GSS  A+ K+++E +      +NF       +K     G
Sbjct: 2   ASSKSYRELIIEGLTALKERKGSSRPALKKFIKENYPIVGSASNFDLYFNNAIKKGVEAG 61

Query: 108 NLIKIR---ASYKLSE 120
           +  + +    + KL++
Sbjct: 62  DFEQPKGPAGAVKLAK 77

>2rqp_A Heterochromatin protein 1-binding protein 3; histone H1, alternative splicing, chromosomal protein, DNA-binding, nucleus, phosphoprotein; NMR {Homo sapiens} Length = 88

 Score = 50.2 bits (120), Expect = 5e-09
 Identities = 18/70 (25%), Positives = 31/70 (44%)

Query: 46  SKTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAA 105
             +   P    ++TEA+ A   KSG+S  AI KY+  K+          +L   LK    
Sbjct: 4   MASSPRPKMDAILTEAIKACFQKSGASVVAIRKYIIHKYPSLELERRGYLLKQALKRELN 63

Query: 106 KGNLIKIRAS 115
           +G + +++  
Sbjct: 64  RGVIKQVKGK 73

>1ghc_A GH1; chromosomal protein; NMR {Gallus gallus} SCOP: a.4.5.13 Length = 75

 Score = 49.3 bits (118), Expect = 1e-08
 Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 7/76 (9%)

Query: 50  SHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNL 109
           + P   ++IT+A+ A +++ G S  A+ K +     D         + + LK   +KG L
Sbjct: 2   AGPSVTELITKAVSASKERKGLSLAALKKALAAGGYD--VEKNNSRIKLGLKSLVSKGTL 59

Query: 110 IKIR-----ASYKLSE 120
           ++ +      S++LS+
Sbjct: 60  VQTKGTGASGSFRLSK 75

>1uss_A Histone H1; DNA binding protein, linker histone, DNA binding domain; NMR {Saccharomyces cerevisiae} SCOP: a.4.5.13 PDB: 1yqa_A Length = 88

 Score = 48.7 bits (116), Expect = 2e-08
 Identities = 19/86 (22%), Positives = 39/86 (45%), Gaps = 2/86 (2%)

Query: 45  QSKTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHK--DELPANFRKILAVQLKH 102
           ++ +PS   Y +MI +++  L D  GSS   + KY+++      +  +NF  +    +K 
Sbjct: 1   KASSPSSLTYKEMILKSMPQLNDGKGSSRIVLKKYVKDTFSSKLKTSSNFDYLFNSAIKK 60

Query: 103 FAAKGNLIKIRASYKLSEAAAGKTKK 128
               G L++ +    + +    K K 
Sbjct: 61  CVENGELVQPKGPSGIIKLNKKKVKL 86

>1hst_A Histone H5; chromosomal protein; 2.60A {Gallus gallus} SCOP: a.4.5.13 Length = 90

 Score = 45.3 bits (107), Expect = 5e-07
 Identities = 23/90 (25%), Positives = 46/90 (51%), Gaps = 7/90 (7%)

Query: 47  KTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAK 106
           ++ SHP Y +MI  A+ A + + GSS  +I KY++  +K    A+ +  + + ++   A 
Sbjct: 3   RSASHPTYSEMIAAAIRAEKSRGGSSRQSIQKYIKSHYKVGHNADLQ--IKLSIRRLLAA 60

Query: 107 GNLIKIRA-----SYKLSEAAAGKTKKEIK 131
           G L + +      S++L+++   K     K
Sbjct: 61  GVLKQTKGVGASGSFRLAKSDKAKRSPGKK 90

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

 Score = 40.6 bits (94), Expect = 2e-04
 Identities = 22/128 (17%), Positives = 38/128 (29%), Gaps = 29/128 (22%)

Query: 16  EEPEKVVTEKKAKAAKEKKPKAPK--------EKKPKQSKTPS-HPPYFQMITEALMALQ 66
            +   VV +    +  EK+PK           E K K     + H    + I +     +
Sbjct: 402 SDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALH----RSIVDHYNIPK 457

Query: 67  --DKSGSSPYAIAKY--------MEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASY 116
             D     P  + +Y        ++     E    FR +  +    F  +    KIR   
Sbjct: 458 TFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVF-LDF-RFLEQ----KIRHDS 511

Query: 117 KLSEAAAG 124
               A+  
Sbjct: 512 TAWNASGS 519

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	192
1uss_A	88	Histone H1; DNA binding protein, linker histone, D	99.93
1uhm_A	78	Histone H1, histone HHO1P; winged helix-turn-helix	99.93
1hst_A	90	Histone H5; chromosomal protein; 2.60A {Gallus gal	99.92
1ust_A	93	Histone H1; DNA binding protein, linker histone, D	99.92
2rqp_A	88	Heterochromatin protein 1-binding protein 3; histo	99.91
1ghc_A	75	GH1; chromosomal protein; NMR {Gallus gallus} SCOP	99.85
2lso_A	83	Histone H1X; structural genomics, northeast struct	99.72
2a07_F	93	Forkhead box protein P2; double-helix, swapping, h	94.95
1vtn_C	102	HNF-3/FORK head DNA-recognition motif; protein-DNA	94.12
2c6y_A	111	Forkhead box protein K2; transcription regulation,	94.06
3bpy_A	85	FORK head domain, forkhead transcription factor FO	93.06
2hfh_A	109	Genesis, HFH-2; HNF-3 homologues, winged helix pro	92.98
2hdc_A	97	Protein (transcription factor); structure, dyanami	92.92
3coa_C	117	Forkhead box protein O1; winged helix, forkhead do	92.81
1kq8_A	100	HFH-1, hepatocyte nuclear factor 3 forkhead homolo	92.53
3l2c_A	110	Forkhead box protein O4; winged helix, transcripti	92.41
1e17_A	150	AFX; DNA binding domain, winged helix; NMR {Homo s	90.76
3g73_A	142	Forkhead box protein M1; DNA-binding domain, forkh	89.81
3fbl_A	82	Putative uncharacterized protein; AFV1, archaeal v	84.41
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	84.23

>1uss_A Histone H1; DNA binding protein, linker histone, DNA binding domain; NMR {Saccharomyces cerevisiae} SCOP: a.4.5.13 PDB: 1yqa_A

Probab=99.93  E-value=1.7e-26  Score=171.47  Aligned_cols=79  Identities=24%  Similarity=0.429  Sum_probs=73.1

Q ss_pred             CCCCCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC--CCchhHHHHHHHHHHHHHhcCceEecCC---ceecCcc
Q 029524           47 KTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD--ELPANFRKILAVQLKHFAAKGNLIKIRA---SYKLSEA  121 (192)
Q Consensus        47 k~~sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~--~lp~nf~~lLk~aLKk~Ve~G~LVqvKG---SFKLs~~  121 (192)
                      ++++||+|.+||.|||.+|+||+|||+++|.+||+++|++  +++.+|+.+|+.+|++||++|.|+|++|   ||+|+..
T Consensus         3 ~~~~hP~y~~MI~eAI~alker~GsS~~AIkKyI~~~y~~~~~~~~~~~~~lk~aLK~~v~~G~lvq~KgasGsfkl~~k   82 (88)
T 1uss_A            3 SSPSSLTYKEMILKSMPQLNDGKGSSRIVLKKYVKDTFSSKLKTSSNFDYLFNSAIKKCVENGELVQPKGPSGIIKLNKK   82 (88)
T ss_dssp             TCCSSCCHHHHHHHHHHHSCCTTSBCHHHHHHHHHHHTTTTSCCSSTHHHHHHHHHHHHHHHSSEECSSTTSSCBEECCS
T ss_pred             CCCCCCCHHHHHHHHHHHhccCCCcCHHHHHHHHHHhCCCcccchHhHHHHHHHHHHHHHHcCCEEeccCCCCceecCcc
Confidence            4568999999999999999999999999999999999986  4578999999999999999999999998   9999987


Q ss_pred             cccc
Q 029524          122 AAGK  125 (192)
Q Consensus       122 ~Kk~  125 (192)
                      .++.
T Consensus        83 ~~~~   86 (88)
T 1uss_A           83 KVKL   86 (88)
T ss_dssp             CCCC
T ss_pred             cccc
Confidence            7553

>1uhm_A Histone H1, histone HHO1P; winged helix-turn-helix, linker histone, riken structural genomics/proteomics initiative, RSGI; NMR {Saccharomyces cerevisiae} SCOP: a.4.5.13

Probab=99.93  E-value=7.5e-26  Score=164.22  Aligned_cols=72  Identities=26%  Similarity=0.372  Sum_probs=67.3

Q ss_pred             CCCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCc-hhHHHHHHHHHHHHHhcCceEecC---CceecCc
Q 029524           49 PSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELP-ANFRKILAVQLKHFAAKGNLIKIR---ASYKLSE  120 (192)
Q Consensus        49 ~sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp-~nf~~lLk~aLKk~Ve~G~LVqvK---GSFKLs~  120 (192)
                      ++||+|.+||.|||.+|+||+|||+++|++||+++|+++++ .+|+.+|+.+|++||++|.|+|++   |||+|+.
T Consensus         2 ~~hP~y~~MI~eAI~~lker~GsS~~AIkKyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~q~KGasgsfkl~~   77 (78)
T 1uhm_A            2 ASSKSYRELIIEGLTALKERKGSSRPALKKFIKENYPIVGSASNFDLYFNNAIKKGVEAGDFEQPKGPAGAVKLAK   77 (78)
T ss_dssp             CCCCCHHHHHHHHHHHHCCSSCEEHHHHHHHHHTTSCTTTSSSTHHHHHHHHHHHHHHTTSEECCCTTSCEEEESC
T ss_pred             CCCCCHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCCCCCchHHHHHHHHHHHHHHHHcCCEEeccCCCcceecCC
Confidence            58999999999999999999999999999999999996555 799999999999999999999976   5999985

>1hst_A Histone H5; chromosomal protein; 2.60A {Gallus gallus} SCOP: a.4.5.13

Probab=99.92  E-value=2.4e-25  Score=166.29  Aligned_cols=76  Identities=28%  Similarity=0.466  Sum_probs=65.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCC-----ceecCc
Q 029524           46 SKTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRA-----SYKLSE  120 (192)
Q Consensus        46 ~k~~sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKG-----SFKLs~  120 (192)
                      .++++||+|.+||.|||.+|+||+|||+++|.+||+++|++  +++|+.+|+.+|++||++|.|+|++|     ||+|+.
T Consensus         2 k~~~~hP~y~~MI~eAI~~lker~GsS~~AI~KyI~~~y~~--~~~~~~~l~~aLk~~v~~G~l~q~Kg~GasGsfkl~~   79 (90)
T 1hst_A            2 RRSASHPTYSEMIAAAIRAEKSRGGSSRQSIQKYIKSHYKV--GHNADLQIKLSIRRLLAAGVLKQTKGVGASGSFRLAK   79 (90)
T ss_dssp             ----CCCCHHHHHHHHHHTCCCSSCEEHHHHHHHHHHHSCC--CTTHHHHHHHHHHHHHHTTSEEEECCSSCCCEEEECC
T ss_pred             CCCCCCCCHHHHHHHHHHHhccCCCCCHHHHHHHHHHHccC--chhHHHHHHHHHHHHHHcCCeeeecCCCccceeecCC
Confidence            34568999999999999999999999999999999999984  35699999999999999999999997     999997


Q ss_pred             ccc
Q 029524          121 AAA  123 (192)
Q Consensus       121 ~~K  123 (192)
                      ..+
T Consensus        80 ~~k   82 (90)
T 1hst_A           80 SDK   82 (90)
T ss_dssp             ---
T ss_pred             CcC
Confidence            653

>2rqp_A Heterochromatin protein 1-binding protein 3; histone H1, alternative splicing, chromosomal protein, DNA-binding, nucleus, phosphoprotein; NMR {Homo sapiens}

Probab=99.91  E-value=5.5e-26  Score=168.22  Aligned_cols=78  Identities=24%  Similarity=0.280  Sum_probs=71.7

Q ss_pred             CCCCCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCC-----ceecCcc
Q 029524           47 KTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRA-----SYKLSEA  121 (192)
Q Consensus        47 k~~sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKG-----SFKLs~~  121 (192)
                      ++.+||+|.+||.|||.+|+||+|||+++|.+||+++|+..++++|+.+|+.+|++||++|.|+|++|     ||+|+..
T Consensus         5 ~~~~hp~y~~MI~eAI~~Lker~GsS~~AI~KyI~~~y~~~~~~~~~~~lk~aLk~~v~~G~l~q~Kg~GasGsfkl~~~   84 (88)
T 2rqp_A            5 ASSPRPKMDAILTEAIKACFQKSGASVVAIRKYIIHKYPSLELERRGYLLKQALKRELNRGVIKQVKGKGASGSFVVVQK   84 (88)
T ss_dssp             SCCCCCCHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHCSTHHHHTTTTTHHHHHHHHHHHHTTCCSSCSSTTTSSCCTTT
T ss_pred             CCCCCCCHHHHHHHHHHHhccCCCcCHHHHHHHHHHhCCCCChhhHHHHHHHHHHHHHhcCcEEeecCCCCcceeecccc
Confidence            45699999999999999999999999999999999999843457899999999999999999999997     9999988


Q ss_pred             ccc
Q 029524          122 AAG  124 (192)
Q Consensus       122 ~Kk  124 (192)
                      .++
T Consensus        85 ~kk   87 (88)
T 2rqp_A           85 SRK   87 (88)
T ss_dssp             TCC
T ss_pred             ccC
Confidence            765

>1ghc_A GH1; chromosomal protein; NMR {Gallus gallus} SCOP: a.4.5.13

Probab=99.85  E-value=5.2e-23  Score=147.34  Aligned_cols=70  Identities=26%  Similarity=0.406  Sum_probs=63.4

Q ss_pred             CCCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCC-----ceecCc
Q 029524           49 PSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRA-----SYKLSE  120 (192)
Q Consensus        49 ~sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKG-----SFKLs~  120 (192)
                      ++||+|.+||.|||.+|+||+|||+++|.+||+++|.. + .+++.+|+.+|++||++|.|+|++|     ||+|+.
T Consensus         1 ~~hP~y~~mI~~AI~alker~GsS~~AI~Kyi~~~~~~-~-~~~~~~l~~aLk~~v~~G~l~~~kg~gasGsfkl~~   75 (75)
T 1ghc_A            1 MAGPSVTELITKAVSASKERKGLSLAALKKALAAGGYD-V-EKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFRLSK   75 (75)
T ss_dssp             CCSSSHHHHHHHHHHHCSSSSCCTTSSGGGSSSSSSCC-S-SSSHHHHHHHTTTHHHHTSSCCCCCSTTSCCCCSCC
T ss_pred             CCCCCHHHHHHHHHHHhccCCcccHHHHHHHHHHccCC-c-hhHHHHHHHHHHHHHhcCCeEeccCCCCccccccCC
Confidence            37999999999999999999999999999999999442 3 3568899999999999999999997     999973

>2lso_A Histone H1X; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, nuclear protein; NMR {Homo sapiens}

Probab=99.72  E-value=4e-22  Score=146.82  Aligned_cols=69  Identities=23%  Similarity=0.297  Sum_probs=64.5

Q ss_pred             CCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCC-----ceecCcc
Q 029524           52 PPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRA-----SYKLSEA  121 (192)
Q Consensus        52 P~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKG-----SFKLs~~  121 (192)
                      ++|.+||.|||.+|+||+|||+++|.+||+++|+. ++++|+.+|+.+|+++|++|.|+|++|     ||+|+..
T Consensus         6 ~~y~~MI~eAI~aLker~GSS~~AI~K~i~~~~~~-~~~~~~~~lk~aLK~~v~~G~Lvq~Kg~GasGsfKl~~k   79 (83)
T 2lso_A            6 GKYSQLVVETIRRLGERNGSSLAKIYTEAKKVPWF-DQQNGRTYLKYSIKALVQNDTLLQVKGTGANGSFKLNRK   79 (83)
Confidence            68999999999999999999999999999999974 568999999999999999999999997     9999864

>2a07_F Forkhead box protein P2; double-helix, swapping, homodimer, monomer, winged-helix, magnesium, transcription/DNA complex; 1.90A {Homo sapiens} SCOP: a.4.5.14 PDB: 2as5_F 2kiu_A 3qrf_F

Probab=94.95  E-value=0.054  Score=40.32  Aligned_cols=58  Identities=12%  Similarity=0.201  Sum_probs=41.3

Q ss_pred             CCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC--CCchhHHHHHHHHHHHHHhcCceEec
Q 029524           51 HPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD--ELPANFRKILAVQLKHFAAKGNLIKI  112 (192)
Q Consensus        51 HP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~--~lp~nf~~lLk~aLKk~Ve~G~LVqv  112 (192)
                      .-+|..||..||.+.. ..+.+..-|-.||+++|+.  ..+..+..-|++.|-   -++-|+++
T Consensus         5 p~SY~~LI~~AI~~sp-~~~ltL~eIY~~i~~~fpyyr~~~~gWkNSIRHNLS---ln~~F~kv   64 (93)
T 2a07_F            5 PFTYATLIRQAIMESS-DRQLTLNEIYSWFTRTFAYFRRNAATWKNAVRHNLS---LHKCFVRV   64 (93)
T ss_dssp             SCCHHHHHHHHHHHST-TSCBCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH---HCTTBCCE
T ss_pred             CCCHHHHHHHHHHhCC-CCCccHHHHHHHHHHhCCccccCCCccccccceeee---hhhceeec
Confidence            4579999999999854 4569999999999999863  234456666666554   34455554

>1vtn_C HNF-3/FORK head DNA-recognition motif; protein-DNA complex, double helix, transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} PDB: 1d5v_A

Probab=94.12  E-value=0.099  Score=39.42  Aligned_cols=58  Identities=14%  Similarity=0.176  Sum_probs=43.1

Q ss_pred             CCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC--CCchhHHHHHHHHHHHHHhcCceEec
Q 029524           51 HPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD--ELPANFRKILAVQLKHFAAKGNLIKI  112 (192)
Q Consensus        51 HP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~--~lp~nf~~lLk~aLKk~Ve~G~LVqv  112 (192)
                      .-+|..||..||.+.. ..+.+..-|-.||+++|+.  ..+..+..-|++.|--   +.-|+++
T Consensus         5 p~SY~~LI~~AI~~sp-~~~LtL~eIY~~I~~~fpyyr~~~~gWqNSIRHNLSl---n~~F~kv   64 (102)
T 1vtn_C            5 PYSYISLITMAIQQAP-GKMLTLSEIYQWIMDLFPYYRENQQRWQNSIRHSLSF---NDCFVKV   64 (102)
T ss_dssp             SSCHHHHHHHHHHTST-TSCBCHHHHHHHHHHHCGGGGSCHHHHHHHHHHHHHH---CTTEEEE
T ss_pred             CCCHHHHHHHHHHhCC-CCCCcHHHHHHHHHHcCCccccCCCchhhhhhhhhhh---ccceEec
Confidence            4579999999999753 4468999999999999974  2344566667766543   5677776

>2c6y_A Forkhead box protein K2; transcription regulation, DNA-binding domain, forkhead transcription factors, interleukin enhancer binding factor; 2.4A {Homo sapiens} SCOP: a.4.5.14 PDB: 1jxs_A 2a3s_A 2d2w_A

Probab=94.06  E-value=0.14  Score=39.12  Aligned_cols=59  Identities=14%  Similarity=0.153  Sum_probs=43.6

Q ss_pred             CCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC--CCchhHHHHHHHHHHHHHhcCceEec
Q 029524           50 SHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD--ELPANFRKILAVQLKHFAAKGNLIKI  112 (192)
Q Consensus        50 sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~--~lp~nf~~lLk~aLKk~Ve~G~LVqv  112 (192)
                      ..-+|..||..||.... ....+..-|-.||+++|+.  ..+..+..-|++.|-   -+.-|+++
T Consensus        17 Pp~SYa~LI~~AI~~sp-~~~LtL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLS---ln~~F~Kv   77 (111)
T 2c6y_A           17 PPYSYAQLIVQAITMAP-DKQLTLNGIYTHITKNYPYYRTADKGWQNSIRHNLS---LNRYFIKV   77 (111)
T ss_dssp             CSSCHHHHHHHHHHTST-TSCEEHHHHHHHHHHHCTTSCTTCHHHHHHHHHHHH---HSTTEEEE
T ss_pred             CCCCHHHHHHHHHHhCC-CCCCcHHHHHHHHHHcCCccccCCCeeecchhHHhh---hhhhhccc
Confidence            34569999999999954 4468999999999999974  233556666666553   45677765

>3bpy_A FORK head domain, forkhead transcription factor FOXO4, DNA binding domain; forkhead BOX, winged helix; 1.87A {Homo sapiens}

Probab=93.06  E-value=0.11  Score=37.93  Aligned_cols=59  Identities=17%  Similarity=0.303  Sum_probs=42.1

Q ss_pred             CCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC--CC-----chhHHHHHHHHHHHHHhcCceEecC
Q 029524           51 HPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD--EL-----PANFRKILAVQLKHFAAKGNLIKIR  113 (192)
Q Consensus        51 HP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~--~l-----p~nf~~lLk~aLKk~Ve~G~LVqvK  113 (192)
                      .-+|..||..||....++ ..+.+.|-.||+++|+.  ..     ...+..-|++.|-   -+.-|++|.
T Consensus         7 ~~SY~~LI~~Ai~~sp~~-~ltL~eIY~~i~~~fpyy~~~~~~~s~~gWqNSIRHNLS---ln~~F~Kv~   72 (85)
T 3bpy_A            7 NQSYAELISQAIESAPEK-RLTLAQIYEWMVRTVPYFKDKGDSNSSAGWKNSIRHNLS---LHSKFIKVH   72 (85)
T ss_dssp             SCCHHHHHHHHHHHSTTS-CBCHHHHHHHHHHHCGGGTTCTTCCTTSHHHHHHHHHHH---HCTTEEEEC
T ss_pred             CCCHHHHHHHHHHhCCcC-CccHHHHHHHHHHhCcchhcCccCccCCCcchhhhhhcc---HhhhheeCC
Confidence            457999999999996654 49999999999999863  11     1245556666543   356677654

>2hfh_A Genesis, HFH-2; HNF-3 homologues, winged helix protein; NMR {Rattus norvegicus} SCOP: a.4.5.14

Probab=92.98  E-value=0.12  Score=39.56  Aligned_cols=58  Identities=16%  Similarity=0.257  Sum_probs=40.1

Q ss_pred             CCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC--CCchhHHHHHHHHHHHHHhcCceEec
Q 029524           51 HPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD--ELPANFRKILAVQLKHFAAKGNLIKI  112 (192)
Q Consensus        51 HP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~--~lp~nf~~lLk~aLKk~Ve~G~LVqv  112 (192)
                      .-+|..||..||.+.. ....+..-|-.||+++|+.  ..+..+..-|+..|-   -+.-|+++
T Consensus         5 p~SYa~LI~~AI~~sp-~~~LtL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLS---ln~~F~Kv   64 (109)
T 2hfh_A            5 PYSYIALITMAILQSP-QKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLS---LNDCFVKI   64 (109)
T ss_dssp             CCCHHHHHHHHHHTCS-SSCBCHHHHHHHHHTTCHHHHTTCGGGHHHHHHHHH---HHTCCBCC
T ss_pred             CCCHHHHHHHHHHhCC-CCCCcHHHHHHHHHHhcchhccCCcccchhhhhhhh---hhhhhhcC
Confidence            4579999999998754 4568999999999999963  223445555555443   33455554

>2hdc_A Protein (transcription factor); structure, dyanamics, genesis, winged helix protein, protein/DNA complex; HET: DNA; NMR {Rattus norvegicus} SCOP: a.4.5.14

Probab=92.92  E-value=0.085  Score=39.45  Aligned_cols=58  Identities=16%  Similarity=0.253  Sum_probs=38.7

Q ss_pred             CCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC--CCchhHHHHHHHHHHHHHhcCceEec
Q 029524           51 HPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD--ELPANFRKILAVQLKHFAAKGNLIKI  112 (192)
Q Consensus        51 HP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~--~lp~nf~~lLk~aLKk~Ve~G~LVqv  112 (192)
                      --+|..||..||.+.. ..+.+..-|-.||+++|+.  ..+..+..-|++.|--   +.-|+++
T Consensus         4 p~SY~~LI~~AI~~sp-~~~ltL~eIY~~i~~~fpyyr~~~~gWqNSIRHNLSl---n~~F~Kv   63 (97)
T 2hdc_A            4 PYSYIALITMAILQSP-QKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSL---NDCFVKI   63 (97)
T ss_dssp             CCCHHHHHHHHHHTCT-TTCBCHHHHHHHHHHHCHHHHHHCSSHHHHHHHHHHH---HHCCEEE
T ss_pred             CCCHHHHHHHHHHhCC-CCCCCHHHHHHHHHHhchhhccCCcceehhhhhhhhh---hhheeec
Confidence            3579999999998754 4568999999999999963  1123344455554432   2445544

>3coa_C Forkhead box protein O1; winged helix, forkhead domain, chromosomal rearrangement; HET: DNA; 2.20A {Homo sapiens} PDB: 3co7_C* 2k86_A 2uzk_A

Probab=92.81  E-value=0.21  Score=38.52  Aligned_cols=60  Identities=15%  Similarity=0.264  Sum_probs=42.7

Q ss_pred             CCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC--CC-----chhHHHHHHHHHHHHHhcCceEecC
Q 029524           50 SHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD--EL-----PANFRKILAVQLKHFAAKGNLIKIR  113 (192)
Q Consensus        50 sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~--~l-----p~nf~~lLk~aLKk~Ve~G~LVqvK  113 (192)
                      ..-+|..||..||..-. ....++.-|-.||+++|+.  .-     ...+..-|++.|-   -+.-|+++.
T Consensus        12 Pp~SYa~LI~~AI~~sp-~~~LTL~eIY~~I~~~fPyyr~~~d~~s~~gWqNSIRHNLS---ln~~F~Kv~   78 (117)
T 3coa_C           12 GNLSYADLITKAIESSA-EKRLTLSQIYEWMVKSVPYFKDKGDSNSSAGWKNSIRHNLS---LHSKFIRVQ   78 (117)
T ss_dssp             BSCCHHHHHHHHHHTST-TSCBCHHHHHHHHHHHCGGGTTCCSHHHHHHHHHHHHHHHH---HCTTEEEEC
T ss_pred             CCCCHHHHHHHHHHhCC-CCCccHHHHHHHHHHhCcccccCCCCcccccchhccchhee---cchhhcccc
Confidence            34689999999999754 4568999999999999863  11     1345555665543   457777763

>1kq8_A HFH-1, hepatocyte nuclear factor 3 forkhead homolog 1, winged; winged helix protein, structure, transcription; NMR {Rattus norvegicus} SCOP: a.4.5.14

Probab=92.53  E-value=0.1  Score=39.20  Aligned_cols=58  Identities=17%  Similarity=0.196  Sum_probs=37.9

Q ss_pred             CCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC--CCchhHHHHHHHHHHHHHhcCceEec
Q 029524           51 HPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD--ELPANFRKILAVQLKHFAAKGNLIKI  112 (192)
Q Consensus        51 HP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~--~lp~nf~~lLk~aLKk~Ve~G~LVqv  112 (192)
                      .-+|..||..||.+..+ ...+.+-|-.||+++|+.  ..+..+..-|++.|-   -+.-|+++
T Consensus         4 p~SY~~LI~~AI~~sp~-~~ltL~eIY~~i~~~fpyyr~~~~gWqNSIRHNLS---ln~~F~kv   63 (100)
T 1kq8_A            4 PYSYIALITMAIRDSAG-GRLTLAEINEYLMGKFPFFRGSYTGWRNSVRHNLS---LNDCFVKV   63 (100)
T ss_dssp             ---CHHHHHHHHTTSSS-SCBCHHHHHHHHHHHCTTGGGTCSCCHHHHHHHHH---HHTCCEEC
T ss_pred             CCCHHHHHHHHHHhCCC-CCCcHHHHHHHHHHhCccccCCCCceecccchhee---hhheeeec
Confidence            34688999999998554 459999999999999974  112334444555443   23456654

>3l2c_A Forkhead box protein O4; winged helix, transcription-DNA COMP; 1.87A {Homo sapiens} SCOP: a.4.5.14 PDB: 3co6_C*

Probab=92.41  E-value=0.14  Score=39.09  Aligned_cols=60  Identities=17%  Similarity=0.300  Sum_probs=43.2

Q ss_pred             CCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC--CC-----chhHHHHHHHHHHHHHhcCceEecC
Q 029524           50 SHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD--EL-----PANFRKILAVQLKHFAAKGNLIKIR  113 (192)
Q Consensus        50 sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~--~l-----p~nf~~lLk~aLKk~Ve~G~LVqvK  113 (192)
                      ..-+|..||..||....++ ..++..|-.||+++|+.  ..     ...+..-|++.|-   -+.-|++|-
T Consensus        25 PpySY~~LI~~AI~~sp~~-~LtL~eIY~~I~~~fPyyr~~~~~~s~~gWqNSIRHNLS---ln~~F~Kv~   91 (110)
T 3l2c_A           25 GNQSYAELISQAIESAPEK-RLTLAQIYEWMVRTVPYFKDKGDSNSSAGWKNSIRHNLS---LHSKFIKVH   91 (110)
T ss_dssp             BSCCHHHHHHHHHHHSTTS-CBCHHHHHHHHHHHCGGGTTCTTCCTTSHHHHHHHHHHH---HCTTEEEEC
T ss_pred             CCCCHHHHHHHHHHhCCcc-CcCHHHHHHHHHHhCchhhcCccccCCCCcccchhhhcc---HhhhheeCC
Confidence            3467999999999996654 49999999999999863  11     1345666666543   456677763

>3g73_A Forkhead box protein M1; DNA-binding domain, forkhead transcription factors, FOXM1, W helix; HET: DNA; 2.21A {Homo sapiens}

Probab=89.81  E-value=0.48  Score=37.69  Aligned_cols=59  Identities=12%  Similarity=0.193  Sum_probs=41.5

Q ss_pred             CCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC--C-CchhHHHHHHHHHHHHHhcCceEec
Q 029524           50 SHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD--E-LPANFRKILAVQLKHFAAKGNLIKI  112 (192)
Q Consensus        50 sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~--~-lp~nf~~lLk~aLKk~Ve~G~LVqv  112 (192)
                      ..-+|..||..||....+ .+.+...|-.||+++|+.  . -...+..-|++.|   .-+.-|+++
T Consensus        19 PpySYa~LI~~AI~~sp~-~~LTL~eIY~~I~~~fPyyr~~~~~gWqNSIRHNL---Sln~~F~r~   80 (142)
T 3g73_A           19 PPYSYMAMIQFAINSTER-KRMTLKDIYTWIEDHFPYFKHIAKPGWKNSIRHNL---SLHDMFVRE   80 (142)
T ss_dssp             CSSCHHHHHHHHHHTSTT-SEECHHHHHHHHHHHCTHHHHTSCTTHHHHHHHHH---HHCTTEEEE
T ss_pred             CCCCHHHHHHHHHHhCCC-CCcCHHHHHHHHHHhCCCccccCCCCccchhhhhh---hhhhhheec
Confidence            345799999999988554 449999999999999973  1 2234555666544   345666664

>3fbl_A Putative uncharacterized protein; AFV1, archaeal virus, extremophiles, lipothrixviridae, structural protein, DNA-binding protein; 1.95A {Acidianus filamentous virus 1}

Probab=84.41  E-value=1.1  Score=32.21  Aligned_cols=29  Identities=24%  Similarity=0.437  Sum_probs=24.2

Q ss_pred             HHHHHHHHHcCCCCCCcH---HHHHHHHHHhC
Q 029524           56 QMITEALMALQDKSGSSP---YAIAKYMEEKH   84 (192)
Q Consensus        56 eMI~EAI~aLkeR~GSS~---~AIkKYIe~~Y   84 (192)
                      +.|.+||.++..|+|.|.   |-|..||.+||
T Consensus        51 eyinnaisafssrtgisqetaqkiadfitsny   82 (82)
T 3fbl_A           51 EYINNAISAFSSRTGISQETAQKIADFITSNY   82 (82)
T ss_dssp             HHHHHHHHHHHTSTTCCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhhcccccHHHHHHHHHHHhcCC
Confidence            445678899999999997   56899999987

>1r7j_A Conserved hypothetical protein SSO10A; winged helix-turn-helix, two-stranded antiparallel coiled CO structural genomics, PSI; 1.47A {Sulfolobus solfataricus} SCOP: a.4.5.49 PDB: 1xsx_A

Probab=84.23  E-value=1.5  Score=31.52  Aligned_cols=62  Identities=15%  Similarity=0.106  Sum_probs=49.5

Q ss_pred             CCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCCceecCccccc
Q 029524           52 PPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKLSEAAAG  124 (192)
Q Consensus        52 P~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKGSFKLs~~~Kk  124 (192)
                      -+..++|.+-|..|.+  |.++..|...+.=+         .+.++..|..+.+.|-|....|.|.|.+.+.+
T Consensus         4 Rs~~eIi~~IL~~i~~--~~~~t~La~~~~ls---------~~~~~~~l~~L~~~GLI~~~~~~~~LT~kG~~   65 (95)
T 1r7j_A            4 KSKLEIIQAILEACKS--GSPKTRIMYGANLS---------YALTGRYIKMLMDLEIIRQEGKQYMLTKKGEE   65 (95)
T ss_dssp             CCHHHHHHHHHHHHTT--CBCHHHHHHHHTCC---------HHHHHHHHHHHHHTTSEEEETTEEEECHHHHH
T ss_pred             CCHHHHHHHHHHHHHc--CCCHHHHHHHhCcC---------HHHHHHHHHHHHHCCCeEEECCeeEEChhHHH
Confidence            4577888888888874  48888887665332         23589999999999999999999999988864

---

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	192
d1hsta_	74	a.4.5.13 (A:) Histone H5, globular domain {Chicken	5e-12
d1ghca_	75	a.4.5.13 (A:) Histone H1, globular domain {Chicken	2e-10
d1ussa_	88	a.4.5.13 (A:) Histone H1 homologue Hho1p {Baker's	7e-09
d1usta_	92	a.4.5.13 (A:) Histone H1 homologue Hho1p {Baker's	2e-08

>d1hsta_ a.4.5.13 (A:) Histone H5, globular domain {Chicken (Gallus gallus) [TaxId: 9031]} Length = 74

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Linker histone H1/H5
domain: Histone H5, globular domain
species: Chicken (Gallus gallus) [TaxId: 9031]

 Score = 56.7 bits (137), Expect = 5e-12
 Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 7/76 (9%)

Query: 50  SHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNL 109
           SHP Y +MI  A+ A + + GSS  +I KY++  +K     N    + + ++   A G L
Sbjct: 1   SHPTYSEMIAAAIRAEKSRGGSSRQSIQKYIKSHYKV--GHNADLQIKLSIRRLLAAGVL 58

Query: 110 IKIR-----ASYKLSE 120
            + +      S++L++
Sbjct: 59  KQTKGVGASGSFRLAK 74

>d1ghca_ a.4.5.13 (A:) Histone H1, globular domain {Chicken (Gallus gallus) [TaxId: 9031]} Length = 75

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Linker histone H1/H5
domain: Histone H1, globular domain
species: Chicken (Gallus gallus) [TaxId: 9031]

 Score = 52.9 bits (127), Expect = 2e-10
 Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 7/76 (9%)

Query: 50  SHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNL 109
           + P   ++IT+A+ A +++ G S  A+ K +     D         + + LK   +KG L
Sbjct: 2   AGPSVTELITKAVSASKERKGLSLAALKKALAAGGYD--VEKNNSRIKLGLKSLVSKGTL 59

Query: 110 IKIRA-----SYKLSE 120
           ++ +      S++LS+
Sbjct: 60  VQTKGTGASGSFRLSK 75

>d1ussa_ a.4.5.13 (A:) Histone H1 homologue Hho1p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 88

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Linker histone H1/H5
domain: Histone H1 homologue Hho1p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 48.7 bits (116), Expect = 7e-09
 Identities = 19/86 (22%), Positives = 39/86 (45%), Gaps = 2/86 (2%)

Query: 45  QSKTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHK--DELPANFRKILAVQLKH 102
           ++ +PS   Y +MI +++  L D  GSS   + KY+++      +  +NF  +    +K 
Sbjct: 1   KASSPSSLTYKEMILKSMPQLNDGKGSSRIVLKKYVKDTFSSKLKTSSNFDYLFNSAIKK 60

Query: 103 FAAKGNLIKIRASYKLSEAAAGKTKK 128
               G L++ +    + +    K K 
Sbjct: 61  CVENGELVQPKGPSGIIKLNKKKVKL 86

>d1usta_ a.4.5.13 (A:) Histone H1 homologue Hho1p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 92

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Linker histone H1/H5
domain: Histone H1 homologue Hho1p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 47.9 bits (114), Expect = 2e-08
 Identities = 22/89 (24%), Positives = 44/89 (49%), Gaps = 4/89 (4%)

Query: 47  KTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHK-DELPANFRKILAVQLKHFAA 105
           +  S   Y ++I E L AL+++ GSS  A+ K+++E +      +NF       +K    
Sbjct: 2   EEASSKSYRELIIEGLTALKERKGSSRPALKKFIKENYPIVGSASNFDLYFNNAIKKGVE 61

Query: 106 KGNLIKIR---ASYKLSEAAAGKTKKEIK 131
            G+  + +    + KL++  + + KKE +
Sbjct: 62  AGDFEQPKGPAGAVKLAKKKSPEVKKEKE 90

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	192
d1hsta_	74	Histone H5, globular domain {Chicken (Gallus gallu	99.93
d1ussa_	88	Histone H1 homologue Hho1p {Baker's yeast (Sacchar	99.92
d1usta_	92	Histone H1 homologue Hho1p {Baker's yeast (Sacchar	99.91
d1ghca_	75	Histone H1, globular domain {Chicken (Gallus gallu	99.88
d2a07f1	82	Forkhead box protein P2, FOXP2 {Human (Homo sapien	95.67
d2fnaa1	73	Hypothetical protein SSO1545, C-terminal domain {S	94.98
d2c6ya1	98	Interleukin enhancer binding factor {Human (Homo s	94.75
d3bpya1	85	Afx (Foxo4) {Human (Homo sapiens) [TaxId: 9606]}	94.03
d1d5va_	94	Adipocyte-transcription factor FREAC-11 (s12, fkh-	94.01
d2hdca_	97	Genesis {Rat (Rattus norvegicus) [TaxId: 10116]}	93.76
d1kq8a_	75	HFH-1 (HNF-3 forkhead homolog-1) {Rat (Rattus norv	93.35
d2v9va2	73	C-terminal fragment of elongation factor SelB {Moo	85.7

>d1hsta_ a.4.5.13 (A:) Histone H5, globular domain {Chicken (Gallus gallus) [TaxId: 9031]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Linker histone H1/H5
domain: Histone H5, globular domain
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=99.93  E-value=3.7e-26  Score=163.16  Aligned_cols=69  Identities=30%  Similarity=0.513  Sum_probs=65.3

Q ss_pred             CCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC-----CceecCc
Q 029524           50 SHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR-----ASYKLSE  120 (192)
Q Consensus        50 sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK-----GSFKLs~  120 (192)
                      +||+|.+||.|||.+|+||+|||+++|++||+++|+  ++.+|+.+|+.+|+++|++|.|+|++     |||||+.
T Consensus         1 sHP~y~~MI~eAI~al~er~GsS~~AI~kyI~~~y~--~~~~~~~~l~~aLk~~v~~G~l~q~kg~GasGsfkl~k   74 (74)
T d1hsta_           1 SHPTYSEMIAAAIRAEKSRGGSSRQSIQKYIKSHYK--VGHNADLQIKLSIRRLLAAGVLKQTKGVGASGSFRLAK   74 (74)
T ss_dssp             CCCCHHHHHHHHHHTCCCSSCEEHHHHHHHHHHHSC--CCTTHHHHHHHHHHHHHHTTSEEEECCSSCCCEEEECC
T ss_pred             CCCCHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCC--CchhHHHHHHHHHHHHHHcCcEEeeccCCCcceeecCC
Confidence            699999999999999999999999999999999998  46789999999999999999999999     5999973

>d1ussa_ a.4.5.13 (A:) Histone H1 homologue Hho1p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Linker histone H1/H5
domain: Histone H1 homologue Hho1p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.92  E-value=1.1e-25  Score=165.69  Aligned_cols=79  Identities=24%  Similarity=0.429  Sum_probs=72.4

Q ss_pred             CCCCCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCC--CchhHHHHHHHHHHHHHhcCceEecCC---ceecCcc
Q 029524           47 KTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDE--LPANFRKILAVQLKHFAAKGNLIKIRA---SYKLSEA  121 (192)
Q Consensus        47 k~~sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~--lp~nf~~lLk~aLKk~Ve~G~LVqvKG---SFKLs~~  121 (192)
                      ..++||+|.+||.|||.+|+||+|||+++|.+||+++|+++  ++.+|+.+|+++|++||++|.|+|++|   +|+|+..
T Consensus         3 ~~~~~~sy~~MI~eAI~~L~er~GsS~~aI~KyI~~~y~~~~~~~~~f~~~l~~aLk~~v~~G~L~q~kG~sG~fkl~kk   82 (88)
T d1ussa_           3 SSPSSLTYKEMILKSMPQLNDGKGSSRIVLKKYVKDTFSSKLKTSSNFDYLFNSAIKKCVENGELVQPKGPSGIIKLNKK   82 (88)
T ss_dssp             TCCSSCCHHHHHHHHHHHSCCTTSBCHHHHHHHHHHHTTTTSCCSSTHHHHHHHHHHHHHHHSSEECSSTTSSCBEECCS
T ss_pred             CCCCCCCHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCCccccchHhHHHHHHHHHHHHHHcCcEEeccCCCceeeeccc
Confidence            45689999999999999999999999999999999999863  467899999999999999999999995   9999988


Q ss_pred             cccc
Q 029524          122 AAGK  125 (192)
Q Consensus       122 ~Kk~  125 (192)
                      .++.
T Consensus        83 ~kk~   86 (88)
T d1ussa_          83 KVKL   86 (88)
T ss_dssp             CCCC
T ss_pred             cccC
Confidence            7664

>d1usta_ a.4.5.13 (A:) Histone H1 homologue Hho1p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Linker histone H1/H5
domain: Histone H1 homologue Hho1p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.91  E-value=2.7e-25  Score=164.75  Aligned_cols=77  Identities=25%  Similarity=0.356  Sum_probs=70.1

Q ss_pred             CCCCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC-CCchhHHHHHHHHHHHHHhcCceEecC---CceecCcccc
Q 029524           48 TPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD-ELPANFRKILAVQLKHFAAKGNLIKIR---ASYKLSEAAA  123 (192)
Q Consensus        48 ~~sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~-~lp~nf~~lLk~aLKk~Ve~G~LVqvK---GSFKLs~~~K  123 (192)
                      ..+||+|.+||.|||.+|+||+|||+++|.+||+++|++ .++.+|+.+|+.+|++||++|.|+|++   |+|+|+...+
T Consensus         3 ~~~~pty~~MI~eAI~~l~er~GsS~~aI~KyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~L~q~kG~sG~fkl~~~~~   82 (92)
T d1usta_           3 EASSKSYRELIIEGLTALKERKGSSRPALKKFIKENYPIVGSASNFDLYFNNAIKKGVEAGDFEQPKGPAGAVKLAKKKS   82 (92)
T ss_dssp             SSCCCCHHHHHHHHHTTTTTTSCEEHHHHHHHHHHHCHHHHTSTTHHHHHHHHHHHHHHTTSEECTTCTTSEEEECSCCC
T ss_pred             CCCCCCHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHCcCcCCHHHHHHHHHHHHHHHHHcCcEEeccCCCCceecCCCCC
Confidence            468999999999999999999999999999999999974 245789999999999999999999999   5999987765


Q ss_pred             c
Q 029524          124 G  124 (192)
Q Consensus       124 k  124 (192)
                      .
T Consensus        83 ~   83 (92)
T d1usta_          83 P   83 (92)
T ss_dssp             S
T ss_pred             C
Confidence            4

>d1ghca_ a.4.5.13 (A:) Histone H1, globular domain {Chicken (Gallus gallus) [TaxId: 9031]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Linker histone H1/H5
domain: Histone H1, globular domain
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=99.88  E-value=1.2e-24  Score=155.96  Aligned_cols=69  Identities=25%  Similarity=0.364  Sum_probs=64.4

Q ss_pred             CCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCC-----ceecCc
Q 029524           50 SHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRA-----SYKLSE  120 (192)
Q Consensus        50 sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKG-----SFKLs~  120 (192)
                      .||+|.+||.|||.+|+||+|||+++|++||+++|.  +..+|+.+|+.+|+++|++|.|+|++|     ||+|+.
T Consensus         2 a~P~y~~MI~eAI~al~er~GsS~~AI~kyI~~~~~--~~~~~~~~l~~aLk~~v~~G~l~q~kG~GasGsfkl~k   75 (75)
T d1ghca_           2 AGPSVTELITKAVSASKERKGLSLAALKKALAAGGY--DVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFRLSK   75 (75)
T ss_dssp             CSSSHHHHHHHHHHHCSSSSCCTTSSGGGSSSSSSC--CSSSSHHHHHHHTTTHHHHTSSCCCCCSTTSCCCCSCC
T ss_pred             CCCCHHHHHHHHHHHcCCCCCcCHHHHHHHHHHhcc--CccchHHHHHHHHHHHHhcCCEEeeccCCccceeeeCC
Confidence            599999999999999999999999999999999987  357889999999999999999999985     999973

>d2a07f1 a.4.5.14 (F:503-584) Forkhead box protein P2, FOXP2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Forkhead DNA-binding domain
domain: Forkhead box protein P2, FOXP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.67  E-value=0.011  Score=41.34  Aligned_cols=50  Identities=14%  Similarity=0.178  Sum_probs=38.1

Q ss_pred             CCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC--CCchhHHHHHHHHHHH
Q 029524           52 PPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD--ELPANFRKILAVQLKH  102 (192)
Q Consensus        52 P~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~--~lp~nf~~lLk~aLKk  102 (192)
                      -+|..||..||.+.. ..+.+..-|-.||+++|+.  .....+..-|++.|..
T Consensus         5 ~sY~~LI~~Ai~~sp-~~~LtL~eIy~~i~~~fpyyr~~~~gWkNSIRHnLS~   56 (82)
T d2a07f1           5 FTYATLIRQAIMESS-DRQLTLNEIYSWFTRTFAYFRRNAATWKNAVRHNLSL   56 (82)
T ss_dssp             CCHHHHHHHHHHHST-TSCBCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhCC-CCCccHHHHHHHHHHhCcccccCCcccchhHhHhccc
Confidence            469999999999864 4559999999999999952  2345566667666644

>d2fnaa1 a.4.5.11 (A:284-356) Hypothetical protein SSO1545, C-terminal domain {Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Helicase DNA-binding domain
domain: Hypothetical protein SSO1545, C-terminal domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=94.98  E-value=0.036  Score=38.23  Aligned_cols=58  Identities=17%  Similarity=0.113  Sum_probs=47.7

Q ss_pred             HHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCCceecCccc
Q 029524           57 MITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKLSEAA  122 (192)
Q Consensus        57 MI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKGSFKLs~~~  122 (192)
                      .|++||.     .|++=..|+.|++.+.+..++   +..|...|++|+.-|-|++..+.|+|.++.
T Consensus        10 ~ILkaia-----~G~rWs~IK~yle~~~G~~I~---d~~ls~lL~nL~k~~~iek~~~~Y~i~DPv   67 (73)
T d2fnaa1          10 NIMRTLS-----KCGKWSDVKRALELEEGIEIS---DSEIYNYLTQLTKHSWIIKEGEKYCPSEPL   67 (73)
T ss_dssp             HHHHHHT-----TCBCHHHHHHHHHHHHCSCCC---HHHHHHHHHHHHHTTSEEESSSCEEESSHH
T ss_pred             HHHHHHH-----ccCcHHHHHHHHHHHcCCCCC---hHHHHHHHHHHHHcCceeecCCeeccCcHH
Confidence            3677776     457899999999999874344   556889999999999999999999998864

>d2c6ya1 a.4.5.14 (A:1-98) Interleukin enhancer binding factor {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Forkhead DNA-binding domain
domain: Interleukin enhancer binding factor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.75  E-value=0.031  Score=40.06  Aligned_cols=57  Identities=16%  Similarity=0.187  Sum_probs=43.7

Q ss_pred             CCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC--CCchhHHHHHHHHHHHHHhcCceEec
Q 029524           52 PPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD--ELPANFRKILAVQLKHFAAKGNLIKI  112 (192)
Q Consensus        52 P~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~--~lp~nf~~lLk~aLKk~Ve~G~LVqv  112 (192)
                      -+|..||..||.+..+ .+.+..-|-.||+++|+.  ..+..+..-|++.|-   .++-|+++
T Consensus         6 ~sY~~LI~~Ai~~sp~-~~ltL~eIy~~i~~~fpyfr~~~~gWkNSIRHnLS---~n~~F~kv   64 (98)
T d2c6ya1           6 YSYAQLIVQAITMAPD-KQLTLNGIYTHITKNYPYYRTADKGWQNSIRHNLS---LNRYFIKV   64 (98)
T ss_dssp             SCHHHHHHHHHHTSTT-SCEEHHHHHHHHHHHCTTSCTTCHHHHHHHHHHHH---HSTTEEEE
T ss_pred             ccHHHHHHHHHHhCCC-CCccHHHHHHHHHHhCcccccCCCCcchhhchhcc---cccceEec
Confidence            5799999999998644 459999999999999975  223456667777665   46667765

>d3bpya1 a.4.5.14 (A:93-177) Afx (Foxo4) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Forkhead DNA-binding domain
domain: Afx (Foxo4)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.03  E-value=0.028  Score=39.50  Aligned_cols=57  Identities=16%  Similarity=0.273  Sum_probs=40.2

Q ss_pred             CCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC--C-----CchhHHHHHHHHHHHHHhcCceEec
Q 029524           52 PPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD--E-----LPANFRKILAVQLKHFAAKGNLIKI  112 (192)
Q Consensus        52 P~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~--~-----lp~nf~~lLk~aLKk~Ve~G~LVqv  112 (192)
                      -+|.+||..||.+. ...+.+++-|-.||+++|+.  .     -...+..-|++.|-   .+.-|+++
T Consensus         8 ~SY~~LI~~Ai~~s-p~~~ltL~eIY~~i~~~fPyyr~~~~~~~~~gWkNSIRHnLS---l~~~F~kv   71 (85)
T d3bpya1           8 QSYAELISQAIESA-PEKRLTLAQIYEWMVRTVPYFKDKGDSNSSAGWKNSIRHNLS---LHSKFIKV   71 (85)
T ss_dssp             CCHHHHHHHHHHHS-TTSCBCHHHHHHHHHHHCGGGTTCTTCCTTSHHHHHHHHHHH---HCTTEEEE
T ss_pred             cCHHHHHHHHHHhC-CCCCccHHHHHHHHHHhChhhhccCcccccccchhhHHHHhh---HhhheeeC
Confidence            37999999999986 44559999999999999963  0     11245666666553   23556654

>d1d5va_ a.4.5.14 (A:) Adipocyte-transcription factor FREAC-11 (s12, fkh-14) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Forkhead DNA-binding domain
domain: Adipocyte-transcription factor FREAC-11 (s12, fkh-14)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.01  E-value=0.036  Score=39.49  Aligned_cols=57  Identities=14%  Similarity=0.231  Sum_probs=42.3

Q ss_pred             CCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC--CCchhHHHHHHHHHHHHHhcCceEec
Q 029524           52 PPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD--ELPANFRKILAVQLKHFAAKGNLIKI  112 (192)
Q Consensus        52 P~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~--~lp~nf~~lLk~aLKk~Ve~G~LVqv  112 (192)
                      -+|..||..||.+.. .++.+..-|-.||+++|+.  .....+..-|++.|-   -+.-|+++
T Consensus         7 ~SYa~LI~~AI~~sp-~~~ltL~eIY~~i~~~fpyfr~~~~gWkNSIRHnLS---ln~~F~kv   65 (94)
T d1d5va_           7 YSYIALITMAIQNAP-EKKITLNGIYQFIMDRFPFYRENKQGWQNSIRHNLS---LNECFVKV   65 (94)
T ss_dssp             SCHHHHHHHHHHTCS-SSSBCHHHHHHHHHHHCTHHHHCCTTHHHHHHHHHH---HCSSEEEC
T ss_pred             CCHHHHHHHHHHhCC-CCCccHHHHHHHHHHHCCccCccccchHHHHHHHcc---ccceEEEc
Confidence            469999999999864 4459999999999999974  123456666777665   45667764

>d2hdca_ a.4.5.14 (A:) Genesis {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Forkhead DNA-binding domain
domain: Genesis
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=93.76  E-value=0.024  Score=40.58  Aligned_cols=49  Identities=16%  Similarity=0.259  Sum_probs=36.4

Q ss_pred             CCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC--CCchhHHHHHHHHHH
Q 029524           52 PPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD--ELPANFRKILAVQLK  101 (192)
Q Consensus        52 P~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~--~lp~nf~~lLk~aLK  101 (192)
                      -+|.+||..||.+..++ +.+.+-|-.||+++|+.  .-...+..-|++.|.
T Consensus         5 ~sY~~LI~~Ai~~sp~~-~ltL~eIY~~i~~~fpyfr~~~~gWkNSIRHnLS   55 (97)
T d2hdca_           5 YSYIALITMAILQSPQK-KLTLSGICEFISNRFPYYREKFPAWQNSIRHNLS   55 (97)
T ss_dssp             CCHHHHHHHHHHTCTTT-CBCHHHHHHHHHHHCHHHHHHCSSHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhCCCc-CccHHHHHHHHHHhCccccCCCCCchhhhhhhcc
Confidence            46999999999986554 69999999999999963  112345555666655

>d1kq8a_ a.4.5.14 (A:) HFH-1 (HNF-3 forkhead homolog-1) {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Forkhead DNA-binding domain
domain: HFH-1 (HNF-3 forkhead homolog-1)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=93.35  E-value=0.033  Score=38.19  Aligned_cols=55  Identities=18%  Similarity=0.229  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC--CCchhHHHHHHHHHHHHHhcCceEec
Q 029524           54 YFQMITEALMALQDKSGSSPYAIAKYMEEKHKD--ELPANFRKILAVQLKHFAAKGNLIKI  112 (192)
Q Consensus        54 Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~--~lp~nf~~lLk~aLKk~Ve~G~LVqv  112 (192)
                      |..||..||.+..+ ...+.+.|-.||+++|+.  ........-|++.|-   .+.-|+++
T Consensus         1 Y~~LI~~Ai~~sp~-~~ltL~eIy~~i~~~fpy~r~~~~gWkNSIRHnLS---~n~~F~kv   57 (75)
T d1kq8a_           1 YIALITMAIRDSAG-GRLTLAEINEYLMGKFPFFRGSYTGWRNSVRHNLS---LNDCFVKV   57 (75)
T ss_dssp             CHHHHHHHHTTSSS-SCBCHHHHHHHHHHHCTTGGGTCSCCHHHHHHHHH---HHTCCEEC
T ss_pred             CHHHHHHHHHhCCC-CCccHHHHHHHHHHhCcccccCCccchhHhheccc---ccceeEec
Confidence            78999999998644 459999999999999975  122334444555443   23445543

>d2v9va2 a.4.5.35 (A:438-510) C-terminal fragment of elongation factor SelB {Moorella thermoacetica [TaxId: 1525]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal fragment of elongation factor SelB
domain: C-terminal fragment of elongation factor SelB
species: Moorella thermoacetica [TaxId: 1525]

Probab=85.70  E-value=0.82  Score=29.68  Aligned_cols=46  Identities=11%  Similarity=0.166  Sum_probs=36.4

Q ss_pred             CCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCCceecC
Q 029524           67 DKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKLS  119 (192)
Q Consensus        67 eR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKGSFKLs  119 (192)
                      ++.|.++..|...+..+.+       ..++...|..+++.|.|+...+.+.|.
T Consensus        23 ~~~G~~keeLr~~l~~~~~-------~~~f~~lL~~l~~~g~l~~~g~~v~L~   68 (73)
T d2v9va2          23 LRPGLAREELRSRYFSRLP-------ARVYQALLEEWSREGRLQLAANTVALA   68 (73)
T ss_dssp             TSSCEEHHHHHHHHCTTSC-------HHHHHHHHHHHHHTTSEEECSSEEEET
T ss_pred             cccCCCHHHHHHHhcccCC-------HHHHHHHHHHHHHCCChheeCCEEECC
Confidence            5999999999988766543       446777888999999999877766664