Citrus Sinensis ID: 006832

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------63
Protein Sequence
MPGAGKKVVKHSESGKSCFPKKDSGSELIASLKFKKGSKISKSKKLRSKSRCQSKTVNSTLLKRTVAESHSKGAGDDFARSKSISQKNLHIKIDRKGSKNWASSKHKGKNSALVISKGNGEVVDGDGETKKLRKGRSKKRRKEKVELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRPEKELQRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRENSCSISRAGTDDDPSSSTSLSWFSDSETFSESMRWEMESNGYKNYSVDSSIGSDETSDGEIICGRRQRRTVDYKKLYDEMFGKDASAFEQLSEDEDWGPAKRRRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESARQVSGSPRISKESSLETEKKNADVLTLKNSLEETLICSPKSLKKIHPKRIQNQSAVAAASRKISRKELL
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccHHHccccccccccccccccHHHHHHcccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccHHHHccccHHHHHccccHHHHcccccccccccccccccccccccHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccccHccccccccccccccccccccccccccccccEEcccHccccccccccccccccccccccccccccccccccHccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHccccccccccccEHHHcccccccccccEEEEcccccccHHHHHcccccccccccccccccccccHHHHHHHHHHHccccccccccHHHHcHHHHHcccccccccccHHcccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccHcccccccEEEcHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHcHccHHHHHHHHHHcccEEccccHccccccccccccccccccccHccHHHHc
Coil and Loop (DISEMBL)
mpgagkkvvkhsesgkscfpkkdsgSELIASLKfkkgskiskskklrsksrcqsktvnsTLLKRTvaeshskgagddfarsksisqknLHIKIdrkgsknwasskhkgknsaLVISkgngevvdgdgetkklrkgrskkrrkEKVELDEASRLQRRTRYLLIKMKLEQNLIDaysgegwkghsrekirPEKELQRAKKQILKCKIGIRDAIRQldslssvgciegsviatdgsvhhEHIICAKCklreafpdndivlcdgtcncafhqkcldppldtesrdqgwfckfCECKMEIIESMNahigtsfsvnsnwqdifkeeaafpdgcSALLNqeeewpsddsedddynperrenscsisragtdddpssstslswfsdsetFSESMRWEMesngyknysvdssigsdetsdgeiicgrrqrrtVDYKKLYDEMFGKDASAFeqlsededwgpakrrrkekESDAVNSLMTLYgseekyskVKTAEVkkklpsnakirrsfhrmppnAVEKLRQVFAenelpsriVKENlskelslepekvNKWFKNARYLALKARKVEsarqvsgspriskessleTEKKNADVLTLKNSLEetlicspkslkkihpkriqNQSAVAAASRKISRKELL
Flexible Loop (DISEMBL)
mpgagkkvvkhsesgkscfpkkdsgseLIASlkfkkgskiskskklrsksrcqsktvnstllkrtvaeshskgagddfarsksisqknlhikidrkgsknwasskhkgknsalviskgngevvdgdgetkklrkgrskkrrkekveldeasrlqrrtRYLLIKMKLEQNLIDaysgegwkghsrekirpekelqRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSviatdgsvhHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSALLNqeeewpsddsedddynperrenscsisragtdddpssstslswfSDSETFSESMRWEMESNGYKNysvdssigsdetsdgeiicgrrqrrtvDYKKLYDEMFGkdasafeqlsededwgpakrrrkekesdavnslmtlygseekyskvktaevkkklpsnakirrsfhrmppnAVEKLRQVfaenelpsrivkenlskelslepekvnkwfKNARYLALKarkvesarqvsgspriskessletekKNADVLTLKNSLEETLICspkslkkihpkriqnqsavaaasrkisrkell
Low Complexity Region (SEG)
MPGAGKKVVKHSESGKSCFPKKDSGSELIAslkfkkgskiskskklrsksrcqskTVNSTLLKRTVAESHSKGAGDDFARSKSISQKNLHIKIDRKGSKNWASSKHKGKNSALVISKGNGEVVDGDGETkklrkgrskkrrkekVELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRPEKELQRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSALLNQeeewpsddsedddynpeRRENSCSISRAGTdddpssstslswfsdsETFSESMRWEMESNGYKNYSVDSSIGSDETSDGEIICGRRQRRTVDYKKLYDEMFGKDASAFEQLSEDEDWGPAKRRRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESARQVSGSPRISKESSLETEKKNADVLTLKNSLEETLICSPKSLKKIHPKRIQNQSAVAAASRKISRKELL
Disordered region (IsUnstruct)
************************************************************************************************************************************************************TRYLLIKMKLEQNLIDAYSGEGW******************KQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSAL***********************************************************************************IICGRRQRRTVDYKKLYDEMF*********************************************************************************************************VNKWFKNARYLALK****************************************************************************
Disordered Region (DISOPRED)
***************************************************************************************************************************************************************************************************************RD***********************SVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKMEIIE*****************************************************************************************************************************************************************************************************************AVEKLRQVFAENELPSRI*KE**SKELSLEPEKVNKWFKN***********************************************************************************
Disordered Region (DISEMBL)
************************GSELIASLKFK**********************NSTLLKRTVAESHSKGAGDDFARSKSISQKNLHIKIDRK**************SALVISKGNGEVVD*************************ASRLQRRTRYLLIKMKLEQNLIDAYSGE********KIRPEKELQRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSALLNQ**************************************************ESMRWEMESNGYKNYSVDSSIGSDETSDGEIICGRRQRRTVDYKKLYDEMFGKDASAFEQLS******************AVNSLMTLYGSEEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR****************************VLTLKNSLEETLICSPKSLKKI************************
Disordered Region (DISPRO)
************************************************************************************************************************************************VELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRPEKELQRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEAAFP*******************************************************************************************CGRRQRRTVDYKKLYDEMFGK***************************************************************FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV************************ADVLTLKNSLEETLICSPKSLK**************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPGAGKKVVKHSESGKSCFPKKDSGSELIASLKFKKGSKISKSKKLRSKSRCQSKTVNSTLLKRTVAESHSKGAGDDFARSKSISQKNLHIKIDRKGSKNWASSKHKGKNSALVISKGNGEVVDGDGETKKLRKGRSKKRRKEKVELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRPEKELQRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRENSCSISRAGTDDDPSSSTSLSWFSDSETFSESMRWEMESNGYKNYSVDSSIGSDETSDGEIICGRRQRRTVDYKKLYDEMFGKDASAFEQLSEDEDWGPAKRRRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESARQVSGSPRISKESSLETEKKNADVLTLKNSLEETLICSPKSLKKIHPKRIQNQSAVAAASRKISRKELL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	629	2.2.26 [Sep-21-2011]
P48785	796	Pathogenesis-related home	yes	no	0.677	0.535	0.584	1e-136
Q04996	723	Homeobox protein HAT3.1 O	no	no	0.298	0.260	0.484	6e-49
P46605	719	Homeobox protein HOX1A OS	N/A	no	0.302	0.264	0.445	2e-46
P48786	1088	Pathogenesis-related home	N/A	no	0.640	0.370	0.300	5e-45
P87233	461	SWM histone demethylase c	yes	no	0.168	0.229	0.283	9e-05
G5EBZ4	1829	Protein let-418 OS=Caenor	yes	no	0.106	0.036	0.337	0.0001
Q09908	538	SWM histone demethylase c	no	no	0.076	0.089	0.423	0.0002
Q96BD5	680	PHD finger protein 21A OS	yes	no	0.093	0.086	0.338	0.0005
Q9P1Y6	1649	PHD and RING finger domai	no	no	0.068	0.026	0.377	0.0009

>sp|P48785|PRH_ARATH Pathogenesis-related homeodomain protein OS=Arabidopsis thaliana GN=PRH PE=2 SV=1

 Score =  487 bits (1254), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 259/443 (58%), Positives = 328/443 (74%), Gaps = 17/443 (3%)

Query: 139 KRRKEKVELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRPEKELQRAKK 198
           +++  KVE+D++ RLQRRTRYLLIKMK++QNLIDAY+ EGWKG SREKIRP+KEL+RA+K
Sbjct: 91  QQKDNKVEVDDSLRLQRRTRYLLIKMKMQQNLIDAYATEGWKGQSREKIRPDKELERARK 150

Query: 199 QILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLC 258
           +IL CK+G+RDAIRQLD LSSVG +E  VIA+DGS+HH+HI CA+C  REAFPDNDI+LC
Sbjct: 151 EILNCKLGLRDAIRQLDLLSSVGSMEEKVIASDGSIHHDHIFCAECNSREAFPDNDIILC 210

Query: 259 DGTCNCAFHQKCLDPPLDTES---RDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQD 315
           DGTCN AFHQKCLDPPL+TES    DQGWFCKFC+CK+EII++MNA IGT F V+SNWQD
Sbjct: 211 DGTCNRAFHQKCLDPPLETESIPPGDQGWFCKFCDCKIEIIDTMNAQIGTHFPVDSNWQD 270

Query: 316 IFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRE----NSCSISRAGTDDDPSSST 371
           IF EEA+ P G  A +N E +WPSDDS+DDDY+PE RE    NS ++S  G  D+   S 
Sbjct: 271 IFNEEASLPIGSEATVNNEADWPSDDSKDDDYDPEMRENGGGNSSNVSGDGGGDNDEESI 330

Query: 372 SLSWFSDSETFSESMRWEMESNGYKNYSVDSSIGSDETSDGEIICGRRQRRTVDYKKLYD 431
           S S    S+  +      + +  ++ + + + +   ETS+ E +CG RQRRTVDY +LY 
Sbjct: 331 STSLSLSSDGVA------LSTGSWEGHRLSNMVEQCETSNEETVCGPRQRRTVDYTQLYY 384

Query: 432 EMFGKDASAFEQLSEDEDWGPAKRRRKEKESDAVNSLMTLYGSEEKYSKV----KTAEVK 487
           EMFGKDA   EQ SEDEDWGP  RR++++ESDA ++L+T+  S +K   V    + +E  
Sbjct: 385 EMFGKDAVLQEQGSEDEDWGPNDRRKRKRESDAGSTLVTMCESSKKDQDVVETLEQSERD 444

Query: 488 KKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNA 547
                N   RR   R+P NAVEKLRQVFAE ELPS+ V++ L+KELSL+PEKVNKWFKN 
Sbjct: 445 SVSVENKGGRRRMFRLPRNAVEKLRQVFAETELPSKAVRDRLAKELSLDPEKVNKWFKNT 504

Query: 548 RYLALKARKVESARQVSGSPRIS 570
           RY+AL+ RK ES +Q   S  +S
Sbjct: 505 RYMALRNRKTESVKQPGDSKTVS 527

Specifically binds to the fungal elicitor-responsive DNA element, 5'-CTAATTGTTTA-3', of the gene PR2 promoter.
Arabidopsis thaliana (taxid: 3702)

>sp|Q04996|HAT31_ARATH Homeobox protein HAT3.1 OS=Arabidopsis thaliana GN=HAT3.1 PE=2 SV=3

 Score =  196 bits (497), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 95/196 (48%), Positives = 130/196 (66%), Gaps = 8/196 (4%)

Query: 135 GRSKKRRK-----EKVELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRP 189
           GR KK+ K     +  E DE +R++++ RY L ++  EQ+LIDAYS EGWKG S EKIRP
Sbjct: 157 GRPKKKNKTMNKGQVREDDEYTRIKKKLRYFLNRINYEQSLIDAYSLEGWKGSSLEKIRP 216

Query: 190 EKELQRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREA 249
           EKEL+RA K+IL+ K+ IRD  + LD+L + G +  S+  TDG +  E I CAKC  ++ 
Sbjct: 217 EKELERATKEILRRKLKIRDLFQHLDTLCAEGSLPESLFDTDGEISSEDIFCAKCGSKDL 276

Query: 250 FPDNDIVLCDGTCNCAFHQKCLDPPL---DTESRDQGWFCKFCECKMEIIESMNAHIGTS 306
             DNDI+LCDG C+  FHQ CL+PPL   D    D+GW C  C+CK + ++ +N  +GT 
Sbjct: 277 SVDNDIILCDGFCDRGFHQYCLEPPLRKEDIPPDDEGWLCPGCDCKDDSLDLLNDSLGTK 336

Query: 307 FSVNSNWQDIFKEEAA 322
           FSV+ +W+ IF E AA
Sbjct: 337 FSVSDSWEKIFPEAAA 352

Binds only to large DNA fragments. Recognizes a DNA fragment carrying 8 copies of box7 motif of the light-induced cab-E promoter of Nicotiana plumbaginifolia. Also recognizes the box7m1 motif.

Arabidopsis thaliana (taxid: 3702)

>sp|P46605|HOX1A_MAIZE Homeobox protein HOX1A OS=Zea mays GN=HOX1A PE=2 SV=1

 Score =  187 bits (476), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 86/193 (44%), Positives = 126/193 (65%), Gaps = 3/193 (1%)

Query: 134 KGRSKKRRKEKVELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRPEKEL 193
           K R   R   K   DE S++++R RY+L +M  EQ+LI+AY+ EGWK  S +KIRPEKEL
Sbjct: 105 KRRKMSRASNKSSTDEFSQIRKRVRYILNRMNYEQSLIEAYASEGWKNQSLDKIRPEKEL 164

Query: 194 QRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDN 253
           +RAK +IL+CK+ IR+  R +DSL S G I+ ++  ++G +  E I C+ C   +A   N
Sbjct: 165 ERAKSEILRCKLRIREVFRNIDSLLSKGKIDETLFDSEGEISCEDIFCSTCGSNDATLGN 224

Query: 254 DIVLCDGTCNCAFHQKCLDPPLDTES---RDQGWFCKFCECKMEIIESMNAHIGTSFSVN 310
           DI+LCDG C+  FHQ CL+PPL TE     D+GW C  C+CK++ I+ +N   G++ S+ 
Sbjct: 225 DIILCDGACDRGFHQNCLNPPLRTEDIPMGDEGWLCPACDCKIDCIDLINELHGSNISIE 284

Query: 311 SNWQDIFKEEAAF 323
            +W+ +F + AA 
Sbjct: 285 DSWEKVFPDAAAM 297

Interacts with the shrunken (SHR) 26 bp feedback control element.

Zea mays (taxid: 4577)

>sp|P48786|PRH_PETCR Pathogenesis-related homeodomain protein OS=Petroselinum crispum GN=PRH PE=2 SV=1

 Score =  183 bits (464), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 151/502 (30%), Positives = 222/502 (44%), Gaps = 99/502 (19%)

Query: 147 LDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRPEKELQRAKKQILKCKIG 206
           +DE  R++   RYLL ++K E+N +DAYSGEGWKG S +KI+PEKEL+RAK +I   K+ 
Sbjct: 487 VDEFCRIRTHLRYLLHRIKYEKNFLDAYSGEGWKGQSLDKIKPEKELKRAKAEIFGRKLK 546

Query: 207 IRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAF 266
           IRD  ++LD   S G +   +  + G +  E I CAKC  ++    NDI+LCDG C+  F
Sbjct: 547 IRDLFQRLDLARSEGRLPEILFDSRGEIDSEDIFCAKCGSKDVTLSNDIILCDGACDRGF 606

Query: 267 HQKCLDPPLDTE---SRDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFK----- 318
           HQ CLDPPL  E     D+GW C  CECK++ I+ +N    T+  +  +W+ +F      
Sbjct: 607 HQFCLDPPLLKEYIPPDDEGWLCPGCECKIDCIKLLNDSQETNILLGDSWEKVFAEEAAA 666

Query: 319 --------EEAAFPDGCSALLNQ-------EEEWPSDDSEDD--DYNPE-------RREN 354
                   + +  P   S   +        +E+   DDS  D  DY  E       R++N
Sbjct: 667 AASGKNLDDNSGLPSDDSEDDDYDPGGPDLDEKVQGDDSSTDESDYQSESDDMQVIRQKN 726

Query: 355 SCSI------------SRAGTDDDPSSSTSLSWFSDSETFSESM---------RWEMESN 393
           S  +            S   TD     S+   + SDSE F+            +  + S 
Sbjct: 727 SRGLPSDDSEDDEYDPSGLVTDQMYKDSSCSDFTSDSEDFTGVFDDYKDTGKAQGPLAST 786

Query: 394 GYKNYSVDSSIGSDETSDGEIICGRRQRRTVDYKKLYDEMFGKDASAFEQLSEDEDWGPA 453
                + +   G  E  D   +  RRQ  ++DYKKL D  F K     + LS   D    
Sbjct: 787 PDHVRNNEEGCGHPEQGDTAPLYPRRQVESLDYKKLNDIEFSKMCDILDILSSQLDVIIC 846

Query: 454 KRRRKE---KESDAVNSLMTLYGSEEKYSKVKTAEVKKK------LPSNAKIRRSFHR-- 502
              ++E     SD+ +    +  S +K +  K A   ++      L  + K R S H   
Sbjct: 847 TGNQEEYGNTSSDSSDEDYMVTSSPDKNNSDKEATAMERGRESGDLELDQKARESTHNRR 906

Query: 503 ---------------------MPP--------------NAVEKLRQVFAENELPSRIVKE 527
                                  P              +A ++L Q F EN+ P R VKE
Sbjct: 907 YIKKFAVEGTDSFLSRSCEDSAAPVAGSKSTSKTLHGEHATQRLLQSFKENQYPQRAVKE 966

Query: 528 NLSKELSLEPEKVNKWFKNARY 549
           +L+ EL+L   +V+ WF N R+
Sbjct: 967 SLAAELALSVRQVSNWFNNRRW 988

Specifically binds to the fungal elicitor-responsive DNA element, 5'-CTAATTGTTTA-3', of the gene PR2 promoter.

Petroselinum crispum (taxid: 4043)

>sp|P87233|PHF1_SCHPO SWM histone demethylase complex subunit phf1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=phf1 PE=1 SV=1

 Score = 49.3 bits (116), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 34/120 (28%), Positives = 52/120 (43%), Gaps = 14/120 (11%)

Query: 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLD---TESRDQGWFCKFCE---CKM 293
           +C+ C+   +   N IV CDG CN  +HQ C  PP+D    +  D  WFC  C+    K 
Sbjct: 192 LCSVCQRGHSPLSNRIVFCDG-CNSPYHQLCHHPPIDDATVQDVDAEWFCMKCQYRRAKQ 250

Query: 294 EIIESMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRE 353
            +   M A       ++ + + ++      P     +L  E+ +PS       YNP  RE
Sbjct: 251 PLETGMTAQ---DLGLSESDKKMYLSSLPTPHLADLILFCEKSYPSLPI----YNPRTRE 303

Component of the SWM histone demethylase complex that specifically demethylates H3K9me2, a specific tag for epigenetic transcriptional activation, thereby acting as a corepressor. Has a role in regulating heterochromatin propagation and euchromatic transcription.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|G5EBZ4|LE418_CAEEL Protein let-418 OS=Caenorhabditis elegans GN=let-418 PE=1 SV=1

 Score = 48.9 bits (115), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 7/74 (9%)

Query: 218 SSVGCIE-GSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLD 276
           S   CIE G  +  +         C  CK  E     +++LCD +C C+FH  C+DPPL 
Sbjct: 296 SCAHCIEHGPEVVKEEPAKQNDEFCKICKETE-----NLLLCD-SCVCSFHAYCIDPPLT 349

Query: 277 TESRDQGWFCKFCE 290
              +++ W C  CE
Sbjct: 350 EVPKEETWSCPRCE 363

Part of a NuRD (Nucleosome Remodeling and Deacetylase) complex which is implicated in the synMuv B pathway that negatively regulates specification of vulval cell fate. This negative regulation is thought to be mediated via interaction with the promoter of lin-39, a key regulator in vulva development, and is dependent on the presence lin-1. Contributes to negative regulation of lag-2 which is expressed in the gut during larval development. Has a broad role in development.

Caenorhabditis elegans (taxid: 6239)

>sp|Q09908|PHF2_SCHPO SWM histone demethylase complex subunit phf2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=phf2 PE=1 SV=1

 Score = 48.1 bits (113), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 28/52 (53%), Gaps = 4/52 (7%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQG---WFCKFC 289
           C+ C+  ++ P N IV CDG CN  FHQ C +P +  E  D     WFC  C
Sbjct: 235 CSVCQRLQSPPKNRIVFCDG-CNTPFHQLCHEPYISDELLDSPNGEWFCDDC 285

Component of the SWM histone demethylase complex that specifically demethylates H3K9me2, a specific tag for epigenetic transcriptional activation, thereby acting as a corepressor. Has a role in regulating heterochromatin propagation and euchromatic transcription.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q96BD5|PF21A_HUMAN PHD finger protein 21A OS=Homo sapiens GN=PHF21A PE=1 SV=1

 Score = 47.0 bits (110), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 9/68 (13%)

Query: 226 SVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWF 285
           S  +TDG +H +   C+ C+         +++CD TC+  +H  CLDPPL T  +   W 
Sbjct: 478 SPTSTDGDIHED--FCSVCRK-----SGQLLMCD-TCSRVYHLDCLDPPLKTIPKGM-WI 528

Query: 286 CKFCECKM 293
           C  C+ +M
Sbjct: 529 CPRCQDQM 536

Component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. The BHC complex is recruited at RE1/NRSE sites by REST and acts by deacetylating and demethylating specific sites on histones, thereby acting as a chromatin modifier. In the BHC complex, it may act as a scaffold. Inhibits KDM1A-mediated demethylation of 'Lys-4' of histone H3 in vitro, suggesting a role in demethylation regulation.

Homo sapiens (taxid: 9606)

>sp|Q9P1Y6|PHRF1_HUMAN PHD and RING finger domain-containing protein 1 OS=Homo sapiens GN=PHRF1 PE=1 SV=3

 Score = 46.2 bits (108), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 27/45 (60%), Gaps = 2/45 (4%)

Query: 252 DNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKMEII 296
           ++ ++LCDG C+  +H +CLDPPL     D+ WFC  C     ++
Sbjct: 195 EDRLLLCDG-CDAGYHMECLDPPLQEVPVDE-WFCPECAAPGVVL 237

Homo sapiens (taxid: 9606)

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	629
225470662	727	PREDICTED: pathogenesis-related homeodom	0.980	0.848	0.618	0.0
255573765	732	conserved hypothetical protein [Ricinus	0.947	0.814	0.609	0.0
224144330	727	predicted protein [Populus trichocarpa]	0.920	0.796	0.635	0.0
224090517	725	predicted protein [Populus trichocarpa]	0.904	0.784	0.620	0.0
449457269	714	PREDICTED: pathogenesis-related homeodom	0.925	0.815	0.587	1e-167
356530336	714	PREDICTED: pathogenesis-related homeodom	0.853	0.752	0.598	1e-161
356558320	600	PREDICTED: pathogenesis-related homeodom	0.887	0.93	0.577	1e-160
449503000	741	PREDICTED: pathogenesis-related homeodom	0.855	0.726	0.561	1e-157
357449593	707	Pathogenesis-related homeodomain protein	0.812	0.722	0.568	1e-151
356564821	617	PREDICTED: pathogenesis-related homeodom	0.818	0.834	0.589	1e-149

>gi|225470662|ref|XP_002269263.1| PREDICTED: pathogenesis-related homeodomain protein [Vitis vinifera] gi|296090281|emb|CBI40100.3| unnamed protein product [Vitis vinifera]

 Score =  736 bits (1899), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 394/637 (61%), Positives = 477/637 (74%), Gaps = 20/637 (3%)

Query: 1   MPGAGKKVVKHSESGKSCFPKKDSGSELIASLKFKKGSKISKSKKLRSKSRCQSKTVNST 60
           M G GKK   H ESGKSCFPK++ G +L A+L+ K GSKIS+++K + KS+  +KT+ + 
Sbjct: 1   MRGTGKKA-GHQESGKSCFPKRNIGPKLNAALQIKNGSKISQTRKCKPKSKSHAKTIGAI 59

Query: 61  LLKRTVAESHSKGAGDDFARSKSISQKNLHIKIDRKGSKNWASSKHKGKNSALVISKGNG 120
           L KRT   S SKG+       K I +K LH  ID + SK  +SSK KG+    + +  NG
Sbjct: 60  LSKRTTTGSPSKGSRSGSTTRKLIHKKTLHKAIDTESSKKESSSKLKGEKPPQISTNKNG 119

Query: 121 EVVDGDGETKKLRKGRSKKRRKEKVELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWK 180
           E VD + + +KL+K   +KRRK+  ELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWK
Sbjct: 120 ETVDKNVKPQKLKKRGKRKRRKDNSELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWK 179

Query: 181 GHSREKIRPEKELQRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHII 240
           GHSREKIRPEKELQRA KQILKCK+GIRDAIRQL+SLSS+GCIE + IA+DGSV+HEHII
Sbjct: 180 GHSREKIRPEKELQRATKQILKCKLGIRDAIRQLESLSSIGCIEDTAIASDGSVYHEHII 239

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES---RDQGWFCKFCECKMEIIE 297
           CAKCKLREAFPDNDI+LCDGTCNCAFHQKCLDPPL+TE+    DQGWFCKFCECKMEI+E
Sbjct: 240 CAKCKLREAFPDNDIILCDGTCNCAFHQKCLDPPLETENIPPGDQGWFCKFCECKMEILE 299

Query: 298 SMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRENSCS 357
           +MNAH+GT FSV+S WQDIFKEEAA PDG SAL   EE+WPSDDS+D DY+PER ENSCS
Sbjct: 300 AMNAHLGTRFSVDSTWQDIFKEEAALPDGGSALPYPEEDWPSDDSQDHDYDPERNENSCS 359

Query: 358 ISRAGTD----DDPSSSTSLSWFSDSETFSESMRWEMESNGYKNYSVDSSIGSDETSDGE 413
           IS AGT+    DD +SS SLSW  + E  S S R           S   S  SDETSD E
Sbjct: 360 ISTAGTEGNASDDTNSSLSLSWSFEDEILSGSKR-----------SGIISADSDETSDCE 408

Query: 414 IICGRRQRRTVDYKKLYDEMFGKDASAFEQLSEDEDWGPAKRRRKEKESDAVNSLMTLYG 473
           II GRRQRR VDY+KLYDEMFGKDA A EQ+SEDEDWGPA +RR+EKESDA ++L+TLY 
Sbjct: 409 IISGRRQRRAVDYRKLYDEMFGKDAHANEQVSEDEDWGPANKRRREKESDAASTLITLYE 468

Query: 474 SEEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKEL 533
            E+K   V+T E K+K+ S+ + +R F R+P +AVEKLRQ F ENELPSR V+ENL+K+L
Sbjct: 469 GEKKLPNVETMEAKQKISSDPQTKRPFSRIPLDAVEKLRQAFGENELPSRDVRENLAKQL 528

Query: 534 SLEPEKVNKWFKNARYLALKARKVESARQVSGSPRISKESSLETEK-KNADVLTLKNSLE 592
            L+ EKVNKWFKNARY+ALK RK E A+Q+  SPRISKES  E  K K  D++  +++  
Sbjct: 529 GLDYEKVNKWFKNARYIALKTRKAERAKQLQTSPRISKESRSEIVKDKTVDLVASRDNSS 588

Query: 593 ETLICSPKSLKKIHPKRIQNQSAVAAASRKISRKELL 629
            +L+ + K+LKK+  ++       +   +K  R+ LL
Sbjct: 589 ASLVRALKNLKKVRRRKNPKPIITSPVKKKHHRRALL 625

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255573765|ref|XP_002527803.1| conserved hypothetical protein [Ricinus communis] gi|223532799|gb|EEF34575.1| conserved hypothetical protein [Ricinus communis]

 Score =  681 bits (1758), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 377/619 (60%), Positives = 451/619 (72%), Gaps = 23/619 (3%)

Query: 1   MPGAGKKVVKHSESGKSCFPKKDSGSELIASLKFKKGSKISKSKKLRSKSRCQSKTVNST 60
           M G GKK  K+ ESGKSCF   ++GS LIASLK +K   I   K+ + K + Q K    +
Sbjct: 1   MRGTGKKA-KNQESGKSCFSNSENGSMLIASLKLRKDKTIPHCKRGKPKPKSQLKATGGS 59

Query: 61  LLKRTVAESHSKGAGDDFA-RSKSISQKNLHIKIDRKGSKNWASSK-HKGKNSALVISKG 118
            LKR   +  SKG  + +   +K I +K L   ID+K S    +SK  +GK    +  + 
Sbjct: 60  RLKRVATDPSSKGIKNGYTTNTKMICKKILQKAIDKKSSTKKLTSKVRRGKRLPAIGCED 119

Query: 119 NGEVVDGDGET---KKLRKGRSKKRRKEKVELDEASRLQRRTRYLLIKMKLEQNLIDAYS 175
           NG+  + D      K  R+ ++K+ +KEKV+LDE SRLQRRT+YL+IKMKLEQNLIDAYS
Sbjct: 120 NGKEPNEDVNVTVKKLNRRKKNKRGQKEKVKLDEPSRLQRRTKYLMIKMKLEQNLIDAYS 179

Query: 176 GEGWKGHSREKIRPEKELQRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVH 235
           GEGWKG SREKI+PEKEL RAKKQILKCK+GIRDAI QLDSLS+VGCIE SVIA DGSV 
Sbjct: 180 GEGWKGQSREKIKPEKELVRAKKQILKCKLGIRDAIHQLDSLSTVGCIEDSVIAPDGSVS 239

Query: 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES---RDQGWFCKFCECK 292
           HEHI CAKCK  E  PDNDIVLCDGTCNC FHQ+CLDPPLDTE+    DQGW+CKFCEC+
Sbjct: 240 HEHIFCAKCKSNEVSPDNDIVLCDGTCNCGFHQRCLDPPLDTENIPPGDQGWYCKFCECR 299

Query: 293 MEIIESMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERR 352
           MEIIE+MNAH+GT FSV+S WQDIF+EEA F DG   LLN EEEWPSDDSEDDDY+P  +
Sbjct: 300 MEIIEAMNAHLGTQFSVDSCWQDIFQEEATFSDGGGILLNPEEEWPSDDSEDDDYDPGSQ 359

Query: 353 ENSCSISRAGTDDD----PSSSTSLSWFSDSETFSESMRWEMESNGYKNYSVDSSIGSDE 408
           +N  SIS AGTDDD     SS+TSL W SD E  S S +W+M    ++N  + SS+ SDE
Sbjct: 360 DN--SISGAGTDDDASDNASSATSLGWSSDGEVLSGSRKWDMGDTYFRNQFIYSSLDSDE 417

Query: 409 TSDGEIICGRRQRRTVDYKKLYDEMFGKDASAFEQLSEDEDWGPAKRRRKEKESDAVNSL 468
           TSDGEI+CGRRQRR VDYKKLYDEMFGKDA   EQ+SEDEDWGP KR+R+EKESDA ++L
Sbjct: 418 TSDGEIVCGRRQRRAVDYKKLYDEMFGKDAQEHEQVSEDEDWGPGKRKRREKESDAASTL 477

Query: 469 MTLYGSEEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKEN 528
           MTLY SE+   KV      KK   + +++R   R+PP+AVEKLRQVFAENELPSR +KEN
Sbjct: 478 MTLYESEKTSKKV------KKHSRDPQVKRPLFRIPPSAVEKLRQVFAENELPSRTIKEN 531

Query: 529 LSKELSLEPEKVNKWFKNARYLALKARKVESARQV-SGSPRISKESSLE-TEKKNADVLT 586
           LSKEL LEP KV+KWFKNARYLALK+RK +   ++ S SP I +E  L+   K  AD+  
Sbjct: 532 LSKELGLEPGKVSKWFKNARYLALKSRKADRTSELYSSSPEIPREPKLDAVNKITADLAE 591

Query: 587 LKNSLEETLICSPKSLKKI 605
           L+ +  ET I SPKSLK+I
Sbjct: 592 LRATSSETKIYSPKSLKQI 610

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224144330|ref|XP_002325264.1| predicted protein [Populus trichocarpa] gi|222866698|gb|EEF03829.1| predicted protein [Populus trichocarpa]

 Score =  670 bits (1728), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 375/590 (63%), Positives = 454/590 (76%), Gaps = 11/590 (1%)

Query: 24  SGSELIASLKFKKGSKISKSKKLRSKSRCQSKTV-NSTLLKRTVAESHSKGAGDDFARSK 82
           +GS LI SLK KKG K+S  K  + K++   KT+ NS++ K+ V  +  KG  +     +
Sbjct: 23  NGSLLIKSLKIKKGGKLSHRKSEKPKTKPHLKTIINSSVSKKKV--TPKKGIRNGSTSRR 80

Query: 83  SISQKNLHIKIDRKGSKNWASSKHKGKNSALVISKGNGEVVDGDGETKKLRKGRSKKRRK 142
            I +K LH  +D+K S+N ASS+ +GK  + + S+GNG+  D +G  KK++K + KKR+K
Sbjct: 81  LIHRKILHKALDKKASRNGASSELQGKQLSTIDSEGNGKNAD-EGAIKKVKKRKPKKRQK 139

Query: 143 EKVELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRPEKELQRAKKQILK 202
           +KV+LDE  RLQRR RYL+IKMKLEQNLIDAYSGEGWKG SREKIRPEKEL RA+KQILK
Sbjct: 140 DKVKLDEPPRLQRRARYLMIKMKLEQNLIDAYSGEGWKGKSREKIRPEKELLRARKQILK 199

Query: 203 CKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTC 262
           CK+G+R+ IRQ+DSLS+VGCIE +V+A DGSV HEHI CAKCKL E   DNDIVLCDGTC
Sbjct: 200 CKLGLREIIRQVDSLSTVGCIEDAVMAPDGSVSHEHIFCAKCKLNEVSQDNDIVLCDGTC 259

Query: 263 NCAFHQKCLDPPLDTES---RDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKE 319
           NCAFHQKCLDPPLDTE+    DQGWFCKFC+C+MEIIE+MNAH+GT FS +S WQDIFKE
Sbjct: 260 NCAFHQKCLDPPLDTENIPPGDQGWFCKFCDCRMEIIEAMNAHLGTHFSEDSGWQDIFKE 319

Query: 320 EAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRENSCS--ISRAGTDDDPSSSTSLSWFS 377
           EAA PDG + LLN EEEWPSDDSEDDDY+PERREN  S   +     DD S+ST LSW S
Sbjct: 320 EAAVPDGGNMLLNPEEEWPSDDSEDDDYDPERRENVMSGAGTDDDASDDTSNSTRLSWSS 379

Query: 378 DSETFSESMRWEMESNGYKNYSVDSSIGSDETSDGEIICGRRQRRTVDYKKLYDEMFGKD 437
           D E FS S RWE++   ++N S+ SS+ SDETSDGEIICGRRQRR VDYKKLY+EMFGKD
Sbjct: 380 DGEVFSGSRRWEVDGLDFRNNSIYSSLDSDETSDGEIICGRRQRRAVDYKKLYNEMFGKD 439

Query: 438 ASAFEQLSEDEDWGPAKRRRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKKKLPSNAKIR 497
           A A EQ SEDEDWGP+KR+R+EKESDA ++LMTLY S+ +     T E   KLP + +IR
Sbjct: 440 APAHEQPSEDEDWGPSKRKRREKESDAASTLMTLYESKRRCKNDATIEGMMKLPRDPQIR 499

Query: 498 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV 557
           R   R+PP+AVEKLRQVFAENELPSR VKENLSKEL LEP KV+KWFKN+RYLALK+RKV
Sbjct: 500 RPIFRLPPDAVEKLRQVFAENELPSRTVKENLSKELGLEPGKVSKWFKNSRYLALKSRKV 559

Query: 558 ESARQVS-GSPRISKESSLETEK-KNADVLTLKNSLEETLICSPKSLKKI 605
           E   QV   S ++S E +L   K K AD+  LK+S  ET +C+P++LK+I
Sbjct: 560 EKGEQVHYSSSKVSAEPTLNVMKDKTADLSLLKDSQAETGVCTPENLKRI 609

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224090517|ref|XP_002309010.1| predicted protein [Populus trichocarpa] gi|222854986|gb|EEE92533.1| predicted protein [Populus trichocarpa]

 Score =  652 bits (1681), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 371/598 (62%), Positives = 449/598 (75%), Gaps = 29/598 (4%)

Query: 24  SGSELIASLKFKKGSKISKSKKLRSKSRCQSK-------TVNSTLLKRTVAESHSKGAGD 76
           +GS LI SLK KK SKIS  K  ++K++ + K        ++S + KR V+    KG G+
Sbjct: 23  TGSLLIKSLKIKKDSKISPRKGQKTKTKSKPKPIPHLKTIISSAVSKRKVS---PKGIGN 79

Query: 77  DFARSKSISQKNLHIKIDRKGSKNWASSKHKGKNSALVISKGNGEVVDGDGETKKLRKGR 136
                K I +K LH  +D+K S+  ASS   G   + + SKGNG+  D +G  KKL+K +
Sbjct: 80  GSTSRKLIHRKILHKALDKKASRKGASS---GLQLSTIDSKGNGKNGD-EGAIKKLKKRK 135

Query: 137 SKKRRKEKVELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRPEKELQRA 196
            KKR+++KV+LDE SRLQRR RYL+IKMKL+QNLIDAYSGEGWKG SREKIRPEKEL RA
Sbjct: 136 PKKRQRDKVKLDEPSRLQRRARYLMIKMKLDQNLIDAYSGEGWKGQSREKIRPEKELLRA 195

Query: 197 KKQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIV 256
           +KQILKCK+G+RD IRQ+DSLS+VGCIE +V+A DGSV HEHI CAKCKL E  PDNDIV
Sbjct: 196 RKQILKCKLGLRDIIRQVDSLSTVGCIEETVMAPDGSVSHEHIFCAKCKLNEVSPDNDIV 255

Query: 257 LCDGTCNCAFHQKCLDPPLDTES---RDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNW 313
           LCDGTCNCAFHQKCL+PPLDTES    DQGWFCKFCEC+M+IIE+MNAH+GT FS +S+W
Sbjct: 256 LCDGTCNCAFHQKCLEPPLDTESIPPGDQGWFCKFCECRMDIIEAMNAHLGTHFSEDSSW 315

Query: 314 QDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRENSCSISRAGT----DDDPSS 369
           QDIF EEAA PD  + LLN EEEWPSDDSEDD+Y+PERR+N   +S AGT     DD SS
Sbjct: 316 QDIFTEEAAIPDAGNVLLNPEEEWPSDDSEDDNYDPERRDN--IMSEAGTDDDASDDISS 373

Query: 370 STSLSWFSDSETFSESMRWEMESNGYKNYSVDSSIGSDETSDGEIICGRRQRRTVDYKKL 429
           STSL W SD E F  S RWEM    ++N S+ SS+ SDETSDGEI+CGRRQRR +DYKKL
Sbjct: 374 STSLGWSSDGEVFLGSRRWEMHGLDFRNNSIYSSLDSDETSDGEIVCGRRQRRAIDYKKL 433

Query: 430 YDEMFGKDASAFEQLSEDEDWGPAKRRRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKKK 489
           YDE+FGKDA A EQ SEDEDWGP KR+R+EKES+A ++LMTL  S++K    +T E    
Sbjct: 434 YDEVFGKDAPAHEQASEDEDWGPGKRKRREKESNAASTLMTLCESKKKSKSDETIEGMMN 493

Query: 490 LPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 549
           LP   + RR   R+PP+AVEKLRQVF ENELPSR VKENLSKEL LEP KV+KWFKN+RY
Sbjct: 494 LP--PQTRRPIFRLPPDAVEKLRQVFVENELPSRTVKENLSKELGLEPGKVSKWFKNSRY 551

Query: 550 LALKARKVESARQV-SGSPRISKESSLET-EKKNADVLTLKNSLEETLICSPKSLKKI 605
           LALK+RKVE   Q+ + S ++S E +L   E K AD+   ++S EET +C PK+LK+I
Sbjct: 552 LALKSRKVEKGEQLHNSSSKVSAEPTLNVMEGKTADL--SQDSWEETEVCIPKNLKRI 607

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449457269|ref|XP_004146371.1| PREDICTED: pathogenesis-related homeodomain protein-like [Cucumis sativus]

 Score =  595 bits (1534), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 352/599 (58%), Positives = 434/599 (72%), Gaps = 17/599 (2%)

Query: 1   MPGAGKKVVKHSESGKSCFPKKDSGSELIASLKFKKGSKISKSKKLRSKSRCQSKTVNST 60
           M GAGK++++ SE  K    K +SGSELI SLK  + SKIS SK+ +S+ +  S+ + ST
Sbjct: 1   MRGAGKRLMEESE--KCSHSKLESGSELIFSLKLTRCSKISHSKQKKSRMKSHSQAICST 58

Query: 61  LLKRTVAESHSKGAGDDFARSKSISQKNLHIKIDRKGSKNWASSKHKGKNS-ALVISKGN 119
             +R + +S SKG  +   R  +  +K L  K+D K SK    SK +G+ S +   +KGN
Sbjct: 59  FKRRPLPKSLSKGNKNVTIRQLA-GKKFLLKKLDTKPSKELLLSKLQGEKSLSSTNTKGN 117

Query: 120 GEVVDGDGETKKLRKGRSKKRRKEKVELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGW 179
            E V+   +  + RK +  K +KEKVELDEASRLQRRTRYL+IKMKLEQNLIDAYSGEGW
Sbjct: 118 AEKVEPVVKINQQRKRKKNKGKKEKVELDEASRLQRRTRYLIIKMKLEQNLIDAYSGEGW 177

Query: 180 KGHSREKIRPEKELQRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHI 239
           KG SREKIRPEKELQRA KQILKCK+GIRDAIRQLD L SVGCIE SVI  DGSV+HEHI
Sbjct: 178 KGQSREKIRPEKELQRAMKQILKCKLGIRDAIRQLDLLGSVGCIEDSVIGPDGSVYHEHI 237

Query: 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES---RDQGWFCKFCECKMEII 296
            CAKCKLREAFPDNDI+LCDGTCNCAFHQKCLDPPLDT+S    DQGWFCKFCECKMEI+
Sbjct: 238 FCAKCKLREAFPDNDIILCDGTCNCAFHQKCLDPPLDTKSIPPGDQGWFCKFCECKMEIL 297

Query: 297 ESMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRENSC 356
           E MNAH+GT FS+N  W+DIFKEEAAFPDG +ALLN EE+WPSDDSEDDDY+P+++EN C
Sbjct: 298 EGMNAHLGTRFSLNIGWEDIFKEEAAFPDGGNALLNHEEDWPSDDSEDDDYDPDKKEN-C 356

Query: 357 SISRAGTDDDPSSSTSLSWFSDSETFSESMRWEMESNGY---KNYSVDSSIGSDETSDGE 413
             + +  ++D       S  +      +     +  NG     ++   +SI SD +++  
Sbjct: 357 HDNASEEENDKEVLEESSSSTSLSWSLDGEDL-VSGNGIGCEDHFGAGTSIVSDGSNEEG 415

Query: 414 IICGRRQRRTVDYKKLYDEMFGKDASAFEQ-LSEDEDWGPAKRRRKEKESDAVNSLMTLY 472
           I CGRRQR  VDYKKLYDEMFGKD  A EQ +SEDEDWGPAKRRR+EKE DA ++LM+L 
Sbjct: 416 ITCGRRQRHAVDYKKLYDEMFGKDTPAHEQEVSEDEDWGPAKRRRREKECDAASTLMSLC 475

Query: 473 GSEEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKE 532
            SE+K   +     KK L S+    RSF R+P +AVEKLR+VFA+NELPSR VKENLSKE
Sbjct: 476 ESEKKSQDIDMEAEKKLLNSHG---RSFFRIPRHAVEKLRKVFADNELPSRDVKENLSKE 532

Query: 533 LSLEPEKVNKWFKNARYLALKARKVESARQVSGSPRISKESSL-ETEKKNADVLTLKNS 590
           L L+ EKV+KWFKNARY AL+ RK E A Q   S + S E  L ++++ + ++L+L+N+
Sbjct: 533 LGLDAEKVSKWFKNARYSALRTRKAEGATQPHSSHKTSNELRLADSKEMSKNLLSLENA 591

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356530336|ref|XP_003533738.1| PREDICTED: pathogenesis-related homeodomain protein-like [Glycine max]

 Score =  574 bits (1479), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 329/550 (59%), Positives = 405/550 (73%), Gaps = 13/550 (2%)

Query: 14  SGKSCFPKKDSGSELIASLKFKKGSKISKSKKLRSKSRCQSKTVNSTLLKRTVAESHSKG 73
           SGKS + ++ + S+L++S KFK  S   + KK + K +       +   K+TV +S  K 
Sbjct: 12  SGKSSYSQEQTMSKLVSS-KFKTSSTKCQEKKHKVKLKSHKHRAGTNKSKKTVTDSSIKA 70

Query: 74  AGDDFARSKSISQKNLHIKIDRKGSKNWASSK-HKGKNSALVISKGNGEVVDGDGETKKL 132
             +D +  K I +K  H K D K S+  +S+K   GKNS     +GN   VDG+ E  K 
Sbjct: 71  PLEDSSNKKVIIRKYRH-KTDGKSSRMLSSTKLEGGKNSHSSGIEGND--VDGE-EKIKK 126

Query: 133 RKGRSKKRRKEKVELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRPEKE 192
            K R KKR++  +++D+ASRL+RRTRYLLIKMKLEQNLIDAYSGEGWKG SREKIRPEKE
Sbjct: 127 HKRRKKKRQRNNMDVDDASRLRRRTRYLLIKMKLEQNLIDAYSGEGWKGQSREKIRPEKE 186

Query: 193 LQRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPD 252
           L RAKKQILKCK+ IRDAIRQLDSLSSVG IE S IA DGSV+HE+I CA CKL EAFPD
Sbjct: 187 LLRAKKQILKCKLNIRDAIRQLDSLSSVGSIEDSAIAPDGSVYHENIFCANCKLHEAFPD 246

Query: 253 NDIVLCDGTCNCAFHQKCLDPPLDTES---RDQGWFCKFCECKMEIIESMNAHIGTSFSV 309
           NDI+LCDGTCN AFHQ+CL+PPLDTE+    DQGWFCKFCECK+EI+E+ NAH+GT FS+
Sbjct: 247 NDIILCDGTCNRAFHQRCLNPPLDTENIPPGDQGWFCKFCECKIEILEATNAHLGTQFSL 306

Query: 310 NSNWQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRENSCSISRAGTDDDPSS 369
           +S WQD+FKEEA+ PDG  ALLN EEEWPSDD EDDDYNPE++E+S SI   G  DD ++
Sbjct: 307 DSTWQDVFKEEASMPDGDIALLNPEEEWPSDDPEDDDYNPEKKEDSHSIDIEG--DDGNA 364

Query: 370 STSLSWFSDSETFSESMRWEMESNGYKNYSVDSSIGSDETSDGEIICGRRQRRTVDYKKL 429
           S   +  S   + +       E   ++ YSV+S I S+E+  GEI CG RQR+ VDYKKL
Sbjct: 365 SNDSTSSSSLWSLNGECPPVDEGVSHEYYSVNSCIDSNES--GEIACGPRQRKAVDYKKL 422

Query: 430 YDEMFGKDASAFEQLSEDEDWGPAKRRRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKKK 489
           YDEMFGKDA   EQ+SEDEDWGP KR+R+EKESDAVN+LMTL+ SE K+S  +  +  ++
Sbjct: 423 YDEMFGKDAPPCEQVSEDEDWGPGKRKRREKESDAVNTLMTLHESENKHSNNEKNDTTRE 482

Query: 490 LPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 549
             S  +IRRS  R+P +AVEKLRQ FAENELP R VK++LSKEL L+PEKV+KWFKNARY
Sbjct: 483 GSSGIQIRRSCFRIPVDAVEKLRQAFAENELPPRSVKDSLSKELGLDPEKVSKWFKNARY 542

Query: 550 LALKARKVES 559
           LALK R+ +S
Sbjct: 543 LALKTRRYQS 552

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356558320|ref|XP_003547455.1| PREDICTED: pathogenesis-related homeodomain protein-like [Glycine max]

 Score =  573 bits (1476), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 332/575 (57%), Positives = 418/575 (72%), Gaps = 17/575 (2%)

Query: 14  SGKSCFPKKDSGSELIASLKFKKGSKISKSKKLRSKSRCQSKTVNSTLLKRTVAESHSKG 73
           SGKS + ++ + S+L++S KFK  S   + KK + +S+       ++  K+TV  S  + 
Sbjct: 12  SGKSSYSQEQTKSKLVSS-KFKTSSTKRQEKKHKVRSKSHKHRAGTSKSKKTVTHSSVEA 70

Query: 74  AGDDFARSKSISQKNLHIKIDRKGSKNWASSK-HKGKNSALVISKGNGEVVDGDGETKKL 132
             +D +  K I +K  H K D K S+  +S+K   GKNS     +GN    D DGE K  
Sbjct: 71  PLEDSSNKKVIIRKYRH-KTDGKSSQMLSSTKLEGGKNSHSSGIEGN----DVDGEAKIK 125

Query: 133 RKGRSKKRRK-EKVELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRPEK 191
           ++ R KK+R+   +++D+ASRL+RRTRYLLIKMKLEQNLIDAYSGEGWKG SREKIRPEK
Sbjct: 126 KRKRRKKKRQRNNIDVDDASRLRRRTRYLLIKMKLEQNLIDAYSGEGWKGQSREKIRPEK 185

Query: 192 ELQRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFP 251
           EL RAKKQILKCK+ IRDAI QLDSLSSVG IE S IA DGSV+HE+I CA CKL EAFP
Sbjct: 186 ELLRAKKQILKCKLSIRDAIHQLDSLSSVGSIEDSAIAPDGSVYHENIFCANCKLHEAFP 245

Query: 252 DNDIVLCDGTCNCAFHQKCLDPPLDTES---RDQGWFCKFCECKMEIIESMNAHIGTSFS 308
           DNDI+LCDGTCN AFHQ+CL+PPLDTE+    DQGWFCKFCECK+EI+E+ NAH+GT FS
Sbjct: 246 DNDIILCDGTCNRAFHQRCLNPPLDTENIPPGDQGWFCKFCECKIEILEATNAHLGTQFS 305

Query: 309 VNSNWQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRENSCSISRAGTDDDPS 368
           ++S WQD+FKEEAA PDG  ALLN EEEWPSDD EDDDYNPER+E++ +    G D++ S
Sbjct: 306 LDSTWQDVFKEEAAMPDGDIALLNPEEEWPSDDPEDDDYNPERKEDNHNFDTEGADENAS 365

Query: 369 SSTSLSWFSDSETFSESMRWEMESNGYKNYSVDSSIGSDETSDGEIICGRRQRRTVDYKK 428
           + ++      S         E   + Y  YSV+S + SDE+  GEI CG RQR+ VDYKK
Sbjct: 366 NDSTSCSSLLSLNGECPPVDEGICHEY--YSVNSCLDSDES--GEIACGPRQRKAVDYKK 421

Query: 429 LYDEMFGKDASAFEQLSEDEDWGPAKRRRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKK 488
           LYDEM+GKDA   EQ+SEDEDWGP KR+R+EKESDAVN+LMTL+ SE K+S  +  +  +
Sbjct: 422 LYDEMYGKDAPPCEQMSEDEDWGPGKRKRREKESDAVNTLMTLHESENKHSDNEKNDRTR 481

Query: 489 KLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 548
           +  S  +IRRS  R+P +AVEKLRQVFAENELP R VK++LSKEL L+PEKV+KWFKNAR
Sbjct: 482 EGSSGIQIRRSCFRIPLDAVEKLRQVFAENELPPRSVKDSLSKELGLDPEKVSKWFKNAR 541

Query: 549 YLALKARKVES--ARQVSGSPRISKESSLETEKKN 581
           YLALK R+ +S   R  S + +I+K+S  + E+K+
Sbjct: 542 YLALKTRRYQSEGERLQSFTSKITKDSISQNEEKD 576

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449503000|ref|XP_004161802.1| PREDICTED: pathogenesis-related homeodomain protein-like [Cucumis sativus]

 Score =  561 bits (1447), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 336/598 (56%), Positives = 411/598 (68%), Gaps = 60/598 (10%)

Query: 1   MPGAGKKVVKHSESGKSCFPKKDSGSELIASLKFKKGSKISKSKKLRSKSRCQSKTVNST 60
           M GAGK++++ SE  K    K +SGSELI SLK  + SKIS SK+ +S+ +  S+ + ST
Sbjct: 73  MRGAGKRLMEESE--KCSHSKLESGSELIFSLKLTRCSKISHSKQKKSRMKSHSQAICST 130

Query: 61  LLKRTVAESHSKGAGDDFARSKSISQKNLHIKIDRKGSKNWASSKHKGKNSALVISKGNG 120
             +R + +S                                             +SKGN 
Sbjct: 131 FKRRPLPKS---------------------------------------------LSKGNK 145

Query: 121 EVVDGDGETKKLRKGRSKKRRKEKVELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWK 180
            V       K  ++   ++R+KEKVELDEASRLQRRTRYL+IKMKLEQNLIDAYSGEGWK
Sbjct: 146 NVTIRQLADKPTKEEEEEQRKKEKVELDEASRLQRRTRYLIIKMKLEQNLIDAYSGEGWK 205

Query: 181 GHSREKIRPEKELQRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHII 240
           G SREKIRPEKELQRA KQILKCK+GIRDAIRQLD L SVGCIE SVI  DGSV+HEHI 
Sbjct: 206 GQSREKIRPEKELQRAMKQILKCKLGIRDAIRQLDLLGSVGCIEDSVIGPDGSVYHEHIF 265

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES---RDQGWFCKFCECKMEIIE 297
           CAKCKLREAFPDNDI+LCDGTCNCAFHQKCLDPPLDT+S    DQGWFCKFCECKMEI+E
Sbjct: 266 CAKCKLREAFPDNDIILCDGTCNCAFHQKCLDPPLDTKSIPPGDQGWFCKFCECKMEILE 325

Query: 298 SMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRENSCS 357
            MNAH+GT FS+N  W+DIFKEEAAFPDG +ALLN EE+WPSDDSEDDDY+P+++EN C 
Sbjct: 326 GMNAHLGTRFSLNIGWEDIFKEEAAFPDGGNALLNHEEDWPSDDSEDDDYDPDKKEN-CH 384

Query: 358 ISRAGTDDDPSSSTSLSWFSDSETFSESMRWEMESNGY---KNYSVDSSIGSDETSDGEI 414
            + +  ++D       S  +      +     +  NG     ++   +SI SD +++  I
Sbjct: 385 DNASEEENDKEVLEESSSSTSLSWSLDGEDL-VSGNGIGCEDHFGAGTSIVSDGSNEEGI 443

Query: 415 ICGRRQRRTVDYKKLYDEMFGKDASAFEQ-LSEDEDWGPAKRRRKEKESDAVNSLMTLYG 473
            CGRRQR  VDYKKLYDEMFGKD  A EQ +SEDEDWGPAKRRR+EKE DA ++LM+L  
Sbjct: 444 TCGRRQRHAVDYKKLYDEMFGKDTPAHEQEVSEDEDWGPAKRRRREKECDAASTLMSLCE 503

Query: 474 SEEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKEL 533
           SE+K   +     KK L S+    RSF R+P +AVEKLR+VFA+NELPSR VKENLSKEL
Sbjct: 504 SEKKSQDIDMEAEKKLLNSHG---RSFFRIPRHAVEKLRKVFADNELPSRDVKENLSKEL 560

Query: 534 SLEPEKVNKWFKNARYLALKARKVESARQVSGSPRISKESSL-ETEKKNADVLTLKNS 590
            L+ EKV+KWFKNARY AL+ RK E A Q   S + S E  L ++++ + ++L+L+N+
Sbjct: 561 GLDAEKVSKWFKNARYSALRTRKAEGATQPHSSHKTSNELRLADSKEMSKNLLSLENA 618

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357449593|ref|XP_003595073.1| Pathogenesis-related homeodomain protein [Medicago truncatula] gi|355484121|gb|AES65324.1| Pathogenesis-related homeodomain protein [Medicago truncatula]

 Score =  542 bits (1396), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 309/544 (56%), Positives = 375/544 (68%), Gaps = 33/544 (6%)

Query: 29  IASLKFKKGSKISKSKKLRSKSRCQSKTVNSTLLKRTVAESHSKGAGDDFARSKSISQKN 88
           + S +FK  S   + KK R KS+       +    RT  +S +K +  D +         
Sbjct: 26  VDSPQFKTSSTKHQRKKHRLKSKSHKLGGCTNASVRTATDSSNKASTKDSSN-------- 77

Query: 89  LHIKIDRKGSKNWASSKHKGKNSALVIS-KGNGEVVDGDGETKKLRKGRSKKRRKEKVEL 147
              K DR  ++   S K +G  ++L    KG  +VVD +G  +K ++ R KKR++  V+L
Sbjct: 78  ---KTDRNSTQVQPSKKIQGGKTSLNNDRKGEKDVVDQEGNIQKRKRRRKKKRQRHNVDL 134

Query: 148 DEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRPEKELQRAKKQILKCKIGI 207
           D+  RLQRRTR +LI+MK EQNLIDAY+GEGWKG SREKIRPE ELQRAKKQILKCK+ I
Sbjct: 135 DDTVRLQRRTRNILIRMKQEQNLIDAYAGEGWKGQSREKIRPEMELQRAKKQILKCKLSI 194

Query: 208 RDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFH 267
           RDAI QLDSLSSVG IEGSVIATDGSV HEHI CA CK+ E  PDNDI+LCDGTCN AFH
Sbjct: 195 RDAIHQLDSLSSVGSIEGSVIATDGSVSHEHIFCANCKINEVSPDNDIILCDGTCNRAFH 254

Query: 268 QKCLDPPLDTES---RDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEAAFP 324
           Q+CLDPPL+TE     DQGWFCK+C+CK+EI+E+ NAH+GT F ++S WQD+FKEEAA P
Sbjct: 255 QRCLDPPLETEDIPPEDQGWFCKYCDCKIEILEATNAHLGTRFPLDSTWQDVFKEEAAIP 314

Query: 325 DGCSALLNQEEEWPSDDSEDDDYNPERRENS-CSISRAGTDDDPSSSTSLS---WFSDSE 380
           DG +ALLNQEEEWPSDD EDDDYNPER+E S    +  G D + S  +S S   W  + E
Sbjct: 315 DGDAALLNQEEEWPSDDPEDDDYNPERKEESHGGFNTEGNDKNASDDSSSSSSMWSLNGE 374

Query: 381 --TFSESMRWEMESNGYKNYSVDSSIGSDETSDGEIICGRRQRRTVDYKKLYDEMFGKDA 438
                E +  E  SN +        I SDE+  GEI CGRRQRR VDYKKLYDEMFGKDA
Sbjct: 375 CSLLDEGINLEYYSNDH--------IDSDES--GEIACGRRQRRAVDYKKLYDEMFGKDA 424

Query: 439 SAFEQLSEDEDWGPAKRRRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKKKLPSNAKIRR 498
              EQ+SEDEDWGP KRRR+EKES+AVN+LMTL+ SE KY   K  +  +   +++ I+R
Sbjct: 425 PPCEQVSEDEDWGPRKRRRREKESEAVNTLMTLHESENKYPNNKNNDRIRG--NSSGIKR 482

Query: 499 SFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE 558
              R    AVEKLRQVFAENELP + VK+ LSKEL L+  KVNKWFKNARY+ALK RK++
Sbjct: 483 PCFRFSHEAVEKLRQVFAENELPPKSVKDALSKELGLDAAKVNKWFKNARYMALKIRKLQ 542

Query: 559 SARQ 562
              Q
Sbjct: 543 EGGQ 546

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356564821|ref|XP_003550646.1| PREDICTED: pathogenesis-related homeodomain protein-like [Glycine max]

 Score =  536 bits (1380), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 312/529 (58%), Positives = 386/529 (72%), Gaps = 14/529 (2%)

Query: 35  KKGSKISKSKKLRSKSRCQSKTVNSTL-LKRTVAESHSKGAGDDFARSKSISQKNLHIKI 93
           KKG    K +K++  S+  +K   + +  KR ++    KG   D +  K I  K L IK 
Sbjct: 23  KKGQ--GKKEKVKVGSKSHTKNAGTDISRKRVISSLKVKGPPKDSSDKKLIIGKKLPIK- 79

Query: 94  DRKGSKNWASSKHKGKNSALVISKGNGEVVDGDGETKKLRKGRSKKRRKEKVELDEASRL 153
             K S    SSK +GK ++L   K  G+  DG  +  K+++ R KKR++  V+LD+ SRL
Sbjct: 80  -NKKSSLKPSSKLQGKKASLSSRKEGGDA-DGAVKLPKMKRKRKKKRQRNNVDLDDPSRL 137

Query: 154 QRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRPEKELQRAKKQILKCKIGIRDAIRQ 213
           QRRTRYLLIKMKLEQNLIDAYSGEGWKG SREKI+PEKELQRA+KQILKC++GIRD IRQ
Sbjct: 138 QRRTRYLLIKMKLEQNLIDAYSGEGWKGQSREKIKPEKELQRARKQILKCRLGIRDVIRQ 197

Query: 214 LDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDP 273
           LDSL S+  IE S IA DGSV+HEHI C KC +RE  PDNDI+LC+GTC  AFHQKCLDP
Sbjct: 198 LDSLGSLSSIEDSAIAPDGSVYHEHIFCVKCTVREELPDNDIILCNGTCKRAFHQKCLDP 257

Query: 274 PLDTES---RDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSAL 330
           PLDTE+    +QGWFCKFCECKMEI+E+ NAH+GT FS++S WQD+FKEEAA PDG +AL
Sbjct: 258 PLDTENIPPGEQGWFCKFCECKMEILEATNAHLGTHFSLHSTWQDVFKEEAAIPDGETAL 317

Query: 331 LNQEEEWPSDDSEDDDYNPERRENSCSISRAGTDDDPSSSTSLSWFSDSETFSESMRWEM 390
           LN EEEWPSDDSEDDDY+PER+E+S +I+  G +D  S   + S    S     S    +
Sbjct: 318 LNPEEEWPSDDSEDDDYDPERKEDSHNINTEGANDSASEDLTSSTSLCSSDGESS---PV 374

Query: 391 ESNGYKNYSVDSSIGSDETSDGEIICGRRQRRTVDYKKLYDEMFGKDASAFEQLSEDEDW 450
           +   ++ +SV SSI SDE+ D    CG RQR+ VDYKKLYDEMFGKDA A+EQLSEDEDW
Sbjct: 375 DGVSHEYFSVKSSIDSDESEDK--ACGCRQRKAVDYKKLYDEMFGKDAPAYEQLSEDEDW 432

Query: 451 GPAKRRRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEK 510
           GP KR+R+EKESDAV+SLMTL+ SE  +   +  ++ +K  S+ KI+R   R+P +AVEK
Sbjct: 433 GPGKRKRREKESDAVDSLMTLHESENMHPNNEHLDMTRKNSSSIKIKRHCFRIPHDAVEK 492

Query: 511 LRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES 559
           LRQVFAENELP R ++E LSKEL L+ EKV+KWFKNARYLALK RK ++
Sbjct: 493 LRQVFAENELPPRSIREGLSKELGLDTEKVSKWFKNARYLALKNRKYQA 541

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	629
TAIR|locus:2005538	796	PRHA "pathogenesis related hom	0.713	0.564	0.532	1e-123
TAIR|locus:2090694	723	HAT3.1 [Arabidopsis thaliana (	0.281	0.244	0.5	2.1e-56
UNIPROTKB|I3LTW3	113	I3LTW3 "Uncharacterized protei	0.066	0.371	0.409	8.8e-05
WB|WBGene00020485	220	ceh-54 [Caenorhabditis elegans	0.166	0.477	0.288	0.00037
WB|WBGene00021913	679	cec-8 [Caenorhabditis elegans	0.341	0.316	0.25	0.00086

TAIR|locus:2005538 PRHA "pathogenesis related homeodomain protein A" [Arabidopsis thaliana (taxid:3702)]

 Score = 1216 (433.1 bits), Expect = 1.0e-123, P = 1.0e-123
 Identities = 245/460 (53%), Positives = 317/460 (68%)

Query:   145 VELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRPEKELQRAKKQILKCK 204
             VE+D++ RLQRRTRYLLIKMK++QNLIDAY+ EGWKG SREKIRP+KEL+RA+K+IL CK
Sbjct:    97 VEVDDSLRLQRRTRYLLIKMKMQQNLIDAYATEGWKGQSREKIRPDKELERARKEILNCK 156

Query:   205 IGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNC 264
             +G+RDAIRQLD LSSVG +E  VIA+DGS+HH+HI CA+C  REAFPDNDI+LCDGTCN 
Sbjct:   157 LGLRDAIRQLDLLSSVGSMEEKVIASDGSIHHDHIFCAECNSREAFPDNDIILCDGTCNR 216

Query:   265 AFHQKCLDPPLDTES---RDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEA 321
             AFHQKCLDPPL+TES    DQGWFCKFC+CK+EII++MNA IGT F V+SNWQDIF EEA
Sbjct:   217 AFHQKCLDPPLETESIPPGDQGWFCKFCDCKIEIIDTMNAQIGTHFPVDSNWQDIFNEEA 276

Query:   322 AFPDGCSALLNQXXXXXXXXXXXXXXXXXRRENSCSISRAGTXXXXXXXXXXXXXXXXET 381
             + P G  A +N                   REN    S   +                  
Sbjct:   277 SLPIGSEATVNNEADWPSDDSKDDDYDPEMRENGGGNSSNVSGDGGGDNDEESISTSLSL 336

Query:   382 FSESMRWEMESNGYKNYSVDSSIGSDETSDGEIICGRRQRRTVDYKKLYDEMFGKDASAF 441
              S+ +   + +  ++ + + + +   ETS+ E +CG RQRRTVDY +LY EMFGKDA   
Sbjct:   337 SSDGVA--LSTGSWEGHRLSNMVEQCETSNEETVCGPRQRRTVDYTQLYYEMFGKDAVLQ 394

Query:   442 EQLSEDEDWGPAKRRRKEKESDAVNSLMTLYGSEEK-YSKVKTAEVKKK---LPSNAKIR 497
             EQ SEDEDWGP  RR++++ESDA ++L+T+  S +K    V+T E  ++      N   R
Sbjct:   395 EQGSEDEDWGPNDRRKRKRESDAGSTLVTMCESSKKDQDVVETLEQSERDSVSVENKGGR 454

Query:   498 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV 557
             R   R+P NAVEKLRQVFAE ELPS+ V++ L+KELSL+PEKVNKWFKN RY+AL+ RK 
Sbjct:   455 RRMFRLPRNAVEKLRQVFAETELPSKAVRDRLAKELSLDPEKVNKWFKNTRYMALRNRKT 514

Query:   558 ESARQVSGSPRISK-ESSLETE-KKNADVLTLKNSLEETL 595
             ES +Q   S  +S  +S  E   + N +   ++++L++T+
Sbjct:   515 ESVKQPGDSKTVSGGDSGPEAVMENNTETNEVQDTLDDTV 554

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

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

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

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2090694 HAT3.1 [Arabidopsis thaliana (taxid:3702)]

 Score = 478 (173.3 bits), Expect = 2.1e-56, Sum P(2) = 2.1e-56
 Identities = 90/180 (50%), Positives = 123/180 (68%)

Query:   146 ELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRPEKELQRAKKQILKCKI 205
             E DE +R++++ RY L ++  EQ+LIDAYS EGWKG S EKIRPEKEL+RA K+IL+ K+
Sbjct:   173 EDDEYTRIKKKLRYFLNRINYEQSLIDAYSLEGWKGSSLEKIRPEKELERATKEILRRKL 232

Query:   206 GIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCA 265
              IRD  + LD+L + G +  S+  TDG +  E I CAKC  ++   DNDI+LCDG C+  
Sbjct:   233 KIRDLFQHLDTLCAEGSLPESLFDTDGEISSEDIFCAKCGSKDLSVDNDIILCDGFCDRG 292

Query:   266 FHQKCLDPPL---DTESRDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEAA 322
             FHQ CL+PPL   D    D+GW C  C+CK + ++ +N  +GT FSV+ +W+ IF E AA
Sbjct:   293 FHQYCLEPPLRKEDIPPDDEGWLCPGCDCKDDSLDLLNDSLGTKFSVSDSWEKIFPEAAA 352

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

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0008284 "positive regulation of cell proliferation" evidence=RCA

GO:0009560 "embryo sac egg cell differentiation" evidence=RCA

GO:0043687 "post-translational protein modification" evidence=RCA

GO:0051276 "chromosome organization" evidence=RCA

GO:0003677 "DNA binding" evidence=IDA

UNIPROTKB|I3LTW3 I3LTW3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 104 (41.7 bits), Expect = 8.8e-05, P = 8.8e-05
 Identities = 18/44 (40%), Positives = 28/44 (63%)

Query:   256 VLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCEC-KMEIIES 298
             VLCD  CN A+H  CL+PPLD    ++ W+C  C+    E++++
Sbjct:     3 VLCD-ECNMAYHIYCLNPPLDKVPEEEYWYCPSCKTDSSEVVKA 45

GO:0008270 "zinc ion binding" evidence=IEA

WB|WBGene00020485 ceh-54 [Caenorhabditis elegans (taxid:6239)]

 Score = 115 (45.5 bits), Expect = 0.00037, P = 0.00037
 Identities = 32/111 (28%), Positives = 58/111 (52%)

Query:   483 TAEVKKKLPSNAKI-RRSFHRMP--PNAVEKLRQVFAENELPSRIVKENLSKELSLEPEK 539
             T ++ +K  +N    R+  +R+    N ++++ +VFAEN+ P  + +E L+ ++ L  E+
Sbjct:    28 TKKITRKRSNNFNPDRKKRNRITFDANQIDEMEKVFAENQYPDTMSREKLANKIQLHEER 87

Query:   540 VNKWFKNARYLALKARKVESARQVSGSPRISKESSLETEKKNADVLTLKNS 590
             V  WF+N R  A   R+ +        P I+K  + E EK   D  TL ++
Sbjct:    88 VQIWFQNRR--AKYRREQKQTGHPYEPPSITKNPTGEKEKTQ-DCTTLTSA 135

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:0005634 "nucleus" evidence=IEA

WB|WBGene00021913 cec-8 [Caenorhabditis elegans (taxid:6239)]

 Score = 120 (47.3 bits), Expect = 0.00086, P = 0.00086
 Identities = 58/232 (25%), Positives = 104/232 (44%)

Query:   407 DETSDGEIICGRRQRRTVDYKKL--YDEMFGKDASAFEQLSEDEDWGPAKRRRKEKESDA 464
             D++SD +    RR++++   KK   + +   +  +  +  S+DED      +R +K   A
Sbjct:   245 DDSSDDDSEMERRRKKSKKSKKSKKFKKSEKRKRAVNDSSSDDEDEEEKPEKRSKKSKKA 304

Query:   465 VNSLMTLYGSEEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRI 524
             V    +    EEK SK ++ + KK+     +   S   +    VE  +   +  + P + 
Sbjct:   305 VIDSSSEDEEEEKSSKKRSKKSKKESDEEQQASDSEEEV----VEVKKNSKSPKKTPKKT 360

Query:   525 -VKENLSKELSLEPEKVNKWFKNARYLALKARKVES--ARQVSGSPRISKESSLETEKKN 581
              VKE   +    E E+V K  K+++    KA++  S    +V  SP+   +S  ++ KK+
Sbjct:   361 AVKEESEESSGDEEEEVVKKKKSSKINKRKAKESSSDEEEEVEESPKKKTKSPRKSSKKS 420

Query:   582 A-----DVLTLKNSLEETLICSPKSLKKIH-PKRIQNQSAVAAASRKISRKE 627
             A     +  +  N  EE +  SPK  KK+  PK+   + A    S + S  E
Sbjct:   421 AAKEESEEESSDNEEEEEVDYSPK--KKVKSPKKSSKKPAAKVESEEPSDNE 470


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.312   0.128   0.366    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      629       556   0.00098  119 3  11 23  0.46    34
                                                     35  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  5
  No. of states in DFA:  621 (66 KB)
  Total size of DFA:  315 KB (2160 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  53.73u 0.13s 53.86t   Elapsed:  00:00:02
  Total cpu time:  53.73u 0.13s 53.86t   Elapsed:  00:00:02
  Start:  Fri May 10 17:43:23 2013   End:  Fri May 10 17:43:25 2013

GO:0005634 "nucleus" evidence=IEA

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00009253001 SubName- Full=Chromosome undetermined scaffold_226, whole genome shotgun sequence; (727 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	629
pfam00628	51	pfam00628, PHD, PHD-finger	2e-11
smart00249	47	smart00249, PHD, PHD zinc finger	2e-08
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	2e-08
smart00389	57	smart00389, HOX, Homeodomain	6e-07
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	5e-04
pfam00046	57	pfam00046, Homeobox, Homeobox domain	6e-04

>gnl|CDD|201356 pfam00628, PHD, PHD-finger

 Score = 58.7 bits (142), Expect = 2e-11
 Identities = 22/54 (40%), Positives = 31/54 (57%), Gaps = 4/54 (7%)

Query: 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQG-WFCKFCECK 292
            CA C   +   D +++LCDG C+  FH  CL PPL+ E   +G W+C  C+ K
Sbjct: 1   YCAVC--GKVDDDGELLLCDG-CDRWFHLACLGPPLEPEEIPEGEWYCPECKPK 51

PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3. Length = 51

>gnl|CDD|214584 smart00249, PHD, PHD zinc finger

 Score = 50.7 bits (121), Expect = 2e-08
 Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 3/50 (6%)

Query: 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFC 289
            C+ C   +     +++ CDG C+  +HQ CL PPL  E  D  W+C  C
Sbjct: 1   YCSVCGKPDD--GGELLQCDG-CDRWYHQTCLGPPLLEEEPDGKWYCPKC 47

The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers. Length = 47

>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 22/53 (41%), Positives = 30/53 (56%)

Query: 497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 549
           RR   R  P  +E+L + F +N  PSR  +E L+KEL L   +V  WF+N R 
Sbjct: 1   RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRA 53

Length = 59

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 46.5 bits (111), Expect = 6e-07
 Identities = 21/55 (38%), Positives = 31/55 (56%), Gaps = 3/55 (5%)

Query: 495 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 549
           + R SF    P  +E+L + F +N  PSR  +E L+K+L L   +V  WF+N R 
Sbjct: 3   RKRTSF---TPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRA 54

DNA-binding factors that are involved in the transcriptional regulation of key developmental processes. Length = 57

>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor [Transcription]

 Score = 40.9 bits (96), Expect = 5e-04
 Identities = 29/130 (22%), Positives = 49/130 (37%), Gaps = 16/130 (12%)

Query: 454 KRRRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQ 513
           K  + ++E +A +S M L   ++  S  K+   +                    +  L +
Sbjct: 24  KTTKNKREVEAADSEMKLERKQDGSSPPKSKRRRTTD---------------EQLMVLER 68

Query: 514 VFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY-LALKARKVESARQVSGSPRISKE 572
            F  N  PS I +  LS  L++ P+ V  WF+N R     K       R       ++K 
Sbjct: 69  EFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQRPGEEEADLAKI 128

Query: 573 SSLETEKKNA 582
            SL T + + 
Sbjct: 129 GSLSTGQISI 138

Length = 156

>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain

 Score = 37.8 bits (89), Expect = 6e-04
 Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 6/62 (9%)

Query: 495 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 554
           + R +F    P  +E+L + F +N  PS   +E L+K+L L   +V  WF+N R    K 
Sbjct: 2   RKRTTFT---PEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRA---KW 55

Query: 555 RK 556
           ++
Sbjct: 56  KR 57

Length = 57

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	629
KOG4299	613	consensus PHD Zn-finger protein [General function	99.9
KOG0842	307	consensus Transcription factor tinman/NKX2-3, cont	99.73
KOG0850	245	consensus Transcription factor DLX and related pro	99.69
KOG0484	125	consensus Transcription factor PHOX2/ARIX, contain	99.66
KOG1244	336	consensus Predicted transcription factor Requiem/N	99.62
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.58
KOG0843	197	consensus Transcription factor EMX1 and related HO	99.56
KOG0489	261	consensus Transcription factor zerknullt and relat	99.51
KOG0492	246	consensus Transcription factor MSH, contains HOX d	99.48
KOG0488	309	consensus Transcription factor BarH and related HO	99.48
KOG0485	268	consensus Transcription factor NKX-5.1/HMX1, conta	99.46
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.46
KOG2251	228	consensus Homeobox transcription factor [Transcrip	99.45
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.45
KOG0493	342	consensus Transcription factor Engrailed, contains	99.44
KOG0487	308	consensus Transcription factor Abd-B, contains HOX	99.43
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.42
KOG0494	332	consensus Transcription factor CHX10 and related H	99.39
KOG0848	317	consensus Transcription factor Caudal, contains HO	99.29
KOG0483	198	consensus Transcription factor HEX, contains HOX a	99.28
COG5576	156	Homeodomain-containing transcription factor [Trans	99.28
KOG0486	351	consensus Transcription factor PTX1, contains HOX	99.2
KOG0491	194	consensus Transcription factor BSH, contains HOX d	99.11
KOG0847	288	consensus Transcription factor, contains HOX domai	99.07
KOG4577	383	consensus Transcription factor LIM3, contains LIM	99.05
KOG0844	408	consensus Transcription factor EVX1, contains HOX	99.05
KOG0490	235	consensus Transcription factor, contains HOX domai	98.97
KOG3802	398	consensus Transcription factor OCT-1, contains POU	98.91
KOG0775	304	consensus Transcription factor SIX and related HOX	98.77
KOG0849	354	consensus Transcription factor PRD and related pro	98.67
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	98.64
KOG0774	334	consensus Transcription factor PBX and related HOX	98.61
KOG0825	1134	consensus PHD Zn-finger protein [General function	98.58
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.54
KOG2252	558	consensus CCAAT displacement protein and related h	98.52
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	98.3
KOG0955	1051	consensus PHD finger protein BR140/LIN-49 [General	98.18
KOG1168	385	consensus Transcription factor ACJ6/BRN-3, contain	98.17
KOG4323	464	consensus Polycomb-like PHD Zn-finger protein [Gen	98.17
KOG4443	694	consensus Putative transcription factor HALR/MLL3,	98.14
COG5034	271	TNG2 Chromatin remodeling protein, contains PhD zi	98.04
KOG1512	381	consensus PHD Zn-finger protein [General function	98.01
KOG1973	274	consensus Chromatin remodeling protein, contains P	97.94
cd04718	148	BAH_plant_2 BAH, or Bromo Adjacent Homology domain	97.91
KOG0383	696	consensus Predicted helicase [General function pre	97.78
COG5141	669	PHD zinc finger-containing protein [General functi	97.75
KOG0773	342	consensus Transcription factor MEIS1 and related H	97.75
KOG0490	235	consensus Transcription factor, contains HOX domai	97.73
KOG0954	893	consensus PHD finger protein [General function pre	97.64
KOG0957	707	consensus PHD finger protein [General function pre	97.62
KOG1245	1404	consensus Chromatin remodeling complex WSTF-ISWI,	97.61
KOG0956	900	consensus PHD finger protein AF10 [General functio	97.53
KOG1146	1406	consensus Homeobox protein [General function predi	96.88
PF13831	36	PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.	96.27
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	96.16
PF15446	175	zf-PHD-like: PHD/FYVE-zinc-finger like domain	95.23
KOG1473	1414	consensus Nucleosome remodeling factor, subunit NU	94.95
KOG3623	1007	consensus Homeobox transcription factor SIP1 [Tran	94.16
KOG0957	707	consensus PHD finger protein [General function pre	93.33
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	93.21
KOG4443	694	consensus Putative transcription factor HALR/MLL3,	90.98
KOG1246	904	consensus DNA-binding protein jumonji/RBP2/SMCY, c	88.41
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	87.02
KOG4299	613	consensus PHD Zn-finger protein [General function	85.93
KOG1512	381	consensus PHD Zn-finger protein [General function	80.35
KOG3612	588	consensus PHD Zn-finger protein [General function	80.33

>KOG4299 consensus PHD Zn-finger protein [General function prediction only]

Probab=99.90  E-value=3.1e-24  Score=236.67  Aligned_cols=193  Identities=34%  Similarity=0.565  Sum_probs=161.7

Q ss_pred             cchhHHHHHHHHHHHHHHHHhhhhhHHhhhcCCCCCCCccc---------CCchHHHHHHHHhhhhhhhhHHHHhhhccc
Q 006832          146 ELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREK---------IRPEKELQRAKKQILKCKIGIRDAIRQLDS  216 (629)
Q Consensus       146 ~~~e~~ri~~r~r~~l~~~~~Eq~l~~Ay~~egwk~~sreK---------~rPekEl~Rak~~i~k~K~~ird~l~~ld~  216 (629)
                      .+.+.-|...+++|+...+..++.++++|+.+||++.+.+|         ++|.++..++..+|+.+++.++.+.+.++.
T Consensus       150 ~~p~~~r~~n~lk~~t~~~~~~~~li~~~s~e~~~a~~~~k~~~r~~~~~~~~~~~sn~tt~~i~~r~~~~~s~~~hl~t  229 (613)
T KOG4299|consen  150 EVPDSFRDKNSLKYLTSLQNDVQELIDISSTEGWKASSDEKPPGRPFELLIRPAKESNVTTKEILNRKLTYRSLPRHLET  229 (613)
T ss_pred             cCCCcchhhhhhhhhhccccccccccchhcccccccCCcccCcccchhhhcCcchhhccchhhhhhhhhhhhhhhhhhhh
Confidence            45677899999999999999999999999999999999999         999999999999999999999999999998


Q ss_pred             cCCCCCCCCCcccCCCCcccccc--cccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCC-CCCceecccCchhh
Q 006832          217 LSSVGCIEGSVIATDGSVHHEHI--ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES-RDQGWFCKFCECKM  293 (629)
Q Consensus       217 l~~~g~le~s~~~~dg~~~~e~~--~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p-~dg~W~C~~C~~k~  293 (629)
                      ....+..++..+..++.....+.  ||..|++.+..  +++||||| |+++|||.||.|||.... +.|.|||+.|.++.
T Consensus       230 ~s~~~t~~e~r~~~D~~~~~~~~~~fCsaCn~~~~F--~~~i~CD~-Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k~  306 (613)
T KOG4299|consen  230 ESKEGTVEEKRRERDKNISVEDIEDFCSACNGSGLF--NDIICCDG-CPRSFHQTCLEPPLEPENIPPGSWFCPECKIKS  306 (613)
T ss_pred             hhhhccchhhhhhhccccccCCHHHHHHHhCCcccc--ccceeecC-CchHHHHhhcCCCCCcccCCCCccccCCCeeee
Confidence            88777777777777776665555  99999999875  78999996 999999999999965544 47999999999986


Q ss_pred             HHHH--------------------hhhccCCccccccchhhhhhccccccCCCCccccCCccCCCCCCCCCCCCCccc
Q 006832          294 EIIE--------------------SMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPER  351 (629)
Q Consensus       294 ~~l~--------------------~~n~~~gtsf~lp~~~~d~F~eva~~~dG~~~~~~~e~~wpsddseD~dydP~~  351 (629)
                      .++.                    .|..+++..|.||..+...|.+|..+          +.+|++|++.+.+|+|..
T Consensus       307 ~in~~~~t~~~~~~~~~i~t~~~~~IDs~np~q~~lPe~i~~~~~~v~~g----------~~~~~sd~~~~~pl~~~~  374 (613)
T KOG4299|consen  307 VINPKMETLSNRGTVVDIFTQFVSKIDSHNPIQKILPENISESFGGVSRG----------DDGQYSDTQDEKPLDPPA  374 (613)
T ss_pred             ecccchhhhhhccchHHHHHHHHHhhhccchhhhhCCHHHHhhccccccC----------CCCccccccCCcCCChhh
Confidence            5332                    34555666666777777777776643          445778999999999944

>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]

Probab=99.73  E-value=2.1e-18  Score=179.71  Aligned_cols=91  Identities=25%  Similarity=0.357  Sum_probs=75.9

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhhhcc--ccCCCC--CC
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESAR--QVSGSP--RI  569 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~~~~~--~l~~~~--~~  569 (629)
                      .++||+|..||..||-+||+.|.++.|++..+|++||..|+||++||+|||||||||.+|+.+....+  .+...+  .-
T Consensus       151 ~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~~~~~~~~r~  230 (307)
T KOG0842|consen  151 RKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALLLASSPPPRR  230 (307)
T ss_pred             ccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcccCCCCCcccc
Confidence            45566788899999999999999999999999999999999999999999999999988887554433  333333  46


Q ss_pred             CCCcchhhcccchhh
Q 006832          570 SKESSLETEKKNADV  584 (629)
Q Consensus       570 s~~~~~~~~~~~~dl  584 (629)
                      .+.+.++.+++++-.
T Consensus       231 v~vpvlvrd~kp~~~  245 (307)
T KOG0842|consen  231 VAVPVLVRDGKPCSG  245 (307)
T ss_pred             cCCceeccCCCcccC
Confidence            888899888876655

>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]

Probab=99.69  E-value=1.8e-17  Score=165.04  Aligned_cols=74  Identities=19%  Similarity=0.291  Sum_probs=69.9

Q ss_pred             cchhhccCCCccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832          483 TAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       483 ~~~~~~~~~~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      +....+.|++.+|.|++||.|+..||+.|.+.|+.++|+-..+|.+||..||||.+||+|||||||.|++|..+
T Consensus       109 E~~e~~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k  182 (245)
T KOG0850|consen  109 EPSERRPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK  182 (245)
T ss_pred             CcceeccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence            44556889999999999999999999999999999999999999999999999999999999999999888887

>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]

Probab=99.66  E-value=4e-17  Score=144.98  Aligned_cols=70  Identities=26%  Similarity=0.434  Sum_probs=63.7

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhhhcccc
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESARQV  563 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~~~~~~l  563 (629)
                      .++||-|+.||..|+.+||++|.+++||+..+|++||-.|.||+..|+|||||||++++|+.++......
T Consensus        15 rKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~~~   84 (125)
T KOG0484|consen   15 RKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAKMA   84 (125)
T ss_pred             HHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHHhh
Confidence            4567889999999999999999999999999999999999999999999999999999999876654433

>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]

Probab=99.62  E-value=2.3e-16  Score=160.05  Aligned_cols=192  Identities=22%  Similarity=0.355  Sum_probs=129.6

Q ss_pred             CCCC-chhhhhhhccccchhh--hccccccccccccccCCcc-ceeccCCCCcccCCcccchhcccccchhhccch--hc
Q 006832           73 GAGD-DFARSKSISQKNLHIK--IDRKGSKNWASSKHKGKNS-ALVISKGNGEVVDGDGETKKLRKGRSKKRRKEK--VE  146 (629)
Q Consensus        73 ~~~~-~~~~~~~~~~~~~~~~--~~~~~~~~~~s~~~~~~~~-~~~~~~~~~~~~d~~~~~~~~k~~rk~kr~~~~--~~  146 (629)
                      ++.+ ++++++||++++|+|+  ++.+++     .+|+..|- ..++++.|.+++|.++++++++.+-+.+.++-.  -.
T Consensus       110 ~~~e~~~~leAll~seglekk~s~dar~e-----eti~d~qkq~~l~~p~dle~eD~eed~pkrknrsk~ka~~v~~~~~  184 (336)
T KOG1244|consen  110 AASEHGACLEALLRSEGLEKKHSNDAREE-----ETINDDQKQSGLIFPTDLESEDLEEDIPKRKNRSKGKATGVGILRK  184 (336)
T ss_pred             CcccccHHHHHHHhcccccccCCCCCCcc-----cchhhhhhccccccCcccchhhccccccccccCCcccceeeecccc
Confidence            4556 7999999999999999  888888     78886663 467888889999999999999999999988543  34


Q ss_pred             chhHHHHHHHHHHHHHHHHhhhhhHHh-hhcCCCCCCCcccCCchHHHHHHHHhhh---------------hhhhh-HHH
Q 006832          147 LDEASRLQRRTRYLLIKMKLEQNLIDA-YSGEGWKGHSREKIRPEKELQRAKKQIL---------------KCKIG-IRD  209 (629)
Q Consensus       147 ~~e~~ri~~r~r~~l~~~~~Eq~l~~A-y~~egwk~~sreK~rPekEl~Rak~~i~---------------k~K~~-ird  209 (629)
                      +...+-+..   |++          ++ +..-+|+.-      ..+.-+|+++-|.               .+|.+ ..+
T Consensus       185 l~~ss~l~~---~~~----------d~~~~~~~~~~g------e~~vkqr~kkd~a~Pn~YCDFclgdsr~nkkt~~pee  245 (336)
T KOG1244|consen  185 LTDSSSLED---YVC----------DTGTKQTVFAPG------EAKVKQRVKKDIAQPNPYCDFCLGDSRENKKTGMPEE  245 (336)
T ss_pred             ccccccccc---hhh----------cccccccccCcc------hhhHHHhhhcccccCCcccceeccccccccccCCchh
Confidence            444444443   333          22 222233321      0122333333111               23333 223


Q ss_pred             Hhhhcc--ccCCCCCCCC--Ccc---cCCCCcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCC
Q 006832          210 AIRQLD--SLSSVGCIEG--SVI---ATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQ  282 (629)
Q Consensus       210 ~l~~ld--~l~~~g~le~--s~~---~~dg~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg  282 (629)
                      ++...|  ...+..++..  .++   ....|.+.++.+|.+|+..++  +++||+|| .|+++||||||.||+...| +|
T Consensus       246 lvscsdcgrsghpsclqft~nm~~avk~yrwqcieck~csicgtsen--ddqllfcd-dcdrgyhmyclsppm~epp-eg  321 (336)
T KOG1244|consen  246 LVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYCSICGTSEN--DDQLLFCD-DCDRGYHMYCLSPPMVEPP-EG  321 (336)
T ss_pred             hcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeecceeccccCcCC--CceeEeec-ccCCceeeEecCCCcCCCC-CC
Confidence            332221  2223333321  122   245699999999999998865  78999999 7999999999999999988 89


Q ss_pred             ceecccCchh
Q 006832          283 GWFCKFCECK  292 (629)
Q Consensus       283 ~W~C~~C~~k  292 (629)
                      .|.|..|...
T Consensus       322 swsc~KOG~~  331 (336)
T KOG1244|consen  322 SWSCHLCLEE  331 (336)
T ss_pred             chhHHHHHHH
Confidence            9999999643

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.58  E-value=1.4e-15  Score=121.04  Aligned_cols=57  Identities=35%  Similarity=0.585  Sum_probs=53.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832          497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  553 (629)
Q Consensus       497 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K  553 (629)
                      ||++++||++|+..|+.+|..++||+..+++.||..|||++.||++||+|+|++.+|
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence            567889999999999999999999999999999999999999999999999996553

; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....

>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]

Probab=99.56  E-value=2.4e-15  Score=145.20  Aligned_cols=62  Identities=24%  Similarity=0.424  Sum_probs=57.6

Q ss_pred             ccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832          495 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       495 k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      +.||.||.||++|+..||..|+.++|....+|++||+.|+|++.||+|||||||.|.+|...
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~  162 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQ  162 (197)
T ss_pred             CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHH
Confidence            56888999999999999999999999999999999999999999999999999997665553

>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]

Probab=99.51  E-value=6e-15  Score=152.11  Aligned_cols=66  Identities=23%  Similarity=0.335  Sum_probs=59.9

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhhh
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES  559 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~~~  559 (629)
                      .+.||.|+.||..|+.+||..|.-|.|+++..|.+||..|.|+++||+|||||||.|.+|..+...
T Consensus       157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~  222 (261)
T KOG0489|consen  157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS  222 (261)
T ss_pred             CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence            446888999999999999999999999999999999999999999999999999997776665443

>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]

Probab=99.48  E-value=2.3e-14  Score=140.96  Aligned_cols=65  Identities=23%  Similarity=0.338  Sum_probs=59.2

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhh
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE  558 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~~  558 (629)
                      +.-|++|+-||.+|+..||+.|.+.+|.++.+|.+++..|.||+.||+|||||||+|.+|...++
T Consensus       142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae  206 (246)
T KOG0492|consen  142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAE  206 (246)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHH
Confidence            44578899999999999999999999999999999999999999999999999999877765443

>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]

Probab=99.48  E-value=3.4e-14  Score=149.71  Aligned_cols=65  Identities=22%  Similarity=0.282  Sum_probs=59.8

Q ss_pred             ccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhh
Q 006832          493 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV  557 (629)
Q Consensus       493 ~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~  557 (629)
                      .+|.|+.|+.||..|+.+||..|+...|.+..+|.+||+.||||-.||++||||||+|++|....
T Consensus       169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~  233 (309)
T KOG0488|consen  169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE  233 (309)
T ss_pred             CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence            36677889999999999999999999999999999999999999999999999999977766644

>KOG0485 consensus Transcription factor NKX-5

Probab=99.46  E-value=6.5e-14  Score=138.63  Aligned_cols=66  Identities=18%  Similarity=0.285  Sum_probs=61.3

Q ss_pred             ccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhh
Q 006832          493 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE  558 (629)
Q Consensus       493 ~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~~  558 (629)
                      ..++||.|+.|+..|+.+||..|....|++..+|..||+.|.||+.||+|||||||.|++|+-+++
T Consensus       101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad  166 (268)
T KOG0485|consen  101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAAD  166 (268)
T ss_pred             ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhh
Confidence            346788899999999999999999999999999999999999999999999999999888887655

1/HMX1, contains HOX domain [Transcription]

>smart00389 HOX Homeodomain

Probab=99.46  E-value=5.8e-14  Score=110.68  Aligned_cols=53  Identities=34%  Similarity=0.597  Sum_probs=50.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006832          498 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  550 (629)
Q Consensus       498 R~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k  550 (629)
                      +.+++|+++|+..|+.+|..++||+..++..||..|||+..||++||+|+|++
T Consensus         2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~   54 (56)
T smart00389        2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAK   54 (56)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhc
Confidence            45677999999999999999999999999999999999999999999999984

DNA-binding factors that are involved in the transcriptional regulation of key developmental processes

>KOG2251 consensus Homeobox transcription factor [Transcription]

Probab=99.45  E-value=7.6e-14  Score=138.78  Aligned_cols=67  Identities=27%  Similarity=0.475  Sum_probs=61.9

Q ss_pred             CccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhh
Q 006832          492 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE  558 (629)
Q Consensus       492 ~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~~  558 (629)
                      ...|.||.||+|+..|+.+||.+|.+++||+...|++||.+|+|.+.+|+|||.|||+|.+++.+.+
T Consensus        33 ~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   33 GPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             cchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            3466788999999999999999999999999999999999999999999999999999888877654

>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner

Probab=99.45  E-value=8.2e-14  Score=110.46  Aligned_cols=56  Identities=38%  Similarity=0.623  Sum_probs=51.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832          498 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  553 (629)
Q Consensus       498 R~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K  553 (629)
                      +.+..|+..|+..|+.+|..++||+..++..||.+|||+..||++||+|+|++.++
T Consensus         2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~   57 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR   57 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence            45567999999999999999999999999999999999999999999999995543

>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]

Probab=99.44  E-value=7.3e-14  Score=141.26  Aligned_cols=62  Identities=23%  Similarity=0.437  Sum_probs=57.2

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      +.-||+|+.||.+|++.|...|++|.|.+...|.+||++|||.+.||+|||||+|+|.+|--
T Consensus       244 ~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT  305 (342)
T KOG0493|consen  244 KEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST  305 (342)
T ss_pred             chhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence            34589999999999999999999999999999999999999999999999999999666543

>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]

Probab=99.43  E-value=7.9e-14  Score=145.80  Aligned_cols=63  Identities=22%  Similarity=0.307  Sum_probs=56.1

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      .+.|++|--||+.|+.+||+.|--|.|.+.+.|.+||+.|+||++||+|||||||.|.+|--+
T Consensus       233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r  295 (308)
T KOG0487|consen  233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR  295 (308)
T ss_pred             cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence            344556677899999999999999999999999999999999999999999999997666553

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.42  E-value=1.9e-13  Score=110.90  Aligned_cols=53  Identities=15%  Similarity=0.292  Sum_probs=50.8

Q ss_pred             cCCCCCCCCHHHHHHHHHHHHhCCC----CCHHHHHHHHHHhCCCcchhhhccchhc
Q 006832          496 IRRSFHRMPPNAVEKLRQVFAENEL----PSRIVKENLSKELSLEPEKVNKWFKNAR  548 (629)
Q Consensus       496 ~kR~r~rft~~Q~~~Le~~F~~~~y----Ps~~~re~LA~~lgLt~~QVkiWFQNrR  548 (629)
                      +||.|+.||++|+..|+.+|..++|    |+..++++||..|||++.+|+|||||.+
T Consensus         1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            3788999999999999999999999    9999999999999999999999999975

This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.

>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]

Probab=99.39  E-value=2.3e-13  Score=137.57  Aligned_cols=72  Identities=24%  Similarity=0.346  Sum_probs=61.8

Q ss_pred             cCCCccccCCC-CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhhhc
Q 006832          489 KLPSNAKIRRS-FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESA  560 (629)
Q Consensus       489 ~~~~~~k~kR~-r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~~~~  560 (629)
                      ++.+.+++||. |+.||..|+.+||..|++-.||+...|+-||-++.|.+.+|+|||||||+|++|..+..+.
T Consensus       133 ~~~kkk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~  205 (332)
T KOG0494|consen  133 DNAKKKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGG  205 (332)
T ss_pred             cccccccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCc
Confidence            33444445554 8899999999999999999999999999999999999999999999999988777665543

>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]

Probab=99.29  E-value=8e-13  Score=134.34  Aligned_cols=59  Identities=22%  Similarity=0.232  Sum_probs=54.0

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhh
Q 006832          499 SFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV  557 (629)
Q Consensus       499 ~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~  557 (629)
                      =|..||..|+.+||..|...+|.+...|-+||.-|||+++||+|||||||+|-+|..+.
T Consensus       202 YRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKK  260 (317)
T KOG0848|consen  202 YRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKK  260 (317)
T ss_pred             eeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHH
Confidence            35679999999999999999999999999999999999999999999999986666543

>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]

Probab=99.28  E-value=1.7e-12  Score=128.90  Aligned_cols=56  Identities=29%  Similarity=0.430  Sum_probs=51.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHH
Q 006832          497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL  552 (629)
Q Consensus       497 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~  552 (629)
                      .+++.|||.+|+..||..|..+.|.....|..||++|||.++||.|||||||++++
T Consensus        51 ~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK  106 (198)
T KOG0483|consen   51 KGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWK  106 (198)
T ss_pred             ccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhcccccc
Confidence            34446789999999999999999999999999999999999999999999999543

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.28  E-value=3.5e-12  Score=122.60  Aligned_cols=63  Identities=29%  Similarity=0.389  Sum_probs=56.0

Q ss_pred             ccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhh
Q 006832          495 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV  557 (629)
Q Consensus       495 k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~  557 (629)
                      ..+++|+|.|.+|+..|++.|..+|||+..+|..||..|||+++-|+|||||+|++.++.+..
T Consensus        50 ~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~  112 (156)
T COG5576          50 PPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG  112 (156)
T ss_pred             cCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence            345555667999999999999999999999999999999999999999999999977766643

>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]

Probab=99.20  E-value=7e-12  Score=130.05  Aligned_cols=64  Identities=25%  Similarity=0.392  Sum_probs=58.8

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhh
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV  557 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~  557 (629)
                      +|+||.|+.||.+|+++||.+|+.|.||++.+|++||-.++||+..|+|||+|||++.+|..+-
T Consensus       110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN  173 (351)
T KOG0486|consen  110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERN  173 (351)
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhh
Confidence            4678889999999999999999999999999999999999999999999999999976665533

>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]

Probab=99.11  E-value=2.1e-11  Score=116.67  Aligned_cols=60  Identities=23%  Similarity=0.368  Sum_probs=54.8

Q ss_pred             cCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          496 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       496 ~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      +++-|+.|+..|+.-|+..|+...|.+..+|.+||..|+|++.||+.||||||.|.+|+-
T Consensus       100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~  159 (194)
T KOG0491|consen  100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQ  159 (194)
T ss_pred             hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence            455688999999999999999999999999999999999999999999999999655543

>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]

Probab=99.07  E-value=5.8e-11  Score=117.99  Aligned_cols=66  Identities=20%  Similarity=0.326  Sum_probs=57.8

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhhh
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES  559 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~~~  559 (629)
                      .+++-.+-.|+-.|++.|+..|.+.+||-..+|.+||..||+++.||+|||||||.|++|+.+++-
T Consensus       165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEm  230 (288)
T KOG0847|consen  165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEM  230 (288)
T ss_pred             ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccch
Confidence            333444556899999999999999999999999999999999999999999999998877776653

>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]

Probab=99.05  E-value=1.1e-10  Score=119.98  Aligned_cols=61  Identities=30%  Similarity=0.495  Sum_probs=56.9

Q ss_pred             cCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832          496 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       496 ~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      .||+|+.+|..|++.|..+|+..|.|.+.+|++|+.++||..+.|+|||||||+|-+|..+
T Consensus       167 nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKK  227 (383)
T KOG4577|consen  167 NKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKK  227 (383)
T ss_pred             cCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhh
Confidence            4889999999999999999999999999999999999999999999999999998665543

>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]

Probab=99.05  E-value=7.4e-11  Score=121.85  Aligned_cols=64  Identities=22%  Similarity=0.389  Sum_probs=59.5

Q ss_pred             ccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832          493 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       493 ~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      ....||=|+.||-+|+..||+.|...+|.++..|-+||..|||++..|+|||||||.|-+|+|-
T Consensus       178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl  241 (408)
T KOG0844|consen  178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL  241 (408)
T ss_pred             cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence            3456788899999999999999999999999999999999999999999999999998888874

>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]

Probab=98.97  E-value=6.1e-10  Score=110.73  Aligned_cols=64  Identities=22%  Similarity=0.331  Sum_probs=58.8

Q ss_pred             ccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832          493 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       493 ~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      ..++||.|+.|+..|+.+|++.|..++||+...|+.||..++|++..|+|||||+|++.++..+
T Consensus        57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~  120 (235)
T KOG0490|consen   57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER  120 (235)
T ss_pred             hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence            4567888999999999999999999999999999999999999999999999999997666653

>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]

Probab=98.91  E-value=7.8e-10  Score=118.52  Aligned_cols=61  Identities=25%  Similarity=0.351  Sum_probs=56.0

Q ss_pred             ccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          495 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       495 k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      |+||+||-|...++.+||.+|..|+.|+..+.-.||.+|+|....|+|||+|||.|.+|-.
T Consensus       293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~  353 (398)
T KOG3802|consen  293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT  353 (398)
T ss_pred             cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence            6777889999999999999999999999999999999999999999999999999544433

>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]

Probab=98.77  E-value=8.9e-09  Score=105.63  Aligned_cols=48  Identities=29%  Similarity=0.459  Sum_probs=45.5

Q ss_pred             CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006832          503 MPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  550 (629)
Q Consensus       503 ft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k  550 (629)
                      |..--...|.+||..++||+..+|.+||+.+||+..||.+||+|||++
T Consensus       183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQR  230 (304)
T KOG0775|consen  183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQR  230 (304)
T ss_pred             hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhh
Confidence            677778899999999999999999999999999999999999999994

>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]

Probab=98.67  E-value=1.2e-08  Score=109.82  Aligned_cols=62  Identities=27%  Similarity=0.450  Sum_probs=57.1

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      .+.+|.|+.|+..|+..|++.|..++||+...|++||.++||++..|++||+|+|++.+|..
T Consensus       174 ~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~  235 (354)
T KOG0849|consen  174 RGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH  235 (354)
T ss_pred             ccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence            44566689999999999999999999999999999999999999999999999999776666

>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.64  E-value=4.8e-09  Score=81.89  Aligned_cols=49  Identities=35%  Similarity=0.960  Sum_probs=40.8

Q ss_pred             cccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCC-CCCceecccCch
Q 006832          240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES-RDQGWFCKFCEC  291 (629)
Q Consensus       240 ~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p-~dg~W~C~~C~~  291 (629)
                      +|.+|+..+  .++.||.|| .|.++||+.|++|++.... ....|+|+.|..
T Consensus         1 ~C~vC~~~~--~~~~~i~C~-~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~   50 (51)
T PF00628_consen    1 YCPVCGQSD--DDGDMIQCD-SCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP   50 (51)
T ss_dssp             EBTTTTSSC--TTSSEEEBS-TTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred             eCcCCCCcC--CCCCeEEcC-CCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence            589999854  478999999 5999999999999988544 235899999975

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....

>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]

Probab=98.61  E-value=3.8e-08  Score=100.36  Aligned_cols=60  Identities=32%  Similarity=0.447  Sum_probs=55.9

Q ss_pred             cCCCCCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          496 IRRSFHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       496 ~kR~r~rft~~Q~~~Le~~F~~---~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      .+|+|+.|+...+.+|..||..   ||||+.+.+++||++.|++..||.+||.|+|.+.+|+.
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~  250 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM  250 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence            4677788999999999999985   59999999999999999999999999999999988887

>KOG0825 consensus PHD Zn-finger protein [General function prediction only]

Probab=98.58  E-value=1.6e-08  Score=114.66  Aligned_cols=53  Identities=32%  Similarity=0.909  Sum_probs=45.9

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCCcc-cccccCCCCCCCCCCCCceecccCchh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCA-FHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~ra-fH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      .+..-|.+|...+.  .+.||+||+ |+.+ ||+|||+|+|..+| -+.|||++|.--
T Consensus       213 ~E~~~C~IC~~~Dp--EdVLLLCDs-CN~~~YH~YCLDPdl~eiP-~~eWYC~NC~dL  266 (1134)
T KOG0825|consen  213 QEEVKCDICTVHDP--EDVLLLCDS-CNKVYYHVYCLDPDLSESP-VNEWYCTNCSLL  266 (1134)
T ss_pred             cccccceeeccCCh--HHhheeecc-cccceeeccccCccccccc-ccceecCcchhh
Confidence            34567999999864  679999996 9999 99999999999998 789999999753

>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants []

Probab=98.54  E-value=2.6e-08  Score=75.32  Aligned_cols=33  Identities=39%  Similarity=0.681  Sum_probs=28.6

Q ss_pred             hCCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006832          517 ENELPSRIVKENLSKELSLEPEKVNKWFKNARY  549 (629)
Q Consensus       517 ~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~  549 (629)
                      .+|||+.++|+.||+++||+..||..||-|.|.
T Consensus         7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRr   39 (40)
T PF05920_consen    7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARR   39 (40)
T ss_dssp             TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHc
Confidence            469999999999999999999999999999997

; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.

>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]

Probab=98.52  E-value=6.4e-08  Score=107.32  Aligned_cols=58  Identities=29%  Similarity=0.401  Sum_probs=55.0

Q ss_pred             ccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006832          493 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  550 (629)
Q Consensus       493 ~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k  550 (629)
                      ....||+|+.||+.|...|..+|++++||+.+..+.|+++|||..+.|.+||.|.|.+
T Consensus       417 ~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRR  474 (558)
T KOG2252|consen  417 MLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRR  474 (558)
T ss_pred             cccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhh
Confidence            4567888999999999999999999999999999999999999999999999999995

>smart00249 PHD PHD zinc finger

Probab=98.30  E-value=5.9e-07  Score=67.20  Aligned_cols=46  Identities=37%  Similarity=1.002  Sum_probs=38.2

Q ss_pred             cccccccCcCCCCCCceEeCCcCCcccccccCCCCCC-CCCCCCceecccC
Q 006832          240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLD-TESRDQGWFCKFC  289 (629)
Q Consensus       240 ~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~-~~p~dg~W~C~~C  289 (629)
                      +|.+|+...  .++.||.|+ .|..+||+.|++++.. ..+ ...|+|+.|
T Consensus         1 ~C~~C~~~~--~~~~~i~C~-~C~~~~H~~C~~~~~~~~~~-~~~~~C~~C   47 (47)
T smart00249        1 YCSVCGKPD--DGGELLQCD-GCDRWYHQTCLGPPLLEEEP-DGKWYCPKC   47 (47)
T ss_pred             CcccCCCcC--CCCCEEECC-CCCchhhhhhCCCcccCCCC-CCCEECcCC
Confidence            488898864  467999999 5999999999999887 333 579999987

The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the

>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]

Probab=98.18  E-value=6e-07  Score=107.00  Aligned_cols=77  Identities=26%  Similarity=0.543  Sum_probs=55.6

Q ss_pred             ccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhhH----HHHhhhccCCcccccc
Q 006832          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKME----IIESMNAHIGTSFSVN  310 (629)
Q Consensus       235 ~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~~----~l~~~n~~~gtsf~lp  310 (629)
                      ..++.+|.+|..++....+.+|+||+ |+.++|+.|++  +..+| +|.|+|..|...+.    |+...+......-++.
T Consensus       216 ~~~D~~C~iC~~~~~~n~n~ivfCD~-Cnl~VHq~Cyg--i~~ip-eg~WlCr~Cl~s~~~~v~c~~cp~~~gAFkqt~d  291 (1051)
T KOG0955|consen  216 LEEDAVCCICLDGECQNSNVIVFCDG-CNLAVHQECYG--IPFIP-EGQWLCRRCLQSPQRPVRCLLCPSKGGAFKQTDD  291 (1051)
T ss_pred             cCCCccceeecccccCCCceEEEcCC-CcchhhhhccC--CCCCC-CCcEeehhhccCcCcccceEeccCCCCcceeccC
Confidence            35678999999998876799999995 99999999999  33444 79999999987543    4444444333333444


Q ss_pred             chhhh
Q 006832          311 SNWQD  315 (629)
Q Consensus       311 ~~~~d  315 (629)
                      ..|.+
T Consensus       292 grw~H  296 (1051)
T KOG0955|consen  292 GRWAH  296 (1051)
T ss_pred             Cceee
Confidence            44433

>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]

Probab=98.17  E-value=7e-07  Score=92.43  Aligned_cols=62  Identities=21%  Similarity=0.307  Sum_probs=53.7

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      ..+||+|+-+-.-....||++|..+|.|+.+....||++|.|....|+|||+|.|.|.+|-.
T Consensus       307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~  368 (385)
T KOG1168|consen  307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK  368 (385)
T ss_pred             cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence            34566677667777889999999999999999999999999999999999999999665533

>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]

Probab=98.17  E-value=5e-07  Score=99.48  Aligned_cols=54  Identities=28%  Similarity=0.648  Sum_probs=47.1

Q ss_pred             cccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCC---CCCceecccCchhhH
Q 006832          240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES---RDQGWFCKFCECKME  294 (629)
Q Consensus       240 ~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p---~dg~W~C~~C~~k~~  294 (629)
                      .|.||..++....|.||.|++ |..+||+.|+.|++...-   +...|||..|...+.
T Consensus       170 qc~vC~~g~~~~~NrmlqC~~-C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~  226 (464)
T KOG4323|consen  170 QCSVCYCGGPGAGNRMLQCDK-CRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPK  226 (464)
T ss_pred             eeeeeecCCcCccceeeeecc-cccHHHHHhccCCCCHhhccCccceEeehhhccchh
Confidence            399999888777899999995 999999999999987765   457999999988765

>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]

Probab=98.14  E-value=1.1e-06  Score=99.34  Aligned_cols=64  Identities=23%  Similarity=0.581  Sum_probs=57.0

Q ss_pred             CCCCcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhhHHHH
Q 006832          230 TDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKMEIIE  297 (629)
Q Consensus       230 ~dg~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~~~l~  297 (629)
                      ..||.+..+.+|..|+.++  +...+++|++ |+-+||.||..|++..++ .+.|+|+.|..+..|-.
T Consensus        60 ~~gWrC~~crvCe~c~~~g--D~~kf~~Ck~-cDvsyh~yc~~P~~~~v~-sg~~~ckk~~~c~qc~~  123 (694)
T KOG4443|consen   60 SGGWRCPSCRVCEACGTTG--DPKKFLLCKR-CDVSYHCYCQKPPNDKVP-SGPWLCKKCTRCRQCDS  123 (694)
T ss_pred             cCCcccCCceeeeeccccC--Cccccccccc-ccccccccccCCcccccc-CcccccHHHHhhhhccc
Confidence            5679999999999999775  4789999995 999999999999999999 79999999998877554

>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]

Probab=98.04  E-value=3.3e-06  Score=86.37  Aligned_cols=50  Identities=28%  Similarity=0.775  Sum_probs=40.6

Q ss_pred             ccccccccccccCcCCCCCCceEeCC-cCCc-ccccccCCCCCCCCCCCCceecccCch
Q 006832          235 HHEHIICAKCKLREAFPDNDIVLCDG-TCNC-AFHQKCLDPPLDTESRDQGWFCKFCEC  291 (629)
Q Consensus       235 ~~e~~~C~vC~~~g~~~~~~lLlCDG-~C~r-afH~~CL~PPL~~~p~dg~W~C~~C~~  291 (629)
                      ..+..+|. |.....   ++||-||+ .|.+ |||+-|++  |...| .|.|||+.|..
T Consensus       218 e~e~lYCf-CqqvSy---GqMVaCDn~nCkrEWFH~~CVG--Lk~pP-KG~WYC~eCk~  269 (271)
T COG5034         218 EGEELYCF-CQQVSY---GQMVACDNANCKREWFHLECVG--LKEPP-KGKWYCPECKK  269 (271)
T ss_pred             cCceeEEE-eccccc---ccceecCCCCCchhheeccccc--cCCCC-CCcEeCHHhHh
Confidence            44667885 766543   79999998 7986 99999999  77777 89999999964

>KOG1512 consensus PHD Zn-finger protein [General function prediction only]

Probab=98.01  E-value=1.9e-06  Score=89.19  Aligned_cols=53  Identities=21%  Similarity=0.466  Sum_probs=47.1

Q ss_pred             cCCCCcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecc
Q 006832          229 ATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCK  287 (629)
Q Consensus       229 ~~dg~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~  287 (629)
                      ....|.+.++..|.+|+.+..  ...+|+|| .|+++||.+|++  |...| .|.|.|-
T Consensus       305 KTY~W~C~~C~lC~IC~~P~~--E~E~~FCD-~CDRG~HT~CVG--L~~lP-~G~WICD  357 (381)
T KOG1512|consen  305 KTYFWKCSSCELCRICLGPVI--ESEHLFCD-VCDRGPHTLCVG--LQDLP-RGEWICD  357 (381)
T ss_pred             hhcchhhcccHhhhccCCccc--chheeccc-cccCCCCccccc--ccccc-Cccchhh
Confidence            345689999999999999865  67999999 799999999999  88888 7999997

>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]

Probab=97.94  E-value=4.6e-06  Score=87.18  Aligned_cols=51  Identities=25%  Similarity=0.652  Sum_probs=38.4

Q ss_pred             cccccccccccCcCCCCCCceEeCC-cCC-cccccccCCCCCCCCCCCCceecccCchhh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDG-TCN-CAFHQKCLDPPLDTESRDQGWFCKFCECKM  293 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG-~C~-rafH~~CL~PPL~~~p~dg~W~C~~C~~k~  293 (629)
                      .+..+|..+...    -+.||.||+ .|+ .|||+.|++  |...| .|.|||+.|....
T Consensus       217 ~e~~yC~Cnqvs----yg~Mi~CDn~~C~~eWFH~~CVG--L~~~P-kgkWyC~~C~~~~  269 (274)
T KOG1973|consen  217 DEPTYCICNQVS----YGKMIGCDNPGCPIEWFHFTCVG--LKTKP-KGKWYCPRCKAEN  269 (274)
T ss_pred             CCCEEEEecccc----cccccccCCCCCCcceEEEeccc--cccCC-CCcccchhhhhhh
Confidence            345666544222    369999995 499 999999999  66666 6889999997653

>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function

Probab=97.91  E-value=4.8e-06  Score=79.64  Aligned_cols=29  Identities=41%  Similarity=1.061  Sum_probs=26.2

Q ss_pred             ccccccCCCCCCCCCCCCceecccCchhhH
Q 006832          265 AFHQKCLDPPLDTESRDQGWFCKFCECKME  294 (629)
Q Consensus       265 afH~~CL~PPL~~~p~dg~W~C~~C~~k~~  294 (629)
                      +||++||+|||..+| +|+|+||.|.....
T Consensus         1 g~H~~CL~Ppl~~~P-~g~W~Cp~C~~~~~   29 (148)
T cd04718           1 GFHLCCLRPPLKEVP-EGDWICPFCEVEKS   29 (148)
T ss_pred             CcccccCCCCCCCCC-CCCcCCCCCcCCCC
Confidence            599999999999999 89999999987643

BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

>KOG0383 consensus Predicted helicase [General function prediction only]

Probab=97.78  E-value=7.6e-06  Score=94.51  Aligned_cols=54  Identities=31%  Similarity=0.778  Sum_probs=47.2

Q ss_pred             CcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhh
Q 006832          233 SVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKM  293 (629)
Q Consensus       233 ~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~  293 (629)
                      |...+..+|.+|+.++     .+|+|| +|+.+||.+|++||+...| .+.|.|+.|.+..
T Consensus        42 ~~~~~~e~c~ic~~~g-----~~l~c~-tC~~s~h~~cl~~pl~~~p-~~~~~c~Rc~~p~   95 (696)
T KOG0383|consen   42 WDDAEQEACRICADGG-----ELLWCD-TCPASFHASCLGPPLTPQP-NGEFICPRCFCPK   95 (696)
T ss_pred             cchhhhhhhhhhcCCC-----cEEEec-cccHHHHHHccCCCCCcCC-ccceeeeeeccCC
Confidence            5567788999999986     799999 7999999999999999999 5569999996654

>COG5141 PHD zinc finger-containing protein [General function prediction only]

Probab=97.75  E-value=1.2e-05  Score=88.38  Aligned_cols=53  Identities=32%  Similarity=0.713  Sum_probs=45.7

Q ss_pred             ccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCch
Q 006832          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCEC  291 (629)
Q Consensus       235 ~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~  291 (629)
                      +.-++.|.+|.+.+....|.||+||| |+-+.|+.|++.+..  | +|.|+|..|.-
T Consensus       190 d~~d~~C~~c~~t~~eN~naiVfCdg-C~i~VHq~CYGI~f~--p-eG~WlCrkCi~  242 (669)
T COG5141         190 DEFDDICTKCTSTHNENSNAIVFCDG-CEICVHQSCYGIQFL--P-EGFWLCRKCIY  242 (669)
T ss_pred             hhhhhhhHhccccccCCcceEEEecC-cchhhhhhcccceec--C-cchhhhhhhcc
Confidence            34678999999998877899999997 999999999996644  4 68999999974

>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]

Probab=97.75  E-value=1.4e-05  Score=85.37  Aligned_cols=62  Identities=32%  Similarity=0.367  Sum_probs=55.3

Q ss_pred             ccCCCCCCCCHHHHHHHHHHHHhC---CCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832          495 KIRRSFHRMPPNAVEKLRQVFAEN---ELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       495 k~kR~r~rft~~Q~~~Le~~F~~~---~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      ..+|++..|+...+.+|+.|+.++   |||+..++..||+++||+..||.+||.|.|.+.++...
T Consensus       238 ~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~  302 (342)
T KOG0773|consen  238 SKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI  302 (342)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence            356667789999999999998874   89999999999999999999999999999998777764

>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]

Probab=97.73  E-value=2.4e-05  Score=77.96  Aligned_cols=64  Identities=31%  Similarity=0.429  Sum_probs=58.0

Q ss_pred             CccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          492 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       492 ~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      ...+.++.++.|+..|+..|...|..++||+...++.|+..+|++...|++||||+|++.++..
T Consensus       149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~  212 (235)
T KOG0490|consen  149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK  212 (235)
T ss_pred             CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence            3456778889999999999999999999999999999999999999999999999999665544

>KOG0954 consensus PHD finger protein [General function prediction only]

Probab=97.64  E-value=1.9e-05  Score=90.28  Aligned_cols=51  Identities=31%  Similarity=0.861  Sum_probs=46.2

Q ss_pred             ccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCch
Q 006832          237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCEC  291 (629)
Q Consensus       237 e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~  291 (629)
                      ++.+|.||..++.+..++||+|| .|+...|+.|++  +..+| ++.|+|..|.-
T Consensus       270 edviCDvCrspD~e~~neMVfCd-~Cn~cVHqaCyG--Ile~p-~gpWlCr~Cal  320 (893)
T KOG0954|consen  270 EDVICDVCRSPDSEEANEMVFCD-KCNICVHQACYG--ILEVP-EGPWLCRTCAL  320 (893)
T ss_pred             ccceeceecCCCccccceeEEec-cchhHHHHhhhc--eeecC-CCCeeehhccc
Confidence            67899999999888889999999 799999999999  77888 79999999954

>KOG0957 consensus PHD finger protein [General function prediction only]

Probab=97.62  E-value=1.8e-05  Score=87.03  Aligned_cols=51  Identities=33%  Similarity=0.849  Sum_probs=43.2

Q ss_pred             ccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCC---CCCceecccCc
Q 006832          237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES---RDQGWFCKFCE  290 (629)
Q Consensus       237 e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p---~dg~W~C~~C~  290 (629)
                      ....|.+|....  +..-++.|| +|...||+.||+|||+..|   ....|.|..|.
T Consensus       543 ~~ysCgiCkks~--dQHll~~CD-tC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECd  596 (707)
T KOG0957|consen  543 MNYSCGICKKST--DQHLLTQCD-TCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECD  596 (707)
T ss_pred             cceeeeeeccch--hhHHHhhcc-hhhceeeccccCCccccCcccccCcceeecccc
Confidence            345699999874  356899999 8999999999999999999   34689999994

>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]

Probab=97.61  E-value=1.3e-05  Score=98.97  Aligned_cols=55  Identities=29%  Similarity=0.799  Sum_probs=48.4

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhhH
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKME  294 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~~  294 (629)
                      .....|.+|...+.  ...|++||+ |..+||++|+.|.+..+| .++|+|+.|.....
T Consensus      1106 ~~~~~c~~cr~k~~--~~~m~lc~~-c~~~~h~~C~rp~~~~~~-~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1106 AVNALCKVCRRKKQ--DEKMLLCDE-CLSGFHLFCLRPALSSVP-PGDWMCPSCRKEHR 1160 (1404)
T ss_pred             cchhhhhhhhhccc--chhhhhhHh-hhhhHHHHhhhhhhccCC-cCCccCCccchhhh
Confidence            44678999999864  579999995 999999999999999999 78999999998765

>KOG0956 consensus PHD finger protein AF10 [General function prediction only]

Probab=97.53  E-value=3.4e-05  Score=87.62  Aligned_cols=50  Identities=34%  Similarity=0.848  Sum_probs=41.1

Q ss_pred             ccccccccCcCCCCCCceEeCC-cCCcccccccCCCCCCCCCCCCceecccCch
Q 006832          239 IICAKCKLREAFPDNDIVLCDG-TCNCAFHQKCLDPPLDTESRDQGWFCKFCEC  291 (629)
Q Consensus       239 ~~C~vC~~~g~~~~~~lLlCDG-~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~  291 (629)
                      .-|.||.+----.+|.||.||| .|.-+.|+.|++  +..+| .|.|||..|..
T Consensus         6 GGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYG--IvqVP-tGpWfCrKCes   56 (900)
T KOG0956|consen    6 GGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYG--IVQVP-TGPWFCRKCES   56 (900)
T ss_pred             cceeeecCcCCCccCceeeecCCCceeeeehhcce--eEecC-CCchhhhhhhh
Confidence            4588887632235799999998 799999999999  66777 79999999954

>KOG1146 consensus Homeobox protein [General function prediction only]

Probab=96.88  E-value=0.00088  Score=81.24  Aligned_cols=63  Identities=19%  Similarity=0.267  Sum_probs=57.7

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      -.+++.|++++..|+..|..+|....||...+-|.|...++|..+.|.+||||.|.+.+|..-
T Consensus       901 ~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~  963 (1406)
T KOG1146|consen  901 MGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL  963 (1406)
T ss_pred             hhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence            345677899999999999999999999999999999999999999999999999997777663

>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A

Probab=96.27  E-value=0.00086  Score=49.79  Aligned_cols=35  Identities=37%  Similarity=0.965  Sum_probs=18.9

Q ss_pred             CCceEeCCcCCcccccccCCCCCCCCCCCCceecccCc
Q 006832          253 NDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCE  290 (629)
Q Consensus       253 ~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~  290 (629)
                      +.||.|++ |....|+.|++......  ...|+|..|.
T Consensus         2 n~ll~C~~-C~v~VH~~CYGv~~~~~--~~~W~C~~C~   36 (36)
T PF13831_consen    2 NPLLFCDN-CNVAVHQSCYGVSEVPD--GDDWLCDRCE   36 (36)
T ss_dssp             CEEEE-SS-S--EEEHHHHT-SS--S--S-----HHH-
T ss_pred             CceEEeCC-CCCcCChhhCCcccCCC--CCcEECCcCC
Confidence            57999995 99999999999654433  2479998883

>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A

Probab=96.16  E-value=0.0035  Score=51.05  Aligned_cols=42  Identities=12%  Similarity=0.295  Sum_probs=32.3

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006832          508 VEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  549 (629)
Q Consensus       508 ~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~  549 (629)
                      ++-|+.+|..++++....-..|..+.||+..||+.||--++.
T Consensus        10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~   51 (56)
T PF11569_consen   10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ   51 (56)
T ss_dssp             -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred             hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence            567999999999999999999999999999999999987765

>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain

Probab=95.23  E-value=0.011  Score=57.91  Aligned_cols=53  Identities=26%  Similarity=0.655  Sum_probs=38.6

Q ss_pred             ccccccc-CcCCCCCCceEeCCcCCcccccccCCCCCCCCC-------CCCceecccCchhh
Q 006832          240 ICAKCKL-REAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES-------RDQGWFCKFCECKM  293 (629)
Q Consensus       240 ~C~vC~~-~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p-------~dg~W~C~~C~~k~  293 (629)
                      .|.+|+. ++...-+.||.|-| |..+||..||+|.....-       ......|..|+...
T Consensus         1 ~C~~C~~~g~~~~kG~Lv~CQG-Cs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig~~   61 (175)
T PF15446_consen    1 TCDTCGYEGDDRNKGPLVYCQG-CSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCIGIA   61 (175)
T ss_pred             CcccccCCCCCccCCCeEEcCc-cChHHHhhhcCCccccceeeEEEcCCceEEechhhcChh
Confidence            4888865 23344689999997 999999999999865443       22456788887543

>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]

Probab=94.95  E-value=0.013  Score=70.45  Aligned_cols=49  Identities=24%  Similarity=0.550  Sum_probs=43.3

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCch
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCEC  291 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~  291 (629)
                      .-++.|.+|...+     +++||. +|++.||+.|+.||+...| ...|-|-.|..
T Consensus       342 ~~ddhcrf~~d~~-----~~lc~E-t~prvvhlEcv~hP~~~~~-s~~~e~evc~~  390 (1414)
T KOG1473|consen  342 EYDDHCRFCHDLG-----DLLCCE-TCPRVVHLECVFHPRFAVP-SAFWECEVCNI  390 (1414)
T ss_pred             eecccccccCccc-----ceeecc-cCCceEEeeecCCccccCC-Cccchhhhhhh
Confidence            3467899999874     899999 7999999999999999999 67899999974

>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]

Probab=94.16  E-value=0.062  Score=62.49  Aligned_cols=47  Identities=21%  Similarity=0.383  Sum_probs=43.3

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006832          508 VEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA  554 (629)
Q Consensus       508 ~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~  554 (629)
                      +..|..+|..|.+|+.++-..+|.++||+...|+.||+++++..+..
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv  614 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSV  614 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhh
Confidence            78999999999999999999999999999999999999999944443

>KOG0957 consensus PHD finger protein [General function prediction only]

Probab=93.33  E-value=0.043  Score=61.34  Aligned_cols=53  Identities=25%  Similarity=0.653  Sum_probs=40.8

Q ss_pred             ccccccccCcCCCCCCceEeCCcCCcccccccCCCCC-CCCC------CCCceecccCchh
Q 006832          239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPL-DTES------RDQGWFCKFCECK  292 (629)
Q Consensus       239 ~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL-~~~p------~dg~W~C~~C~~k  292 (629)
                      .+|.||.+....+-++||.|| .|.-..|-.|++.-- ..+|      ....|||-.|.+-
T Consensus       120 ~iCcVClg~rs~da~ei~qCd-~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~G  179 (707)
T KOG0957|consen  120 VICCVCLGQRSVDAGEILQCD-KCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLYG  179 (707)
T ss_pred             eEEEEeecCccccccceeecc-ccCceecccccccccccccCCCCccCCCCchhhhhHhcC
Confidence            389999987767779999999 699999999998641 1111      2257999999764

>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere

Probab=93.21  E-value=0.15  Score=40.86  Aligned_cols=48  Identities=17%  Similarity=0.279  Sum_probs=36.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006832          497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  549 (629)
Q Consensus       497 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~  549 (629)
                      ||+|..||.++.-.+-..+...+     ...+||+++|++.++|..|..|+..
T Consensus         1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~~   48 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKDK   48 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHHH
Confidence            46677889999888888888776     6899999999999999999999753

Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.

>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]

Probab=90.98  E-value=0.057  Score=62.17  Aligned_cols=61  Identities=16%  Similarity=0.400  Sum_probs=47.7

Q ss_pred             ccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhhHHH
Q 006832          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKMEII  296 (629)
Q Consensus       235 ~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~~~l  296 (629)
                      ...+..|.+|+..|....+.|+.|. .|...||.+|+..-+.....-+.|-|+.|..+-.|.
T Consensus        15 ~~~~~mc~l~~s~G~~~ag~m~ac~-~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~   75 (694)
T KOG4443|consen   15 IIVCLMCPLCGSSGKGRAGRLLACS-DCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEACG   75 (694)
T ss_pred             hhhhhhhhhhccccccccCcchhhh-hhcccCCcchhhHHHhHHHhcCCcccCCceeeeecc
Confidence            4557789999998887889999999 699999999999655444212569999998765443

>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]

Probab=88.41  E-value=0.31  Score=59.17  Aligned_cols=51  Identities=31%  Similarity=0.829  Sum_probs=42.6

Q ss_pred             ccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832          237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       237 e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      ....|..|..+..  . .+++|++ |...||.+|+.||+..++ ++.|.|+.|..-
T Consensus       154 ~~~~~~~~~k~~~--~-~~~~~~~-~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~  204 (904)
T KOG1246|consen  154 DYPQCNTCSKGKE--E-KLLLCDS-CDDSYHTYCLRPPLTRVP-DGDWRCPKCIPT  204 (904)
T ss_pred             cchhhhccccCCC--c-cceeccc-ccCcccccccCCCCCcCC-cCcccCCccccc
Confidence            3456899988764  2 3449995 999999999999999999 899999999865

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=87.02  E-value=0.35  Score=39.30  Aligned_cols=35  Identities=29%  Similarity=0.741  Sum_probs=28.9

Q ss_pred             ccccccccccCcCCCCCCceEeCCcCCcccccccCCC
Q 006832          237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDP  273 (629)
Q Consensus       237 e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~P  273 (629)
                      ....|.+|+..- .+.+++|.|. .|...||..|+..
T Consensus         4 ~~~~C~~Cg~~~-~~~dDiVvCp-~CgapyHR~C~~~   38 (54)
T PF14446_consen    4 EGCKCPVCGKKF-KDGDDIVVCP-ECGAPYHRDCWEK   38 (54)
T ss_pred             cCccChhhCCcc-cCCCCEEECC-CCCCcccHHHHhh
Confidence            446799999863 3468999999 7999999999864

>KOG4299 consensus PHD Zn-finger protein [General function prediction only]

Probab=85.93  E-value=0.44  Score=54.96  Aligned_cols=49  Identities=29%  Similarity=0.712  Sum_probs=41.1

Q ss_pred             cccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832          238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       238 ~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      ...|.+|..++     ++++|+ .|+.+||+.|..+++........|.|..|...
T Consensus        47 ~ts~~~~~~~g-----n~~~~~-~~~~s~h~~~~~~~~sp~~~~~~~~~~~~~~~   95 (613)
T KOG4299|consen   47 ATSCGICKSGG-----NLLCCD-HCPASFHLECDKPPLSPDLKGSEINCSRCPKG   95 (613)
T ss_pred             hhhcchhhhcC-----Cccccc-cCccccchhccCcccCcccccccccccCCCcc
Confidence            56799999875     799999 69999999999999984434578999999763

>KOG1512 consensus PHD Zn-finger protein [General function prediction only]

Probab=80.35  E-value=0.43  Score=50.49  Aligned_cols=59  Identities=15%  Similarity=0.227  Sum_probs=41.6

Q ss_pred             ccccccccccCcC----CCCCCceEeCCcCCcccccccCCCCCCCCC--CCCceecccCchhhHHH
Q 006832          237 EHIICAKCKLREA----FPDNDIVLCDGTCNCAFHQKCLDPPLDTES--RDQGWFCKFCECKMEII  296 (629)
Q Consensus       237 e~~~C~vC~~~g~----~~~~~lLlCDG~C~rafH~~CL~PPL~~~p--~dg~W~C~~C~~k~~~l  296 (629)
                      ....|..|-.+-.    ..-+.||+|- .|..+||.+|+..+..-+.  ....|.|-.|.-+.-|+
T Consensus       257 ~~~~~~~~~~~~~~~~~~r~~S~I~C~-~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~lC~IC~  321 (381)
T KOG1512|consen  257 RRNERKHFWDIQTNIIQSRRNSWIVCK-PCATRPHPYCVAMIPELVGQYKTYFWKCSSCELCRICL  321 (381)
T ss_pred             chhhhhhhhcchhhhhhhhhccceeec-ccccCCCCcchhcCHHHHhHHhhcchhhcccHhhhccC
Confidence            3456777765421    0136799999 7999999999987754433  34689999998776554

>KOG3612 consensus PHD Zn-finger protein [General function prediction only]

Probab=80.33  E-value=1.1  Score=51.00  Aligned_cols=55  Identities=16%  Similarity=0.288  Sum_probs=42.8

Q ss_pred             CcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhh
Q 006832          233 SVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKM  293 (629)
Q Consensus       233 ~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~  293 (629)
                      .....+++|.-|.-.+     ..|.|+ .|.+.||..|+.|.-........|.|+.|....
T Consensus        55 ~~~N~d~~cfechlpg-----~vl~c~-vc~Rs~h~~c~sp~~q~r~~s~p~~~p~p~s~k  109 (588)
T KOG3612|consen   55 PSSNIDPFCFECHLPG-----AVLKCI-VCHRSFHENCQSPDPQKRNYSVPSDKPQPYSFK  109 (588)
T ss_pred             cccCCCcccccccCCc-----ceeeee-hhhccccccccCcchhhccccccccCCcccccC
Confidence            3445679999999865     788999 699999999998865444434579999997643

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	629
2yt5_A	66	Metal-response element-binding transcription facto	2e-15
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-15
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-08
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	2e-14
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	5e-12
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	3e-11
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	3e-11
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	4e-11
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	1e-10
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	2e-10
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	3e-10
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	4e-10
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	1e-09
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	2e-09
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	3e-09
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	3e-09
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	2e-08
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	2e-08
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	4e-08
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	2e-07
3ask_A	226	E3 ubiquitin-protein ligase UHRF1; histone reader	4e-07
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	7e-07
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	1e-06
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	3e-06
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	3e-06
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	3e-06
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	1e-04
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	3e-06
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	5e-06
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	1e-05
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	2e-05
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	3e-05
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	6e-05
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	8e-05
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	8e-05
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	2e-04
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	3e-04
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	4e-04
1x4i_A	70	Inhibitor of growth protein 3; structural genomics	5e-04
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	5e-04
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	5e-04
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	6e-04
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	7e-04

>2yt5_A Metal-response element-binding transcription factor 2; zinc-regulated factor 1, ZIRF1, metal-response element DNA-binding protein M96; NMR {Mus musculus} Length = 66

 Score = 70.3 bits (172), Expect = 2e-15
 Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESR--DQGWFCKFC 289
              +C  C+   +   N++V+CD  C   +HQ C  P +D+     D+ W C+ C
Sbjct: 5   SSGVCTICQEEYSEAPNEMVICDK-CGQGYHQLCHTPHIDSSVIDSDEKWLCRQC 58

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

 Score = 78.0 bits (191), Expect = 5e-15
 Identities = 93/601 (15%), Positives = 173/601 (28%), Gaps = 176/601 (29%)

Query: 142 KEKVE--LDEASRLQRRTRYLLIKMKLEQ-NLIDAYSGE------GW---------KGHS 183
           KE+++  +     +   T  L   +  +Q  ++  +  E       +         +  S
Sbjct: 48  KEEIDHIIMSKDAVSG-TLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPS 106

Query: 184 REKIRPEKELQR--------AKKQI--LKCKIGIRDAIRQLDSLSSV------GCIEG-S 226
                  ++  R        AK  +  L+  + +R A+ +L    +V      G   G +
Sbjct: 107 MMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGS--GKT 164

Query: 227 VIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFC 286
            +A D        +C   K++         L    CN    +  L+       +    + 
Sbjct: 165 WVALD--------VCLSYKVQCKMDFKIFWLNLKNCNSP--ETVLEMLQKLLYQIDPNWT 214

Query: 287 KFCECKMEI---IESMNAHIGTSFS-------------VNSNWQDIFKEEAAFPDGCSAL 330
              +    I   I S+ A +                  V +     +    AF   C  L
Sbjct: 215 SRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAK--AWN---AFNLSCKIL 269

Query: 331 L-------------NQEEEWPSDDSEDDDYNPERRENSCSISRAGTDDDPSSSTSLSWFS 377
           L                     D         E +            D P    + +   
Sbjct: 270 LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRR 329

Query: 378 DSETFSESM-----RWEMESNGYKNYSVD-------SSIGSDETSDGEIICGRRQRRTVD 425
            S   +ES+      W+     +K+ + D       SS+   E ++              
Sbjct: 330 LS-IIAESIRDGLATWD----NWKHVNCDKLTTIIESSLNVLEPAE-------------- 370

Query: 426 YKKLYDEM--FGKDA----SAFEQLSEDEDWGPAKRRRKEKESDAVNSLMTLYGSEEKYS 479
           Y+K++D +  F   A         +     W       K      VN L   Y   EK  
Sbjct: 371 YRKMFDRLSVFPPSAHIPTILLSLI-----WFDVI---KSDVMVVVNKLHK-YSLVEKQP 421

Query: 480 KVKTA-------EVKKKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKEN---- 528
           K  T        E+K KL +      + HR   +     +   +++ +P  +  +     
Sbjct: 422 KESTISIPSIYLELKVKLEN----EYALHRSIVDHYNIPKTFDSDDLIPPYL--DQYFYS 475

Query: 529 -----LSK-ELSLEPEKVNKWFKNARYLALKARKVESARQVSGS------------PRIS 570
                L   E           F + R+L  K R   +A   SGS            P I 
Sbjct: 476 HIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYIC 535

Query: 571 KESSLETEKKNADVLTLKNSLEETLICSPKSLKKIHPKRIQ------NQSAVAAASRKIS 624
             +  + E+    +L     +EE LICS       +   ++      +++    A +++ 
Sbjct: 536 D-NDPKYERLVNAILDFLPKIEENLICSK------YTDLLRIALMAEDEAIFEEAHKQVQ 588

Query: 625 R 625
           R
Sbjct: 589 R 589

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

 Score = 55.2 bits (132), Expect = 5e-08
 Identities = 81/574 (14%), Positives = 139/574 (24%), Gaps = 204/574 (35%)

Query: 1   MPGAGKKV----VKHSESGKSCFPKKDSGSELIASLKFKKGSKISKSKKLRSKSRCQSKT 56
           + G+GK      V  S   +     K      I  L                   C S  
Sbjct: 158 VLGSGKTWVALDVCLSYKVQCKMDFK------IFWLNL---------------KNCNSP- 195

Query: 57  VNSTLLKRTVAESHSKGAGDDFARSKSISQKNLHIKIDRKGSKNWASSKHKGKNSALVIS 116
              T+L+                       + L  +ID     NW S      N      
Sbjct: 196 --ETVLEM---------------------LQKLLYQID----PNWTSRSDHSSNI----- 223

Query: 117 KGNGEVVDGDGETKKLRKGRSKKRRKEKVELDEASRLQRRTRY---LLIKMKLEQNLIDA 173
                                 K R   ++  E  RL +   Y   LL+       L++ 
Sbjct: 224 ----------------------KLRIHSIQ-AELRRLLKSKPYENCLLV-------LLNV 253

Query: 174 YSGEGWKGHSREKIRPEKELQRAKKQILKCKIGI--RDAIRQLDSLSSVGCIEGSVIATD 231
            + + W   +                 L CKI +  R   +  D LS+      S+    
Sbjct: 254 QNAKAWNAFN-----------------LSCKILLTTRFK-QVTDFLSAATTTHISLDHHS 295

Query: 232 GSVHHEHI--ICAKC-KLR-EAFPDNDIVLCDGTCNCAFHQKCLDPPL----------DT 277
            ++  + +  +  K    R +  P                +     P           D 
Sbjct: 296 MTLTPDEVKSLLLKYLDCRPQDLP---------------REVLTTNPRRLSIIAESIRDG 340

Query: 278 ESRDQGWFCKFCECKMEIIESMNAHIGTSFSVN----SNWQDIFKEEAAFPDGC---SAL 330
            +    W    C+    IIES         S+N    + ++ +F   + FP      + L
Sbjct: 341 LATWDNWKHVNCDKLTTIIES---------SLNVLEPAEYRKMFDRLSVFPPSAHIPTIL 391

Query: 331 LNQEEEWPSDDSEDDDYNPERRENSCSISRAGTDDDPSSSTSLSWFSDSETFSESMRWEM 390
           L     W      D         N              S+ S+              + +
Sbjct: 392 L--SLIWFDVIKSD----VMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYAL 445

Query: 391 ESNGYKNYSV----DSSIGSDETSDGEIICGRRQRRTVDYKKL-Y----DEMFGKDASAF 441
             +   +Y++    DS        D              Y  + +     E   +    F
Sbjct: 446 HRSIVDHYNIPKTFDSDDLIPPYLDQYF-----------YSHIGHHLKNIEHPERMTL-F 493

Query: 442 EQLSEDEDWGPAKRRRKEKESDAVNSLMTLYGSEEKYSK----------VKTAEVKKKLP 491
             +  D  +   K R      +A  S++      + Y                 +   LP
Sbjct: 494 RMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLP 553

Query: 492 S-NAKIRRSFHR-------MPPNAV---EKLRQV 514
                +  S +        M  +     E  +QV
Sbjct: 554 KIEENLICSKYTDLLRIALMAEDEAIFEEAHKQV 587

>1wev_A Riken cDNA 1110020M19; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: g.50.1.2 Length = 88

 Score = 68.2 bits (166), Expect = 2e-14
 Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 4/69 (5%)

Query: 229 ATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESR---DQGWF 285
             D       + C  C+       N +V C   C+  +HQ C  P +  +        W+
Sbjct: 7   GADDFAMEMGLACVVCRQMTVASGNQLVECQE-CHNLYHQDCHKPQVTDKEVNDPRLVWY 65

Query: 286 CKFCECKME 294
           C  C  +M+
Sbjct: 66  CARCTRQMK 74

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens} Length = 71

 Score = 60.7 bits (147), Expect = 5e-12
 Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 4/63 (6%)

Query: 230 TDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFC 289
              S+  E  +C+ C   E+   N I+ CD  CN A HQ+C   P   E +   W C+ C
Sbjct: 8   HMQSLIDEDAVCSICMDGESQNSNVILFCDM-CNLAVHQECYGVPYIPEGQ---WLCRHC 63

Query: 290 ECK 292
              
Sbjct: 64  LQS 66

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens} Length = 60

 Score = 58.2 bits (141), Expect = 3e-11
 Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 8/60 (13%)

Query: 235 HHEHI-ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKM 293
           H  H   C+ C+         +++CD  C+  +H  CLDPPL T  +   W C  C+ +M
Sbjct: 1   HMIHEDFCSVCRK-----SGQLLMCDT-CSRVYHLDCLDPPLKTIPKGM-WICPRCQDQM 53

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens} Length = 88

 Score = 58.9 bits (142), Expect = 3e-11
 Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 4/69 (5%)

Query: 224 EGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQG 283
            G    +  S+  E  +C+ C   E+   N I+ CD  CN A HQ+C   P   E +   
Sbjct: 11  TGGSSGSSQSLIDEDAVCSICMDGESQNSNVILFCDM-CNLAVHQECYGVPYIPEGQ--- 66

Query: 284 WFCKFCECK 292
           W C+ C   
Sbjct: 67  WLCRHCLQS 75

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 56

 Score = 57.4 bits (139), Expect = 4e-11
 Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 8/64 (12%)

Query: 229 ATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKF 288
            + GS  HE   C+ C+         +++CD  C+  +H  CLDPPL T  +   W C  
Sbjct: 1   GSSGSSGHEDF-CSVCRK-----SGQLLMCDT-CSRVYHLDCLDPPLKTIPKGM-WICPR 52

Query: 289 CECK 292
           C+ +
Sbjct: 53  CQDQ 56

>1mm2_A MI2-beta; PHD, zinc finger, protein scaffold, DNA binding protein; NMR {Homo sapiens} SCOP: g.50.1.2 PDB: 2l75_A* 1mm3_A Length = 61

 Score = 56.2 bits (136), Expect = 1e-10
 Identities = 20/64 (31%), Positives = 27/64 (42%), Gaps = 8/64 (12%)

Query: 229 ATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKF 288
              GS HH    C  CK        +++ CD  C  ++H  CL+PPL      + W C  
Sbjct: 1   GPLGSDHHMEF-CRVCKD-----GGELLCCDT-CPSSYHIHCLNPPLPEIPNGE-WLCPR 52

Query: 289 CECK 292
           C C 
Sbjct: 53  CTCP 56

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A Length = 66

 Score = 55.9 bits (135), Expect = 2e-10
 Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 8/62 (12%)

Query: 232 GSVHHEHI-ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCE 290
           G++  ++   CA C+        +++ CDG C  AFH  CL PPL        W C  C 
Sbjct: 1   GAMAQKNEDECAVCRD-----GGELICCDG-CPRAFHLACLSPPLREIPSGT-WRCSSCL 53

Query: 291 CK 292
             
Sbjct: 54  QA 55

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2 Length = 88

 Score = 56.5 bits (136), Expect = 3e-10
 Identities = 19/76 (25%), Positives = 29/76 (38%), Gaps = 8/76 (10%)

Query: 224 EGSVIATDGSVHHEHI-ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQ 282
            GS I  +     +   IC  C+        D+V+C+  C   FH  C  P L     ++
Sbjct: 10  HGSDIIDEFGTLDDSATICRVCQK-----PGDLVMCNQ-CEFCFHLDCHLPALQDVPGEE 63

Query: 283 GWFCKFCECKMEIIES 298
            W C  C    ++ E 
Sbjct: 64  -WSCSLCHVLPDLKEE 78

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens} Length = 61

 Score = 54.7 bits (132), Expect = 4e-10
 Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 7/52 (13%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK 292
           C  C+        +I+LCD  C  A+H  CLDP ++     + W C  CE +
Sbjct: 14  CEVCQQ-----GGEIILCDT-CPRAYHMVCLDPDMEKAPEGK-WSCPHCEKE 58

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 77

 Score = 54.4 bits (131), Expect = 1e-09
 Identities = 19/50 (38%), Positives = 27/50 (54%), Gaps = 3/50 (6%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCE 290
           C  C  +     N  +LCD  CN A+H  CL+PPLD    ++ W+C  C+
Sbjct: 29  CRVCGGKHE--PNMQLLCDE-CNVAYHIYCLNPPLDKVPEEEYWYCPSCK 75

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens} Length = 77

 Score = 53.7 bits (129), Expect = 2e-09
 Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 3/50 (6%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCE 290
           C  C  R+    +  ++CD  C+ AFH  CLDPPL +   +  W+C  C 
Sbjct: 29  CHLCGGRQD--PDKQLMCDE-CDMAFHIYCLDPPLSSVPSEDEWYCPECR 75

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2 Length = 51

 Score = 52.0 bits (125), Expect = 3e-09
 Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 4/50 (8%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCE 290
           C  C+ +    D+ ++LCD  CN AFH  CL P L      + W C  C+
Sbjct: 3   CKVCRKKGE--DDKLILCDE-CNKAFHLFCLRPALYEVPDGE-WQCPACQ 48

>3asl_A E3 ubiquitin-protein ligase UHRF1; histone reader module, epigenetic regulation, LI binding protein complex; 1.41A {Homo sapiens} PDB: 3sou_A 3sow_A* 3sox_A 3zvy_A 2lgg_A 2lgk_A* 2lgl_A 3t6r_A 3zvz_B Length = 70

 Score = 52.5 bits (126), Expect = 3e-09
 Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 3/50 (6%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCE 290
           C  C  R+    +  ++CD  C+ AFH  CLDPPL +   +  W+C  C 
Sbjct: 21  CHLCGGRQD--PDKQLMCDE-CDMAFHIYCLDPPLSSVPSEDEWYCPECR 67

>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A* Length = 114

 Score = 52.0 bits (124), Expect = 2e-08
 Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 4/58 (6%)

Query: 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKME 294
           E   C  C   E   D+ ++ CD  C+  +H  CL+PP+        W C  C   ++
Sbjct: 57  ECKSCILCGTSEN--DDQLLFCDD-CDRGYHMYCLNPPVAEPPEGS-WSCHLCWELLK 110

>2e6r_A Jumonji/ARID domain-containing protein 1D; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 51.1 bits (122), Expect = 2e-08
 Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 4/56 (7%)

Query: 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK 292
           +  IC  C   +   D+ ++ CDG C+  +H  CL PPL    R   W C  C   
Sbjct: 15  DSYICQVCSRGD--EDDKLLFCDG-CDDNYHIFCLLPPLPEIPRGI-WRCPKCILA 66

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A Length = 112

 Score = 50.8 bits (121), Expect = 4e-08
 Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 3/57 (5%)

Query: 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK 292
            E   C+ C+  +    ++++ CD  C+  FH +C DPPL    +   W C+ C  +
Sbjct: 59  IECKTCSSCR-DQGKNADNMLFCDS-CDRGFHMECCDPPLTRMPKGM-WICQICRPR 112

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens} Length = 189

 Score = 50.6 bits (120), Expect = 2e-07
 Identities = 28/169 (16%), Positives = 45/169 (26%), Gaps = 21/169 (12%)

Query: 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKMEIIESM 299
           IC  C+        D+V+C+  C   FH  C  P L     ++ W C  C    ++ E  
Sbjct: 4   ICRVCQK-----PGDLVMCN-QCEFCFHLDCHLPALQDVPGEE-WSCSLCHVLPDLKEED 56

Query: 300 NAHIGTSFSVNSNWQDIFKEEAAFPDG-CSALLNQEEEW----PSDDSEDDDYNPERREN 354
            +              +        +    AL   E        + DS      P    +
Sbjct: 57  GSLSLDGADSTGVVAKLSPANQRKCERVLLALFCHEPCRPLHQLATDSTFSLDQPGGTLD 116

Query: 355 SCSISRAGTDDDPSSSTSLSWF-SDSETFSESMRWEMESNGYKNYSVDS 402
              I     +      +S   F  D       +   M     K     +
Sbjct: 117 LTLIRARLQEKLSPPYSSPQEFAQD-------VGR-MFKQFNKLTEDKA 157

>3ask_A E3 ubiquitin-protein ligase UHRF1; histone reader modules, epigenetic regulation, trimethylaion of lysine residue, ligase-DNA binding protein; HET: M3L; 2.90A {Homo sapiens} Length = 226

 Score = 50.5 bits (120), Expect = 4e-07
 Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 3/50 (6%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCE 290
           C  C  R+    +  ++CD  C+ AFH  CLDPPL +   +  W+C  C 
Sbjct: 177 CHLCGGRQD--PDKQLMCDE-CDMAFHIYCLDPPLSSVPSEDEWYCPECR 223

>2xb1_A Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro; fusion protein, signal transduction, transcription, metal BI WNT proteins; 1.90A {Homo sapiens} Length = 105

 Score = 47.2 bits (111), Expect = 7e-07
 Identities = 18/67 (26%), Positives = 26/67 (38%), Gaps = 6/67 (8%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKC--LDPP---LDTESRDQGWFCKFCECKMEI 295
           C  C+  E   D D +LC+ +C   FH++C  +      L T      W C  C    E 
Sbjct: 6   CGACR-SEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTKEG 64

Query: 296 IESMNAH 302
             S +  
Sbjct: 65  SGSGSGS 71

>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway, WNT signaling complex, chromosomal rearrangement, signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A 2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A* Length = 65

 Score = 45.5 bits (107), Expect = 1e-06
 Identities = 16/54 (29%), Positives = 21/54 (38%), Gaps = 6/54 (11%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKC--LDPP---LDTESRDQGWFCKFC 289
           C  C   E   D D +LC+ +C   FH+ C  +      L T      W C  C
Sbjct: 11  CGICT-NEVNDDQDAILCEASCQKWFHRICTGMTETAYGLLTAEASAVWGCDTC 63

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A Length = 164

 Score = 46.8 bits (110), Expect = 3e-06
 Identities = 15/58 (25%), Positives = 27/58 (46%)

Query: 491 PSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 548
                 ++            L  +F EN+ PS+ ++  +S++L LE   V+ +F NAR
Sbjct: 92  DRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 149

>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 76

 Score = 44.3 bits (105), Expect = 3e-06
 Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 5/75 (6%)

Query: 492 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA 551
           S A I +  ++     +  L+  F  N+ P +   E+L+K   L   +V KWF + RY  
Sbjct: 6   SGASIYK--NKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRY-- 61

Query: 552 LKARKVESARQVSGS 566
              R ++ +R    S
Sbjct: 62  -HCRNLKGSRSGPSS 75

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens} Length = 111

 Score = 45.4 bits (107), Expect = 3e-06
 Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 4/53 (7%)

Query: 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFC 289
           E  +C  CK      D+ +++CD  C+  +H  CL P + +   + GW CK C
Sbjct: 53  ECKVCQNCKQSGE--DSKMLVCDT-CDKGYHTFCLQPVMKSVPTN-GWKCKNC 101

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens} Length = 111

 Score = 41.1 bits (96), Expect = 1e-04
 Identities = 17/66 (25%), Positives = 22/66 (33%), Gaps = 7/66 (10%)

Query: 232 GSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCK---F 288
           GS       CA C         D   C   C   +H  CLD  + T  +  GW C     
Sbjct: 1   GSSGSSGANCAVCDSPGD--LLDQFFCTT-CGQHYHGMCLDIAV-TPLKRAGWQCPECKV 56

Query: 289 CECKME 294
           C+   +
Sbjct: 57  CQNCKQ 62

>3ql9_A Transcriptional regulator ATRX; zinc finger, transcription, lysine trimethylation, protein, histone-binding protein, transcription-structural complex; HET: M3L; 0.93A {Homo sapiens} PDB: 3qla_A* 3qlc_A 3qln_A 2jm1_A Length = 129

 Score = 45.9 bits (108), Expect = 3e-06
 Identities = 13/59 (22%), Positives = 21/59 (35%), Gaps = 12/59 (20%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQ------GWFCKFCECKM 293
           C  C         +++ CD  C+ AF +KC+   L              W+C  C  + 
Sbjct: 60  CRWCAE-----GGNLICCD-FCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHPEP 112

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} Length = 164

 Score = 46.2 bits (109), Expect = 5e-06
 Identities = 19/74 (25%), Positives = 27/74 (36%)

Query: 475 EEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELS 534
           EE  S   +     K+ +  + R+    +       L   F +   PS      L+  L 
Sbjct: 78  EETDSSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQ 137

Query: 535 LEPEKVNKWFKNAR 548
           LE E V  WF N R
Sbjct: 138 LEKEVVRVWFCNRR 151

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A* Length = 75

 Score = 42.9 bits (101), Expect = 1e-05
 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 8/61 (13%)

Query: 236 HEHIICAKCKLREAFPDND--IVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKM 293
           ++  IC  C      PD+   ++ CD  C+  +H  C+          Q WFC  C  K+
Sbjct: 16  NQIWICPGCNK----PDDGSPMIGCDD-CDDWYHWPCVGIMAAPPEEMQ-WFCPKCANKI 69

Query: 294 E 294
           +
Sbjct: 70  K 70

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A Length = 142

 Score = 44.0 bits (103), Expect = 2e-05
 Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 12/59 (20%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQ------GWFCKFCECKM 293
           C  C         +++ CD  C+ AF +KC+   L  +           W+C  C  + 
Sbjct: 66  CRWCAE-----GGNLICCD-FCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPEP 118

>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens} Length = 66

 Score = 41.3 bits (97), Expect = 3e-05
 Identities = 11/56 (19%), Positives = 21/56 (37%)

Query: 494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 549
           A       +     +  L+  F +++ P       L +   L   ++ KWF + RY
Sbjct: 2   AHHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRY 57

>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 89

 Score = 41.1 bits (96), Expect = 6e-05
 Identities = 8/74 (10%), Positives = 21/74 (28%)

Query: 500 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES 559
           F       +  L+  F  + + +      L  +  L   +++ WF   +       +   
Sbjct: 15  FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKME 74

Query: 560 ARQVSGSPRISKES 573
             + +        S
Sbjct: 75  IDESNAGSSSGPSS 88

>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 89

 Score = 40.7 bits (95), Expect = 8e-05
 Identities = 15/74 (20%), Positives = 28/74 (37%), Gaps = 2/74 (2%)

Query: 500 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES 559
           F       V+ L   F ++  P++   + L  E  L   +++ WF   R   L+    ++
Sbjct: 17  FKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERR--KLRDSMEQA 74

Query: 560 ARQVSGSPRISKES 573
                GS +    S
Sbjct: 75  VLDSMGSGKSGPSS 88

>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 75

 Score = 40.3 bits (94), Expect = 8e-05
 Identities = 15/69 (21%), Positives = 26/69 (37%), Gaps = 1/69 (1%)

Query: 497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 556
              +    P  +  L   FA+N LP     + L  E  +   +++ WF   R     A +
Sbjct: 8   PTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKV-NAEE 66

Query: 557 VESARQVSG 565
            + +   SG
Sbjct: 67  TKKSGPSSG 75

>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 71

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 4/66 (6%)

Query: 492 SNAKIRRSFHRMPPNAVEKLRQVFAE-NELPSRIVKENLSKELSLEPEKVNKWFKNARYL 550
           S +   RS  ++   A+  L+    +    P +     LS +L L    + K+F+N RY 
Sbjct: 3   SGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRY- 61

Query: 551 ALKARK 556
               + 
Sbjct: 62  --HVKH 65

>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 66

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 3/68 (4%)

Query: 495 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 554
           K  R    +    +  LR  +A N  P  ++KE L +   L P  +  WF+N R    K 
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKR---CKD 58

Query: 555 RKVESARQ 562
           +K     +
Sbjct: 59  KKRSIMMK 66

>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 80

 Score = 38.6 bits (90), Expect = 4e-04
 Identities = 14/57 (24%), Positives = 29/57 (50%)

Query: 492 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 548
              + +R    + P  +E L Q +  +  P+R + ++++ E+ L+   V  WF+N R
Sbjct: 13  EPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTR 69

>1x4i_A Inhibitor of growth protein 3; structural genomics, PHD domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 70

 Score = 37.9 bits (88), Expect = 5e-04
 Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 7/46 (15%)

Query: 252 DNDIVLCDGTCNCA---FHQKCLDPPLDTESRDQGWFCKFCECKME 294
             ++V CD   +C    FH  C+   L    + + W+C  C   M+
Sbjct: 16  YGEMVGCDN-QDCPIEWFHYGCVG--LTEAPKGK-WYCPQCTAAMK 57

>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain, hoogsteen base PAIR, transcription/DNA complex; HET: 5IU; 2.10A {Synthetic} SCOP: a.4.1.1 Length = 60

 Score = 37.7 bits (88), Expect = 5e-04
 Identities = 16/51 (31%), Positives = 19/51 (37%), Gaps = 3/51 (5%)

Query: 501 HRMPPNAVEKLRQVFAENEL---PSRIVKENLSKELSLEPEKVNKWFKNAR 548
           HR     V  L   FA+N           ENL K  SL   ++  W  N R
Sbjct: 3   HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR 53

>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens} Length = 96

 Score = 38.6 bits (89), Expect = 5e-04
 Identities = 16/77 (20%), Positives = 28/77 (36%), Gaps = 1/77 (1%)

Query: 474 SEEKYSKVKTAEVKKKLPSNA-KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKE 532
           +   +      EV  + P+          +  P  +  L+  F   + PS    + L+KE
Sbjct: 2   AHHHHHHSSGLEVLFQGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKE 61

Query: 533 LSLEPEKVNKWFKNARY 549
             L    +  WF + RY
Sbjct: 62  SGLARTDIVSWFGDTRY 78

>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding, transcription, nucleus, phosphoprotein, DNA bindi protein; 1.95A {Homo sapiens} Length = 67

 Score = 37.7 bits (88), Expect = 6e-04
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 502 RMPPNAVEKLRQVFAENEL---PSRIVKENLSKELSLEPEKVNKWFKNAR 548
             P  A   +R    ++     PS   K+ L+++  L   +VN WF NAR
Sbjct: 4   IFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINAR 53

>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1 Length = 64

 Score = 37.3 bits (87), Expect = 7e-04
 Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 5/60 (8%)

Query: 492 SNAKIRRSFHRMPPNAVEKLRQVFAENEL---PSRIVKENLSKELSLEPEKVNKWFKNAR 548
           S+  I      M   A E L + F  +     PS   KE L+K+  +   +V+ WF N R
Sbjct: 1   SSGHIEGR--HMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKR 58

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	629
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.74
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.73
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.73
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.73
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.73
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.73
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.73
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.72
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.72
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.71
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.71
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.7
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.7
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.7
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.7
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.7
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.7
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.69
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.69
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.69
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.69
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.68
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.68
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.68
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.68
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.68
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.68
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.68
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.68
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.68
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.68
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.67
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.67
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.67
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.67
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.67
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.66
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.66
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.66
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.65
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.65
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.65
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.65
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.65
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.65
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.65
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.64
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.64
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.64
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.63
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.63
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.63
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.63
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.62
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.62
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.6
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.6
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.59
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.59
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.57
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.56
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.56
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.55
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.55
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.54
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.54
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.53
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.53
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.53
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.52
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.5
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.49
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.4
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	99.37
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	99.36
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.36
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.33
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	99.28
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	99.27
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	99.27
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	99.27
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	99.26
2yt5_A	66	Metal-response element-binding transcription facto	99.26
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	99.25
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.24
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	99.23
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	99.21
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	99.21
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	99.21
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	99.2
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	99.18
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	99.13
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	99.13
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	99.11
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.1
3ask_A	226	E3 ubiquitin-protein ligase UHRF1; histone reader	99.09
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	99.08
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	99.07
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	99.02
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	99.01
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	98.95
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	98.83
4gne_A	107	Histone-lysine N-methyltransferase NSD3; zinc fing	98.69
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	98.6
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	98.59
1weu_A	91	Inhibitor of growth family, member 4; structural g	98.51
2vnf_A	60	ING 4, P29ING4, inhibitor of growth protein 4; ace	98.49
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	98.47
3c6w_A	59	P28ING5, inhibitor of growth protein 5; chromatin,	98.45
2jmi_A	90	Protein YNG1, ING1 homolog 1; PHD, histone, recogn	98.42
2g6q_A	62	Inhibitor of growth protein 2; protein-peptide com	98.35
1we9_A	64	PHD finger family protein; structural genomics, PH	98.28
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	98.21
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	98.15
1x4i_A	70	Inhibitor of growth protein 3; structural genomics	98.13
1wee_A	72	PHD finger family protein; structural genomics, PH	98.08
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	98.03
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.03
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	97.91
2rsd_A	68	E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant	97.91
1wem_A	76	Death associated transcription factor 1; structura	97.88
1wew_A	78	DNA-binding family protein; structural genomics, P	97.86
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	97.84
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	97.82
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	97.78
3kqi_A	75	GRC5, PHD finger protein 2; metal-binding, zinc-fi	97.76
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	97.73
3o7a_A	52	PHD finger protein 13 variant; PHF13, zinc finger,	97.65
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	97.58
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	97.57
3pur_A	528	Lysine-specific demethylase 7 homolog; oxidoreduct	97.24
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	97.15
3kv5_D	488	JMJC domain-containing histone demethylation prote	97.12
3kv4_A	447	PHD finger protein 8; epigenetics, histone CODE, c	96.2
4bbq_A	117	Lysine-specific demethylase 2A; oxidoreductase, ub	95.81
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	94.93
4gne_A	107	Histone-lysine N-methyltransferase NSD3; zinc fing	94.36
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	93.53
3a1b_A	159	DNA (cytosine-5)-methyltransferase 3A, histone H3;	87.6
3rsn_A	177	SET1/ASH2 histone methyltransferase complex subun;	87.09
2pv0_B	386	DNA (cytosine-5)-methyltransferase 3-like; DNMT3L,	84.74

>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=1.9e-18  Score=142.57  Aligned_cols=65  Identities=29%  Similarity=0.438  Sum_probs=59.2

Q ss_pred             CccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832          492 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       492 ~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      .+.+.+|.|++||.+|+.+||.+|..++||+..+++.||..|||++.||+|||||||++.+|..+
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2dmu_A            3 SGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP   67 (70)
T ss_dssp             STTSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTST
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccCC
Confidence            34556788899999999999999999999999999999999999999999999999997776653

>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=3.7e-18  Score=144.08  Aligned_cols=66  Identities=20%  Similarity=0.255  Sum_probs=60.0

Q ss_pred             CccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhh
Q 006832          492 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV  557 (629)
Q Consensus       492 ~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~  557 (629)
                      +..+.+|.|++||.+|+.+||.+|..++||+..+++.||..|||++.||+|||||||++.+|....
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (80)
T 2dmq_A            3 SGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLR   68 (80)
T ss_dssp             CCCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHH
Confidence            345678889999999999999999999999999999999999999999999999999977776543

>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.73  E-value=3.9e-18  Score=144.25  Aligned_cols=65  Identities=23%  Similarity=0.442  Sum_probs=59.2

Q ss_pred             CccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832          492 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       492 ~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      ...+.+|.|++||.+|+.+||.+|..++||+..+++.||..|||++.||+|||||||++.+|..+
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~   67 (80)
T 2dms_A            3 SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQ   67 (80)
T ss_dssp             CCCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHH
Confidence            34667888999999999999999999999999999999999999999999999999997666553

>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.73  E-value=1.4e-18  Score=143.40  Aligned_cols=64  Identities=20%  Similarity=0.332  Sum_probs=58.1

Q ss_pred             CccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          492 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       492 ~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      +..+.+|+|++||..|+.+||.+|..++||+..+++.||..|||++.||+|||||||++.+|..
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~   66 (70)
T 2cra_A            3 SGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSG   66 (70)
T ss_dssp             SSCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccC
Confidence            4456788899999999999999999999999999999999999999999999999999655543

>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.73  E-value=4.1e-18  Score=144.20  Aligned_cols=67  Identities=21%  Similarity=0.409  Sum_probs=60.7

Q ss_pred             CccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhh
Q 006832          492 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE  558 (629)
Q Consensus       492 ~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~~  558 (629)
                      ++...+|.|++||..|+.+||.+|..++||+..+++.||..|||++.||+|||||||++.+|..+..
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~   69 (80)
T 2cue_A            3 SGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLR   69 (80)
T ss_dssp             SCCSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhh
Confidence            3456688889999999999999999999999999999999999999999999999999877776544

>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.73  E-value=3.3e-18  Score=141.22  Aligned_cols=64  Identities=22%  Similarity=0.306  Sum_probs=58.5

Q ss_pred             CccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          492 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       492 ~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      ++...++++++||.+|+.+||.+|..++||+..+++.||..|||++.||++||||||++.++..
T Consensus         3 ~~~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~   66 (70)
T 2e1o_A            3 SGSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSG   66 (70)
T ss_dssp             CCCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCC
Confidence            3455677889999999999999999999999999999999999999999999999999776655

>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}

Probab=99.73  E-value=1.8e-18  Score=142.57  Aligned_cols=64  Identities=31%  Similarity=0.369  Sum_probs=58.4

Q ss_pred             CccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          492 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       492 ~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      +..+.+|+|++||..|+.+||.+|..++||+..+++.||..|||++.||++||||||++.+|..
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2da2_A            3 SGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSG   66 (70)
T ss_dssp             CSCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhcc
Confidence            4466788899999999999999999999999999999999999999999999999999655543

>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}

Probab=99.72  E-value=2.4e-18  Score=141.81  Aligned_cols=64  Identities=22%  Similarity=0.393  Sum_probs=58.4

Q ss_pred             CccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          492 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       492 ~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      ...+.+|+|++||.+|+.+||.+|..++||+..++..||..|||++.||++||||||++.+|..
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2da1_A            3 SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSG   66 (70)
T ss_dssp             SSCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhc
Confidence            4456788899999999999999999999999999999999999999999999999999665543

>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic development, complex (homeodomain/DNA); HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P* 1vnd_A 1qry_A

Probab=99.72  E-value=7.4e-18  Score=141.67  Aligned_cols=65  Identities=25%  Similarity=0.381  Sum_probs=59.2

Q ss_pred             CccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832          492 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       492 ~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      ...+.+|.|++||..|+..||.+|..++||+..+++.||..|||++.||+|||||||++.+|...
T Consensus         5 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~   69 (77)
T 1nk2_P            5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQN   69 (77)
T ss_dssp             CSCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhc
Confidence            34566788899999999999999999999999999999999999999999999999997766654

>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=2.1e-18  Score=142.39  Aligned_cols=64  Identities=20%  Similarity=0.285  Sum_probs=58.1

Q ss_pred             CccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          492 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       492 ~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      .+.+.+|+|++||..|+.+||.+|..++||+..+++.||..|||++.||++||||||++.+|..
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2djn_A            3 SGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSG   66 (70)
T ss_dssp             SCCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccC
Confidence            4466788899999999999999999999999999999999999999999999999999655443

>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=4.1e-18  Score=144.25  Aligned_cols=63  Identities=24%  Similarity=0.283  Sum_probs=57.8

Q ss_pred             ccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          493 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       493 ~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      ..+.+|.|+.||..|+.+||.+|..++||+..+|+.||..|||++.||+|||||||++.+|..
T Consensus        14 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   76 (80)
T 2dmt_A           14 AKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSG   76 (80)
T ss_dssp             CCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhccc
Confidence            456678899999999999999999999999999999999999999999999999999665544

>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus}

Probab=99.70  E-value=9.6e-18  Score=135.72  Aligned_cols=59  Identities=24%  Similarity=0.291  Sum_probs=54.1

Q ss_pred             cCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006832          496 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA  554 (629)
Q Consensus       496 ~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~  554 (629)
                      .+|+|++||..|+..||.+|..++||+..++..||..|||++.||++||||||++.+|.
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   61 (63)
T 2h1k_A            3 NKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE   61 (63)
T ss_dssp             --CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhh
Confidence            46788999999999999999999999999999999999999999999999999966554

>1wh5_A ZF-HD homeobox family protein; structural genomics, zinc finger homeobox family protein, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} SCOP: a.4.1.1

Probab=99.70  E-value=6.3e-18  Score=143.74  Aligned_cols=60  Identities=10%  Similarity=0.181  Sum_probs=55.6

Q ss_pred             ccccCCCCCCCCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHhCCCcchhhhccchhccHHH
Q 006832          493 NAKIRRSFHRMPPNAVEKLRQVFAE----NELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL  552 (629)
Q Consensus       493 ~~k~kR~r~rft~~Q~~~Le~~F~~----~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~  552 (629)
                      ..+.||.|+.||.+|+.+||.+|..    ++||+..+|++||..|||++.||+|||||||++.+
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~   77 (80)
T 1wh5_A           14 GGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGP   77 (80)
T ss_dssp             CCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSS
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCC
Confidence            3567888999999999999999999    99999999999999999999999999999999543

>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1

Probab=99.70  E-value=1.2e-17  Score=132.67  Aligned_cols=57  Identities=25%  Similarity=0.372  Sum_probs=53.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832          497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  553 (629)
Q Consensus       497 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K  553 (629)
                      ||+|+.||..|+..||.+|..++||+..++..||..|||++.||++||||||++.+|
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            467899999999999999999999999999999999999999999999999996554

>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA binding protein/DNA), transcription/DNA complex; HET: DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A 1du0_A* 1ztr_A 1enh_A 2p81_A

Probab=99.70  E-value=8e-18  Score=135.22  Aligned_cols=58  Identities=28%  Similarity=0.462  Sum_probs=51.6

Q ss_pred             cCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832          496 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  553 (629)
Q Consensus       496 ~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K  553 (629)
                      .+|+|+.||..|+..||.+|..++||+..+++.||..|||++.||++||||||++.+|
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            4778899999999999999999999999999999999999999999999999995543

>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}

Probab=99.70  E-value=5.6e-18  Score=142.72  Aligned_cols=63  Identities=24%  Similarity=0.408  Sum_probs=57.4

Q ss_pred             ccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          493 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       493 ~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      ..+.+|.|++||.+|+.+||.+|..++||+..++++||..|||++.||+|||||||++.+|..
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   76 (80)
T 2da3_A           14 PQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSG   76 (80)
T ss_dssp             CCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhc
Confidence            356678899999999999999999999999999999999999999999999999999655543

>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens}

Probab=99.70  E-value=8.5e-18  Score=143.12  Aligned_cols=64  Identities=20%  Similarity=0.276  Sum_probs=58.1

Q ss_pred             CccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          492 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       492 ~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      ...+.+|.|+.||..|+.+||.+|..++||+..+|+.||..|||++.||+|||||||++.+|..
T Consensus        18 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   81 (84)
T 2kt0_A           18 VPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQ   81 (84)
T ss_dssp             CCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHh
Confidence            3456788899999999999999999999999999999999999999999999999999655543

>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA complex, transcription/DNA complex; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1

Probab=99.69  E-value=1.2e-17  Score=133.82  Aligned_cols=58  Identities=22%  Similarity=0.392  Sum_probs=54.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006832          497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA  554 (629)
Q Consensus       497 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~  554 (629)
                      ||.|+.||..|+..||.+|..++||+..++..||..|||++.||++||||+|++.+|+
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   59 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHhHhhcc
Confidence            6788999999999999999999999999999999999999999999999999976664

>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A 1hom_A 1ftz_A

Probab=99.69  E-value=1.2e-17  Score=137.28  Aligned_cols=61  Identities=23%  Similarity=0.313  Sum_probs=56.7

Q ss_pred             cCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832          496 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       496 ~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      ++|.|+.||..|+..||.+|..++||+..++..||..|||++.||+|||||||++.+|..+
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~   62 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK   62 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhcc
Confidence            3677899999999999999999999999999999999999999999999999997776653

>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus}

Probab=99.69  E-value=9.6e-18  Score=135.18  Aligned_cols=59  Identities=20%  Similarity=0.298  Sum_probs=50.6

Q ss_pred             ccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832          495 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  553 (629)
Q Consensus       495 k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K  553 (629)
                      +.+|+|+.||..|+.+||.+|..++||+..++..||..|||++.||+|||||||++.+|
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   60 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR   60 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGG
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhh
Confidence            35778899999999999999999999999999999999999999999999999995443

>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster}

Probab=99.69  E-value=2.1e-17  Score=144.11  Aligned_cols=68  Identities=18%  Similarity=0.300  Sum_probs=61.1

Q ss_pred             CccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhhhh
Q 006832          492 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES  559 (629)
Q Consensus       492 ~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~~~  559 (629)
                      ...+.+|+|+.||..|+..||.+|..++||+..+|..||..|||++.||+|||||||++.+|....+.
T Consensus        13 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~   80 (93)
T 3a01_A           13 TPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEER   80 (93)
T ss_dssp             CCCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC-
T ss_pred             CCCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHHH
Confidence            34567888999999999999999999999999999999999999999999999999998877765443

>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix, helix-turn-helix; NMR {Drosophila melanogaster} SCOP: a.4.1.1

Probab=99.68  E-value=2.3e-17  Score=135.51  Aligned_cols=62  Identities=24%  Similarity=0.325  Sum_probs=57.3

Q ss_pred             cCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhh
Q 006832          496 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV  557 (629)
Q Consensus       496 ~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~  557 (629)
                      .+|.|+.||..|+..||.+|..++||+..++..||..|||++.||+|||||||++.++....
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~   63 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ   63 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhcc
Confidence            46788999999999999999999999999999999999999999999999999977766543

>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription regulation; HET: DNA; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 3a01_B

Probab=99.68  E-value=2.3e-17  Score=139.75  Aligned_cols=64  Identities=23%  Similarity=0.455  Sum_probs=57.9

Q ss_pred             ccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832          493 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       493 ~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      ..+.+|.|++||..|+..||.+|..++||+..++..||..|||++.||++||||||++.+|...
T Consensus        15 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~   78 (81)
T 1fjl_A           15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   78 (81)
T ss_dssp             --CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhcc
Confidence            3556788999999999999999999999999999999999999999999999999997776653

>1puf_A HOX-1.7, homeobox protein HOX-A9; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Mus musculus} SCOP: a.4.1.1 PDB: 1san_A

Probab=99.68  E-value=3.3e-17  Score=137.74  Aligned_cols=63  Identities=22%  Similarity=0.281  Sum_probs=58.2

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      .+.+|.|++||..|+.+||.+|..++||+..+++.||..|||++.||+|||||||++.+|..+
T Consensus        11 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k   73 (77)
T 1puf_A           11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINK   73 (77)
T ss_dssp             CTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhh
Confidence            456778899999999999999999999999999999999999999999999999997776654

>2dmn_A Homeobox protein TGIF2LX; TGFB-induced factor 2-like protein, X-linked TGF(beta) induced transcription factor 2-like protein, TGIF-like on the X; NMR {Homo sapiens}

Probab=99.68  E-value=3.8e-17  Score=139.59  Aligned_cols=64  Identities=27%  Similarity=0.377  Sum_probs=58.1

Q ss_pred             CccccCCCCCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          492 SNAKIRRSFHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       492 ~~~k~kR~r~rft~~Q~~~Le~~F~~---~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      +..+.+|++++|+.+|+.+|+.+|.+   +|||+..+|++||..|||++.||+|||||+|++.++..
T Consensus         3 ~~~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~   69 (83)
T 2dmn_A            3 SGSSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDM   69 (83)
T ss_dssp             CCCCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHH
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHH
Confidence            44567788899999999999999998   59999999999999999999999999999999776654

>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1

Probab=99.68  E-value=2.3e-17  Score=135.48  Aligned_cols=61  Identities=26%  Similarity=0.418  Sum_probs=56.6

Q ss_pred             cCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832          496 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       496 ~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      ++|++++||..|+..||.+|..++||+..++..||..|||++.||+|||||||++.+|..+
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~   62 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK   62 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhh
Confidence            4678899999999999999999999999999999999999999999999999997666653

>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P 2lkx_A* 2l7m_P

Probab=99.68  E-value=1e-17  Score=137.49  Aligned_cols=62  Identities=24%  Similarity=0.388  Sum_probs=57.3

Q ss_pred             ccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832          495 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       495 k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      +.+|+|+.||..|+..||.+|..++||+..++..||..|||++.||+|||||||++.+|..+
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~   63 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREE   63 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhh
Confidence            45778899999999999999999999999999999999999999999999999997666653

>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1

Probab=99.68  E-value=1.2e-17  Score=136.24  Aligned_cols=59  Identities=29%  Similarity=0.476  Sum_probs=54.9

Q ss_pred             ccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832          495 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  553 (629)
Q Consensus       495 k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K  553 (629)
                      +.+|+|+.||.+|+..||.+|..++||+..+++.||..|||++.||++||||||++.+|
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKK   60 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhH
Confidence            35788899999999999999999999999999999999999999999999999995443

>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding proteins/DNA), complex, DNA- binding protein, DNA; HET: DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1f43_A 1yrn_A*

Probab=99.68  E-value=1.3e-17  Score=133.73  Aligned_cols=57  Identities=26%  Similarity=0.405  Sum_probs=47.3

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  550 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k  550 (629)
                      .+.+|++++||..|+..||.+|..++||+..++..||..|||++.||++||||+|++
T Consensus         3 ~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k   59 (61)
T 1akh_A            3 EKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR   59 (61)
T ss_dssp             ---------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhc
Confidence            456778899999999999999999999999999999999999999999999999994

>1x2n_A Homeobox protein pknox1; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.68  E-value=3.4e-17  Score=136.01  Aligned_cols=63  Identities=22%  Similarity=0.352  Sum_probs=57.6

Q ss_pred             ccccCCCCCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          493 NAKIRRSFHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       493 ~~k~kR~r~rft~~Q~~~Le~~F~~---~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      .++.+|.+++|+..|+..|+.+|.+   ++||+..+|++||..|||++.||++||||+|++.++..
T Consensus         4 ~~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~   69 (73)
T 1x2n_A            4 GSSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSG   69 (73)
T ss_dssp             CSSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhccccc
Confidence            4556778899999999999999988   99999999999999999999999999999999776654

>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A*

Probab=99.68  E-value=2.3e-17  Score=137.39  Aligned_cols=61  Identities=20%  Similarity=0.307  Sum_probs=56.2

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA  554 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~  554 (629)
                      .+.+|.|++||..|+..||.+|..++||+..++..||..|||++.||++||||||++.+|.
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   65 (73)
T 2l7z_A            5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKV   65 (73)
T ss_dssp             SCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHH
Confidence            4567888999999999999999999999999999999999999999999999999955544

>1wh7_A ZF-HD homeobox family protein; homeobox domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: a.4.1.1

Probab=99.67  E-value=1.6e-17  Score=141.45  Aligned_cols=59  Identities=17%  Similarity=0.289  Sum_probs=54.4

Q ss_pred             ccccCCCCCCCCHHHHHHHHHHHHh-----CCCCCHHHHHHHHHHhCCCcchhhhccchhccHHH
Q 006832          493 NAKIRRSFHRMPPNAVEKLRQVFAE-----NELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL  552 (629)
Q Consensus       493 ~~k~kR~r~rft~~Q~~~Le~~F~~-----~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~  552 (629)
                      ..+.||.|+.||.+|+.+|| .|.+     ++||+..+|++||..|||++.||+|||||||++.+
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~   77 (80)
T 1wh7_A           14 GGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGP   77 (80)
T ss_dssp             CCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSC
T ss_pred             CCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCC
Confidence            45678889999999999999 7999     99999999999999999999999999999999543

>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=4.9e-17  Score=136.21  Aligned_cols=58  Identities=21%  Similarity=0.418  Sum_probs=53.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          498 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       498 R~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      +++.+||.+|+.+||.+|..++||+..+|..||..|||++.||+|||||||++.+|..
T Consensus         9 ~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~   66 (75)
T 2da5_A            9 TKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEE   66 (75)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSS
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhh
Confidence            3456789999999999999999999999999999999999999999999999766655

>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA binding, homeodomain, homeotic proteins, development, specificity; HET: DNA; 2.40A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 9ant_A*

Probab=99.67  E-value=2.6e-17  Score=139.78  Aligned_cols=62  Identities=23%  Similarity=0.312  Sum_probs=53.1

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      ...+|.|+.||..|+..||.+|..++||+..+|+.||..|||++.||+|||||||++.+|..
T Consensus        18 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   79 (81)
T 1b8i_A           18 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEI   79 (81)
T ss_dssp             ------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhc
Confidence            45678889999999999999999999999999999999999999999999999999666543

>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor, structural genomics, loop insertion, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.67  E-value=6.2e-17  Score=141.30  Aligned_cols=65  Identities=22%  Similarity=0.333  Sum_probs=59.9

Q ss_pred             CccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhC---------------CCcchhhhccchhccHHHHhhh
Q 006832          492 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELS---------------LEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       492 ~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lg---------------Lt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      +..+.+|.|+.||+.|+.+||.+|..++||+..+|++||..||               |++.||++||||||++.+|..+
T Consensus         3 ~~~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~   82 (95)
T 2cuf_A            3 SGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRAN   82 (95)
T ss_dssp             SSSCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhh
Confidence            4567788999999999999999999999999999999999999               9999999999999997766654

>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=2.5e-17  Score=139.24  Aligned_cols=62  Identities=16%  Similarity=0.210  Sum_probs=57.0

Q ss_pred             ccccCCCCCCCCHHHHHHHHHHHHhC----CCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006832          493 NAKIRRSFHRMPPNAVEKLRQVFAEN----ELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA  554 (629)
Q Consensus       493 ~~k~kR~r~rft~~Q~~~Le~~F~~~----~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~  554 (629)
                      ..+.+|.|+.||.+|+.+||.+|..+    +||+..++++||..|||++.||+|||||||++.+|.
T Consensus         5 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~   70 (80)
T 2da4_A            5 SSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLM   70 (80)
T ss_dssp             CCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhc
Confidence            35567888999999999999999999    999999999999999999999999999999966553

>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens}

Probab=99.66  E-value=4.4e-17  Score=128.77  Aligned_cols=55  Identities=25%  Similarity=0.407  Sum_probs=52.5

Q ss_pred             cCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006832          496 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  550 (629)
Q Consensus       496 ~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k  550 (629)
                      ++|.+++||..|+..||.+|..++||+..++.+||..|||++.||++||||||++
T Consensus         2 ~rr~Rt~~t~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   56 (58)
T 3rkq_A            2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYK   56 (58)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             cCCCCCCcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhhcc
Confidence            4677899999999999999999999999999999999999999999999999995

>3a02_A Homeobox protein aristaless; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.00A {Drosophila melanogaster} PDB: 3lnq_A 3cmy_A

Probab=99.66  E-value=3.7e-17  Score=130.94  Aligned_cols=57  Identities=23%  Similarity=0.445  Sum_probs=49.7

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          499 SFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       499 ~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      +|++||.+|+..||.+|..++||+..++..||..|||++.||++||||||++.+|..
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~   58 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE   58 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC---
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhc
Confidence            357899999999999999999999999999999999999999999999999766654

>2m0c_A Homeobox protein aristaless-like 4; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.66  E-value=8.8e-17  Score=133.64  Aligned_cols=62  Identities=27%  Similarity=0.440  Sum_probs=56.9

Q ss_pred             ccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006832          493 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA  554 (629)
Q Consensus       493 ~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~  554 (629)
                      .++.+|.+++||..|+..||.+|..++||+..++..||..|||++.||+|||||||++.+|.
T Consensus         6 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   67 (75)
T 2m0c_A            6 KGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKR   67 (75)
T ss_dssp             CSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHH
Confidence            35567889999999999999999999999999999999999999999999999999955544

>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.65  E-value=7.1e-17  Score=136.40  Aligned_cols=55  Identities=18%  Similarity=0.311  Sum_probs=50.8

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006832          500 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA  554 (629)
Q Consensus       500 r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~  554 (629)
                      +.+||.+|+.+|+.+|..|+||+..+|++||..|||++.||+|||||+|++.++.
T Consensus         7 r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~   61 (76)
T 2ecc_A            7 GKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHH
Confidence            3568999999999999999999999999999999999999999999999955443

>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.65  E-value=9.8e-17  Score=133.50  Aligned_cols=59  Identities=22%  Similarity=0.265  Sum_probs=54.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          497 RRSFHRMPPNAVEKLRQVFA-ENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       497 kR~r~rft~~Q~~~Le~~F~-~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      ++.|++||..|+.+||.+|. .++||+..+++.||..|||++.||+|||||||++.+|..
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~   62 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   62 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhc
Confidence            45678899999999999999 599999999999999999999999999999999766655

>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant, DNA binding protein, developmental protein, disease mutation, DNA-binding; NMR {Homo sapiens}

Probab=99.65  E-value=5.6e-17  Score=132.60  Aligned_cols=58  Identities=31%  Similarity=0.519  Sum_probs=54.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006832          497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA  554 (629)
Q Consensus       497 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~  554 (629)
                      ||+|++||+.|+..||.+|..++||+..++..||..|||++.||++||||||++.+|.
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRS   59 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCS
T ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHh
Confidence            6778999999999999999999999999999999999999999999999999955443

>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens}

Probab=99.65  E-value=7.9e-17  Score=127.54  Aligned_cols=54  Identities=20%  Similarity=0.351  Sum_probs=49.8

Q ss_pred             CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006832          501 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA  554 (629)
Q Consensus       501 ~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~  554 (629)
                      +.||..|+..||.+|..++||+..+|.+||..|||++.||++||||||++.+|+
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~   55 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ   55 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhhccc
Confidence            579999999999999999999999999999999999999999999999976653

>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A*

Probab=99.65  E-value=5.1e-17  Score=139.86  Aligned_cols=61  Identities=21%  Similarity=0.304  Sum_probs=53.3

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA  554 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~  554 (629)
                      .+.+|.|++||..|+.+||.+|..++||+..+|+.||..|||++.||+|||||||++.+|.
T Consensus        26 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~   86 (88)
T 2r5y_A           26 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   86 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhh
Confidence            4567888999999999999999999999999999999999999999999999999966554

>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.65  E-value=9.5e-17  Score=139.45  Aligned_cols=55  Identities=11%  Similarity=0.235  Sum_probs=50.8

Q ss_pred             CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          501 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       501 ~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      .+||.+|+.+||..|..++||+..+|++||..|||++.||+|||||||++.+|..
T Consensus        16 k~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~   70 (89)
T 2ecb_A           16 KEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE   70 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCC
T ss_pred             ccCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHH
Confidence            3789999999999999999999999999999999999999999999999554443

>1puf_B PRE-B-cell leukemia transcription factor-1; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Homo sapiens} SCOP: a.4.1.1 PDB: 1b8i_B* 2r5y_B* 2r5z_B*

Probab=99.65  E-value=8.6e-17  Score=133.62  Aligned_cols=60  Identities=32%  Similarity=0.434  Sum_probs=55.9

Q ss_pred             CCCCCCCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832          497 RRSFHRMPPNAVEKLRQVF---AENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       497 kR~r~rft~~Q~~~Le~~F---~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      ||++++||..|+..|+.+|   ..++||+..++..||..|||++.||++||||+|++.++...
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~   64 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG   64 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcccccc
Confidence            6778899999999999999   89999999999999999999999999999999997776653

>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac development, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.64  E-value=1.1e-16  Score=132.75  Aligned_cols=58  Identities=24%  Similarity=0.304  Sum_probs=53.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          498 RSFHRMPPNAVEKLRQVFAE-NELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       498 R~r~rft~~Q~~~Le~~F~~-~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      +.+++||..|+.+||.+|.. ++||+..+++.||..|||++.||+|||||||++.+|..
T Consensus         3 k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~   61 (72)
T 1uhs_A            3 EGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhc
Confidence            45688999999999999996 99999999999999999999999999999999766655

>1b72_B Protein (PBX1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1 PDB: 1lfu_P

Probab=99.64  E-value=9.5e-17  Score=137.49  Aligned_cols=61  Identities=31%  Similarity=0.418  Sum_probs=56.0

Q ss_pred             CCCCCCCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhh
Q 006832          497 RRSFHRMPPNAVEKLRQVF---AENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV  557 (629)
Q Consensus       497 kR~r~rft~~Q~~~Le~~F---~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~  557 (629)
                      ||+|++|+..|+.+|+.+|   ..++||+..+|+.||..|||++.||++||||+|++.+|....
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~   65 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGK   65 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGG
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhcccc
Confidence            6778899999999999999   899999999999999999999999999999999987776643

>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.64  E-value=1.3e-16  Score=131.59  Aligned_cols=58  Identities=26%  Similarity=0.383  Sum_probs=55.4

Q ss_pred             CccccCCCCCCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006832          492 SNAKIRRSFHRMPPNAVEKLRQVFAE-NELPSRIVKENLSKELSLEPEKVNKWFKNARY  549 (629)
Q Consensus       492 ~~~k~kR~r~rft~~Q~~~Le~~F~~-~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~  549 (629)
                      +.+..||.|+.|+.+|+.+|+.+|+. ++||+...|+.||++|||++++|+|||||+|+
T Consensus         3 ~~~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~   61 (71)
T 1wi3_A            3 SGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRY   61 (71)
T ss_dssp             CCCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhcccee
Confidence            44667899999999999999999999 99999999999999999999999999999999

>1b72_A Protein (homeobox protein HOX-B1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1

Probab=99.63  E-value=1.3e-16  Score=139.77  Aligned_cols=62  Identities=21%  Similarity=0.300  Sum_probs=54.3

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      ...+|.|+.||..|+..||.+|..++||+..+|+.||..|||++.||+|||||||++.+|..
T Consensus        32 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   93 (97)
T 1b72_A           32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRE   93 (97)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHh
Confidence            45677889999999999999999999999999999999999999999999999999766654

>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.63  E-value=5.9e-17  Score=131.21  Aligned_cols=58  Identities=31%  Similarity=0.387  Sum_probs=53.3

Q ss_pred             cCCCCCCCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832          496 IRRSFHRMPPNAVEKLRQVF---AENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  553 (629)
Q Consensus       496 ~kR~r~rft~~Q~~~Le~~F---~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K  553 (629)
                      .++.+++|+..|+..|+.+|   ..++||+..++++||..|||++.||++||||+|++.+|
T Consensus         3 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A            3 GHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             CCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            35677889999999999999   89999999999999999999999999999999995443

>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration calorimetry, protein-DNA complex, transcription/DNA complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1akh_B* 1apl_C* 1yrn_B*

Probab=99.63  E-value=1.4e-16  Score=135.95  Aligned_cols=58  Identities=26%  Similarity=0.263  Sum_probs=52.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          498 RSFHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       498 R~r~rft~~Q~~~Le~~F~~---~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      +++++||..|+..|+.+|..   ++||+..+|..||..|||++.||++||||||++.++..
T Consensus         4 krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~   64 (83)
T 1le8_B            4 YRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTIT   64 (83)
T ss_dssp             -CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHccccccc
Confidence            44566999999999999999   99999999999999999999999999999999665554

>2ly9_A Zinc fingers and homeoboxes protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.63  E-value=1.7e-16  Score=132.00  Aligned_cols=61  Identities=18%  Similarity=0.317  Sum_probs=55.2

Q ss_pred             ccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          495 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       495 k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      ..++.|+.||.+|+..||.+|..++||+..++++||..|||++.||++||||||++.+|..
T Consensus         5 ~~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   65 (74)
T 2ly9_A            5 DSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSK   65 (74)
T ss_dssp             CCCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTT
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhC
Confidence            3466788999999999999999999999999999999999999999999999999554443

>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=2.4e-16  Score=132.07  Aligned_cols=59  Identities=24%  Similarity=0.442  Sum_probs=53.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       497 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      .+.|++||.+|+.+||.+|..++||+..+|++||..|||++.||++||||||++.+|..
T Consensus         9 ~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~   67 (76)
T 2dn0_A            9 SIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLK   67 (76)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCC
T ss_pred             CCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhc
Confidence            33468899999999999999999999999999999999999999999999999554443

>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain, hoogsteen base PAIR, transcription/DNA complex; HET: 5IU; 2.10A {Synthetic} SCOP: a.4.1.1

Probab=99.62  E-value=2.1e-16  Score=126.36  Aligned_cols=53  Identities=30%  Similarity=0.337  Sum_probs=50.2

Q ss_pred             CCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhCCCcchhhhccchhccHHH
Q 006832          500 FHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL  552 (629)
Q Consensus       500 r~rft~~Q~~~Le~~F~~---~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~  552 (629)
                      +++||..|+.+|+.+|..   ++||+..+++.||..|||++.||++||||+|++.+
T Consensus         2 r~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~k   57 (60)
T 1k61_A            2 GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK   57 (60)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_pred             cCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHcccc
Confidence            468999999999999999   99999999999999999999999999999999544

>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.60  E-value=5.2e-16  Score=134.27  Aligned_cols=56  Identities=21%  Similarity=0.421  Sum_probs=50.8

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          500 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       500 r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      +.+||.+|+.+||.+|..++||+..+|+.||..|||++.||+|||||||++.++..
T Consensus        17 ~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~   72 (89)
T 2dmp_A           17 FKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSME   72 (89)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSC
T ss_pred             cccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHh
Confidence            34589999999999999999999999999999999999999999999999544444

>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens}

Probab=99.60  E-value=4e-16  Score=136.54  Aligned_cols=61  Identities=21%  Similarity=0.403  Sum_probs=53.6

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA  554 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~  554 (629)
                      ...+|.|++||..|+..||.+|..++||+..++++||..|||++.||+|||||||++.+|.
T Consensus        23 ~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~   83 (96)
T 3nar_A           23 SGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNG   83 (96)
T ss_dssp             ----CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhh
Confidence            3456778999999999999999999999999999999999999999999999999965543

>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.1

Probab=99.59  E-value=7e-16  Score=132.45  Aligned_cols=58  Identities=28%  Similarity=0.299  Sum_probs=53.4

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhCCCcchhhhccchhccHH
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARYLA  551 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~---~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~  551 (629)
                      .++++++++|+..|+..|+.+|..   ++||+..+|+.||..|||++.||++||||||++.
T Consensus        25 ~~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~   85 (87)
T 1mnm_C           25 STKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKE   85 (87)
T ss_dssp             ESSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhc
Confidence            345566789999999999999999   9999999999999999999999999999999943

>2da6_A Hepatocyte nuclear factor 1-beta; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=1.8e-15  Score=134.40  Aligned_cols=65  Identities=25%  Similarity=0.336  Sum_probs=58.7

Q ss_pred             CccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHh---------------------CCCcchhhhccchhccH
Q 006832          492 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKEL---------------------SLEPEKVNKWFKNARYL  550 (629)
Q Consensus       492 ~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~l---------------------gLt~~QVkiWFQNrR~k  550 (629)
                      +.+++||.|+.|++.|+.+||.+|..++||+..+|++||..|                     +|++.||+|||||||++
T Consensus         2 ~~~~~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k   81 (102)
T 2da6_A            2 SSGSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKE   81 (102)
T ss_dssp             TTCCSCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHH
Confidence            446678899999999999999999999999999999999999                     79999999999999996


Q ss_pred             HHHhhh
Q 006832          551 ALKARK  556 (629)
Q Consensus       551 ~~K~~~  556 (629)
                      .++..+
T Consensus        82 ~kr~~~   87 (102)
T 2da6_A           82 EAFRQK   87 (102)
T ss_dssp             HHHHHH
T ss_pred             HHHhhH
Confidence            655543

>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens}

Probab=99.57  E-value=1.3e-15  Score=125.27  Aligned_cols=49  Identities=20%  Similarity=0.454  Sum_probs=47.0

Q ss_pred             CHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHH
Q 006832          504 PPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL  552 (629)
Q Consensus       504 t~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~  552 (629)
                      |.+|+.+||..|..++||+..+|.+||..|||+..||++||||||++.+
T Consensus        12 ~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~K   60 (66)
T 3nau_A           12 TKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQ   60 (66)
T ss_dssp             CHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhh
Confidence            8999999999999999999999999999999999999999999999444

>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.56  E-value=4.6e-16  Score=129.76  Aligned_cols=55  Identities=22%  Similarity=0.349  Sum_probs=50.1

Q ss_pred             CCCCCCCHHHHHHHHHHH-HhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHH
Q 006832          498 RSFHRMPPNAVEKLRQVF-AENELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL  552 (629)
Q Consensus       498 R~r~rft~~Q~~~Le~~F-~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~  552 (629)
                      +.+.+++..|+.+||.+| ..++||+..+|++||..|||++.||+|||||||++.+
T Consensus        10 k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r   65 (72)
T 2cqx_A           10 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK   65 (72)
T ss_dssp             CCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCC
Confidence            344567999999999999 9999999999999999999999999999999999433

>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens}

Probab=99.56  E-value=1.8e-15  Score=142.37  Aligned_cols=61  Identities=31%  Similarity=0.493  Sum_probs=56.2

Q ss_pred             ccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832          493 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  553 (629)
Q Consensus       493 ~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K  553 (629)
                      ..++||+|+.||..|+..||.+|..++||+..+|..||..|||++.||+|||||||++.+|
T Consensus        90 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           90 PSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            3566788899999999999999999999999999999999999999999999999995543

>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1

Probab=99.55  E-value=1.4e-15  Score=142.76  Aligned_cols=61  Identities=30%  Similarity=0.409  Sum_probs=53.3

Q ss_pred             ccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832          493 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  553 (629)
Q Consensus       493 ~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K  553 (629)
                      ..++||+|+.||..|+..||.+|..++||+..+|..||..|||++.||+|||||||++.+|
T Consensus        84 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr  144 (146)
T 1au7_A           84 NERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR  144 (146)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhc
Confidence            3566778999999999999999999999999999999999999999999999999995544

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus}

Probab=99.55  E-value=1.3e-15  Score=145.67  Aligned_cols=62  Identities=24%  Similarity=0.293  Sum_probs=50.3

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      .++||+|++||..|+..||.+|..++||+..+|++||..|||++.||+|||||||++.+|..
T Consensus        97 ~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~  158 (164)
T 2xsd_C           97 GRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMT  158 (164)
T ss_dssp             ---------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSC
T ss_pred             ccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhcc
Confidence            55677899999999999999999999999999999999999999999999999999665554

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A

Probab=99.54  E-value=2.2e-15  Score=143.23  Aligned_cols=60  Identities=23%  Similarity=0.387  Sum_probs=52.6

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  553 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K  553 (629)
                      .++||+|+.||..|+.+||.+|..++||+..+|+.||..|||++.||+|||||||++.+|
T Consensus        99 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr  158 (160)
T 1e3o_C           99 SRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR  158 (160)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTS
T ss_pred             CCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhc
Confidence            466788999999999999999999999999999999999999999999999999996544

>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding, transcription, nucleus, phosphoprotein, DNA bindi protein; 1.95A {Homo sapiens} SCOP: a.4.1.1

Probab=99.54  E-value=2.7e-15  Score=123.32  Aligned_cols=55  Identities=27%  Similarity=0.381  Sum_probs=49.5

Q ss_pred             CCCHHHHHHHHHHHH---hCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832          502 RMPPNAVEKLRQVFA---ENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       502 rft~~Q~~~Le~~F~---~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      +||.+|+..|+.+|.   .+|||+..+|++||..|||++.||++||||+|++.+|...
T Consensus         4 ~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~   61 (67)
T 3k2a_A            4 IFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMI   61 (67)
T ss_dssp             --CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC-
T ss_pred             cCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHH
Confidence            689999999999999   9999999999999999999999999999999997766543

>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A

Probab=99.53  E-value=1.5e-15  Score=134.26  Aligned_cols=59  Identities=29%  Similarity=0.430  Sum_probs=50.3

Q ss_pred             ccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHH------------------hC---CCcchhhhccchhccHH
Q 006832          493 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKE------------------LS---LEPEKVNKWFKNARYLA  551 (629)
Q Consensus       493 ~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~------------------lg---Lt~~QVkiWFQNrR~k~  551 (629)
                      .++.||.|+.||+.|+..||.+|..++||+..+|++||..                  ||   |++.||+|||||||++.
T Consensus         6 ~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k~   85 (99)
T 1lfb_A            6 TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEE   85 (99)
T ss_dssp             -------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHHH
Confidence            3567888999999999999999999999999999999999                  98   99999999999999943

>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=3.9e-15  Score=121.53  Aligned_cols=50  Identities=22%  Similarity=0.319  Sum_probs=47.5

Q ss_pred             CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006832          501 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  550 (629)
Q Consensus       501 ~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k  550 (629)
                      ..++..|+..||.+|..++||+..+|++||..|||++.||+|||||||++
T Consensus         8 ~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak   57 (64)
T 2e19_A            8 QPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAG   57 (64)
T ss_dssp             CCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCC
Confidence            45689999999999999999999999999999999999999999999993

>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.53  E-value=4.6e-15  Score=123.06  Aligned_cols=54  Identities=28%  Similarity=0.475  Sum_probs=50.0

Q ss_pred             CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006832          501 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA  554 (629)
Q Consensus       501 ~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~  554 (629)
                      ..+|..|+.+||..|..++||+..+|.+||..|||++.||+|||||||++.+|.
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~   62 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRK   62 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCS
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhh
Confidence            468999999999999999999999999999999999999999999999954443

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A

Probab=99.52  E-value=2.9e-15  Score=142.49  Aligned_cols=62  Identities=26%  Similarity=0.364  Sum_probs=53.2

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      .+.||+|+.||..|+..|+.+|..++||+..+|++||..|||++.||+|||||||++.++..
T Consensus        95 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~  156 (164)
T 2d5v_A           95 NTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKW  156 (164)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC-
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccC
Confidence            55678889999999999999999999999999999999999999999999999999655444

>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.50  E-value=3.4e-15  Score=122.28  Aligned_cols=46  Identities=28%  Similarity=0.491  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHH-HhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006832          505 PNAVEKLRQVF-AENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  550 (629)
Q Consensus       505 ~~Q~~~Le~~F-~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k  550 (629)
                      +.|+.+||.+| ..++||+..+|.+||.+|||+++||+|||||||++
T Consensus         9 ~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k   55 (64)
T 1x2m_A            9 AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQ   55 (64)
T ss_dssp             SCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence            45899999999 57899999999999999999999999999999993

>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A

Probab=99.49  E-value=8.5e-15  Score=138.63  Aligned_cols=60  Identities=22%  Similarity=0.323  Sum_probs=55.6

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  553 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K  553 (629)
                      .+.||.|+.|+..|+..||.+|..++||+..+|..||..|||++.||+|||||||++.+|
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr  153 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKR  153 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC
T ss_pred             cCCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccccC
Confidence            456778899999999999999999999999999999999999999999999999995543

>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens}

Probab=99.40  E-value=2.8e-13  Score=117.62  Aligned_cols=56  Identities=36%  Similarity=0.461  Sum_probs=52.0

Q ss_pred             CCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832          501 HRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       501 ~rft~~Q~~~Le~~F~~---~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      .-|+..++..|+.||.+   +|||+..+|++||+.+||++.||++||||+|.+.++...
T Consensus        10 ~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~   68 (89)
T 2lk2_A           10 HMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDML   68 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHH
Confidence            45899999999999998   899999999999999999999999999999998777653

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=99.37  E-value=2.7e-13  Score=117.43  Aligned_cols=59  Identities=27%  Similarity=0.737  Sum_probs=50.7

Q ss_pred             cCCCCcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhhH
Q 006832          229 ATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKME  294 (629)
Q Consensus       229 ~~dg~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~~  294 (629)
                      ....+...++++|.+|+.++     +||+||+ |+++||++||.|||..+| .+.|||+.|.....
T Consensus        16 ~~~~~~d~n~~~C~vC~~~g-----~LL~CD~-C~~~fH~~Cl~PpL~~~P-~g~W~C~~C~~~~~   74 (88)
T 1fp0_A           16 DEFGTLDDSATICRVCQKPG-----DLVMCNQ-CEFCFHLDCHLPALQDVP-GEEWSCSLCHVLPD   74 (88)
T ss_dssp             CCCCSSSSSSSCCSSSCSSS-----CCEECTT-SSCEECTTSSSTTCCCCC-SSSCCCCSCCCCCS
T ss_pred             ccccccCCCCCcCcCcCCCC-----CEEECCC-CCCceecccCCCCCCCCc-CCCcCCccccCCCc
Confidence            34456677889999999874     7999995 999999999999999999 79999999986544

>1wev_A Riken cDNA 1110020M19; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: g.50.1.2

Probab=99.36  E-value=1.3e-13  Score=119.38  Aligned_cols=63  Identities=22%  Similarity=0.635  Sum_probs=51.3

Q ss_pred             ccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCC----CCCCCceecccCchhhHHHHhh
Q 006832          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDT----ESRDQGWFCKFCECKMEIIESM  299 (629)
Q Consensus       235 ~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~----~p~dg~W~C~~C~~k~~~l~~~  299 (629)
                      ..++.+|.+|+.++...++.||+||+ |+++||++||+|||..    +| .+.|||+.|.........+
T Consensus        13 ~e~~~~C~vC~~~~~~~~~~ll~CD~-C~~~yH~~Cl~Ppl~~~~~~~p-~g~W~C~~C~~~~~~~~~~   79 (88)
T 1wev_A           13 MEMGLACVVCRQMTVASGNQLVECQE-CHNLYHQDCHKPQVTDKEVNDP-RLVWYCARCTRQMKRMAQK   79 (88)
T ss_dssp             HHHCCSCSSSCCCCCCTTCCEEECSS-SCCEEETTTSSSCCCHHHHHCT-TCCCCCHHHHHHHCCSTTC
T ss_pred             CCCCCcCCCCCCCCCCCCCceEECCC-CCCeEcCccCCCcccccccCCC-CCCeeCccccchhhhhccc
Confidence            34578999999986555689999995 9999999999999985    66 7999999998765544333

>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1

Probab=99.36  E-value=1.1e-13  Score=135.79  Aligned_cols=59  Identities=27%  Similarity=0.404  Sum_probs=51.8

Q ss_pred             CccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhC---------------------CCcchhhhccchhccH
Q 006832          492 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELS---------------------LEPEKVNKWFKNARYL  550 (629)
Q Consensus       492 ~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lg---------------------Lt~~QVkiWFQNrR~k  550 (629)
                      ...+.||.|+.|++.|+.+||.+|..++||+..+|++||..||                     |++.||+|||||||++
T Consensus       111 ~~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~  190 (194)
T 1ic8_A          111 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE  190 (194)
T ss_dssp             ------CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHH
T ss_pred             ccccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhh
Confidence            4466788899999999999999999999999999999999999                     9999999999999984

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens}

Probab=99.33  E-value=5.6e-13  Score=132.78  Aligned_cols=61  Identities=30%  Similarity=0.496  Sum_probs=52.5

Q ss_pred             cCCCccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhC---------------------CCcchhhhccchh
Q 006832          489 KLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELS---------------------LEPEKVNKWFKNA  547 (629)
Q Consensus       489 ~~~~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lg---------------------Lt~~QVkiWFQNr  547 (629)
                      ..+..++.||.|+.|++.|+.+|+.+|..++||+..+|++||..+|                     ||+.||++|||||
T Consensus       135 ~~~~~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNR  214 (221)
T 2h8r_A          135 SEPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANR  214 (221)
T ss_dssp             -------CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHH
T ss_pred             cccccCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHh
Confidence            3445567788999999999999999999999999999999999998                     8999999999999


Q ss_pred             cc
Q 006832          548 RY  549 (629)
Q Consensus       548 R~  549 (629)
                      |+
T Consensus       215 R~  216 (221)
T 2h8r_A          215 RK  216 (221)
T ss_dssp             HT
T ss_pred             hh
Confidence            98

>2e6r_A Jumonji/ARID domain-containing protein 1D; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.28  E-value=1e-12  Score=114.61  Aligned_cols=57  Identities=30%  Similarity=0.727  Sum_probs=49.6

Q ss_pred             CCcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832          232 GSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       232 g~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      .+...++.+|.+|+.++.  .+.||+||+ |+++||++||+|||..+| .+.|||+.|...
T Consensus        10 ~~~~~~~~~C~vC~~~~~--~~~ll~CD~-C~~~~H~~Cl~Ppl~~~P-~g~W~C~~C~~~   66 (92)
T 2e6r_A           10 SAQFIDSYICQVCSRGDE--DDKLLFCDG-CDDNYHIFCLLPPLPEIP-RGIWRCPKCILA   66 (92)
T ss_dssp             CCCCCCCCCCSSSCCSGG--GGGCEECTT-TCCEECSSSSSSCCSSCC-SSCCCCHHHHHH
T ss_pred             hhhccCCCCCccCCCcCC--CCCEEEcCC-CCchhccccCCCCcccCC-CCCcCCccCcCc
Confidence            355677889999998863  568999995 999999999999999999 789999999754

>1mm2_A MI2-beta; PHD, zinc finger, protein scaffold, DNA binding protein; NMR {Homo sapiens} SCOP: g.50.1.2 PDB: 2l75_A* 1mm3_A

Probab=99.27  E-value=1.9e-12  Score=104.73  Aligned_cols=51  Identities=33%  Similarity=0.946  Sum_probs=44.9

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKM  293 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~  293 (629)
                      .++.+|.+|+.+     +.||+||+ |+++||++||+|||..+| .+.|||+.|..+.
T Consensus         7 ~~~~~C~vC~~~-----g~ll~Cd~-C~~~fH~~Cl~ppl~~~p-~g~W~C~~C~~~~   57 (61)
T 1mm2_A            7 HHMEFCRVCKDG-----GELLCCDT-CPSSYHIHCLNPPLPEIP-NGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC-----SSCBCCSS-SCCCBCSSSSSSCCSSCC-SSCCCCTTTTTTC
T ss_pred             CCCCcCCCCCCC-----CCEEEcCC-CCHHHcccccCCCcCcCC-CCccCChhhcCch
Confidence            457889999975     48999995 999999999999999998 7899999998653

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=99.27  E-value=1.5e-12  Score=101.22  Aligned_cols=48  Identities=40%  Similarity=0.920  Sum_probs=43.1

Q ss_pred             cccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCch
Q 006832          240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCEC  291 (629)
Q Consensus       240 ~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~  291 (629)
                      +|.+|+.++.  ++.||+||+ |+++||++||+|||..+| .+.|||+.|..
T Consensus         2 ~C~vC~~~~~--~~~ll~Cd~-C~~~~H~~Cl~p~l~~~P-~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGE--DDKLILCDE-CNKAFHLFCLRPALYEVP-DGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSC--CSCCEECTT-TCCEECHHHHCTTCCSCC-SSCCSCTTTSC
T ss_pred             CCCCCCCCCC--CCCEEECCC-CChhhCcccCCCCcCCCC-CCcEECcCccc
Confidence            6999998763  579999995 999999999999999998 78999999974

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=99.27  E-value=1.3e-12  Score=107.17  Aligned_cols=50  Identities=36%  Similarity=0.828  Sum_probs=44.5

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      .++++|.+|+.++     +||+||+ |+++||++||+|||..+| .+.|||+.|...
T Consensus         6 ~~~~~C~vC~~~g-----~ll~CD~-C~~~fH~~Cl~ppl~~~P-~g~W~C~~C~~~   55 (66)
T 1xwh_A            6 KNEDECAVCRDGG-----ELICCDG-CPRAFHLACLSPPLREIP-SGTWRCSSCLQA   55 (66)
T ss_dssp             SCCCSBSSSSCCS-----SCEECSS-CCCEECTTTSSSCCSSCC-SSCCCCHHHHHT
T ss_pred             CCCCCCccCCCCC-----CEEEcCC-CChhhcccccCCCcCcCC-CCCeECccccCc
Confidence            4678999999763     8999995 999999999999999998 789999999754

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=99.26  E-value=1.7e-12  Score=104.42  Aligned_cols=51  Identities=33%  Similarity=0.898  Sum_probs=45.0

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKM  293 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~  293 (629)
                      .++++|.+|+.+     +.||+||+ |+++||+.||+|||..+| .+.|||+.|....
T Consensus         3 ~~~~~C~vC~~~-----g~ll~Cd~-C~~~fH~~Cl~ppl~~~p-~g~W~C~~C~~~~   53 (60)
T 2puy_A            3 IHEDFCSVCRKS-----GQLLMCDT-CSRVYHLDCLDPPLKTIP-KGMWICPRCQDQM   53 (60)
T ss_dssp             CCCSSCTTTCCC-----SSCEECSS-SSCEECGGGSSSCCSSCC-CSCCCCHHHHHHH
T ss_pred             CCCCCCcCCCCC-----CcEEEcCC-CCcCEECCcCCCCcCCCC-CCceEChhccChh
Confidence            356899999986     38999995 999999999999999998 7899999997654

>2yt5_A Metal-response element-binding transcription factor 2; zinc-regulated factor 1, ZIRF1, metal-response element DNA-binding protein M96; NMR {Mus musculus}

Probab=99.26  E-value=9.2e-13  Score=107.43  Aligned_cols=55  Identities=31%  Similarity=0.788  Sum_probs=46.8

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCC--C-CCCCceecccCchh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDT--E-SRDQGWFCKFCECK  292 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~--~-p~dg~W~C~~C~~k  292 (629)
                      .++.+|.+|+.+....++.||+||+ |+++||++||+||+..  + | .+.|||+.|...
T Consensus         4 ~~~~~C~vC~~~~~~~~~~ll~Cd~-C~~~~H~~C~~p~l~~~~~~p-~~~W~C~~C~~~   61 (66)
T 2yt5_A            4 GSSGVCTICQEEYSEAPNEMVICDK-CGQGYHQLCHTPHIDSSVIDS-DEKWLCRQCVFA   61 (66)
T ss_dssp             CCCCCBSSSCCCCCBTTBCEEECSS-SCCEEETTTSSSCCCHHHHHS-SCCCCCHHHHHT
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCC-CChHHHhhhCCCcccccccCC-CCCEECCCCcCc
Confidence            4578999999875555689999995 9999999999999986  2 5 789999999754

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=99.25  E-value=2.8e-12  Score=103.73  Aligned_cols=52  Identities=35%  Similarity=0.858  Sum_probs=45.4

Q ss_pred             CcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCch
Q 006832          233 SVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCEC  291 (629)
Q Consensus       233 ~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~  291 (629)
                      ....++.+|.+|+.+     +.||+|| .|+++||++||+||+..+| .+.|||+.|..
T Consensus         6 ~~~~~~~~C~vC~~~-----g~ll~CD-~C~~~fH~~Cl~p~l~~~p-~g~W~C~~C~~   57 (61)
T 2l5u_A            6 YETDHQDYCEVCQQG-----GEIILCD-TCPRAYHMVCLDPDMEKAP-EGKWSCPHCEK   57 (61)
T ss_dssp             CSSCCCSSCTTTSCC-----SSEEECS-SSSCEEEHHHHCTTCCSCC-CSSCCCTTGGG
T ss_pred             ccCCCCCCCccCCCC-----CcEEECC-CCChhhhhhccCCCCCCCC-CCceECccccc
Confidence            345567899999975     4899999 5999999999999999988 78999999974

>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.24  E-value=3e-12  Score=106.21  Aligned_cols=45  Identities=22%  Similarity=0.353  Sum_probs=43.9

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006832          505 PNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  549 (629)
Q Consensus       505 ~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~  549 (629)
                      .+|+..|+.+|..|+||+.+++..||..|||+.++|+|||||+|+
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa   58 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKV   58 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhccc
Confidence            578999999999999999999999999999999999999999998

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.23  E-value=6.1e-12  Score=106.46  Aligned_cols=56  Identities=36%  Similarity=0.838  Sum_probs=47.4

Q ss_pred             CCCcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCC-ceecccCch
Q 006832          231 DGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQ-GWFCKFCEC  291 (629)
Q Consensus       231 dg~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg-~W~C~~C~~  291 (629)
                      ..|.+.+. +|.+|+..+  +++.||+||+ |+++||++||+|||..+| .+ .|||+.|..
T Consensus        20 ~~w~C~~c-~C~vC~~~~--~~~~ll~CD~-C~~~yH~~Cl~Ppl~~~P-~g~~W~C~~C~~   76 (77)
T 2e6s_A           20 PEKKCHSC-SCRVCGGKH--EPNMQLLCDE-CNVAYHIYCLNPPLDKVP-EEEYWYCPSCKT   76 (77)
T ss_dssp             SSSCCSSS-SCSSSCCCC--CSTTEEECSS-SCCEEETTSSSSCCSSCC-CSSCCCCTTTCC
T ss_pred             CCeECCCC-CCcCcCCcC--CCCCEEEcCC-CCccccccccCCCccCCC-CCCCcCCcCccC
Confidence            34666665 899999864  3679999995 999999999999999999 67 999999963

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.21  E-value=4.1e-12  Score=100.88  Aligned_cols=49  Identities=35%  Similarity=0.917  Sum_probs=43.5

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCch
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCEC  291 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~  291 (629)
                      .++++|.+|+.++     .||+|| .|+++||+.||+|||..+| .+.|||+.|..
T Consensus         7 ~~~~~C~vC~~~g-----~ll~Cd-~C~~~~H~~Cl~ppl~~~p-~g~W~C~~C~~   55 (56)
T 2yql_A            7 GHEDFCSVCRKSG-----QLLMCD-TCSRVYHLDCLDPPLKTIP-KGMWICPRCQD   55 (56)
T ss_dssp             SSCCSCSSSCCSS-----CCEECS-SSSCEECSSSSSSCCCSCC-CSSCCCHHHHC
T ss_pred             CCCCCCccCCCCC-----eEEEcC-CCCcceECccCCCCcCCCC-CCceEChhhhC
Confidence            4578999999863     899999 5999999999999999998 78999999963

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=99.21  E-value=5.4e-12  Score=103.80  Aligned_cols=49  Identities=27%  Similarity=0.618  Sum_probs=43.0

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCch
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCEC  291 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~  291 (629)
                      .....|.+|+.+     ++||+|| .|+++||++||+|||..+| .+.|||+.|..
T Consensus        10 ~~~~~C~vC~~~-----~~ll~Cd-~C~~~~H~~Cl~P~l~~~P-~g~W~C~~C~~   58 (66)
T 2lri_C           10 APGARCGVCGDG-----TDVLRCT-HCAAAFHWRCHFPAGTSRP-GTGLRCRSCSG   58 (66)
T ss_dssp             CTTCCCTTTSCC-----TTCEECS-SSCCEECHHHHCTTTCCCC-SSSCCCTTTTT
T ss_pred             CCCCCcCCCCCC-----CeEEECC-CCCCceecccCCCccCcCC-CCCEECccccC
Confidence            345679999875     4799999 5999999999999999999 78999999974

>3asl_A E3 ubiquitin-protein ligase UHRF1; histone reader module, epigenetic regulation, LI binding protein complex; 1.41A {Homo sapiens} PDB: 3sou_A 3sow_A* 3sox_A 3zvy_A 2lgg_A 2lgk_A* 2lgl_A 3t6r_A 3zvz_B

Probab=99.21  E-value=6.4e-12  Score=104.41  Aligned_cols=56  Identities=32%  Similarity=0.816  Sum_probs=47.4

Q ss_pred             CCCcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCC-ceecccCch
Q 006832          231 DGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQ-GWFCKFCEC  291 (629)
Q Consensus       231 dg~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg-~W~C~~C~~  291 (629)
                      ..|..... +|.+|+..+.  ++.||+||+ |+++||++||+|||..+| .+ .|||+.|..
T Consensus        12 ~~w~C~~C-~C~~C~~~~~--~~~ll~CD~-C~~~yH~~Cl~Ppl~~~P-~g~~W~C~~C~~   68 (70)
T 3asl_A           12 VNRLCRVC-ACHLCGGRQD--PDKQLMCDE-CDMAFHIYCLDPPLSSVP-SEDEWYCPECRN   68 (70)
T ss_dssp             TTSCCTTT-SBTTTCCCSC--GGGEEECTT-TCCEEEGGGSSSCCSSCC-SSSCCCCTTTSC
T ss_pred             CCeECCCC-CCcCCCCcCC--CCCEEEcCC-CCCceecccCCCCcCCCC-CCCCcCCcCccC
Confidence            34666666 8889997643  679999995 999999999999999999 67 999999974

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=99.20  E-value=3.5e-12  Score=106.35  Aligned_cols=54  Identities=33%  Similarity=0.755  Sum_probs=46.2

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKM  293 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~  293 (629)
                      .++.+|.+|+.++...++.||+||+ |+++||++||+||+  +| .+.|||+.|....
T Consensus        14 ~~~~~C~vC~~~~s~~~~~ll~CD~-C~~~~H~~Cl~~~~--vP-~g~W~C~~C~~~~   67 (71)
T 2ku3_A           14 DEDAVCSICMDGESQNSNVILFCDM-CNLAVHQECYGVPY--IP-EGQWLCRHCLQSR   67 (71)
T ss_dssp             CSSCSCSSSCCCCCCSSSCEEECSS-SCCEEEHHHHTCSS--CC-SSCCCCHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCC-CCCccccccCCCCc--CC-CCCcCCccCcCcC
Confidence            4578999999887556789999995 99999999999985  56 6899999998653

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=99.18  E-value=3.8e-12  Score=110.20  Aligned_cols=55  Identities=33%  Similarity=0.728  Sum_probs=46.7

Q ss_pred             ccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhh
Q 006832          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKM  293 (629)
Q Consensus       235 ~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~  293 (629)
                      ..++.+|.+|+.++...++.||+||+ |+.+||++||+||+  +| .+.|||+.|....
T Consensus        22 ~~~~~~C~vC~~~~s~~~~~ll~CD~-C~~~fH~~Cl~p~~--vP-~g~W~C~~C~~~~   76 (88)
T 2l43_A           22 IDEDAVCSICMDGESQNSNVILFCDM-CNLAVHQECYGVPY--IP-EGQWLCRHCLQSR   76 (88)
T ss_dssp             CCCCCCCSSCCSSSSCSEEEEEECSS-SCCCCCHHHHTCSS--CC-SSCCCCHHHHHHT
T ss_pred             CCCCCcCCcCCCCCCCCCCCEEECCC-CCchhhcccCCCCc--cC-CCceECccccCcc
Confidence            34678999999887556789999995 99999999999996  56 6899999998653

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens}

Probab=99.13  E-value=2.2e-11  Score=103.08  Aligned_cols=56  Identities=32%  Similarity=0.821  Sum_probs=47.2

Q ss_pred             CCCcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCc-eecccCch
Q 006832          231 DGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQG-WFCKFCEC  291 (629)
Q Consensus       231 dg~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~-W~C~~C~~  291 (629)
                      ..|.+... .|.+|+..+.  ++.||+||+ |+++||++||+|||..+| .+. |||+.|..
T Consensus        20 ~~W~C~~C-~C~vC~~~~d--~~~ll~CD~-C~~~yH~~Cl~PpL~~~P-~g~~W~C~~C~~   76 (77)
T 3shb_A           20 VNRLCRVC-ACHLCGGRQD--PDKQLMCDE-CDMAFHIYCLDPPLSSVP-SEDEWYCPECRN   76 (77)
T ss_dssp             TTSCCTTT-SBTTTCCCSC--GGGEEECTT-TCCEEETTTSSSCCSSCC-SSSCCCCTTTC-
T ss_pred             CCCCCCCC-cCCccCCCCC--CcceeEeCC-CCCccCcccCCCcccCCC-CCCceECcCccc
Confidence            34667777 7899988753  679999995 999999999999999999 677 99999974

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A

Probab=99.13  E-value=2.2e-11  Score=117.65  Aligned_cols=50  Identities=28%  Similarity=0.719  Sum_probs=44.4

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      .++++|.+|+.+|     +||+||+ |+++||+.||.||+...| .+.|+|+.|...
T Consensus         2 ~~~~~C~~C~~~g-----~ll~Cd~-C~~~~H~~C~~p~l~~~p-~~~W~C~~C~~~   51 (184)
T 3o36_A            2 PNEDWCAVCQNGG-----ELLCCEK-CPKVFHLSCHVPTLTNFP-SGEWICTFCRDL   51 (184)
T ss_dssp             CSCSSCTTTCCCS-----SCEECSS-SSCEECTTTSSSCCSSCC-SSCCCCTTTSCS
T ss_pred             CCCCccccCCCCC-----eeeecCC-CCcccCccccCCCCCCCC-CCCEECccccCc
Confidence            3578999999764     7999995 999999999999999998 789999999854

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A*

Probab=99.11  E-value=2.2e-11  Score=119.87  Aligned_cols=50  Identities=30%  Similarity=0.718  Sum_probs=44.8

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      .++++|.+|+.+|     +||+||+ |+++||+.||+||+..+| .|.|+|+.|...
T Consensus         5 ~~~~~C~~C~~~g-----~ll~Cd~-C~~~~H~~Cl~p~l~~~p-~~~W~C~~C~~~   54 (207)
T 3u5n_A            5 PNEDWCAVCQNGG-----DLLCCEK-CPKVFHLTCHVPTLLSFP-SGDWICTFCRDI   54 (207)
T ss_dssp             SSCSSBTTTCCCE-----EEEECSS-SSCEECTTTSSSCCSSCC-SSCCCCTTTSCS
T ss_pred             CCCCCCCCCCCCC-----ceEEcCC-CCCccCCccCCCCCCCCC-CCCEEeCceeCc
Confidence            4578999999775     7999995 999999999999999999 789999999854

>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding cooperativity, maltose binding protein, MBP, sugar binding, DNA binding protein; 2.10A {Escherichia coli} SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A

Probab=99.10  E-value=2.2e-11  Score=127.82  Aligned_cols=54  Identities=28%  Similarity=0.413  Sum_probs=50.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006832          497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  550 (629)
Q Consensus       497 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k  550 (629)
                      ++.+..|+..|+..|++.|..++||+..+|++||++|||+++||+|||||||+|
T Consensus       366 ~~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~  419 (421)
T 1mh3_A          366 TAAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR  419 (421)
T ss_dssp             HHHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCC
T ss_pred             hhhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccc
Confidence            445567899999999999999999999999999999999999999999999984

>3ask_A E3 ubiquitin-protein ligase UHRF1; histone reader modules, epigenetic regulation, trimethylaion of lysine residue, ligase-DNA binding protein; HET: M3L; 2.90A {Homo sapiens}

Probab=99.09  E-value=4.2e-11  Score=119.75  Aligned_cols=55  Identities=33%  Similarity=0.848  Sum_probs=43.0

Q ss_pred             CCcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCC-ceecccCch
Q 006832          232 GSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQ-GWFCKFCEC  291 (629)
Q Consensus       232 g~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg-~W~C~~C~~  291 (629)
                      .|.+..+ +|.+|+..+.  ++.||+||+ |+++||++||+|||..+| .| .|||+.|..
T Consensus       169 ~w~C~~c-~C~vC~~~~~--~~~lL~CD~-C~~~yH~~CL~PPL~~vP-~G~~W~Cp~C~~  224 (226)
T 3ask_A          169 NRLCRVC-ACHLCGGRQD--PDKQLMCDE-CDMAFHIYCLDPPLSSVP-SEDEWYCPECRN  224 (226)
T ss_dssp             TSCCTTT-SCSSSCCCCC----CCEECSS-SCCEECSCC--CCCCSCC-SSSCCCCGGGC-
T ss_pred             CEecCCC-CCcCCCCCCC--CCCeEEcCC-CCcceeCccCCCCcccCC-CCCCCCCcCCcC
Confidence            3555555 8999998753  679999995 999999999999999999 67 999999974

>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A*

Probab=99.08  E-value=4.2e-11  Score=107.95  Aligned_cols=61  Identities=28%  Similarity=0.691  Sum_probs=52.5

Q ss_pred             cCCCCcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhh
Q 006832          229 ATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKM  293 (629)
Q Consensus       229 ~~dg~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~  293 (629)
                      ....|.+.+..+|.+|+..+.  ++.||+||+ |+++||++||+|||..+| .+.|||+.|....
T Consensus        49 ~~~~W~C~~C~~C~~C~~~~~--~~~ll~Cd~-C~~~yH~~Cl~ppl~~~P-~g~W~C~~C~~~~  109 (114)
T 2kwj_A           49 KTYKWQCIECKSCILCGTSEN--DDQLLFCDD-CDRGYHMYCLNPPVAEPP-EGSWSCHLCWELL  109 (114)
T ss_dssp             HHTTCCCGGGCCCTTTTCCTT--TTTEEECSS-SCCEEETTTSSSCCSSCC-SSCCCCHHHHHHH
T ss_pred             CCCccCccccCccCcccccCC--CCceEEcCC-CCccccccccCCCccCCC-CCCeECccccchh
Confidence            455688888889999998753  679999995 999999999999999999 7899999997543

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=99.07  E-value=7.1e-11  Score=106.06  Aligned_cols=60  Identities=27%  Similarity=0.712  Sum_probs=52.1

Q ss_pred             cCCCCcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCch
Q 006832          229 ATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCEC  291 (629)
Q Consensus       229 ~~dg~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~  291 (629)
                      ....|.+.+..+|.+|+..+. +++.||+|| .|+++||++||+|||..+| .+.|||+.|..
T Consensus        52 ~~~~W~C~~C~~C~vC~~~~~-~~~~ll~Cd-~C~~~yH~~Cl~p~l~~~P-~~~W~C~~C~~  111 (112)
T 3v43_A           52 KALRWQCIECKTCSSCRDQGK-NADNMLFCD-SCDRGFHMECCDPPLTRMP-KGMWICQICRP  111 (112)
T ss_dssp             HTSCCCCTTTCCBTTTCCCCC-TTCCCEECT-TTCCEECGGGCSSCCSSCC-SSCCCCTTTSC
T ss_pred             hccccccccCCccccccCcCC-CccceEEcC-CCCCeeecccCCCCCCCCC-CCCeECCCCCC
Confidence            456788888999999998642 357899999 5999999999999999999 78999999975

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens}

Probab=99.02  E-value=9.1e-11  Score=114.42  Aligned_cols=48  Identities=31%  Similarity=0.861  Sum_probs=43.2

Q ss_pred             cccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832          238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       238 ~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      +++|.+|+.++     +||+||+ |+++||++||.||+...| .|.|+|+.|...
T Consensus         2 ~~~C~~C~~~g-----~ll~Cd~-C~~~~H~~Cl~p~l~~~p-~g~W~C~~C~~~   49 (189)
T 2ro1_A            2 ATICRVCQKPG-----DLVMCNQ-CEFCFHLDCHLPALQDVP-GEEWSCSLCHVL   49 (189)
T ss_dssp             CCCBTTTCCCS-----SCCCCTT-TCCBCCSTTSTTCCSSCC-CTTCCTTTTSCS
T ss_pred             CCcCccCCCCC-----ceeECCC-CCchhccccCCCCcccCC-CCCCCCcCccCC
Confidence            46899999764     7999995 999999999999999998 799999999854

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=99.01  E-value=1.4e-10  Score=96.79  Aligned_cols=55  Identities=24%  Similarity=0.655  Sum_probs=46.3

Q ss_pred             ccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhh
Q 006832          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKM  293 (629)
Q Consensus       235 ~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~  293 (629)
                      ..+..+|.+|+..+.  +..||+||+ |+.+||+.|+++++...+ .+.|||+.|..+.
T Consensus        15 ~~~~~~C~~C~~~~~--~~~mi~CD~-C~~wfH~~Cv~~~~~~~~-~~~w~C~~C~~~~   69 (75)
T 2k16_A           15 GNQIWICPGCNKPDD--GSPMIGCDD-CDDWYHWPCVGIMAAPPE-EMQWFCPKCANKI   69 (75)
T ss_dssp             SCEEECBTTTTBCCS--SCCEEECSS-SSSEEEHHHHTCSSCCCS-SSCCCCTTTHHHH
T ss_pred             CCCCcCCCCCCCCCC--CCCEEEcCC-CCcccccccCCCCccCCC-CCCEEChhccCch
Confidence            345688999998753  457999995 999999999999998877 6899999997653

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=98.95  E-value=3.6e-10  Score=100.87  Aligned_cols=60  Identities=32%  Similarity=0.774  Sum_probs=52.1

Q ss_pred             cCCCCcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832          229 ATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       229 ~~dg~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      ....|...+..+|.+|+..+.  ++.||+|| .|+++||++||+|||..+| .+.|||+.|...
T Consensus        45 ~~~~W~C~~C~~C~~C~~~~~--~~~ll~Cd-~C~~~yH~~Cl~ppl~~~P-~g~W~C~~C~~c  104 (111)
T 2ysm_A           45 KRAGWQCPECKVCQNCKQSGE--DSKMLVCD-TCDKGYHTFCLQPVMKSVP-TNGWKCKNCRIC  104 (111)
T ss_dssp             TSTTCCCTTTCCCTTTCCCSC--CTTEEECS-SSCCEEEGGGSSSCCSSCC-SSCCCCHHHHCC
T ss_pred             cccCccCCcCCcccccCccCC--CCCeeECC-CCCcHHhHHhcCCccccCC-CCCcCCcCCcCc
Confidence            346788888889999998764  56899999 5999999999999999999 789999999754

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=98.83  E-value=2.3e-09  Score=94.39  Aligned_cols=55  Identities=22%  Similarity=0.572  Sum_probs=44.0

Q ss_pred             CCcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832          232 GSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       232 g~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      |....+.+.| +|+..+.  ++.||+|| .|+.+||+.|++|++..+|  ..|||+.|..+
T Consensus        22 g~~~~d~vrC-iC~~~~~--~~~mi~Cd-~C~~w~H~~C~~~~~~~~p--~~w~C~~C~~~   76 (98)
T 2lv9_A           22 GSYGTDVTRC-ICGFTHD--DGYMICCD-KCSVWQHIDCMGIDRQHIP--DTYLCERCQPR   76 (98)
T ss_dssp             CCCCCCBCCC-TTSCCSC--SSCEEEBT-TTCBEEETTTTTCCTTSCC--SSBCCTTTSSS
T ss_pred             CCCCCCCEEe-ECCCccC--CCcEEEcC-CCCCcCcCcCCCCCccCCC--CCEECCCCcCC
Confidence            3334445668 7887653  67999999 5999999999999998887  48999999754

>4gne_A Histone-lysine N-methyltransferase NSD3; zinc finger, transcription, nuclear protein, transf nuclear protein complex; 1.47A {Homo sapiens} PDB: 4gnd_A 4gnf_A 4gng_A*

Probab=98.69  E-value=6.7e-09  Score=93.01  Aligned_cols=49  Identities=29%  Similarity=0.763  Sum_probs=42.3

Q ss_pred             ccccccccccccCcCCCCCCceEeC--CcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832          235 HHEHIICAKCKLREAFPDNDIVLCD--GTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       235 ~~e~~~C~vC~~~g~~~~~~lLlCD--G~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      ..++++|.+|+.+     ++||+||  + |+++||+.||+  |..+| .|.|||+.|.+.
T Consensus        12 ~~~~~~C~~C~~~-----G~ll~CD~~~-Cp~~fH~~Cl~--L~~~P-~g~W~Cp~c~C~   62 (107)
T 4gne_A           12 QMHEDYCFQCGDG-----GELVMCDKKD-CPKAYHLLCLN--LTQPP-YGKWECPWHQCD   62 (107)
T ss_dssp             CSSCSSCTTTCCC-----SEEEECCSTT-CCCEECTGGGT--CSSCC-SSCCCCGGGBCT
T ss_pred             CCCCCCCCcCCCC-----CcEeEECCCC-CCcccccccCc--CCcCC-CCCEECCCCCCC
Confidence            4567899999965     4899999  6 99999999999  78888 799999999754

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=98.60  E-value=2.9e-08  Score=88.51  Aligned_cols=56  Identities=27%  Similarity=0.552  Sum_probs=46.5

Q ss_pred             cccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhh
Q 006832          234 VHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKM  293 (629)
Q Consensus       234 ~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~  293 (629)
                      ...++++|.+|+.++.  .++||+|+ .|+++||+.||+|++..++ .+.|+|+.|....
T Consensus         3 ~~~~~~~C~~C~~~g~--~~~ll~C~-~C~~~~H~~Cl~~~~~~~~-~~~W~C~~C~~C~   58 (111)
T 2ysm_A            3 SGSSGANCAVCDSPGD--LLDQFFCT-TCGQHYHGMCLDIAVTPLK-RAGWQCPECKVCQ   58 (111)
T ss_dssp             CCCCCSCBTTTCCCCC--TTTSEECS-SSCCEECTTTTTCCCCTTT-STTCCCTTTCCCT
T ss_pred             CCCCCCCCcCCCCCCC--CcCCeECC-CCCCCcChHHhCCcccccc-ccCccCCcCCccc
Confidence            3457789999999873  35789999 5999999999999988776 6899999997443

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=98.59  E-value=5.8e-09  Score=97.71  Aligned_cols=52  Identities=25%  Similarity=0.676  Sum_probs=44.1

Q ss_pred             ccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCC-------CCCCCceecccCchhh
Q 006832          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDT-------ESRDQGWFCKFCECKM  293 (629)
Q Consensus       235 ~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~-------~p~dg~W~C~~C~~k~  293 (629)
                      +..+++|.+|+.+|     +||+|| .|+++||+.||.||+..       .| .+.|+|+.|...+
T Consensus        60 Dg~~d~C~vC~~GG-----~LlcCD-~Cpr~Fh~~Cl~p~l~~~~l~~i~~p-~~~W~C~~C~~~p  118 (142)
T 2lbm_A           60 DGMDEQCRWCAEGG-----NLICCD-FCHNAFCKKCILRNLGRKELSTIMDE-NNQWYCYICHPEP  118 (142)
T ss_dssp             TSCBCSCSSSCCCS-----SEEECS-SSCCEEEHHHHHHHTCHHHHHHHHTS-TTCCCCTTTCCCT
T ss_pred             CCCCCeecccCCCC-----cEEeCC-CCCCeeeHhhcCCCCChhhhhhcccC-CCCCEeecccCcc
Confidence            34578999999875     799999 69999999999999973       34 6899999998754

>1weu_A Inhibitor of growth family, member 4; structural genomics, PHD domain, ING1-like protein, DNA binding protein, NPPSFA; NMR {Mus musculus} SCOP: g.50.1.2

Probab=98.51  E-value=8.9e-08  Score=83.44  Aligned_cols=49  Identities=31%  Similarity=0.769  Sum_probs=39.5

Q ss_pred             cccccccccccCcCCCCCCceEeCCc--CC-cccccccCCCCCCCCCCCCceecccCchh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGT--CN-CAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~--C~-rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      .+..+| +|+...   .+.||+|| .  |+ .|||+.|++  |...| .+.|||+.|...
T Consensus        34 ~e~~yC-iC~~~~---~g~MI~CD-~~dC~~~WfH~~CVg--l~~~p-~g~W~Cp~C~~~   85 (91)
T 1weu_A           34 NEPTYC-LCHQVS---YGEMIGCD-NPDCSIEWFHFACVG--LTTKP-RGKWFCPRCSQE   85 (91)
T ss_dssp             CCCBCS-TTCCBC---CSCCCCCS-CSSCSCCCCCSTTTT--CSSCC-CSSCCCTTTCCC
T ss_pred             CCCcEE-ECCCCC---CCCEeEec-CCCCCCCCEecccCC--cCcCC-CCCEECcCccCc
Confidence            456788 999865   36899999 6  66 799999999  55666 589999999754

>2vnf_A ING 4, P29ING4, inhibitor of growth protein 4; acetylation, alternative splicing, anti-oncogene, cell cycle, coiled C nucleus, zinc, zinc-finger, ING4; HET: M3L; 1.76A {Homo sapiens} SCOP: g.50.1.2 PDB: 2k1j_A 2jmq_A 2qic_A*

Probab=98.49  E-value=2.7e-08  Score=80.16  Aligned_cols=48  Identities=31%  Similarity=0.776  Sum_probs=38.4

Q ss_pred             ccccccccccCcCCCCCCceEeCCc--CC-cccccccCCCCCCCCCCCCceecccCchh
Q 006832          237 EHIICAKCKLREAFPDNDIVLCDGT--CN-CAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       237 e~~~C~vC~~~g~~~~~~lLlCDG~--C~-rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      +..+| +|+...   .+.||+|| .  |+ .+||+.|++  |...| .+.|||+.|..+
T Consensus         9 e~~~C-~C~~~~---~g~mi~CD-~cdC~~~wfH~~Cvg--l~~~p-~g~w~C~~C~~~   59 (60)
T 2vnf_A            9 EPTYC-LCHQVS---YGEMIGCD-NPDCSIEWFHFACVG--LTTKP-RGKWFCPRCSQE   59 (60)
T ss_dssp             CCEET-TTTEEC---CSEEEECS-CTTCSSCEEETGGGT--CSSCC-SSCCCCHHHHC-
T ss_pred             CCCEE-ECCCcC---CCCEEEeC-CCCCCCceEehhcCC--CCcCC-CCCEECcCccCc
Confidence            45788 899865   36899999 6  55 799999999  66677 689999999754

>1wen_A Inhibitor of growth family, member 4; ING1-like protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.50.1.2 PDB: 1wes_A

Probab=98.47  E-value=6.6e-08  Score=80.48  Aligned_cols=49  Identities=31%  Similarity=0.769  Sum_probs=39.7

Q ss_pred             cccccccccccCcCCCCCCceEeCCc--CC-cccccccCCCCCCCCCCCCceecccCchh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGT--CN-CAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~--C~-rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      .+..+| +|+...   .+.||+|| .  |+ .+||+.|++  |...| .+.|||+.|...
T Consensus        14 ~~~~~C-~C~~~~---~g~MI~CD-~~~C~~~wfH~~Cvg--l~~~p-~g~w~Cp~C~~~   65 (71)
T 1wen_A           14 NEPTYC-LCHQVS---YGEMIGCD-NPDCSIEWFHFACVG--LTTKP-RGKWFCPRCSQE   65 (71)
T ss_dssp             TSCCCS-TTCCCS---CSSEECCS-CSSCSCCCEETTTTT--CSSCC-SSCCCCTTTSSC
T ss_pred             CCCCEE-ECCCCC---CCCEeEee-CCCCCCccEecccCC--cCcCC-CCCEECCCCCcc
Confidence            356789 799864   36899999 7  77 699999999  66666 689999999754

>3c6w_A P28ING5, inhibitor of growth protein 5; chromatin, PHD, ING, epigenetics, alternative splicing, metal-binding, phosphoprotein, zinc; HET: M3L; 1.75A {Homo sapiens} PDB: 2pnx_A*

Probab=98.45  E-value=3.8e-08  Score=79.10  Aligned_cols=48  Identities=33%  Similarity=0.787  Sum_probs=38.9

Q ss_pred             ccccccccccCcCCCCCCceEeCCc--CC-cccccccCCCCCCCCCCCCceecccCchh
Q 006832          237 EHIICAKCKLREAFPDNDIVLCDGT--CN-CAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       237 e~~~C~vC~~~g~~~~~~lLlCDG~--C~-rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      +..+| +|+...   .+.||.|| .  |+ .+||+.|++  |...| .+.|||+.|..+
T Consensus         8 e~~yC-~C~~~~---~g~mi~CD-~~~C~~~wfH~~Cvg--l~~~p-~~~w~Cp~C~~~   58 (59)
T 3c6w_A            8 EPTYC-LCHQVS---YGEMIGCD-NPDCPIEWFHFACVD--LTTKP-KGKWFCPRCVQE   58 (59)
T ss_dssp             CCEET-TTTEEC---CSEEEECS-CTTCSSCEEETGGGT--CSSCC-SSCCCCHHHHCC
T ss_pred             CCcEE-ECCCCC---CCCeeEee-CCCCCCCCEecccCC--cccCC-CCCEECcCccCc
Confidence            45788 899864   36899999 7  76 699999999  66666 689999999653

>2jmi_A Protein YNG1, ING1 homolog 1; PHD, histone, recognition, yeast, protein binding; NMR {Saccharomyces cerevisiae} PDB: 2jmj_A*

Probab=98.42  E-value=8e-08  Score=83.58  Aligned_cols=47  Identities=28%  Similarity=0.714  Sum_probs=38.0

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCC---cccccccCCCCCCCCCCCCceeccc-Cc
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCN---CAFHQKCLDPPLDTESRDQGWFCKF-CE  290 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~---rafH~~CL~PPL~~~p~dg~W~C~~-C~  290 (629)
                      .+..+| +|+...   .+.||+|| .|+   .|||+.|++  |...| .+.|||+. |.
T Consensus        24 ~~~~yC-iC~~~~---~g~MI~CD-~c~C~~eWfH~~CVg--l~~~p-~~~W~Cp~cC~   74 (90)
T 2jmi_A           24 QEEVYC-FCRNVS---YGPMVACD-NPACPFEWFHYGCVG--LKQAP-KGKWYCSKDCK   74 (90)
T ss_dssp             CCSCCS-TTTCCC---SSSEECCC-SSSCSCSCEETTTSS--CSSCT-TSCCCSSHHHH
T ss_pred             CCCcEE-EeCCCC---CCCEEEec-CCCCccccCcCccCC--CCcCC-CCCccCChhhc
Confidence            456789 899864   35799999 577   899999999  55666 68999999 86

>2g6q_A Inhibitor of growth protein 2; protein-peptide complex, gene regulation, apoptosis; HET: M3L; 2.00A {Mus musculus}

Probab=98.35  E-value=9.3e-08  Score=77.61  Aligned_cols=48  Identities=27%  Similarity=0.732  Sum_probs=38.0

Q ss_pred             ccccccccccCcCCCCCCceEeCCc--CC-cccccccCCCCCCCCCCCCceecccCchh
Q 006832          237 EHIICAKCKLREAFPDNDIVLCDGT--CN-CAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       237 e~~~C~vC~~~g~~~~~~lLlCDG~--C~-rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      +..+| +|+...   .+.||.|| .  |+ .+||+.|++  |...| .+.|||+.|...
T Consensus        10 e~~yC-~C~~~~---~g~MI~CD-~c~C~~~WfH~~Cvg--l~~~p-~~~w~Cp~C~~~   60 (62)
T 2g6q_A           10 EPTYC-LCNQVS---YGEMIGCD-NEQCPIEWFHFSCVS--LTYKP-KGKWYCPKCRGD   60 (62)
T ss_dssp             CCEET-TTTEEC---CSEEEECS-CTTCSSCEEETGGGT--CSSCC-SSCCCCHHHHTC
T ss_pred             CCcEE-ECCCCC---CCCeeeee-CCCCCcccEecccCC--cCcCC-CCCEECcCcccC
Confidence            45788 899864   35899999 6  44 999999999  45556 689999999753

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=98.28  E-value=2.2e-07  Score=75.06  Aligned_cols=56  Identities=25%  Similarity=0.457  Sum_probs=43.0

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKM  293 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~  293 (629)
                      .+..+|.+|+.... +++.||.|| .|..|||..|++...........|+|+.|..+.
T Consensus         4 ~e~~~C~~C~~~~~-~~~~mI~Cd-~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k~   59 (64)
T 1we9_A            4 GSSGQCGACGESYA-ADEFWICCD-LCEMWFHGKCVKITPARAEHIKQYKCPSCSNKS   59 (64)
T ss_dssp             SSCCCCSSSCCCCC-SSSCEEECS-SSCCEEETTTTTCCTTGGGGCSSCCCHHHHTTT
T ss_pred             CCCCCCCCCCCccC-CCCCEEEcc-CCCCCCCccccCcChhHhcCCCcEECCCCcCcC
Confidence            45678999998752 346899999 599999999999765543212689999998653

>3ql9_A Transcriptional regulator ATRX; zinc finger, transcription, lysine trimethylation, protein, histone-binding protein, transcription-structural complex; HET: M3L; 0.93A {Homo sapiens} PDB: 3qla_A* 3qlc_A 3qln_A 2jm1_A

Probab=98.21  E-value=8.5e-08  Score=88.48  Aligned_cols=53  Identities=26%  Similarity=0.629  Sum_probs=43.5

Q ss_pred             ccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCC-----CC--CCCCceecccCchhhH
Q 006832          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLD-----TE--SRDQGWFCKFCECKME  294 (629)
Q Consensus       235 ~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~-----~~--p~dg~W~C~~C~~k~~  294 (629)
                      +..+.+|.+|+.++     +||+|| .|+++||..|+.|++.     .+  | .+.|+|..|..++.
T Consensus        54 Dg~~~~C~vC~dGG-----~LlcCd-~Cpr~Fc~~Cl~~~lg~~~l~~i~~~-~~~W~C~~C~~~pl  113 (129)
T 3ql9_A           54 DGMDEQCRWCAEGG-----NLICCD-FCHNAFCKKCILRNLGRRELSTIMDE-NNQWYCYICHPEPL  113 (129)
T ss_dssp             TSCBSSCTTTCCCS-----EEEECS-SSSCEEEHHHHHHHTCHHHHHHHTCT-TSCCCCTTTCCGGG
T ss_pred             CCCCCcCeecCCCC-----eeEecC-CCchhhhHHHhCCCcchhHHHHhccC-CCCeEcCCcCCHHH
Confidence            34567899999875     899999 5999999999999864     22  4 68999999987653

>3o70_A PHD finger protein 13; PHF13, structural genomics consortium, SGC, structural genom type zinc finger, protein binding, zinc ION binding; 1.85A {Homo sapiens}

Probab=98.15  E-value=9.4e-07  Score=72.91  Aligned_cols=52  Identities=17%  Similarity=0.443  Sum_probs=41.8

Q ss_pred             cccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCch
Q 006832          234 VHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCEC  291 (629)
Q Consensus       234 ~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~  291 (629)
                      ...+..+| +|+....  ++.||.|| .|..|||..|++......|  ..|+|+.|..
T Consensus        15 ~~~~~~~C-iC~~~~~--~~~MIqCd-~C~~WfH~~Cvgi~~~~~~--~~~~C~~C~~   66 (68)
T 3o70_A           15 YFQGLVTC-FCMKPFA--GRPMIECN-ECHTWIHLSCAKIRKSNVP--EVFVCQKCRD   66 (68)
T ss_dssp             TTTTCCCS-TTCCCCT--TCCEEECT-TTCCEEETTTTTCCTTSCC--SSCCCHHHHT
T ss_pred             CCCCceEe-ECCCcCC--CCCEEECC-CCCccccccccCcCcccCC--CcEECCCCCC
Confidence            34456789 9998753  56799999 5999999999998776555  6899999963

>1x4i_A Inhibitor of growth protein 3; structural genomics, PHD domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.13  E-value=8.2e-07  Score=73.70  Aligned_cols=51  Identities=24%  Similarity=0.584  Sum_probs=39.3

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCC---cccccccCCCCCCCCCCCCceecccCchhhH
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCN---CAFHQKCLDPPLDTESRDQGWFCKFCECKME  294 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~---rafH~~CL~PPL~~~p~dg~W~C~~C~~k~~  294 (629)
                      .+..+|. |+...   .+.||.||+ |+   .+||+.|++.  ...| .+.|||+.|.....
T Consensus         4 ~~~~yC~-C~~~~---~g~MI~CD~-cdC~~~WfH~~Cvgl--~~~p-~~~w~Cp~C~~~~~   57 (70)
T 1x4i_A            4 GSSGYCI-CNQVS---YGEMVGCDN-QDCPIEWFHYGCVGL--TEAP-KGKWYCPQCTAAMK   57 (70)
T ss_dssp             SCCCCST-TSCCC---CSSEECCSC-TTCSCCCEEHHHHTC--SSCC-SSCCCCHHHHHHHH
T ss_pred             CCCeEEE-cCCCC---CCCEeEeCC-CCCCccCCccccccc--CcCC-CCCEECCCCCcccc
Confidence            3457885 88764   459999994 75   8999999994  4455 68999999987654

>1wee_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=98.08  E-value=1.9e-06  Score=71.37  Aligned_cols=53  Identities=19%  Similarity=0.498  Sum_probs=39.8

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      ....+| +|+.... ++..||.|| .|..|||..|++....... ...|+|+.|..+
T Consensus        14 ~~~~~C-~C~~~~~-~g~~mI~Cd-~C~~W~H~~Cvg~~~~~~~-~~~~~C~~C~~~   66 (72)
T 1wee_A           14 NWKVDC-KCGTKDD-DGERMLACD-GCGVWHHTRCIGINNADAL-PSKFLCFRCIEL   66 (72)
T ss_dssp             SSEECC-TTCCCSC-CSSCEEECS-SSCEEEETTTTTCCTTSCC-CSCCCCHHHHHH
T ss_pred             CcceEe-eCCCccC-CCCcEEECC-CCCCccCCeeeccCccccC-CCcEECCCccCC
Confidence            445789 6998742 234699999 5999999999997754322 378999999754

>2ri7_A Nucleosome-remodeling factor subunit BPTF; zinc finger, alpha-helical bundle, dimethyl-lysine, bromodom chromatin regulator, metal-binding, nucleus; HET: MLY; 1.45A {Homo sapiens} PDB: 2fsa_A* 2f6n_A 2f6j_A* 3qzv_A* 3uv2_A* 3qzt_A* 3qzs_A* 2fui_A 2fuu_A*

Probab=98.03  E-value=4.3e-07  Score=86.58  Aligned_cols=55  Identities=20%  Similarity=0.507  Sum_probs=41.0

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKM  293 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~  293 (629)
                      .+..+| +|+.++. .++.||+|| .|+.|||..|++.+.......+.|+|+.|....
T Consensus         6 ~~~~~C-~C~~~~~-~~~~mi~Cd-~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~~~   60 (174)
T 2ri7_A            6 DTKLYC-ICKTPED-ESKFYIGCD-RCQNWYHGRCVGILQSEAELIDEYVCPQCQSTE   60 (174)
T ss_dssp             -CCEET-TTTEECC-TTSCEEECT-TTCCEEEHHHHTCCHHHHTTCSSCCCHHHHHHH
T ss_pred             CCCcEe-eCCCCCC-CCCCEeECC-CCCchhChhhcCCchhhccCccCeecCCCcchh
Confidence            356789 9998752 356799999 599999999998654322113789999998754

>2nzz_A Penetratin conjugated GAS (374-394) peptide; conformational analysis, G protein, GAS subunit, A2A adenosine receptor, cell-penetrating peptides; NMR {Synthetic} PDB: 2o00_A

Probab=98.03  E-value=7.8e-07  Score=65.29  Aligned_cols=20  Identities=25%  Similarity=0.358  Sum_probs=15.8

Q ss_pred             chhhhccchhccHHHHhhhh
Q 006832          538 EKVNKWFKNARYLALKARKV  557 (629)
Q Consensus       538 ~QVkiWFQNrR~k~~K~~~~  557 (629)
                      +||+|||||||++.+|....
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~   20 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFN   20 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHH
T ss_pred             CCceeccHHHHHHHHHHhHH
Confidence            59999999999966655543

>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A*

Probab=97.91  E-value=1.5e-06  Score=78.07  Aligned_cols=53  Identities=23%  Similarity=0.488  Sum_probs=40.3

Q ss_pred             ccccccccCcC-----CCCCCceEeCCcCCcccccccCCCCCC---CCCCCCceecccCchhh
Q 006832          239 IICAKCKLREA-----FPDNDIVLCDGTCNCAFHQKCLDPPLD---TESRDQGWFCKFCECKM  293 (629)
Q Consensus       239 ~~C~vC~~~g~-----~~~~~lLlCDG~C~rafH~~CL~PPL~---~~p~dg~W~C~~C~~k~  293 (629)
                      .+|.+|..++.     ...+.||+|++ |++.||+.||.+++.   .++ .+.|+|+.|....
T Consensus         2 ~~C~~C~~~~~~n~k~g~~~~Li~C~~-C~~~~H~~Cl~~~~~~~~~~~-~~~W~C~~C~~C~   62 (114)
T 2kwj_A            2 SYCDFCLGGSNMNKKSGRPEELVSCAD-CGRSGHPTCLQFTLNMTEAVK-TYKWQCIECKSCI   62 (114)
T ss_dssp             CCCSSSCCBTTBCTTTCCCCCCEECSS-SCCEECTTTTTCCHHHHHHHH-HTTCCCGGGCCCT
T ss_pred             CcCccCCCCccccccCCCCCCCeEeCC-CCCccchhhCCChhhhhhccC-CCccCccccCccC
Confidence            57899987642     23579999995 999999999998753   233 5789999996443

>2rsd_A E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant homeodomain (PHD), histone binding; NMR {Oryza sativa japonica group}

Probab=97.91  E-value=6.2e-06  Score=67.71  Aligned_cols=54  Identities=17%  Similarity=0.561  Sum_probs=38.3

Q ss_pred             cccccccccccCcCCCCCCceEeCC-cCCcccccccCCCCCCCCC---CCCceecccCchh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDG-TCNCAFHQKCLDPPLDTES---RDQGWFCKFCECK  292 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG-~C~rafH~~CL~PPL~~~p---~dg~W~C~~C~~k  292 (629)
                      .+..+| +|+....  ++.||.||+ .|..|||..|++.+.....   ....|||+.|...
T Consensus         8 e~~v~C-~C~~~~~--~g~mI~CD~~~C~~W~H~~Cvgi~~~~~~~~~~p~~~~C~~Cr~~   65 (68)
T 2rsd_A            8 EAKVRC-ICSSTMV--NDSMIQCEDQRCQVWQHLNCVLIPDKPGESAEVPPVFYCELCRLS   65 (68)
T ss_dssp             SCEECC-TTCCCSC--CSCEEECSCTTTCEEEETTTSCCCSSTTSCCCCCSSCCCHHHHHH
T ss_pred             CCCEEe-ECCCCcC--CCCEEEECCCCCCCeEchhhCCCCcccccccCCCCcEECcCccCc
Confidence            445778 7987643  578999993 4999999999985432211   1147999999753

>1wem_A Death associated transcription factor 1; structural genomics, PHD domain, death inducer- obliterator 1(DIO-1); NMR {Mus musculus} SCOP: g.50.1.2

Probab=97.88  E-value=1.8e-06  Score=72.12  Aligned_cols=53  Identities=19%  Similarity=0.560  Sum_probs=39.4

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCC----CCCCceecccCchh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTE----SRDQGWFCKFCECK  292 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~----p~dg~W~C~~C~~k  292 (629)
                      .+..+| +|+....  ++.||.|| .|..|||..|++......    +....|+|+.|...
T Consensus        14 ~~~~~C-~C~~~~~--~~~MI~Cd-~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~   70 (76)
T 1wem_A           14 PNALYC-ICRQPHN--NRFMICCD-RCEEWFHGDCVGISEARGRLLERNGEDYICPNCTIL   70 (76)
T ss_dssp             TTCCCS-TTCCCCC--SSCEEECS-SSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHH
T ss_pred             CCCCEE-ECCCccC--CCCEEEeC-CCCCcEeCeEEccchhhhhhccCCCCeEECcCCcCc
Confidence            345788 7998753  46899999 599999999999654321    01268999999754

>1wew_A DNA-binding family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=97.86  E-value=5.5e-06  Score=69.79  Aligned_cols=53  Identities=17%  Similarity=0.532  Sum_probs=40.6

Q ss_pred             cccccccccccCcCCCCCCceEeC--CcCCcccccccCCCCCCCC----CCCCceecccCchh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCD--GTCNCAFHQKCLDPPLDTE----SRDQGWFCKFCECK  292 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCD--G~C~rafH~~CL~PPL~~~----p~dg~W~C~~C~~k  292 (629)
                      .+..+| +|+...  ..+.||.||  . |..|||..|++.+....    .....|||+.|...
T Consensus        14 ~~~~~C-iC~~~~--~~g~MI~CD~~~-C~~W~H~~CVgi~~~~~~~~~~~~~~~~C~~C~~~   72 (78)
T 1wew_A           14 EIKVRC-VCGNSL--ETDSMIQCEDPR-CHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLT   72 (78)
T ss_dssp             CCCCCC-SSCCCC--CCSCEEECSSTT-TCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHC
T ss_pred             CCCEEe-ECCCcC--CCCCEEEECCcc-CCccccCEEEccccccccccccCCCCEECCCCCcc
Confidence            456789 799874  357999999  7 99999999999765431    11268999999754

>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway, WNT signaling complex, chromosomal rearrangement, signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A 2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A*

Probab=97.84  E-value=2.6e-06  Score=69.73  Aligned_cols=52  Identities=27%  Similarity=0.613  Sum_probs=39.0

Q ss_pred             cccccccccccCcCCCCCCceEeC-CcCCcccccccCCCCCCC------CCCCCceecccCc
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCD-GTCNCAFHQKCLDPPLDT------ESRDQGWFCKFCE  290 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCD-G~C~rafH~~CL~PPL~~------~p~dg~W~C~~C~  290 (629)
                      .....|.+|+.... ++..||.|| + |..+||..|++.....      .| .+.|+|+.|.
T Consensus         6 ~~~~~C~~C~~p~~-~~~~mI~CD~~-C~~WfH~~Cvglt~~~~~~l~~e~-~~~w~C~~C~   64 (65)
T 2vpb_A            6 DPVYPCGICTNEVN-DDQDAILCEAS-CQKWFHRICTGMTETAYGLLTAEA-SAVWGCDTCM   64 (65)
T ss_dssp             ---CBCTTTCSBCC-TTSCEEEBTTT-TCCEEEHHHHTCCHHHHHHHHHCT-TEEECCHHHH
T ss_pred             CCcCcCccCCCccC-CCCCeEecccC-ccccCchhccCCCHHHHHHhhccC-CCcEECcCcc
Confidence            44578999999753 456899999 7 9999999999954321      24 5699999995

>1wep_A PHF8; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: g.50.1.2

Probab=97.82  E-value=3.7e-06  Score=70.91  Aligned_cols=54  Identities=19%  Similarity=0.431  Sum_probs=40.1

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      .+..+| +|+.... .++.||.|| .|..|||..|++...........|+|+.|...
T Consensus        10 ~~~~~C-~C~~~~d-~~~~MIqCd-~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~   63 (79)
T 1wep_A           10 LVPVYC-LCRQPYN-VNHFMIECG-LCQDWFHGSCVGIEEENAVDIDIYHCPDCEAV   63 (79)
T ss_dssp             CCCCCS-TTSCSCC-SSSCEEEBT-TTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTT
T ss_pred             CCccEE-EcCCccC-CCCceEEcC-CCCCcEEeeecCcccccccCCCeEECCCcccc
Confidence            345678 8998752 357899999 59999999999865433211268999999854

>2xb1_A Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro; fusion protein, signal transduction, transcription, metal BI WNT proteins; 1.90A {Homo sapiens}

Probab=97.78  E-value=5.8e-06  Score=73.60  Aligned_cols=54  Identities=30%  Similarity=0.694  Sum_probs=41.0

Q ss_pred             cccccccccCcCCCCCCceEeC-CcCCcccccccCCCCCC------CCCCCCceecccCchhhH
Q 006832          238 HIICAKCKLREAFPDNDIVLCD-GTCNCAFHQKCLDPPLD------TESRDQGWFCKFCECKME  294 (629)
Q Consensus       238 ~~~C~vC~~~g~~~~~~lLlCD-G~C~rafH~~CL~PPL~------~~p~dg~W~C~~C~~k~~  294 (629)
                      ...|.+|+.... +++.||.|| + |..|||..|++....      ..| ...|+|+.|.....
T Consensus         3 ~~~C~iC~~p~~-~~~~mi~Cdd~-C~~WfH~~CVglt~~~~~~i~~~~-~~~~~Cp~C~~~~~   63 (105)
T 2xb1_A            3 VYPCGACRSEVN-DDQDAILCEAS-CQKWFHRECTGMTESAYGLLTTEA-SAVWACDLCLKTKE   63 (105)
T ss_dssp             CCBCTTTCSBCC-TTSCEEECTTT-TCCEEEGGGTTCCHHHHHHHHHCT-TEEECCHHHHHTTT
T ss_pred             cCCCCCCCCccC-CCCCEEEecCC-cccccccccCCcCHHHHHhhccCC-CCCEECccccCcCC
Confidence            467999999843 346799997 6 999999999995531      123 57899999987643

>3kqi_A GRC5, PHD finger protein 2; metal-binding, zinc-finger, histone-binding, NUC protein; HET: M3L; 1.78A {Homo sapiens} SCOP: g.50.1.2

Probab=97.76  E-value=5.2e-06  Score=69.35  Aligned_cols=54  Identities=22%  Similarity=0.508  Sum_probs=39.9

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      ....+| +|+.... .++.||.|| .|..+||..|++......+....|+|+.|...
T Consensus         8 ~~~~yC-iC~~~~~-~~~~MI~Cd-~C~~WfH~~Cvg~~~~~~~~~~~~~C~~C~~~   61 (75)
T 3kqi_A            8 TVPVYC-VCRLPYD-VTRFMIECD-ACKDWFHGSCVGVEEEEAPDIDIYHCPNCEKT   61 (75)
T ss_dssp             CCCEET-TTTEECC-TTSCEEECT-TTCCEEEHHHHTCCTTTGGGBSSCCCHHHHHH
T ss_pred             CCeeEE-ECCCcCC-CCCCEEEcC-CCCCCEecccccccccccCCCCEEECCCCccc
Confidence            344667 7887642 356899999 69999999999966554332257999999754

>1wil_A KIAA1045 protein; ring finger domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: g.50.1.3

Probab=97.73  E-value=7.6e-06  Score=70.02  Aligned_cols=53  Identities=23%  Similarity=0.703  Sum_probs=42.5

Q ss_pred             ccccccccccccCcCCCCCCceEeCCcCCcccccccCCCC------------CCCCCCCCceecccCchh
Q 006832          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPP------------LDTESRDQGWFCKFCECK  292 (629)
Q Consensus       235 ~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PP------------L~~~p~dg~W~C~~C~~k  292 (629)
                      ..++..|.||....   .+.|+-|. .|.+.||..||.++            +...+ ...|.|+.|..-
T Consensus        12 ~~~D~~C~VC~~~t---~~~l~pCR-vC~RvfH~~CL~r~gy~~~~~a~e~~l~A~T-~~GWSC~~CenL   76 (89)
T 1wil_A           12 VVNDEMCDVCEVWT---AESLFPCR-VCTRVFHDGCLRRMGYIQGDSAAEVTEMAHT-ETGWSCHYCDNI   76 (89)
T ss_dssp             CCCSCCCTTTCCCC---SSCCSSCS-SSSSCCCHHHHHHHTSCCCCCCCSCSCCCSS-SSSCCCTTTCCC
T ss_pred             CCCCcccCcccccc---ccceeccc-cccccccHhhcccccccccHHHHHHHHccCC-CCCccccccchh
Confidence            34678999999875   47899999 89999999999875            33333 689999999643

>3o7a_A PHD finger protein 13 variant; PHF13, zinc finger, PHD domain, nuclear protein, structural structural genomics consortium, SGC, protein binding; HET: M3L; 1.67A {Homo sapiens}

Probab=97.65  E-value=1.3e-05  Score=62.45  Aligned_cols=46  Identities=20%  Similarity=0.543  Sum_probs=37.0

Q ss_pred             ccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCc
Q 006832          239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCE  290 (629)
Q Consensus       239 ~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~  290 (629)
                      .+| +|+....  ++.||.|| .|..+||..|++.+....|  ..|+|+.|.
T Consensus         5 ~~C-~C~~~~~--~~~MI~Cd-~C~~W~H~~Cvgi~~~~~~--~~~~C~~C~   50 (52)
T 3o7a_A            5 VTC-FCMKPFA--GRPMIECN-ECHTWIHLSCAKIRKSNVP--EVFVCQKCR   50 (52)
T ss_dssp             BCS-TTCCBCT--TCCEEECT-TTCCEEETTTTTCCGGGCC--SSCCCHHHH
T ss_pred             eEE-EeCCcCC--CCCEEEcC-CCCccccccccCCCcccCC--CcEECcCCC
Confidence            456 5887643  56999999 5999999999997766555  689999995

>2kgg_A Histone demethylase jarid1A; PHD finger, histone modification, leukemia, alternative splicing, chromatin regulator, developmental protein; NMR {Homo sapiens} PDB: 2kgi_A* 3gl6_A*

Probab=97.58  E-value=9.9e-06  Score=63.17  Aligned_cols=48  Identities=27%  Similarity=0.639  Sum_probs=35.5

Q ss_pred             cccccccCcCCCCCCceEeC-CcCCcccccccCCCCCCCCCCCCceecccCc
Q 006832          240 ICAKCKLREAFPDNDIVLCD-GTCNCAFHQKCLDPPLDTESRDQGWFCKFCE  290 (629)
Q Consensus       240 ~C~vC~~~g~~~~~~lLlCD-G~C~rafH~~CL~PPL~~~p~dg~W~C~~C~  290 (629)
                      -|.+|+.+.. ++..||.|| + |..+||..|++....... ...|+|+.|.
T Consensus         4 ~cc~C~~p~~-~~~~mI~Cd~~-C~~WfH~~Cvgl~~~~~~-~~~~~C~~C~   52 (52)
T 2kgg_A            4 AAQNCQRPCK-DKVDWVQCDGG-CDEWFHQVCVGVSPEMAE-NEDYICINCA   52 (52)
T ss_dssp             SCTTCCCCCC-TTCCEEECTTT-TCCEEETTTTTCCHHHHH-HSCCCCSCC-
T ss_pred             cCCCCcCccC-CCCcEEEeCCC-CCccCcccccCCCccccC-CCCEECCCCC
Confidence            3677887752 356799999 6 999999999996433222 2689999994

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=97.57  E-value=4.8e-06  Score=74.54  Aligned_cols=55  Identities=22%  Similarity=0.471  Sum_probs=39.7

Q ss_pred             cccccccccCcC----CCCCCceEeCCcCCcccccccCCCC--CC-CCCCCCceecccCchhhH
Q 006832          238 HIICAKCKLREA----FPDNDIVLCDGTCNCAFHQKCLDPP--LD-TESRDQGWFCKFCECKME  294 (629)
Q Consensus       238 ~~~C~vC~~~g~----~~~~~lLlCDG~C~rafH~~CL~PP--L~-~~p~dg~W~C~~C~~k~~  294 (629)
                      ..+|.+|...+.    ...+.||.|++ |++.||++||++.  +. .++ .+.|+|+.|.....
T Consensus         5 ~~~C~~C~~~~~~~~~g~~~~Ll~C~~-C~~~~H~~Cl~~~~~~~~~~~-~~~W~C~~C~~C~v   66 (112)
T 3v43_A            5 IPICSFCLGTKEQNREKKPEELISCAD-CGNSGHPSCLKFSPELTVRVK-ALRWQCIECKTCSS   66 (112)
T ss_dssp             CSSBTTTCCCTTCCTTSCCCCCEECTT-TCCEECHHHHTCCHHHHHHHH-TSCCCCTTTCCBTT
T ss_pred             CccccccCCchhhCcCCCchhceEhhh-cCCCCCCchhcCCHHHHHHhh-ccccccccCCcccc
Confidence            467888876531    13569999995 9999999999752  22 223 57999999975443

>3pur_A Lysine-specific demethylase 7 homolog; oxidoreductase-oxidoreductase inhibitor complex; HET: 2HG; 2.10A {Caenorhabditis elegans} PDB: 3n9l_A 3n9m_A* 3n9o_A* 3n9p_A* 3n9q_A* 3n9n_A* 3puq_A*

Probab=97.24  E-value=9.4e-05  Score=81.93  Aligned_cols=41  Identities=22%  Similarity=0.387  Sum_probs=31.6

Q ss_pred             CCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832          251 PDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       251 ~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      ++..||+|| .|..|||..|++...........|+||.|...
T Consensus        54 ~~~~mI~CD-~C~~WfH~~CVgi~~~~a~~~~~y~Cp~C~~~   94 (528)
T 3pur_A           54 NDFQWIGCD-SCQTWYHFLCSGLEQFEYYLYEKFFCPKCVPH   94 (528)
T ss_dssp             STTSEEECT-TTCCEEEGGGTTCCGGGTTTEEECCCTTTHHH
T ss_pred             cCCCEEECC-CCCcCCCCcCCCCChhHhcCCCeEECcCCcCC
Confidence            346899999 59999999999965433221368999999864

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A

Probab=97.15  E-value=0.00012  Score=71.07  Aligned_cols=54  Identities=17%  Similarity=0.416  Sum_probs=38.3

Q ss_pred             ccccccccCcCCC--CCCceEeCCcCCcccccccCCCCCC------CCCCCCceecccCchhh
Q 006832          239 IICAKCKLREAFP--DNDIVLCDGTCNCAFHQKCLDPPLD------TESRDQGWFCKFCECKM  293 (629)
Q Consensus       239 ~~C~vC~~~g~~~--~~~lLlCDG~C~rafH~~CL~PPL~------~~p~dg~W~C~~C~~k~  293 (629)
                      .+|.+|+......  +..||.|| .|..|||..|++..-.      ..|....|+|+.|....
T Consensus         3 ~~CpiC~k~Y~~~~~~~~MIqCd-~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~   64 (183)
T 3lqh_A            3 NFCPLCDKCYDDDDYESKMMQCG-KCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERH   64 (183)
T ss_dssp             CBCTTTCCBCTTCCTTCCEEECT-TTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSS
T ss_pred             CcCCCCcCccCCcccCCCeEECC-CCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCC
Confidence            4799999876422  12499999 5999999999986421      11211379999998753

>3kv5_D JMJC domain-containing histone demethylation protein 1D; epigenetics, histone CODE, jumonji lysine demethylase, metal-binding, zinc, zinc-finger; HET: OGA; 2.39A {Homo sapiens} PDB: 3kv6_A*

Probab=97.12  E-value=5.4e-05  Score=83.53  Aligned_cols=55  Identities=18%  Similarity=0.426  Sum_probs=40.2

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKM  293 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~  293 (629)
                      .+..+| +|+.... .++.||.|| .|..|||..|++..-........|+|+.|....
T Consensus        35 ~~~~yC-~C~~~~d-~~~~MIqCd-~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~   89 (488)
T 3kv5_D           35 PPPVYC-VCRQPYD-VNRFMIECD-ICKDWFHGSCVGVEEHHAVDIDLYHCPNCAVLH   89 (488)
T ss_dssp             CCCEET-TTTEECC-TTSCEEEBT-TTCCEEEHHHHTCCGGGGGGEEEBCCHHHHHHH
T ss_pred             CCCeEE-eCCCcCC-CCCCeEEcc-CCCCceeeeecCcCcccccCCCEEECCCCcCCc
Confidence            445677 8988642 357899999 599999999998654332212579999998653

>3kv4_A PHD finger protein 8; epigenetics, histone CODE, covalent histone modifications, jumonji demethylase, mental retardation, metal-binding, zinc; HET: M3L MLY OGA; 2.19A {Homo sapiens}

Probab=96.20  E-value=0.00037  Score=76.11  Aligned_cols=52  Identities=23%  Similarity=0.540  Sum_probs=37.6

Q ss_pred             ccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhh
Q 006832          239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKM  293 (629)
Q Consensus       239 ~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~  293 (629)
                      .+| +|+.... .++.||.|| .|..+||..|++......+....|+|+.|....
T Consensus         6 ~yC-iC~~~~d-~~~~MIqCD-~C~~WfH~~CVgi~~~~~~~~~~y~C~~C~~~~   57 (447)
T 3kv4_A            6 VYC-LCRLPYD-VTRFMIECD-MCQDWFHGSCVGVEEEKAADIDLYHCPNCEVLH   57 (447)
T ss_dssp             EET-TTTEECC-TTSCEEECT-TTCCEEEHHHHTCCHHHHTTEEECCCHHHHHHH
T ss_pred             eEE-eCCCcCC-CCCCeEEcC-CCCcccccccCCcCcccccCCCEEECCCCcccc
Confidence            445 7887642 357899999 599999999998553332212689999997653

>4bbq_A Lysine-specific demethylase 2A; oxidoreductase, ubiquitin, ligase, ubiquitination, demethyla ZF-CXXC DNA binding domain, CPG island, chromatin; 2.24A {Homo sapiens}

Probab=95.81  E-value=0.0035  Score=55.84  Aligned_cols=40  Identities=23%  Similarity=0.472  Sum_probs=30.3

Q ss_pred             CCCceEeCCcCCcccccccCCCCCCCCC---CCCceecccCchh
Q 006832          252 DNDIVLCDGTCNCAFHQKCLDPPLDTES---RDQGWFCKFCECK  292 (629)
Q Consensus       252 ~~~lLlCDG~C~rafH~~CL~PPL~~~p---~dg~W~C~~C~~k  292 (629)
                      +..||.|+ .|..+||..|++++....+   ....|+|+.|...
T Consensus        72 ~~~m~~C~-~C~~~~H~~C~~~~~~~~~~~~~~~~~~C~~C~~~  114 (117)
T 4bbq_A           72 EKKLMECC-ICNEIVHPGCLQMDGEGLLNEELPNCWECPKCYQE  114 (117)
T ss_dssp             GGSCEEET-TTCCEECGGGCCSCCCCEECSSSSSEEECTTTC--
T ss_pred             CcceEEee-ecCCeEECCCCCCCccccccccCCCCeECCCCcCC
Confidence            35699999 6999999999998865433   1246999999754

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=94.93  E-value=0.0049  Score=54.83  Aligned_cols=38  Identities=18%  Similarity=0.486  Sum_probs=28.5

Q ss_pred             CceEeCCcCCcccccccCCCCC------CCCCCCCceecccCchh
Q 006832          254 DIVLCDGTCNCAFHQKCLDPPL------DTESRDQGWFCKFCECK  292 (629)
Q Consensus       254 ~lLlCDG~C~rafH~~CL~PPL------~~~p~dg~W~C~~C~~k  292 (629)
                      .||.|| .|..|||..|....-      ...|....|.|+.|...
T Consensus         1 ~mi~c~-~c~~w~H~~c~~~~~~~~~~l~~lp~~~~~~c~~C~~~   44 (140)
T 2ku7_A            1 SMMQCG-KCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTER   44 (140)
T ss_dssp             CCCCCS-CCSSCHHHHHCCCCHHHHHHHHSSCTTTTCCSSCCTTT
T ss_pred             Cccccc-cCCCccCCcccccCHHHHHHHhhccccceeeCcccccc
Confidence            389999 599999999998542      22232357999999754

>4gne_A Histone-lysine N-methyltransferase NSD3; zinc finger, transcription, nuclear protein, transf nuclear protein complex; 1.47A {Homo sapiens} PDB: 4gnd_A 4gnf_A 4gng_A*

Probab=94.36  E-value=0.035  Score=49.56  Aligned_cols=47  Identities=19%  Similarity=0.430  Sum_probs=35.6

Q ss_pred             CCCcccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceec
Q 006832          231 DGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFC  286 (629)
Q Consensus       231 dg~~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C  286 (629)
                      ..|.+..+ .|.+|+...      .+.|. .|+.+||..|+.+.|...+ ...|+|
T Consensus        52 g~W~Cp~c-~C~~C~k~~------~~~C~-~Cp~sfC~~c~~g~l~~~~-~~~~~c   98 (107)
T 4gne_A           52 GKWECPWH-QCDECSSAA------VSFCE-FCPHSFCKDHEKGALVPSA-LEGRLC   98 (107)
T ss_dssp             SCCCCGGG-BCTTTCSBC------CEECS-SSSCEECTTTCTTSCEECT-TTTCEE
T ss_pred             CCEECCCC-CCCcCCCCC------CcCcC-CCCcchhhhccCCcceecC-CCCcee
Confidence            33544433 366676652      38899 7999999999999999888 689998

>2ys9_A Homeobox and leucine zipper protein homez; homeodomain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=93.53  E-value=0.047  Score=45.27  Aligned_cols=45  Identities=22%  Similarity=0.417  Sum_probs=40.4

Q ss_pred             CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchh
Q 006832          503 MPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNA  547 (629)
Q Consensus       503 ft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNr  547 (629)
                      .++.-.+.|+++|..+..+....-..|..+.+|+..||+-||--+
T Consensus        13 ~~p~~~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~k   57 (70)
T 2ys9_A           13 PPPPDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSR   57 (70)
T ss_dssp             CCCCCCHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             CCCCcchHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHhc
Confidence            355556799999999999999999999999999999999999654

>3a1b_A DNA (cytosine-5)-methyltransferase 3A, histone H3; zinc-finger, histone binding, chromosomal protein, DNA damag repair, DNA-binding, methylation; HET: DNA; 2.29A {Homo sapiens} PDB: 3a1a_A*

Probab=87.60  E-value=0.094  Score=49.89  Aligned_cols=52  Identities=21%  Similarity=0.626  Sum_probs=39.8

Q ss_pred             ccccccccccCcCCCCCCceEeCC-cCCcccccccCCCCCCCCC-----CCCceecccCchhh
Q 006832          237 EHIICAKCKLREAFPDNDIVLCDG-TCNCAFHQKCLDPPLDTES-----RDQGWFCKFCECKM  293 (629)
Q Consensus       237 e~~~C~vC~~~g~~~~~~lLlCDG-~C~rafH~~CL~PPL~~~p-----~dg~W~C~~C~~k~  293 (629)
                      .+.+|.+|+.++     .||+||. .|.++|=..|+.--+....     ....|.|--|...+
T Consensus        78 ~~~yC~wC~~Gg-----~l~~Cdn~~C~r~FC~~CI~~nvG~~~~~~i~~~d~W~Cy~C~P~~  135 (159)
T 3a1b_A           78 YQSYCTICCGGR-----EVLMCGNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKG  135 (159)
T ss_dssp             SBSSCTTTSCCS-----EEEECSSTTTCCEEEHHHHHHHTCTTHHHHHHTSSSCCCTTTCSSC
T ss_pred             CcceeeEecCCC-----eEEeeCCCCCCCchhHHHHHHhcCHhHHHHHhccCCCEEEecCCcc
Confidence            367899999874     8999992 2999999999865444422     35789999998764

>3rsn_A SET1/ASH2 histone methyltransferase complex subun; PHD domain, winged helix domain, binding, transcription; 2.10A {Homo sapiens} PDB: 3s32_A

Probab=87.09  E-value=0.4  Score=46.36  Aligned_cols=50  Identities=10%  Similarity=0.174  Sum_probs=31.6

Q ss_pred             ccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCC---CCCceecccCch
Q 006832          239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES---RDQGWFCKFCEC  291 (629)
Q Consensus       239 ~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p---~dg~W~C~~C~~  291 (629)
                      .+|. |+..+. -.-.||.|+ .|.++||..|+..+....-   .--...|..|..
T Consensus         6 ~yCY-CG~~~~-~~~~mLqC~-~C~qWFH~~Cl~~~~~~~lp~~~fY~F~C~~C~~   58 (177)
T 3rsn_A            6 GSVD-EENGRQ-LGEVELQCG-ICTKWFTADTFGIDTSSCLPFMTNYSFHCNVCHH   58 (177)
T ss_dssp             ------CTTCC-TTSCEEECT-TTCCEEEGGGGTCCCTTCCTTCCSEEEECTTTST
T ss_pred             eEEE-cCCCCC-CCceeEeec-cccceecHHHhcccccCccccceeEEEEccccCC
Confidence            3453 666542 356899999 5999999999986543322   123567999965

>2pv0_B DNA (cytosine-5)-methyltransferase 3-like; DNMT3L, unmethylated H3K4, de novo DNA methylation, transferase regulator; HET: DNA; 3.30A {Homo sapiens} PDB: 2pvc_B*

Probab=84.74  E-value=0.16  Score=54.59  Aligned_cols=51  Identities=20%  Similarity=0.610  Sum_probs=40.0

Q ss_pred             ccccccccccCcCCCCCCceEeC--CcCCcccccccCCCCCCCCC-----CCCceecccCchhh
Q 006832          237 EHIICAKCKLREAFPDNDIVLCD--GTCNCAFHQKCLDPPLDTES-----RDQGWFCKFCECKM  293 (629)
Q Consensus       237 e~~~C~vC~~~g~~~~~~lLlCD--G~C~rafH~~CL~PPL~~~p-----~dg~W~C~~C~~k~  293 (629)
                      .+.+|..|+.++     .+|+||  . |.++|-..|+.--+...-     ....|.|--|...+
T Consensus        92 ~~~yCr~C~~Gg-----~l~~Cdn~~-C~r~FC~~Ci~~n~g~~~~~~i~~~d~W~Cf~C~p~p  149 (386)
T 2pv0_B           92 YQSYCSICCSGE-----TLLICGNPD-CTRCYCFECVDSLVGPGTSGKVHAMSNWVCYLCLPSS  149 (386)
T ss_dssp             SBCSCTTTCCCS-----SCEECCSTT-CCCEECHHHHHHHTCTTHHHHHHHCSSCCCTTTSSCC
T ss_pred             CcccceEcCCCC-----eEEEeCCCC-CCcchHHHHHHHhcChhHHHHhhccCCceEEEcCCcc
Confidence            467899999875     799999  6 999999999975553322     23689999998765

---

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	629
d1fp0a1	70	g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-	5e-10
d1f62a_	51	g.50.1.2 (A:) Williams-Beuren syndrome transcripti	2e-09
d1weva_	88	g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus mu	2e-09
d1mm2a_	61	g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens	2e-08
d1we9a_	64	g.50.1.2 (A:) PHD finger protein At5g26210 {Thale	5e-08
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	2e-06
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	2e-06
d1weea_	72	g.50.1.2 (A:) PHD finger protein At1g33420 {Thale	3e-06
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	8e-06
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	1e-04
d1wema_	76	g.50.1.2 (A:) Death associated transcription facto	1e-04
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	1e-04
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	2e-04
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	3e-04
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	3e-04
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	3e-04
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	4e-04
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	4e-04
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	7e-04
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	7e-04
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	8e-04
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	0.001
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	0.001
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	0.001
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	0.002
d1wepa_	79	g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus mus	0.002
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	0.004

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]} Length = 70

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Nuclear corepressor KAP-1 (TIF-1beta)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.9 bits (129), Expect = 5e-10
 Identities = 17/67 (25%), Positives = 27/67 (40%), Gaps = 7/67 (10%)

Query: 232 GSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCEC 291
           G++     IC  C+        D+V+C+  C   FH  C  P L     ++ W C  C  
Sbjct: 1   GTLDDSATICRVCQK-----PGDLVMCNQ-CEFCFHLDCHLPALQDVPGEE-WSCSLCHV 53

Query: 292 KMEIIES 298
             ++ E 
Sbjct: 54  LPDLKEE 60

>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]} Length = 51

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Williams-Beuren syndrome transcription factor, WSTF
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.5 bits (123), Expect = 2e-09
 Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 4/50 (8%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCE 290
           C  C+ +    D+ ++LCD  CN AFH  CL P L      + W C  C+
Sbjct: 3   CKVCRKKG--EDDKLILCDE-CNKAFHLFCLRPALYEVPDGE-WQCPACQ 48

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]} Length = 88

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 22
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.5 bits (125), Expect = 2e-09
 Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 4/69 (5%)

Query: 229 ATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES---RDQGWF 285
             D       + C  C+       N +V C   C+  +HQ C  P +  +        W+
Sbjct: 7   GADDFAMEMGLACVVCRQMTVASGNQLVECQE-CHNLYHQDCHKPQVTDKEVNDPRLVWY 65

Query: 286 CKFCECKME 294
           C  C  +M+
Sbjct: 66  CARCTRQMK 74

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]} Length = 61

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.8 bits (116), Expect = 2e-08
 Identities = 17/58 (29%), Positives = 24/58 (41%), Gaps = 7/58 (12%)

Query: 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKM 293
           H    C  CK        +++ CD  C  ++H  CL+PPL      + W C  C C  
Sbjct: 7   HHMEFCRVCKD-----GGELLCCDT-CPSSYHIHCLNPPLPEIPNGE-WLCPRCTCPA 57

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 64

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 47.7 bits (113), Expect = 5e-08
 Identities = 14/52 (26%), Positives = 18/52 (34%), Gaps = 2/52 (3%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK 292
           C  C    A  D   + CD  C   FH KC+          + + C  C  K
Sbjct: 9   CGACGESYA-ADEFWICCDL-CEMWFHGKCVKITPARAEHIKQYKCPSCSNK 58

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Length = 62

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.2 bits (102), Expect = 2e-06
 Identities = 13/55 (23%), Positives = 26/55 (47%), Gaps = 3/55 (5%)

Query: 497 RRSFHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNAR 548
           +     +P +A   +R    +   +  P+   K+ ++ + +L   +VN WF NAR
Sbjct: 3   KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINAR 57

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 43.2 bits (102), Expect = 2e-06
 Identities = 16/51 (31%), Positives = 19/51 (37%), Gaps = 3/51 (5%)

Query: 501 HRMPPNAVEKLRQVFAENEL---PSRIVKENLSKELSLEPEKVNKWFKNAR 548
           HR     V  L   FA+N           ENL K  SL   ++  W  N R
Sbjct: 3   HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR 53

>d1weea_ g.50.1.2 (A:) PHD finger protein At1g33420 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 72

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At1g33420
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 43.1 bits (101), Expect = 3e-06
 Identities = 9/52 (17%), Positives = 15/52 (28%), Gaps = 1/52 (1%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK 292
              CK      D + +L    C    H +C+          + + C  C   
Sbjct: 16  KVDCKCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSK-FLCFRCIEL 66

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 80

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 41.9 bits (98), Expect = 8e-06
 Identities = 8/63 (12%), Positives = 17/63 (26%), Gaps = 4/63 (6%)

Query: 491 PSNAKIRRSFHRMPPNAVEKLRQVFAE----NELPSRIVKENLSKELSLEPEKVNKWFKN 546
            S    +R   +      EK+           +    +  E    E  +  + +  W  N
Sbjct: 12  SSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHN 71

Query: 547 ARY 549
            + 
Sbjct: 72  NKN 74

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 50

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.9 bits (88), Expect = 1e-04
 Identities = 15/41 (36%), Positives = 25/41 (60%)

Query: 508 VEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 548
              L  +F EN+ PS+ ++  +S++L LE   V+ +F NAR
Sbjct: 10  RRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>d1wema_ g.50.1.2 (A:) Death associated transcription factor 1, Datf1 (DIO-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 76

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Death associated transcription factor 1, Datf1 (DIO-1)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.5 bits (89), Expect = 1e-04
 Identities = 11/53 (20%), Positives = 18/53 (33%), Gaps = 5/53 (9%)

Query: 244 CKLREAFPDNDIVLCDGTCNCAFHQKCL----DPPLDTESRDQGWFCKFCECK 292
           C  R+   +  ++ CD  C   FH  C+          E   + + C  C   
Sbjct: 19  CICRQPHNNRFMICCDR-CEEWFHGDCVGISEARGRLLERNGEDYICPNCTIL 70

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (89), Expect = 1e-04
 Identities = 14/66 (21%), Positives = 28/66 (42%)

Query: 497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 556
           +R+        +E L + F     P    +E L+ ++ L   ++  WF N R    +  K
Sbjct: 2   QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 61

Query: 557 VESARQ 562
           + + R+
Sbjct: 62  LRNQRR 67

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 66

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 37.5 bits (87), Expect = 2e-04
 Identities = 16/54 (29%), Positives = 24/54 (44%)

Query: 495 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 548
           K  R    +    +  LR  +A N  P  ++KE L +   L P  +  WF+N R
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKR 55

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 37.3 bits (86), Expect = 3e-04
 Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 3/73 (4%)

Query: 495 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 554
           K R+           +L + F +    S   +E+L+  + L P +V  WF+N RY   K 
Sbjct: 8   KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRY---KT 64

Query: 555 RKVESARQVSGSP 567
           ++ ++ +   G P
Sbjct: 65  KRAQNEKGYEGHP 77

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 53

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

 Score = 36.8 bits (85), Expect = 3e-04
 Identities = 14/42 (33%), Positives = 24/42 (57%)

Query: 508 VEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 549
           + +L++ F EN   +   ++ LS EL L   ++  WF+NAR 
Sbjct: 11  LARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARA 52

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 59

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: LAG1 longevity assurance homolog 5, LASS5
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.7 bits (85), Expect = 3e-04
 Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 3/49 (6%)

Query: 501 HRMPPNAVEKLRQVFA-ENELPSRIVKENLSKELSLEPEKVNKWFKNAR 548
           +++ PN    L +VF    + P     + LSK+L     K+  WF++ R
Sbjct: 8   NKVEPNDT--LEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRR 54

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 56

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Antennapedia Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

 Score = 36.7 bits (85), Expect = 4e-04
 Identities = 11/41 (26%), Positives = 20/41 (48%)

Query: 508 VEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 548
             +L + F  N   +R  +  ++  LSL   ++  WF+N R
Sbjct: 9   TLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRR 49

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-a9
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.1 bits (86), Expect = 4e-04
 Identities = 15/72 (20%), Positives = 29/72 (40%), Gaps = 3/72 (4%)

Query: 491 PSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL 550
                 R+       +   +L + F  N   +R  +  +++ L+L   +V  WF+N R  
Sbjct: 8   LHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRM- 66

Query: 551 ALKARKVESARQ 562
             K +K+   R 
Sbjct: 67  --KMKKINKDRA 76

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 53

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 36.0 bits (83), Expect = 7e-04
 Identities = 15/48 (31%), Positives = 23/48 (47%)

Query: 502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 549
            + P A   L QVF   +  +   KE ++K+  + P +V  WF N R 
Sbjct: 3   SISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRM 50

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 65

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 36.0 bits (83), Expect = 7e-04
 Identities = 15/62 (24%), Positives = 28/62 (45%)

Query: 495 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 554
           K RRS      + +++L + F   + P    +E L++  +L   ++  WF+N R    K 
Sbjct: 1   KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 60

Query: 555 RK 556
             
Sbjct: 61  HT 62

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Thyroid transcription factor 1 homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 36.1 bits (83), Expect = 8e-04
 Identities = 18/66 (27%), Positives = 33/66 (50%)

Query: 497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 556
           R+         V +L + F + +  S   +E+L+  + L P +V  WF+N RY   +  K
Sbjct: 3   RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62

Query: 557 VESARQ 562
            ++A+Q
Sbjct: 63  DKAAQQ 68

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.3 bits (81), Expect = 0.001
 Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 3/62 (4%)

Query: 497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 556
           RR         +++L   F  N  P    +E ++   +L   +V  WFKN R    K RK
Sbjct: 2   RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRA---KWRK 58

Query: 557 VE 558
            E
Sbjct: 59  RE 60

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein prh
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.2 bits (81), Expect = 0.001
 Identities = 13/52 (25%), Positives = 23/52 (44%)

Query: 497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 548
           +    R   +   +L + F   +  S   ++ L+K L L   +V  WF+N R
Sbjct: 1   KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRR 52

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 52

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.1 bits (81), Expect = 0.001
 Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 3/45 (6%)

Query: 505 PNAVEKLRQVFAE-NELPSRIVKENLSKELSLEPEKVNKWFKNAR 548
           PNA+  L +VF    + P     E LSK+L  +   + +WF+  R
Sbjct: 4   PNAI--LEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRR 46

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Length = 73

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.3 bits (81), Expect = 0.002
 Identities = 20/69 (28%), Positives = 28/69 (40%), Gaps = 6/69 (8%)

Query: 497 RRSFHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 553
           RR        A E L + F     N  PS   KE L+K+  +   +V+ WF N R    +
Sbjct: 2   RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRI---R 58

Query: 554 ARKVESARQ 562
            +K     Q
Sbjct: 59  YKKNIGKFQ 67

>d1wepa_ g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus musculus) [TaxId: 10090]} Length = 79

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 8
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 11/49 (22%), Positives = 18/49 (36%)

Query: 244 CKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK 292
           C  R+ +  N  ++  G C   FH  C+    +       + C  CE  
Sbjct: 15  CLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAV 63

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 33.7 bits (77), Expect = 0.004
 Identities = 11/41 (26%), Positives = 21/41 (51%)

Query: 508 VEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 548
           + +L + F +    SR  +  L+ +L+L    +  WF+N R
Sbjct: 11  LGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRR 51

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	629
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.76
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.76
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.76
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.75
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.75
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.75
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.75
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.75
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.75
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.74
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.73
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.72
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.71
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.7
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.7
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.7
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.7
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.69
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.68
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.67
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.66
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.65
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.64
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.64
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.64
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.62
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.6
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.57
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.56
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.54
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.52
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.47
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	99.13
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	99.06
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	99.03
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	98.96
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	98.41
d1weea_	72	PHD finger protein At1g33420 {Thale cress (Arabido	98.37
d2pnxa1	51	Inhibitor of growth protein 4, Ing4 {Homo sapiens	98.26
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	98.22
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	98.2
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	98.06
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	97.63
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	94.97
d1hlva1	66	DNA-binding domain of centromere binding protein B	87.86
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	84.77
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	82.65

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein prh
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.5e-19  Score=142.85  Aligned_cols=57  Identities=23%  Similarity=0.347  Sum_probs=53.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832          497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  553 (629)
Q Consensus       497 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K  553 (629)
                      |++|++||+.|+.+||.+|..|+||+..++++||..|||++.||+|||||||++.+|
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k~kk   57 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR   57 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhhccC
Confidence            567899999999999999999999999999999999999999999999999996554

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=8.5e-20  Score=144.86  Aligned_cols=56  Identities=20%  Similarity=0.363  Sum_probs=52.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHH
Q 006832          497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL  552 (629)
Q Consensus       497 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~  552 (629)
                      ||+|++||++|+.+||.+|..|+||+..+|++||..|||++.||+|||||||++.+
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~k   57 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK   57 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhcc
Confidence            56778999999999999999999999999999999999999999999999999543

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=1.9e-19  Score=142.54  Aligned_cols=57  Identities=25%  Similarity=0.372  Sum_probs=53.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832          497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  553 (629)
Q Consensus       497 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K  553 (629)
                      ||+|+.||++|+.+||..|+.|+||+..+|++||..|||++.||+|||||+|++.+|
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            567889999999999999999999999999999999999999999999999996654

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-a9
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.75  E-value=3.3e-19  Score=149.03  Aligned_cols=63  Identities=22%  Similarity=0.281  Sum_probs=57.9

Q ss_pred             cccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832          494 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       494 ~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      ...||+|++||++|+.+||.+|..++||+..+|++||..|||++.||+|||||||++.+|..+
T Consensus        11 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~   73 (77)
T d1pufa_          11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINK   73 (77)
T ss_dssp             CTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHH
Confidence            345677899999999999999999999999999999999999999999999999998777654

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.75  E-value=2e-19  Score=140.11  Aligned_cols=53  Identities=28%  Similarity=0.510  Sum_probs=51.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006832          498 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  550 (629)
Q Consensus       498 R~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k  550 (629)
                      |+|+.||++|+.+||..|..++||+..+|.+||..|||++.||+|||||||+|
T Consensus         1 R~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~lgL~~~qV~vWFqNrRaK   53 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK   53 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             CCCccCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChHHhhhcccccCCC
Confidence            56889999999999999999999999999999999999999999999999983

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.75  E-value=4.2e-19  Score=143.73  Aligned_cols=61  Identities=25%  Similarity=0.476  Sum_probs=57.0

Q ss_pred             ccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          495 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       495 k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      ++||.|++||++|+.+||.+|..|+||+..++..||..|||++.||++||||+|++.+|..
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~   61 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH   61 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhcc
Confidence            4577899999999999999999999999999999999999999999999999999776655

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.75  E-value=3.6e-19  Score=144.97  Aligned_cols=61  Identities=25%  Similarity=0.344  Sum_probs=56.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhhh
Q 006832          497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV  557 (629)
Q Consensus       497 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~~  557 (629)
                      ||+|++||++|+.+||.+|..++||+..+|.+||..|||++.||+|||||||++.+|....
T Consensus         2 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~~   62 (67)
T d1zq3p1           2 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ   62 (67)
T ss_dssp             SCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhhh
Confidence            5678999999999999999999999999999999999999999999999999977765543

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.75  E-value=3.4e-19  Score=140.77  Aligned_cols=56  Identities=21%  Similarity=0.379  Sum_probs=53.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832          498 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  553 (629)
Q Consensus       498 R~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K  553 (629)
                      |.|+.||+.|+.+||..|..++||+..+|++||..|||++.||+|||||+|++.+|
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk   56 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR   56 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhc
Confidence            56789999999999999999999999999999999999999999999999997665

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Antennapedia Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.75  E-value=2.9e-19  Score=140.88  Aligned_cols=55  Identities=22%  Similarity=0.293  Sum_probs=52.0

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006832          500 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA  554 (629)
Q Consensus       500 r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~  554 (629)
                      |+.||++|+..||.+|..|+||+..+|++||..|||++.||+|||||||++.+|+
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk~   55 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   55 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhhc
Confidence            5789999999999999999999999999999999999999999999999976653

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Thyroid transcription factor 1 homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.74  E-value=5.3e-19  Score=144.40  Aligned_cols=60  Identities=25%  Similarity=0.407  Sum_probs=56.1

Q ss_pred             cCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          496 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       496 ~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      +||+|+.||+.|+.+|+.+|..|+||+..+|.+||..|||++.||+|||||+|++.+|..
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~   61 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA   61 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhcc
Confidence            467889999999999999999999999999999999999999999999999999776654

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.73  E-value=6.3e-19  Score=147.26  Aligned_cols=64  Identities=23%  Similarity=0.334  Sum_probs=58.0

Q ss_pred             CCCccccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832          490 LPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  553 (629)
Q Consensus       490 ~~~~~k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K  553 (629)
                      ++...+++|.|++||++|+.+||.+|..++||+..++++||..|||++.||+|||||+|++.+|
T Consensus         3 ~g~p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr   66 (77)
T d1vnda_           3 DGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR   66 (77)
T ss_dssp             SCCSSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSS
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHH
Confidence            3445667788999999999999999999999999999999999999999999999999995544

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1.8e-18  Score=141.22  Aligned_cols=60  Identities=22%  Similarity=0.448  Sum_probs=56.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhhh
Q 006832          497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  556 (629)
Q Consensus       497 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~~  556 (629)
                      ||+|+.||++|+.+||.+|..|+||+..+|++||..|||++.||+|||||+|++.++..+
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~   61 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK   61 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhh
Confidence            567899999999999999999999999999999999999999999999999998776653

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.1e-18  Score=139.04  Aligned_cols=59  Identities=25%  Similarity=0.398  Sum_probs=55.0

Q ss_pred             cCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006832          496 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA  554 (629)
Q Consensus       496 ~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~  554 (629)
                      .||+|++||++|+.+|+.+|..|+||+..++..||..|||++.||++||||+|++.+|.
T Consensus         1 Qrr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1           1 QRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             SSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            36788999999999999999999999999999999999999999999999999966553

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=1.6e-18  Score=142.39  Aligned_cols=61  Identities=23%  Similarity=0.335  Sum_probs=54.8

Q ss_pred             ccccCCCCCCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832          493 NAKIRRSFHRMPPNAVEKLRQVFAE-NELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  553 (629)
Q Consensus       493 ~~k~kR~r~rft~~Q~~~Le~~F~~-~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K  553 (629)
                      +...+|+|++||++|+.+|+.+|.+ ++||+..++++||++|||++.||++||||+|++.+|
T Consensus         4 ~~~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk   65 (71)
T d1wi3a_           4 GSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             CCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhcc
Confidence            3445678899999999999999975 999999999999999999999999999999995544

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=3.7e-18  Score=145.93  Aligned_cols=61  Identities=21%  Similarity=0.303  Sum_probs=54.0

Q ss_pred             ccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          495 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       495 k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      +.+|.|++||++|+.+||.+|..|+||+..+|++||..|||++.||+|||||+|++.+|..
T Consensus        26 ~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~   86 (88)
T d1b72a_          26 SPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRE   86 (88)
T ss_dssp             ----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhc
Confidence            3467788999999999999999999999999999999999999999999999999766654

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeodomain-only protein, Hop
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.70  E-value=4.6e-18  Score=140.29  Aligned_cols=59  Identities=24%  Similarity=0.298  Sum_probs=53.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          497 RRSFHRMPPNAVEKLRQVFAE-NELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       497 kR~r~rft~~Q~~~Le~~F~~-~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      ++.+++||++|+.+||..|.. |+||+..+|++||.+|||++.||+|||||||++.+|..
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~   61 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhcc
Confidence            467789999999999999986 78999999999999999999999999999999666543

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.70  E-value=3.2e-18  Score=138.94  Aligned_cols=59  Identities=29%  Similarity=0.476  Sum_probs=54.9

Q ss_pred             ccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832          495 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  553 (629)
Q Consensus       495 k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K  553 (629)
                      +.+|.|++||++|+..|+.+|..|+||+..+++.||.+|||++.||++||||+|++.++
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk   60 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKK   60 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSS
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHH
Confidence            45788999999999999999999999999999999999999999999999999995443

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.69  E-value=5e-18  Score=132.10  Aligned_cols=51  Identities=29%  Similarity=0.435  Sum_probs=49.3

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006832          500 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  550 (629)
Q Consensus       500 r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k  550 (629)
                      |++||++|+.+|+.+|..++||+..++.+||..|||++.||++||||+|++
T Consensus         1 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k   51 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR   51 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhc
Confidence            578999999999999999999999999999999999999999999999994

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-3 POU Homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.68  E-value=4.9e-18  Score=138.27  Aligned_cols=58  Identities=22%  Similarity=0.288  Sum_probs=54.1

Q ss_pred             ccCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHH
Q 006832          495 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL  552 (629)
Q Consensus       495 k~kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~  552 (629)
                      .+||+|++|+++|+..|+.+|..|+||+..++++||..|||++.||+|||||+|++.+
T Consensus         7 ~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~K   64 (67)
T d1ocpa_           7 ARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGK   64 (67)
T ss_dssp             CSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSS
T ss_pred             ccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHh
Confidence            3567789999999999999999999999999999999999999999999999999543

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-containing protein 1, HMBOX1 (Flj21616)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.7e-17  Score=139.91  Aligned_cols=59  Identities=22%  Similarity=0.366  Sum_probs=54.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhC---------------CCcchhhhccchhccHHHHhh
Q 006832          497 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELS---------------LEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       497 kR~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lg---------------Lt~~QVkiWFQNrR~k~~K~~  555 (629)
                      ||.|+.||++|+.+||.+|.+|+||+..+|++||..+|               |++.||+|||||||++.+|..
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~   74 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRA   74 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhh
Confidence            57789999999999999999999999999999999875               999999999999999776654

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.66  E-value=1.5e-17  Score=131.60  Aligned_cols=55  Identities=29%  Similarity=0.382  Sum_probs=51.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHH
Q 006832          498 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL  552 (629)
Q Consensus       498 R~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~  552 (629)
                      |.|+.|+++|+.+||.+|..|+||+..++.+||..|||++.||+|||||+|++.+
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k   55 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREK   55 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHH
Confidence            4678899999999999999999999999999999999999999999999999543

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.65  E-value=1.9e-17  Score=127.16  Aligned_cols=50  Identities=30%  Similarity=0.436  Sum_probs=48.9

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhc
Q 006832          499 SFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR  548 (629)
Q Consensus       499 ~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR  548 (629)
                      +|+.||++|+.+||.+|..|+||+..++.+||..|||++.||++||||+|
T Consensus         1 PRt~ft~~Q~~~Le~~F~~n~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1           1 PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             CCSCCCHHHHHHHHHHTTSSCSSTHHHHHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhhcCCcCc
Confidence            57899999999999999999999999999999999999999999999998

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=4.4e-17  Score=128.54  Aligned_cols=55  Identities=24%  Similarity=0.369  Sum_probs=51.5

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832          499 SFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  553 (629)
Q Consensus       499 ~r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K  553 (629)
                      +|+.|+++|+..||.+|..++||+..+++.||..|||++.||++||||+|++.+|
T Consensus         1 kRT~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk   55 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR   55 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTS
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHc
Confidence            4688999999999999999999999999999999999999999999999995543

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Zinc fingers and homeoboxes protein 1, ZHX1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=5.8e-17  Score=134.75  Aligned_cols=50  Identities=12%  Similarity=0.276  Sum_probs=47.5

Q ss_pred             CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHH
Q 006832          502 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA  551 (629)
Q Consensus       502 rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~  551 (629)
                      ++|++|+.+|+.+|..|+||+..++++||..|||++.||++||||||++.
T Consensus        10 ~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~   59 (76)
T d2ecba1          10 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSK   59 (76)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHH
Confidence            35999999999999999999999999999999999999999999999843

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.64  E-value=3.6e-17  Score=137.30  Aligned_cols=59  Identities=14%  Similarity=0.227  Sum_probs=54.3

Q ss_pred             CccccCCCCCCCCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006832          492 SNAKIRRSFHRMPPNAVEKLRQVFAE----NELPSRIVKENLSKELSLEPEKVNKWFKNARYL  550 (629)
Q Consensus       492 ~~~k~kR~r~rft~~Q~~~Le~~F~~----~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k  550 (629)
                      ...++||.|++||.+|+++|+.+|+.    ++||+..++++||++|||++.||+|||||+|++
T Consensus        13 ~~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~   75 (80)
T d1wh7a_          13 SGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNS   75 (80)
T ss_dssp             CCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCC
T ss_pred             CccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCC
Confidence            34556788999999999999999996    899999999999999999999999999999984

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=1.2e-16  Score=131.70  Aligned_cols=59  Identities=32%  Similarity=0.442  Sum_probs=53.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHhh
Q 006832          497 RRSFHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  555 (629)
Q Consensus       497 kR~r~rft~~Q~~~Le~~F~~---~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~~  555 (629)
                      ||+|++||++|++.|+.+|.+   +|||+..++++||..|||++.||++||||+|++.++..
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~   63 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccc
Confidence            566788999999999999986   78999999999999999999999999999999766543

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-leucine zipper protein Homez
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=3.2e-16  Score=130.16  Aligned_cols=54  Identities=19%  Similarity=0.349  Sum_probs=50.4

Q ss_pred             CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHHh
Q 006832          501 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA  554 (629)
Q Consensus       501 ~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K~  554 (629)
                      .+||++|+.+|+.+|..|+||+..++..||..|||++.||++||||+|++.++.
T Consensus         8 ~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~   61 (76)
T d2ecca1           8 KRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             CCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhc
Confidence            467999999999999999999999999999999999999999999999965553

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=1e-15  Score=122.60  Aligned_cols=57  Identities=25%  Similarity=0.405  Sum_probs=51.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhCCCcchhhhccchhccHHHH
Q 006832          497 RRSFHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  553 (629)
Q Consensus       497 kR~r~rft~~Q~~~Le~~F~~---~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~~K  553 (629)
                      |++|++|+++|+.+|+.+|.+   ||||+..++..||..+||+..||++||+|+|++.++
T Consensus         3 krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R~lq   62 (62)
T d1x2na1           3 KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQ   62 (62)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcC
Confidence            344568999999999999996   799999999999999999999999999999997653

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.56  E-value=9.8e-16  Score=121.81  Aligned_cols=50  Identities=32%  Similarity=0.406  Sum_probs=47.1

Q ss_pred             CCCCHHHHHHHHHHHHhC---CCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006832          501 HRMPPNAVEKLRQVFAEN---ELPSRIVKENLSKELSLEPEKVNKWFKNARYL  550 (629)
Q Consensus       501 ~rft~~Q~~~Le~~F~~~---~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k  550 (629)
                      .|||.+|+..|+.+|.++   |||+..++++||..+||++.||++||||+|++
T Consensus         3 ~Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r   55 (60)
T d1k61a_           3 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRK   55 (60)
T ss_dssp             CSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhccc
Confidence            458999999999999876   79999999999999999999999999999984

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Rat (Rattus rattus) [TaxId: 10117]

Probab=99.54  E-value=4.7e-16  Score=129.98  Aligned_cols=54  Identities=24%  Similarity=0.355  Sum_probs=50.1

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhC---------------------CCcchhhhccchhccHHHH
Q 006832          500 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELS---------------------LEPEKVNKWFKNARYLALK  553 (629)
Q Consensus       500 r~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lg---------------------Lt~~QVkiWFQNrR~k~~K  553 (629)
                      |++||++|+.+||.+|+.|+||+..+|++||++||                     |++.||++||||||++.++
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr   75 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAF   75 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSC
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999999999994                     9999999999999995443

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.52  E-value=7.9e-16  Score=119.19  Aligned_cols=48  Identities=25%  Similarity=0.477  Sum_probs=44.8

Q ss_pred             CHHHHHHHHHHHHh-CCCCCHHHHHHHHHHhCCCcchhhhccchhccHH
Q 006832          504 PPNAVEKLRQVFAE-NELPSRIVKENLSKELSLEPEKVNKWFKNARYLA  551 (629)
Q Consensus       504 t~~Q~~~Le~~F~~-~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k~  551 (629)
                      |.+|+..||.+|.. ++||+..+++.||..|||++.||+|||||||++.
T Consensus         1 T~~q~~iLE~~F~~~~~~P~~~~~~~LA~~~~ls~~qV~~WFqNrR~k~   49 (52)
T d1x2ma1           1 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQE   49 (52)
T ss_dssp             SSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHS
T ss_pred             ChhHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhccc
Confidence            56899999999987 6999999999999999999999999999999943

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: LAG1 longevity assurance homolog 5, LASS5
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.47  E-value=3.9e-15  Score=118.07  Aligned_cols=52  Identities=23%  Similarity=0.374  Sum_probs=47.8

Q ss_pred             CCCCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHhCCCcchhhhccchhccH
Q 006832          499 SFHRMPPNAVEKLRQVFAE-NELPSRIVKENLSKELSLEPEKVNKWFKNARYL  550 (629)
Q Consensus       499 ~r~rft~~Q~~~Le~~F~~-~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~k  550 (629)
                      .+.+|+.+|..+||.+|.. ++||+..+++.||++|||++.||++||||||++
T Consensus         4 ~~~~~k~~~~~iLE~~F~~~~~yPs~~~~~~LA~~lgls~~qV~~WFqNrR~k   56 (59)
T d2cqxa1           4 DSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQ   56 (59)
T ss_dssp             CCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCccccHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcc
Confidence            3466788999999999986 689999999999999999999999999999994

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Nuclear corepressor KAP-1 (TIF-1beta)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.13  E-value=1.4e-11  Score=100.18  Aligned_cols=52  Identities=29%  Similarity=0.813  Sum_probs=44.7

Q ss_pred             cccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832          234 VHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       234 ~~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      .+....+|.+|+.++     +||+||+ |+++||+.|+.||+..+| .+.|+|+.|...
T Consensus         3 ~Dd~c~~C~~C~~~~-----~ll~Cd~-C~~~~H~~C~~p~l~~~p-~~~W~C~~C~~~   54 (70)
T d1fp0a1           3 LDDSATICRVCQKPG-----DLVMCNQ-CEFCFHLDCHLPALQDVP-GEEWSCSLCHVL   54 (70)
T ss_dssp             SSSSSSCCSSSCSSS-----CCEECTT-SSCEECTTSSSTTCCCCC-SSSCCCCSCCCC
T ss_pred             cCCCCCCCCCCCCcC-----EEEECCC-CChhhccccCCCCcCcCC-CCCEECcCCcCc
Confidence            455678899998754     7999995 999999999999999998 789999999754

>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Williams-Beuren syndrome transcription factor, WSTF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.06  E-value=2.3e-11  Score=92.68  Aligned_cols=48  Identities=40%  Similarity=0.925  Sum_probs=42.3

Q ss_pred             cccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCch
Q 006832          240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCEC  291 (629)
Q Consensus       240 ~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~  291 (629)
                      .|.+|+..+.  ++.||+|| .|+.+||+.|++||+..+| .+.|||+.|..
T Consensus         2 ~C~vC~~~~~--~~~~i~Cd-~C~~~~H~~C~~p~~~~~p-~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGE--DDKLILCD-ECNKAFHLFCLRPALYEVP-DGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSC--CSCCEECT-TTCCEECHHHHCTTCCSCC-SSCCSCTTTSC
T ss_pred             CCcCcCCCCC--CCCEEEcC-CCCCCCCCCCCCCCCCcCC-CCCEECcCCcC
Confidence            4889988764  67899999 5999999999999999998 78999999974

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.03  E-value=5.3e-11  Score=94.11  Aligned_cols=51  Identities=35%  Similarity=0.970  Sum_probs=43.9

Q ss_pred             cccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchhh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECKM  293 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k~  293 (629)
                      .+.++|.+|+.+     +.||+|| .|+++||+.|++|++...| .+.|||+.|..+.
T Consensus         7 ~~~~~C~~C~~~-----g~lv~Cd-~C~~~~H~~C~~~~~~~~~-~~~W~C~~C~~~~   57 (61)
T d1mm2a_           7 HHMEFCRVCKDG-----GELLCCD-TCPSSYHIHCLNPPLPEIP-NGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC-----SSCBCCS-SSCCCBCSSSSSSCCSSCC-SSCCCCTTTTTTC
T ss_pred             CCcCCCcCCCCC-----CeEEEeC-CCCccCchhhcCCCcCcCC-CCcEECCCCcCcc
Confidence            346789999865     4799999 5999999999999999888 6799999998653

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 22
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.96  E-value=1e-10  Score=98.43  Aligned_cols=57  Identities=23%  Similarity=0.661  Sum_probs=45.4

Q ss_pred             ccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCC---CCCceecccCchh
Q 006832          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES---RDQGWFCKFCECK  292 (629)
Q Consensus       235 ~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p---~dg~W~C~~C~~k  292 (629)
                      .....+|.+|+.......+.||+||+ |..+||+.||+|++....   +++.|||+.|...
T Consensus        13 ~~~~~~C~iC~~~~~~~~~~~v~Cd~-C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~   72 (88)
T d1weva_          13 MEMGLACVVCRQMTVASGNQLVECQE-CHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQ   72 (88)
T ss_dssp             HHHCCSCSSSCCCCCCTTCCEEECSS-SCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHH
T ss_pred             CcCcCCccCCCCccCCCCCeEEEcCC-CCCccccccCCCcccccccccCCCeEECcccCch
Confidence            34567899999866555678999995 999999999999986321   2678999999754

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=98.41  E-value=3.5e-08  Score=78.00  Aligned_cols=54  Identities=26%  Similarity=0.492  Sum_probs=42.6

Q ss_pred             ccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832          237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       237 e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      ....|.+|+.... .+..||.|| .|..+||+.|++++....+....|+|+.|..+
T Consensus         5 ~~~~C~~C~~~~~-~~~~~I~Cd-~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           5 SSGQCGACGESYA-ADEFWICCD-LCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SCCCCSSSCCCCC-SSSCEEECS-SSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCcCcCcCCCCC-CCCCEEEcC-CCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            3567999998653 335689999 59999999999998776653368999999754

>d1weea_ g.50.1.2 (A:) PHD finger protein At1g33420 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At1g33420
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=98.37  E-value=9.3e-08  Score=77.17  Aligned_cols=50  Identities=20%  Similarity=0.544  Sum_probs=39.8

Q ss_pred             ccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832          239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       239 ~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      ..| +|+.... ....||+|+ .|.++||+.|++++....+ .+.|+|+.|...
T Consensus        17 ~~C-~C~~~~~-~~~~mv~Cd-~C~~w~H~~C~g~~~~~~~-~~~~~C~~C~~~   66 (72)
T d1weea_          17 VDC-KCGTKDD-DGERMLACD-GCGVWHHTRCIGINNADAL-PSKFLCFRCIEL   66 (72)
T ss_dssp             ECC-TTCCCSC-CSSCEEECS-SSCEEEETTTTTCCTTSCC-CSCCCCHHHHHH
T ss_pred             EEe-eCCCCcC-CCCeEEEeC-CCCCcCchhhcCCccccCC-CCcEECcCCcCc
Confidence            347 6876542 345699999 5999999999999887776 579999999765

>d2pnxa1 g.50.1.2 (A:195-245) Inhibitor of growth protein 4, Ing4 {Homo sapiens [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Inhibitor of growth protein 4, Ing4
species: Homo sapiens [TaxId: 9606]

Probab=98.26  E-value=9.4e-08  Score=72.75  Aligned_cols=46  Identities=30%  Similarity=0.756  Sum_probs=35.7

Q ss_pred             ccccccccCcCCCCCCceEeCC-cC-CcccccccCCCCCCCCCCCCceecccCch
Q 006832          239 IICAKCKLREAFPDNDIVLCDG-TC-NCAFHQKCLDPPLDTESRDQGWFCKFCEC  291 (629)
Q Consensus       239 ~~C~vC~~~g~~~~~~lLlCDG-~C-~rafH~~CL~PPL~~~p~dg~W~C~~C~~  291 (629)
                      .+| +|+...   +++||.||. .| ..+||+.|++  |...| .+.|||+.|..
T Consensus         3 ~yC-~C~~~~---~~~mi~Cd~~~C~~~WfH~~Cvg--l~~~p-~~~w~C~~C~~   50 (51)
T d2pnxa1           3 TYC-LCHQVS---YGEMIGCDNPDCSIEWFHFACVG--LTTKP-RGKWFCPRCSQ   50 (51)
T ss_dssp             EET-TTTEEC---CSEEEECSCTTCSSCEEEGGGGT--CSSCC-SSCCCCHHHHC
T ss_pred             cEE-EcCCCC---CCCEEEEecCCCCCCCEeCCccC--CCcCC-CCcEECcCCCC
Confidence            589 798764   467999983 24 5799999998  55666 68999999964

>d1wesa_ g.50.1.2 (A:) PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD Inhibitor of growth protein 2, Ing2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.22  E-value=3e-07  Score=74.55  Aligned_cols=48  Identities=27%  Similarity=0.728  Sum_probs=35.6

Q ss_pred             ccccccccccCcCCCCCCceEeCC-cCC-cccccccCCCCCCCCCCCCceecccCch
Q 006832          237 EHIICAKCKLREAFPDNDIVLCDG-TCN-CAFHQKCLDPPLDTESRDQGWFCKFCEC  291 (629)
Q Consensus       237 e~~~C~vC~~~g~~~~~~lLlCDG-~C~-rafH~~CL~PPL~~~p~dg~W~C~~C~~  291 (629)
                      +..+| +|+...   ++.||+|+. .|. .+||+.|+.  |...| .+.|||+.|..
T Consensus        15 e~~~C-iC~~~~---~~~~i~c~~~~C~~~wfH~~Cvg--l~~~p-~~~w~C~~C~~   64 (71)
T d1wesa_          15 EPTYC-LCNQVS---YGEMIGCDNEQCPIEWFHFSCVS--LTYKP-KGKWYCPKCRG   64 (71)
T ss_dssp             SCCCS-TTCCCC---CSSEECCSCTTCSCCCEETTTTT--CSSCC-SSCCCCTTTSS
T ss_pred             CCCEE-EeCCCC---CCCEEEEECCCCCCcCccCccCC--CCcCC-CCcEECcCCcc
Confidence            44678 898764   346666641 476 689999995  67777 68999999974

>d1wepa_ g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 8
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.20  E-value=1.1e-07  Score=78.31  Aligned_cols=51  Identities=20%  Similarity=0.488  Sum_probs=39.1

Q ss_pred             ccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832          239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       239 ~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      .+| +|+.... .+..||.|| .|..+||..|++++....+..+.|+|+.|...
T Consensus        13 v~C-iC~~~~~-~~~~mI~Cd-~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~   63 (79)
T d1wepa_          13 VYC-LCRQPYN-VNHFMIECG-LCQDWFHGSCVGIEEENAVDIDIYHCPDCEAV   63 (79)
T ss_dssp             CCS-TTSCSCC-SSSCEEEBT-TTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTT
T ss_pred             eEe-ECCCccC-CCCcEEECC-CCCCcEeccccCcchhcCCCCCEEECccCcCC
Confidence            567 8998643 345699999 59999999999987555443367999999754

>d1wema_ g.50.1.2 (A:) Death associated transcription factor 1, Datf1 (DIO-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Death associated transcription factor 1, Datf1 (DIO-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.06  E-value=1.3e-07  Score=76.81  Aligned_cols=53  Identities=19%  Similarity=0.575  Sum_probs=38.7

Q ss_pred             ccccccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCC----CCCceecccCch
Q 006832          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES----RDQGWFCKFCEC  291 (629)
Q Consensus       235 ~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p----~dg~W~C~~C~~  291 (629)
                      +.+..+| +|+..+.  ++.||.|| .|..+||+.|++.+.....    ....|+|+.|..
T Consensus        13 d~~~~~C-iC~~~~~--~~~mi~Cd-~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~   69 (76)
T d1wema_          13 DPNALYC-ICRQPHN--NRFMICCD-RCEEWFHGDCVGISEARGRLLERNGEDYICPNCTI   69 (76)
T ss_dssp             CTTCCCS-TTCCCCC--SSCEEECS-SSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHH
T ss_pred             CCCcCEE-ECCCccC--CCeEEEEC-CCCCcCCccccCCCcccccccCCCCCcEECCCCcC
Confidence            3456789 8988753  56799999 6999999999985432111    235799999963

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Sumoylation ligase E3, SIZ1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.63  E-value=1.2e-05  Score=65.60  Aligned_cols=54  Identities=17%  Similarity=0.541  Sum_probs=37.3

Q ss_pred             cccccccccccCcCCCCCCceEeCC-cCCcccccccCCCCCC---CCC-CCCceecccCchh
Q 006832          236 HEHIICAKCKLREAFPDNDIVLCDG-TCNCAFHQKCLDPPLD---TES-RDQGWFCKFCECK  292 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lLlCDG-~C~rafH~~CL~PPL~---~~p-~dg~W~C~~C~~k  292 (629)
                      .+..+| +|+....  ++.||+|+. .|..|||+.|++.+-.   ..+ ....|+|+.|...
T Consensus        14 ~~~~~C-~C~~~~~--~~~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~   72 (78)
T d1wewa_          14 EIKVRC-VCGNSLE--TDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLT   72 (78)
T ss_dssp             CCCCCC-SSCCCCC--CSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHC
T ss_pred             CCccEe-ECCCccC--CCcEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCc
Confidence            345788 8998653  567888872 4999999999975322   111 1246999999743

>d1wila_ g.50.1.3 (A:) Hypothetical protein KIAA1045 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: variant PHD-like domain
domain: Hypothetical protein KIAA1045
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.97  E-value=0.0085  Score=49.11  Aligned_cols=54  Identities=22%  Similarity=0.719  Sum_probs=39.7

Q ss_pred             ccccccccccccCcCCCCCCceEeCCcCCcccccccCCCC--------CCCCC---CCCceecccCchh
Q 006832          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPP--------LDTES---RDQGWFCKFCECK  292 (629)
Q Consensus       235 ~~e~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PP--------L~~~p---~dg~W~C~~C~~k  292 (629)
                      ..++..|.+|....   .+.++-|- .|.+.||-.||.--        +....   .+-.|-|..|..-
T Consensus        12 v~~D~mC~vC~v~t---~~~l~pCR-vCtRv~H~~CL~r~gyl~~e~a~e~~e~A~T~~GWSC~~C~nl   76 (89)
T d1wila_          12 VVNDEMCDVCEVWT---AESLFPCR-VCTRVFHDGCLRRMGYIQGDSAAEVTEMAHTETGWSCHYCDNI   76 (89)
T ss_dssp             CCCSCCCTTTCCCC---SSCCSSCS-SSSSCCCHHHHHHHTSCCCCCCCSCSCCCSSSSSCCCTTTCCC
T ss_pred             CCcCccccccCccc---ccceecce-eecchhhHHHHHHhcccccHHHHHHHHhhcCCCCcchhhhcch
Confidence            45678899997765   47899999 89999999998321        11111   4568999999854

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.86  E-value=0.3  Score=38.05  Aligned_cols=46  Identities=17%  Similarity=0.291  Sum_probs=40.1

Q ss_pred             CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCcchhhhccchhcc
Q 006832          501 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  549 (629)
Q Consensus       501 ~rft~~Q~~~Le~~F~~~~yPs~~~re~LA~~lgLt~~QVkiWFQNrR~  549 (629)
                      ..||..+.-.+-+.|..++-.+   +.+||+.+||...+|..|..|+..
T Consensus         6 k~LT~~eK~~ii~~~e~g~k~s---q~eIA~~fGv~~STvs~IlKnK~k   51 (66)
T d1hlva1           6 RQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNKRA   51 (66)
T ss_dssp             CCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTHHH
T ss_pred             ccCCHHHHHHHHHHHHcCCcch---HHHHHHHhCCChhHHHHHHHHHHH
Confidence            3579999888888999887666   678999999999999999999765

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

Probab=84.77  E-value=0.028  Score=42.42  Aligned_cols=51  Identities=20%  Similarity=0.413  Sum_probs=33.8

Q ss_pred             cccccccccccCcCCCCCCce--EeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832          236 HEHIICAKCKLREAFPDNDIV--LCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       236 ~e~~~C~vC~~~g~~~~~~lL--lCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      .+..+|.+|.....  +..+.  .|.| |...||..||..=+..   .+.+.||.|...
T Consensus         4 ed~~~C~IC~~~~~--~~~~~~c~c~~-c~h~~H~~Cl~~W~~~---~~~~~CP~Cr~~   56 (60)
T d1vyxa_           4 EDVPVCWICNEELG--NERFRACGCTG-ELENVHRSCLSTWLTI---SRNTACQICGVV   56 (60)
T ss_dssp             CSCCEETTTTEECS--CCCCCSCCCSS-GGGSCCHHHHHHHHHH---HTCSBCTTTCCB
T ss_pred             CCCCCCccCCccCC--CceeEecccCC-CCCEEcHHHHHHHHhh---CCCCCCcccCCe
Confidence            34578999987643  22223  4665 8899999999853322   145679999865

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

Probab=82.65  E-value=0.28  Score=36.41  Aligned_cols=48  Identities=25%  Similarity=0.569  Sum_probs=34.8

Q ss_pred             cccccccccCcCCCCCCceEeCCcCCcccccccCCCCCCCCCCCCceecccCchh
Q 006832          238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESRDQGWFCKFCECK  292 (629)
Q Consensus       238 ~~~C~vC~~~g~~~~~~lLlCDG~C~rafH~~CL~PPL~~~p~dg~W~C~~C~~k  292 (629)
                      ...|.+|...-. .++.++.+. .|...||..|+..=+....     .||.|+..
T Consensus         5 ~~~C~ICl~~~~-~~~~~~~l~-~C~H~Fh~~Ci~~Wl~~~~-----~CP~CR~~   52 (55)
T d1iyma_           5 GVECAVCLAELE-DGEEARFLP-RCGHGFHAECVDMWLGSHS-----TCPLCRLT   52 (55)
T ss_dssp             SCCCTTTCCCCC-TTSCCEECS-SSCCEECTTHHHHTTTTCC-----SCSSSCCC
T ss_pred             CCCCeEECcccc-CCCEEEEeC-CCCCcccHHHHHHHHHhCC-----cCCCCCCE
Confidence            356999987643 334566676 4999999999997665532     59999854