Psyllid ID: psy14921

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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-------15
Protein Sequence
LCITYKTGNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAIDYNHTADDGPSKKKVKLPRVSPYSPVECNNSNSSSDVHNSKPPTSISSVPNTVSFFSDPLQ
Secondary Structure (PSIPRED)
ccccccccccccccHHHHHHHHHHHHcccccccHHHHHHHHHcccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHcccHHHcHHHHHHHHHccccccccEEEEcccccccccccEEEEccccccccccHHHHHHccccccccccHHccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
lcityktgnikctSSYASLIRLAISNAPQGRMTLNEIYQFITHtfpyyreanagwknsirhnlslnkcftkvarpkddpgkgsywaidynhtaddgpskkkvklprvspyspvecnnsnsssdvhnskpptsissvpntvsffsdplq
Flexible Loop (DISEMBL)
lcityktgnikctssYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTkvarpkddpgkGSYWAIDYnhtaddgpskkkvkLPRVSPYSPVEcnnsnsssdvhnskpptsissvpntvsffsdplq
Low Complexity Region (SEG)
LCITYKTGNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAIDYNHTADDGPSKKKVKLPRVSPYSPVECnnsnsssDVHNSKPPTSISSVPNTVSFFSDPLQ
Disordered region (IsUnstruct)
*CITYKTGNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR******KGSYWAIDYN**********************************************************
Disordered Region (DISOPRED)
*********IKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARP**DPGKGSYWAIDYNHTAD******************************************************
Disordered Region (DISEMBL)
LCITYKTGNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAIDYNHTADDGPSKKKVKLPRVSPYSPVEC******************SSVPNTVSFFSDPLQ
Disordered Region (DISPRO)
*****KTGNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAIDYNHTADDGPSKKKVKLPR******************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
LCITYKTGNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAIDYNHTADDGPSKKKVKLPRVSPYSPVECNNSNSSSDVHNSKPPTSISSVPNTVSFFSDPLQ
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	148	2.2.26 [Sep-21-2011]
Q8BUR3	623	Forkhead box protein J3 O	yes	N/A	0.831	0.197	0.532	3e-31
Q9UPW0	622	Forkhead box protein J3 O	yes	N/A	0.831	0.197	0.532	3e-31
Q28EM1	512	Forkhead box protein J2 O	no	N/A	0.770	0.222	0.552	1e-27
Q68EZ2	512	Forkhead box protein J2 O	N/A	N/A	0.777	0.224	0.532	1e-27
Q9ES18	565	Forkhead box protein J2 O	no	N/A	0.831	0.217	0.468	4e-26
Q9P0K8	574	Forkhead box protein J2 O	no	N/A	0.621	0.160	0.552	1e-25
Q8JIT5	381	Forkhead box protein I1c	N/A	N/A	0.513	0.199	0.592	1e-24
Q9YHC5	436	Forkhead box protein G1 O	N/A	N/A	0.5	0.169	0.648	2e-24
P56260	387	Transforming protein Qin	N/A	N/A	0.5	0.191	0.648	2e-24
Q90964	451	Forkhead box protein G1 O	no	N/A	0.5	0.164	0.648	2e-24

>sp|Q8BUR3|FOXJ3_MOUSE Forkhead box protein J3 OS=Mus musculus GN=Foxj3 PE=2 SV=1

 Score =  134 bits (336), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 74/139 (53%), Positives = 93/139 (66%), Gaps = 16/139 (11%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SYASLI  AI+++P+ +MTL+EIYQ+I   FPYYREA +GWKNSIRHNLSLNKCF KV R
Sbjct: 82  SYASLITFAINSSPKKKMTLSEIYQWICDNFPYYREAGSGWKNSIRHNLSLNKCFLKVPR 141

Query: 75  PKDDPGKGSYWAIDYNHTADDGPSKKKVKLPRV----SPYS------PVECNNSNSSSDV 124
            KDDPGKGSYWAID N   D  P++ K +   V    +PYS       +EC  S S+S  
Sbjct: 142 SKDDPGKGSYWAIDTNPKEDTLPTRPKKRARSVERASTPYSIDSDSLGMECIISGSAS-- 199

Query: 125 HNSKPPTSISSVPNTVSFF 143
               P  +I++V N V+ +
Sbjct: 200 ----PTLAINTVTNKVTLY 214

Mus musculus (taxid: 10090)

>sp|Q9UPW0|FOXJ3_HUMAN Forkhead box protein J3 OS=Homo sapiens GN=FOXJ3 PE=1 SV=2

 Score =  133 bits (335), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 74/139 (53%), Positives = 93/139 (66%), Gaps = 16/139 (11%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SYASLI  AI+++P+ +MTL+EIYQ+I   FPYYREA +GWKNSIRHNLSLNKCF KV R
Sbjct: 82  SYASLITFAINSSPKKKMTLSEIYQWICDNFPYYREAGSGWKNSIRHNLSLNKCFLKVPR 141

Query: 75  PKDDPGKGSYWAIDYNHTADDGPSKKKVKLPRV----SPYS------PVECNNSNSSSDV 124
            KDDPGKGSYWAID N   D  P++ K +   V    +PYS       +EC  S S+S  
Sbjct: 142 SKDDPGKGSYWAIDTNPKEDVLPTRPKKRARSVERASTPYSIDSDSLGMECIISGSAS-- 199

Query: 125 HNSKPPTSISSVPNTVSFF 143
               P  +I++V N V+ +
Sbjct: 200 ----PTLAINTVTNKVTLY 214

Homo sapiens (taxid: 9606)

>sp|Q28EM1|FOXJ2_XENTR Forkhead box protein J2 OS=Xenopus tropicalis GN=foxj2 PE=2 SV=1

 Score =  122 bits (305), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 68/123 (55%), Positives = 80/123 (65%), Gaps = 9/123 (7%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SYA+LI+ AI++AP  RMTL+EIY++I   FPYYR A  GWKNSIRHNLSLNKCF KV R
Sbjct: 63  SYANLIQYAINSAPAKRMTLSEIYRWICDNFPYYRNAGVGWKNSIRHNLSLNKCFRKVPR 122

Query: 75  PKDDPGKGSYWAIDYNHTADDGPSKKKVKLPRVS-PYSPVECNNSNSSSDVHNSKPPTSI 133
           P+DDPGKGSYW ID          K+ V LPR   P+   E +  +   DV N  P  S 
Sbjct: 123 PRDDPGKGSYWMIDSC-------PKEDVALPRRKRPHPDDEVSQDSFEQDV-NKSPLRSA 174

Query: 134 SSV 136
           S V
Sbjct: 175 SEV 177

Transcriptional activator.

Xenopus tropicalis (taxid: 8364)

>sp|Q68EZ2|FOXJ2_XENLA Forkhead box protein J2 OS=Xenopus laevis GN=foxj2 PE=2 SV=1

 Score =  121 bits (304), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 65/122 (53%), Positives = 79/122 (64%), Gaps = 7/122 (5%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SYA+LI+ AI++AP  RMTL+EIY++I   FPYYR A  GWKNSIRHNLSLNKCF KV R
Sbjct: 63  SYANLIQYAINSAPAKRMTLSEIYRWICDNFPYYRSAGVGWKNSIRHNLSLNKCFRKVPR 122

Query: 75  PKDDPGKGSYWAIDYNHTADDGPSKKKVKLPRVSPYSPVECNNSNSSSDVHNSKPPTSIS 134
           P+DDPGKGSYW ID          K+ + LPR     P +  + +S     N  P +S S
Sbjct: 123 PRDDPGKGSYWMIDSC-------PKEDITLPRRKRPHPDDEVSQDSFEQEVNKSPLSSAS 175

Query: 135 SV 136
            V
Sbjct: 176 EV 177

Transcriptional activator.

Xenopus laevis (taxid: 8355)

>sp|Q9ES18|FOXJ2_MOUSE Forkhead box protein J2 OS=Mus musculus GN=Foxj2 PE=2 SV=1

 Score =  116 bits (291), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 67/143 (46%), Positives = 85/143 (59%), Gaps = 20/143 (13%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SYA+LI  AI+++P  +MTL+EIY++I   FPYY+ A  GWKNSIRHNLSLNKCF KV R
Sbjct: 70  SYATLITYAINSSPAKKMTLSEIYRWICDNFPYYKNAGIGWKNSIRHNLSLNKCFRKVPR 129

Query: 75  PKDDPGKGSYWAID--------YNHTAD-----DGPSKKKVKLPRVSPYSPVECNNSNSS 121
           P+DDPGKGSYW ID          H  D     D P ++  K PR           S  +
Sbjct: 130 PRDDPGKGSYWTIDTCPDISRKRRHPPDDDLSQDSPEQEASKSPRGG------VPGSGEA 183

Query: 122 SDVHNSKPPTSISSVPNTVSFFS 144
           S  H   P  S+ S P++V+ +S
Sbjct: 184 SLSHEGTPQMSLQS-PSSVANYS 205

Transcriptional activator. Able to bind to two different type of DNA binding sites.

Mus musculus (taxid: 10090)

>sp|Q9P0K8|FOXJ2_HUMAN Forkhead box protein J2 OS=Homo sapiens GN=FOXJ2 PE=1 SV=1

 Score =  115 bits (287), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 58/105 (55%), Positives = 70/105 (66%), Gaps = 13/105 (12%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SYA+LI  AI+++P  +MTL+EIY++I   FPYY+ A  GWKNSIRHNLSLNKCF KV R
Sbjct: 70  SYATLITYAINSSPAKKMTLSEIYRWICDNFPYYKNAGIGWKNSIRHNLSLNKCFRKVPR 129

Query: 75  PKDDPGKGSYWAID--------YNHTAD-----DGPSKKKVKLPR 106
           P+DDPGKGSYW ID          H  D     D P ++  K PR
Sbjct: 130 PRDDPGKGSYWTIDTCPDISRKRRHPPDDDLSQDSPEQEASKSPR 174

Transcriptional activator. Able to bind to two different type of DNA binding sites. Isoform FOXJ2.L behaves as a more potent transactivator than FOXJ2.S.

Homo sapiens (taxid: 9606)

>sp|Q8JIT5|FXI1C_XENLA Forkhead box protein I1c OS=Xenopus laevis GN=foxi1c PE=2 SV=1

 Score =  112 bits (279), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 45/76 (59%), Positives = 62/76 (81%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SY++LI +AI NAP+ ++TL++IYQ++   FP+Y+ + AGW+NSIRHNLSLN CF KV R
Sbjct: 133 SYSALIAMAIQNAPEKKLTLSQIYQYVAENFPFYKRSKAGWQNSIRHNLSLNDCFKKVPR 192

Query: 75  PKDDPGKGSYWAIDYN 90
            +DDPGKG+YW +D N
Sbjct: 193 DEDDPGKGNYWTLDPN 208

Probable transcription factor.

Xenopus laevis (taxid: 8355)

>sp|Q9YHC5|FOXG1_XENLA Forkhead box protein G1 OS=Xenopus laevis GN=foxg1 PE=2 SV=1

 Score =  111 bits (277), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 48/74 (64%), Positives = 57/74 (77%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SY +LI +AI  +P+ R+TLN IY+FI   FPYYRE   GW+NSIRHNLSLNKCF KV R
Sbjct: 132 SYNALIMMAIRQSPEKRLTLNGIYEFIMKNFPYYRENKQGWQNSIRHNLSLNKCFVKVPR 191

Query: 75  PKDDPGKGSYWAID 88
             DDPGKG+YW +D
Sbjct: 192 HYDDPGKGNYWMLD 205

A neural-specific transcription factor that can act as both a transcriptional activator and a transcriptional repressor. Both represses and activates neuronal differentiation in a dose-dependent manner, independently regulating cell fate choice and cell proliferation. Converts ectoderm to a neural fate. Suppresses the transcription of the cell cycle inhibitor p27xic1 and promotes the proliferation of neuroectodermal cells at a high concentration. Promotes the transcription of p27xic1 and inhibits ectodermal proliferation at low concentrations. The transcription factors foxd1 and foxg1 mutually repress each other to pattern the forebrain.

Xenopus laevis (taxid: 8355)

>sp|P56260|QIN_AVIS3 Transforming protein Qin OS=Avian sarcoma virus (strain 31) GN=V-QIN PE=2 SV=1

 Score =  111 bits (277), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 48/74 (64%), Positives = 57/74 (77%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SY +LI +AI  +P+ R+TLN IY+FI   FPYYRE   GW+NSIRHNLSLNKCF KV R
Sbjct: 147 SYNALIMMAIRQSPEKRLTLNGIYEFIMKNFPYYRENKQGWQNSIRHNLSLNKCFVKVPR 206

Query: 75  PKDDPGKGSYWAID 88
             DDPGKG+YW +D
Sbjct: 207 HYDDPGKGNYWMLD 220

Galliformes (taxid: 8976)

>sp|Q90964|FOXG1_CHICK Forkhead box protein G1 OS=Gallus gallus GN=FOXG1 PE=2 SV=1

 Score =  111 bits (277), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 48/74 (64%), Positives = 57/74 (77%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SY +LI +AI  +P+ R+TLN IY+FI   FPYYRE   GW+NSIRHNLSLNKCF KV R
Sbjct: 147 SYNALIMMAIRQSPEKRLTLNGIYEFIMKNFPYYRENKQGWQNSIRHNLSLNKCFVKVPR 206

Query: 75  PKDDPGKGSYWAID 88
             DDPGKG+YW +D
Sbjct: 207 HYDDPGKGNYWMLD 220

May determine the nasotemporal axis of the retina, and consequently specify the topographical projection of the retinal ganglion-cell axons to the tectum by controlling expression of their target genes.

Gallus gallus (taxid: 9031)

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	148
47211273	342	unnamed protein product [Tetraodon nigro	0.831	0.359	0.553	2e-30
118601042	483	forkhead transcription factor J2 [Strong	0.716	0.219	0.629	3e-30
291222693	438	PREDICTED: fork-head box J2/3 transcript	0.662	0.223	0.638	3e-30
283464173	361	fork-head box J2/3 transcription factor	0.662	0.271	0.638	4e-30
432857929	575	PREDICTED: forkhead box protein J3-like,	0.824	0.212	0.542	5e-30
189525242	592	PREDICTED: forkhead box protein J3-like	0.858	0.214	0.555	5e-30
348521676	604	PREDICTED: forkhead box protein J3 isofo	0.824	0.201	0.542	7e-30
395526752	729	PREDICTED: forkhead box protein J3 [Sarc	0.831	0.168	0.539	9e-30
354479361	613	PREDICTED: forkhead box protein J3-like	0.831	0.200	0.532	1e-29
403291975	640	PREDICTED: forkhead box protein J3 isofo	0.831	0.192	0.532	1e-29

>gi|47211273|emb|CAF96645.1| unnamed protein product [Tetraodon nigroviridis]

 Score =  137 bits (344), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 78/141 (55%), Positives = 93/141 (65%), Gaps = 18/141 (12%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SYASLI  AI+ +P+ RMTL+EIYQ+I   FPYYREA +GWKNSIRHNLSLNKCF KV R
Sbjct: 79  SYASLITFAINGSPRKRMTLSEIYQWICDNFPYYREAGSGWKNSIRHNLSLNKCFLKVPR 138

Query: 75  PKDDPGKGSYWAIDYNHTADDGPSKKKVKLPR-----VSPYS------PVECNNSNSSSD 123
            KDDPGKGSYWAID N   D  PS+ K K PR      +PYS       V+C  S  +S 
Sbjct: 139 SKDDPGKGSYWAIDTNPKEDTVPSRPK-KRPRSGERASTPYSLESESLRVDCIMSGGAS- 196

Query: 124 VHNSKPPTSISSVPNTVSFFS 144
                P  +I++V N V+ +S
Sbjct: 197 -----PTLAINAVTNKVALYS 212

Source: Tetraodon nigroviridis

Species: Tetraodon nigroviridis

Genus: Tetraodon

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|118601042|ref|NP_001073017.1| forkhead transcription factor J2 [Strongylocentrotus purpuratus] gi|82706182|gb|ABB89475.1| forkhead transcription factor J2 [Strongylocentrotus purpuratus]

 Score =  136 bits (342), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 68/108 (62%), Positives = 80/108 (74%), Gaps = 2/108 (1%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SYA+LI  AI+++P+ +MTL+EIYQ+I   FPYYREA  GWKNSIRHNLSLNKCF KV R
Sbjct: 67  SYANLITFAINSSPKKKMTLSEIYQWICENFPYYREAGNGWKNSIRHNLSLNKCFMKVPR 126

Query: 75  PKDDPGKGSYWAIDYNHTADDGPSKKKVKLPRVSPYSPVECNNSNSSS 122
            KDDPGKGSYWAID N   D    +KK + P +SPYSP E   S+  S
Sbjct: 127 SKDDPGKGSYWAIDNNPQDDS--LRKKRRHPGMSPYSPEESLESSGGS 172

Source: Strongylocentrotus purpuratus

Species: Strongylocentrotus purpuratus

Genus: Strongylocentrotus

Family: Strongylocentrotidae

Order: Echinoida

Class: Echinoidea

Phylum: Echinodermata

Superkingdom: Eukaryota

>gi|291222693|ref|XP_002731348.1| PREDICTED: fork-head box J2/3 transcription factor [Saccoglossus kowalevskii]

 Score =  136 bits (342), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 67/105 (63%), Positives = 78/105 (74%), Gaps = 7/105 (6%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SYA+LI  AI+++P+ +MTL+EIYQ+I   FP+YREA  GWKNSIRHNLSLNKCF KV R
Sbjct: 69  SYANLITFAINSSPKKKMTLSEIYQWICENFPFYREAGNGWKNSIRHNLSLNKCFLKVPR 128

Query: 75  PKDDPGKGSYWAIDYNHTADDGPSKKKVKLPRV-------SPYSP 112
            KDDPGKGSYWAID N   D  PS+ K K PR+       SPYSP
Sbjct: 129 SKDDPGKGSYWAIDNNPPDDPLPSRNKAKKPRIGCSRGGSSPYSP 173

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|283464173|gb|ADB22670.1| fork-head box J2/3 transcription factor [Saccoglossus kowalevskii]

 Score =  135 bits (341), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 67/105 (63%), Positives = 78/105 (74%), Gaps = 7/105 (6%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SYA+LI  AI+++P+ +MTL+EIYQ+I   FP+YREA  GWKNSIRHNLSLNKCF KV R
Sbjct: 69  SYANLITFAINSSPKKKMTLSEIYQWICENFPFYREAGNGWKNSIRHNLSLNKCFLKVPR 128

Query: 75  PKDDPGKGSYWAIDYNHTADDGPSKKKVKLPRV-------SPYSP 112
            KDDPGKGSYWAID N   D  PS+ K K PR+       SPYSP
Sbjct: 129 SKDDPGKGSYWAIDNNPPDDPLPSRNKAKKPRIGCSRGGSSPYSP 173

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|432857929|ref|XP_004068796.1| PREDICTED: forkhead box protein J3-like, partial [Oryzias latipes]

 Score =  135 bits (341), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 76/140 (54%), Positives = 95/140 (67%), Gaps = 18/140 (12%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SYASLI  AI+++P+ +MTL+EIYQ+I   FPYYREA +GWKNSIRHNLSLNKCF KVAR
Sbjct: 72  SYASLITFAINSSPKKKMTLSEIYQWICDNFPYYREAGSGWKNSIRHNLSLNKCFLKVAR 131

Query: 75  PKDDPGKGSYWAIDYNHTADDGPSKKKVKLPR-----VSPYS------PVECNNSNSSSD 123
            KDDPGKGSYWAID N   D  P++ K K PR      +PYS       ++C  S S+S 
Sbjct: 132 SKDDPGKGSYWAIDTNPKEDALPTRPK-KRPRSGERASTPYSLDSESLGMDCMISGSAS- 189

Query: 124 VHNSKPPTSISSVPNTVSFF 143
                P  +I++V N V+ +
Sbjct: 190 -----PTLAINTVTNKVALY 204

Source: Oryzias latipes

Species: Oryzias latipes

Genus: Oryzias

Family: Adrianichthyidae

Order: Beloniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|189525242|ref|XP_001922273.1| PREDICTED: forkhead box protein J3-like [Danio rerio]

 Score =  135 bits (340), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 75/135 (55%), Positives = 94/135 (69%), Gaps = 8/135 (5%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SYASLI  AI+++P+ +MTL+EIYQ+I   FPYYREA +GWKNSIRHNLSLNKCF KV R
Sbjct: 66  SYASLITFAINSSPKKKMTLSEIYQWICDNFPYYREAGSGWKNSIRHNLSLNKCFLKVPR 125

Query: 75  PKDDPGKGSYWAIDYNHTADDGPSKKKVKLPR-----VSPYSPVECNNSNSSSDVHNSKP 129
            KDDPGKGSYWAID N   D  P++ K K PR      +PYS +E +N      +  S  
Sbjct: 126 SKDDPGKGSYWAIDTNPKEDTLPTRPK-KRPRSGERASTPYS-LESDNLGMDCIISGSAS 183

Query: 130 PT-SISSVPNTVSFF 143
           PT +I++V N V+ +
Sbjct: 184 PTLAINTVTNKVALY 198

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|348521676|ref|XP_003448352.1| PREDICTED: forkhead box protein J3 isoform 1 [Oreochromis niloticus]

 Score =  135 bits (339), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 76/140 (54%), Positives = 94/140 (67%), Gaps = 18/140 (12%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SYASLI  AI+++P+ +MTL+EIYQ+I   FPYYREA +GWKNSIRHNLSLNKCF KV R
Sbjct: 66  SYASLITFAINSSPKKKMTLSEIYQWICDNFPYYREAGSGWKNSIRHNLSLNKCFLKVPR 125

Query: 75  PKDDPGKGSYWAIDYNHTADDGPSKKKVKLPR-----VSPYS------PVECNNSNSSSD 123
            KDDPGKGSYWAID N   D  P++ K K PR      +PYS       +EC  S S+S 
Sbjct: 126 SKDDPGKGSYWAIDTNPKEDALPTRPK-KRPRSGERASTPYSLESESLGMECMISGSAS- 183

Query: 124 VHNSKPPTSISSVPNTVSFF 143
                P  +I++V N V+ +
Sbjct: 184 -----PTLAINTVTNKVALY 198

Source: Oreochromis niloticus

Species: Oreochromis niloticus

Genus: Oreochromis

Family: Cichlidae

Order: Perciformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|395526752|ref|XP_003765520.1| PREDICTED: forkhead box protein J3 [Sarcophilus harrisii]

 Score =  134 bits (338), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 75/139 (53%), Positives = 93/139 (66%), Gaps = 16/139 (11%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SYASLI  AI+++P+ +MTL+EIYQ+I   FPYYREA +GWKNSIRHNLSLNKCF KV R
Sbjct: 187 SYASLITFAINSSPKKKMTLSEIYQWICDNFPYYREAGSGWKNSIRHNLSLNKCFLKVPR 246

Query: 75  PKDDPGKGSYWAIDYNHTADDGPSKKKVKLPRV----SPYS------PVECNNSNSSSDV 124
            KDDPGKGSYWAID N   D  PS+ K +   V    +PYS       +EC  S S+S  
Sbjct: 247 SKDDPGKGSYWAIDNNPKEDTLPSRPKKRARSVERASTPYSIDSDSLGMECIISGSAS-- 304

Query: 125 HNSKPPTSISSVPNTVSFF 143
               P  +I++V N V+ +
Sbjct: 305 ----PTLAINTVTNKVTLY 319

Source: Sarcophilus harrisii

Species: Sarcophilus harrisii

Genus: Sarcophilus

Family: Dasyuridae

Order: Dasyuromorphia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|354479361|ref|XP_003501880.1| PREDICTED: forkhead box protein J3-like [Cricetulus griseus]

 Score =  134 bits (338), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 74/139 (53%), Positives = 93/139 (66%), Gaps = 16/139 (11%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SYASLI  AI+++P+ +MTL+EIYQ+I   FPYYREA +GWKNSIRHNLSLNKCF KV R
Sbjct: 74  SYASLITFAINSSPKKKMTLSEIYQWICDNFPYYREAGSGWKNSIRHNLSLNKCFLKVPR 133

Query: 75  PKDDPGKGSYWAIDYNHTADDGPSKKKVKLPRV----SPYS------PVECNNSNSSSDV 124
            KDDPGKGSYWAID N   D  P++ K +   V    +PYS       +EC  S S+S  
Sbjct: 134 SKDDPGKGSYWAIDTNPKEDTLPTRSKKRARSVERASTPYSIDSDSLGMECIISGSAS-- 191

Query: 125 HNSKPPTSISSVPNTVSFF 143
               P  +I++V N V+ +
Sbjct: 192 ----PTLAINTVTNKVTLY 206

Source: Cricetulus griseus

Species: Cricetulus griseus

Genus: Cricetulus

Family: Cricetidae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|403291975|ref|XP_003937035.1| PREDICTED: forkhead box protein J3 isoform 3 [Saimiri boliviensis boliviensis]

 Score =  134 bits (337), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 74/139 (53%), Positives = 93/139 (66%), Gaps = 16/139 (11%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SYASLI  AI+++P+ +MTL+EIYQ+I   FPYYREA +GWKNSIRHNLSLNKCF KV R
Sbjct: 100 SYASLITFAINSSPKKKMTLSEIYQWICDNFPYYREAGSGWKNSIRHNLSLNKCFLKVPR 159

Query: 75  PKDDPGKGSYWAIDYNHTADDGPSKKKVKLPRV----SPYS------PVECNNSNSSSDV 124
            KDDPGKGSYWAID N   D  P++ K +   V    +PYS       +EC  S S+S  
Sbjct: 160 SKDDPGKGSYWAIDTNPKEDALPTRPKKRARSVERASTPYSIDSDSLGMECIISGSAS-- 217

Query: 125 HNSKPPTSISSVPNTVSFF 143
               P  +I++V N V+ +
Sbjct: 218 ----PTLAINTVTNKVTLY 232

Source: Saimiri boliviensis boliviensis

Species: Saimiri boliviensis

Genus: Saimiri

Family: Cebidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	148
UNIPROTKB|Q2V894	483	FoxJ2 "Forkhead transcription	0.662	0.202	0.67	1.6e-31
UNIPROTKB|F1M3L2	621	Foxj3 "Protein Foxj3" [Rattus	0.871	0.207	0.540	1.2e-30
MGI|MGI:2443432	623	Foxj3 "forkhead box J3" [Mus m	0.871	0.207	0.540	1.2e-30
UNIPROTKB|E1BK17	610	FOXJ3 "Uncharacterized protein	0.871	0.211	0.540	1.4e-30
UNIPROTKB|E2R0F1	622	FOXJ3 "Uncharacterized protein	0.871	0.207	0.540	1.6e-30
UNIPROTKB|Q9UPW0	622	FOXJ3 "Forkhead box protein J3	0.871	0.207	0.540	2e-30
UNIPROTKB|C9JVP0	382	FOXJ3 "Forkhead box protein J3	0.824	0.319	0.552	2.3e-30
RGD|1311770	587	Foxj3 "forkhead box J3" [Rattu	0.824	0.207	0.552	5.6e-30
UNIPROTKB|Q28EM1	512	foxj2 "Forkhead box protein J2	0.770	0.222	0.560	2.2e-27
UNIPROTKB|Q4H3I3	560	Ci-FoxJ2 "Transcription factor	0.540	0.142	0.712	3.2e-27

UNIPROTKB|Q2V894 FoxJ2 "Forkhead transcription factor J2" [Strongylocentrotus purpuratus (taxid:7668)]

 Score = 346 (126.9 bits), Expect = 1.6e-31, P = 1.6e-31
 Identities = 67/100 (67%), Positives = 79/100 (79%)

Query:    15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
             SYA+LI  AI+++P+ +MTL+EIYQ+I   FPYYREA  GWKNSIRHNLSLNKCF KV R
Sbjct:    67 SYANLITFAINSSPKKKMTLSEIYQWICENFPYYREAGNGWKNSIRHNLSLNKCFMKVPR 126

Query:    75 PKDDPGKGSYWAIDYNHTADDGPSKKKVKLPRVSPYSPVE 114
              KDDPGKGSYWAID N+  DD   KK+ + P +SPYSP E
Sbjct:   127 SKDDPGKGSYWAID-NNPQDDSLRKKR-RHPGMSPYSPEE 164

GO:0003690 "double-stranded DNA binding" evidence=IBA

GO:0003705 "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" evidence=IBA

GO:0005667 "transcription factor complex" evidence=IBA

GO:0007389 "pattern specification process" evidence=IBA

GO:0008134 "transcription factor binding" evidence=IBA

GO:0008301 "DNA binding, bending" evidence=IBA

GO:0009790 "embryo development" evidence=IBA

GO:0009888 "tissue development" evidence=IBA

GO:0019904 "protein domain specific binding" evidence=IBA

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

GO:0048513 "organ development" evidence=IBA

GO:0051090 "regulation of sequence-specific DNA binding transcription factor activity" evidence=IBA

UNIPROTKB|F1M3L2 Foxj3 "Protein Foxj3" [Rattus norvegicus (taxid:10116)]

 Score = 344 (126.2 bits), Expect = 1.2e-30, P = 1.2e-30
 Identities = 73/135 (54%), Positives = 94/135 (69%)

Query:    15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
             SYASLI  AI+++P+ +MTL+EIYQ+I   FPYYREA +GWKNSIRHNLSLNKCF KV R
Sbjct:    81 SYASLITFAINSSPKKKMTLSEIYQWICDNFPYYREAGSGWKNSIRHNLSLNKCFLKVPR 140

Query:    75 PKDDPGKGSYWAIDYNHTADDGPS--KKKVK-LPRVS-PYSPVECXXXXXXXDVHNSKPP 130
              KDDPGKGSYWAID N   D  P+  KK+ + + R S PYS ++         +  S  P
Sbjct:   141 SKDDPGKGSYWAIDTNPKEDTLPTRPKKRARSVERASTPYS-IDSDSLGMECIISGSASP 199

Query:   131 T-SISSVPNTVSFFS 144
             T +I++V N V+ ++
Sbjct:   200 TLAINTVTNKVTLYN 214

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

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

MGI|MGI:2443432 Foxj3 "forkhead box J3" [Mus musculus (taxid:10090)]

 Score = 344 (126.2 bits), Expect = 1.2e-30, P = 1.2e-30
 Identities = 73/135 (54%), Positives = 94/135 (69%)

Query:    15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
             SYASLI  AI+++P+ +MTL+EIYQ+I   FPYYREA +GWKNSIRHNLSLNKCF KV R
Sbjct:    82 SYASLITFAINSSPKKKMTLSEIYQWICDNFPYYREAGSGWKNSIRHNLSLNKCFLKVPR 141

Query:    75 PKDDPGKGSYWAIDYNHTADDGPS--KKKVK-LPRVS-PYSPVECXXXXXXXDVHNSKPP 130
              KDDPGKGSYWAID N   D  P+  KK+ + + R S PYS ++         +  S  P
Sbjct:   142 SKDDPGKGSYWAIDTNPKEDTLPTRPKKRARSVERASTPYS-IDSDSLGMECIISGSASP 200

Query:   131 T-SISSVPNTVSFFS 144
             T +I++V N V+ ++
Sbjct:   201 TLAINTVTNKVTLYN 215

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

GO:0003677 "DNA binding" evidence=IEA

GO:0003690 "double-stranded DNA binding" evidence=IBA

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

GO:0003705 "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" evidence=IBA

GO:0005634 "nucleus" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IBA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

GO:0007389 "pattern specification process" evidence=IBA

GO:0008134 "transcription factor binding" evidence=IBA

GO:0008301 "DNA binding, bending" evidence=IBA

GO:0009790 "embryo development" evidence=IBA

GO:0009888 "tissue development" evidence=IBA

GO:0019904 "protein domain specific binding" evidence=IBA

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

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

GO:0048513 "organ development" evidence=IBA

GO:0051090 "regulation of sequence-specific DNA binding transcription factor activity" evidence=IBA

UNIPROTKB|E1BK17 FOXJ3 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 343 (125.8 bits), Expect = 1.4e-30, P = 1.4e-30
 Identities = 73/135 (54%), Positives = 94/135 (69%)

Query:    15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
             SYASLI  AI+++P+ +MTL+EIYQ+I   FPYYREA +GWKNSIRHNLSLNKCF KV R
Sbjct:    67 SYASLITFAINSSPKKKMTLSEIYQWICDNFPYYREAGSGWKNSIRHNLSLNKCFLKVPR 126

Query:    75 PKDDPGKGSYWAIDYNHTADDGPS--KKKVK-LPRVS-PYSPVECXXXXXXXDVHNSKPP 130
              KDDPGKGSYWAID N   D  P+  KK+ + + R S PYS ++         +  S  P
Sbjct:   127 SKDDPGKGSYWAIDTNPKEDALPTRPKKRARSVERASTPYS-IDSDSLGMECIISGSASP 185

Query:   131 T-SISSVPNTVSFFS 144
             T +I++V N V+ ++
Sbjct:   186 TLAINTVTNKVTLYN 200

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

UNIPROTKB|E2R0F1 FOXJ3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 343 (125.8 bits), Expect = 1.6e-30, P = 1.6e-30
 Identities = 73/135 (54%), Positives = 94/135 (69%)

Query:    15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
             SYASLI  AI+++P+ +MTL+EIYQ+I   FPYYREA +GWKNSIRHNLSLNKCF KV R
Sbjct:    82 SYASLITFAINSSPKKKMTLSEIYQWICDNFPYYREAGSGWKNSIRHNLSLNKCFLKVPR 141

Query:    75 PKDDPGKGSYWAIDYNHTADDGPS--KKKVK-LPRVS-PYSPVECXXXXXXXDVHNSKPP 130
              KDDPGKGSYWAID N   D  P+  KK+ + + R S PYS ++         +  S  P
Sbjct:   142 SKDDPGKGSYWAIDTNPKEDALPTRPKKRARSVERASTPYS-IDSDSLGMECIISGSASP 200

Query:   131 T-SISSVPNTVSFFS 144
             T +I++V N V+ ++
Sbjct:   201 TLAINTVTNKVTLYN 215

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

UNIPROTKB|Q9UPW0 FOXJ3 "Forkhead box protein J3" [Homo sapiens (taxid:9606)]

 Score = 342 (125.4 bits), Expect = 2.0e-30, P = 2.0e-30
 Identities = 73/135 (54%), Positives = 94/135 (69%)

Query:    15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
             SYASLI  AI+++P+ +MTL+EIYQ+I   FPYYREA +GWKNSIRHNLSLNKCF KV R
Sbjct:    82 SYASLITFAINSSPKKKMTLSEIYQWICDNFPYYREAGSGWKNSIRHNLSLNKCFLKVPR 141

Query:    75 PKDDPGKGSYWAIDYNHTADDGPS--KKKVK-LPRVS-PYSPVECXXXXXXXDVHNSKPP 130
              KDDPGKGSYWAID N   D  P+  KK+ + + R S PYS ++         +  S  P
Sbjct:   142 SKDDPGKGSYWAIDTNPKEDVLPTRPKKRARSVERASTPYS-IDSDSLGMECIISGSASP 200

Query:   131 T-SISSVPNTVSFFS 144
             T +I++V N V+ ++
Sbjct:   201 TLAINTVTNKVTLYN 215

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

GO:0003690 "double-stranded DNA binding" evidence=IBA

GO:0003705 "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" evidence=IBA

GO:0005667 "transcription factor complex" evidence=IBA

GO:0007389 "pattern specification process" evidence=IBA

GO:0008134 "transcription factor binding" evidence=IBA

GO:0008301 "DNA binding, bending" evidence=IBA

GO:0009790 "embryo development" evidence=IBA

GO:0009888 "tissue development" evidence=IBA

GO:0019904 "protein domain specific binding" evidence=IBA

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

GO:0048513 "organ development" evidence=IBA

GO:0051090 "regulation of sequence-specific DNA binding transcription factor activity" evidence=IBA

UNIPROTKB|C9JVP0 FOXJ3 "Forkhead box protein J3" [Homo sapiens (taxid:9606)]

 Score = 335 (123.0 bits), Expect = 2.3e-30, P = 2.3e-30
 Identities = 69/125 (55%), Positives = 88/125 (70%)

Query:    15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
             SYASLI  AI+++P+ +MTL+EIYQ+I   FPYYREA +GWKNSIRHNLSLNKCF KV R
Sbjct:    82 SYASLITFAINSSPKKKMTLSEIYQWICDNFPYYREAGSGWKNSIRHNLSLNKCFLKVPR 141

Query:    75 PKDDPGKGSYWAIDYNHTADDGPS--KKKVK-LPRVSPYSPVECXXXXXXXDVHNSKPPT 131
              KDDPGKGSYWAID N   D  P+  KK+ + + RV+ Y+  +         ++NS    
Sbjct:   142 SKDDPGKGSYWAIDTNPKEDVLPTRPKKRARSVERVTLYNTDQDGSDSPRSSLNNSLSDQ 201

Query:   132 SISSV 136
             S++SV
Sbjct:   202 SLASV 206

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

RGD|1311770 Foxj3 "forkhead box J3" [Rattus norvegicus (taxid:10116)]

 Score = 337 (123.7 bits), Expect = 5.6e-30, P = 5.6e-30
 Identities = 69/125 (55%), Positives = 88/125 (70%)

Query:    15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
             SYASLI  AI+++P+ +MTL+EIYQ+I   FPYYREA +GWKNSIRHNLSLNKCF KV R
Sbjct:    81 SYASLITFAINSSPKKKMTLSEIYQWICDNFPYYREAGSGWKNSIRHNLSLNKCFLKVPR 140

Query:    75 PKDDPGKGSYWAIDYNHTADDGPS--KKKVK-LPRVSPYSPVECXXXXXXXDVHNSKPPT 131
              KDDPGKGSYWAID N   D  P+  KK+ + + RV+ Y+  +         ++NS    
Sbjct:   141 SKDDPGKGSYWAIDTNPKEDTLPTRPKKRARSVERVTLYNTDQDGSDSPRSSLNNSLSDQ 200

Query:   132 SISSV 136
             S++SV
Sbjct:   201 SLASV 205

GO:0003690 "double-stranded DNA binding" evidence=IBA

GO:0003705 "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" evidence=IBA

GO:0005667 "transcription factor complex" evidence=IBA

GO:0007389 "pattern specification process" evidence=IBA

GO:0008134 "transcription factor binding" evidence=IBA

GO:0008301 "DNA binding, bending" evidence=IBA

GO:0009790 "embryo development" evidence=IBA

GO:0009888 "tissue development" evidence=IBA

GO:0019904 "protein domain specific binding" evidence=IBA

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

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

GO:0048513 "organ development" evidence=IBA

GO:0051090 "regulation of sequence-specific DNA binding transcription factor activity" evidence=IBA

UNIPROTKB|Q28EM1 foxj2 "Forkhead box protein J2" [Xenopus (Silurana) tropicalis (taxid:8364)]

 Score = 311 (114.5 bits), Expect = 2.2e-27, P = 2.2e-27
 Identities = 69/123 (56%), Positives = 79/123 (64%)

Query:    15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
             SYA+LI+ AI++AP  RMTL+EIY++I   FPYYR A  GWKNSIRHNLSLNKCF KV R
Sbjct:    63 SYANLIQYAINSAPAKRMTLSEIYRWICDNFPYYRNAGVGWKNSIRHNLSLNKCFRKVPR 122

Query:    75 PKDDPGKGSYWAIDYNHTADDGPSKKKVKLPRVS-PYSPVECXXXXXXXDVHNSKPPTSI 133
             P+DDPGKGSYW ID        P K+ V LPR   P+   E        DV N  P  S 
Sbjct:   123 PRDDPGKGSYWMID------SCP-KEDVALPRRKRPHPDDEVSQDSFEQDV-NKSPLRSA 174

Query:   134 SSV 136
             S V
Sbjct:   175 SEV 177

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

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

UNIPROTKB|Q4H3I3 Ci-FoxJ2 "Transcription factor protein" [Ciona intestinalis (taxid:7719)]

 Score = 300 (110.7 bits), Expect = 3.2e-27, Sum P(2) = 3.2e-27
 Identities = 57/80 (71%), Positives = 64/80 (80%)

Query:    15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
             SYASLI LAI+++ + +MTL+EIYQ+I  TFPYY  A  GWKNSIRHNLSLNKCF KV R
Sbjct:    80 SYASLISLAINSSNEKKMTLSEIYQWICKTFPYYSGAGTGWKNSIRHNLSLNKCFMKVPR 139

Query:    75 PKDDPGKGSYWAIDYNHTAD 94
              KDDPGKGSYWAID N   D
Sbjct:   140 AKDDPGKGSYWAIDSNPQED 159

GO:0003690 "double-stranded DNA binding" evidence=IBA

GO:0003705 "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity" evidence=IBA

GO:0005667 "transcription factor complex" evidence=IBA

GO:0007389 "pattern specification process" evidence=IBA

GO:0008134 "transcription factor binding" evidence=IBA

GO:0008301 "DNA binding, bending" evidence=IBA

GO:0009790 "embryo development" evidence=IBA

GO:0009888 "tissue development" evidence=IBA

GO:0019904 "protein domain specific binding" evidence=IBA

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

GO:0048513 "organ development" evidence=IBA

GO:0051090 "regulation of sequence-specific DNA binding transcription factor activity" evidence=IBA

---

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)
Q8BUR3	FOXJ3_MOUSE	No assigned EC number	0.5323	0.8310	0.1974	yes	N/A
Q9UPW0	FOXJ3_HUMAN	No assigned EC number	0.5323	0.8310	0.1977	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	148
cd00059	78	cd00059, FH, Forkhead (FH), also known as a "winge	4e-43
smart00339	89	smart00339, FH, FORKHEAD	3e-42
pfam00250	96	pfam00250, Fork_head, Fork head domain	7e-40
COG5025	610	COG5025, COG5025, Transcription factor of the Fork	2e-21
COG5025	610	COG5025, COG5025, Transcription factor of the Fork	2e-13

>gnl|CDD|238016 cd00059, FH, Forkhead (FH), also known as a "winged helix"

 Score =  136 bits (346), Expect = 4e-43
 Identities = 47/74 (63%), Positives = 63/74 (85%)

Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
          SY++LI +AI ++P+ R+TL+EIY++I+  FPY+R+A AGW+NSIRHNLSLNKCF KV R
Sbjct: 5  SYSALIAMAIQSSPEKRLTLSEIYKWISDNFPYFRDAPAGWQNSIRHNLSLNKCFVKVPR 64

Query: 75 PKDDPGKGSYWAID 88
            D+PGKGSYW +D
Sbjct: 65 EPDEPGKGSYWTLD 78

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. Length = 78

>gnl|CDD|214627 smart00339, FH, FORKHEAD

 Score =  134 bits (340), Expect = 3e-42
 Identities = 47/74 (63%), Positives = 57/74 (77%)

Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
          SY +LI +AI ++P  R+TL+EIY++I   FPYYRE  AGW+NSIRHNLSLN CF KV R
Sbjct: 5  SYIALIAMAILSSPDKRLTLSEIYKWIEDNFPYYRENRAGWQNSIRHNLSLNDCFVKVPR 64

Query: 75 PKDDPGKGSYWAID 88
            D PGKGSYW +D
Sbjct: 65 EGDRPGKGSYWTLD 78

FORKHEAD, also known as a "winged helix". Length = 89

>gnl|CDD|189470 pfam00250, Fork_head, Fork head domain

 Score =  129 bits (326), Expect = 7e-40
 Identities = 46/74 (62%), Positives = 56/74 (75%)

Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
          SY +LI +AI  +P+  +TL+EIYQ+I   FPYYR+   GW+NSIRHNLSLNKCF KV R
Sbjct: 5  SYIALITMAIQQSPEKMLTLSEIYQWIMDLFPYYRQNKQGWQNSIRHNLSLNKCFIKVPR 64

Query: 75 PKDDPGKGSYWAID 88
            D PGKGSYW +D
Sbjct: 65 SPDKPGKGSYWTLD 78

Length = 96

>gnl|CDD|227358 COG5025, COG5025, Transcription factor of the Forkhead/HNF3 family [Transcription]

 Score = 89.1 bits (221), Expect = 2e-21
 Identities = 44/95 (46%), Positives = 57/95 (60%)

Query: 9   NIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKC 68
             K   SYA+ I  AI ++P G+MTL+EIY +I+   PYYR     W+NSIRHNLSLNK 
Sbjct: 335 TSKPAFSYANSITQAILSSPSGKMTLSEIYSWISSNLPYYRHKPTAWQNSIRHNLSLNKS 394

Query: 69  FTKVARPKDDPGKGSYWAIDYNHTADDGPSKKKVK 103
           F KV R    PGKG +W IDY++  +    +    
Sbjct: 395 FEKVPRSASQPGKGCFWKIDYSYIYEKESKRNPRS 429

Length = 610

>gnl|CDD|227358 COG5025, COG5025, Transcription factor of the Forkhead/HNF3 family [Transcription]

 Score = 66.0 bits (161), Expect = 2e-13
 Identities = 35/77 (45%), Positives = 48/77 (62%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SYA+   LAI N+P   +TL++IY +I +TF YY +  + W+NSIRHNLSLN  F K+  
Sbjct: 90  SYATGRGLAILNSPDKPLTLSKIYTWIHNTFFYYAKVVSRWQNSIRHNLSLNDAFIKIEG 149

Query: 75  PKDDPGKGSYWAIDYNH 91
                 KG +W+I   H
Sbjct: 150 RNGAKVKGHFWSIGPGH 166

Length = 610

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	148
cd00059	78	FH Forkhead (FH), also known as a "winged helix".	100.0
PF00250	96	Fork_head: Fork head domain; InterPro: IPR001766 T	100.0
smart00339	89	FH FORKHEAD. FORKHEAD, also known as a "winged hel	100.0
KOG3563|consensus	454		100.0
KOG3562|consensus	277		100.0
KOG2294|consensus	454		100.0
KOG4385|consensus	581		99.94
COG5025	610	Transcription factor of the Forkhead/HNF3 family [	99.88
COG5025	610	Transcription factor of the Forkhead/HNF3 family [	99.61
PF00538	77	Linker_histone: linker histone H1 and H5 family; I	95.94
smart00526	66	H15 Domain in histone families 1 and 5.	95.61
cd00073	88	H15 linker histone 1 and histone 5 domains; the ba	94.82
PF05066	72	HARE-HTH: HB1, ASXL, restriction endonuclease HTH	90.46
KOG4012|consensus	243		89.34

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

Probab=100.00  E-value=1.8e-42  Score=240.96  Aligned_cols=78  Identities=62%  Similarity=1.173  Sum_probs=76.7

Q ss_pred             CCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeeec
Q psy14921         11 KCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAID   88 (148)
Q Consensus        11 KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~id   88 (148)
                      ||||||++||++||+++|+++|||+|||+||+++||||+.+..|||||||||||+|+||+||+|+.+++|||+||+||
T Consensus         1 kP~~sY~~LI~~Ai~~sp~~~lTL~eIy~~I~~~~pyyr~~~~gWknSIRHnLS~n~~F~kv~r~~~~~gkg~~W~i~   78 (78)
T cd00059           1 KPPYSYSALIAMAIQSSPEKRLTLSEIYKWISDNFPYFRDAPAGWQNSIRHNLSLNKCFVKVPREPDEPGKGSYWTLD   78 (78)
T ss_pred             CCCCCHHHHHHHHHHhCCCCCeeHHHHHHHHHHhCCccccCCCCCccceeEecccccceEECCCCCCCCCCCCeeeeC
Confidence            899999999999999999999999999999999999999999999999999999999999999998889999999997

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.

>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=100.00  E-value=5.9e-42  Score=246.34  Aligned_cols=89  Identities=56%  Similarity=1.005  Sum_probs=81.0

Q ss_pred             CCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeeecCC
Q psy14921         11 KCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAIDYN   90 (148)
Q Consensus        11 KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~id~~   90 (148)
                      ||||||++||+|||+++|+++|||+|||+||+++||||+.+..|||||||||||+|+||+||+++.+++|||+||+|+++
T Consensus         1 KPp~sY~~LI~~Ai~~sp~~~Ltl~eIy~~i~~~~pyyr~~~~~WknSIRHnLS~~~~F~kv~~~~~~~gkg~~W~i~~~   80 (96)
T PF00250_consen    1 KPPYSYATLIAMAILSSPDKRLTLSEIYEWIEENFPYYRDASKGWKNSIRHNLSLNKCFVKVPRDPSEPGKGSYWTIDPE   80 (96)
T ss_dssp             -SSS-HHHHHHHHHHTSTTSEBEHHHHHHHHHHHCGHHHCTHCHHHHHHHHHHHHSTTEEEESCCTSSSSSSEEEEE-CT
T ss_pred             CCCCcHHHHHHHHHHhCCCCCccHHHHHHHHHHhhccccccchhhhhHHhhhccccceeeecCcCCCCCCCceeEEeCHH
Confidence            89999999999999999999999999999999999999999999999999999999999999998888999999999999


Q ss_pred             CCCCCCCCc
Q psy14921         91 HTADDGPSK   99 (148)
Q Consensus        91 ~~~~~~~~r   99 (148)
                      +.......+
T Consensus        81 ~~~~~~~~~   89 (96)
T PF00250_consen   81 AIEEFEKGR   89 (96)
T ss_dssp             HHHHHHHSC
T ss_pred             HHHHHhcch
Confidence            987554433

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 ....

>smart00339 FH FORKHEAD

Probab=100.00  E-value=2.9e-40  Score=234.78  Aligned_cols=83  Identities=58%  Similarity=1.051  Sum_probs=80.7

Q ss_pred             CCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeeecCC
Q psy14921         11 KCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAIDYN   90 (148)
Q Consensus        11 KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~id~~   90 (148)
                      |||+||++||++||+++|+++|||+|||+||+++||||+.+..|||||||||||+|+||+||+|+.+.+|||+||+|+++
T Consensus         1 kP~~sY~~lI~~ai~~sp~~~ltl~~Iy~~I~~~~pyy~~~~~~WknSIRHnLS~n~~F~kv~~~~~~~gkg~~W~i~~~   80 (89)
T smart00339        1 KPPYSYIALIAMAILSSPDKRLTLSEIYKWIEDNFPYYRENRAGWQNSIRHNLSLNDCFVKVPREGDRPGKGSYWTLDPD   80 (89)
T ss_pred             CCCCCHHHHHHHHHHhCCCCCeeHHHHHHHHHHhCchhhcCccccccccccccchhhceeecCcCCCCCCCCCEEEECcc
Confidence            89999999999999999999999999999999999999999999999999999999999999998888899999999999


Q ss_pred             CCC
Q psy14921         91 HTA   93 (148)
Q Consensus        91 ~~~   93 (148)
                      +..
T Consensus        81 ~~~   83 (89)
T smart00339       81 AEN   83 (89)
T ss_pred             HHH
Confidence            875

FORKHEAD, also known as a "winged helix"

>KOG3563|consensus

Probab=100.00  E-value=3.4e-38  Score=269.25  Aligned_cols=87  Identities=51%  Similarity=0.901  Sum_probs=84.7

Q ss_pred             CCCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeee
Q psy14921          8 GNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAI   87 (148)
Q Consensus         8 ~~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~i   87 (148)
                      .+.||||||+.||.|||+.+|.++|||+|||+||++.|||||.+...|||||||.||+|+|||||+|.+|+||||+||+|
T Consensus       170 ~haKPPYSYISLITMAIQ~~pskmLTLSEIYqwIMDLFPyYrqNQQRWQNSIRHSLSFNDCFVKVaRSPDKPGKGSfWTL  249 (454)
T KOG3563|consen  170 THAKPPYSYISLITMAIQQAPSKMLTLSEIYQWIMDLFPYYRQNQQRWQNSIRHSLSFNDCFVKVARSPDKPGKGSFWTL  249 (454)
T ss_pred             cCCCCChhHHHHHHHHHHhCCccceeHHHHHHHHHHhhhHhhhhHHHHHhhhhhhccccceeeeccCCCCCCCCccceee
Confidence            48899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q psy14921         88 DYNHTAD   94 (148)
Q Consensus        88 d~~~~~~   94 (148)
                      .|++..-
T Consensus       250 HpdsGNM  256 (454)
T KOG3563|consen  250 HPDSGNM  256 (454)
T ss_pred             cCCcCcc
Confidence            9999863

>KOG3562|consensus

Probab=100.00  E-value=1e-36  Score=246.80  Aligned_cols=97  Identities=44%  Similarity=0.855  Sum_probs=88.9

Q ss_pred             CCCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeee
Q psy14921          8 GNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAI   87 (148)
Q Consensus         8 ~~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~i   87 (148)
                      +++||||||+.|.+|||++||+++|.|+|||+||+++|||||.++..||||+|||||.|+||+||+|..+.+|||+||++
T Consensus        10 ~dQKPPYSYIsLTaMAI~~SpekmLPLseIYkfImDrFPfYRkNTQrWQNSLRHNLSFNDCFIKiPRr~drpGKGsyWal   89 (277)
T KOG3562|consen   10 GDQKPPYSYISLTAMAIQSSPEKMLPLSEIYKFIMDRFPFYRKNTQRWQNSLRHNLSFNDCFIKIPRRPDRPGKGSYWAL   89 (277)
T ss_pred             cccCCCceeeehhhHHhhcChhhcCcHHHHHHHHHhhCchhhhchHHHHHHhhccccccceeeecCCCCCCCCCccceee
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCC--CCCCCccccCC
Q psy14921         88 DYNHTA--DDGPSKKKVKL  104 (148)
Q Consensus        88 d~~~~~--~~~~~rkk~r~  104 (148)
                      .|.+..  |+++-.+|+||
T Consensus        90 HP~a~dMFENGS~LRRrKR  108 (277)
T KOG3562|consen   90 HPSAFDMFENGSLLRRRKR  108 (277)
T ss_pred             ccchhhhcccchHHHHhhh
Confidence            999986  45543333333

>KOG2294|consensus

Probab=100.00  E-value=6.3e-36  Score=258.15  Aligned_cols=86  Identities=55%  Similarity=1.000  Sum_probs=82.9

Q ss_pred             CCCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHh-hCCCccccc-ccccccchhhcccccccccccCCCCCCCCccee
Q psy14921          8 GNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITH-TFPYYREAN-AGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYW   85 (148)
Q Consensus         8 ~~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~-~fPyyr~~~-~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W   85 (148)
                      ...||||||++||+|||+.+++++|||+|||+||.. +||||++.. .|||||||||||||+||+||+|..+++|||+||
T Consensus       127 ~~~kpp~SY~~LI~mAI~~Sp~krLtLs~Iy~~i~~~~fpyyr~~~~~gWqNSIRHNLSLn~cF~Kvpr~~~~~gKg~~W  206 (454)
T KOG2294|consen  127 AGVKPPYSYSGLIAMAIRLSPGKRLTLGGIYFYILLEHFPYYRDANMPGWKNSIRHNLSLNKCFVKVPRERGRPGKGNYW  206 (454)
T ss_pred             CCcCCccccccccccccccCCCcceeecCeeEEEEeccccccccCCCccchhhcccccccccCccccCCcccCCCCCCcc
Confidence            468999999999999999999999999999999995 999999999 999999999999999999999988889999999


Q ss_pred             eecCCCCC
Q psy14921         86 AIDYNHTA   93 (148)
Q Consensus        86 ~id~~~~~   93 (148)
                      +||++...
T Consensus       207 ~ldP~~~~  214 (454)
T KOG2294|consen  207 TLDPDDEN  214 (454)
T ss_pred             ccCcchhc
Confidence            99998886

>KOG4385|consensus

Probab=99.94  E-value=3.8e-28  Score=213.37  Aligned_cols=85  Identities=47%  Similarity=0.869  Sum_probs=80.7

Q ss_pred             ecCCCCCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcc
Q psy14921          4 TYKTGNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGS   83 (148)
Q Consensus         4 ~y~~~~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~   83 (148)
                      |||+.+.+|||+||.||.+||.++|++.|||+|||.|+.+.|.|||.+.+.|||+||||||+++||++|+-     -||.
T Consensus       361 fyk~~dvRPPfTYAsLIRqAIlESpdkQLTLNEIY~WFTrtFAYFRRNaATWKnAVRHNLSLHKCF~RVEn-----vkga  435 (581)
T KOG4385|consen  361 FYKNADVRPPFTYASLIRQAILESPDKQLTLNEIYNWFTRTFAYFRRNAATWKNAVRHNLSLHKCFVRVEN-----VKGA  435 (581)
T ss_pred             hhhccccCCchhHHHHHHHHHhcCchhhccHHHHHHHHHHHHHHHhccchhHhHHHhhhhHHHHHHHHHHH-----Hhcc
Confidence            79999999999999999999999999999999999999999999999999999999999999999999983     6899


Q ss_pred             eeeecCCCCC
Q psy14921         84 YWAIDYNHTA   93 (148)
Q Consensus        84 ~W~id~~~~~   93 (148)
                      -|++|+...-
T Consensus       436 vwtvDe~e~~  445 (581)
T KOG4385|consen  436 VWTVDEREFQ  445 (581)
T ss_pred             eeeeehhhhh
Confidence            9999976543

>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]

Probab=99.88  E-value=8.4e-24  Score=191.71  Aligned_cols=94  Identities=47%  Similarity=0.843  Sum_probs=88.8

Q ss_pred             CCCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeee
Q psy14921          8 GNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAI   87 (148)
Q Consensus         8 ~~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~i   87 (148)
                      ...||+.+|+.||++||..+++++|+|.+||.||..+||||+.+..+|+||||||||+|++|.||+|...++|||+||.|
T Consensus       334 ~~~kP~~sya~~iT~ail~s~~~kmsls~Iy~~i~s~~pyYr~~p~~w~nSiRhnlSlNksf~kvP~sa~~pGKg~fw~i  413 (610)
T COG5025         334 RTSKPAFSYANSITQAILSSPSGKMTLSEIYSWISSNLPYYRHKPTAWQNSIRHNLSLNKSFEKVPRSASQPGKGCFWKI  413 (610)
T ss_pred             cCccCCcchhhhhHHHhhcCcccccccccccccccccchhhccCCcccCchhhhhhhhccccccCCCCcCCCCCcccCcc
Confidence            37899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCCCCCccc
Q psy14921         88 DYNHTADDGPSKKK  101 (148)
Q Consensus        88 d~~~~~~~~~~rkk  101 (148)
                      +.++..+..+.+.+
T Consensus       414 ~~s~~~~~~sk~~~  427 (610)
T COG5025         414 DYSYIYEKESKRNP  427 (610)
T ss_pred             Chhhhhhhcccccc
Confidence            99999877654443

>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]

Probab=99.61  E-value=5e-17  Score=147.81  Aligned_cols=89  Identities=39%  Similarity=0.602  Sum_probs=83.9

Q ss_pred             CCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeeec
Q psy14921          9 NIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAID   88 (148)
Q Consensus         9 ~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~id   88 (148)
                      -.||+|+|+.+|.++|..++.+.|||..||.||-..|.||.....+|+|||||||++++.|.|+.++.+..++|.||.|.
T Consensus        84 ~~v~~~s~a~gr~~~il~s~~~~lt~s~~~~~~~~~~~~~~k~~~~~~~sIr~Nls~~~a~~~i~g~~g~~~~g~~~~ig  163 (610)
T COG5025          84 YYVPPYSYATGRGLAILNSPDKPLTLSKIYTWIHNTFFYYAKVVSRWQNSIRHNLSLNDAFIKIEGRNGAKVKGHFWSIG  163 (610)
T ss_pred             cccCCeeeeeccccccccCcccCCcccceeeeeeecccccccccchhhhhhhcccccCceEEEEeccCCccccceeeccC
Confidence            36999999999999999999999999999999999999999999999999999999999999999998989999999999


Q ss_pred             CCCCCCCCC
Q psy14921         89 YNHTADDGP   97 (148)
Q Consensus        89 ~~~~~~~~~   97 (148)
                      |+.......
T Consensus       164 P~~~~~~l~  172 (610)
T COG5025         164 PGHETQFLK  172 (610)
T ss_pred             CCccceeec
Confidence            988865443

>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=95.94  E-value=0.012  Score=40.07  Aligned_cols=33  Identities=21%  Similarity=0.362  Sum_probs=29.3

Q ss_pred             hHHHHHHHHHhhCCC-CCcCHHHHHHHHHhhCCC
Q psy14921         15 SYASLIRLAISNAPQ-GRMTLNEIYQFITHTFPY   47 (148)
Q Consensus        15 SYa~LI~~AI~~sp~-~~LtL~eIY~~i~~~fPy   47 (148)
                      +|.+||.+||.+..+ +..++..|..||+++|+.
T Consensus         4 ~y~~mI~eAI~~l~er~GsS~~aI~kyI~~~y~~   37 (77)
T PF00538_consen    4 PYSDMILEAIKALKERKGSSLQAIKKYIKAKYKV   37 (77)
T ss_dssp             CHHHHHHHHHHHCCSSSSEEHHHHHHHHHHHSSC
T ss_pred             CHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhcCc
Confidence            589999999999666 559999999999999975

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.

>smart00526 H15 Domain in histone families 1 and 5

Probab=95.61  E-value=0.024  Score=37.37  Aligned_cols=33  Identities=24%  Similarity=0.440  Sum_probs=29.0

Q ss_pred             hHHHHHHHHHhhCCCCC-cCHHHHHHHHHhhCCC
Q psy14921         15 SYASLIRLAISNAPQGR-MTLNEIYQFITHTFPY   47 (148)
Q Consensus        15 SYa~LI~~AI~~sp~~~-LtL~eIY~~i~~~fPy   47 (148)
                      +|..||.+||.+..++. .++..|..||+.+|+.
T Consensus         6 ~~~~mI~eAI~~l~er~GsS~~aI~kyi~~~~~~   39 (66)
T smart00526        6 PYSEMITEAISALKERKGSSLQAIKKYIEANYKV   39 (66)
T ss_pred             CHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCC
Confidence            79999999999976644 9999999999999663

>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=94.82  E-value=0.051  Score=38.00  Aligned_cols=35  Identities=17%  Similarity=0.319  Sum_probs=29.6

Q ss_pred             hHHHHHHHHHhhCCCC-CcCHHHHHHHHHhhCCCcc
Q psy14921         15 SYASLIRLAISNAPQG-RMTLNEIYQFITHTFPYYR   49 (148)
Q Consensus        15 SYa~LI~~AI~~sp~~-~LtL~eIY~~i~~~fPyyr   49 (148)
                      +|..||.+||.+..++ ..++..|..||+.+|+.-.
T Consensus         6 ~y~~MI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~   41 (88)
T cd00073           6 PYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDD   41 (88)
T ss_pred             CHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCCcch
Confidence            7899999999995544 4999999999999988643

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

Probab=90.46  E-value=0.26  Score=32.80  Aligned_cols=58  Identities=21%  Similarity=0.249  Sum_probs=38.0

Q ss_pred             chHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcc-----ccccccccc
Q psy14921         14 SSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLS-----LNKCFTKVA   73 (148)
Q Consensus        14 ~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS-----~n~~F~Kv~   73 (148)
                      +||..++...|+... +.|+.+||++.|.+.--+ ....+...++|+-.|.     .+..|++|.
T Consensus         1 mt~~eaa~~vL~~~~-~pm~~~eI~~~i~~~~~~-~~~~k~p~~~i~a~ly~~~~~~d~~F~~vg   63 (72)
T PF05066_consen    1 MTFKEAAYEVLEEAG-RPMTFKEIWEEIQERGLY-KKSGKTPEATIAAQLYTDIKNEDSRFVKVG   63 (72)
T ss_dssp             S-HHHHHHHHHHHH--S-EEHHHHHHHHHHHHTS----GGGGGHHHH-HHHHHHH-T-SS-EESS
T ss_pred             CCHHHHHHHHHHhcC-CCcCHHHHHHHHHHhCCC-CcccCCHHHHHHHHHHHHcccCCCCEEEeC
Confidence            478888998898886 779999999999987655 2225566777773333     445898874

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.

>KOG4012|consensus

Probab=89.34  E-value=0.39  Score=40.05  Aligned_cols=66  Identities=24%  Similarity=0.396  Sum_probs=46.2

Q ss_pred             CchHHHHHHHHHhhCCCCC-cCHHHHHHHHHhhCCCcccccccccccchhhccccc-----ccccccCCCCCCCCcceee
Q psy14921         13 TSSYASLIRLAISNAPQGR-MTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNK-----CFTKVARPKDDPGKGSYWA   86 (148)
Q Consensus        13 p~SYa~LI~~AI~~sp~~~-LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~-----~F~Kv~r~~~~~gkg~~W~   86 (148)
                      .-+|.+||..||....++. .++.-|+.||..+|+.|.-..    +--|.+++|+.     .|+++-      |.|.-|.
T Consensus        44 ~P~~~~mi~eAi~a~keR~GsS~aAikK~i~~~Y~g~~v~k----~n~~lk~alK~~v~~g~l~Qtk------G~GAsGs  113 (243)
T KOG4012|consen   44 HPPYSEMITEAISALKERKGSSLAAIKKYIAANYPGDDVEK----NNSRLKLALKKGVSKGVLVQTK------GTGASGS  113 (243)
T ss_pred             CCcHHHHHHHHHHHhhhcccchHHHHHHHHhhcCccchhhh----hhHHHHHHHHhhhccCceeeec------cCCcccc
Confidence            4479999999999987776 999999999999998876432    12355555543     454433      5555555


Q ss_pred             ec
Q psy14921         87 ID   88 (148)
Q Consensus        87 id   88 (148)
                      +.
T Consensus       114 Fk  115 (243)
T KOG4012|consen  114 FK  115 (243)
T ss_pred             cc
Confidence            44

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	148
1d5v_A	94	Solution Structure Of The Forkhead Domain Of The Ad		2e-24
1vtn_C	102	Co-Crystal Structure Of The Hnf-3FORK HEAD DNA-Reco		4e-22
2c6y_A	111	Crystal Structure Of Interleukin Enhancer-Binding F		9e-22
1jxs_A	98	Solution Structure Of The Dna-Binding Domain Of Int		1e-21
2a3s_A	101	Solution Structure And Dynamics Of Dna-Binding Doma		1e-20
2hfh_A	109	The Nmr Structures Of A Winged Helix Protein: Genes		1e-20
2hdc_A	97	Structure Of Transcription Factor GenesisDNA COMPLE		2e-20
1kq8_A	100	Solution Structure Of Winged Helix Protein Hfh-1 Le		5e-17
2kiu_A	87	Solution Structure And Backbone Dynamics Of The Dna		1e-16
3qrf_F	82	Structure Of A Domain-Swapped Foxp3 Dimer Length =		2e-16
2a07_F	93	Crystal Structure Of Foxp2 Bound Specifically To Dn		4e-16
1e17_A	150	Solution Structure Of The Dna Binding Domain Of The		1e-14
3l2c_A	110	Crystal Structure Of The Dna Binding Domain Of Foxo		1e-14
2uzk_A	97	Crystal Structure Of The Human Foxo3a-Dbd Bound To		3e-13
2k86_A	103	Solution Structure Of Foxo3a Forkhead Domain Length		3e-13
3co6_C	100	Crystal Structure Of Foxo1 Dbd Bound To Dbe1 Dna Le		4e-13
3co7_C	117	Crystal Structure Of Foxo1 Dbd Bound To Dbe2 Dna Le		4e-13
3g73_A	142	Structure Of The Foxm1 Dna Binding Length = 142		2e-12

>pdb|1D5V|A Chain A, Solution Structure Of The Forkhead Domain Of The Adipocyte- Transcription Factor Freac-11 (S12) Length = 94

Iteration: 1
 Score =  107 bits (267), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 48/79 (60%), Positives = 58/79 (73%)
Query: 10 IKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCF 69
          +K   SY +LI +AI NAP+ ++TLN IYQFI   FP+YRE   GW+NSIRHNLSLN+CF
Sbjct: 3  VKPPYSYIALITMAIQNAPEKKITLNGIYQFIMDRFPFYRENKQGWQNSIRHNLSLNECF 62
Query: 70 TKVARPKDDPGKGSYWAID 88
           KV R    PGKGSYW +D
Sbjct: 63 VKVPRDDKKPGKGSYWTLD 81

>pdb|1VTN|C Chain C, Co-Crystal Structure Of The Hnf-3FORK HEAD DNA-Recognition Motif Resembles Histone H5 Length = 102

Iteration: 1
 Score =  100 bits (248), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 46/73 (63%), Positives = 53/73 (72%)
Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
          SY SLI +AI  AP   +TL+EIYQ+I   FPYYRE    W+NSIRH+LS N CF KVAR
Sbjct: 7  SYISLITMAIQQAPGKMLTLSEIYQWIMDLFPYYRENQQRWQNSIRHSLSFNDCFVKVAR 66
Query: 75 PKDDPGKGSYWAI 87
            D PGKGSYWA+
Sbjct: 67 SPDKPGKGSYWAL 79

>pdb|2C6Y|A Chain A, Crystal Structure Of Interleukin Enhancer-Binding Factor 1 Bound To Dna Length = 111

Iteration: 1
 Score = 99.0 bits (245), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 45/74 (60%), Positives = 56/74 (75%)
Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
          SYA LI  AI+ AP  ++TLN IY  IT  +PYYR A+ GW+NSIRHNLSLN+ F KV R
Sbjct: 20 SYAQLIVQAITMAPDKQLTLNGIYTHITKNYPYYRTADKGWQNSIRHNLSLNRYFIKVPR 79
Query: 75 PKDDPGKGSYWAID 88
           +++PGKGS+W ID
Sbjct: 80 SQEEPGKGSFWRID 93

>pdb|1JXS|A Chain A, Solution Structure Of The Dna-Binding Domain Of Interleukin Enhancer Binding Factor Length = 98

Iteration: 1
 Score = 98.6 bits (244), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 45/74 (60%), Positives = 56/74 (75%)
Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
          SYA LI  AI+ AP  ++TLN IY  IT  +PYYR A+ GW+NSIRHNLSLN+ F KV R
Sbjct: 7  SYAQLIVQAITMAPDKQLTLNGIYTHITKNYPYYRTADKGWQNSIRHNLSLNRYFIKVPR 66
Query: 75 PKDDPGKGSYWAID 88
           +++PGKGS+W ID
Sbjct: 67 SQEEPGKGSFWRID 80

>pdb|2A3S|A Chain A, Solution Structure And Dynamics Of Dna-Binding Domain Of Myocyte Nuclear Factor Length = 101

Iteration: 1
 Score = 95.5 bits (236), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 44/74 (59%), Positives = 56/74 (75%)
Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
          SYA LI  AIS+A   ++TL+ IY  IT  +PYYR A+ GW+NSIRHNLSLN+ F KV R
Sbjct: 7  SYAQLIVQAISSAQDRQLTLSGIYAHITKHYPYYRTADKGWQNSIRHNLSLNRYFIKVPR 66
Query: 75 PKDDPGKGSYWAID 88
           +++PGKGS+W ID
Sbjct: 67 SQEEPGKGSFWRID 80

>pdb|2HFH|A Chain A, The Nmr Structures Of A Winged Helix Protein: Genesis, 20 Structures Length = 109

Iteration: 1
 Score = 95.1 bits (235), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 42/79 (53%), Positives = 57/79 (72%)
Query: 10 IKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCF 69
          +K   SY +LI +AI  +PQ ++TL+ I +FI++ FPYYRE    W+NSIRHNLSLN CF
Sbjct: 2  VKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDCF 61
Query: 70 TKVARPKDDPGKGSYWAID 88
           K+ R   +PGKG+YW +D
Sbjct: 62 VKIPREPGNPGKGNYWTLD 80

>pdb|2HDC|A Chain A, Structure Of Transcription Factor GenesisDNA COMPLEX Length = 97

Iteration: 1
 Score = 94.4 bits (233), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 41/74 (55%), Positives = 55/74 (74%)
Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
          SY +LI +AI  +PQ ++TL+ I +FI++ FPYYRE    W+NSIRHNLSLN CF K+ R
Sbjct: 6  SYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDCFVKIPR 65
Query: 75 PKDDPGKGSYWAID 88
             +PGKG+YW +D
Sbjct: 66 EPGNPGKGNYWTLD 79

>pdb|1KQ8|A Chain A, Solution Structure Of Winged Helix Protein Hfh-1 Length = 100

Iteration: 1
 Score = 83.2 bits (204), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 40/90 (44%), Positives = 60/90 (66%), Gaps = 3/90 (3%)
Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
           SY +LI +AI ++  GR+TL EI +++   FP++R +  GW+NS+RHNLSLN CF KV R
Sbjct: 6   SYIALITMAIRDSAGGRLTLAEINEYLMGKFPFFRGSYTGWRNSVRHNLSLNDCFVKVLR 65
Query: 75  PKDDP-GKGSYWAIDYN--HTADDGPSKKK 101
               P GK +YW ++ N  +T  DG  +++
Sbjct: 66  DPSRPWGKDNYWMLNPNSEYTFADGVFRRR 95

>pdb|2KIU|A Chain A, Solution Structure And Backbone Dynamics Of The Dna-Binding Domain Of Foxp1: Insight Into Its Domain Swapping Length = 87

Iteration: 1
 Score = 82.0 bits (201), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 39/85 (45%), Positives = 53/85 (62%), Gaps = 5/85 (5%)
Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
          +YASLIR AI  +P+ ++TLNEIY + T  FPY+R   A WKN++RHNLSL+K F +V  
Sbjct: 8  TYASLIRQAILESPEKQLTLNEIYNWFTRMFPYFRRNAATWKNAVRHNLSLHKYFVRV-- 65
Query: 75 PKDDPGKGSYWAIDYNHTADDGPSK 99
             +  KG+ W +D        P K
Sbjct: 66 ---ENVKGAVWTVDEVEFQKRRPQK 87

>pdb|3QRF|F Chain F, Structure Of A Domain-Swapped Foxp3 Dimer Length = 82

Iteration: 1
 Score = 81.3 bits (199), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 37/74 (50%), Positives = 50/74 (67%), Gaps = 5/74 (6%)
Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
          +YA+LIR AI  AP+ + TLNEIY + T  F ++R   A WKN+IRHNLSL+KCF +V  
Sbjct: 6  TYATLIRWAILEAPEKQRTLNEIYHWFTRMFAFFRNHPATWKNAIRHNLSLHKCFVRV-- 63
Query: 75 PKDDPGKGSYWAID 88
             +  KG+ W +D
Sbjct: 64 ---ESEKGAVWTVD 74

>pdb|2A07|F Chain F, Crystal Structure Of Foxp2 Bound Specifically To Dna. Length = 93

Iteration: 1
 Score = 80.1 bits (196), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 36/74 (48%), Positives = 50/74 (67%), Gaps = 5/74 (6%)
Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
          +YA+LIR AI  +   ++TLNEIY + T TF Y+R   A WKN++RHNLSL+KCF +V  
Sbjct: 7  TYATLIRQAIMESSDRQLTLNEIYSWFTRTFAYFRRNAATWKNAVRHNLSLHKCFVRV-- 64
Query: 75 PKDDPGKGSYWAID 88
             +  KG+ W +D
Sbjct: 65 ---ENVKGAVWTVD 75

>pdb|3L2C|A Chain A, Crystal Structure Of The Dna Binding Domain Of Foxo4 Bound To Dna Length = 110

Iteration: 1
 Score = 75.1 bits (183), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 38/85 (44%), Positives = 55/85 (64%), Gaps = 7/85 (8%)
Query: 9   NIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYRE-----ANAGWKNSIRHNL 63
           N     SYA LI  AI +AP+ R+TL +IY+++  T PY+++     ++AGWKNSIRHNL
Sbjct: 22  NAWGNQSYAELISQAIESAPEKRLTLAQIYEWMVRTVPYFKDKGDSNSSAGWKNSIRHNL 81
Query: 64  SLNKCFTKVARPKDDPGKGSYWAID 88
           SL+  F KV    +  GK S+W ++
Sbjct: 82  SLHSKFIKVH--NEATGKSSWWMLN 104

>pdb|2UZK|A Chain A, Crystal Structure Of The Human Foxo3a-Dbd Bound To Dna Length = 97

Iteration: 1
 Score = 70.9 bits (172), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 41/99 (41%), Positives = 60/99 (60%), Gaps = 11/99 (11%)
Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYRE-----ANAGWKNSIRHNLSLNKCF 69
           SYA LI  AI ++P  R+TL++IY+++    PY+++     ++AGWKNSIRHNLSL+  F
Sbjct: 5   SYADLITRAIESSPDKRLTLSQIYEWMVRCVPYFKDKGDSNSSAGWKNSIRHNLSLHSRF 64
Query: 70  TKVARPKDDPGKGSYWAIDYNHTADDGPSKKKVKLPRVS 108
            +V    +  GK S+W I+     D G S K  +   VS
Sbjct: 65  MRV--QNEGTGKSSWWIIN----PDGGKSGKAPRRRAVS 97

>pdb|2K86|A Chain A, Solution Structure Of Foxo3a Forkhead Domain Length = 103

Iteration: 1
 Score = 70.9 bits (172), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 35/79 (44%), Positives = 53/79 (67%), Gaps = 7/79 (8%)
Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYRE-----ANAGWKNSIRHNLSLNKCF 69
          SYA LI  AI ++P  R+TL++IY+++    PY+++     ++AGWKNSIRHNLSL+  F
Sbjct: 13 SYADLITRAIESSPDKRLTLSQIYEWMVRCVPYFKDKGDSNSSAGWKNSIRHNLSLHSRF 72
Query: 70 TKVARPKDDPGKGSYWAID 88
           +V    +  GK S+W I+
Sbjct: 73 MRV--QNEGTGKSSWWIIN 89

>pdb|3CO6|C Chain C, Crystal Structure Of Foxo1 Dbd Bound To Dbe1 Dna Length = 100

Iteration: 1
 Score = 70.1 bits (170), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 33/79 (41%), Positives = 54/79 (68%), Gaps = 7/79 (8%)
Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYRE-----ANAGWKNSIRHNLSLNKCF 69
          SYA LI  AI ++ + R+TL++IY+++  + PY+++     ++AGWKNSIRHNLSL+  F
Sbjct: 15 SYADLITKAIESSAEKRLTLSQIYEWMVKSVPYFKDKGDSNSSAGWKNSIRHNLSLHSKF 74
Query: 70 TKVARPKDDPGKGSYWAID 88
           +V    +  GK S+W ++
Sbjct: 75 IRV--QNEGTGKSSWWMLN 91

>pdb|3CO7|C Chain C, Crystal Structure Of Foxo1 Dbd Bound To Dbe2 Dna Length = 117

Iteration: 1
 Score = 70.1 bits (170), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 33/79 (41%), Positives = 54/79 (68%), Gaps = 7/79 (8%)
Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYRE-----ANAGWKNSIRHNLSLNKCF 69
          SYA LI  AI ++ + R+TL++IY+++  + PY+++     ++AGWKNSIRHNLSL+  F
Sbjct: 15 SYADLITKAIESSAEKRLTLSQIYEWMVKSVPYFKDKGDSNSSAGWKNSIRHNLSLHSKF 74
Query: 70 TKVARPKDDPGKGSYWAID 88
           +V    +  GK S+W ++
Sbjct: 75 IRV--QNEGTGKSSWWMLN 91

>pdb|3G73|A Chain A, Structure Of The Foxm1 Dna Binding Length = 142

Iteration: 1
 Score = 67.8 bits (164), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 35/74 (47%), Positives = 47/74 (63%), Gaps = 4/74 (5%)
Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYRE-ANAGWKNSIRHNLSLNKCFTKVA 73
          SY ++I+ AI++  + RMTL +IY +I   FPY++  A  GWKNSIRHNLSL+  F    
Sbjct: 22 SYMAMIQFAINSTERKRMTLKDIYTWIEDHFPYFKHIAKPGWKNSIRHNLSLHDMF---V 78
Query: 74 RPKDDPGKGSYWAI 87
          R     GK S+W I
Sbjct: 79 RETSANGKVSFWTI 92

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	148
1vtn_C	102	HNF-3/FORK head DNA-recognition motif; protein-DNA	1e-45
2hdc_A	97	Protein (transcription factor); structure, dyanami	1e-45
2c6y_A	111	Forkhead box protein K2; transcription regulation,	2e-45
2hfh_A	109	Genesis, HFH-2; HNF-3 homologues, winged helix pro	5e-45
1kq8_A	100	HFH-1, hepatocyte nuclear factor 3 forkhead homolo	2e-42
2a07_F	93	Forkhead box protein P2; double-helix, swapping, h	1e-40
3bpy_A	85	FORK head domain, forkhead transcription factor FO	5e-40
3g73_A	142	Forkhead box protein M1; DNA-binding domain, forkh	6e-39
3l2c_A	110	Forkhead box protein O4; winged helix, transcripti	4e-38
3coa_C	117	Forkhead box protein O1; winged helix, forkhead do	7e-36
1e17_A	150	AFX; DNA binding domain, winged helix; NMR {Homo s	6e-35

>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 Length = 102

 Score =  143 bits (363), Expect = 1e-45
 Identities = 46/74 (62%), Positives = 53/74 (71%)

Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
          SY SLI +AI  AP   +TL+EIYQ+I   FPYYRE    W+NSIRH+LS N CF KVAR
Sbjct: 7  SYISLITMAIQQAPGKMLTLSEIYQWIMDLFPYYRENQQRWQNSIRHSLSFNDCFVKVAR 66

Query: 75 PKDDPGKGSYWAID 88
            D PGKGSYWA+ 
Sbjct: 67 SPDKPGKGSYWALH 80

>2hdc_A Protein (transcription factor); structure, dyanamics, genesis, winged helix protein, protein/DNA complex; HET: DNA; NMR {Rattus norvegicus} SCOP: a.4.5.14 Length = 97

 Score =  143 bits (362), Expect = 1e-45
 Identities = 41/77 (53%), Positives = 55/77 (71%)

Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
          SY +LI +AI  +PQ ++TL+ I +FI++ FPYYRE    W+NSIRHNLSLN CF K+ R
Sbjct: 6  SYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDCFVKIPR 65

Query: 75 PKDDPGKGSYWAIDYNH 91
             +PGKG+YW +D   
Sbjct: 66 EPGNPGKGNYWTLDPQS 82

>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 Length = 111

 Score =  143 bits (362), Expect = 2e-45
 Identities = 45/77 (58%), Positives = 56/77 (72%)

Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
          SYA LI  AI+ AP  ++TLN IY  IT  +PYYR A+ GW+NSIRHNLSLN+ F KV R
Sbjct: 20 SYAQLIVQAITMAPDKQLTLNGIYTHITKNYPYYRTADKGWQNSIRHNLSLNRYFIKVPR 79

Query: 75 PKDDPGKGSYWAIDYNH 91
           +++PGKGS+W ID   
Sbjct: 80 SQEEPGKGSFWRIDPAS 96

>2hfh_A Genesis, HFH-2; HNF-3 homologues, winged helix protein; NMR {Rattus norvegicus} SCOP: a.4.5.14 Length = 109

 Score =  142 bits (359), Expect = 5e-45
 Identities = 41/77 (53%), Positives = 55/77 (71%)

Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
          SY +LI +AI  +PQ ++TL+ I +FI++ FPYYRE    W+NSIRHNLSLN CF K+ R
Sbjct: 7  SYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDCFVKIPR 66

Query: 75 PKDDPGKGSYWAIDYNH 91
             +PGKG+YW +D   
Sbjct: 67 EPGNPGKGNYWTLDPQS 83

>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 Length = 100

 Score =  135 bits (341), Expect = 2e-42
 Identities = 37/78 (47%), Positives = 53/78 (67%), Gaps = 1/78 (1%)

Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
          SY +LI +AI ++  GR+TL EI +++   FP++R +  GW+NS+RHNLSLN CF KV R
Sbjct: 6  SYIALITMAIRDSAGGRLTLAEINEYLMGKFPFFRGSYTGWRNSVRHNLSLNDCFVKVLR 65

Query: 75 PKDDP-GKGSYWAIDYNH 91
              P GK +YW ++ N 
Sbjct: 66 DPSRPWGKDNYWMLNPNS 83

>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 Length = 93

 Score =  130 bits (328), Expect = 1e-40
 Identities = 36/74 (48%), Positives = 49/74 (66%), Gaps = 5/74 (6%)

Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVAR 74
          +YA+LIR AI  +   ++TLNEIY + T TF Y+R   A WKN++RHNLSL+KCF +V  
Sbjct: 7  TYATLIRQAIMESSDRQLTLNEIYSWFTRTFAYFRRNAATWKNAVRHNLSLHKCFVRVEN 66

Query: 75 PKDDPGKGSYWAID 88
                KG+ W +D
Sbjct: 67 -----VKGAVWTVD 75

>3bpy_A FORK head domain, forkhead transcription factor FOXO4, DNA binding domain; forkhead BOX, winged helix; 1.87A {Homo sapiens} SCOP: a.4.5.14 Length = 85

 Score =  128 bits (324), Expect = 5e-40
 Identities = 37/79 (46%), Positives = 54/79 (68%), Gaps = 7/79 (8%)

Query: 15 SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYRE-----ANAGWKNSIRHNLSLNKCF 69
          SYA LI  AI +AP+ R+TL +IY+++  T PY+++     ++AGWKNSIRHNLSL+  F
Sbjct: 9  SYAELISQAIESAPEKRLTLAQIYEWMVRTVPYFKDKGDSNSSAGWKNSIRHNLSLHSKF 68

Query: 70 TKVARPKDDPGKGSYWAID 88
           KV    +  GK S+W ++
Sbjct: 69 IKV--HNEATGKSSWWMLN 85

>3g73_A Forkhead box protein M1; DNA-binding domain, forkhead transcription factors, FOXM1, W helix; HET: DNA; 2.21A {Homo sapiens} Length = 142

 Score =  127 bits (321), Expect = 6e-39
 Identities = 40/124 (32%), Positives = 59/124 (47%), Gaps = 4/124 (3%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREAN-AGWKNSIRHNLSLNKCFTKVA 73
           SY ++I+ AI++  + RMTL +IY +I   FPY++     GWKNSIRHNLSL+  F    
Sbjct: 22  SYMAMIQFAINSTERKRMTLKDIYTWIEDHFPYFKHIAKPGWKNSIRHNLSLHDMFV--- 78

Query: 74  RPKDDPGKGSYWAIDYNHTADDGPSKKKVKLPRVSPYSPVECNNSNSSSDVHNSKPPTSI 133
           R     GK S+W I  +        +    L   SP  P    +     +    +  T  
Sbjct: 79  RETSANGKVSFWTIHPSANRYLTLDQVFKPLDPGSPQLPEHLESQQKRPNPELRRNMTIK 138

Query: 134 SSVP 137
           + +P
Sbjct: 139 TELP 142

>3l2c_A Forkhead box protein O4; winged helix, transcription-DNA COMP; 1.87A {Homo sapiens} PDB: 3co6_C* Length = 110

 Score =  124 bits (313), Expect = 4e-38
 Identities = 37/79 (46%), Positives = 54/79 (68%), Gaps = 7/79 (8%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYRE-----ANAGWKNSIRHNLSLNKCF 69
           SYA LI  AI +AP+ R+TL +IY+++  T PY+++     ++AGWKNSIRHNLSL+  F
Sbjct: 28  SYAELISQAIESAPEKRLTLAQIYEWMVRTVPYFKDKGDSNSSAGWKNSIRHNLSLHSKF 87

Query: 70  TKVARPKDDPGKGSYWAID 88
            KV    +  GK S+W ++
Sbjct: 88  IKV--HNEATGKSSWWMLN 104

>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 Length = 117

 Score =  119 bits (299), Expect = 7e-36
 Identities = 35/92 (38%), Positives = 58/92 (63%), Gaps = 8/92 (8%)

Query: 15  SYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYRE-----ANAGWKNSIRHNLSLNKCF 69
           SYA LI  AI ++ + R+TL++IY+++  + PY+++     ++AGWKNSIRHNLSL+  F
Sbjct: 15  SYADLITKAIESSAEKRLTLSQIYEWMVKSVPYFKDKGDSNSSAGWKNSIRHNLSLHSKF 74

Query: 70  TKVARPKDDPGKGSYWAIDYNHTADDGPSKKK 101
            +V    +  GK S+W ++       G S ++
Sbjct: 75  IRV--QNEGTGKSSWWMLNPEG-GKSGKSPRR 103

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	148
1vtn_C	102	HNF-3/FORK head DNA-recognition motif; protein-DNA	100.0
2hdc_A	97	Protein (transcription factor); structure, dyanami	100.0
1kq8_A	100	HFH-1, hepatocyte nuclear factor 3 forkhead homolo	100.0
2hfh_A	109	Genesis, HFH-2; HNF-3 homologues, winged helix pro	100.0
2c6y_A	111	Forkhead box protein K2; transcription regulation,	100.0
3coa_C	117	Forkhead box protein O1; winged helix, forkhead do	100.0
3bpy_A	85	FORK head domain, forkhead transcription factor FO	100.0
3l2c_A	110	Forkhead box protein O4; winged helix, transcripti	100.0
1e17_A	150	AFX; DNA binding domain, winged helix; NMR {Homo s	100.0
2a07_F	93	Forkhead box protein P2; double-helix, swapping, h	100.0
3g73_A	142	Forkhead box protein M1; DNA-binding domain, forkh	100.0
1uss_A	88	Histone H1; DNA binding protein, linker histone, D	93.69
1uhm_A	78	Histone H1, histone HHO1P; winged helix-turn-helix	93.18
1hst_A	90	Histone H5; chromosomal protein; 2.60A {Gallus gal	92.9
1ust_A	93	Histone H1; DNA binding protein, linker histone, D	91.8
2rqp_A	88	Heterochromatin protein 1-binding protein 3; histo	91.33
2lso_A	83	Histone H1X; structural genomics, northeast struct	84.37

>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=100.00  E-value=7.3e-46  Score=268.55  Aligned_cols=87  Identities=54%  Similarity=0.903  Sum_probs=83.6

Q ss_pred             CCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeeec
Q psy14921          9 NIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAID   88 (148)
Q Consensus         9 ~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~id   88 (148)
                      +.||||||++||+|||+++|+++|||+|||+||+++||||+.+..|||||||||||+|+||+||+|+.+++|||+||+||
T Consensus         1 h~KPp~SY~~LI~~AI~~sp~~~LtL~eIY~~I~~~fpyyr~~~~gWqNSIRHNLSln~~F~kv~r~~~~~GKG~~W~l~   80 (102)
T 1vtn_C            1 HAKPPYSYISLITMAIQQAPGKMLTLSEIYQWIMDLFPYYRENQQRWQNSIRHSLSFNDCFVKVARSPDKPGKGSYWALH   80 (102)
T ss_dssp             CCCCSSCHHHHHHHHHHTSTTSCBCHHHHHHHHHHHCGGGGSCHHHHHHHHHHHHHHCTTEEEECCCSCSSCSSCEEEEC
T ss_pred             CcCcCCCHHHHHHHHHHhCCCCCCcHHHHHHHHHHcCCccccCCCchhhhhhhhhhhccceEecCCCCCCCCCcceEEEC
Confidence            58999999999999999999999999999999999999999999999999999999999999999998999999999999


Q ss_pred             CCCCCCC
Q psy14921         89 YNHTADD   95 (148)
Q Consensus        89 ~~~~~~~   95 (148)
                      +++....
T Consensus        81 p~~~~~f   87 (102)
T 1vtn_C           81 PSSGNMF   87 (102)
T ss_dssp             GGGCSTT
T ss_pred             cCHHHHh
Confidence            9987633

>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=100.00  E-value=5.3e-46  Score=267.14  Aligned_cols=84  Identities=50%  Similarity=0.959  Sum_probs=81.8

Q ss_pred             CCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeeecC
Q psy14921         10 IKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAIDY   89 (148)
Q Consensus        10 ~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~id~   89 (148)
                      .||||||++||+|||+++|+++|||+|||+||+++||||+.+..|||||||||||+|+||+||+|+.+++|||+||+||+
T Consensus         1 ~KPp~SY~~LI~~AI~~sp~~~ltL~eIY~~i~~~fpyyr~~~~gWqNSIRHNLSln~~F~Kv~r~~~~~gKg~~W~l~p   80 (97)
T 2hdc_A            1 VKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDP   80 (97)
T ss_dssp             CCCCCCHHHHHHHHHHTCTTTCBCHHHHHHHHHHHCHHHHHHCSSHHHHHHHHHHHHHCCEEECSCTTCSSSCCEEECCT
T ss_pred             CcCCCCHHHHHHHHHHhCCCCCCCHHHHHHHHHHhchhhccCCcceehhhhhhhhhhhheeecCCCCCCCCCcceEEECc
Confidence            59999999999999999999999999999999999999999999999999999999999999999988999999999999


Q ss_pred             CCCC
Q psy14921         90 NHTA   93 (148)
Q Consensus        90 ~~~~   93 (148)
                      ++.+
T Consensus        81 ~~~~   84 (97)
T 2hdc_A           81 QSED   84 (97)
T ss_dssp             THHH
T ss_pred             CHHH
Confidence            9875

>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=100.00  E-value=2.9e-45  Score=264.61  Aligned_cols=86  Identities=44%  Similarity=0.837  Sum_probs=72.8

Q ss_pred             CCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCC-CCcceeeec
Q psy14921         10 IKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDP-GKGSYWAID   88 (148)
Q Consensus        10 ~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~-gkg~~W~id   88 (148)
                      +||||||++||+|||+++|+++|||+|||+||+++||||+.+..|||||||||||+|+||+||+|+.+++ |||+||+||
T Consensus         1 ~KPp~SY~~LI~~AI~~sp~~~ltL~eIY~~i~~~fpyyr~~~~gWqNSIRHNLSln~~F~kv~r~~~~p~gkg~~W~l~   80 (100)
T 1kq8_A            1 PKPPYSYIALITMAIRDSAGGRLTLAEINEYLMGKFPFFRGSYTGWRNSVRHNLSLNDCFVKVLRDPSRPWGKDNYWMLN   80 (100)
T ss_dssp             ------CHHHHHHHHTTSSSSCBCHHHHHHHHHHHCTTGGGTCSCCHHHHHHHHHHHTCCEECSSCSCCSSSCCCCEECC
T ss_pred             CcCCCCHHHHHHHHHHhCCCCCCcHHHHHHHHHHhCccccCCCCceecccchheehhheeeecCCCCCCCCCCCeEEEEC
Confidence            5999999999999999999999999999999999999999999999999999999999999999988887 999999999


Q ss_pred             CCCCCCC
Q psy14921         89 YNHTADD   95 (148)
Q Consensus        89 ~~~~~~~   95 (148)
                      |+++...
T Consensus        81 p~~~~~f   87 (100)
T 1kq8_A           81 PNSEYTF   87 (100)
T ss_dssp             C------
T ss_pred             cCHHHHH
Confidence            9987643

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

Probab=100.00  E-value=3.3e-45  Score=267.84  Aligned_cols=84  Identities=50%  Similarity=0.959  Sum_probs=82.2

Q ss_pred             CCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeeecC
Q psy14921         10 IKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAIDY   89 (148)
Q Consensus        10 ~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~id~   89 (148)
                      .||||||++||+|||+++|+++|||+|||+||+++||||+.+..|||||||||||+|+||+||+|+.+++|||+||+||+
T Consensus         2 ~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSln~~F~Kv~r~~~~~GKG~~W~l~p   81 (109)
T 2hfh_A            2 VKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDP   81 (109)
T ss_dssp             CCCCCCHHHHHHHHHHTCSSSCBCHHHHHHHHHTTCHHHHTTCGGGHHHHHHHHHHHTCCBCCTTCTTSCSSCCCBBCCT
T ss_pred             CCCCCCHHHHHHHHHHhCCCCCCcHHHHHHHHHHhcchhccCCcccchhhhhhhhhhhhhhcCCCCCCCCCCceeEEECc
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy14921         90 NHTA   93 (148)
Q Consensus        90 ~~~~   93 (148)
                      ++.+
T Consensus        82 ~~~~   85 (109)
T 2hfh_A           82 QSED   85 (109)
T ss_dssp             TCCH
T ss_pred             cHHH
Confidence            9985

>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=100.00  E-value=1.6e-45  Score=270.32  Aligned_cols=90  Identities=51%  Similarity=0.881  Sum_probs=82.9

Q ss_pred             ecCCCCCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcc
Q psy14921          4 TYKTGNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGS   83 (148)
Q Consensus         4 ~y~~~~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~   83 (148)
                      ...+.+.||||||++||+|||+++|+++|||+|||+||+++||||+.+..|||||||||||+|+||+||+|+.+++|||+
T Consensus         9 ~~~~~~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSln~~F~Kv~r~~~~~GKG~   88 (111)
T 2c6y_A            9 MGRGSDSKPPYSYAQLIVQAITMAPDKQLTLNGIYTHITKNYPYYRTADKGWQNSIRHNLSLNRYFIKVPRSQEEPGKGS   88 (111)
T ss_dssp             -----CCCCSSCHHHHHHHHHHTSTTSCEEHHHHHHHHHHHCTTSCTTCHHHHHHHHHHHHHSTTEEEECCCTTSCCSSC
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHhCCCCCCcHHHHHHHHHHcCCccccCCCeeecchhHHhhhhhhhccccCCCCCCCCcc
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999988999999


Q ss_pred             eeeecCCCCC
Q psy14921         84 YWAIDYNHTA   93 (148)
Q Consensus        84 ~W~id~~~~~   93 (148)
                      ||+||++++.
T Consensus        89 ~W~l~p~~~~   98 (111)
T 2c6y_A           89 FWRIDPASES   98 (111)
T ss_dssp             EEEECHHHHH
T ss_pred             eEEeChhHHH
Confidence            9999998864

>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=100.00  E-value=2.2e-42  Score=255.70  Aligned_cols=86  Identities=40%  Similarity=0.747  Sum_probs=76.9

Q ss_pred             CCCCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCccccc-----ccccccchhhcccccccccccCCCCCCCC
Q psy14921          7 TGNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREAN-----AGWKNSIRHNLSLNKCFTKVARPKDDPGK   81 (148)
Q Consensus         7 ~~~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~-----~gWknSIRHnLS~n~~F~Kv~r~~~~~gk   81 (148)
                      ..+.||||||++||+|||+++|+++|||+|||+||+++||||+.+.     .|||||||||||+|+||+||+|  +++||
T Consensus         7 ~~n~kPp~SYa~LI~~AI~~sp~~~LTL~eIY~~I~~~fPyyr~~~d~~s~~gWqNSIRHNLSln~~F~Kv~~--~~~GK   84 (117)
T 3coa_C            7 RRNAWGNLSYADLITKAIESSAEKRLTLSQIYEWMVKSVPYFKDKGDSNSSAGWKNSIRHNLSLHSKFIRVQN--EGTGK   84 (117)
T ss_dssp             CCBTTBSCCHHHHHHHHHHTSTTSCBCHHHHHHHHHHHCGGGTTCCSHHHHHHHHHHHHHHHHHCTTEEEECC--SSTTC
T ss_pred             CCCCCCCCCHHHHHHHHHHhCCCCCccHHHHHHHHHHhCcccccCCCCcccccchhccchheecchhhccccc--CCCCC
Confidence            4588999999999999999999999999999999999999999864     7999999999999999999997  46899


Q ss_pred             cceeeecCCCCCC
Q psy14921         82 GSYWAIDYNHTAD   94 (148)
Q Consensus        82 g~~W~id~~~~~~   94 (148)
                      |+||+||+++...
T Consensus        85 g~~W~l~p~~~~~   97 (117)
T 3coa_C           85 SSWWMLNPEGGKS   97 (117)
T ss_dssp             CCEEEECC-----
T ss_pred             cceEEECcccccc
Confidence            9999999998754

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

Probab=100.00  E-value=3e-42  Score=242.30  Aligned_cols=79  Identities=48%  Similarity=0.879  Sum_probs=74.6

Q ss_pred             CCCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccc-----cccccccchhhcccccccccccCCCCCCCCc
Q psy14921          8 GNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREA-----NAGWKNSIRHNLSLNKCFTKVARPKDDPGKG   82 (148)
Q Consensus         8 ~~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~-----~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg   82 (148)
                      .+.||||||++||+|||+++|+++|||+|||+||+++||||+.+     ..|||||||||||+|+||+||+|  +++|||
T Consensus         2 rn~kp~~SY~~LI~~Ai~~sp~~~ltL~eIY~~i~~~fpyy~~~~~~~s~~gWqNSIRHNLSln~~F~Kv~r--~~~GKg   79 (85)
T 3bpy_A            2 RNAWGNQSYAELISQAIESAPEKRLTLAQIYEWMVRTVPYFKDKGDSNSSAGWKNSIRHNLSLHSKFIKVHN--EATGKS   79 (85)
T ss_dssp             CBTTBSCCHHHHHHHHHHHSTTSCBCHHHHHHHHHHHCGGGTTCTTCCTTSHHHHHHHHHHHHCTTEEEECC--CSTTCC
T ss_pred             CCCcCCCCHHHHHHHHHHhCCcCCccHHHHHHHHHHhCcchhcCccCccCCCcchhhhhhccHhhhheeCCC--CCCCCC
Confidence            47899999999999999999999999999999999999999975     46999999999999999999997  468999


Q ss_pred             ceeeec
Q psy14921         83 SYWAID   88 (148)
Q Consensus        83 ~~W~id   88 (148)
                      +||+||
T Consensus        80 ~~W~ld   85 (85)
T 3bpy_A           80 SWWMLN   85 (85)
T ss_dssp             CEEEEC
T ss_pred             CceecC
Confidence            999997

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

Probab=100.00  E-value=1.1e-41  Score=249.62  Aligned_cols=84  Identities=45%  Similarity=0.806  Sum_probs=75.0

Q ss_pred             CCCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccc-----cccccccchhhcccccccccccCCCCCCCCc
Q psy14921          8 GNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREA-----NAGWKNSIRHNLSLNKCFTKVARPKDDPGKG   82 (148)
Q Consensus         8 ~~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~-----~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg   82 (148)
                      .+.||||||++||+|||+++|+++|||+|||+||+++||||+.+     ..|||||||||||+|+||+||+|  +++|||
T Consensus        21 ~~~kPpySY~~LI~~AI~~sp~~~LtL~eIY~~I~~~fPyyr~~~~~~s~~gWqNSIRHNLSln~~F~Kv~r--~~~GKG   98 (110)
T 3l2c_A           21 RNAWGNQSYAELISQAIESAPEKRLTLAQIYEWMVRTVPYFKDKGDSNSSAGWKNSIRHNLSLHSKFIKVHN--EATGKS   98 (110)
T ss_dssp             CBTTBSCCHHHHHHHHHHHSTTSCBCHHHHHHHHHHHCGGGTTCTTCCTTSHHHHHHHHHHHHCTTEEEECC--CSTTCC
T ss_pred             CCCCCCCCHHHHHHHHHHhCCccCcCHHHHHHHHHHhCchhhcCccccCCCCcccchhhhccHhhhheeCCC--CCCCCC
Confidence            47899999999999999999999999999999999999999975     57999999999999999999997  468999


Q ss_pred             ceeeecCCCCC
Q psy14921         83 SYWAIDYNHTA   93 (148)
Q Consensus        83 ~~W~id~~~~~   93 (148)
                      +||+|||+++.
T Consensus        99 ~~W~l~p~~~~  109 (110)
T 3l2c_A           99 SWWMLNPEGGK  109 (110)
T ss_dssp             CEEEEC-----
T ss_pred             ceEEECccccC
Confidence            99999998863

>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=100.00  E-value=4.2e-41  Score=240.03  Aligned_cols=77  Identities=47%  Similarity=0.874  Sum_probs=73.9

Q ss_pred             CCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeeecC
Q psy14921         10 IKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAIDY   89 (148)
Q Consensus        10 ~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~id~   89 (148)
                      .||||||++||+|||+++|+++|||+|||+||+++||||+.+..|||||||||||+|+||+||++     |||+||+||+
T Consensus         2 ~KPp~SY~~LI~~AI~~sp~~~ltL~eIY~~i~~~fpyyr~~~~gWkNSIRHNLSln~~F~kv~~-----gkG~~W~l~~   76 (93)
T 2a07_F            2 VRPPFTYATLIRQAIMESSDRQLTLNEIYSWFTRTFAYFRRNAATWKNAVRHNLSLHKCFVRVEN-----VKGAVWTVDE   76 (93)
T ss_dssp             CCCSCCHHHHHHHHHHHSTTSCBCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCTTBCCEEC-----SSSEECCBCH
T ss_pred             CCCCCCHHHHHHHHHHhCCCCCccHHHHHHHHHHhCCccccCCCccccccceeeehhhceeecCC-----CCCCeeEECh
Confidence            69999999999999999999999999999999999999999999999999999999999999984     8999999998


Q ss_pred             CC
Q psy14921         90 NH   91 (148)
Q Consensus        90 ~~   91 (148)
                      +.
T Consensus        77 ~~   78 (93)
T 2a07_F           77 VE   78 (93)
T ss_dssp             HH
T ss_pred             HH
Confidence            53

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

Probab=100.00  E-value=8.4e-40  Score=248.86  Aligned_cols=87  Identities=39%  Similarity=0.761  Sum_probs=79.0

Q ss_pred             cCCC-CCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCccc-ccccccccchhhcccccccccccCCCCCCCCc
Q psy14921          5 YKTG-NIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYRE-ANAGWKNSIRHNLSLNKCFTKVARPKDDPGKG   82 (148)
Q Consensus         5 y~~~-~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~-~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg   82 (148)
                      +... ..||||||++||+|||+++++++|||+|||+||+++||||+. +..|||||||||||+|+||+|+.   +++|||
T Consensus        11 ~~~~~~~KPpySYa~LI~~AI~~sp~~~LTL~eIY~~I~~~fPyyr~~~~~gWqNSIRHNLSln~~F~r~~---~~~GKg   87 (142)
T 3g73_A           11 WQNSVSERPPYSYMAMIQFAINSTERKRMTLKDIYTWIEDHFPYFKHIAKPGWKNSIRHNLSLHDMFVRET---SANGKV   87 (142)
T ss_dssp             ---CTTSCCSSCHHHHHHHHHHTSTTSEECHHHHHHHHHHHCTHHHHTSCTTHHHHHHHHHHHCTTEEEEE---CTTSCC
T ss_pred             CCccCCCCCCCCHHHHHHHHHHhCCCCCcCHHHHHHHHHHhCCCccccCCCCccchhhhhhhhhhhheecC---CCCCCC
Confidence            4444 779999999999999999999999999999999999999998 89999999999999999999874   568999


Q ss_pred             ceeeecCCCCCC
Q psy14921         83 SYWAIDYNHTAD   94 (148)
Q Consensus        83 ~~W~id~~~~~~   94 (148)
                      +||+||++++..
T Consensus        88 ~~W~i~p~~~~~   99 (142)
T 3g73_A           88 SFWTIHPSANRY   99 (142)
T ss_dssp             EEEEECTTTCCC
T ss_pred             ceEEECcccccc
Confidence            999999999764

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

Probab=93.69  E-value=0.088  Score=36.07  Aligned_cols=33  Identities=15%  Similarity=0.333  Sum_probs=29.0

Q ss_pred             hHHHHHHHHHhhCCCC-CcCHHHHHHHHHhhCCC
Q psy14921         15 SYASLIRLAISNAPQG-RMTLNEIYQFITHTFPY   47 (148)
Q Consensus        15 SYa~LI~~AI~~sp~~-~LtL~eIY~~i~~~fPy   47 (148)
                      +|..||..||.+..++ ..++..|..||+.+|+.
T Consensus         9 ~y~~MI~eAI~alker~GsS~~AIkKyI~~~y~~   42 (88)
T 1uss_A            9 TYKEMILKSMPQLNDGKGSSRIVLKKYVKDTFSS   42 (88)
T ss_dssp             CHHHHHHHHHHHSCCTTSBCHHHHHHHHHHHTTT
T ss_pred             CHHHHHHHHHHHhccCCCcCHHHHHHHHHHhCCC
Confidence            7899999999996665 49999999999999764

>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=93.18  E-value=0.071  Score=35.62  Aligned_cols=33  Identities=21%  Similarity=0.385  Sum_probs=28.7

Q ss_pred             hHHHHHHHHHhhCCCC-CcCHHHHHHHHHhhCCC
Q psy14921         15 SYASLIRLAISNAPQG-RMTLNEIYQFITHTFPY   47 (148)
Q Consensus        15 SYa~LI~~AI~~sp~~-~LtL~eIY~~i~~~fPy   47 (148)
                      +|..||..||.+..++ ..++..|-.||+.+|+.
T Consensus         6 ~y~~MI~eAI~~lker~GsS~~AIkKyI~~~y~~   39 (78)
T 1uhm_A            6 SYRELIIEGLTALKERKGSSRPALKKFIKENYPI   39 (78)
T ss_dssp             CHHHHHHHHHHHHCCSSCEEHHHHHHHHHTTSCT
T ss_pred             CHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCCC
Confidence            7999999999995554 49999999999999774

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

Probab=92.90  E-value=0.11  Score=35.80  Aligned_cols=32  Identities=19%  Similarity=0.365  Sum_probs=28.6

Q ss_pred             hHHHHHHHHHhhCCCC-CcCHHHHHHHHHhhCC
Q psy14921         15 SYASLIRLAISNAPQG-RMTLNEIYQFITHTFP   46 (148)
Q Consensus        15 SYa~LI~~AI~~sp~~-~LtL~eIY~~i~~~fP   46 (148)
                      +|.+||..||.+..++ ..++..|-.||+.+|+
T Consensus         9 ~y~~MI~eAI~~lker~GsS~~AI~KyI~~~y~   41 (90)
T 1hst_A            9 TYSEMIAAAIRAEKSRGGSSRQSIQKYIKSHYK   41 (90)
T ss_dssp             CHHHHHHHHHHTCCCSSCEEHHHHHHHHHHHSC
T ss_pred             CHHHHHHHHHHHhccCCCCCHHHHHHHHHHHcc
Confidence            7899999999996665 4999999999999976

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

Probab=91.33  E-value=0.078  Score=36.21  Aligned_cols=35  Identities=20%  Similarity=0.365  Sum_probs=29.2

Q ss_pred             chHHHHHHHHHhhCCC-CCcCHHHHHHHHHhhCCCc
Q psy14921         14 SSYASLIRLAISNAPQ-GRMTLNEIYQFITHTFPYY   48 (148)
Q Consensus        14 ~SYa~LI~~AI~~sp~-~~LtL~eIY~~i~~~fPyy   48 (148)
                      -+|.+||..||.+..+ +..++..|..||+.+|+-+
T Consensus        10 p~y~~MI~eAI~~Lker~GsS~~AI~KyI~~~y~~~   45 (88)
T 2rqp_A           10 PKMDAILTEAIKACFQKSGASVVAIRKYIIHKYPSL   45 (88)
T ss_dssp             CCHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHCSTH
T ss_pred             CCHHHHHHHHHHHhccCCCcCHHHHHHHHHHhCCCC
Confidence            3789999999998444 3489999999999999844

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

Probab=84.37  E-value=0.21  Score=33.87  Aligned_cols=34  Identities=18%  Similarity=0.187  Sum_probs=28.5

Q ss_pred             CchHHHHHHHHHhhCCCCC-cCHHHHHHHHHhhCC
Q psy14921         13 TSSYASLIRLAISNAPQGR-MTLNEIYQFITHTFP   46 (148)
Q Consensus        13 p~SYa~LI~~AI~~sp~~~-LtL~eIY~~i~~~fP   46 (148)
                      |-+|..||..||.+-.++. -++..|..+|..++.
T Consensus         5 ~~~y~~MI~eAI~aLker~GSS~~AI~K~i~~~~~   39 (83)
T 2lso_A            5 PGKYSQLVVETIRRLGERNGSSLAKIYTEAKKVPW   39 (83)
Confidence            3489999999999865554 899999999999875

---

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	148
d2c6ya1	98	a.4.5.14 (A:1-98) Interleukin enhancer binding fac	9e-36
d1d5va_	94	a.4.5.14 (A:) Adipocyte-transcription factor FREAC	1e-35
d2hdca_	97	a.4.5.14 (A:) Genesis {Rat (Rattus norvegicus) [Ta	2e-35
d1kq8a_	75	a.4.5.14 (A:) HFH-1 (HNF-3 forkhead homolog-1) {Ra	4e-34
d3bpya1	85	a.4.5.14 (A:93-177) Afx (Foxo4) {Human (Homo sapie	5e-32
d2a07f1	82	a.4.5.14 (F:503-584) Forkhead box protein P2, FOXP	2e-30

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

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]

 Score =  117 bits (294), Expect = 9e-36
 Identities = 46/80 (57%), Positives = 58/80 (72%)

Query: 9  NIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKC 68
          + K   SYA LI  AI+ AP  ++TLN IY  IT  +PYYR A+ GW+NSIRHNLSLN+ 
Sbjct: 1  DSKPPYSYAQLIVQAITMAPDKQLTLNGIYTHITKNYPYYRTADKGWQNSIRHNLSLNRY 60

Query: 69 FTKVARPKDDPGKGSYWAID 88
          F KV R +++PGKGS+W ID
Sbjct: 61 FIKVPRSQEEPGKGSFWRID 80

>d1d5va_ a.4.5.14 (A:) Adipocyte-transcription factor FREAC-11 (s12, fkh-14) {Human (Homo sapiens) [TaxId: 9606]} Length = 94

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]

 Score =  116 bits (292), Expect = 1e-35
 Identities = 49/89 (55%), Positives = 62/89 (69%), Gaps = 2/89 (2%)

Query: 10 IKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCF 69
          +K   SY +LI +AI NAP+ ++TLN IYQFI   FP+YRE   GW+NSIRHNLSLN+CF
Sbjct: 3  VKPPYSYIALITMAIQNAPEKKITLNGIYQFIMDRFPFYRENKQGWQNSIRHNLSLNECF 62

Query: 70 TKVARPKDDPGKGSYWAID--YNHTADDG 96
           KV R    PGKGSYW +D    +  ++G
Sbjct: 63 VKVPRDDKKPGKGSYWTLDPDSYNMFENG 91

>d2hdca_ a.4.5.14 (A:) Genesis {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 97

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]

 Score =  116 bits (291), Expect = 2e-35
 Identities = 45/96 (46%), Positives = 63/96 (65%), Gaps = 2/96 (2%)

Query: 10  IKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCF 69
           +K   SY +LI +AI  +PQ ++TL+ I +FI++ FPYYRE    W+NSIRHNLSLN CF
Sbjct: 1   VKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDCF 60

Query: 70  TKVARPKDDPGKGSYWAID--YNHTADDGPSKKKVK 103
            K+ R   +PGKG+YW +D       D+G   ++ K
Sbjct: 61  VKIPREPGNPGKGNYWTLDPQSEDMFDNGSFLRRRK 96

>d1kq8a_ a.4.5.14 (A:) HFH-1 (HNF-3 forkhead homolog-1) {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 75

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]

 Score =  112 bits (281), Expect = 4e-34
 Identities = 35/74 (47%), Positives = 51/74 (68%), Gaps = 1/74 (1%)

Query: 16 YASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARP 75
          Y +LI +AI ++  GR+TL EI +++   FP++R +  GW+NS+RHNLSLN CF KV R 
Sbjct: 1  YIALITMAIRDSAGGRLTLAEINEYLMGKFPFFRGSYTGWRNSVRHNLSLNDCFVKVLRD 60

Query: 76 KDDP-GKGSYWAID 88
             P GK +YW ++
Sbjct: 61 PSRPWGKDNYWMLN 74

>d3bpya1 a.4.5.14 (A:93-177) Afx (Foxo4) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

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]

 Score =  107 bits (268), Expect = 5e-32
 Identities = 38/85 (44%), Positives = 55/85 (64%), Gaps = 7/85 (8%)

Query: 9  NIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYRE-----ANAGWKNSIRHNL 63
          N     SYA LI  AI +AP+ R+TL +IY+++  T PY+++     ++AGWKNSIRHNL
Sbjct: 3  NAWGNQSYAELISQAIESAPEKRLTLAQIYEWMVRTVPYFKDKGDSNSSAGWKNSIRHNL 62

Query: 64 SLNKCFTKVARPKDDPGKGSYWAID 88
          SL+  F KV    +  GK S+W ++
Sbjct: 63 SLHSKFIKV--HNEATGKSSWWMLN 85

>d2a07f1 a.4.5.14 (F:503-584) Forkhead box protein P2, FOXP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 82

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]

 Score =  102 bits (257), Expect = 2e-30
 Identities = 36/79 (45%), Positives = 52/79 (65%), Gaps = 5/79 (6%)

Query: 10 IKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCF 69
          ++   +YA+LIR AI  +   ++TLNEIY + T TF Y+R   A WKN++RHNLSL+KCF
Sbjct: 1  VRPPFTYATLIRQAIMESSDRQLTLNEIYSWFTRTFAYFRRNAATWKNAVRHNLSLHKCF 60

Query: 70 TKVARPKDDPGKGSYWAID 88
           +V     +  KG+ W +D
Sbjct: 61 VRV-----ENVKGAVWTVD 74

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	148
d2c6ya1	98	Interleukin enhancer binding factor {Human (Homo s	100.0
d2hdca_	97	Genesis {Rat (Rattus norvegicus) [TaxId: 10116]}	100.0
d1d5va_	94	Adipocyte-transcription factor FREAC-11 (s12, fkh-	100.0
d1kq8a_	75	HFH-1 (HNF-3 forkhead homolog-1) {Rat (Rattus norv	100.0
d2a07f1	82	Forkhead box protein P2, FOXP2 {Human (Homo sapien	100.0
d3bpya1	85	Afx (Foxo4) {Human (Homo sapiens) [TaxId: 9606]}	100.0
d1ussa_	88	Histone H1 homologue Hho1p {Baker's yeast (Sacchar	95.86
d1hsta_	74	Histone H5, globular domain {Chicken (Gallus gallu	95.79
d1usta_	92	Histone H1 homologue Hho1p {Baker's yeast (Sacchar	95.61
d1ghca_	75	Histone H1, globular domain {Chicken (Gallus gallu	90.64

>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=100.00  E-value=1.5e-45  Score=263.44  Aligned_cols=86  Identities=53%  Similarity=0.934  Sum_probs=82.8

Q ss_pred             CCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeeec
Q psy14921          9 NIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAID   88 (148)
Q Consensus         9 ~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~id   88 (148)
                      +.||||||++||+|||+++|+++|||+|||+||+++||||+.+..|||||||||||+|+||+||+|+.+++|||+||+||
T Consensus         1 ~~KP~~sY~~LI~~Ai~~sp~~~ltL~eIy~~i~~~fpyfr~~~~gWkNSIRHnLS~n~~F~kv~r~~~~~gKg~~W~l~   80 (98)
T d2c6ya1           1 DSKPPYSYAQLIVQAITMAPDKQLTLNGIYTHITKNYPYYRTADKGWQNSIRHNLSLNRYFIKVPRSQEEPGKGSFWRID   80 (98)
T ss_dssp             CCCCSSCHHHHHHHHHHTSTTSCEEHHHHHHHHHHHCTTSCTTCHHHHHHHHHHHHHSTTEEEECCCTTSCCSSCEEEEC
T ss_pred             CCCCCccHHHHHHHHHHhCCCCCccHHHHHHHHHHhCcccccCCCCcchhhchhcccccceEeccCCCCCCCCCceEEEC
Confidence            57999999999999999999999999999999999999999999999999999999999999999998999999999999


Q ss_pred             CCCCCC
Q psy14921         89 YNHTAD   94 (148)
Q Consensus        89 ~~~~~~   94 (148)
                      |++..+
T Consensus        81 p~~~~~   86 (98)
T d2c6ya1          81 PASESK   86 (98)
T ss_dssp             HHHHHH
T ss_pred             ccHHhh
Confidence            987754

>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=100.00  E-value=1.2e-44  Score=258.33  Aligned_cols=84  Identities=50%  Similarity=0.959  Sum_probs=81.6

Q ss_pred             CCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeeecC
Q psy14921         10 IKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAIDY   89 (148)
Q Consensus        10 ~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~id~   89 (148)
                      .||||||++||++||+++|+++|||+|||+||+++||||+.+..|||||||||||+|+||+||+|+.+++|||+||+||+
T Consensus         1 vKPp~sY~~LI~~Ai~~sp~~~ltL~eIY~~i~~~fpyfr~~~~gWkNSIRHnLSln~~F~kv~~~~~~~gKg~~W~l~p   80 (97)
T d2hdca_           1 VKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDP   80 (97)
T ss_dssp             CCCCCCHHHHHHHHHHTCTTTCBCHHHHHHHHHHHCHHHHHHCSSHHHHHHHHHHHHHCCEEECSCTTCSSSCCEEECCT
T ss_pred             CCCCCcHHHHHHHHHHhCCCcCccHHHHHHHHHHhCccccCCCCCchhhhhhhcchhhhhcccCCCCCCCCCCcEEEECc
Confidence            59999999999999999999999999999999999999999999999999999999999999999988899999999999


Q ss_pred             CCCC
Q psy14921         90 NHTA   93 (148)
Q Consensus        90 ~~~~   93 (148)
                      ++..
T Consensus        81 ~~~~   84 (97)
T d2hdca_          81 QSED   84 (97)
T ss_dssp             THHH
T ss_pred             cHHH
Confidence            9875

>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=100.00  E-value=1.6e-43  Score=251.24  Aligned_cols=87  Identities=55%  Similarity=0.983  Sum_probs=83.8

Q ss_pred             CCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeeecC
Q psy14921         10 IKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAIDY   89 (148)
Q Consensus        10 ~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~id~   89 (148)
                      .||||||++||++||+++|+++|||+|||+||+++||||+.+..|||||||||||+|+||+||+|..+++|||+||+|++
T Consensus         3 ~KP~~SYa~LI~~AI~~sp~~~ltL~eIY~~i~~~fpyfr~~~~gWkNSIRHnLSln~~F~kv~~~~~~~gkg~~W~l~p   82 (94)
T d1d5va_           3 VKPPYSYIALITMAIQNAPEKKITLNGIYQFIMDRFPFYRENKQGWQNSIRHNLSLNECFVKVPRDDKKPGKGSYWTLDP   82 (94)
T ss_dssp             CCCSSCHHHHHHHHHHTCSSSSBCHHHHHHHHHHHCTHHHHCCTTHHHHHHHHHHHCSSEEECCCCTTSCSCCCCEEECC
T ss_pred             CCCCCCHHHHHHHHHHhCCCCCccHHHHHHHHHHHCCccCccccchHHHHHHHccccceEEEcCcCCCCCCCCceEEECc
Confidence            69999999999999999999999999999999999999999999999999999999999999999988899999999999


Q ss_pred             CCCCCCC
Q psy14921         90 NHTADDG   96 (148)
Q Consensus        90 ~~~~~~~   96 (148)
                      ++.....
T Consensus        83 ~~~~~f~   89 (94)
T d1d5va_          83 DSYNMFE   89 (94)
T ss_dssp             SCSSTTS
T ss_pred             cHHHHHh
Confidence            9987643

>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=100.00  E-value=1.6e-40  Score=227.02  Aligned_cols=74  Identities=47%  Similarity=0.996  Sum_probs=71.8

Q ss_pred             HHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCC-CCcceeeecC
Q psy14921         16 YASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDP-GKGSYWAIDY   89 (148)
Q Consensus        16 Ya~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~-gkg~~W~id~   89 (148)
                      |++||+|||+++|+++|||+|||+||+++||||+.+..|||||||||||+|+||+||+|+.+++ |||+||+|||
T Consensus         1 Y~~LI~~Ai~~sp~~~ltL~eIy~~i~~~fpy~r~~~~gWkNSIRHnLS~n~~F~kv~r~~~~~~gKg~~W~l~P   75 (75)
T d1kq8a_           1 YIALITMAIRDSAGGRLTLAEINEYLMGKFPFFRGSYTGWRNSVRHNLSLNDCFVKVLRDPSRPWGKDNYWMLNP   75 (75)
T ss_dssp             CHHHHHHHHTTSSSSCBCHHHHHHHHHHHCTTGGGTCSCCHHHHHHHHHHHTCCEECSSCSCCSSSCCCCEECCC
T ss_pred             CHHHHHHHHHhCCCCCccHHHHHHHHHHhCcccccCCccchhHhhecccccceeEecCCCCCCCCCCccEEEeCc
Confidence            8999999999999999999999999999999999999999999999999999999999987776 9999999997

>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=100.00  E-value=1.1e-40  Score=231.25  Aligned_cols=76  Identities=47%  Similarity=0.884  Sum_probs=73.2

Q ss_pred             CCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccccccccccchhhcccccccccccCCCCCCCCcceeeecC
Q psy14921         10 IKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREANAGWKNSIRHNLSLNKCFTKVARPKDDPGKGSYWAIDY   89 (148)
Q Consensus        10 ~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg~~W~id~   89 (148)
                      .||||||++||++||+++|+++|||+|||+||+++||||+.+.+|||||||||||+|+||+||++     |||+||+||+
T Consensus         1 vKP~~sY~~LI~~Ai~~sp~~~LtL~eIy~~i~~~fpyyr~~~~gWkNSIRHnLS~n~~F~kv~~-----~kG~~W~i~~   75 (82)
T d2a07f1           1 VRPPFTYATLIRQAIMESSDRQLTLNEIYSWFTRTFAYFRRNAATWKNAVRHNLSLHKCFVRVEN-----VKGAVWTVDE   75 (82)
T ss_dssp             CCCSCCHHHHHHHHHHHSTTSCBCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCTTBCCEEC-----SSSEECCBCH
T ss_pred             CcCCCcHHHHHHHHHHhCCCCCccHHHHHHHHHHhCcccccCCcccchhHhHhcccccceEeCCC-----CCCCEEEECH
Confidence            59999999999999999999999999999999999999999999999999999999999999984     8999999987


Q ss_pred             C
Q psy14921         90 N   90 (148)
Q Consensus        90 ~   90 (148)
                      +
T Consensus        76 ~   76 (82)
T d2a07f1          76 V   76 (82)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=100.00  E-value=1.5e-39  Score=226.92  Aligned_cols=79  Identities=48%  Similarity=0.865  Sum_probs=73.6

Q ss_pred             CCCCCCchHHHHHHHHHhhCCCCCcCHHHHHHHHHhhCCCcccc-----cccccccchhhcccccccccccCCCCCCCCc
Q psy14921          8 GNIKCTSSYASLIRLAISNAPQGRMTLNEIYQFITHTFPYYREA-----NAGWKNSIRHNLSLNKCFTKVARPKDDPGKG   82 (148)
Q Consensus         8 ~~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~i~~~fPyyr~~-----~~gWknSIRHnLS~n~~F~Kv~r~~~~~gkg   82 (148)
                      .+.+|++||++||++||+++|+++|||+|||+||+++|||||..     ..|||||||||||+|+||+||+|+  .+|||
T Consensus         2 ~n~~~~~SY~~LI~~Ai~~sp~~~ltL~eIY~~i~~~fPyyr~~~~~~~~~gWkNSIRHnLSl~~~F~kv~r~--~~gKg   79 (85)
T d3bpya1           2 RNAWGNQSYAELISQAIESAPEKRLTLAQIYEWMVRTVPYFKDKGDSNSSAGWKNSIRHNLSLHSKFIKVHNE--ATGKS   79 (85)
T ss_dssp             CBTTBSCCHHHHHHHHHHHSTTSCBCHHHHHHHHHHHCGGGTTCTTCCTTSHHHHHHHHHHHHCTTEEEECCC--STTCC
T ss_pred             CCCCCCcCHHHHHHHHHHhCCCCCccHHHHHHHHHHhChhhhccCcccccccchhhHHHHhhHhhheeeCCCC--CCCCC
Confidence            47899999999999999999999999999999999999999953     468999999999999999999975  47999


Q ss_pred             ceeeec
Q psy14921         83 SYWAID   88 (148)
Q Consensus        83 ~~W~id   88 (148)
                      +||+||
T Consensus        80 ~~W~i~   85 (85)
T d3bpya1          80 SWWMLN   85 (85)
T ss_dssp             CEEEEC
T ss_pred             ceeecC
Confidence            999997

>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=95.86  E-value=0.0051  Score=40.84  Aligned_cols=35  Identities=11%  Similarity=0.235  Sum_probs=30.9

Q ss_pred             CchHHHHHHHHHhhCCC-CCcCHHHHHHHHHhhCCC
Q psy14921         13 TSSYASLIRLAISNAPQ-GRMTLNEIYQFITHTFPY   47 (148)
Q Consensus        13 p~SYa~LI~~AI~~sp~-~~LtL~eIY~~i~~~fPy   47 (148)
                      -.||..||..||.+..+ +..++..|-.||+.+||.
T Consensus         7 ~~sy~~MI~eAI~~L~er~GsS~~aI~KyI~~~y~~   42 (88)
T d1ussa_           7 SLTYKEMILKSMPQLNDGKGSSRIVLKKYVKDTFSS   42 (88)
T ss_dssp             SCCHHHHHHHHHHHSCCTTSBCHHHHHHHHHHHTTT
T ss_pred             CCCHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCCc
Confidence            46899999999999655 559999999999999986

>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=95.79  E-value=0.0046  Score=39.67  Aligned_cols=33  Identities=18%  Similarity=0.343  Sum_probs=29.0

Q ss_pred             hHHHHHHHHHhhCCCCC-cCHHHHHHHHHhhCCC
Q psy14921         15 SYASLIRLAISNAPQGR-MTLNEIYQFITHTFPY   47 (148)
Q Consensus        15 SYa~LI~~AI~~sp~~~-LtL~eIY~~i~~~fPy   47 (148)
                      +|..||..||.+..++. .++..|..||+.+|+-
T Consensus         4 ~y~~MI~eAI~al~er~GsS~~AI~kyI~~~y~~   37 (74)
T d1hsta_           4 TYSEMIAAAIRAEKSRGGSSRQSIQKYIKSHYKV   37 (74)
T ss_dssp             CHHHHHHHHHHTCCCSSCEEHHHHHHHHHHHSCC
T ss_pred             CHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCCC
Confidence            58899999999976654 9999999999999974

>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=95.61  E-value=0.004  Score=41.66  Aligned_cols=34  Identities=21%  Similarity=0.411  Sum_probs=29.8

Q ss_pred             chHHHHHHHHHhhCCCCC-cCHHHHHHHHHhhCCC
Q psy14921         14 SSYASLIRLAISNAPQGR-MTLNEIYQFITHTFPY   47 (148)
Q Consensus        14 ~SYa~LI~~AI~~sp~~~-LtL~eIY~~i~~~fPy   47 (148)
                      -||..||..||.+..++. .++..|..||+.+||-
T Consensus         7 pty~~MI~eAI~~l~er~GsS~~aI~KyI~~~y~~   41 (92)
T d1usta_           7 KSYRELIIEGLTALKERKGSSRPALKKFIKENYPI   41 (92)
T ss_dssp             CCHHHHHHHHHTTTTTTSCEEHHHHHHHHHHHCHH
T ss_pred             CCHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHCcC
Confidence            479999999999965554 9999999999999984

>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=90.64  E-value=0.013  Score=37.62  Aligned_cols=31  Identities=19%  Similarity=0.250  Sum_probs=27.1

Q ss_pred             hHHHHHHHHHhhCCCCC-cCHHHHHHHHHhhC
Q psy14921         15 SYASLIRLAISNAPQGR-MTLNEIYQFITHTF   45 (148)
Q Consensus        15 SYa~LI~~AI~~sp~~~-LtL~eIY~~i~~~f   45 (148)
                      +|..||..||.+..+++ .++..|..||+.++
T Consensus         5 ~y~~MI~eAI~al~er~GsS~~AI~kyI~~~~   36 (75)
T d1ghca_           5 SVTELITKAVSASKERKGLSLAALKKALAAGG   36 (75)
T ss_dssp             SHHHHHHHHHHHCSSSSCCTTSSGGGSSSSSS
T ss_pred             CHHHHHHHHHHHcCCCCCcCHHHHHHHHHHhc
Confidence            69999999999965555 99999999999875