Psyllid ID: psy9499

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------29
Protein Sequence
MEDSGRLYLGFHHSPHLLPQPHHTGPRTSFDSPLDLRGAPHPGDMCNLSSPSPSSEDDSDADINVESDDGDEQGMSNVRRNIAEFHKHFSNCESDVNGCPTDGSISPGPEGDSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDFLLRDPHAAAMASFLGSDPYHHGLLPHSLQHGGFSFMSPLPPAVPLLPPSELVVQSISLCLRS
Secondary Structure (PSIPRED)
ccccccEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHccccccccHHHHHHHHHHcccccccccccHHHHHHccccccccEEccccccccccccccccccccccccccccccHHHHHccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHccHHHHccHHHHHHHHccccccccEEEEcccccccccccEEEEccccccccccccHHHHHHccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcc
Coil and Loop (DISEMBL)
medsgrlylgfhhsphllpqphhtgprtsfdspldlrgaphpgdmcnlsspspsseddsdadinvesddgdeqgMSNVRRNIAEFHKHFsncesdvngcptdgsispgpegdsdkqdgknsivkppySYIALITMAILqsphkkltlSGICEFImsrfpyyrekfpawqnsirhnlslndcfvkiprepgnpgkgnywtldpmaedmfdngsflrrrkrykrtppdfllrdpHAAAMASflgsdpyhhgllphslqhggfsfmsplppavpllppselVVQSISLCLRS
Flexible Loop (DISEMBL)
MEDSGRLYLGFHHSPHLLPQPHHTGPRTSFDSPLDLRGAPHPGDMCNLSSPSPSSEDDSDADINVESDDGDEQGMSNVRRNIAEFHKHFSNCESDVNGCPTDGSISPGpegdsdkqdgknSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDFLLRDPHAAAMASFLGSDPYHHGLLPHSLQHGGFSFMSPLPPAVPLLPPSELVVQSISLCLRS
Low Complexity Region (SEG)
MEDSGRLYLGFhhsphllpqphhTGPRTSFDSPLDLRGAPHPGDMCNLsspspsseddsdadINVESDDGDEQGMSNVRRNIAEFHKHFSNCESDVNGCPTDGSISPGPEGDSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDFLLRDPHAAAMASFLGSDPYHHGLLPHSLQHGGFSFMsplppavpllppselvvqsISLCLRS
Disordered region (IsUnstruct)
**************************************************************************************************************************VKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPRE****GKGNYWTLDPMAEDMFDNGSFLRR*********DFLLRDPHAAAMASFLGSDPYHHGLLPHSLQHGGFSFMSPLPPAVPLLP*SELVVQSISLC***
Disordered Region (DISOPRED)
****GRL***FH*******************************************************************************************************************SYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFL**********************************************************************L****
Disordered Region (DISEMBL)
MEDSGRLYLGFHHSPHLLPQPHHTGPRTSFDSPLDLRGAPHPGDMCN**************DINVESDDGDEQGMSNVRRNIAEFHKHFSNCESDVNGCPTDGSI************GKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDFLLRDPHAAAMASFLGSDPYHHGLLPHSLQHGGFSFMSPLPPAVPLLPPSELVVQSISLCLRS
Disordered Region (DISPRO)
***SGRLYLGFHHSPHLLPQPHHTGP********************************************************************************************KNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKR*******************************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MEDSGRLYLGFHHSPHLLPQPHHTGPRTSFDSPLDLRGAPHPGDMCNLSSPSPSSEDDSDADINVESDDGDEQGMSNVRRNIAEFHKHFSNCESDVNGCPTDGSISPGPEGDSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDFLLRDPHAAAMASFLGSDPYHHGLLPHSLQHGGFSFMSPLPPAVPLLPPSELVVQSISLCLRS
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	289	2.2.26 [Sep-21-2011]
Q9DEN3	371	Forkhead box protein D3-B	N/A	N/A	0.761	0.592	0.574	5e-57
Q9DEN4	371	Forkhead box protein D3-A	N/A	N/A	0.809	0.630	0.544	6e-57
Q5M7L9	369	Forkhead box protein D3 O	yes	N/A	0.764	0.598	0.578	2e-56
Q02361	456	Fork head domain-containi	yes	N/A	0.356	0.225	0.912	4e-55
P79772	394	Forkhead box protein D3 O	yes	N/A	0.550	0.403	0.691	7e-51
Q90WN4	346	Forkhead box protein D2 O	N/A	N/A	0.723	0.604	0.548	9e-50
Q61060	465	Forkhead box protein D3 O	yes	N/A	0.325	0.202	0.936	2e-49
Q9UJU5	478	Forkhead box protein D3 O	yes	N/A	0.325	0.196	0.936	4e-49
Q12950	439	Forkhead box protein D4 O	no	N/A	0.429	0.282	0.728	7e-49
Q61345	456	Forkhead box protein D1 O	no	N/A	0.411	0.260	0.837	5e-48

>sp|Q9DEN3|FXD3B_XENLA Forkhead box protein D3-B OS=Xenopus laevis GN=foxd3-b PE=2 SV=1

 Score =  221 bits (563), Expect = 5e-57,   Method: Compositional matrix adjust.
 Identities = 142/247 (57%), Positives = 160/247 (64%), Gaps = 27/247 (10%)

Query: 55  SEDDSDADINVESD---DGDEQGMSNV-------RRNIAEFHKHFSNCESDVNGCPTDGS 104
           S DD+D D+  E D   D D +  S V            E  +  S   +D  G     S
Sbjct: 19  SADDADIDVVGEGDEALDKDSECESPVGHHDEVDALGGKEIPRSPSGSSTDAEG--KGES 76

Query: 105 ISPGPEGDSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREK 164
                EG  +K   KNS+VKPPYSYIALITM+ILQSP KKLTLSGICEFI SRFPYYREK
Sbjct: 77  QQQQQEGIQNKP--KNSVVKPPYSYIALITMSILQSPQKKLTLSGICEFISSRFPYYREK 134

Query: 165 FPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTP 224
           FPAWQNSIRHNLSLNDCF+KIPREPGNPGKGNYWTLDP +EDMFDNGSFLRRRKR+KR  
Sbjct: 135 FPAWQNSIRHNLSLNDCFIKIPREPGNPGKGNYWTLDPQSEDMFDNGSFLRRRKRFKRQQ 194

Query: 225 PDFLLRDPHAAAMASFLG---SDPY--HHGLLPHSLQHGG---FSFMSP----LPPAVPL 272
            D  LR+  A  M SF     + PY  H+GL P +  H     + ++ P    LPPAVPL
Sbjct: 195 QD-TLREQTALMMQSFGAYSLASPYGRHYGLHPAAYTHPAALQYPYIPPVGPMLPPAVPL 253

Query: 273 LPPSELV 279
           LP SEL 
Sbjct: 254 LPSSELT 260

Transcriptional repressor that is an essential upstream regulator of neural crest determination and mesoderm induction. Functions by recruiting the transcriptional corepressor tle4. Also acts in a negative auto-regulator loop by inhibiting the transcription of its own gene.
Xenopus laevis (taxid: 8355)

>sp|Q9DEN4|FXD3A_XENLA Forkhead box protein D3-A OS=Xenopus laevis GN=foxd3-a PE=1 SV=1

 Score =  221 bits (562), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 140/257 (54%), Positives = 164/257 (63%), Gaps = 23/257 (8%)

Query: 43  GDMCNLSSPSPSSEDDSDADINVESD-----DGDEQGMSNVRRNIAEFHKHFSNCESDVN 97
           G   ++S  +  S DD+D D+  E D     D + +  +     + E            +
Sbjct: 7   GSASDMSGQTVLSADDADIDVVGEGDEALDKDSECESTAGHTDEVGELGGKEIPRSPSGS 66

Query: 98  GCPTDG---SISPGPEGDSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFI 154
           G   +G   S     EG  +K   KNS+VKPPYSYIALITM+ILQSP KKLTLSGICEFI
Sbjct: 67  GTEAEGKGESQQQQQEGIQNKP--KNSLVKPPYSYIALITMSILQSPQKKLTLSGICEFI 124

Query: 155 MSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFL 214
            +RFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDP +EDMFDNGSFL
Sbjct: 125 SNRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPQSEDMFDNGSFL 184

Query: 215 RRRKRYKRTPPDFLLRDPHAAAMASFLG---SDPY--HHGLLPHSLQHGG---FSFMSP- 265
           RRRKR+KR   D  LR+  A  M SF     + PY  H+GL P +  H     + ++ P 
Sbjct: 185 RRRKRFKRQQQDS-LREQTALMMQSFGAYSLASPYGRHYGLHPAAYTHPAALQYPYIPPV 243

Query: 266 ---LPPAVPLLPPSELV 279
              LPPAVPLLP SEL 
Sbjct: 244 GHMLPPAVPLLPSSELT 260

Transcriptional repressor that is an essential upstream regulator of neural crest determination and mesoderm induction. Functions by recruiting the transcriptional corepressor tle4. Also acts in a negative auto-regulator loop by inhibiting the transcription of its own gene.

Xenopus laevis (taxid: 8355)

>sp|Q5M7L9|FOXD3_XENTR Forkhead box protein D3 OS=Xenopus tropicalis GN=foxd3 PE=2 SV=1

 Score =  219 bits (557), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 140/242 (57%), Positives = 162/242 (66%), Gaps = 21/242 (8%)

Query: 55  SEDDSDADINVESDDG-DEQGMSNVRRNIAEFHKHFSNCESDVNGCPTDGSISPGPEGDS 113
           S DD+D D+  E D+  D+          AE        E  +   P+  +     +G+S
Sbjct: 19  SADDADIDVVGEGDEPLDKDSECGSPAGHAEEADELGGKE--IARSPSGSANEAEGKGES 76

Query: 114 DKQDG-----KNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAW 168
            +Q+G     KNS+VKPPYSYIALITMAILQSP KKLTLSGICEFI +RFPYYREKFPAW
Sbjct: 77  QQQEGMQNKPKNSLVKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAW 136

Query: 169 QNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDFL 228
           QNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDP +EDMFDNGSFLRRRKR+KR  PD  
Sbjct: 137 QNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPQSEDMFDNGSFLRRRKRFKRQQPDS- 195

Query: 229 LRDPHAAAMASFLG---SDPYH--HGLLPHSLQHGG---FSFMSP----LPPAVPLLPPS 276
           LR+  A  M SF     + PY   +GL P +  H     + ++ P    LPPAVPLLP S
Sbjct: 196 LREQTALMMQSFGAYSLAGPYGRPYGLHPAAYTHPAALQYPYIPPVGPMLPPAVPLLPSS 255

Query: 277 EL 278
           EL
Sbjct: 256 EL 257

Transcriptional repressor that is an essential upstream regulator of neural crest determination. Also acts in a negative auto-regulator loop by inhibiting the transcription of its own gene.

Xenopus tropicalis (taxid: 8364)

>sp|Q02361|FD3_DROME Fork head domain-containing protein FD3 OS=Drosophila melanogaster GN=fd59A PE=2 SV=2

 Score =  215 bits (547), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 94/103 (91%), Positives = 102/103 (99%)

Query: 122 IVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDC 181
           +VKPPYSYIALITMAILQSPHKKLTLSGIC+FIMSRFPYY++KFPAWQNSIRHNLSLNDC
Sbjct: 83  LVKPPYSYIALITMAILQSPHKKLTLSGICDFIMSRFPYYKDKFPAWQNSIRHNLSLNDC 142

Query: 182 FVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTP 224
           F+K+PREPGNPGKGN+WTLDP+AEDMFDNGSFLRRRKRYKR P
Sbjct: 143 FIKVPREPGNPGKGNFWTLDPLAEDMFDNGSFLRRRKRYKRAP 185

Involved in development during embryogenesis.

Drosophila melanogaster (taxid: 7227)

>sp|P79772|FOXD3_CHICK Forkhead box protein D3 OS=Gallus gallus GN=FOXD3 PE=2 SV=1

 Score =  201 bits (510), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 119/172 (69%), Positives = 131/172 (76%), Gaps = 13/172 (7%)

Query: 119 KNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSL 178
           K+S+VKPPYSYIALITMAILQSP KKLTLSGICEFI +RFPYYREKFPAWQNSIRHNLSL
Sbjct: 112 KSSLVKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSL 171

Query: 179 NDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDFLLRDPHAAAMA 238
           NDCFVKIPREPGNPGKGNYWTLDP +EDMFDNGSFLRRRKR+KR   +  LRD  A  M 
Sbjct: 172 NDCFVKIPREPGNPGKGNYWTLDPQSEDMFDNGSFLRRRKRFKRHQQEH-LRDQTALMMQ 230

Query: 239 SFLG---SDPYH--HGLLPHSLQHGG---FSFMSP----LPPAVPLLPPSEL 278
            F     + PY   +GL P +  H     + ++ P    LPPA PLLP  EL
Sbjct: 231 GFGAYGLAGPYGRPYGLPPGAYPHPAALQYPYIPPVGPMLPPACPLLPSGEL 282

Binds to the consensus sequence 5'-A[AT]T[AG]TTTGTTT-3' and acts as a transcriptional repressor. Also acts as a transcriptional activator. Promotes development of neural crest cells from neural tube progenitors. Restricts neural progenitor cells to the neural crest lineage while suppressing interneuron differentiation. Required for maintenance of pluripotent cells in the pre-implantation and peri-implantation stages of embryogenesis.

Gallus gallus (taxid: 9031)

>sp|Q90WN4|FOXD2_XENLA Forkhead box protein D2 OS=Xenopus laevis GN=foxd2 PE=2 SV=1

 Score =  197 bits (500), Expect = 9e-50,   Method: Compositional matrix adjust.
 Identities = 125/228 (54%), Positives = 152/228 (66%), Gaps = 19/228 (8%)

Query: 60  DADINVESDDGDEQGMSNVRRNIAEFHKHFSNCESDVN------GCPTDGSISPGPEGDS 113
           D DI+V  D G + G         ++  + S+ +SD N      G P    +S G E + 
Sbjct: 16  DTDIDVVGDMGAKDG---------KYSDYHSDNDSDDNVARTPRGDPASPDLSSGSESNQ 66

Query: 114 DKQDG-KNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSI 172
             +   KN++VKPPYSYIALITM+ILQSP K+LTLS ICEFI +RFPYYREKFPAWQNSI
Sbjct: 67  RAEKSPKNALVKPPYSYIALITMSILQSPKKRLTLSEICEFISNRFPYYREKFPAWQNSI 126

Query: 173 RHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDFLLRDP 232
           RHNLSLNDCFVKIPREPGNPGKGNYWTLDP + DMFDNGSFLRRRKR+KR   + +LRDP
Sbjct: 127 RHNLSLNDCFVKIPREPGNPGKGNYWTLDPESADMFDNGSFLRRRKRFKRQQSNEILRDP 186

Query: 233 HAAAMASFLGSDPYHHGLLP--HSLQHGGFSFMSPLPPAVPLLPPSEL 278
            +   A+F      ++  L   +  QH G +F S  P   PL PP+ +
Sbjct: 187 SSFMPAAFGYGPYGYNYGLQLHNYQQHPGATF-SFQPSHCPLPPPASV 233

Probable transcription factor.

Xenopus laevis (taxid: 8355)

>sp|Q61060|FOXD3_MOUSE Forkhead box protein D3 OS=Mus musculus GN=Foxd3 PE=2 SV=3

 Score =  196 bits (497), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 88/94 (93%), Positives = 91/94 (96%)

Query: 119 KNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSL 178
           KNS+VKPPYSYIALITMAILQSP KKLTLSGICEFI +RFPYYREKFPAWQNSIRHNLSL
Sbjct: 126 KNSLVKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSL 185

Query: 179 NDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGS 212
           NDCFVKIPREPGNPGKGNYWTLDP +EDMFDNGS
Sbjct: 186 NDCFVKIPREPGNPGKGNYWTLDPQSEDMFDNGS 219

Binds to the consensus sequence 5'-A[AT]T[AG]TTTGTTT-3' and acts as a transcriptional repressor. Also acts as a transcriptional activator. Promotes development of neural crest cells from neural tube progenitors. Restricts neural progenitor cells to the neural crest lineage while suppressing interneuron differentiation. Required for maintenance of pluripotent cells in the pre-implantation and peri-implantation stages of embryogenesis.

Mus musculus (taxid: 10090)

>sp|Q9UJU5|FOXD3_HUMAN Forkhead box protein D3 OS=Homo sapiens GN=FOXD3 PE=1 SV=1

 Score =  194 bits (494), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 88/94 (93%), Positives = 91/94 (96%)

Query: 119 KNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSL 178
           KNS+VKPPYSYIALITMAILQSP KKLTLSGICEFI +RFPYYREKFPAWQNSIRHNLSL
Sbjct: 136 KNSLVKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSL 195

Query: 179 NDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGS 212
           NDCFVKIPREPGNPGKGNYWTLDP +EDMFDNGS
Sbjct: 196 NDCFVKIPREPGNPGKGNYWTLDPQSEDMFDNGS 229

Binds to the consensus sequence 5'-A[AT]T[AG]TTTGTTT-3' and acts as a transcriptional repressor. Also acts as a transcriptional activator. Promotes development of neural crest cells from neural tube progenitors. Restricts neural progenitor cells to the neural crest lineage while suppressing interneuron differentiation. Required for maintenance of pluripotent cells in the pre-implantation and peri-implantation stages of embryogenesis.

Homo sapiens (taxid: 9606)

>sp|Q12950|FOXD4_HUMAN Forkhead box protein D4 OS=Homo sapiens GN=FOXD4 PE=2 SV=4

 Score =  194 bits (492), Expect = 7e-49,   Method: Compositional matrix adjust.
 Identities = 91/125 (72%), Positives = 100/125 (80%), Gaps = 1/125 (0%)

Query: 109 PEGDSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAW 168
           P   +  +D +    KPP SYIALITMAILQSPHK+LTLSGIC FI  RFPYYR KFPAW
Sbjct: 90  PRSAAASEDARQP-AKPPSSYIALITMAILQSPHKRLTLSGICAFISDRFPYYRRKFPAW 148

Query: 169 QNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDFL 228
           QNSIRHNLSLNDCFVKIPREPG PGKGNYW+LDP ++DMFDNGSFLRRRKR++R  P   
Sbjct: 149 QNSIRHNLSLNDCFVKIPREPGRPGKGNYWSLDPASQDMFDNGSFLRRRKRFQRHQPTPG 208

Query: 229 LRDPH 233
              PH
Sbjct: 209 AHLPH 213

Homo sapiens (taxid: 9606)

>sp|Q61345|FOXD1_MOUSE Forkhead box protein D1 OS=Mus musculus GN=Foxd1 PE=2 SV=2

 Score =  191 bits (485), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 103/123 (83%), Positives = 107/123 (86%), Gaps = 4/123 (3%)

Query: 119 KNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSL 178
           KN +VKPPYSYIALITMAILQSP K+LTLS ICEFI SRFPYYREKFPAWQNSIRHNLSL
Sbjct: 125 KNPLVKPPYSYIALITMAILQSPKKRLTLSEICEFISSRFPYYREKFPAWQNSIRHNLSL 184

Query: 179 NDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDFLLRDPHAAAMA 238
           NDCFVKIPREPGNPGKGNYWTLDP + DMFDNGSFLRRRKR+KR P    L  PHAAA A
Sbjct: 185 NDCFVKIPREPGNPGKGNYWTLDPESADMFDNGSFLRRRKRFKRQP----LLAPHAAAEA 240

Query: 239 SFL 241
             L
Sbjct: 241 LLL 243

Transcription factor required for formation of positional identity in the developing retina, regionalization of the optic chiasm and morphogenesis of the kidney. Can neuralize ectodermal cells directly.

Mus musculus (taxid: 10090)

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	289
242021691	410	Forkhead box protein D3, putative [Pedic	0.930	0.656	0.547	5e-82
270010909	271	hypothetical protein TcasGA2_TC015957 [T	0.602	0.642	0.681	3e-63
18858703	371	forkhead box protein D3 [Danio rerio] gi	0.792	0.617	0.566	2e-57
63102195	371	Forkhead box D3 [Danio rerio]	0.792	0.617	0.566	3e-57
284005018	388	fork-head box D transcription factor [Sa	0.446	0.332	0.794	6e-57
328709854	561	PREDICTED: hypothetical protein LOC10016	0.415	0.213	0.860	9e-57
238054009	398	forkhead box D3 [Oryzias latipes] gi|226	0.712	0.517	0.579	9e-56
319740954	247	forkhead box d [Patiria miniata]	0.463	0.542	0.766	1e-55
147903421	371	forkhead box protein D3-B [Xenopus laevi	0.761	0.592	0.574	3e-55
405963400	430	Forkhead box protein D3-B [Crassostrea g	0.519	0.348	0.674	4e-55

>gi|242021691|ref|XP_002431277.1| Forkhead box protein D3, putative [Pediculus humanus corporis] gi|212516534|gb|EEB18539.1| Forkhead box protein D3, putative [Pediculus humanus corporis]

 Score =  310 bits (794), Expect = 5e-82,   Method: Compositional matrix adjust.
 Identities = 177/323 (54%), Positives = 210/323 (65%), Gaps = 54/323 (16%)

Query: 1   MEDSGRLYLGF------HHSPHLLPQPHHTGP------RTSFDSPLDLRGAP-------- 40
           M+++GRL +G+        +  +L  P  T P        S +SPLDLRG          
Sbjct: 1   MDETGRLVIGYRDLQQSQTTTPILINPILTVPIRNSEISNSSESPLDLRGNVGGEHLSPM 60

Query: 41  HPGDMCNLSSPSPSSEDDSDADINVESDDGDEQGMSNVRRNIAEFHKHFSN-CESDVNGC 99
            P  +C L+       D  ++D+NV+SDD     +   R  IAEFH+HF+N   +++N  
Sbjct: 61  SPVSVCRLT-------DSEESDVNVDSDDECSPSLMQARHTIAEFHRHFANSLATEMNPN 113

Query: 100 PTDGSISPGPEGDSDKQDG----------------KNSIVKPPYSYIALITMAILQSPHK 143
                  P PE   D+ DG                  ++VKPPYSYIALITMAILQSP K
Sbjct: 114 ------QPSPES-PDQNDGGLDETSPSSPTDSSKKSLALVKPPYSYIALITMAILQSPRK 166

Query: 144 KLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPM 203
           KLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCF+KIPREPGNPGKGNYWTLDPM
Sbjct: 167 KLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFIKIPREPGNPGKGNYWTLDPM 226

Query: 204 AEDMFDNGSFLRRRKRYKRTPPDFLLRDPHAAAMASFLG-SDPYHHGLL--PHSLQHGGF 260
           AEDMFDNGSFLRRRKRYKR PPDF+LR+ HAAAM+ FLG SDPYHH  L   H   H  +
Sbjct: 227 AEDMFDNGSFLRRRKRYKRQPPDFVLREHHAAAMSQFLGSSDPYHHASLLGSHPALHNPY 286

Query: 261 SFMSPLPPAVPLLPPSELVVQSI 283
            ++SPLPPA+PLL P+EL   S+
Sbjct: 287 QYLSPLPPAIPLLSPAELARLSL 309

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270010909|gb|EFA07357.1| hypothetical protein TcasGA2_TC015957 [Tribolium castaneum]

 Score =  248 bits (632), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 122/179 (68%), Positives = 145/179 (81%), Gaps = 5/179 (2%)

Query: 110 EGDSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQ 169
           E  + ++D K+ ++KPPYSYIALITMAILQSP KKLTLSGICEFIM+RF YYREKFPAWQ
Sbjct: 24  ERKTPEKDKKHQLIKPPYSYIALITMAILQSPQKKLTLSGICEFIMTRFQYYREKFPAWQ 83

Query: 170 NSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDFLL 229
           NSIRHNLSLNDCF+KIPREPGNPGKGNYWTLDP+AEDMFDNGSFLRRRKRYKR  P+ +L
Sbjct: 84  NSIRHNLSLNDCFIKIPREPGNPGKGNYWTLDPLAEDMFDNGSFLRRRKRYKRPSPNIML 143

Query: 230 RDPHAAAM-ASFLGSDPYHHGLLPHSLQHGGFSFMSPLPPAVPLLPPSELVVQSISLCL 287
           RD HA+AM ASFL  + Y H L   +L H  +S++  +P   P+LPP +L   ++ L +
Sbjct: 144 RDHHASAMVASFLTQENYQHSLFSPNL-HNPYSYIPGIP---PMLPPMDLSRLNLGLGI 198

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|18858703|ref|NP_571365.1| forkhead box protein D3 [Danio rerio] gi|2982349|gb|AAC06366.1| fork head domain protein FKD6 [Danio rerio]

 Score =  228 bits (582), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 144/254 (56%), Positives = 169/254 (66%), Gaps = 25/254 (9%)

Query: 47  NLSSPSPSSEDDSDADINVESDDGDEQG-------MSNVRRNIAEFH---KHFSNCESDV 96
           N+S  +  + DD D D+  E D+G EQ        M +    + E     +  S CES+ 
Sbjct: 11  NMSGQTVLTADDVDIDVVGEGDEGMEQDSDCESQCMQDRGDEVEEIEVKERSTSPCESNA 70

Query: 97  NGCPTDGSISPGPEGDSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMS 156
           +G  T G       G    +  K+S+VKPPYSYIALITMAILQSP KKLTLSGICEFI +
Sbjct: 71  DG-ETKGDAQESSTGPMQNKP-KSSLVKPPYSYIALITMAILQSPQKKLTLSGICEFISN 128

Query: 157 RFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRR 216
           RFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDP +EDMFDNGSFLRR
Sbjct: 129 RFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPQSEDMFDNGSFLRR 188

Query: 217 RKRYKRTPPDFLLRDPHAAAMASFLG---SDPY--HHGLLPHSLQHGG---FSFMSP--- 265
           RKR+KR  PD +LRD  A  M SF      +PY  H+G+ P +  H     + ++ P   
Sbjct: 189 RKRFKRHQPD-ILRDQTALMMQSFGAYGIGNPYGRHYGIHPAAYTHPAALQYPYIPPVGP 247

Query: 266 -LPPAVPLLPPSEL 278
            LPPAVPLLP +EL
Sbjct: 248 MLPPAVPLLPSAEL 261

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|63102195|gb|AAH95603.1| Forkhead box D3 [Danio rerio]

 Score =  228 bits (580), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 144/254 (56%), Positives = 169/254 (66%), Gaps = 25/254 (9%)

Query: 47  NLSSPSPSSEDDSDADINVESDDGDEQG-------MSNVRRNIAEFH---KHFSNCESDV 96
           N+S  +  + DD D D+  E D+G EQ        M +    + E     +  S CES+ 
Sbjct: 11  NMSGQTVLTADDVDIDVVGEGDEGMEQDSDCESQCMQDRGDEVEEIEVKERSDSPCESNA 70

Query: 97  NGCPTDGSISPGPEGDSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMS 156
           +G  T G       G    +  K+S+VKPPYSYIALITMAILQSP KKLTLSGICEFI +
Sbjct: 71  DG-ETKGDAQESSTGPMQNKP-KSSLVKPPYSYIALITMAILQSPQKKLTLSGICEFISN 128

Query: 157 RFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRR 216
           RFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDP +EDMFDNGSFLRR
Sbjct: 129 RFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPQSEDMFDNGSFLRR 188

Query: 217 RKRYKRTPPDFLLRDPHAAAMASFLG---SDPY--HHGLLPHSLQHGG---FSFMSP--- 265
           RKR+KR  PD +LRD  A  M SF      +PY  H+G+ P +  H     + ++ P   
Sbjct: 189 RKRFKRHQPD-ILRDQTALMMQSFGAYGIGNPYGRHYGIHPAAYTHPAALQYPYIPPVGP 247

Query: 266 -LPPAVPLLPPSEL 278
            LPPAVPLLP +EL
Sbjct: 248 MLPPAVPLLPSTEL 261

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|284005018|ref|NP_001164677.1| fork-head box D transcription factor [Saccoglossus kowalevskii] gi|283464169|gb|ADB22668.1| fork-head box D transcription factor [Saccoglossus kowalevskii]

 Score =  226 bits (577), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 108/136 (79%), Positives = 118/136 (86%), Gaps = 7/136 (5%)

Query: 119 KNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSL 178
           KN++VKPPYSYIALITMA+LQSP K+LTLSGICEFIM+RFPYYRE+FP WQNSIRHNLSL
Sbjct: 131 KNNLVKPPYSYIALITMAVLQSPQKRLTLSGICEFIMNRFPYYRERFPVWQNSIRHNLSL 190

Query: 179 NDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDFLLRDPHAAAMA 238
           NDCFVKIPREPGNPGKGNYWTLDP +EDMFDNGSFLRRRKRYKR  PD  LR+P A    
Sbjct: 191 NDCFVKIPREPGNPGKGNYWTLDPASEDMFDNGSFLRRRKRYKRQHPD-PLREPTA---- 245

Query: 239 SFLGSDPY-HHGLLPH 253
            F+ +DPY HH L  H
Sbjct: 246 -FMTTDPYGHHFLFGH 260

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|328709854|ref|XP_003244090.1| PREDICTED: hypothetical protein LOC100167072 [Acyrthosiphon pisum]

 Score =  226 bits (576), Expect = 9e-57,   Method: Compositional matrix adjust.
 Identities = 105/122 (86%), Positives = 109/122 (89%), Gaps = 2/122 (1%)

Query: 110 EGDSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQ 169
           +GD     G  S VKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYR+KFPAWQ
Sbjct: 188 DGDKASGAGNGSPVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYRDKFPAWQ 247

Query: 170 NSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKR--TPPDF 227
           NSIRHNLSLNDCF+KIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKR   P DF
Sbjct: 248 NSIRHNLSLNDCFIKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRMQAPSDF 307

Query: 228 LL 229
            +
Sbjct: 308 FI 309

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|238054009|ref|NP_001153925.1| forkhead box D3 [Oryzias latipes] gi|226441715|gb|ACO57460.1| forkhead box D3 [Oryzias latipes]

 Score =  223 bits (567), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 142/245 (57%), Positives = 163/245 (66%), Gaps = 39/245 (15%)

Query: 54  SSEDDSDADINVESDDGDEQGMSNVRRNIAEFHKHFSNCESDVNGCPTDG-------SIS 106
           + +DD + +I VE +D    G S               CES   G P  G       S +
Sbjct: 59  TGDDDLEDEIEVEKEDMGSGGGSPC-------------CESSGEGEPGTGKGEGHDHSTT 105

Query: 107 PGPEGDSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFP 166
           PG       Q  K+S+VKPPYSYIALITMAILQSP KKLTLSGICEFI +RFPYYREKFP
Sbjct: 106 PG----GTMQKPKSSLVKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFP 161

Query: 167 AWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPD 226
           AWQNSIRHNLSLNDCF+KIPREPGNPGKGNYWT+DP +EDMFDNGSFLRRRKR+KR  PD
Sbjct: 162 AWQNSIRHNLSLNDCFIKIPREPGNPGKGNYWTMDPASEDMFDNGSFLRRRKRFKRVQPD 221

Query: 227 FLLRDPHAAAMASF----LGSDPY--HHGLLPHSLQHGG---FSFMSP----LPPAVPLL 273
            +LRD  A  M SF    LGS PY  H+G+ P +  H     + ++SP    LPP VPLL
Sbjct: 222 -VLRDQTALMMQSFGAYSLGS-PYGRHYGIHPAAYSHPAALQYPYISPVGPMLPPGVPLL 279

Query: 274 PPSEL 278
           P +EL
Sbjct: 280 PSAEL 284

Source: Oryzias latipes

Species: Oryzias latipes

Genus: Oryzias

Family: Adrianichthyidae

Order: Beloniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|319740954|gb|ADV68997.1| forkhead box d [Patiria miniata]

 Score =  223 bits (567), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 105/137 (76%), Positives = 113/137 (82%), Gaps = 3/137 (2%)

Query: 110 EGDSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQ 169
           +  SD +  K+S VKPPYSYIALITMAILQSP K+LTLSGICEFIM+RFPYYREKFP WQ
Sbjct: 113 DASSDGKKAKSSTVKPPYSYIALITMAILQSPQKRLTLSGICEFIMNRFPYYREKFPIWQ 172

Query: 170 NSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDFLL 229
           NSIRHNLSLNDCF+KIPREPGNPGKGNYWTLDP +EDMFDNGSFLRRRKRYKR  PD  L
Sbjct: 173 NSIRHNLSLNDCFIKIPREPGNPGKGNYWTLDPASEDMFDNGSFLRRRKRYKRHQPDLGL 232

Query: 230 RDPHAAAMASFLGSDPY 246
                +A   FL   PY
Sbjct: 233 SLREHSA---FLAGSPY 246

Source: Patiria miniata

Species: Patiria miniata

Genus: Patiria

Family: Asterinidae

Order: Valvatida

Class: Asteroidea

Phylum: Echinodermata

Superkingdom: Eukaryota

>gi|147903421|ref|NP_001079078.1| forkhead box protein D3-B [Xenopus laevis] gi|82247047|sp|Q9DEN3.1|FXD3B_XENLA RecName: Full=Forkhead box protein D3-B; Short=FoxD3-B; Short=FoxD3b; AltName: Full=Fork head domain-related protein 6'; Short=xFD-6' gi|10799935|emb|CAC12895.1| winged helix transcription factor [Xenopus laevis] gi|49257271|gb|AAH72772.1| Foxd3b-A protein [Xenopus laevis]

 Score =  221 bits (563), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 142/247 (57%), Positives = 160/247 (64%), Gaps = 27/247 (10%)

Query: 55  SEDDSDADINVESD---DGDEQGMSNV-------RRNIAEFHKHFSNCESDVNGCPTDGS 104
           S DD+D D+  E D   D D +  S V            E  +  S   +D  G     S
Sbjct: 19  SADDADIDVVGEGDEALDKDSECESPVGHHDEVDALGGKEIPRSPSGSSTDAEG--KGES 76

Query: 105 ISPGPEGDSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREK 164
                EG  +K   KNS+VKPPYSYIALITM+ILQSP KKLTLSGICEFI SRFPYYREK
Sbjct: 77  QQQQQEGIQNKP--KNSVVKPPYSYIALITMSILQSPQKKLTLSGICEFISSRFPYYREK 134

Query: 165 FPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTP 224
           FPAWQNSIRHNLSLNDCF+KIPREPGNPGKGNYWTLDP +EDMFDNGSFLRRRKR+KR  
Sbjct: 135 FPAWQNSIRHNLSLNDCFIKIPREPGNPGKGNYWTLDPQSEDMFDNGSFLRRRKRFKRQQ 194

Query: 225 PDFLLRDPHAAAMASFLG---SDPY--HHGLLPHSLQHGG---FSFMSP----LPPAVPL 272
            D  LR+  A  M SF     + PY  H+GL P +  H     + ++ P    LPPAVPL
Sbjct: 195 QD-TLREQTALMMQSFGAYSLASPYGRHYGLHPAAYTHPAALQYPYIPPVGPMLPPAVPL 253

Query: 273 LPPSELV 279
           LP SEL 
Sbjct: 254 LPSSELT 260

Source: Xenopus laevis

Species: Xenopus laevis

Genus: Xenopus

Family: Pipidae

Order: Anura

Class: Amphibia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|405963400|gb|EKC28977.1| Forkhead box protein D3-B [Crassostrea gigas]

 Score =  221 bits (562), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 110/163 (67%), Positives = 125/163 (76%), Gaps = 13/163 (7%)

Query: 112 DSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNS 171
           DS+K   K+++VKPPYSYIALITMAILQS  K+LTLSGICEFI++RFPYYREKFPAWQNS
Sbjct: 108 DSEKNSSKSNLVKPPYSYIALITMAILQSSQKRLTLSGICEFIINRFPYYREKFPAWQNS 167

Query: 172 IRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDFLLRD 231
           IRHNLSLNDCFVKIPREPGNPGKGNYWTLDP +EDMFDNGSFLRRRKRYKR P +     
Sbjct: 168 IRHNLSLNDCFVKIPREPGNPGKGNYWTLDPRSEDMFDNGSFLRRRKRYKRNPIEM---- 223

Query: 232 PHAAAMASFLGSDPY--HHGLLP------HSLQHGGFSFMSPL 266
            H  + A    ++ Y  HH  LP      HS     + +MSP+
Sbjct: 224 -HQQSTAFMSSAEQYLHHHPFLPSPMHAHHSRPGVPYPYMSPM 265

Source: Crassostrea gigas

Species: Crassostrea gigas

Genus: Crassostrea

Family: Ostreidae

Order: Ostreoida

Class: Bivalvia

Phylum: Mollusca

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	289
ZFIN|ZDB-GENE-980526-143	371	foxd3 "forkhead box D3" [Danio	0.657	0.512	0.623	2.5e-58
UNIPROTKB|Q90WN4	346	foxd2 "Forkhead box protein D2	0.674	0.563	0.582	1.2e-56
UNIPROTKB|Q5M7L9	369	foxd3 "Forkhead box protein D3	0.508	0.398	0.727	6.8e-56
UNIPROTKB|Q9DEN3	371	foxd3-b "Forkhead box protein	0.546	0.425	0.684	8.6e-56
UNIPROTKB|Q9DEN4	371	foxd3-a "Forkhead box protein	0.501	0.390	0.738	4.8e-55
FB|FBgn0004896	456	fd59A "forkhead domain 59A" [D	0.543	0.344	0.683	7.8e-55
ZFIN|ZDB-GENE-040426-2094	343	foxd1 "forkhead box D1" [Danio	0.605	0.510	0.629	2.6e-54
UNIPROTKB|E2QS90	411	FOXD3 "Uncharacterized protein	0.512	0.360	0.716	7e-54
UNIPROTKB|F6USR8	439	FOXD3 "Uncharacterized protein	0.512	0.337	0.716	7e-54
UNIPROTKB|J9P9K1	370	FOXD3 "Uncharacterized protein	0.512	0.4	0.716	7e-54

ZFIN|ZDB-GENE-980526-143 foxd3 "forkhead box D3" [Danio rerio (taxid:7955)]

 Score = 599 (215.9 bits), Expect = 2.5e-58, P = 2.5e-58
 Identities = 126/202 (62%), Positives = 144/202 (71%)

Query:    65 VESD-DGDEQGMSNVRRNIAEFH---KHFSNCESDVNGCPTDGSISPGPEGDSDKQDGKN 120
             +E D D + Q M +    + E     +  S CES+ +G  T G       G    +  K+
Sbjct:    35 MEQDSDCESQCMQDRGDEVEEIEVKERSDSPCESNADG-ETKGDAQESSTGPMQNKP-KS 92

Query:   121 SIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLND 180
             S+VKPPYSYIALITMAILQSP KKLTLSGICEFI +RFPYYREKFPAWQNSIRHNLSLND
Sbjct:    93 SLVKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSLND 152

Query:   181 CFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDFLLRDPHAAAMASF 240
             CFVKIPREPGNPGKGNYWTLDP +EDMFDNGSFLRRRKR+KR  PD +LRD  A  M SF
Sbjct:   153 CFVKIPREPGNPGKGNYWTLDPQSEDMFDNGSFLRRRKRFKRHQPD-ILRDQTALMMQSF 211

Query:   241 --LG-SDPY--HHGLLPHSLQH 257
                G  +PY  H+G+ P +  H
Sbjct:   212 GAYGIGNPYGRHYGIHPAAYTH 233

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

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

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

GO:0005667 "transcription factor complex" evidence=IBA

GO:0008134 "transcription factor binding" evidence=IBA

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

GO:0009790 "embryo development" evidence=IBA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IBA

GO:0007389 "pattern specification process" evidence=IBA

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

GO:0001822 "kidney development" evidence=IBA

GO:0048846 "axon extension involved in axon guidance" evidence=IBA

GO:0001658 "branching involved in ureteric bud morphogenesis" evidence=IBA

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

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

GO:0030318 "melanocyte differentiation" evidence=IGI

GO:0010629 "negative regulation of gene expression" evidence=IGI;IMP

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IDA

GO:0060351 "cartilage development involved in endochondral bone morphogenesis" evidence=IMP

GO:0014032 "neural crest cell development" evidence=IGI;IMP

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

GO:0001071 "nucleic acid binding transcription factor activity" evidence=IDA

GO:0051216 "cartilage development" evidence=IMP

GO:0048937 "lateral line nerve glial cell development" evidence=IMP

GO:0048484 "enteric nervous system development" evidence=IMP

GO:0050935 "iridophore differentiation" evidence=IMP

GO:0007422 "peripheral nervous system development" evidence=IMP

GO:0050931 "pigment cell differentiation" evidence=IGI;IMP

GO:0048485 "sympathetic nervous system development" evidence=IMP

GO:0001755 "neural crest cell migration" evidence=IMP

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|Q90WN4 foxd2 "Forkhead box protein D2" [Xenopus laevis (taxid:8355)]

 Score = 583 (210.3 bits), Expect = 1.2e-56, P = 1.2e-56
 Identities = 120/206 (58%), Positives = 147/206 (71%)

Query:    67 SDDGDEQGMSNVRRNIAEFHKHFSNCESDVN------GCPTDGSISPGPEGDSDKQDG-K 119
             S+D D   + ++     ++  + S+ +SD N      G P    +S G E +   +   K
Sbjct:    14 SEDTDIDVVGDMGAKDGKYSDYHSDNDSDDNVARTPRGDPASPDLSSGSESNQRAEKSPK 73

Query:   120 NSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLN 179
             N++VKPPYSYIALITM+ILQSP K+LTLS ICEFI +RFPYYREKFPAWQNSIRHNLSLN
Sbjct:    74 NALVKPPYSYIALITMSILQSPKKRLTLSEICEFISNRFPYYREKFPAWQNSIRHNLSLN 133

Query:   180 DCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDFLLRDPHAAAMAS 239
             DCFVKIPREPGNPGKGNYWTLDP + DMFDNGSFLRRRKR+KR   + +LRDP +   A+
Sbjct:   134 DCFVKIPREPGNPGKGNYWTLDPESADMFDNGSFLRRRKRFKRQQSNEILRDPSSFMPAA 193

Query:   240 FLGSDPY--HHGLLPHSLQ-HGGFSF 262
             F G  PY  ++GL  H+ Q H G +F
Sbjct:   194 F-GYGPYGYNYGLQLHNYQQHPGATF 218

GO:0003677 "DNA binding" evidence=NAS

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

GO:0005634 "nucleus" evidence=NAS

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

UNIPROTKB|Q5M7L9 foxd3 "Forkhead box protein D3" [Xenopus (Silurana) tropicalis (taxid:8364)]

 Score = 576 (207.8 bits), Expect = 6.8e-56, P = 6.8e-56
 Identities = 115/158 (72%), Positives = 127/158 (80%)

Query:   110 EGDSDKQDG-----KNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREK 164
             +G+S +Q+G     KNS+VKPPYSYIALITMAILQSP KKLTLSGICEFI +RFPYYREK
Sbjct:    73 KGESQQQEGMQNKPKNSLVKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREK 132

Query:   165 FPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTP 224
             FPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDP +EDMFDNGSFLRRRKR+KR  
Sbjct:   133 FPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPQSEDMFDNGSFLRRRKRFKRQQ 192

Query:   225 PDFLLRDPHAAAMASFLG---SDPYH--HGLLPHSLQH 257
             PD L R+  A  M SF     + PY   +GL P +  H
Sbjct:   193 PDSL-REQTALMMQSFGAYSLAGPYGRPYGLHPAAYTH 229

GO:0001658 "branching involved in ureteric bud morphogenesis" evidence=IBA

GO:0001755 "neural crest cell migration" evidence=IBA

GO:0001822 "kidney development" evidence=IBA

GO:0003677 "DNA binding" evidence=ISS

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:0007422 "peripheral nervous system development" evidence=IBA

GO:0008134 "transcription factor binding" evidence=IBA

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

GO:0009790 "embryo development" evidence=IBA

GO:0014034 "neural crest cell fate commitment" evidence=ISS

GO:0030318 "melanocyte differentiation" evidence=IBA

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=ISS

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IBA

GO:0048484 "enteric nervous system development" evidence=IBA

GO:0048485 "sympathetic nervous system development" evidence=IBA

GO:0048846 "axon extension involved in axon guidance" evidence=IBA

GO:0048937 "lateral line nerve glial cell development" evidence=IBA

GO:0050768 "negative regulation of neurogenesis" evidence=ISS

GO:0050769 "positive regulation of neurogenesis" evidence=ISS

GO:0050935 "iridophore differentiation" evidence=IBA

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

GO:0051216 "cartilage development" evidence=IBA

UNIPROTKB|Q9DEN3 foxd3-b "Forkhead box protein D3-B" [Xenopus laevis (taxid:8355)]

 Score = 575 (207.5 bits), Expect = 8.6e-56, P = 8.6e-56
 Identities = 117/171 (68%), Positives = 129/171 (75%)

Query:    97 NGCPTDGSISPGPEGDSDKQDG-----KNSIVKPPYSYIALITMAILQSPHKKLTLSGIC 151
             +G  TD     G E    +Q+G     KNS+VKPPYSYIALITM+ILQSP KKLTLSGIC
Sbjct:    64 SGSSTDAE-GKG-ESQQQQQEGIQNKPKNSVVKPPYSYIALITMSILQSPQKKLTLSGIC 121

Query:   152 EFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNG 211
             EFI SRFPYYREKFPAWQNSIRHNLSLNDCF+KIPREPGNPGKGNYWTLDP +EDMFDNG
Sbjct:   122 EFISSRFPYYREKFPAWQNSIRHNLSLNDCFIKIPREPGNPGKGNYWTLDPQSEDMFDNG 181

Query:   212 SFLRRRKRYKRTPPDFLLRDPHAAAMASFLG---SDPY--HHGLLPHSLQH 257
             SFLRRRKR+KR   D  LR+  A  M SF     + PY  H+GL P +  H
Sbjct:   182 SFLRRRKRFKRQQQD-TLREQTALMMQSFGAYSLASPYGRHYGLHPAAYTH 231

GO:0003677 "DNA binding" evidence=IDA

GO:0014034 "neural crest cell fate commitment" evidence=ISS

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IDA

GO:0050768 "negative regulation of neurogenesis" evidence=IMP

GO:0050769 "positive regulation of neurogenesis" evidence=ISS

UNIPROTKB|Q9DEN4 foxd3-a "Forkhead box protein D3-A" [Xenopus laevis (taxid:8355)]

 Score = 568 (205.0 bits), Expect = 4.8e-55, P = 4.8e-55
 Identities = 113/153 (73%), Positives = 123/153 (80%)

Query:   110 EGDSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQ 169
             EG  +K   KNS+VKPPYSYIALITM+ILQSP KKLTLSGICEFI +RFPYYREKFPAWQ
Sbjct:    82 EGIQNKP--KNSLVKPPYSYIALITMSILQSPQKKLTLSGICEFISNRFPYYREKFPAWQ 139

Query:   170 NSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDFLL 229
             NSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDP +EDMFDNGSFLRRRKR+KR   D L 
Sbjct:   140 NSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPQSEDMFDNGSFLRRRKRFKRQQQDSL- 198

Query:   230 RDPHAAAMASFLG---SDPY--HHGLLPHSLQH 257
             R+  A  M SF     + PY  H+GL P +  H
Sbjct:   199 REQTALMMQSFGAYSLASPYGRHYGLHPAAYTH 231

GO:0001707 "mesoderm formation" evidence=IMP

GO:0003677 "DNA binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0014034 "neural crest cell fate commitment" evidence=IMP

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IMP;IDA

GO:0050768 "negative regulation of neurogenesis" evidence=IMP

GO:0050769 "positive regulation of neurogenesis" evidence=IMP

FB|FBgn0004896 fd59A "forkhead domain 59A" [Drosophila melanogaster (taxid:7227)]

 Score = 566 (204.3 bits), Expect = 7.8e-55, P = 7.8e-55
 Identities = 108/158 (68%), Positives = 120/158 (75%)

Query:    67 SDDGDEQGMSNVRRNIAEFHKHFSNCESDVNGCPTDGSISPGPEGDSDKQDGKNSIVKPP 126
             S  G+  G S   R  A         +SD+      GS + G  GD     G   +VKPP
Sbjct:    29 SSIGNGIGCSASSRTAAADAMSMGCDDSDIEPSSMGGSGAAGGNGDGSGSSG-GPLVKPP 87

Query:   127 YSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIP 186
             YSYIALITMAILQSPHKKLTLSGIC+FIMSRFPYY++KFPAWQNSIRHNLSLNDCF+K+P
Sbjct:    88 YSYIALITMAILQSPHKKLTLSGICDFIMSRFPYYKDKFPAWQNSIRHNLSLNDCFIKVP 147

Query:   187 REPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTP 224
             REPGNPGKGN+WTLDP+AEDMFDNGSFLRRRKRYKR P
Sbjct:   148 REPGNPGKGNFWTLDPLAEDMFDNGSFLRRRKRYKRAP 185

GO:0005634 "nucleus" evidence=ISS;NAS

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

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0009790 "embryo development" evidence=IBA;NAS

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

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IBA

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

GO:0048485 "sympathetic nervous system development" evidence=IBA

GO:0007389 "pattern specification process" evidence=IBA

GO:0009888 "tissue development" 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:0048846 "axon extension involved in axon guidance" evidence=IBA

GO:0048484 "enteric nervous system development" evidence=IBA

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

GO:0008134 "transcription factor binding" evidence=IBA

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

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

GO:0048937 "lateral line nerve glial cell development" evidence=IBA

GO:0007422 "peripheral nervous system development" evidence=IBA

ZFIN|ZDB-GENE-040426-2094 foxd1 "forkhead box D1" [Danio rerio (taxid:7955)]

 Score = 561 (202.5 bits), Expect = 2.6e-54, P = 2.6e-54
 Identities = 117/186 (62%), Positives = 131/186 (70%)

Query:    66 ESDDGDEQGMSNVRRNIAEFHKHFSNCESDVNGCPTDGSISPGPEGDSDKQDGKNSIVKP 125
             E DDGD    S V   +A+ H      E  +NG P    +   P  D  K   KN++VKP
Sbjct:    24 EGDDGDGHTRSYVDE-VAQMHD-----EILLNGSPP--GVDASPARDPYKPASKNTLVKP 75

Query:   126 PYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKI 185
             PYSYIALITMAILQSP K+LTLS IC+FI +RFPYYREKFPAWQNSIRHNLSLNDCFVKI
Sbjct:    76 PYSYIALITMAILQSPKKRLTLSEICDFISNRFPYYREKFPAWQNSIRHNLSLNDCFVKI 135

Query:   186 PREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDFLLRDPHAAAM--ASFLGS 243
             PREPGNPGKGNYWTLDP + DMFDNGSFLRRRKR+KR     LLR+ H   +  A+  G 
Sbjct:   136 PREPGNPGKGNYWTLDPESADMFDNGSFLRRRKRFKRQQAPELLRE-HGGFLPSAAAYGY 194

Query:   244 DPYHHG 249
              PY  G
Sbjct:   195 GPYGCG 200

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

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

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

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

GO:0090184 "positive regulation of kidney development" evidence=IBA

GO:0009790 "embryo development" evidence=IBA

GO:0005667 "transcription factor complex" evidence=IBA

GO:0048485 "sympathetic nervous system development" evidence=IBA

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

GO:0060678 "dichotomous subdivision of terminal units involved in ureteric bud branching" evidence=IBA

GO:0030513 "positive regulation of BMP signaling pathway" evidence=IBA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IBA

GO:0050935 "iridophore differentiation" evidence=IBA

GO:0001755 "neural crest cell migration" evidence=IBA

GO:0030318 "melanocyte differentiation" evidence=IBA

GO:0008134 "transcription factor binding" evidence=IBA

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

GO:0048846 "axon extension involved in axon guidance" evidence=IBA

GO:0007389 "pattern specification process" evidence=IBA

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

GO:0007422 "peripheral nervous system development" evidence=IBA

GO:0051216 "cartilage development" evidence=IBA

GO:0048937 "lateral line nerve glial cell development" evidence=IBA

GO:0048484 "enteric nervous system development" evidence=IBA

GO:0005634 "nucleus" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E2QS90 FOXD3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 557 (201.1 bits), Expect = 7.0e-54, P = 7.0e-54
 Identities = 111/155 (71%), Positives = 118/155 (76%)

Query:    92 CESDVNGCPTDGSISPGPEGDSDKQDG------KNSIVKPPYSYIALITMAILQSPHKKL 145
             C+  V G    GS   GP        G      KNS+VKPPYSYIALITMAILQSP KKL
Sbjct:   104 CKGGVGGEEGGGSGGGGPGAGGGAAGGLAPSKPKNSLVKPPYSYIALITMAILQSPQKKL 163

Query:   146 TLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAE 205
             TLSGICEFI +RFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDP +E
Sbjct:   164 TLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPQSE 223

Query:   206 DMFDNGSFLRRRKRYKRTPPDFLLRDPHAAAMASF 240
             DMFDNGSFLRRRKR+KR   + L R+  A  M SF
Sbjct:   224 DMFDNGSFLRRRKRFKRHQQEHL-REQTALMMQSF 257

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0044212 "transcription regulatory region DNA binding" evidence=IEA

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

GO:0001892 "embryonic placenta development" evidence=IEA

GO:0001829 "trophectodermal cell differentiation" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

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

UNIPROTKB|F6USR8 FOXD3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 557 (201.1 bits), Expect = 7.0e-54, P = 7.0e-54
 Identities = 111/155 (71%), Positives = 118/155 (76%)

Query:    92 CESDVNGCPTDGSISPGPEGDSDKQDG------KNSIVKPPYSYIALITMAILQSPHKKL 145
             C+  V G    GS   GP        G      KNS+VKPPYSYIALITMAILQSP KKL
Sbjct:   104 CKGGVGGEEGGGSGGGGPGAGGGAAGGLAPSKPKNSLVKPPYSYIALITMAILQSPQKKL 163

Query:   146 TLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAE 205
             TLSGICEFI +RFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDP +E
Sbjct:   164 TLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPQSE 223

Query:   206 DMFDNGSFLRRRKRYKRTPPDFLLRDPHAAAMASF 240
             DMFDNGSFLRRRKR+KR   + L R+  A  M SF
Sbjct:   224 DMFDNGSFLRRRKRFKRHQQEHL-REQTALMMQSF 257

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|J9P9K1 FOXD3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 557 (201.1 bits), Expect = 7.0e-54, P = 7.0e-54
 Identities = 111/155 (71%), Positives = 118/155 (76%)

Query:    92 CESDVNGCPTDGSISPGPEGDSDKQDG------KNSIVKPPYSYIALITMAILQSPHKKL 145
             C+  V G    GS   GP        G      KNS+VKPPYSYIALITMAILQSP KKL
Sbjct:    87 CKGGVGGEEGGGSGGGGPGAGGGAAGGLAPSKPKNSLVKPPYSYIALITMAILQSPQKKL 146

Query:   146 TLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAE 205
             TLSGICEFI +RFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDP +E
Sbjct:   147 TLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPQSE 206

Query:   206 DMFDNGSFLRRRKRYKRTPPDFLLRDPHAAAMASF 240
             DMFDNGSFLRRRKR+KR   + L R+  A  M SF
Sbjct:   207 DMFDNGSFLRRRKRFKRHQQEHL-REQTALMMQSF 240

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

---

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)
Q63245	FOXD3_RAT	No assigned EC number	0.9340	0.3148	0.9009	no	N/A
Q63251	FOXD1_RAT	No assigned EC number	0.9010	0.3148	0.9009	no	N/A
P79772	FOXD3_CHICK	No assigned EC number	0.6918	0.5501	0.4035	yes	N/A
Q5M7L9	FOXD3_XENTR	No assigned EC number	0.5785	0.7647	0.5989	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	289
pfam00250	96	pfam00250, Fork_head, Fork head domain	2e-62
smart00339	89	smart00339, FH, FORKHEAD	1e-53
cd00059	78	cd00059, FH, Forkhead (FH), also known as a "winge	5e-53
COG5025	610	COG5025, COG5025, Transcription factor of the Fork	2e-24
COG5025	610	COG5025, COG5025, Transcription factor of the Fork	3e-16

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

 Score =  191 bits (488), Expect = 2e-62
 Identities = 68/96 (70%), Positives = 79/96 (82%)

Query: 124 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFV 183
           KPPYSYIALITMAI QSP K LTLS I ++IM  FPYYR+    WQNSIRHNLSLN CF+
Sbjct: 1   KPPYSYIALITMAIQQSPEKMLTLSEIYQWIMDLFPYYRQNKQGWQNSIRHNLSLNKCFI 60

Query: 184 KIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKR 219
           K+PR P  PGKG+YWTLDP +E+MF+NG +L+RRKR
Sbjct: 61  KVPRSPDKPGKGSYWTLDPESENMFENGKYLKRRKR 96

Length = 96

>gnl|CDD|214627 smart00339, FH, FORKHEAD

 Score =  168 bits (429), Expect = 1e-53
 Identities = 65/89 (73%), Positives = 73/89 (82%)

Query: 124 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFV 183
           KPPYSYIALI MAIL SP K+LTLS I ++I   FPYYRE    WQNSIRHNLSLNDCFV
Sbjct: 1   KPPYSYIALIAMAILSSPDKRLTLSEIYKWIEDNFPYYRENRAGWQNSIRHNLSLNDCFV 60

Query: 184 KIPREPGNPGKGNYWTLDPMAEDMFDNGS 212
           K+PRE   PGKG+YWTLDP AE+MF+NG+
Sbjct: 61  KVPREGDRPGKGSYWTLDPAAENMFENGN 89

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

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

 Score =  167 bits (425), Expect = 5e-53
 Identities = 54/78 (69%), Positives = 61/78 (78%)

Query: 124 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFV 183
           KPPYSY ALI MAI  SP K+LTLS I ++I   FPY+R+    WQNSIRHNLSLN CFV
Sbjct: 1   KPPYSYSALIAMAIQSSPEKRLTLSEIYKWISDNFPYFRDAPAGWQNSIRHNLSLNKCFV 60

Query: 184 KIPREPGNPGKGNYWTLD 201
           K+PREP  PGKG+YWTLD
Sbjct: 61  KVPREPDEPGKGSYWTLD 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|227358 COG5025, COG5025, Transcription factor of the Forkhead/HNF3 family [Transcription]

 Score =  102 bits (255), Expect = 2e-24
 Identities = 51/107 (47%), Positives = 60/107 (56%), Gaps = 2/107 (1%)

Query: 113 SDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSI 172
           SD     N   KP +SY   IT AIL SP  K+TLS I  +I S  PYYR K  AWQNSI
Sbjct: 326 SDLSADVNRTSKPAFSYANSITQAILSSPSGKMTLSEIYSWISSNLPYYRHKPTAWQNSI 385

Query: 173 RHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKR 219
           RHNLSLN  F K+PR    PGKG +W +D     +++  S    R  
Sbjct: 386 RHNLSLNKSFEKVPRSASQPGKGCFWKIDY--SYIYEKESKRNPRSP 430

Length = 610

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

 Score = 78.3 bits (193), Expect = 3e-16
 Identities = 43/85 (50%), Positives = 52/85 (61%)

Query: 124 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFV 183
            PPYSY     +AIL SP K LTLS I  +I + F YY +    WQNSIRHNLSLND F+
Sbjct: 86  VPPYSYATGRGLAILNSPDKPLTLSKIYTWIHNTFFYYAKVVSRWQNSIRHNLSLNDAFI 145

Query: 184 KIPREPGNPGKGNYWTLDPMAEDMF 208
           KI    G   KG++W++ P  E  F
Sbjct: 146 KIEGRNGAKVKGHFWSIGPGHETQF 170

Length = 610

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	289
KOG3563|consensus	454		100.0
KOG3562|consensus	277		100.0
PF00250	96	Fork_head: Fork head domain; InterPro: IPR001766 T	100.0
cd00059	78	FH Forkhead (FH), also known as a "winged helix".	100.0
smart00339	89	FH FORKHEAD. FORKHEAD, also known as a "winged hel	100.0
KOG2294|consensus	454		100.0
KOG4385|consensus	581		99.88
COG5025	610	Transcription factor of the Forkhead/HNF3 family [	99.83
COG5025	610	Transcription factor of the Forkhead/HNF3 family [	99.56
PF00538	77	Linker_histone: linker histone H1 and H5 family; I	93.75
smart00526	66	H15 Domain in histone families 1 and 5.	93.14
cd00073	88	H15 linker histone 1 and histone 5 domains; the ba	91.67
PF05066	72	HARE-HTH: HB1, ASXL, restriction endonuclease HTH	82.03

>KOG3563|consensus

Probab=100.00  E-value=1.8e-41  Score=323.50  Aligned_cols=109  Identities=58%  Similarity=1.058  Sum_probs=104.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCCceeE
Q psy9499         119 KNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYW  198 (289)
Q Consensus       119 ~~~~~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~W  198 (289)
                      .-.+.||||||+.||+|||+.+|.|+|||+|||+||++.|||||.+...|||||||.||+|+||+||+|.+++||||+||
T Consensus       168 sY~haKPPYSYISLITMAIQ~~pskmLTLSEIYqwIMDLFPyYrqNQQRWQNSIRHSLSFNDCFVKVaRSPDKPGKGSfW  247 (454)
T KOG3563|consen  168 SYTHAKPPYSYISLITMAIQQAPSKMLTLSEIYQWIMDLFPYYRQNQQRWQNSIRHSLSFNDCFVKVARSPDKPGKGSFW  247 (454)
T ss_pred             cccCCCCChhHHHHHHHHHHhCCccceeHHHHHHHHHHhhhHhhhhHHHHHhhhhhhccccceeeeccCCCCCCCCccce
Confidence            34679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeCCCchhcccCccchhcccccCCCCCCc
Q psy9499         199 TLDPMAEDMFDNGSFLRRRKRYKRTPPDF  227 (289)
Q Consensus       199 tldP~~e~~f~~g~~~RrRkr~kr~~p~~  227 (289)
                      +|+|++..|||||.|+||+||||...++.
T Consensus       248 TLHpdsGNMFENGCYLRRQKRFK~ekk~~  276 (454)
T KOG3563|consen  248 TLHPDSGNMFENGCYLRRQKRFKCEKKEA  276 (454)
T ss_pred             eecCCcCcccccchhehhhhhhhhhhhhc
Confidence            99999999999999999999999876654

>KOG3562|consensus

Probab=100.00  E-value=2.8e-40  Score=299.50  Aligned_cols=115  Identities=58%  Similarity=1.029  Sum_probs=105.7

Q ss_pred             CCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCCceeEEe
Q psy9499         121 SIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTL  200 (289)
Q Consensus       121 ~~~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~Wtl  200 (289)
                      ..+||||||+.|.+|||++||+|+|.|+|||+||+++|||||.+.+.||||+|||||+|+||+||+|..+.+|||+||.|
T Consensus        10 ~dQKPPYSYIsLTaMAI~~SpekmLPLseIYkfImDrFPfYRkNTQrWQNSLRHNLSFNDCFIKiPRr~drpGKGsyWal   89 (277)
T KOG3562|consen   10 GDQKPPYSYISLTAMAIQSSPEKMLPLSEIYKFIMDRFPFYRKNTQRWQNSLRHNLSFNDCFIKIPRRPDRPGKGSYWAL   89 (277)
T ss_pred             cccCCCceeeehhhHHhhcChhhcCcHHHHHHHHHhhCchhhhchHHHHHHhhccccccceeeecCCCCCCCCCccceee
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCchhcccCccchhcccccCCCC-CCccCCCchhH
Q psy9499         201 DPMAEDMFDNGSFLRRRKRYKRTP-PDFLLRDPHAA  235 (289)
Q Consensus       201 dP~~e~~f~~g~~~RrRkr~kr~~-p~~~~r~~~~~  235 (289)
                      +|.+.+|||||+++|||||+|..+ .+......+.+
T Consensus        90 HP~a~dMFENGS~LRRrKRFrv~k~~d~d~~n~~l~  125 (277)
T KOG3562|consen   90 HPSAFDMFENGSLLRRRKRFRVLKSDDKDPSNTHLP  125 (277)
T ss_pred             ccchhhhcccchHHHHhhhhhhccccccCccccccc
Confidence            999999999999999999998765 33333333333

>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=1.4e-39  Score=261.16  Aligned_cols=96  Identities=66%  Similarity=1.208  Sum_probs=89.7

Q ss_pred             CCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCCceeEEeCCC
Q psy9499         124 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPM  203 (289)
Q Consensus       124 KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~WtldP~  203 (289)
                      ||||||++||+|||+++|+++|||+|||+||+++||||+.+..+||||||||||+|+||+||++..+++|||+||+|+++
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             chhcccCccchhcccc
Q psy9499         204 AEDMFDNGSFLRRRKR  219 (289)
Q Consensus       204 ~e~~f~~g~~~RrRkr  219 (289)
                      +...|+++.++|+|||
T Consensus        81 ~~~~~~~~~~~~~~~~   96 (96)
T PF00250_consen   81 AIEEFEKGRFKRRRKR   96 (96)
T ss_dssp             HHHHHHHSCCSSSSSS
T ss_pred             HHHHHhcchhhhhhcc
Confidence            9999999998888765

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

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

Probab=100.00  E-value=2.4e-38  Score=246.06  Aligned_cols=78  Identities=69%  Similarity=1.249  Sum_probs=76.7

Q ss_pred             CCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCCceeEEeC
Q psy9499         124 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLD  201 (289)
Q Consensus       124 KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~Wtld  201 (289)
                      ||||||++||++||+++|+++|||+|||+||+++||||+.+..|||||||||||+|+||+||+|..+++|||+||+||
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            899999999999999999999999999999999999999999999999999999999999999999889999999997

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

>smart00339 FH FORKHEAD

Probab=100.00  E-value=2.7e-37  Score=245.12  Aligned_cols=87  Identities=74%  Similarity=1.277  Sum_probs=83.0

Q ss_pred             CCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCCceeEEeCCC
Q psy9499         124 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPM  203 (289)
Q Consensus       124 KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~WtldP~  203 (289)
                      ||||||++||++||+++|+++|||+|||+||+++||||+.+.+|||||||||||+|+||+||++..+.+|||+||+|+|+
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             chhcccC
Q psy9499         204 AEDMFDN  210 (289)
Q Consensus       204 ~e~~f~~  210 (289)
                      ++.+|+.
T Consensus        81 ~~~~~~~   87 (89)
T smart00339       81 AENMFEN   87 (89)
T ss_pred             HHHHHhc
Confidence            9875553

FORKHEAD, also known as a "winged helix"

>KOG2294|consensus

Probab=100.00  E-value=2.5e-37  Score=296.82  Aligned_cols=104  Identities=65%  Similarity=1.146  Sum_probs=98.1

Q ss_pred             CCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHh-cCCCcccCC-CccccccccccccccccccccCCCCCCCCcee
Q psy9499         120 NSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMS-RFPYYREKF-PAWQNSIRHNLSLNDCFVKIPREPGNPGKGNY  197 (289)
Q Consensus       120 ~~~~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~-~fPyyr~~~-~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~  197 (289)
                      ...+||||||++||+|||+.+++|+|||+|||+||+. +|||||++. .|||||||||||||+||+||+|+.+.+|||+|
T Consensus       126 ~~~~kpp~SY~~LI~mAI~~Sp~krLtLs~Iy~~i~~~~fpyyr~~~~~gWqNSIRHNLSLn~cF~Kvpr~~~~~gKg~~  205 (454)
T KOG2294|consen  126 GAGVKPPYSYSGLIAMAIRLSPGKRLTLGGIYFYILLEHFPYYRDANMPGWKNSIRHNLSLNKCFVKVPRERGRPGKGNY  205 (454)
T ss_pred             CCCcCCccccccccccccccCCCcceeecCeeEEEEeccccccccCCCccchhhcccccccccCccccCCcccCCCCCCc
Confidence            4579999999999999999999999999999999995 999999999 99999999999999999999999889999999


Q ss_pred             EEeCCCchh-cccCccchhcccccCCC
Q psy9499         198 WTLDPMAED-MFDNGSFLRRRKRYKRT  223 (289)
Q Consensus       198 WtldP~~e~-~f~~g~~~RrRkr~kr~  223 (289)
                      |+|||+.++ ||++|.|+|||+++++.
T Consensus       206 W~ldP~~~~~~~~~g~~~rr~~~~~~~  232 (454)
T KOG2294|consen  206 WTLDPDDENNMFDNGSFRRRRRSKSNG  232 (454)
T ss_pred             cccCcchhccccccccccccccccccc
Confidence            999999998 99999999988875543

>KOG4385|consensus

Probab=99.88  E-value=3.4e-24  Score=210.95  Aligned_cols=84  Identities=44%  Similarity=0.841  Sum_probs=79.2

Q ss_pred             ccCCCCCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCC
Q psy9499         115 KQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGK  194 (289)
Q Consensus       115 ~~~~~~~~~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGK  194 (289)
                      .+..++..+||||+|+.||.+||+.+|++.|||+|||.|+.+.|.|||.+...|||+||||||||+||++|+.     -|
T Consensus       359 ~dfyk~~dvRPPfTYAsLIRqAIlESpdkQLTLNEIY~WFTrtFAYFRRNaATWKnAVRHNLSLHKCF~RVEn-----vk  433 (581)
T KOG4385|consen  359 MDFYKNADVRPPFTYASLIRQAILESPDKQLTLNEIYNWFTRTFAYFRRNAATWKNAVRHNLSLHKCFVRVEN-----VK  433 (581)
T ss_pred             hhhhhccccCCchhHHHHHHHHHhcCchhhccHHHHHHHHHHHHHHHhccchhHhHHHhhhhHHHHHHHHHHH-----Hh
Confidence            3467788899999999999999999999999999999999999999999999999999999999999999988     49


Q ss_pred             ceeEEeCCC
Q psy9499         195 GNYWTLDPM  203 (289)
Q Consensus       195 G~~WtldP~  203 (289)
                      |--|++|..
T Consensus       434 gavwtvDe~  442 (581)
T KOG4385|consen  434 GAVWTVDER  442 (581)
T ss_pred             cceeeeehh
Confidence            999999954

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

Probab=99.83  E-value=1.5e-21  Score=198.49  Aligned_cols=101  Identities=48%  Similarity=0.722  Sum_probs=92.3

Q ss_pred             CccCCCCCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCC
Q psy9499         114 DKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPG  193 (289)
Q Consensus       114 ~~~~~~~~~~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pG  193 (289)
                      ......+...||+++|+.||+.||+.+++++|+|.+||.||..+|||||.+..+||||||||||+|++|.||++..+.+|
T Consensus       327 ~~s~~~~~~~kP~~sya~~iT~ail~s~~~kmsls~Iy~~i~s~~pyYr~~p~~w~nSiRhnlSlNksf~kvP~sa~~pG  406 (610)
T COG5025         327 DLSADVNRTSKPAFSYANSITQAILSSPSGKMTLSEIYSWISSNLPYYRHKPTAWQNSIRHNLSLNKSFEKVPRSASQPG  406 (610)
T ss_pred             ccccccccCccCCcchhhhhHHHhhcCcccccccccccccccccchhhccCCcccCchhhhhhhhccccccCCCCcCCCC
Confidence            34455678899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CceeEEeCCCchhcccCccch
Q psy9499         194 KGNYWTLDPMAEDMFDNGSFL  214 (289)
Q Consensus       194 KG~~WtldP~~e~~f~~g~~~  214 (289)
                      ||+||+++.+....++.....
T Consensus       407 Kg~fw~i~~s~~~~~~sk~~~  427 (610)
T COG5025         407 KGCFWKIDYSYIYEKESKRNP  427 (610)
T ss_pred             CcccCccChhhhhhhcccccc
Confidence            999999999887666654433

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

Probab=99.56  E-value=3.5e-16  Score=159.54  Aligned_cols=90  Identities=48%  Similarity=0.781  Sum_probs=84.8

Q ss_pred             CCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCCceeEEeC
Q psy9499         122 IVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLD  201 (289)
Q Consensus       122 ~~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~Wtld  201 (289)
                      ..||||+|+.+|.++|++++++.|||..||.||-..|.||.....+|||||||||++|++|.||.+..+..+||.||.+.
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            47999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCchhcccCc
Q psy9499         202 PMAEDMFDNG  211 (289)
Q Consensus       202 P~~e~~f~~g  211 (289)
                      |+.+..|...
T Consensus       164 P~~~~~~l~~  173 (610)
T COG5025         164 PGHETQFLKS  173 (610)
T ss_pred             CCccceeecc
Confidence            9887666433

>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=93.75  E-value=0.08  Score=40.55  Aligned_cols=33  Identities=24%  Similarity=0.356  Sum_probs=28.9

Q ss_pred             CHHHHHHHHHhcCC-CCCCCHHHHHHHHHhcCCC
Q psy9499         128 SYIALITMAILQSP-HKKLTLSGICEFIMSRFPY  160 (289)
Q Consensus       128 SYa~LI~~AI~sSp-~k~LTL~eIY~~I~~~fPy  160 (289)
                      +|..||.+||.+.. .+..+++.|..||+.+|+.
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            49999999999844 4789999999999999964

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=93.14  E-value=0.16  Score=37.63  Aligned_cols=32  Identities=28%  Similarity=0.388  Sum_probs=28.2

Q ss_pred             CHHHHHHHHHhcCCC-CCCCHHHHHHHHHhcCC
Q psy9499         128 SYIALITMAILQSPH-KKLTLSGICEFIMSRFP  159 (289)
Q Consensus       128 SYa~LI~~AI~sSp~-k~LTL~eIY~~I~~~fP  159 (289)
                      +|..||.+||....+ +..+++.|..||+.+|.
T Consensus         6 ~~~~mI~eAI~~l~er~GsS~~aI~kyi~~~~~   38 (66)
T smart00526        6 PYSEMITEAISALKERKGSSLQAIKKYIEANYK   38 (66)
T ss_pred             CHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCC
Confidence            799999999998544 67999999999999965

>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=91.67  E-value=0.28  Score=38.63  Aligned_cols=34  Identities=24%  Similarity=0.366  Sum_probs=29.6

Q ss_pred             CHHHHHHHHHhc-CCCCCCCHHHHHHHHHhcCCCc
Q psy9499         128 SYIALITMAILQ-SPHKKLTLSGICEFIMSRFPYY  161 (289)
Q Consensus       128 SYa~LI~~AI~s-Sp~k~LTL~eIY~~I~~~fPyy  161 (289)
                      +|..||.+||.. ...+..+++.|..||+.+|+.-
T Consensus         6 ~y~~MI~eAI~~l~er~GsS~~aI~kyI~~~y~~~   40 (88)
T cd00073           6 PYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVD   40 (88)
T ss_pred             CHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCCcc
Confidence            699999999997 5567889999999999998743

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

Probab=82.03  E-value=0.88  Score=34.08  Aligned_cols=58  Identities=19%  Similarity=0.198  Sum_probs=37.4

Q ss_pred             CCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccc-----ccccccccc
Q psy9499         127 YSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLS-----LNDCFVKIP  186 (289)
Q Consensus       127 ySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLS-----lNkcF~Kvp  186 (289)
                      +||..++...|+... +.|+.+||++.|.+.--| ....+...++|+-.|.     .+..|++|.
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            478888888888876 899999999999976543 3235567777773333     455899874

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	289
2hdc_A	97	Structure Of Transcription Factor GenesisDNA COMPLE		2e-50
2hfh_A	109	The Nmr Structures Of A Winged Helix Protein: Genes		7e-47
1d5v_A	94	Solution Structure Of The Forkhead Domain Of The Ad		2e-35
1vtn_C	102	Co-Crystal Structure Of The Hnf-3FORK HEAD DNA-Reco		2e-33
1kq8_A	100	Solution Structure Of Winged Helix Protein Hfh-1 Le		1e-27
2c6y_A	111	Crystal Structure Of Interleukin Enhancer-Binding F		1e-25
1jxs_A	98	Solution Structure Of The Dna-Binding Domain Of Int		3e-24
2a3s_A	101	Solution Structure And Dynamics Of Dna-Binding Doma		4e-24
2kiu_A	87	Solution Structure And Backbone Dynamics Of The Dna		3e-15
3g73_A	142	Structure Of The Foxm1 Dna Binding Length = 142		5e-15
2a07_F	93	Crystal Structure Of Foxp2 Bound Specifically To Dn		3e-14
3qrf_F	82	Structure Of A Domain-Swapped Foxp3 Dimer Length =		3e-14
3co7_C	117	Crystal Structure Of Foxo1 Dbd Bound To Dbe2 Dna Le		9e-13
1e17_A	150	Solution Structure Of The Dna Binding Domain Of The		1e-12
3co6_C	100	Crystal Structure Of Foxo1 Dbd Bound To Dbe1 Dna Le		1e-12
3l2c_A	110	Crystal Structure Of The Dna Binding Domain Of Foxo		1e-12
2k86_A	103	Solution Structure Of Foxo3a Forkhead Domain Length		6e-12
2uzk_A	97	Crystal Structure Of The Human Foxo3a-Dbd Bound To		7e-12

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

Iteration: 1
 Score =  195 bits (496), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 91/96 (94%), Positives = 93/96 (96%)
Query: 124 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFV 183
           KPPYSYIALITMAILQSP KKLTLSGICEFI +RFPYYREKFPAWQNSIRHNLSLNDCFV
Sbjct: 2   KPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDCFV 61
Query: 184 KIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKR 219
           KIPREPGNPGKGNYWTLDP +EDMFDNGSFLRRRKR
Sbjct: 62  KIPREPGNPGKGNYWTLDPQSEDMFDNGSFLRRRKR 97

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

Iteration: 1
 Score =  184 bits (466), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 85/90 (94%), Positives = 87/90 (96%)
Query: 123 VKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCF 182
           VKPPYSYIALITMAILQSP KKLTLSGICEFI +RFPYYREKFPAWQNSIRHNLSLNDCF
Sbjct: 2   VKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDCF 61
Query: 183 VKIPREPGNPGKGNYWTLDPMAEDMFDNGS 212
           VKIPREPGNPGKGNYWTLDP +EDMFDNGS
Sbjct: 62  VKIPREPGNPGKGNYWTLDPQSEDMFDNGS 91

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

Iteration: 1
 Score =  146 bits (368), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 66/93 (70%), Positives = 79/93 (84%)
Query: 122 IVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDC 181
           +VKPPYSYIALITMAI  +P KK+TL+GI +FIM RFP+YRE    WQNSIRHNLSLN+C
Sbjct: 2   LVKPPYSYIALITMAIQNAPEKKITLNGIYQFIMDRFPFYRENKQGWQNSIRHNLSLNEC 61
Query: 182 FVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFL 214
           FVK+PR+   PGKG+YWTLDP + +MF+NGSFL
Sbjct: 62  FVKVPRDDKKPGKGSYWTLDPDSYNMFENGSFL 94

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

Iteration: 1
 Score =  139 bits (350), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 64/99 (64%), Positives = 77/99 (77%)
Query: 123 VKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCF 182
            KPPYSYI+LITMAI Q+P K LTLS I ++IM  FPYYRE    WQNSIRH+LS NDCF
Sbjct: 2   AKPPYSYISLITMAIQQAPGKMLTLSEIYQWIMDLFPYYRENQQRWQNSIRHSLSFNDCF 61
Query: 183 VKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYK 221
           VK+ R P  PGKG+YW L P + +MF+NG +LRR+KR+K
Sbjct: 62  VKVARSPDKPGKGSYWALHPSSGNMFENGCYLRRQKRFK 100

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

Iteration: 1
 Score =  120 bits (300), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 57/97 (58%), Positives = 72/97 (74%), Gaps = 1/97 (1%)
Query: 124 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFV 183
           KPPYSYIALITMAI  S   +LTL+ I E++M +FP++R  +  W+NS+RHNLSLNDCFV
Sbjct: 2   KPPYSYIALITMAIRDSAGGRLTLAEINEYLMGKFPFFRGSYTGWRNSVRHNLSLNDCFV 61
Query: 184 KIPREPGNP-GKGNYWTLDPMAEDMFDNGSFLRRRKR 219
           K+ R+P  P GK NYW L+P +E  F +G F RRR R
Sbjct: 62  KVLRDPSRPWGKDNYWMLNPNSEYTFADGVFRRRRYR 98

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

Iteration: 1
 Score =  113 bits (282), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 53/105 (50%), Positives = 67/105 (63%)
Query: 115 KQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRH 174
           +Q G+ S  KPPYSY  LI  AI  +P K+LTL+GI   I   +PYYR     WQNSIRH
Sbjct: 7   QQMGRGSDSKPPYSYAQLIVQAITMAPDKQLTLNGIYTHITKNYPYYRTADKGWQNSIRH 66
Query: 175 NLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKR 219
           NLSLN  F+K+PR    PGKG++W +DP +E      +F +RR R
Sbjct: 67  NLSLNRYFIKVPRSQEEPGKGSFWRIDPASESKLIEQAFRKRRPR 111

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

Iteration: 1
 Score =  108 bits (271), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 50/96 (52%), Positives = 62/96 (64%)
Query: 124 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFV 183
           KPPYSY  LI  AI  +P K+LTL+GI   I   +PYYR     WQNSIRHNLSLN  F+
Sbjct: 3   KPPYSYAQLIVQAITMAPDKQLTLNGIYTHITKNYPYYRTADKGWQNSIRHNLSLNRYFI 62
Query: 184 KIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKR 219
           K+PR    PGKG++W +DP +E      +F +RR R
Sbjct: 63  KVPRSQEEPGKGSFWRIDPASESKLIEQAFRKRRPR 98

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

Iteration: 1
 Score =  108 bits (270), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 49/96 (51%), Positives = 62/96 (64%)
Query: 124 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFV 183
           KPPYSY  LI  AI  +  ++LTLSGI   I   +PYYR     WQNSIRHNLSLN  F+
Sbjct: 3   KPPYSYAQLIVQAISSAQDRQLTLSGIYAHITKHYPYYRTADKGWQNSIRHNLSLNRYFI 62
Query: 184 KIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKR 219
           K+PR    PGKG++W +DP +E      +F +RR+R
Sbjct: 63  KVPRSQEEPGKGSFWRIDPASEAKLVEQAFRKRRQR 98

>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 = 78.6 bits (192), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 35/79 (44%), Positives = 51/79 (64%), Gaps = 5/79 (6%)
Query: 123 VKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCF 182
           V+PP++Y +LI  AIL+SP K+LTL+ I  +    FPY+R     W+N++RHNLSL+  F
Sbjct: 3   VRPPFTYASLIRQAILESPEKQLTLNEIYNWFTRMFPYFRRNAATWKNAVRHNLSLHKYF 62
Query: 183 VKIPREPGNPGKGNYWTLD 201
           V++        KG  WT+D
Sbjct: 63  VRVENV-----KGAVWTVD 76

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

Iteration: 1
 Score = 78.2 bits (191), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 45/100 (45%), Positives = 61/100 (61%), Gaps = 7/100 (7%)
Query: 107 PGPEGDSDKQDGKNSIV-KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYRE-K 164
           PGP   S     +NS+  +PPYSY+A+I  AI  +  K++TL  I  +I   FPY++   
Sbjct: 2   PGPSRPS--ASWQNSVSERPPYSYMAMIQFAINSTERKRMTLKDIYTWIEDHFPYFKHIA 59
Query: 165 FPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMA 204
            P W+NSIRHNLSL+D FV   RE    GK ++WT+ P A
Sbjct: 60  KPGWKNSIRHNLSLHDMFV---RETSANGKVSFWTIHPSA 96

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

Iteration: 1
 Score = 75.9 bits (185), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 33/80 (41%), Positives = 50/80 (62%), Gaps = 5/80 (6%)
Query: 122 IVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDC 181
           IV+PP++Y  LI  AI++S  ++LTL+ I  +    F Y+R     W+N++RHNLSL+ C
Sbjct: 1   IVRPPFTYATLIRQAIMESSDRQLTLNEIYSWFTRTFAYFRRNAATWKNAVRHNLSLHKC 60
Query: 182 FVKIPREPGNPGKGNYWTLD 201
           FV++        KG  WT+D
Sbjct: 61  FVRVENV-----KGAVWTVD 75

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

Iteration: 1
 Score = 75.5 bits (184), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 33/81 (40%), Positives = 51/81 (62%), Gaps = 5/81 (6%)
Query: 123 VKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCF 182
           ++PP++Y  LI  AIL++P K+ TL+ I  +    F ++R     W+N+IRHNLSL+ CF
Sbjct: 1   MRPPFTYATLIRWAILEAPEKQRTLNEIYHWFTRMFAFFRNHPATWKNAIRHNLSLHKCF 60
Query: 183 VKIPREPGNPGKGNYWTLDPM 203
           V++  E     KG  WT+D +
Sbjct: 61  VRVESE-----KGAVWTVDEL 76

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 35/80 (43%), Positives = 50/80 (62%), Gaps = 7/80 (8%)
Query: 128 SYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREK-----FPAWQNSIRHNLSLNDCF 182
           SY  LIT AI  S  K+LTLS I E+++   PY+++K        W+NSIRHNLSL+  F
Sbjct: 15  SYADLITKAIESSAEKRLTLSQIYEWMVKSVPYFKDKGDSNSSAGWKNSIRHNLSLHSKF 74
Query: 183 VKIPREPGNPGKGNYWTLDP 202
           +++  E    GK ++W L+P
Sbjct: 75  IRVQNE--GTGKSSWWMLNP 92

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 35/80 (43%), Positives = 50/80 (62%), Gaps = 7/80 (8%)
Query: 128 SYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREK-----FPAWQNSIRHNLSLNDCF 182
           SY  LIT AI  S  K+LTLS I E+++   PY+++K        W+NSIRHNLSL+  F
Sbjct: 15  SYADLITKAIESSAEKRLTLSQIYEWMVKSVPYFKDKGDSNSSAGWKNSIRHNLSLHSKF 74
Query: 183 VKIPREPGNPGKGNYWTLDP 202
           +++  E    GK ++W L+P
Sbjct: 75  IRVQNE--GTGKSSWWMLNP 92

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/80 (42%), Positives = 51/80 (63%), Gaps = 7/80 (8%)
Query: 128 SYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREK-----FPAWQNSIRHNLSLNDCF 182
           SY  LI+ AI  +P K+LTL+ I E+++   PY+++K        W+NSIRHNLSL+  F
Sbjct: 28  SYAELISQAIESAPEKRLTLAQIYEWMVRTVPYFKDKGDSNSSAGWKNSIRHNLSLHSKF 87
Query: 183 VKIPREPGNPGKGNYWTLDP 202
           +K+  E    GK ++W L+P
Sbjct: 88  IKVHNEA--TGKSSWWMLNP 105

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 40/95 (42%), Positives = 57/95 (60%), Gaps = 10/95 (10%)
Query: 128 SYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREK-----FPAWQNSIRHNLSLNDCF 182
           SY  LIT AI  SP K+LTLS I E+++   PY+++K        W+NSIRHNLSL+  F
Sbjct: 13  SYADLITRAIESSPDKRLTLSQIYEWMVRCVPYFKDKGDSNSSAGWKNSIRHNLSLHSRF 72
Query: 183 VKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRR 217
           +++  E    GK ++W ++P   D   +G   RRR
Sbjct: 73  MRVQNE--GTGKSSWWIINP---DGGKSGKAPRRR 102

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

Iteration: 1
 Score = 67.8 bits (164), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 40/95 (42%), Positives = 57/95 (60%), Gaps = 10/95 (10%)
Query: 128 SYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREK-----FPAWQNSIRHNLSLNDCF 182
           SY  LIT AI  SP K+LTLS I E+++   PY+++K        W+NSIRHNLSL+  F
Sbjct: 5   SYADLITRAIESSPDKRLTLSQIYEWMVRCVPYFKDKGDSNSSAGWKNSIRHNLSLHSRF 64
Query: 183 VKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRR 217
           +++  E    GK ++W ++P   D   +G   RRR
Sbjct: 65  MRVQNE--GTGKSSWWIINP---DGGKSGKAPRRR 94

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	289
2hfh_A	109	Genesis, HFH-2; HNF-3 homologues, winged helix pro	1e-74
2c6y_A	111	Forkhead box protein K2; transcription regulation,	2e-74
1vtn_C	102	HNF-3/FORK head DNA-recognition motif; protein-DNA	1e-73
2hdc_A	97	Protein (transcription factor); structure, dyanami	2e-73
1kq8_A	100	HFH-1, hepatocyte nuclear factor 3 forkhead homolo	1e-68
3g73_A	142	Forkhead box protein M1; DNA-binding domain, forkh	5e-59
2a07_F	93	Forkhead box protein P2; double-helix, swapping, h	1e-58
3coa_C	117	Forkhead box protein O1; winged helix, forkhead do	4e-54
1e17_A	150	AFX; DNA binding domain, winged helix; NMR {Homo s	1e-53
3bpy_A	85	FORK head domain, forkhead transcription factor FO	3e-51
3l2c_A	110	Forkhead box protein O4; winged helix, transcripti	1e-50

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

 Score =  222 bits (568), Expect = 1e-74
 Identities = 94/103 (91%), Positives = 98/103 (95%)

Query: 122 IVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDC 181
           +VKPPYSYIALITMAILQSP KKLTLSGICEFI +RFPYYREKFPAWQNSIRHNLSLNDC
Sbjct: 1   MVKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDC 60

Query: 182 FVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTP 224
           FVKIPREPGNPGKGNYWTLDP +EDMFDNGSFLRRRKR+KR  
Sbjct: 61  FVKIPREPGNPGKGNYWTLDPQSEDMFDNGSFLRRRKRFKRLQ 103

>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 =  222 bits (568), Expect = 2e-74
 Identities = 53/108 (49%), Positives = 67/108 (62%)

Query: 112 DSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNS 171
              +Q G+ S  KPPYSY  LI  AI  +P K+LTL+GI   I   +PYYR     WQNS
Sbjct: 4   TGGQQMGRGSDSKPPYSYAQLIVQAITMAPDKQLTLNGIYTHITKNYPYYRTADKGWQNS 63

Query: 172 IRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKR 219
           IRHNLSLN  F+K+PR    PGKG++W +DP +E      +F +RR R
Sbjct: 64  IRHNLSLNRYFIKVPRSQEEPGKGSFWRIDPASESKLIEQAFRKRRPR 111

>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 =  219 bits (561), Expect = 1e-73
 Identities = 64/98 (65%), Positives = 77/98 (78%)

Query: 124 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFV 183
           KPPYSYI+LITMAI Q+P K LTLS I ++IM  FPYYRE    WQNSIRH+LS NDCFV
Sbjct: 3   KPPYSYISLITMAIQQAPGKMLTLSEIYQWIMDLFPYYRENQQRWQNSIRHSLSFNDCFV 62

Query: 184 KIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYK 221
           K+ R P  PGKG+YW L P + +MF+NG +LRR+KR+K
Sbjct: 63  KVARSPDKPGKGSYWALHPSSGNMFENGCYLRRQKRFK 100

>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 =  219 bits (559), Expect = 2e-73
 Identities = 92/97 (94%), Positives = 94/97 (96%)

Query: 123 VKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCF 182
           VKPPYSYIALITMAILQSP KKLTLSGICEFI +RFPYYREKFPAWQNSIRHNLSLNDCF
Sbjct: 1   VKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDCF 60

Query: 183 VKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKR 219
           VKIPREPGNPGKGNYWTLDP +EDMFDNGSFLRRRKR
Sbjct: 61  VKIPREPGNPGKGNYWTLDPQSEDMFDNGSFLRRRKR 97

>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 =  207 bits (529), Expect = 1e-68
 Identities = 57/98 (58%), Positives = 72/98 (73%), Gaps = 1/98 (1%)

Query: 124 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFV 183
           KPPYSYIALITMAI  S   +LTL+ I E++M +FP++R  +  W+NS+RHNLSLNDCFV
Sbjct: 2   KPPYSYIALITMAIRDSAGGRLTLAEINEYLMGKFPFFRGSYTGWRNSVRHNLSLNDCFV 61

Query: 184 KIPREPGNP-GKGNYWTLDPMAEDMFDNGSFLRRRKRY 220
           K+ R+P  P GK NYW L+P +E  F +G F RRR R 
Sbjct: 62  KVLRDPSRPWGKDNYWMLNPNSEYTFADGVFRRRRYRL 99

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

 Score =  183 bits (467), Expect = 5e-59
 Identities = 45/128 (35%), Positives = 62/128 (48%), Gaps = 5/128 (3%)

Query: 107 PGPEGDSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREK-F 165
           PGP   S      +   +PPYSY+A+I  AI  +  K++TL  I  +I   FPY++    
Sbjct: 2   PGPSRPSASWQ-NSVSERPPYSYMAMIQFAINSTERKRMTLKDIYTWIEDHFPYFKHIAK 60

Query: 166 PAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPP 225
           P W+NSIRHNLSL+D FV   RE    GK ++WT+ P A          +         P
Sbjct: 61  PGWKNSIRHNLSLHDMFV---RETSANGKVSFWTIHPSANRYLTLDQVFKPLDPGSPQLP 117

Query: 226 DFLLRDPH 233
           + L     
Sbjct: 118 EHLESQQK 125

>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 =  181 bits (461), Expect = 1e-58
 Identities = 36/106 (33%), Positives = 56/106 (52%), Gaps = 13/106 (12%)

Query: 122 IVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDC 181
           IV+PP++Y  LI  AI++S  ++LTL+ I  +    F Y+R     W+N++RHNLSL+ C
Sbjct: 1   IVRPPFTYATLIRQAIMESSDRQLTLNEIYSWFTRTFAYFRRNAATWKNAVRHNLSLHKC 60

Query: 182 FVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDF 227
           FV++        KG  WT+D           + +RR +     P  
Sbjct: 61  FVRVEN-----VKGAVWTVDE--------VEYQKRRSQKITGSPTL 93

>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 =  170 bits (433), Expect = 4e-54
 Identities = 41/119 (34%), Positives = 58/119 (48%), Gaps = 10/119 (8%)

Query: 115 KQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREK-----FPAWQ 169
           K            SY  LIT AI  S  K+LTLS I E+++   PY+++K        W+
Sbjct: 2   KSSSSRRNAWGNLSYADLITKAIESSAEKRLTLSQIYEWMVKSVPYFKDKGDSNSSAGWK 61

Query: 170 NSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKRYKRTPPDFL 228
           NSIRHNLSL+  F+++  E    GK ++W L+P   +   +G   RRR         F 
Sbjct: 62  NSIRHNLSLHSKFIRVQNE--GTGKSSWWMLNP---EGGKSGKSPRRRAASMDNNSKFA 115

>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 =  162 bits (412), Expect = 3e-51
 Identities = 33/83 (39%), Positives = 51/83 (61%), Gaps = 7/83 (8%)

Query: 124 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPA-----WQNSIRHNLSL 178
               SY  LI+ AI  +P K+LTL+ I E+++   PY+++K  +     W+NSIRHNLSL
Sbjct: 5   WGNQSYAELISQAIESAPEKRLTLAQIYEWMVRTVPYFKDKGDSNSSAGWKNSIRHNLSL 64

Query: 179 NDCFVKIPREPGNPGKGNYWTLD 201
           +  F+K+  E    GK ++W L+
Sbjct: 65  HSKFIKVHNEA--TGKSSWWMLN 85

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

 Score =  161 bits (410), Expect = 1e-50
 Identities = 35/109 (32%), Positives = 55/109 (50%), Gaps = 7/109 (6%)

Query: 102 DGSISPGPEGDSDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYY 161
              +         ++ G         SY  LI+ AI  +P K+LTL+ I E+++   PY+
Sbjct: 2   SHMLEDPGAVTGPRKGGSRRNAWGNQSYAELISQAIESAPEKRLTLAQIYEWMVRTVPYF 61

Query: 162 REK-----FPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPMAE 205
           ++K        W+NSIRHNLSL+  F+K+  E    GK ++W L+P   
Sbjct: 62  KDKGDSNSSAGWKNSIRHNLSLHSKFIKVHNEA--TGKSSWWMLNPEGG 108

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	289
1vtn_C	102	HNF-3/FORK head DNA-recognition motif; protein-DNA	100.0
2hdc_A	97	Protein (transcription factor); structure, dyanami	100.0
2hfh_A	109	Genesis, HFH-2; HNF-3 homologues, winged helix pro	100.0
1kq8_A	100	HFH-1, hepatocyte nuclear factor 3 forkhead homolo	100.0
2c6y_A	111	Forkhead box protein K2; transcription regulation,	100.0
3l2c_A	110	Forkhead box protein O4; winged helix, transcripti	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
2a07_F	93	Forkhead box protein P2; double-helix, swapping, h	100.0
1e17_A	150	AFX; DNA binding domain, winged helix; NMR {Homo s	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	87.97
1uhm_A	78	Histone H1, histone HHO1P; winged helix-turn-helix	87.9
1hst_A	90	Histone H5; chromosomal protein; 2.60A {Gallus gal	85.8
2rqp_A	88	Heterochromatin protein 1-binding protein 3; histo	84.52
1ust_A	93	Histone H1; DNA binding protein, linker histone, D	83.85

>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=4.4e-46  Score=301.44  Aligned_cols=101  Identities=63%  Similarity=1.154  Sum_probs=97.9

Q ss_pred             CCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCCceeEEeC
Q psy9499         122 IVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLD  201 (289)
Q Consensus       122 ~~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~Wtld  201 (289)
                      ++||||||++||+|||+++|+++|||+|||+||+++||||+.+..|||||||||||||+||+||++..+++|||+||+|+
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            47999999999999999999999999999999999999999999999999999999999999999998999999999999


Q ss_pred             CCchhcccCccchhcccccCC
Q psy9499         202 PMAEDMFDNGSFLRRRKRYKR  222 (289)
Q Consensus       202 P~~e~~f~~g~~~RrRkr~kr  222 (289)
                      |+++++|++|.|+|||+|+|+
T Consensus        81 p~~~~~f~~g~~~rr~~~~~~  101 (102)
T 1vtn_C           81 PSSGNMFENGCYLRRQKRFKL  101 (102)
T ss_dssp             GGGCSTTCSSCSSSCSSCCCC
T ss_pred             cCHHHHhhcCCeecccccccc
Confidence            999999999999999998875

>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=5e-46  Score=298.70  Aligned_cols=97  Identities=95%  Similarity=1.596  Sum_probs=94.3

Q ss_pred             CCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCCceeEEeCC
Q psy9499         123 VKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDP  202 (289)
Q Consensus       123 ~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~WtldP  202 (289)
                      +||||||++||+|||+++|+++|||+|||+||+++||||+.+..|||||||||||||+||+||+|+.+++|||+||+|||
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            59999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CchhcccCccchhcccc
Q psy9499         203 MAEDMFDNGSFLRRRKR  219 (289)
Q Consensus       203 ~~e~~f~~g~~~RrRkr  219 (289)
                      +++++|++|.|+|||+|
T Consensus        81 ~~~~~f~~g~~~rrr~r   97 (97)
T 2hdc_A           81 QSEDMFDNGSFLRRRKR   97 (97)
T ss_dssp             THHHHHHHSCCCSSSCC
T ss_pred             CHHHHHhCCCccCCCCC
Confidence            99999999999888875

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

Probab=100.00  E-value=1.6e-45  Score=301.34  Aligned_cols=103  Identities=91%  Similarity=1.548  Sum_probs=91.3

Q ss_pred             CCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCCceeEEeC
Q psy9499         122 IVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLD  201 (289)
Q Consensus       122 ~~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~Wtld  201 (289)
                      .+||||||++||+|||+++|+++|||+|||+||+++||||+.+..|||||||||||||+||+||+|+.+++|||+||+||
T Consensus         1 ~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSln~~F~Kv~r~~~~~GKG~~W~l~   80 (109)
T 2hfh_A            1 MVKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLD   80 (109)
T ss_dssp             CCCCCCCHHHHHHHHHHTCSSSCBCHHHHHHHHHTTCHHHHTTCGGGHHHHHHHHHHHTCCBCCTTCTTSCSSCCCBBCC
T ss_pred             CCCCCCCHHHHHHHHHHhCCCCCCcHHHHHHHHHHhcchhccCCcccchhhhhhhhhhhhhhcCCCCCCCCCCceeEEEC
Confidence            37999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCchhcccCccchhcccccCCCC
Q psy9499         202 PMAEDMFDNGSFLRRRKRYKRTP  224 (289)
Q Consensus       202 P~~e~~f~~g~~~RrRkr~kr~~  224 (289)
                      |+++++|++|.|+|||+++++-+
T Consensus        81 p~~~~~f~~g~~~Rrr~~~~~~~  103 (109)
T 2hfh_A           81 PQSEDMFDNGSFLRRRKRFKRLQ  103 (109)
T ss_dssp             TTCCHHHHSSSCC----------
T ss_pred             ccHHHHHhCCCcccCcccccccc
Confidence            99999999999999998876643

>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=2.3e-45  Score=296.25  Aligned_cols=98  Identities=58%  Similarity=1.091  Sum_probs=73.1

Q ss_pred             CCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCC-CCceeEEeC
Q psy9499         123 VKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNP-GKGNYWTLD  201 (289)
Q Consensus       123 ~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~p-GKG~~Wtld  201 (289)
                      +||||||++||+|||+++|+++|||+|||+||+++||||+.+..|||||||||||||+||+||+++.+++ |||+||+||
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            5999999999999999999999999999999999999999999999999999999999999999998888 999999999


Q ss_pred             CCchhcccCccchhccccc
Q psy9499         202 PMAEDMFDNGSFLRRRKRY  220 (289)
Q Consensus       202 P~~e~~f~~g~~~RrRkr~  220 (289)
                      |+++++|++|.|+|||+|+
T Consensus        81 p~~~~~f~~g~~~rrr~r~   99 (100)
T 1kq8_A           81 PNSEYTFADGVFRRRRYRL   99 (100)
T ss_dssp             C------------------
T ss_pred             cCHHHHHhCCCcccCCCCC
Confidence            9999999999999988874

>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=1.1e-44  Score=297.28  Aligned_cols=102  Identities=51%  Similarity=0.934  Sum_probs=95.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCCcee
Q psy9499         118 GKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNY  197 (289)
Q Consensus       118 ~~~~~~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~  197 (289)
                      +.....||||||++||+|||+++|+++|||+|||+||+++||||+.+..|||||||||||||+||+||+|..+++|||+|
T Consensus        10 ~~~~~~KPp~SYa~LI~~AI~~sp~~~LtL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSln~~F~Kv~r~~~~~GKG~~   89 (111)
T 2c6y_A           10 GRGSDSKPPYSYAQLIVQAITMAPDKQLTLNGIYTHITKNYPYYRTADKGWQNSIRHNLSLNRYFIKVPRSQEEPGKGSF   89 (111)
T ss_dssp             ----CCCCSSCHHHHHHHHHHTSTTSCEEHHHHHHHHHHHCTTSCTTCHHHHHHHHHHHHHSTTEEEECCCTTSCCSSCE
T ss_pred             CCCCCCCCCCCHHHHHHHHHHhCCCCCCcHHHHHHHHHHcCCccccCCCeeecchhHHhhhhhhhccccCCCCCCCCcce
Confidence            44567999999999999999999999999999999999999999999999999999999999999999999889999999


Q ss_pred             EEeCCCchhcccCccchhcccc
Q psy9499         198 WTLDPMAEDMFDNGSFLRRRKR  219 (289)
Q Consensus       198 WtldP~~e~~f~~g~~~RrRkr  219 (289)
                      |+|||+++++|+++.|+|||+|
T Consensus        90 W~l~p~~~~~~~~~~~r~rr~r  111 (111)
T 2c6y_A           90 WRIDPASESKLIEQAFRKRRPR  111 (111)
T ss_dssp             EEECHHHHHHHHHHHTCCCCCC
T ss_pred             EEeChhHHHhhhcccccccCCC
Confidence            9999999999999999888764

>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=7.1e-39  Score=262.29  Aligned_cols=88  Identities=40%  Similarity=0.736  Sum_probs=76.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccC-----CCccccccccccccccccccccCCCCC
Q psy9499         117 DGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREK-----FPAWQNSIRHNLSLNDCFVKIPREPGN  191 (289)
Q Consensus       117 ~~~~~~~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~-----~~gWqNSIRHNLSlNkcF~Kvpr~~~~  191 (289)
                      .......||||||++||+|||+++|+++|||+|||+||+++||||+.+     ..|||||||||||||+||+||+++  +
T Consensus        17 ~~~~~~~kPpySY~~LI~~AI~~sp~~~LtL~eIY~~I~~~fPyyr~~~~~~s~~gWqNSIRHNLSln~~F~Kv~r~--~   94 (110)
T 3l2c_A           17 GGSRRNAWGNQSYAELISQAIESAPEKRLTLAQIYEWMVRTVPYFKDKGDSNSSAGWKNSIRHNLSLHSKFIKVHNE--A   94 (110)
T ss_dssp             ---CCBTTBSCCHHHHHHHHHHHSTTSCBCHHHHHHHHHHHCGGGTTCTTCCTTSHHHHHHHHHHHHCTTEEEECCC--S
T ss_pred             CccCCCCCCCCCHHHHHHHHHHhCCccCcCHHHHHHHHHHhCchhhcCccccCCCCcccchhhhccHhhhheeCCCC--C
Confidence            345567999999999999999999999999999999999999999986     469999999999999999999985  7


Q ss_pred             CCCceeEEeCCCchh
Q psy9499         192 PGKGNYWTLDPMAED  206 (289)
Q Consensus       192 pGKG~~WtldP~~e~  206 (289)
                      +|||+||+|||++++
T Consensus        95 ~GKG~~W~l~p~~~~  109 (110)
T 3l2c_A           95 TGKSSWWMLNPEGGK  109 (110)
T ss_dssp             TTCCCEEEEC-----
T ss_pred             CCCCceEEECccccC
Confidence            899999999999864

>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=1e-38  Score=263.96  Aligned_cols=86  Identities=41%  Similarity=0.711  Sum_probs=77.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCC-----CccccccccccccccccccccCCCCCC
Q psy9499         118 GKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKF-----PAWQNSIRHNLSLNDCFVKIPREPGNP  192 (289)
Q Consensus       118 ~~~~~~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~-----~gWqNSIRHNLSlNkcF~Kvpr~~~~p  192 (289)
                      ......||||||++||+|||+++|+++|||+|||+||+++||||+.+.     .|||||||||||||+||+||+++  ++
T Consensus         5 ~s~~n~kPp~SYa~LI~~AI~~sp~~~LTL~eIY~~I~~~fPyyr~~~d~~s~~gWqNSIRHNLSln~~F~Kv~~~--~~   82 (117)
T 3coa_C            5 SSRRNAWGNLSYADLITKAIESSAEKRLTLSQIYEWMVKSVPYFKDKGDSNSSAGWKNSIRHNLSLHSKFIRVQNE--GT   82 (117)
T ss_dssp             --CCBTTBSCCHHHHHHHHHHTSTTSCBCHHHHHHHHHHHCGGGTTCCSHHHHHHHHHHHHHHHHHCTTEEEECCS--ST
T ss_pred             cCCCCCCCCCCHHHHHHHHHHhCCCCCccHHHHHHHHHHhCcccccCCCCcccccchhccchheecchhhcccccC--CC
Confidence            345678999999999999999999999999999999999999999875     79999999999999999999985  68


Q ss_pred             CCceeEEeCCCch
Q psy9499         193 GKGNYWTLDPMAE  205 (289)
Q Consensus       193 GKG~~WtldP~~e  205 (289)
                      |||+||+|||++.
T Consensus        83 GKg~~W~l~p~~~   95 (117)
T 3coa_C           83 GKSSWWMLNPEGG   95 (117)
T ss_dssp             TCCCEEEECC---
T ss_pred             CCcceEEECcccc
Confidence            9999999999874

>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=2.3e-38  Score=248.71  Aligned_cols=78  Identities=42%  Similarity=0.776  Sum_probs=74.2

Q ss_pred             CCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccC-----CCccccccccccccccccccccCCCCCCCCce
Q psy9499         122 IVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREK-----FPAWQNSIRHNLSLNDCFVKIPREPGNPGKGN  196 (289)
Q Consensus       122 ~~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~-----~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~  196 (289)
                      ..||||||++||+|||+++|+++|||+|||+||+++||||+.+     ..|||||||||||||+||+||+++  ++|||+
T Consensus         3 n~kp~~SY~~LI~~Ai~~sp~~~ltL~eIY~~i~~~fpyy~~~~~~~s~~gWqNSIRHNLSln~~F~Kv~r~--~~GKg~   80 (85)
T 3bpy_A            3 NAWGNQSYAELISQAIESAPEKRLTLAQIYEWMVRTVPYFKDKGDSNSSAGWKNSIRHNLSLHSKFIKVHNE--ATGKSS   80 (85)
T ss_dssp             BTTBSCCHHHHHHHHHHHSTTSCBCHHHHHHHHHHHCGGGTTCTTCCTTSHHHHHHHHHHHHCTTEEEECCC--STTCCC
T ss_pred             CCcCCCCHHHHHHHHHHhCCcCCccHHHHHHHHHHhCcchhcCccCccCCCcchhhhhhccHhhhheeCCCC--CCCCCC
Confidence            5899999999999999999999999999999999999999986     469999999999999999999985  789999


Q ss_pred             eEEeC
Q psy9499         197 YWTLD  201 (289)
Q Consensus       197 ~Wtld  201 (289)
                      ||+||
T Consensus        81 ~W~ld   85 (85)
T 3bpy_A           81 WWMLN   85 (85)
T ss_dssp             EEEEC
T ss_pred             ceecC
Confidence            99997

>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=6.3e-39  Score=255.87  Aligned_cols=87  Identities=39%  Similarity=0.854  Sum_probs=76.7

Q ss_pred             CCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCCceeEEeCC
Q psy9499         123 VKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDP  202 (289)
Q Consensus       123 ~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~WtldP  202 (289)
                      +||||||++||+|||+++|+++|||+|||+||+++||||+.+..|||||||||||||+||+||++     |||+||+|||
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            79999999999999999999999999999999999999999999999999999999999999974     7999999997


Q ss_pred             CchhcccCccchhcccccCC
Q psy9499         203 MAEDMFDNGSFLRRRKRYKR  222 (289)
Q Consensus       203 ~~e~~f~~g~~~RrRkr~kr  222 (289)
                      +        .+.+||.+...
T Consensus        77 ~--------~~~k~r~~~~~   88 (93)
T 2a07_F           77 V--------EYQKRRSQKIT   88 (93)
T ss_dssp             H--------HHHHHC-----
T ss_pred             H--------Hhhcccccccc
Confidence            4        35555544433

>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=4e-37  Score=261.84  Aligned_cols=96  Identities=40%  Similarity=0.757  Sum_probs=81.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCccc-CCCccccccccccccccccccccCCCCCCCCcee
Q psy9499         119 KNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYRE-KFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNY  197 (289)
Q Consensus       119 ~~~~~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~-~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~  197 (289)
                      ....+||||||++||+|||+++++++|||+|||+||+++||||+. +..|||||||||||||+||+|+.   +++|||+|
T Consensus        13 ~~~~~KPpySYa~LI~~AI~~sp~~~LTL~eIY~~I~~~fPyyr~~~~~gWqNSIRHNLSln~~F~r~~---~~~GKg~~   89 (142)
T 3g73_A           13 NSVSERPPYSYMAMIQFAINSTERKRMTLKDIYTWIEDHFPYFKHIAKPGWKNSIRHNLSLHDMFVRET---SANGKVSF   89 (142)
T ss_dssp             -CTTSCCSSCHHHHHHHHHHTSTTSEECHHHHHHHHHHHCTHHHHTSCTTHHHHHHHHHHHCTTEEEEE---CTTSCCEE
T ss_pred             ccCCCCCCCCHHHHHHHHHHhCCCCCcCHHHHHHHHHHhCCCccccCCCCccchhhhhhhhhhhheecC---CCCCCCce
Confidence            455689999999999999999999999999999999999999998 88999999999999999999864   46899999


Q ss_pred             EEeCCCchhcc-cCccchhcc
Q psy9499         198 WTLDPMAEDMF-DNGSFLRRR  217 (289)
Q Consensus       198 WtldP~~e~~f-~~g~~~RrR  217 (289)
                      |+|||+++..+ .++.|++.+
T Consensus        90 W~i~p~~~~~l~~d~~~k~~~  110 (142)
T 3g73_A           90 WTIHPSANRYLTLDQVFKPLD  110 (142)
T ss_dssp             EEECTTTCCCCCCC-------
T ss_pred             EEECccccccchhhhhhcccc
Confidence            99999997654 555555444

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

Probab=87.97  E-value=0.55  Score=36.21  Aligned_cols=32  Identities=16%  Similarity=0.218  Sum_probs=28.0

Q ss_pred             CHHHHHHHHHhcCC-CCCCCHHHHHHHHHhcCC
Q psy9499         128 SYIALITMAILQSP-HKKLTLSGICEFIMSRFP  159 (289)
Q Consensus       128 SYa~LI~~AI~sSp-~k~LTL~eIY~~I~~~fP  159 (289)
                      +|..||..||.... .+..+++-|..||+.+|.
T Consensus         9 ~y~~MI~eAI~alker~GsS~~AIkKyI~~~y~   41 (88)
T 1uss_A            9 TYKEMILKSMPQLNDGKGSSRIVLKKYVKDTFS   41 (88)
T ss_dssp             CHHHHHHHHHHHSCCTTSBCHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHhccCCCcCHHHHHHHHHHhCC
Confidence            69999999999744 458899999999999976

>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=87.90  E-value=0.44  Score=35.79  Aligned_cols=33  Identities=24%  Similarity=0.390  Sum_probs=28.6

Q ss_pred             CHHHHHHHHHhc-CCCCCCCHHHHHHHHHhcCCC
Q psy9499         128 SYIALITMAILQ-SPHKKLTLSGICEFIMSRFPY  160 (289)
Q Consensus       128 SYa~LI~~AI~s-Sp~k~LTL~eIY~~I~~~fPy  160 (289)
                      +|..||..||.. ...+..+++.|-.||+.+|+.
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            699999999997 455678999999999999763

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

Probab=85.80  E-value=0.7  Score=35.87  Aligned_cols=32  Identities=22%  Similarity=0.324  Sum_probs=28.1

Q ss_pred             CHHHHHHHHHhcCCC-CCCCHHHHHHHHHhcCC
Q psy9499         128 SYIALITMAILQSPH-KKLTLSGICEFIMSRFP  159 (289)
Q Consensus       128 SYa~LI~~AI~sSp~-k~LTL~eIY~~I~~~fP  159 (289)
                      +|..||..||....+ +..+++-|-.||+.+|.
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            699999999998544 57899999999999976

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

Probab=84.52  E-value=0.47  Score=36.42  Aligned_cols=34  Identities=21%  Similarity=0.343  Sum_probs=29.0

Q ss_pred             CHHHHHHHHHhc-CCCCCCCHHHHHHHHHhcCCCc
Q psy9499         128 SYIALITMAILQ-SPHKKLTLSGICEFIMSRFPYY  161 (289)
Q Consensus       128 SYa~LI~~AI~s-Sp~k~LTL~eIY~~I~~~fPyy  161 (289)
                      +|..||.+||.. ...+.-+++.|..||+.+|+-+
T Consensus        11 ~y~~MI~eAI~~Lker~GsS~~AI~KyI~~~y~~~   45 (88)
T 2rqp_A           11 KMDAILTEAIKACFQKSGASVVAIRKYIIHKYPSL   45 (88)
T ss_dssp             CHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHCSTH
T ss_pred             CHHHHHHHHHHHhccCCCcCHHHHHHHHHHhCCCC
Confidence            699999999997 3446789999999999999843

---

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	289
d2hdca_	97	a.4.5.14 (A:) Genesis {Rat (Rattus norvegicus) [Ta	1e-54
d2c6ya1	98	a.4.5.14 (A:1-98) Interleukin enhancer binding fac	2e-51
d1d5va_	94	a.4.5.14 (A:) Adipocyte-transcription factor FREAC	2e-51
d2a07f1	82	a.4.5.14 (F:503-584) Forkhead box protein P2, FOXP	4e-39
d1kq8a_	75	a.4.5.14 (A:) HFH-1 (HNF-3 forkhead homolog-1) {Ra	6e-38
d3bpya1	85	a.4.5.14 (A:93-177) Afx (Foxo4) {Human (Homo sapie	3e-37

>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 =  170 bits (432), Expect = 1e-54
 Identities = 92/97 (94%), Positives = 94/97 (96%)

Query: 123 VKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCF 182
           VKPPYSYIALITMAILQSP KKLTLSGICEFI +RFPYYREKFPAWQNSIRHNLSLNDCF
Sbjct: 1   VKPPYSYIALITMAILQSPQKKLTLSGICEFISNRFPYYREKFPAWQNSIRHNLSLNDCF 60

Query: 183 VKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKR 219
           VKIPREPGNPGKGNYWTLDP +EDMFDNGSFLRRRKR
Sbjct: 61  VKIPREPGNPGKGNYWTLDPQSEDMFDNGSFLRRRKR 97

>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 =  162 bits (411), Expect = 2e-51
 Identities = 50/96 (52%), Positives = 62/96 (64%)

Query: 124 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFV 183
           KPPYSY  LI  AI  +P K+LTL+GI   I   +PYYR     WQNSIRHNLSLN  F+
Sbjct: 3   KPPYSYAQLIVQAITMAPDKQLTLNGIYTHITKNYPYYRTADKGWQNSIRHNLSLNRYFI 62

Query: 184 KIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRRKR 219
           K+PR    PGKG++W +DP +E      +F +RR R
Sbjct: 63  KVPRSQEEPGKGSFWRIDPASESKLIEQAFRKRRPR 98

>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 =  161 bits (410), Expect = 2e-51
 Identities = 66/93 (70%), Positives = 79/93 (84%)

Query: 122 IVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDC 181
           +VKPPYSYIALITMAI  +P KK+TL+GI +FIM RFP+YRE    WQNSIRHNLSLN+C
Sbjct: 2   LVKPPYSYIALITMAIQNAPEKKITLNGIYQFIMDRFPFYRENKQGWQNSIRHNLSLNEC 61

Query: 182 FVKIPREPGNPGKGNYWTLDPMAEDMFDNGSFL 214
           FVK+PR+   PGKG+YWTLDP + +MF+NGSFL
Sbjct: 62  FVKVPRDDKKPGKGSYWTLDPDSYNMFENGSFL 94

>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 =  129 bits (327), Expect = 4e-39
 Identities = 34/95 (35%), Positives = 54/95 (56%), Gaps = 13/95 (13%)

Query: 123 VKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCF 182
           V+PP++Y  LI  AI++S  ++LTL+ I  +    F Y+R     W+N++RHNLSL+ CF
Sbjct: 1   VRPPFTYATLIRQAIMESSDRQLTLNEIYSWFTRTFAYFRRNAATWKNAVRHNLSLHKCF 60

Query: 183 VKIPREPGNPGKGNYWTLDPMAEDMFDNGSFLRRR 217
           V++        KG  WT+D +         + +RR
Sbjct: 61  VRVEN-----VKGAVWTVDEVE--------YQKRR 82

>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 =  126 bits (319), Expect = 6e-38
 Identities = 44/75 (58%), Positives = 57/75 (76%), Gaps = 1/75 (1%)

Query: 129 YIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPRE 188
           YIALITMAI  S   +LTL+ I E++M +FP++R  +  W+NS+RHNLSLNDCFVK+ R+
Sbjct: 1   YIALITMAIRDSAGGRLTLAEINEYLMGKFPFFRGSYTGWRNSVRHNLSLNDCFVKVLRD 60

Query: 189 PGNP-GKGNYWTLDP 202
           P  P GK NYW L+P
Sbjct: 61  PSRPWGKDNYWMLNP 75

>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 =  125 bits (315), Expect = 3e-37
 Identities = 33/83 (39%), Positives = 50/83 (60%), Gaps = 7/83 (8%)

Query: 124 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKF-----PAWQNSIRHNLSL 178
               SY  LI+ AI  +P K+LTL+ I E+++   PY+++K        W+NSIRHNLSL
Sbjct: 5   WGNQSYAELISQAIESAPEKRLTLAQIYEWMVRTVPYFKDKGDSNSSAGWKNSIRHNLSL 64

Query: 179 NDCFVKIPREPGNPGKGNYWTLD 201
           +  F+K+  E    GK ++W L+
Sbjct: 65  HSKFIKVHNEA--TGKSSWWMLN 85

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	289
d2hdca_	97	Genesis {Rat (Rattus norvegicus) [TaxId: 10116]}	100.0
d2c6ya1	98	Interleukin enhancer binding factor {Human (Homo s	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	93.34
d1hsta_	74	Histone H5, globular domain {Chicken (Gallus gallu	92.98
d1usta_	92	Histone H1 homologue Hho1p {Baker's yeast (Sacchar	92.77
d1ghca_	75	Histone H1, globular domain {Chicken (Gallus gallu	81.93

>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=1.6e-43  Score=282.18  Aligned_cols=97  Identities=95%  Similarity=1.596  Sum_probs=94.1

Q ss_pred             CCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCCceeEEeCC
Q psy9499         123 VKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDP  202 (289)
Q Consensus       123 ~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~WtldP  202 (289)
                      +||||||++||++||+++|+++|||+|||+||+++||||+.+..|||||||||||+|+||+||+++.+++|||+||+|+|
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            59999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CchhcccCccchhcccc
Q psy9499         203 MAEDMFDNGSFLRRRKR  219 (289)
Q Consensus       203 ~~e~~f~~g~~~RrRkr  219 (289)
                      ++++.|++|.++|||+|
T Consensus        81 ~~~~~~~~~~~~rrrkr   97 (97)
T d2hdca_          81 QSEDMFDNGSFLRRRKR   97 (97)
T ss_dssp             THHHHHHHSCCCSSSCC
T ss_pred             cHHHHhhcCCccccCCC
Confidence            99999999999888765

>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=6.9e-43  Score=278.94  Aligned_cols=97  Identities=52%  Similarity=0.954  Sum_probs=92.9

Q ss_pred             CCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCCceeEEeCC
Q psy9499         123 VKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDP  202 (289)
Q Consensus       123 ~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~WtldP  202 (289)
                      .||||||++||+|||+++|+++|||+|||+||+++||||+.+..|||||||||||+|+||+||++..+++|||+||+|+|
T Consensus         2 ~KP~~sY~~LI~~Ai~~sp~~~ltL~eIy~~i~~~fpyfr~~~~gWkNSIRHnLS~n~~F~kv~r~~~~~gKg~~W~l~p   81 (98)
T d2c6ya1           2 SKPPYSYAQLIVQAITMAPDKQLTLNGIYTHITKNYPYYRTADKGWQNSIRHNLSLNRYFIKVPRSQEEPGKGSFWRIDP   81 (98)
T ss_dssp             CCCSSCHHHHHHHHHHTSTTSCEEHHHHHHHHHHHCTTSCTTCHHHHHHHHHHHHHSTTEEEECCCTTSCCSSCEEEECH
T ss_pred             CCCCccHHHHHHHHHHhCCCCCccHHHHHHHHHHhCcccccCCCCcchhhchhcccccceEeccCCCCCCCCCceEEECc
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CchhcccCccchhcccc
Q psy9499         203 MAEDMFDNGSFLRRRKR  219 (289)
Q Consensus       203 ~~e~~f~~g~~~RrRkr  219 (289)
                      +++..|.++.++|||+|
T Consensus        82 ~~~~~~~~~~~~krr~r   98 (98)
T d2c6ya1          82 ASESKLIEQAFRKRRPR   98 (98)
T ss_dssp             HHHHHHHHHHTCCCCCC
T ss_pred             cHHhhhhcchhhccCCC
Confidence            99999998888777654

>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=6.1e-42  Score=271.73  Aligned_cols=93  Identities=71%  Similarity=1.295  Sum_probs=90.6

Q ss_pred             CCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCCceeEEeC
Q psy9499         122 IVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLD  201 (289)
Q Consensus       122 ~~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~Wtld  201 (289)
                      .+||||||++||++||+++|+++|||+|||+||+++|||||.+..|||||||||||+|+||+||++..+++|||+||+|+
T Consensus         2 l~KP~~SYa~LI~~AI~~sp~~~ltL~eIY~~i~~~fpyfr~~~~gWkNSIRHnLSln~~F~kv~~~~~~~gkg~~W~l~   81 (94)
T d1d5va_           2 LVKPPYSYIALITMAIQNAPEKKITLNGIYQFIMDRFPFYRENKQGWQNSIRHNLSLNECFVKVPRDDKKPGKGSYWTLD   81 (94)
T ss_dssp             CCCCSSCHHHHHHHHHHTCSSSSBCHHHHHHHHHHHCTHHHHCCTTHHHHHHHHHHHCSSEEECCCCTTSCSCCCCEEEC
T ss_pred             CCCCCCCHHHHHHHHHHhCCCCCccHHHHHHHHHHHCCccCccccchHHHHHHHccccceEEEcCcCCCCCCCCceEEEC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCchhcccCccch
Q psy9499         202 PMAEDMFDNGSFL  214 (289)
Q Consensus       202 P~~e~~f~~g~~~  214 (289)
                      |++++.|++|.|+
T Consensus        82 p~~~~~f~~g~~~   94 (94)
T d1d5va_          82 PDSYNMFENGSFL   94 (94)
T ss_dssp             CSCSSTTSCSSCC
T ss_pred             ccHHHHHhcCCCC
Confidence            9999999999885

>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=4.3e-37  Score=234.82  Aligned_cols=74  Identities=59%  Similarity=1.167  Sum_probs=72.2

Q ss_pred             HHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCC-CCceeEEeCC
Q psy9499         129 YIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNP-GKGNYWTLDP  202 (289)
Q Consensus       129 Ya~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~p-GKG~~WtldP  202 (289)
                      |++||+|||+++|+++|||+|||+||+++|||||.+..|||||||||||+|+||+||+|+.+++ |||+||+|||
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            8999999999999999999999999999999999999999999999999999999999998887 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=3.3e-37  Score=239.03  Aligned_cols=76  Identities=42%  Similarity=0.920  Sum_probs=73.3

Q ss_pred             CCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCCceeEEeCC
Q psy9499         123 VKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDP  202 (289)
Q Consensus       123 ~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~WtldP  202 (289)
                      +||||||++||++||+++|+++|||+|||+||+++||||+.+.+|||||||||||+|+||+||++     |||+||+|||
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            59999999999999999999999999999999999999999999999999999999999999975     8999999997


Q ss_pred             C
Q psy9499         203 M  203 (289)
Q Consensus       203 ~  203 (289)
                      +
T Consensus        76 ~   76 (82)
T d2a07f1          76 V   76 (82)
T ss_dssp             H
T ss_pred             H
Confidence            5

>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=1.3e-35  Score=231.37  Aligned_cols=78  Identities=42%  Similarity=0.776  Sum_probs=73.1

Q ss_pred             CCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccC-----CCccccccccccccccccccccCCCCCCCCce
Q psy9499         122 IVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREK-----FPAWQNSIRHNLSLNDCFVKIPREPGNPGKGN  196 (289)
Q Consensus       122 ~~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~-----~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~  196 (289)
                      ..+|++||++||++||+++|+++|||+|||+||+++|||||..     ..|||||||||||+|+||+||+++  .+|||+
T Consensus         3 n~~~~~SY~~LI~~Ai~~sp~~~ltL~eIY~~i~~~fPyyr~~~~~~~~~gWkNSIRHnLSl~~~F~kv~r~--~~gKg~   80 (85)
T d3bpya1           3 NAWGNQSYAELISQAIESAPEKRLTLAQIYEWMVRTVPYFKDKGDSNSSAGWKNSIRHNLSLHSKFIKVHNE--ATGKSS   80 (85)
T ss_dssp             BTTBSCCHHHHHHHHHHHSTTSCBCHHHHHHHHHHHCGGGTTCTTCCTTSHHHHHHHHHHHHCTTEEEECCC--STTCCC
T ss_pred             CCCCCcCHHHHHHHHHHhCCCCCccHHHHHHHHHHhChhhhccCcccccccchhhHHHHhhHhhheeeCCCC--CCCCCc
Confidence            4789999999999999999999999999999999999999964     458999999999999999999987  579999


Q ss_pred             eEEeC
Q psy9499         197 YWTLD  201 (289)
Q Consensus       197 ~Wtld  201 (289)
                      ||+||
T Consensus        81 ~W~i~   85 (85)
T d3bpya1          81 WWMLN   85 (85)
T ss_dssp             EEEEC
T ss_pred             eeecC
Confidence            99997

>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=93.34  E-value=0.036  Score=41.20  Aligned_cols=35  Identities=14%  Similarity=0.216  Sum_probs=30.7

Q ss_pred             CCCHHHHHHHHHhc-CCCCCCCHHHHHHHHHhcCCC
Q psy9499         126 PYSYIALITMAILQ-SPHKKLTLSGICEFIMSRFPY  160 (289)
Q Consensus       126 PySYa~LI~~AI~s-Sp~k~LTL~eIY~~I~~~fPy  160 (289)
                      -.||..||..||.+ ...+..++..|-.||+.+|+.
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            45799999999998 445789999999999999985

>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=92.98  E-value=0.041  Score=39.50  Aligned_cols=32  Identities=22%  Similarity=0.343  Sum_probs=28.2

Q ss_pred             CHHHHHHHHHhcC-CCCCCCHHHHHHHHHhcCC
Q psy9499         128 SYIALITMAILQS-PHKKLTLSGICEFIMSRFP  159 (289)
Q Consensus       128 SYa~LI~~AI~sS-p~k~LTL~eIY~~I~~~fP  159 (289)
                      +|..||.+||.+. ..+.-++..|..||+.+|+
T Consensus         4 ~y~~MI~eAI~al~er~GsS~~AI~kyI~~~y~   36 (74)
T d1hsta_           4 TYSEMIAAAIRAEKSRGGSSRQSIQKYIKSHYK   36 (74)
T ss_dssp             CHHHHHHHHHHTCCCSSCEEHHHHHHHHHHHSC
T ss_pred             CHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCC
Confidence            5999999999984 4467899999999999987

>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=92.77  E-value=0.033  Score=41.71  Aligned_cols=34  Identities=24%  Similarity=0.358  Sum_probs=29.7

Q ss_pred             CCHHHHHHHHHhc-CCCCCCCHHHHHHHHHhcCCC
Q psy9499         127 YSYIALITMAILQ-SPHKKLTLSGICEFIMSRFPY  160 (289)
Q Consensus       127 ySYa~LI~~AI~s-Sp~k~LTL~eIY~~I~~~fPy  160 (289)
                      -||..||..||.. ...+..++..|..||+.+|+-
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            4699999999997 445688999999999999983

>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=81.93  E-value=0.087  Score=37.95  Aligned_cols=31  Identities=26%  Similarity=0.239  Sum_probs=27.0

Q ss_pred             CHHHHHHHHHhc-CCCCCCCHHHHHHHHHhcC
Q psy9499         128 SYIALITMAILQ-SPHKKLTLSGICEFIMSRF  158 (289)
Q Consensus       128 SYa~LI~~AI~s-Sp~k~LTL~eIY~~I~~~f  158 (289)
                      +|..||.+||.+ ...+..++..|..||+.+|
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            599999999997 5557889999999999875