Citrus Sinensis ID: 008193

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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----
Protein Sequence
MPGAGKKVVKHSESGKSCFPKKDSGSELIASLKFKKGSKISKSKKLRSKSRCQSKTVNSTLLKRTVAESHSKGAGDDFARSKSISQKNLHIKIDRKGSKNWASSKHKGKNSALVISKGNGEVVDGDGETKKLRKGRSKKRRKEKVELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRPEKELQRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRENSCSISRAGTDDDPSSSTSLSWFSDSETFSESMSEDEDWGPAKRRRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESARQVSGSPRISKESSLETEKKNADVLTLKNSLEETLICSPKSLKKIHPKRIQNQSAVAAASRKISRKELL
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccEEEEcccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccHHHccccccccHHHHHHHHHHHHccccccHHHHHHHHHHHcccHHHHHHcccHHHHHHHHHHHHHHHccccccccccccccHHHHcccHHHHHccccccccHHcccccccccccccccccHHHccHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccccHccccccccccccccccccccccccccccccEEcccHccccccccccccccccccccccccccccccccccHHcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHcccccccccHccEEEHHcccccccccccEEEEcccccccHHHHHccccccHcccccccccccccccccHHHHHHHHHHHccccccccccHHHHccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHccHHHHHHHHHHcccEEEcccHcccccccHcccHHHcHHHHHHHHHHHHc
Coil and Loop (DISEMBL)
mpgagkkvvkhsesgkscfpkkdsgSELIASLKfkkgskiskskklrsksrcqsktvnsTLLKRTvaeshskgagddfarsksisqknLHIKIdrkgsknwasskhkgknsaLVISkgngevvdgdgetkklrkgrskkrrkEKVELDEASRLQRRTRYLLIKMKLEQNLIDaysgegwkghsrekirPEKELQRAKKQILKCKIGIRDAIRQldslssvgciegsviatdgsvhhEHIICAKCklreafpdndivlcdgtcncafhqkcldppldtesippgdqgwfckfCECKMEIIESMNahigtsfsvnsnwqdifkeeaafpdgcSALLNqeeewpsddsedddynperrenscsisragtdddpssstslswfsdsetfsesmsededwgpakrrrkekESDAVNSLMTLYgseekyskVKTAEVkkklpsnakirrsfhrmppnAVEKLRQVFAenelpsriVKENlskelslepekvNKWFKNARYLALKARKVEsarqvsgspriskessleTEKKNADVLTLKNSLEetlicspkslkkihpkriqNQSAVAAASRKISRKELL
Flexible Loop (DISEMBL)
mpgagkkvvkhsesgkscfpkkdsgseLIASlkfkkgskiskskklrsksrcqsktvnstllkrtvaeshskgagddfarsksisqknlhikidrkgsknwasskhkgknsalviskgngevvdgdgetkklrkgrskkrrkekveldeasrlqrrtRYLLIKMKLEQNLIDaysgegwkghsrekirpekelqRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSviatdgsvhHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSALLNqeeewpsddsedddynperrenscsisragtdddpssstslswfsdsetfsesmsededwgpakrrrkekesdavNSLMtlygseekyskvktaevkkklpsnakirrsfhrmppnAVEKLRQVfaenelpsrivkenlskelslepekvnkwfKNARYLALKarkvesarqvsgspriskessletekKNADVLTLKNSLEETLICspkslkkihpkriqnqsavaaasrkisrkell
Low Complexity Region (SEG)
MPGAGKKVVKHSESGKSCFPKKDSGSELIAslkfkkgskiskskklrsksrcqskTVNSTLLKRTVAESHSKGAGDDFARSKSISQKNLHIKIDRKGSKNWASSKHKGKNSALVISKGNGEVVDGDGETkklrkgrskkrrkekVELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRPEKELQRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSALLNQeeewpsddsedddynpeRRENSCSISRAGTdddpssstslswfsdsETFSESMSEDEDWGPAKRRRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESARQVSGSPRISKESSLETEKKNADVLTLKNSLEETLICSPKSLKKIHPKRIQNQSAVAAASRKISRKELL
Disordered region (IsUnstruct)
************************************************************************************************************************************************************TRYLLIKMKLEQNLIDAYSGEGW******************KQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSAL*******************************************************************************************************************************************************VNKWFKNARYLALK****************************************************************************
Disordered Region (DISOPRED)
****************************************************************************************************************************************************************************************************************DAI************************HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEI****************NWQDIFKEEA***********************************************************************************************************************************************************LEPEKVNKWFK***********************************************************************************L
Disordered Region (DISEMBL)
************************GSELIASLKFK**********************NSTLLKRTVAESHSKGAGDDFARSKSISQKNLHIKIDRK**************SALVISKGNGEVVD*************************ASRLQRRTRYLLIKMKLEQNLIDAYSGE********KIRPEKELQRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSALLNQ************************************************************************AVNSLMTLYGSEEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR****************************VLTLKNSLEETLICSPKSLKKI************************
Disordered Region (DISPRO)
************************************************************************************************************************************************VELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRPEKELQRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEAA***********************************************************************************************************************FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE*********************KNADVLTLKNSLEETLICSPKSLKKIHPK*******V**AS**I******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPGAGKKVVKHSESGKSCFPKKDSGSELIASLKFKKGSKISKSKKLRSKSRCQSKTVNSTLLKRTVAESHSKGAGDDFARSKSISQKNLHIKIDRKGSKNWASSKHKGKNSALVISKGNGEVVDGDGETKKLRKGRSKKRRKEKVELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRPEKELQRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRENSCSISRAGTDDDPSSSTSLSWFSDSETFSESMSEDEDWGPAKRRRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESARQVSGSPRISKESSLETEKKNADVLTLKNSLEETLICSPKSLKKIHPKRIQNQSAVAAASRKISRKELL
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	574	2.2.26 [Sep-21-2011]
P48785	796	Pathogenesis-related home	yes	no	0.656	0.473	0.546	1e-124
Q04996	723	Homeobox protein HAT3.1 O	no	no	0.332	0.264	0.5	1e-52
P46605	719	Homeobox protein HOX1A OS	N/A	no	0.325	0.260	0.461	3e-50
P48786	1088	Pathogenesis-related home	N/A	no	0.303	0.159	0.465	8e-44
P87233	461	SWM histone demethylase c	yes	no	0.189	0.236	0.283	1e-05
Q04779	684	Transcriptional regulator	yes	no	0.095	0.080	0.396	3e-05
Q09908	538	SWM histone demethylase c	no	no	0.088	0.094	0.403	0.0001
Q09819	404	Uncharacterized protein C	no	no	0.081	0.116	0.436	0.0001
Q96BD5	680	PHD finger protein 21A OS	yes	no	0.102	0.086	0.366	0.0002
O97159	1982	Chromodomain-helicase-DNA	yes	no	0.078	0.022	0.436	0.0006

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

 Score =  445 bits (1145), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 239/437 (54%), Positives = 297/437 (67%), Gaps = 60/437 (13%)

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 DGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQD 318
           DGTCN AFHQKCLDPPL+TESIPPGDQGWFCKFC+CK+EII++MNA IGT F V+SNWQD
Sbjct: 211 DGTCNRAFHQKCLDPPLETESIPPGDQGWFCKFCDCKIEIIDTMNAQIGTHFPVDSNWQD 270

Query: 319 IFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRE----NSCSISRAGTDD------ 368
           IF EEA+ P G  A +N E +WPSDDS+DDDY+PE RE    NS ++S  G  D      
Sbjct: 271 IFNEEASLPIGSEATVNNEADWPSDDSKDDDYDPEMRENGGGNSSNVSGDGGGDNDEESI 330

Query: 369 --------DPSSSTSLSW--------------------------------------FSDS 382
                   D  + ++ SW                                      F   
Sbjct: 331 STSLSLSSDGVALSTGSWEGHRLSNMVEQCETSNEETVCGPRQRRTVDYTQLYYEMFGKD 390

Query: 383 ETFSESMSEDEDWGPAKRRRKEKESDAVNSLMTLYGSEEKYSKV----KTAEVKKKLPSN 438
               E  SEDEDWGP  RR++++ESDA ++L+T+  S +K   V    + +E       N
Sbjct: 391 AVLQEQGSEDEDWGPNDRRKRKRESDAGSTLVTMCESSKKDQDVVETLEQSERDSVSVEN 450

Query: 439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 498
              RR   R+P NAVEKLRQVFAE ELPS+ V++ L+KELSL+PEKVNKWFKN RY+AL+
Sbjct: 451 KGGRRRMFRLPRNAVEKLRQVFAETELPSKAVRDRLAKELSLDPEKVNKWFKNTRYMALR 510

Query: 499 ARKVESARQVSGSPRIS 515
            RK ES +Q   S  +S
Sbjct: 511 NRKTESVKQPGDSKTVS 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 =  208 bits (529), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 98/196 (50%), Positives = 133/196 (67%), Gaps = 5/196 (2%)

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 FPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTS 309
             DNDI+LCDG C+  FHQ CL+PPL  E IPP D+GW C  C+CK + ++ +N  +GT 
Sbjct: 277 SVDNDIILCDGFCDRGFHQYCLEPPLRKEDIPPDDEGWLCPGCDCKDDSLDLLNDSLGTK 336

Query: 310 FSVNSNWQDIFKEEAA 325
           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 =  200 bits (508), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 89/193 (46%), Positives = 129/193 (66%)

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 DIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFSVN 313
           DI+LCDG C+  FHQ CL+PPL TE IP GD+GW C  C+CK++ I+ +N   G++ S+ 
Sbjct: 225 DIILCDGACDRGFHQNCLNPPLRTEDIPMGDEGWLCPACDCKIDCIDLINELHGSNISIE 284

Query: 314 SNWQDIFKEEAAF 326
            +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 =  178 bits (452), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 81/174 (46%), Positives = 113/174 (64%)

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 HQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIF 320
           HQ CLDPPL  E IPP D+GW C  CECK++ I+ +N    T+  +  +W+ +F
Sbjct: 607 HQFCLDPPLLKEYIPPDDEGWLCPGCECKIDCIKLLNDSQETNILLGDSWEKVF 660

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 = 52.0 bits (123), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 34/120 (28%), Positives = 53/120 (44%), Gaps = 11/120 (9%)

Query: 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCE---CKM 296
           +C+ C+   +   N IV CDG CN  +HQ C  PP+D  ++   D  WFC  C+    K 
Sbjct: 192 LCSVCQRGHSPLSNRIVFCDG-CNSPYHQLCHHPPIDDATVQDVDAEWFCMKCQYRRAKQ 250

Query: 297 EIIESMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRE 356
            +   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|Q04779|RCO1_YEAST Transcriptional regulatory protein RCO1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RCO1 PE=1 SV=1

 Score = 50.8 bits (120), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/63 (39%), Positives = 33/63 (52%), Gaps = 8/63 (12%)

Query: 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEII 299
            C+ C    +F      LC  TC  +FH  CLDPP+D  ++P GD  W C  C+ K+ I 
Sbjct: 262 FCSACNQSGSF------LCCDTCPKSFHFLCLDPPIDPNNLPKGD--WHCNECKFKIFIN 313

Query: 300 ESM 302
            SM
Sbjct: 314 NSM 316

Catalytic component of the RPD3C(S) histone deacetylase complex responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression, DNA damage response, osmotic stress response and developmental events.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

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

 Score = 48.9 bits (115), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFC 292
           C+ C+  ++ P N IV CDG CN  FHQ C +P +  E +   +  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|Q09819|YAC5_SCHPO Uncharacterized protein C16C9.05 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC16C9.05 PE=1 SV=1

 Score = 48.5 bits (114), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 30/55 (54%), Gaps = 8/55 (14%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK 295
           C+ C  R  F     + C+G C C+FH  CL+PPL  E+IP G   WFC  C  K
Sbjct: 120 CSACGGRGLF-----ICCEG-CPCSFHLSCLEPPLTPENIPEG--SWFCVTCSIK 166

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 = 47.8 bits (112), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 38/71 (53%), Gaps = 12/71 (16%)

Query: 226 SVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQ 285
           S  +TDG +H +   C+ C+         +++CD TC+  +H  CLDPPL T  IP G  
Sbjct: 478 SPTSTDGDIHED--FCSVCRK-----SGQLLMCD-TCSRVYHLDCLDPPLKT--IPKG-- 525

Query: 286 GWFCKFCECKM 296
            W C  C+ +M
Sbjct: 526 MWICPRCQDQM 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|O97159|CHDM_DROME Chromodomain-helicase-DNA-binding protein Mi-2 homolog OS=Drosophila melanogaster GN=Mi-2 PE=1 SV=2

 Score = 46.6 bits (109), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 28/55 (50%), Gaps = 10/55 (18%)

Query: 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC 294
            C  CK      D   +LC  +C  A+H  CL+PPLDT  IP GD  W C  C C
Sbjct: 439 FCRVCK------DGGELLCCDSCPSAYHTFCLNPPLDT--IPDGD--WRCPRCSC 483

Vital role in development. Protein binds to a portion of Hunchback (HB) protein that is critical for repression of bithorax complex (BXC) genes. May also function in polycomb group (PcG) repression of Hox genes.

Drosophila melanogaster (taxid: 7227)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

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	574
225470662	727	PREDICTED: pathogenesis-related homeodom	0.998	0.788	0.579	0.0
255573765	732	conserved hypothetical protein [Ricinus	0.952	0.747	0.533	1e-153
356558320	600	PREDICTED: pathogenesis-related homeodom	0.883	0.845	0.520	1e-137
356530336	714	PREDICTED: pathogenesis-related homeodom	0.846	0.680	0.538	1e-137
357449593	707	Pathogenesis-related homeodomain protein	0.811	0.659	0.520	1e-133
356564821	617	PREDICTED: pathogenesis-related homeodom	0.810	0.753	0.549	1e-133
356550724	699	PREDICTED: pathogenesis-related homeodom	0.794	0.652	0.538	1e-131
302398843	404	HD domain class transcription factor [Ma	0.621	0.883	0.598	1e-126
15233766	796	Pathogenesis-related homeodomain protein	0.656	0.473	0.546	1e-122
334187017	769	Pathogenesis-related homeodomain protein	0.656	0.490	0.546	1e-122

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

 Score =  675 bits (1742), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/626 (57%), Positives = 445/626 (71%), Gaps = 53/626 (8%)

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 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIE 300
           CAKCKLREAFPDNDI+LCDGTCNCAFHQKCLDPPL+TE+IPPGDQGWFCKFCECKMEI+E
Sbjct: 240 CAKCKLREAFPDNDIILCDGTCNCAFHQKCLDPPLETENIPPGDQGWFCKFCECKMEILE 299

Query: 301 SMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRENSCS 360
           +MNAH+GT FSV+S WQDIFKEEAA PDG SAL   EE+WPSDDS+D DY+PER ENSCS
Sbjct: 300 AMNAHLGTRFSVDSTWQDIFKEEAALPDGGSALPYPEEDWPSDDSQDHDYDPERNENSCS 359

Query: 361 ISRAGTD----DDPSSSTSLSWFSDSETFS------------------------------ 386
           IS AGT+    DD +SS SLSW  + E  S                              
Sbjct: 360 ISTAGTEGNASDDTNSSLSLSWSFEDEILSGSKRSGIISADSDETSDCEIISGRRQRRAV 419

Query: 387 -----------------ESMSEDEDWGPAKRRRKEKESDAVNSLMTLYGSEEKYSKVKTA 429
                            E +SEDEDWGPA +RR+EKESDA ++L+TLY  E+K   V+T 
Sbjct: 420 DYRKLYDEMFGKDAHANEQVSEDEDWGPANKRRREKESDAASTLITLYEGEKKLPNVETM 479

Query: 430 EVKKKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWF 489
           E K+K+ S+ + +R F R+P +AVEKLRQ F ENELPSR V+ENL+K+L L+ EKVNKWF
Sbjct: 480 EAKQKISSDPQTKRPFSRIPLDAVEKLRQAFGENELPSRDVRENLAKQLGLDYEKVNKWF 539

Query: 490 KNARYLALKARKVESARQVSGSPRISKESSLETEK-KNADVLTLKNSLEETLICSPKSLK 548
           KNARY+ALK RK E A+Q+  SPRISKES  E  K K  D++  +++   +L+ + K+LK
Sbjct: 540 KNARYIALKTRKAERAKQLQTSPRISKESRSEIVKDKTVDLVASRDNSSASLVRALKNLK 599

Query: 549 KIHPKRIQNQSAVAAASRKISRKELL 574
           K+  ++       +   +K  R+ LL
Sbjct: 600 KVRRRKNPKPIITSPVKKKHHRRALL 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 =  547 bits (1409), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 327/613 (53%), Positives = 397/613 (64%), Gaps = 66/613 (10%)

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 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK 295
           HEHI CAKCK  E  PDNDIVLCDGTCNC FHQ+CLDPPLDTE+IPPGDQGW+CKFCEC+
Sbjct: 240 HEHIFCAKCKSNEVSPDNDIVLCDGTCNCGFHQRCLDPPLDTENIPPGDQGWYCKFCECR 299

Query: 296 MEIIESMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERR 355
           MEIIE+MNAH+GT FSV+S WQDIF+EEA F DG   LLN EEEWPSDDSEDDDY+P  +
Sbjct: 300 MEIIEAMNAHLGTQFSVDSCWQDIFQEEATFSDGGGILLNPEEEWPSDDSEDDDYDPGSQ 359

Query: 356 ENSCSISRAGTDDD----PSSSTSLSWFSDSETFS------------------ESMSEDE 393
           +N  SIS AGTDDD     SS+TSL W SD E  S                   S+  DE
Sbjct: 360 DN--SISGAGTDDDASDNASSATSLGWSSDGEVLSGSRKWDMGDTYFRNQFIYSSLDSDE 417

Query: 394 --DWGPAKRRRKEKESDAVNSLMTLYGSEEK----------------------------- 422
             D      RR+ +  D       ++G + +                             
Sbjct: 418 TSDGEIVCGRRQRRAVDYKKLYDEMFGKDAQEHEQVSEDEDWGPGKRKRREKESDAASTL 477

Query: 423 ---YSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELS 479
              Y   KT++  KK   + +++R   R+PP+AVEKLRQVFAENELPSR +KENLSKEL 
Sbjct: 478 MTLYESEKTSKKVKKHSRDPQVKRPLFRIPPSAVEKLRQVFAENELPSRTIKENLSKELG 537

Query: 480 LEPEKVNKWFKNARYLALKARKVESARQV-SGSPRISKESSLE-TEKKNADVLTLKNSLE 537
           LEP KV+KWFKNARYLALK+RK +   ++ S SP I +E  L+   K  AD+  L+ +  
Sbjct: 538 LEPGKVSKWFKNARYLALKSRKADRTSELYSSSPEIPREPKLDAVNKITADLAELRATSS 597

Query: 538 ETLICSPKSLKKI 550
           ET I SPKSLK+I
Sbjct: 598 ETKIYSPKSLKQI 610

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  495 bits (1275), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 297/571 (52%), Positives = 381/571 (66%), Gaps = 64/571 (11%)

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 DNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFS 311
           DNDI+LCDGTCN AFHQ+CL+PPLDTE+IPPGDQGWFCKFCECK+EI+E+ NAH+GT FS
Sbjct: 246 DNDIILCDGTCNRAFHQRCLNPPLDTENIPPGDQGWFCKFCECKIEILEATNAHLGTQFS 305

Query: 312 VNSNWQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRENSCSISRAGTDDDPS 371
           ++S WQD+FKEEAA PDG  ALLN EEEWPSDD EDDDYNPER+E++ +    G D++ S
Sbjct: 306 LDSTWQDVFKEEAAMPDGDIALLNPEEEWPSDDPEDDDYNPERKEDNHNFDTEGADENAS 365

Query: 372 SSTSLS--------------------WFSDSETFSESMSEDEDWGPAKR----------- 400
           + ++                      ++S +       S +   GP +R           
Sbjct: 366 NDSTSCSSLLSLNGECPPVDEGICHEYYSVNSCLDSDESGEIACGPRQRKAVDYKKLYDE 425

Query: 401 -----------------------RRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKKKLPS 437
                                  +R+EKESDAVN+LMTL+ SE K+S  +  +  ++  S
Sbjct: 426 MYGKDAPPCEQMSEDEDWGPGKRKRREKESDAVNTLMTLHESENKHSDNEKNDRTREGSS 485

Query: 438 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL 497
             +IRRS  R+P +AVEKLRQVFAENELP R VK++LSKEL L+PEKV+KWFKNARYLAL
Sbjct: 486 GIQIRRSCFRIPLDAVEKLRQVFAENELPPRSVKDSLSKELGLDPEKVSKWFKNARYLAL 545

Query: 498 KARKVES--ARQVSGSPRISKESSLETEKKN 526
           K R+ +S   R  S + +I+K+S  + E+K+
Sbjct: 546 KTRRYQSEGERLQSFTSKITKDSISQNEEKD 576

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  494 bits (1273), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 294/546 (53%), Positives = 366/546 (67%), Gaps = 60/546 (10%)

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 NDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFSV 312
           NDI+LCDGTCN AFHQ+CL+PPLDTE+IPPGDQGWFCKFCECK+EI+E+ NAH+GT FS+
Sbjct: 247 NDIILCDGTCNRAFHQRCLNPPLDTENIPPGDQGWFCKFCECKIEILEATNAHLGTQFSL 306

Query: 313 NSNWQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRENSCSISRAGTDDDPSS 372
           +S WQD+FKEEA+ PDG  ALLN EEEWPSDD EDDDYNPE++E+S SI   G D + S+
Sbjct: 307 DSTWQDVFKEEASMPDGDIALLNPEEEWPSDDPEDDDYNPEKKEDSHSIDIEGDDGNASN 366

Query: 373 --------------------STSLSWFSDSETFSESMSEDEDWGPAKR------------ 400
                                 S  ++S +     + S +   GP +R            
Sbjct: 367 DSTSSSSLWSLNGECPPVDEGVSHEYYSVNSCIDSNESGEIACGPRQRKAVDYKKLYDEM 426

Query: 401 ----------------------RRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKKKLPSN 438
                                 +R+EKESDAVN+LMTL+ SE K+S  +  +  ++  S 
Sbjct: 427 FGKDAPPCEQVSEDEDWGPGKRKRREKESDAVNTLMTLHESENKHSNNEKNDTTREGSSG 486

Query: 439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 498
            +IRRS  R+P +AVEKLRQ FAENELP R VK++LSKEL L+PEKV+KWFKNARYLALK
Sbjct: 487 IQIRRSCFRIPVDAVEKLRQAFAENELPPRSVKDSLSKELGLDPEKVSKWFKNARYLALK 546

Query: 499 ARKVES 504
            R+ +S
Sbjct: 547 TRRYQS 552

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  481 bits (1239), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 278/534 (52%), Positives = 339/534 (63%), Gaps = 68/534 (12%)

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 QKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEAAFP 327
           Q+CLDPPL+TE IPP DQGWFCK+C+CK+EI+E+ NAH+GT F ++S WQD+FKEEAA P
Sbjct: 255 QRCLDPPLETEDIPPEDQGWFCKYCDCKIEILEATNAHLGTRFPLDSTWQDVFKEEAAIP 314

Query: 328 DGCSALLNQEEEWPSDDSEDDDYNPERRENS----------------------------- 358
           DG +ALLNQEEEWPSDD EDDDYNPER+E S                             
Sbjct: 315 DGDAALLNQEEEWPSDDPEDDDYNPERKEESHGGFNTEGNDKNASDDSSSSSSMWSLNGE 374

Query: 359 CSISRAG----------TDDDPSSSTSLS---------------WFSDSETFSESMSEDE 393
           CS+   G           D D S   +                  F       E +SEDE
Sbjct: 375 CSLLDEGINLEYYSNDHIDSDESGEIACGRRQRRAVDYKKLYDEMFGKDAPPCEQVSEDE 434

Query: 394 DWGPAKRRRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAV 453
           DWGP KRRR+EKES+AVN+LMTL+ SE KY   K  +  +   +++ I+R   R    AV
Sbjct: 435 DWGPRKRRRREKESEAVNTLMTLHESENKYPNNKNNDRIRG--NSSGIKRPCFRFSHEAV 492

Query: 454 EKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESARQ 507
           EKLRQVFAENELP + VK+ LSKEL L+  KVNKWFKNARY+ALK RK++   Q
Sbjct: 493 EKLRQVFAENELPPKSVKDALSKELGLDAAKVNKWFKNARYMALKIRKLQEGGQ 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 =  481 bits (1239), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 288/524 (54%), Positives = 355/524 (67%), Gaps = 59/524 (11%)

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 PLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEAAFPDGCSAL 333
           PLDTE+IPPG+QGWFCKFCECKMEI+E+ NAH+GT FS++S WQD+FKEEAA PDG +AL
Sbjct: 258 PLDTENIPPGEQGWFCKFCECKMEILEATNAHLGTHFSLHSTWQDVFKEEAAIPDGETAL 317

Query: 334 LNQEEEWPSDDSEDDDYNPERRENSCSISRAGTDD-------------------DPSSST 374
           LN EEEWPSDDSEDDDY+PER+E+S +I+  G +D                    P    
Sbjct: 318 LNPEEEWPSDDSEDDDYDPERKEDSHNINTEGANDSASEDLTSSTSLCSSDGESSPVDGV 377

Query: 375 SLSWFS-----DS-----------------------ETFS------ESMSEDEDWGPAKR 400
           S  +FS     DS                       E F       E +SEDEDWGP KR
Sbjct: 378 SHEYFSVKSSIDSDESEDKACGCRQRKAVDYKKLYDEMFGKDAPAYEQLSEDEDWGPGKR 437

Query: 401 RRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQVF 460
           +R+EKESDAV+SLMTL+ SE  +   +  ++ +K  S+ KI+R   R+P +AVEKLRQVF
Sbjct: 438 KRREKESDAVDSLMTLHESENMHPNNEHLDMTRKNSSSIKIKRHCFRIPHDAVEKLRQVF 497

Query: 461 AENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES 504
           AENELP R ++E LSKEL L+ EKV+KWFKNARYLALK RK ++
Sbjct: 498 AENELPPRSIREGLSKELGLDTEKVSKWFKNARYLALKNRKYQA 541

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356550724|ref|XP_003543734.1| PREDICTED: pathogenesis-related homeodomain protein-like [Glycine max]

 Score =  474 bits (1221), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 289/537 (53%), Positives = 355/537 (66%), Gaps = 81/537 (15%)

Query: 36  KGSKISKSKKLRSKSRCQSKTVNSTLLKRTVAESHSKGAGDDFARSKSISQKNLHIKIDR 95
           KGSK S   K+R K + + + V      +  ++SH+K AG D +R + IS  +L +K  R
Sbjct: 11  KGSKKSSPLKVRKKGQGKKEKV------KVGSKSHTKNAGTDISRKRVIS--SLKVKGPR 62

Query: 96  KGS--KNWASSKH----------------KGKNSALVISKGNGEVVDGDGETKKLRKGRS 137
           K S  K   + K                 +GK ++L   K  G+  DG  + +K+++ R 
Sbjct: 63  KDSSDKKLITGKKLPMKNKKSSQKSSSKLQGKKASLSSRKEGGDA-DGAVKLQKMKRKRK 121

Query: 138 KKRRKEKVELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREKIRPEKELQRAK 197
           KKR +  V+LD+ SRLQRRTRYLLIKMKLEQNLIDAYSGEGWKG SREKIRPEKELQRA+
Sbjct: 122 KKRPRNNVDLDDPSRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGQSREKIRPEKELQRAR 181

Query: 198 KQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVL 257
           KQILKC++GIRDAIRQLDSL S+  IE S IA DGSV HEHI+C KCK+ E  PDNDI+L
Sbjct: 182 KQILKCRLGIRDAIRQLDSLGSLSSIEDSAIALDGSVCHEHILCVKCKVHEELPDNDIIL 241

Query: 258 CDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQ 317
           C+G C  AFHQKCLDPPLDTE+I PG+QGWFCKFCECKMEI+E+ NAH+GT FS++S WQ
Sbjct: 242 CNGKCERAFHQKCLDPPLDTENISPGEQGWFCKFCECKMEILEATNAHLGTHFSLHSTWQ 301

Query: 318 DIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRENSCSISRAGTDD--------- 368
           D+FKEEAA PDG  ALLN E+EWPSDDSEDDDY+PER+E+S +I+  GT+D         
Sbjct: 302 DVFKEEAAIPDGEIALLNPEQEWPSDDSEDDDYDPERKEDSHNINIEGTNDSASEDLSSS 361

Query: 369 ----------DPSSSTSLSWFS-----DS-----------------------ETFS---- 386
                      P    S  +FS     DS                       E F     
Sbjct: 362 TSLCSSDGECSPIDGVSHEYFSVNSSIDSDESEDKACGRRQRKAVDYKKLYDEMFGKDAP 421

Query: 387 --ESMSEDEDWGPAKRRRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKKKLPSNAKIRRS 444
             E +SEDEDWGP KR+R+EKESDAV+SLMTL+ SE ++       +  K  S+ KI+R 
Sbjct: 422 AYELLSEDEDWGPGKRKRREKESDAVDSLMTLHESENRHPN-NEHNMTSKDSSSIKIKRH 480

Query: 445 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 501
             R+P +AVE+LRQVFAENELP R ++E LSKEL L+ EKV+KWFKNARYLALK RK
Sbjct: 481 CFRIPRDAVERLRQVFAENELPPRSIREGLSKELGLDTEKVSKWFKNARYLALKNRK 537

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302398843|gb|ADL36716.1| HD domain class transcription factor [Malus x domestica]

 Score =  457 bits (1177), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 236/394 (59%), Positives = 280/394 (71%), Gaps = 37/394 (9%)

Query: 192 ELQRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFP 251
           ELQRA KQIL CK+GIRDAI QLDSLSSVG I  S I+ DGSV HEHI CAKCKL EAFP
Sbjct: 2   ELQRANKQILNCKLGIRDAIHQLDSLSSVGSIADSFISPDGSVSHEHIFCAKCKLNEAFP 61

Query: 252 DNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFS 311
           DNDI+LCDGTCNCAFHQKCLDPPLDTE+IP G+QGWFCKFCECKMEI+E +NAH+GT F 
Sbjct: 62  DNDIILCDGTCNCAFHQKCLDPPLDTENIPRGEQGWFCKFCECKMEILELVNAHLGTCFP 121

Query: 312 VNSNWQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRENSCSISRAGTDDDPS 371
           +NS WQD+FKEEA FP G ++LLN +EEWPSDDSEDDDYNPER ENSCSISR G+DD  S
Sbjct: 122 MNSGWQDVFKEEATFPHGKNSLLNPDEEWPSDDSEDDDYNPERNENSCSISRGGSDDIAS 181

Query: 372 S---STSLSWFSDSET-----------------------------FSESMSEDEDWGPAK 399
               ST +S  SD  T                               E +S+DEDWGP K
Sbjct: 182 EEELSTDVSVGSDVSTDGEIVSSRRQKRSVDYKKLYDEMFGKDGPLLEQISDDEDWGPGK 241

Query: 400 RRRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQV 459
           R+R+  ESDA ++LMTLY SE      ++ +   +  S+ ++RRS  R+P NAVEKLRQV
Sbjct: 242 RKRRGNESDAASTLMTLYESERNPDVDRSEKKSSQHSSDTQVRRSCFRIPRNAVEKLRQV 301

Query: 460 FAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESARQV-SGSPRISKES 518
           F+ENELPSR VK+NLSKEL L PEKV+KWFKNARYLALK RK  S + + + +P ISK  
Sbjct: 302 FSENELPSRAVKDNLSKELGLNPEKVSKWFKNARYLALKTRKGASGKDLDTFTPGISKAP 361

Query: 519 SLE-TEKKNADVL---TLKNSLEETLICSPKSLK 548
             E    K AD++   +  ++L ET++ SPK+ K
Sbjct: 362 GYENVTGKAADLMASDSDDDTLAETVVHSPKNAK 395

Source: Malus x domestica

Species: Malus x domestica

Genus: Malus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15233766|ref|NP_194723.1| Pathogenesis-related homeodomain protein [Arabidopsis thaliana] gi|1346790|sp|P48785.1|PRH_ARATH RecName: Full=Pathogenesis-related homeodomain protein; Short=PRHA gi|507220|gb|AAA32843.1| homeodomain protein [Arabidopsis thaliana] gi|2501810|gb|AAC49836.1| PRHA [Arabidopsis thaliana] gi|4914418|emb|CAB43669.1| pathogenesis related homeodomain protein (PRHA) [Arabidopsis thaliana] gi|7269893|emb|CAB79752.1| pathogenesis related homeodomain protein (PRHA) [Arabidopsis thaliana] gi|332660298|gb|AEE85698.1| Pathogenesis-related homeodomain protein [Arabidopsis thaliana]

 Score =  445 bits (1145), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 239/437 (54%), Positives = 297/437 (67%), Gaps = 60/437 (13%)

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 DGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQD 318
           DGTCN AFHQKCLDPPL+TESIPPGDQGWFCKFC+CK+EII++MNA IGT F V+SNWQD
Sbjct: 211 DGTCNRAFHQKCLDPPLETESIPPGDQGWFCKFCDCKIEIIDTMNAQIGTHFPVDSNWQD 270

Query: 319 IFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRE----NSCSISRAGTDD------ 368
           IF EEA+ P G  A +N E +WPSDDS+DDDY+PE RE    NS ++S  G  D      
Sbjct: 271 IFNEEASLPIGSEATVNNEADWPSDDSKDDDYDPEMRENGGGNSSNVSGDGGGDNDEESI 330

Query: 369 --------DPSSSTSLSW--------------------------------------FSDS 382
                   D  + ++ SW                                      F   
Sbjct: 331 STSLSLSSDGVALSTGSWEGHRLSNMVEQCETSNEETVCGPRQRRTVDYTQLYYEMFGKD 390

Query: 383 ETFSESMSEDEDWGPAKRRRKEKESDAVNSLMTLYGSEEKYSKV----KTAEVKKKLPSN 438
               E  SEDEDWGP  RR++++ESDA ++L+T+  S +K   V    + +E       N
Sbjct: 391 AVLQEQGSEDEDWGPNDRRKRKRESDAGSTLVTMCESSKKDQDVVETLEQSERDSVSVEN 450

Query: 439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 498
              RR   R+P NAVEKLRQVFAE ELPS+ V++ L+KELSL+PEKVNKWFKN RY+AL+
Sbjct: 451 KGGRRRMFRLPRNAVEKLRQVFAETELPSKAVRDRLAKELSLDPEKVNKWFKNTRYMALR 510

Query: 499 ARKVESARQVSGSPRIS 515
            RK ES +Q   S  +S
Sbjct: 511 NRKTESVKQPGDSKTVS 527

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334187017|ref|NP_001190867.1| Pathogenesis-related homeodomain protein [Arabidopsis thaliana] gi|332660299|gb|AEE85699.1| Pathogenesis-related homeodomain protein [Arabidopsis thaliana]

 Score =  444 bits (1143), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 239/437 (54%), Positives = 297/437 (67%), Gaps = 60/437 (13%)

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 DGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQD 318
           DGTCN AFHQKCLDPPL+TESIPPGDQGWFCKFC+CK+EII++MNA IGT F V+SNWQD
Sbjct: 211 DGTCNRAFHQKCLDPPLETESIPPGDQGWFCKFCDCKIEIIDTMNAQIGTHFPVDSNWQD 270

Query: 319 IFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRE----NSCSISRAGTDD------ 368
           IF EEA+ P G  A +N E +WPSDDS+DDDY+PE RE    NS ++S  G  D      
Sbjct: 271 IFNEEASLPIGSEATVNNEADWPSDDSKDDDYDPEMRENGGGNSSNVSGDGGGDNDEESI 330

Query: 369 --------DPSSSTSLSW--------------------------------------FSDS 382
                   D  + ++ SW                                      F   
Sbjct: 331 STSLSLSSDGVALSTGSWEGHRLSNMVEQCETSNEETVCGPRQRRTVDYTQLYYEMFGKD 390

Query: 383 ETFSESMSEDEDWGPAKRRRKEKESDAVNSLMTLYGSEEKYSKV----KTAEVKKKLPSN 438
               E  SEDEDWGP  RR++++ESDA ++L+T+  S +K   V    + +E       N
Sbjct: 391 AVLQEQGSEDEDWGPNDRRKRKRESDAGSTLVTMCESSKKDQDVVETLEQSERDSVSVEN 450

Query: 439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 498
              RR   R+P NAVEKLRQVFAE ELPS+ V++ L+KELSL+PEKVNKWFKN RY+AL+
Sbjct: 451 KGGRRRMFRLPRNAVEKLRQVFAETELPSKAVRDRLAKELSLDPEKVNKWFKNTRYMALR 510

Query: 499 ARKVESARQVSGSPRIS 515
            RK ES +Q   S  +S
Sbjct: 511 NRKTESVKQPGDSKTVS 527

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	574
TAIR|locus:2005538	796	PRHA "pathogenesis related hom	0.332	0.239	0.753	1.3e-115
TAIR|locus:2090694	723	HAT3.1 [Arabidopsis thaliana (	0.313	0.248	0.516	1.3e-59
UNIPROTKB|J3QQU3	129	PHF12 "PHD finger protein 12"	0.094	0.418	0.354	6.4e-06
UNIPROTKB|K7EQP5	117	PHF12 "PHD finger protein 12"	0.076	0.376	0.403	7.6e-05
TAIR|locus:2089606	343	AT3G14740 [Arabidopsis thalian	0.165	0.276	0.320	0.00012
POMBASE|SPCC4G3.07c	461	phf1 "PHD finger containing pr	0.123	0.154	0.355	0.00026
WB|WBGene00020485	220	ceh-54 [Caenorhabditis elegans	0.182	0.477	0.288	0.00032
SGD|S000004680	684	RCO1 "Essential subunit of the	0.250	0.210	0.304	0.00035
UNIPROTKB|I3LTW3	113	I3LTW3 "Uncharacterized protei	0.073	0.371	0.404	0.00043
POMBASE|SPAC16C9.05	404	cph1 "Clr6 histone deacetylase	0.081	0.116	0.436	0.00045

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

 Score = 815 (292.0 bits), Expect = 1.3e-115, Sum P(2) = 1.3e-115
 Identities = 144/191 (75%), Positives = 170/191 (89%)

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 AFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEA 324
             AFHQKCLDPPL+TESIPPGDQGWFCKFC+CK+EII++MNA IGT F V+SNWQDIF EEA
Sbjct:   217 AFHQKCLDPPLETESIPPGDQGWFCKFCDCKIEIIDTMNAQIGTHFPVDSNWQDIFNEEA 276

Query:   325 AFPDGCSALLN 335
             + P G  A +N
Sbjct:   277 SLPIGSEATVN 287

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 = 509 (184.2 bits), Expect = 1.3e-59, Sum P(2) = 1.3e-59
 Identities = 93/180 (51%), Positives = 126/180 (70%)

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 FHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNWQDIFKEEAA 325
             FHQ CL+PPL  E IPP 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|J3QQU3 PHF12 "PHD finger protein 12" [Homo sapiens (taxid:9606)]

 Score = 114 (45.2 bits), Expect = 6.4e-06, P = 6.4e-06
 Identities = 22/62 (35%), Positives = 32/62 (51%)

Query:   238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKME 297
             H  C  CK        D++ CD  C  AFH +C +PPL  E +PPG+  W C  C  + +
Sbjct:    56 HDSCDSCK-----EGGDLLCCDH-CPAAFHLQCCNPPLSEEMLPPGE--WMCHRCTVRRK 107

Query:   298 II 299
             ++
Sbjct:   108 VL 109

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|K7EQP5 PHF12 "PHD finger protein 12" [Homo sapiens (taxid:9606)]

 Score = 104 (41.7 bits), Expect = 7.6e-05, P = 7.6e-05
 Identities = 21/52 (40%), Positives = 27/52 (51%)

Query:   238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFC 289
             H  C  CK        D++ CD  C  AFH +C +PPL  E +PPG+  W C
Sbjct:    74 HDSCDSCK-----EGGDLLCCDH-CPAAFHLQCCNPPLSEEMLPPGE--WMC 117

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2089606 AT3G14740 [Arabidopsis thaliana (taxid:3702)]

 Score = 123 (48.4 bits), Expect = 0.00012, P = 0.00012
 Identities = 34/106 (32%), Positives = 53/106 (50%)

Query:   190 EKELQRAKKQILKCKIGIRDAIRQLDSLSSVGCI-EGSVI-ATDGSVHHEH-IICAKCKL 246
             EK ++  KK  L  +  +   + + D   ++  + +G  +  +D  V  E  I+CA C+ 
Sbjct:   103 EKSIE--KKSTLNVESSLE--VEEDDDKENIDPLGKGKALDLSDREVEDEDGIMCAVCQS 158

Query:   247 REAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFC 292
              +  P N IV CDG C+   H  C   PL  ++IP GD  WFC+ C
Sbjct:   159 TDGDPLNPIVFCDG-CDLMVHASCYGNPL-VKAIPEGD--WFCRQC 200

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

POMBASE|SPCC4G3.07c phf1 "PHD finger containing protein Phf1" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 122 (48.0 bits), Expect = 0.00026, P = 0.00026
 Identities = 27/76 (35%), Positives = 38/76 (50%)

Query:   240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCE---CKM 296
             +C+ C+   +   N IV CDG CN  +HQ C  PP+D  ++   D  WFC  C+    K 
Sbjct:   192 LCSVCQRGHSPLSNRIVFCDG-CNSPYHQLCHHPPIDDATVQDVDAEWFCMKCQYRRAKQ 250

Query:   297 EIIESMNAH-IGTSFS 311
              +   M A  +G S S
Sbjct:   251 PLETGMTAQDLGLSES 266

GO:0005634 "nucleus" evidence=IDA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0019787 "small conjugating protein ligase activity" evidence=ISM

GO:0033169 "histone H3-K9 demethylation" evidence=IMP

GO:0033193 "Lsd1/2 complex" evidence=IDA

GO:0034605 "cellular response to heat" evidence=IEP

GO:0031491 "nucleosome binding" evidence=IDA

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

 Score = 115 (45.5 bits), Expect = 0.00032, P = 0.00032
 Identities = 32/111 (28%), Positives = 58/111 (52%)

Query:   428 TAEVKKKLPSNAKI-RRSFHRMP--PNAVEKLRQVFAENELPSRIVKENLSKELSLEPEK 484
             T ++ +K  +N    R+  +R+    N ++++ +VFAEN+ P  + +E L+ ++ L  E+
Sbjct:    28 TKKITRKRSNNFNPDRKKRNRITFDANQIDEMEKVFAENQYPDTMSREKLANKIQLHEER 87

Query:   485 VNKWFKNARYLALKARKVESARQVSGSPRISKESSLETEKKNADVLTLKNS 535
             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

SGD|S000004680 RCO1 "Essential subunit of the histone deacetylase Rpd3S complex" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 123 (48.4 bits), Expect = 0.00035, P = 0.00035
 Identities = 52/171 (30%), Positives = 74/171 (43%)

Query:   159 YLLIKMKLEQNLIDAYSGEGWKGH--SREKIR-PEKELQRAKKQILKCKIGIRDAIRQLD 215
             +L   M  E N+    S  GW G   +R + R PE +    K   ++ KI I       D
Sbjct:   170 FLTENMTEESNI---RSTIGWNGDIINRTRDREPESDRDNKKLSNIRTKI-ILSTNATYD 225

Query:   216 SLSSV-GCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIV---------LCDGTCNCA 265
             S S + G  + S+ +T  +   E I   K      F + D           LC  TC  +
Sbjct:   226 SKSKLFG--QNSIKSTSNA--SEKIFRDKNNSTIDFENEDFCSACNQSGSFLCCDTCPKS 281

Query:   266 FHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFSVNSNW 316
             FH  CLDPP+D  ++P GD  W C   ECK +I   +N  + T   + SN+
Sbjct:   282 FHFLCLDPPIDPNNLPKGD--WHCN--ECKFKIF--INNSMATLKKIESNF 326

GO:0005634 "nucleus" evidence=IEA;IDA

GO:0060195 "negative regulation of antisense RNA transcription" evidence=IMP

GO:0016568 "chromatin modification" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

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

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

GO:0033698 "Rpd3L complex" evidence=IDA

GO:0016575 "histone deacetylation" evidence=IMP

GO:0032221 "Rpd3S complex" evidence=IDA

GO:0000118 "histone deacetylase complex" evidence=IDA

GO:0030174 "regulation of DNA-dependent DNA replication initiation" evidence=IMP

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=IGI

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 97 (39.2 bits), Expect = 0.00043, P = 0.00043
 Identities = 19/47 (40%), Positives = 29/47 (61%)

Query:   256 VLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC-KMEIIES 301
             VLCD  CN A+H  CL+PPLD     P ++ W+C  C+    E++++
Sbjct:     3 VLCD-ECNMAYHIYCLNPPLDKV---PEEEYWYCPSCKTDSSEVVKA 45

GO:0008270 "zinc ion binding" evidence=IEA

POMBASE|SPAC16C9.05 cph1 "Clr6 histone deacetylase associated PHD protein-1 Cph1" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 119 (46.9 bits), Expect = 0.00045, P = 0.00045
 Identities = 24/55 (43%), Positives = 30/55 (54%)

Query:   241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK 295
             C+ C  R  F     + C+G C C+FH  CL+PPL  E+IP G   WFC  C  K
Sbjct:   120 CSACGGRGLF-----ICCEG-CPCSFHLSCLEPPLTPENIPEGS--WFCVTCSIK 166

GO:0005634 "nucleus" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0006338 "chromatin remodeling" evidence=IPI

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016575 "histone deacetylation" evidence=ISO

GO:0019787 "small conjugating protein ligase activity" evidence=ISM

GO:0032221 "Rpd3S complex" evidence=IDA

GO:0071276 "cellular response to cadmium ion" evidence=IMP

GO:0071585 "detoxification of cadmium ion" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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	574
pfam00628	51	pfam00628, PHD, PHD-finger	8e-13
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	2e-08
smart00249	47	smart00249, PHD, PHD zinc finger	3e-07
smart00389	57	smart00389, HOX, Homeodomain	5e-07
pfam00046	57	pfam00046, Homeobox, Homeobox domain	4e-04
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	5e-04

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

 Score = 62.5 bits (152), Expect = 8e-13
 Identities = 24/56 (42%), Positives = 33/56 (58%), Gaps = 5/56 (8%)

Query: 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK 295
            CA C   +   D +++LCDG C+  FH  CL PPL+ E IP G+  W+C  C+ K
Sbjct: 1   YCAVC--GKVDDDGELLLCDG-CDRWFHLACLGPPLEPEEIPEGE--WYCPECKPK 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|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: 442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494
           RR   R  P  +E+L + F +N  PSR  +E L+KEL L   +V  WF+N R 
Sbjct: 1   RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRA 53

Length = 59

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

 Score = 46.8 bits (111), Expect = 3e-07
 Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 6/53 (11%)

Query: 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFC 292
            C+ C   +     +++ CDG C+  +HQ CL PPL  E  P G   W+C  C
Sbjct: 1   YCSVCGKPDD--GGELLQCDG-CDRWYHQTCLGPPLL-EEEPDGK--WYCPKC 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|197696 smart00389, HOX, Homeodomain

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

Query: 440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494
           + 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|200956 pfam00046, Homeobox, Homeobox domain

 Score = 38.2 bits (90), Expect = 4e-04
 Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 6/62 (9%)

Query: 440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 499
           + 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: 500 RK 501
           ++
Sbjct: 56  KR 57

Length = 57

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

 Score = 40.5 bits (95), Expect = 5e-04
 Identities = 29/130 (22%), Positives = 49/130 (37%), Gaps = 16/130 (12%)

Query: 399 KRRRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQ 458
           K  + ++E +A +S M L   ++  S  K+   +                    +  L +
Sbjct: 24  KTTKNKREVEAADSEMKLERKQDGSSPPKSKRRRTTD---------------EQLMVLER 68

Query: 459 VFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY-LALKARKVESARQVSGSPRISKE 517
            F  N  PS I +  LS  L++ P+ V  WF+N R     K       R       ++K 
Sbjct: 69  EFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQRPGEEEADLAKI 128

Query: 518 SSLETEKKNA 527
            SL T + + 
Sbjct: 129 GSLSTGQISI 138

Length = 156

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	574
KOG4299	613	consensus PHD Zn-finger protein [General function	99.88
KOG1244	336	consensus Predicted transcription factor Requiem/N	99.63
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.61
KOG0843	197	consensus Transcription factor EMX1 and related HO	99.57
KOG0842	307	consensus Transcription factor tinman/NKX2-3, cont	99.57
KOG0488	309	consensus Transcription factor BarH and related HO	99.56
KOG0487	308	consensus Transcription factor Abd-B, contains HOX	99.56
KOG0489	261	consensus Transcription factor zerknullt and relat	99.54
KOG0493	342	consensus Transcription factor Engrailed, contains	99.51
KOG0485	268	consensus Transcription factor NKX-5.1/HMX1, conta	99.51
KOG0850	245	consensus Transcription factor DLX and related pro	99.5
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.5
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.49
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.46
KOG0484	125	consensus Transcription factor PHOX2/ARIX, contain	99.46
KOG0492	246	consensus Transcription factor MSH, contains HOX d	99.45
KOG0483	198	consensus Transcription factor HEX, contains HOX a	99.41
KOG2251	228	consensus Homeobox transcription factor [Transcrip	99.37
KOG0848	317	consensus Transcription factor Caudal, contains HO	99.3
KOG0494	332	consensus Transcription factor CHX10 and related H	99.28
COG5576	156	Homeodomain-containing transcription factor [Trans	99.27
KOG4577	383	consensus Transcription factor LIM3, contains LIM	99.26
KOG0491	194	consensus Transcription factor BSH, contains HOX d	99.26
KOG3802	398	consensus Transcription factor OCT-1, contains POU	99.17
KOG0844	408	consensus Transcription factor EVX1, contains HOX	99.17
KOG0847	288	consensus Transcription factor, contains HOX domai	99.01
KOG0486	351	consensus Transcription factor PTX1, contains HOX	98.89
KOG0490	235	consensus Transcription factor, contains HOX domai	98.8
KOG0775	304	consensus Transcription factor SIX and related HOX	98.76
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	98.69
KOG0849	354	consensus Transcription factor PRD and related pro	98.65
KOG0825	1134	consensus PHD Zn-finger protein [General function	98.6
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.58
KOG0774	334	consensus Transcription factor PBX and related HOX	98.4
KOG2252	558	consensus CCAAT displacement protein and related h	98.37
KOG1168	385	consensus Transcription factor ACJ6/BRN-3, contain	98.36
KOG1512	381	consensus PHD Zn-finger protein [General function	98.29
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	98.27
KOG4323	464	consensus Polycomb-like PHD Zn-finger protein [Gen	98.15
KOG0955	1051	consensus PHD finger protein BR140/LIN-49 [General	98.13
KOG1973	274	consensus Chromatin remodeling protein, contains P	97.96
KOG4443	694	consensus Putative transcription factor HALR/MLL3,	97.94
cd04718	148	BAH_plant_2 BAH, or Bromo Adjacent Homology domain	97.93
KOG0490	235	consensus Transcription factor, contains HOX domai	97.85
COG5141	669	PHD zinc finger-containing protein [General functi	97.82
KOG0954	893	consensus PHD finger protein [General function pre	97.8
KOG0773	342	consensus Transcription factor MEIS1 and related H	97.79
KOG1245	1404	consensus Chromatin remodeling complex WSTF-ISWI,	97.78
KOG0383	696	consensus Predicted helicase [General function pre	97.74
COG5034	271	TNG2 Chromatin remodeling protein, contains PhD zi	97.69
KOG0956	900	consensus PHD finger protein AF10 [General functio	97.54
KOG1246	904	consensus DNA-binding protein jumonji/RBP2/SMCY, c	97.43
KOG0957	707	consensus PHD finger protein [General function pre	97.32
KOG1146	1406	consensus Homeobox protein [General function predi	96.86
PF13831	36	PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.	96.43
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	96.12
KOG1473	1414	consensus Nucleosome remodeling factor, subunit NU	95.97
KOG3623	1007	consensus Homeobox transcription factor SIP1 [Tran	94.91
KOG0957	707	consensus PHD finger protein [General function pre	94.59
PF15446	175	zf-PHD-like: PHD/FYVE-zinc-finger like domain	93.27
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	92.97
KOG4443	694	consensus Putative transcription factor HALR/MLL3,	91.46
KOG3612	588	consensus PHD Zn-finger protein [General function	87.37
KOG4299	613	consensus PHD Zn-finger protein [General function	86.66
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	83.44
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	81.58

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

Probab=99.88  E-value=2e-23  Score=228.03  Aligned_cols=203  Identities=37%  Similarity=0.621  Sum_probs=162.6

Q ss_pred             cchhHHHHHHHHHHHHHHHHHHhhhHhhhhcCcccccCccc---------CCChHHHHHHHHHHhhhhhhHHHHHhhhcc
Q 008193          146 ELDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKGHSREK---------IRPEKELQRAKKQILKCKIGIRDAIRQLDS  216 (574)
Q Consensus       146 ~~~~~~ri~~r~r~~l~~~~~eq~l~dAy~~egWk~~sreK---------~rp~~Elerak~~ilk~k~~ir~~i~~~d~  216 (574)
                      .+++.-|+..+++|++..+..+++++++|+.+||++.+.++         ++|.++...+..+|+.+++.++.+.++++.
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            56788999999999999999999999999999999999999         999999999999999999999999999988


Q ss_pred             CCCCCCCcCCcccCCCCcccccc--cccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193          217 LSSVGCIEGSVIATDGSVHHEHI--ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC  294 (574)
Q Consensus       217 l~~~~~l~~s~l~~dg~~~~ed~--~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~  294 (574)
                      ....+..++..+..|+....++.  ||..|++.+.+  +++||||+ |+++|||+||.|||..+.+|.|.  |||+.|.+
T Consensus       230 ~s~~~t~~e~r~~~D~~~~~~~~~~fCsaCn~~~~F--~~~i~CD~-Cp~sFH~~CLePPl~~eniP~g~--W~C~ec~~  304 (613)
T KOG4299|consen  230 ESKEGTVEEKRRERDKNISVEDIEDFCSACNGSGLF--NDIICCDG-CPRSFHQTCLEPPLEPENIPPGS--WFCPECKI  304 (613)
T ss_pred             hhhhccchhhhhhhccccccCCHHHHHHHhCCcccc--ccceeecC-CchHHHHhhcCCCCCcccCCCCc--cccCCCee
Confidence            88877788888888887766665  99999998766  78899996 99999999999999999999998  99999999


Q ss_pred             hhhhhhhhh--------ccCCceec--ccCc--cccccccccCCCCCCccccCCCCCCCCCCCCCCCCCcccc
Q 008193          295 KMEIIESMN--------AHIGTSFS--VNSN--WQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERR  355 (574)
Q Consensus       295 k~~~~~~~n--------~~~g~~f~--l~~~--~~~~F~e~a~~~~g~~~~~~~~~~~psddsEDeD~dp~~~  355 (574)
                      +..+.+..+        ...++.|.  |+..  |...|++.....-+...  +....+++++..+.+|++...
T Consensus       305 k~~in~~~~t~~~~~~~~~i~t~~~~~IDs~np~q~~lPe~i~~~~~~v~--~g~~~~~sd~~~~~pl~~~~~  375 (613)
T KOG4299|consen  305 KSVINPKMETLSNRGTVVDIFTQFVSKIDSHNPIQKILPENISESFGGVS--RGDDGQYSDTQDEKPLDPPAL  375 (613)
T ss_pred             eeecccchhhhhhccchHHHHHHHHHhhhccchhhhhCCHHHHhhccccc--cCCCCccccccCCcCCChhhh
Confidence            876554443        23333333  3333  44445443322222211  334456688888888988443

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

Probab=99.63  E-value=4.4e-17  Score=163.65  Aligned_cols=191  Identities=21%  Similarity=0.352  Sum_probs=133.3

Q ss_pred             CCCC-chhhhhhhccccchhh--hccccccccccccccCCCc-cccccCCCCcccCCCchhhhhhcccchhhhcccc--c
Q 008193           73 GAGD-DFARSKSISQKNLHIK--IDRKGSKNWASSKHKGKNS-ALVISKGNGEVVDGDGETKKLRKGRSKKRRKEKV--E  146 (574)
Q Consensus        73 ~~~~-~~~~~~~~~~~~~~~~--~~~~~~~~~~s~~~~~~~~-~~~~~~~~~~~~~~~~~~~k~~~r~~~k~~~~~~--~  146 (574)
                      ++.+ ++++++||++++|+|+  ++.+++     .+|+..+. .-+..++|.+++|.+++++||++|-+.+.++-+.  .
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            5556 7999999999999999  888888     67886653 4677888889999999999999999999885543  4


Q ss_pred             chhHHHHHHHHHHHHHHHHHHhhhHhhhhcCcccc-cCcccCCChHHHHHHHHH--HhhhhhhHH--------------H
Q 008193          147 LDEASRLQRRTRYLLIKMKLEQNLIDAYSGEGWKG-HSREKIRPEKELQRAKKQ--ILKCKIGIR--------------D  209 (574)
Q Consensus       147 ~~~~~ri~~r~r~~l~~~~~eq~l~dAy~~egWk~-~sreK~rp~~Elerak~~--ilk~k~~ir--------------~  209 (574)
                      +.+.+.+..   |++         .--|.+-+|.. +...+       +++++.  +...|..|+              +
T Consensus       185 l~~ss~l~~---~~~---------d~~~~~~~~~~ge~~vk-------qr~kkd~a~Pn~YCDFclgdsr~nkkt~~pee  245 (336)
T KOG1244|consen  185 LTDSSSLED---YVC---------DTGTKQTVFAPGEAKVK-------QRVKKDIAQPNPYCDFCLGDSRENKKTGMPEE  245 (336)
T ss_pred             ccccccccc---hhh---------cccccccccCcchhhHH-------HhhhcccccCCcccceeccccccccccCCchh
Confidence            444444333   222         12234444444 23333       333332  222222222              2


Q ss_pred             HHh--hhccCCCCCCCcCC--ccc---CCCCcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCC
Q 008193          210 AIR--QLDSLSSVGCIEGS--VIA---TDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPP  282 (574)
Q Consensus       210 ~i~--~~d~l~~~~~l~~s--~l~---~dg~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~  282 (574)
                      ++.  .|....|.+||...  +++   ...|.+.++.+|.+|+..+  .+++||+||. |+++||+|||.||+-  ..|+
T Consensus       246 lvscsdcgrsghpsclqft~nm~~avk~yrwqcieck~csicgtse--nddqllfcdd-cdrgyhmyclsppm~--eppe  320 (336)
T KOG1244|consen  246 LVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYCSICGTSE--NDDQLLFCDD-CDRGYHMYCLSPPMV--EPPE  320 (336)
T ss_pred             hcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeecceeccccCcC--CCceeEeecc-cCCceeeEecCCCcC--CCCC
Confidence            222  45556777777522  222   3568899999999999875  5689999995 999999999999998  6888


Q ss_pred             CCCccccCcccc
Q 008193          283 GDQGWFCKFCEC  294 (574)
Q Consensus       283 gde~W~C~~C~~  294 (574)
                      |.  |.|..|..
T Consensus       321 gs--wsc~KOG~  330 (336)
T KOG1244|consen  321 GS--WSCHLCLE  330 (336)
T ss_pred             Cc--hhHHHHHH
Confidence            98  99999974

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.61  E-value=7.9e-16  Score=121.03  Aligned_cols=55  Identities=35%  Similarity=0.600  Sum_probs=52.2

Q ss_pred             CCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193          442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA  496 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~  496 (574)
                      ||+|+.||++|+.+|+.+|..++||+..++++||.+|||+..||++||||+|++.
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~   55 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKE   55 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHh
Confidence            4678999999999999999999999999999999999999999999999999943

; 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=99.57  E-value=2.2e-15  Score=144.01  Aligned_cols=63  Identities=27%  Similarity=0.425  Sum_probs=56.8

Q ss_pred             ccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhh
Q 008193          440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE  503 (574)
Q Consensus       440 ~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e  503 (574)
                      +.||.||.||++|+..||.+|+.|.|....+|.+||+.|+|++.||+|||||||++. |+...+
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~-kr~~~e  163 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKH-KRMQQE  163 (197)
T ss_pred             CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHH-HHHHHH
Confidence            457888999999999999999999999999999999999999999999999999944 444444

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

Probab=99.57  E-value=1.2e-15  Score=157.54  Aligned_cols=64  Identities=28%  Similarity=0.429  Sum_probs=58.2

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhh
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV  502 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~  502 (574)
                      .++||+|.-||..|+-+||+-|....|++..+|++||..|+||+.||||||||||++-+|.++.
T Consensus       151 ~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~d  214 (307)
T KOG0842|consen  151 RKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKD  214 (307)
T ss_pred             ccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhh
Confidence            4677788999999999999999999999999999999999999999999999999966555544

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

Probab=99.56  E-value=2.9e-15  Score=156.03  Aligned_cols=74  Identities=22%  Similarity=0.319  Sum_probs=66.7

Q ss_pred             CccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhhccccCCCC
Q 008193          437 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESARQVSGS  511 (574)
Q Consensus       437 ~~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e~~~~~~~~  511 (574)
                      .++++|+.|+.||..|+..||..|....|++..+|.+||..|||+..||++||||||+ +||+...++.+-++.-
T Consensus       168 ~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRt-KWKrq~a~g~~~~~~~  241 (309)
T KOG0488|consen  168 TPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRT-KWKRQTAEGGELLYQA  241 (309)
T ss_pred             CCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhH-HHHHHHHhhhcccccc
Confidence            3477888999999999999999999999999999999999999999999999999999 8888888765555533

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

Probab=99.56  E-value=1.8e-15  Score=156.46  Aligned_cols=65  Identities=23%  Similarity=0.291  Sum_probs=57.2

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhhc
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES  504 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e~  504 (574)
                      .+.||+|..+|+.|+.+||..|..|.|++.+.|.+||+.|+|+++||+|||||||+ ++|+..+|.
T Consensus       233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRM-K~KK~~re~  297 (308)
T KOG0487|consen  233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRM-KEKKVNREN  297 (308)
T ss_pred             cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhh-HHhhhhhhh
Confidence            45567779999999999999999999999999999999999999999999999999 444444433

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

Probab=99.54  E-value=2.8e-15  Score=152.79  Aligned_cols=65  Identities=20%  Similarity=0.334  Sum_probs=58.0

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhhc
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES  504 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e~  504 (574)
                      ...||.|+.||..|+.+||..|..|.|+++.+|.+||..|.|+++||+|||||||| +||+.....
T Consensus       157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRM-K~Kk~~k~~  221 (261)
T KOG0489|consen  157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRM-KWKKENKAK  221 (261)
T ss_pred             CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHH-HHHHhhccc
Confidence            34678889999999999999999999999999999999999999999999999999 555444443

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

Probab=99.51  E-value=2.2e-14  Score=143.63  Aligned_cols=55  Identities=24%  Similarity=0.500  Sum_probs=53.4

Q ss_pred             ccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       440 ~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      ..||+||.||.+|++.|...|.+|.|++...|++||.+|||.+.||+|||||+|+
T Consensus       245 eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRA  299 (342)
T KOG0493|consen  245 EEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRA  299 (342)
T ss_pred             hhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhh
Confidence            4578999999999999999999999999999999999999999999999999999

>KOG0485 consensus Transcription factor NKX-5

Probab=99.51  E-value=4e-14  Score=138.79  Aligned_cols=63  Identities=21%  Similarity=0.317  Sum_probs=58.2

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhh
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV  502 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~  502 (574)
                      -++||+||.|+..||-.||..|....|++..+|..||+.|.|++.||+|||||||. +||...+
T Consensus       102 ~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRn-KwKRq~a  164 (268)
T KOG0485|consen  102 DRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRN-KWKRQYA  164 (268)
T ss_pred             cccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhH-HHHHHHh
Confidence            46788999999999999999999999999999999999999999999999999999 5565544

1/HMX1, contains HOX domain [Transcription]

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

Probab=99.50  E-value=1.7e-14  Score=142.65  Aligned_cols=70  Identities=21%  Similarity=0.304  Sum_probs=62.4

Q ss_pred             ccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhhcccc
Q 008193          438 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVESARQ  507 (574)
Q Consensus       438 ~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e~~~~  507 (574)
                      +++.|++||.|+.-||+.|.+.|+.+.|+--.+|.+||..|||+..||+|||||||.+-+|..+..++.+
T Consensus       119 ~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~~~  188 (245)
T KOG0850|consen  119 GKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSGPV  188 (245)
T ss_pred             cccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCCcc
Confidence            4678899999999999999999999999999999999999999999999999999997766666443333

>smart00389 HOX Homeodomain

Probab=99.50  E-value=2.7e-14  Score=111.31  Aligned_cols=52  Identities=35%  Similarity=0.622  Sum_probs=50.1

Q ss_pred             CCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          443 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       443 r~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      +.|+.|+++|+.+|+.+|..|+||+..++.+||.+|||+..||++||+|+|+
T Consensus         2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~   53 (56)
T smart00389        2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRA   53 (56)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhh
Confidence            4567899999999999999999999999999999999999999999999998

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

>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=99.49  E-value=3.4e-14  Score=111.33  Aligned_cols=54  Identities=39%  Similarity=0.642  Sum_probs=50.9

Q ss_pred             CCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193          443 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA  496 (574)
Q Consensus       443 r~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~  496 (574)
                      +.+..|+++|+.+||.+|..|+||+..+++.||.+|||+..||++||+|+|++.
T Consensus         2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~   55 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKL   55 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            456789999999999999999999999999999999999999999999999943

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.46  E-value=5.6e-14  Score=112.81  Aligned_cols=53  Identities=15%  Similarity=0.292  Sum_probs=50.8

Q ss_pred             CCCccCCCHHHHHHHHHHHHhCCC----CCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          442 RRSFHRMPPNAVEKLRQVFAENEL----PSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F~~~~y----Ps~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      ||.||.||++|++.||.+|..++|    |+...|++||.+|||++++|+|||||-++
T Consensus         2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k~   58 (58)
T TIGR01565         2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNKK   58 (58)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCCC
Confidence            678899999999999999999999    99999999999999999999999999753

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.

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

Probab=99.46  E-value=3e-14  Score=125.62  Aligned_cols=64  Identities=27%  Similarity=0.466  Sum_probs=57.3

Q ss_pred             ccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhh
Q 008193          440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE  503 (574)
Q Consensus       440 ~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e  503 (574)
                      +.||-|+.||..|+.+||.+|.+..||+.-+|++||..+.|++-.|+|||||||++-.|+.++.
T Consensus        16 KQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a   79 (125)
T KOG0484|consen   16 KQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAA   79 (125)
T ss_pred             HhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHH
Confidence            4567789999999999999999999999999999999999999999999999999555555443

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

Probab=99.45  E-value=5.3e-14  Score=137.16  Aligned_cols=65  Identities=23%  Similarity=0.338  Sum_probs=59.7

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhh
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE  503 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e  503 (574)
                      ...|++|+.||.+|+..||..|.+..|++..+|.+++..|.|++.||+|||||||++++|-..+|
T Consensus       142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae  206 (246)
T KOG0492|consen  142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAE  206 (246)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHH
Confidence            45678999999999999999999999999999999999999999999999999999777666553

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

Probab=99.41  E-value=1.2e-13  Score=135.47  Aligned_cols=58  Identities=31%  Similarity=0.539  Sum_probs=55.0

Q ss_pred             cCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhhc
Q 008193          446 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES  504 (574)
Q Consensus       446 ~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e~  504 (574)
                      .||+.+|+..||..|..+.|+++.+|..||++|||.++||.|||||||+ +||.+..|.
T Consensus        55 ~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRA-RwK~kqlE~  112 (198)
T KOG0483|consen   55 RRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRA-RWKTKQLEK  112 (198)
T ss_pred             ccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccc-cccchhhhh
Confidence            5899999999999999999999999999999999999999999999999 888887764

>KOG2251 consensus Homeobox transcription factor [Transcription]

Probab=99.37  E-value=6.6e-13  Score=130.84  Aligned_cols=64  Identities=28%  Similarity=0.494  Sum_probs=58.0

Q ss_pred             ccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhh
Q 008193          438 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  501 (574)
Q Consensus       438 ~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~  501 (574)
                      +.+.||-||.|+-.|+++||..|.++.||+...|++||.+|+|++.+|+|||.|||++..++.+
T Consensus        34 pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~   97 (228)
T KOG2251|consen   34 PRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQ   97 (228)
T ss_pred             chhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhh
Confidence            4567888999999999999999999999999999999999999999999999999995444444

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

Probab=99.30  E-value=7.6e-13  Score=133.22  Aligned_cols=61  Identities=21%  Similarity=0.246  Sum_probs=54.4

Q ss_pred             CCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhh
Q 008193          443 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE  503 (574)
Q Consensus       443 r~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e  503 (574)
                      |=|..+|+.|.-+||..|-.++|++..++-+||..|||++|||+|||||||++..|..+..
T Consensus       201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk  261 (317)
T KOG0848|consen  201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK  261 (317)
T ss_pred             ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence            4467899999999999999999999999999999999999999999999999655544443

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

Probab=99.28  E-value=2.6e-12  Score=128.85  Aligned_cols=60  Identities=23%  Similarity=0.373  Sum_probs=54.0

Q ss_pred             CCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhh
Q 008193          443 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV  502 (574)
Q Consensus       443 r~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~  502 (574)
                      +-||.||..|+++||.+|.+-.||+-.-|+.||-.|.|++..|+|||||||++..|..+.
T Consensus       143 h~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~  202 (332)
T KOG0494|consen  143 HFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR  202 (332)
T ss_pred             cccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence            348999999999999999999999999999999999999999999999999944444444

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.27  E-value=3.2e-12  Score=121.49  Aligned_cols=56  Identities=29%  Similarity=0.427  Sum_probs=51.9

Q ss_pred             cCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193          441 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA  496 (574)
Q Consensus       441 ~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~  496 (574)
                      .+++|+|.|..|+.+|++.|..+|||+...|..||..|||+++-|++||||+|+..
T Consensus        51 ~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~  106 (156)
T COG5576          51 PKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKE  106 (156)
T ss_pred             CcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHH
Confidence            34556889999999999999999999999999999999999999999999999933

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

Probab=99.26  E-value=3.2e-12  Score=129.77  Aligned_cols=65  Identities=28%  Similarity=0.452  Sum_probs=60.1

Q ss_pred             ccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhhc
Q 008193          440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES  504 (574)
Q Consensus       440 ~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e~  504 (574)
                      ..||+||.||..|++.|..+|...|.|.+.+|++||.++||+.++|||||||||++.+|-++..+
T Consensus       166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAG  230 (383)
T KOG4577|consen  166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAG  230 (383)
T ss_pred             ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcc
Confidence            45789999999999999999999999999999999999999999999999999997777666554

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

Probab=99.26  E-value=2e-12  Score=122.38  Aligned_cols=62  Identities=23%  Similarity=0.373  Sum_probs=56.6

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  500 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~  500 (574)
                      -++++.|+.|+..|+..||..|+...|++..+|++||..|+|++.||++||||||++.+|.-
T Consensus        98 ~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~  159 (194)
T KOG0491|consen   98 CRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQ  159 (194)
T ss_pred             HHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence            45677889999999999999999999999999999999999999999999999999554443

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

Probab=99.17  E-value=1.3e-11  Score=130.66  Aligned_cols=58  Identities=26%  Similarity=0.378  Sum_probs=55.2

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA  496 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~  496 (574)
                      .|+||+||.|...+..+||.+|..|+.|+.+++.+||.+|+|+.++|+|||+|||++.
T Consensus       292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQke  349 (398)
T KOG3802|consen  292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKE  349 (398)
T ss_pred             ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeecccccc
Confidence            4778889999999999999999999999999999999999999999999999999943

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

Probab=99.17  E-value=8.6e-12  Score=127.47  Aligned_cols=65  Identities=22%  Similarity=0.362  Sum_probs=58.7

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhh
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE  503 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e  503 (574)
                      ..-||=||.||.+||..||..|....|.++.+|-+||.+|+|++..|+|||||||++-+|+|-+.
T Consensus       179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlam  243 (408)
T KOG0844|consen  179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAM  243 (408)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhc
Confidence            34567789999999999999999999999999999999999999999999999999777766553

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

Probab=99.01  E-value=1.6e-10  Score=113.84  Aligned_cols=64  Identities=20%  Similarity=0.340  Sum_probs=55.3

Q ss_pred             ccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhh
Q 008193          440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE  503 (574)
Q Consensus       440 ~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e  503 (574)
                      +++-.|..|+-.||..||..|....||-..+|.+||..|||++.||+|||||||++..|+..+|
T Consensus       166 ~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaE  229 (288)
T KOG0847|consen  166 QRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAE  229 (288)
T ss_pred             cccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccc
Confidence            4455666799999999999999999999999999999999999999999999999444444444

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

Probab=98.89  E-value=7.2e-10  Score=114.16  Aligned_cols=61  Identities=26%  Similarity=0.468  Sum_probs=56.0

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  500 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~  500 (574)
                      .+.||.|+-|+.+|+++||.+|..|.||+-.+|++||--++|++..|.|||.|||+ +||+|
T Consensus       110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrra-kwrkr  170 (351)
T KOG0486|consen  110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRA-KWRKR  170 (351)
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchh-hhhhh
Confidence            35678889999999999999999999999999999999999999999999999999 44444

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

Probab=98.80  E-value=1.9e-09  Score=105.90  Aligned_cols=61  Identities=21%  Similarity=0.324  Sum_probs=55.4

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  500 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~  500 (574)
                      .+.++.|+.|+..|+++||.+|..++||+...|+.||..++|++..|+|||||||+ ++++.
T Consensus        58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrra-k~r~~  118 (235)
T KOG0490|consen   58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRA-KDRKE  118 (235)
T ss_pred             ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcH-hhhhh
Confidence            45577889999999999999999999999999999999999999999999999999 44433

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

Probab=98.76  E-value=7.4e-09  Score=105.14  Aligned_cols=55  Identities=27%  Similarity=0.428  Sum_probs=49.6

Q ss_pred             cCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhh
Q 008193          446 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE  503 (574)
Q Consensus       446 ~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e  503 (574)
                      +.|.+.-...|..||..|+||+..++.+||+.+||+..||-+||.|||+   |.|.++
T Consensus       181 yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQ---RDRa~~  235 (304)
T KOG0775|consen  181 YCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQ---RDRAAA  235 (304)
T ss_pred             eehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhh---hhhhcc
Confidence            4567777899999999999999999999999999999999999999999   666443

>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=98.69  E-value=2.2e-09  Score=82.83  Aligned_cols=50  Identities=42%  Similarity=1.097  Sum_probs=41.3

Q ss_pred             cccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193          240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC  294 (574)
Q Consensus       240 ~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~  294 (574)
                      +|.+|+..+  +++.||.||. |..+||+.|++|++....++.+.  |+|+.|..
T Consensus         1 ~C~vC~~~~--~~~~~i~C~~-C~~~~H~~C~~~~~~~~~~~~~~--w~C~~C~~   50 (51)
T PF00628_consen    1 YCPVCGQSD--DDGDMIQCDS-CNRWYHQECVGPPEKAEEIPSGD--WYCPNCRP   50 (51)
T ss_dssp             EBTTTTSSC--TTSSEEEBST-TSCEEETTTSTSSHSHHSHHSSS--BSSHHHHH
T ss_pred             eCcCCCCcC--CCCCeEEcCC-CChhhCcccCCCChhhccCCCCc--EECcCCcC
Confidence            588999843  5689999995 99999999999998754555555  99999974

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 ....

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

Probab=98.65  E-value=1.8e-08  Score=107.32  Aligned_cols=61  Identities=28%  Similarity=0.461  Sum_probs=54.9

Q ss_pred             ccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193          440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  500 (574)
Q Consensus       440 ~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~  500 (574)
                      ..+|.|+.|+.+|+..||.+|..++||+...|++||+++||++..|+|||+|||++..|..
T Consensus       175 ~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~  235 (354)
T KOG0849|consen  175 GGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH  235 (354)
T ss_pred             cccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence            3445579999999999999999999999999999999999999999999999999554444

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

Probab=98.60  E-value=1.3e-08  Score=114.42  Aligned_cols=52  Identities=37%  Similarity=1.049  Sum_probs=44.9

Q ss_pred             cccccccccccCCCCCCCCccccCCCcCCc-ccccccCCCCCCCCCCCCCCccccCcccc
Q 008193          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCA-FHQKCLDPPLDTESIPPGDQGWFCKFCEC  294 (574)
Q Consensus       236 ~ed~~C~vC~~~~~~~~g~lLlCDg~C~ra-fH~~Cl~PPL~~~~iP~gde~W~C~~C~~  294 (574)
                      .+..-|.+|...+  ..+.||+||+ |+.+ ||+|||+|+|-  ++|.+.  |||+.|.-
T Consensus       213 ~E~~~C~IC~~~D--pEdVLLLCDs-CN~~~YH~YCLDPdl~--eiP~~e--WYC~NC~d  265 (1134)
T KOG0825|consen  213 QEEVKCDICTVHD--PEDVLLLCDS-CNKVYYHVYCLDPDLS--ESPVNE--WYCTNCSL  265 (1134)
T ss_pred             cccccceeeccCC--hHHhheeecc-cccceeeccccCcccc--cccccc--eecCcchh
Confidence            3456799999986  4578999996 9999 99999999998  799988  99999974

>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=98.58  E-value=2.7e-08  Score=74.41  Aligned_cols=33  Identities=39%  Similarity=0.681  Sum_probs=28.9

Q ss_pred             hCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          462 ENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       462 ~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      .||||+.+++++||.++||+..||.+||-|.|.
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            589999999999999999999999999999997

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

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

Probab=98.40  E-value=1.7e-07  Score=94.75  Aligned_cols=61  Identities=31%  Similarity=0.428  Sum_probs=54.7

Q ss_pred             CCCccCCCHHHHHHHHHHHH---hCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhh
Q 008193          442 RRSFHRMPPNAVEKLRQVFA---ENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV  502 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F~---~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~  502 (574)
                      +|+|..|+....++|..+|-   .||||+.+.+++||++.|++..||.+||-|+|.+.+|+...
T Consensus       189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k  252 (334)
T KOG0774|consen  189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGK  252 (334)
T ss_pred             HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhh
Confidence            45567899999999999995   58999999999999999999999999999999977776543

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

Probab=98.37  E-value=5.9e-07  Score=98.83  Aligned_cols=58  Identities=29%  Similarity=0.401  Sum_probs=54.7

Q ss_pred             ccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193          438 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  495 (574)
Q Consensus       438 ~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~  495 (574)
                      ....||+|+.||+.|...|..+|.++++|+.+..+.||.+|||..+.|.+||-|.|.|
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            3456889999999999999999999999999999999999999999999999999993

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

Probab=98.36  E-value=1.1e-07  Score=97.28  Aligned_cols=60  Identities=22%  Similarity=0.306  Sum_probs=55.3

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHH
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  498 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k  498 (574)
                      ..+||+||.|-.-....||++|...|-|+.+....||..|.|-..+|+|||+|.|++.+|
T Consensus       307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR  366 (385)
T KOG1168|consen  307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR  366 (385)
T ss_pred             cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence            456778899999999999999999999999999999999999999999999999995544

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

Probab=98.29  E-value=1.8e-07  Score=95.70  Aligned_cols=72  Identities=21%  Similarity=0.499  Sum_probs=57.4

Q ss_pred             hhccCCCCCCCc-----CCcccCCCCcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCcc
Q 008193          213 QLDSLSSVGCIE-----GSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGW  287 (574)
Q Consensus       213 ~~d~l~~~~~l~-----~s~l~~dg~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W  287 (574)
                      .|...+|..|++     ..++....|.+.++..|.+|+++..  +.+||+|| .|+++||.+|++  |.  .+|.|.  |
T Consensus       284 ~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~lC~IC~~P~~--E~E~~FCD-~CDRG~HT~CVG--L~--~lP~G~--W  354 (381)
T KOG1512|consen  284 PCATRPHPYCVAMIPELVGQYKTYFWKCSSCELCRICLGPVI--ESEHLFCD-VCDRGPHTLCVG--LQ--DLPRGE--W  354 (381)
T ss_pred             ccccCCCCcchhcCHHHHhHHhhcchhhcccHhhhccCCccc--chheeccc-cccCCCCccccc--cc--cccCcc--c
Confidence            455667777765     3344456789999999999999863  58999999 699999999999  55  799999  9


Q ss_pred             ccC-ccc
Q 008193          288 FCK-FCE  293 (574)
Q Consensus       288 ~C~-~C~  293 (574)
                      .|. .|.
T Consensus       355 ICD~~C~  361 (381)
T KOG1512|consen  355 ICDMRCR  361 (381)
T ss_pred             hhhhHHH
Confidence            997 454

>smart00249 PHD PHD zinc finger

Probab=98.27  E-value=6.6e-07  Score=66.15  Aligned_cols=47  Identities=40%  Similarity=1.096  Sum_probs=37.5

Q ss_pred             cccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcc
Q 008193          240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFC  292 (574)
Q Consensus       240 ~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C  292 (574)
                      +|.+|+...  +++.||.|++ |+.+||+.|++++.. ...+...  |+|+.|
T Consensus         1 ~C~~C~~~~--~~~~~i~C~~-C~~~~H~~C~~~~~~-~~~~~~~--~~C~~C   47 (47)
T smart00249        1 YCSVCGKPD--DGGELLQCDG-CDRWYHQTCLGPPLL-EEEPDGK--WYCPKC   47 (47)
T ss_pred             CcccCCCcC--CCCCEEECCC-CCchhhhhhCCCccc-CCCCCCC--EECcCC
Confidence            488898864  4689999995 999999999998865 2344444  999987

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

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

Probab=98.15  E-value=5.6e-07  Score=98.07  Aligned_cols=60  Identities=25%  Similarity=0.584  Sum_probs=49.5

Q ss_pred             ccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchhhhh
Q 008193          239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEII  299 (574)
Q Consensus       239 ~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~~~~  299 (574)
                      ..|.||..+.....+.||.|++ |..+||+.|+.|++..+..-+-...|||..|...+..+
T Consensus       169 ~qc~vC~~g~~~~~NrmlqC~~-C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~~~  228 (464)
T KOG4323|consen  169 LQCSVCYCGGPGAGNRMLQCDK-CRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPKKV  228 (464)
T ss_pred             ceeeeeecCCcCccceeeeecc-cccHHHHHhccCCCCHhhccCccceEeehhhccchhhc
Confidence            4499999887777899999997 99999999999999865555544469999998876543

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

Probab=98.13  E-value=1e-06  Score=103.96  Aligned_cols=77  Identities=31%  Similarity=0.640  Sum_probs=56.7

Q ss_pred             ccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchhh----hhhhhhccCCcee
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKME----IIESMNAHIGTSF  310 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~~----~~~~~n~~~g~~f  310 (574)
                      .+++.+|.+|..+++..-+.||+||+ |+.++|+.|++-|    .+|+|.  |+|..|.....    |....+....+.-
T Consensus       216 ~~~D~~C~iC~~~~~~n~n~ivfCD~-Cnl~VHq~Cygi~----~ipeg~--WlCr~Cl~s~~~~v~c~~cp~~~gAFkq  288 (1051)
T KOG0955|consen  216 LEEDAVCCICLDGECQNSNVIVFCDG-CNLAVHQECYGIP----FIPEGQ--WLCRRCLQSPQRPVRCLLCPSKGGAFKQ  288 (1051)
T ss_pred             cCCCccceeecccccCCCceEEEcCC-CcchhhhhccCCC----CCCCCc--EeehhhccCcCcccceEeccCCCCccee
Confidence            35678999999998877789999996 9999999999944    588998  99999987543    3333333333333


Q ss_pred             cccCcccc
Q 008193          311 SVNSNWQD  318 (574)
Q Consensus       311 ~l~~~~~~  318 (574)
                      +++-.|..
T Consensus       289 t~dgrw~H  296 (1051)
T KOG0955|consen  289 TDDGRWAH  296 (1051)
T ss_pred             ccCCceee
Confidence            45455543

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

Probab=97.96  E-value=4e-06  Score=86.61  Aligned_cols=52  Identities=27%  Similarity=0.703  Sum_probs=38.3

Q ss_pred             ccccccccccccCCCCCCCCccccCC-CcC-CcccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDG-TCN-CAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM  296 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg-~C~-rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~  296 (574)
                      .++-.+|..+...    -|.||.||+ .|+ .|||+.|++  |.  ..|.|.  |||+.|....
T Consensus       216 ~~e~~yC~Cnqvs----yg~Mi~CDn~~C~~eWFH~~CVG--L~--~~Pkgk--WyC~~C~~~~  269 (274)
T KOG1973|consen  216 PDEPTYCICNQVS----YGKMIGCDNPGCPIEWFHFTCVG--LK--TKPKGK--WYCPRCKAEN  269 (274)
T ss_pred             CCCCEEEEecccc----cccccccCCCCCCcceEEEeccc--cc--cCCCCc--ccchhhhhhh
Confidence            3445566444222    399999994 499 899999999  44  578888  9999998644

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

Probab=97.94  E-value=4.5e-06  Score=93.42  Aligned_cols=80  Identities=23%  Similarity=0.571  Sum_probs=62.4

Q ss_pred             hhccCCCCCCCc---CCcccCCCCcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCcccc
Q 008193          213 QLDSLSSVGCIE---GSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFC  289 (574)
Q Consensus       213 ~~d~l~~~~~l~---~s~l~~dg~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C  289 (574)
                      .|..++|..|+.   .......+|.+..+.+|..|+.+.  ++..+++|++ |+-.||.||..|+++  .||.|.  |+|
T Consensus        40 ~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~~~g--D~~kf~~Ck~-cDvsyh~yc~~P~~~--~v~sg~--~~c  112 (694)
T KOG4443|consen   40 DCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEACGTTG--DPKKFLLCKR-CDVSYHCYCQKPPND--KVPSGP--WLC  112 (694)
T ss_pred             hhcccCCcchhhHHHhHHHhcCCcccCCceeeeeccccC--Cccccccccc-ccccccccccCCccc--cccCcc--ccc
Confidence            455666666654   111123568899999999999653  6688999996 999999999999999  799998  999


Q ss_pred             Ccccchhhhh
Q 008193          290 KFCECKMEII  299 (574)
Q Consensus       290 ~~C~~k~~~~  299 (574)
                      +.|...+.|-
T Consensus       113 kk~~~c~qc~  122 (694)
T KOG4443|consen  113 KKCTRCRQCD  122 (694)
T ss_pred             HHHHhhhhcc
Confidence            9998766543

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

Probab=97.93  E-value=4.1e-06  Score=79.20  Aligned_cols=28  Identities=54%  Similarity=1.351  Sum_probs=25.8

Q ss_pred             cccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193          265 AFHQKCLDPPLDTESIPPGDQGWFCKFCECKM  296 (574)
Q Consensus       265 afH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~  296 (574)
                      +||++||+|||.  .+|+|+  |+||.|..+.
T Consensus         1 g~H~~CL~Ppl~--~~P~g~--W~Cp~C~~~~   28 (148)
T cd04718           1 GFHLCCLRPPLK--EVPEGD--WICPFCEVEK   28 (148)
T ss_pred             CcccccCCCCCC--CCCCCC--cCCCCCcCCC
Confidence            699999999998  899999  9999999764

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.

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

Probab=97.85  E-value=1.2e-05  Score=79.06  Aligned_cols=60  Identities=32%  Similarity=0.442  Sum_probs=55.4

Q ss_pred             CccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193          437 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA  496 (574)
Q Consensus       437 ~~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~  496 (574)
                      ...+.++.++.|+..|+..|...|..++||+...+++|+..+|+++..|++||||+|+..
T Consensus       149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~  208 (235)
T KOG0490|consen  149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKL  208 (235)
T ss_pred             CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHH
Confidence            345667888999999999999999999999999999999999999999999999999933

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

Probab=97.82  E-value=6.7e-06  Score=89.36  Aligned_cols=57  Identities=33%  Similarity=0.732  Sum_probs=48.3

Q ss_pred             CCcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          232 GSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       232 g~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      +..+.-++.|.+|...++...+.||+||| |+-+.|+.|++.+    -+|+|-  |+|..|...
T Consensus       187 ~~~d~~d~~C~~c~~t~~eN~naiVfCdg-C~i~VHq~CYGI~----f~peG~--WlCrkCi~~  243 (669)
T COG5141         187 EPSDEFDDICTKCTSTHNENSNAIVFCDG-CEICVHQSCYGIQ----FLPEGF--WLCRKCIYG  243 (669)
T ss_pred             CCchhhhhhhHhccccccCCcceEEEecC-cchhhhhhcccce----ecCcch--hhhhhhccc
Confidence            33345678999999998776788999997 9999999999987    589998  999999753

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

Probab=97.80  E-value=1.4e-05  Score=90.41  Aligned_cols=52  Identities=35%  Similarity=0.919  Sum_probs=46.1

Q ss_pred             cccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC  294 (574)
Q Consensus       236 ~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~  294 (574)
                      .++.+|.||..+++...++||+||. |+...|+.|++.  .  .+|+|.  |+|..|.-
T Consensus       269 dedviCDvCrspD~e~~neMVfCd~-Cn~cVHqaCyGI--l--e~p~gp--WlCr~Cal  320 (893)
T KOG0954|consen  269 DEDVICDVCRSPDSEEANEMVFCDK-CNICVHQACYGI--L--EVPEGP--WLCRTCAL  320 (893)
T ss_pred             cccceeceecCCCccccceeEEecc-chhHHHHhhhce--e--ecCCCC--eeehhccc
Confidence            3678999999999888899999995 999999999994  3  699987  99999964

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

Probab=97.79  E-value=9.2e-06  Score=85.74  Aligned_cols=64  Identities=33%  Similarity=0.364  Sum_probs=57.1

Q ss_pred             ccCCCccCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhh
Q 008193          440 KIRRSFHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE  503 (574)
Q Consensus       440 ~~kr~r~r~t~~Q~~~Le~~F~~---~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e  503 (574)
                      ..+|++..|+...+.+|+.|+.+   +|||+..++..||+++||+..||.+||.|.|.+.|+....+
T Consensus       238 ~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~  304 (342)
T KOG0773|consen  238 SKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIEE  304 (342)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchHHH
Confidence            35566779999999999999876   58999999999999999999999999999999888877654

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

Probab=97.78  E-value=7.7e-06  Score=99.86  Aligned_cols=55  Identities=38%  Similarity=1.001  Sum_probs=48.3

Q ss_pred             cccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchhh
Q 008193          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKME  297 (574)
Q Consensus       236 ~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~~  297 (574)
                      .....|.+|....  .+..|++|++ |..+||++|+.|.+.  .+|.|+  |+|+.|+....
T Consensus      1106 ~~~~~c~~cr~k~--~~~~m~lc~~-c~~~~h~~C~rp~~~--~~~~~d--W~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1106 AVNALCKVCRRKK--QDEKMLLCDE-CLSGFHLFCLRPALS--SVPPGD--WMCPSCRKEHR 1160 (1404)
T ss_pred             cchhhhhhhhhcc--cchhhhhhHh-hhhhHHHHhhhhhhc--cCCcCC--ccCCccchhhh
Confidence            3468999999974  4578999996 999999999999998  799999  99999997765

>KOG0383 consensus Predicted helicase [General function prediction only]

Probab=97.74  E-value=8.7e-06  Score=93.06  Aligned_cols=54  Identities=35%  Similarity=0.858  Sum_probs=47.6

Q ss_pred             CcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193          233 SVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM  296 (574)
Q Consensus       233 ~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~  296 (574)
                      +...+..+|.+|+.+     +.+|+|| +|+.+||.+|++||+.  .+|.++  |.|+.|.+..
T Consensus        42 ~~~~~~e~c~ic~~~-----g~~l~c~-tC~~s~h~~cl~~pl~--~~p~~~--~~c~Rc~~p~   95 (696)
T KOG0383|consen   42 WDDAEQEACRICADG-----GELLWCD-TCPASFHASCLGPPLT--PQPNGE--FICPRCFCPK   95 (696)
T ss_pred             cchhhhhhhhhhcCC-----CcEEEec-cccHHHHHHccCCCCC--cCCccc--eeeeeeccCC
Confidence            556777899999987     8999999 6999999999999998  799888  9999996544

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

Probab=97.69  E-value=2.5e-05  Score=79.27  Aligned_cols=49  Identities=33%  Similarity=0.868  Sum_probs=39.0

Q ss_pred             cccccccccccCCCCCCCCccccCC-CcCC-cccccccCCCCCCCCCCCCCCccccCcccc
Q 008193          236 HEHIICAKCKLREAFPDNDIVLCDG-TCNC-AFHQKCLDPPLDTESIPPGDQGWFCKFCEC  294 (574)
Q Consensus       236 ~ed~~C~vC~~~~~~~~g~lLlCDg-~C~r-afH~~Cl~PPL~~~~iP~gde~W~C~~C~~  294 (574)
                      ++..+| .|+..-   =|+||-||+ .|.+ |||+-|++  |.  ..|.|-  |||+.|..
T Consensus       219 ~e~lYC-fCqqvS---yGqMVaCDn~nCkrEWFH~~CVG--Lk--~pPKG~--WYC~eCk~  269 (271)
T COG5034         219 GEELYC-FCQQVS---YGQMVACDNANCKREWFHLECVG--LK--EPPKGK--WYCPECKK  269 (271)
T ss_pred             CceeEE-Eecccc---cccceecCCCCCchhheeccccc--cC--CCCCCc--EeCHHhHh
Confidence            344556 687763   299999998 7986 89999999  44  688898  99999964

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

Probab=97.54  E-value=3e-05  Score=87.19  Aligned_cols=50  Identities=38%  Similarity=0.959  Sum_probs=42.7

Q ss_pred             ccccccccCCCCCCCCccccCC-CcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193          239 IICAKCKLREAFPDNDIVLCDG-TCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC  294 (574)
Q Consensus       239 ~~C~vC~~~~~~~~g~lLlCDg-~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~  294 (574)
                      .-|+||.....-.++.||.||| .|.-+.||.|++..    .||.|.  |||..|..
T Consensus         6 GGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIv----qVPtGp--WfCrKCes   56 (900)
T KOG0956|consen    6 GGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIV----QVPTGP--WFCRKCES   56 (900)
T ss_pred             cceeeecCcCCCccCceeeecCCCceeeeehhcceeE----ecCCCc--hhhhhhhh
Confidence            4599998854445799999998 89999999999965    799998  99999954

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

Probab=97.43  E-value=0.00015  Score=85.96  Aligned_cols=216  Identities=20%  Similarity=0.229  Sum_probs=142.4

Q ss_pred             cccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchhhhhhhhhccCCceecccCc
Q 008193          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEIIESMNAHIGTSFSVNSN  315 (574)
Q Consensus       236 ~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~~~~~~~n~~~g~~f~l~~~  315 (574)
                      .....|..|..+...  ..+ +|++ |...||.+|..|++.  .+|.++  |.|+.|..-...  .....+|+.......
T Consensus       153 ~~~~~~~~~~k~~~~--~~~-~~~~-~~~~~~~~~~~~~~~--~~~~~~--~~~~~~~~~~~~--~~~~~~gf~~~~~~y  222 (904)
T KOG1246|consen  153 IDYPQCNTCSKGKEE--KLL-LCDS-CDDSYHTYCLRPPLT--RVPDGD--WRCPKCIPTPES--KPNYKFGFEQGSREY  222 (904)
T ss_pred             ccchhhhccccCCCc--cce-eccc-ccCcccccccCCCCC--cCCcCc--ccCCcccccccC--CcccccCcCCCCCcc
Confidence            344679999987532  345 9996 999999999999998  799998  999999876221  112344555555555


Q ss_pred             cccccccccCCCCCCccccCCCCCCCCCCCCCCCCCcccccCCcccCCCCCCCCCCCCCCCCCCCCCcCC-----ccccc
Q 008193          316 WQDIFKEEAAFPDGCSALLNQEEEWPSDDSEDDDYNPERRENSCSISRAGTDDDPSSSTSLSWFSDSETF-----SESMS  390 (574)
Q Consensus       316 ~~~~F~e~a~~~~g~~~~~~~~~~~psddsEDeD~dp~~~~~s~s~~~~G~dd~~s~S~s~S~Spn~e~~-----s~~~S  390 (574)
                      -...|...+......|+.......-..++.|-+.|+..........+.+|.+..  ...-+++.|.....     ..+.+
T Consensus       223 t~~~f~~~~~~~~~~~~~~~~~~~~~~~~vE~e~w~~v~~~~~~~~~~~g~d~~--~~~~~s~~~~~~~~~~~~~~~~~y  300 (904)
T KOG1246|consen  223 TLPKFEEYADNFKKDYFPKSKNSPDSTEDVEKEFWRLVASNLESVEVLYGADLS--TKEFGSGFPKSASGPLLGSEAEKY  300 (904)
T ss_pred             ccchhhhHhhhhhccccccccCCCCchHHHHHHHHHhhcccccceeeeeccchh--hccccccccccCCCCCCCcchhhh
Confidence            567777777777777765432221113477778888776665545556775433  33333344443333     35799


Q ss_pred             cCCCCCccccccccccc----cccccchh---hccccccCCchhhhhhhccCCC---ccccCCCccCCCHHHHHHHHHHH
Q 008193          391 EDEDWGPAKRRRKEKES----DAVNSLMT---LYGSEEKYSKVKTAEVKKKLPS---NAKIRRSFHRMPPNAVEKLRQVF  460 (574)
Q Consensus       391 dDeDwgp~~RrrRe~eS----d~~~~~m~---~~es~~gs~~~~~~~~~~~~~~---~~~~kr~r~r~t~~Q~~~Le~~F  460 (574)
                      -+..|+.+...+....-    +....+|+   +|.++..+...++-+....++-   .-...+.++.++....++||.+-
T Consensus       301 ~~s~wnL~~i~~~~~svl~~~~~di~g~~~p~l~~gm~fs~~~wh~ed~~~~slny~h~g~pk~wy~v~~~~ae~~e~~~  380 (904)
T KOG1246|consen  301 SNSGWNLNNIPRLEGSVLSHIDTDISGVTVPWLYIGMCFSTFCWHVEDHSLYSLNYLHLGEPKTWYSVPGSAAEKFEKAM  380 (904)
T ss_pred             ccCcccccccccCCccccccccCCcCccccccccccccccccccccCCccccccchhhcCCceEEEecCcchHHHHHHHH
Confidence            99999999998644331    11123332   4888888888888776554443   23556788999999999999776


Q ss_pred             HhC
Q 008193          461 AEN  463 (574)
Q Consensus       461 ~~~  463 (574)
                      ...
T Consensus       381 ~~~  383 (904)
T KOG1246|consen  381 NKL  383 (904)
T ss_pred             Hhh
Confidence            543

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

Probab=97.32  E-value=7.5e-05  Score=81.57  Aligned_cols=53  Identities=34%  Similarity=0.852  Sum_probs=42.9

Q ss_pred             ccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCC--CCccccCcccc
Q 008193          237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPG--DQGWFCKFCEC  294 (574)
Q Consensus       237 ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~g--de~W~C~~C~~  294 (574)
                      ....|.+|....  +-.-++.|| +|...||+-||+|||+  .+|..  +.+|.|..|..
T Consensus       543 ~~ysCgiCkks~--dQHll~~CD-tC~lhYHlGCL~PPLT--R~Pkk~kn~gWqCsECdk  597 (707)
T KOG0957|consen  543 MNYSCGICKKST--DQHLLTQCD-TCHLHYHLGCLSPPLT--RLPKKNKNFGWQCSECDK  597 (707)
T ss_pred             cceeeeeeccch--hhHHHhhcc-hhhceeeccccCCccc--cCcccccCcceeeccccc
Confidence            346799999873  345688899 7999999999999999  67753  45899999943

>KOG1146 consensus Homeobox protein [General function prediction only]

Probab=96.86  E-value=0.00091  Score=80.31  Aligned_cols=62  Identities=19%  Similarity=0.282  Sum_probs=56.5

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  500 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~  500 (574)
                      -.+++.|++++..|+..|..+|....||..++.+.|...++|+.+.|.+||||.|.+.+|..
T Consensus       901 ~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~  962 (1406)
T KOG1146|consen  901 MGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAK  962 (1406)
T ss_pred             hhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhh
Confidence            35677889999999999999999999999999999999999999999999999999555444

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

Probab=96.43  E-value=0.00051  Score=50.43  Aligned_cols=35  Identities=46%  Similarity=1.187  Sum_probs=19.6

Q ss_pred             CCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCccc
Q 008193          253 NDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCE  293 (574)
Q Consensus       253 g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~  293 (574)
                      +.||.|++ |.-.+|+.|++-.    .+|.++ .|+|..|.
T Consensus         2 n~ll~C~~-C~v~VH~~CYGv~----~~~~~~-~W~C~~C~   36 (36)
T PF13831_consen    2 NPLLFCDN-CNVAVHQSCYGVS----EVPDGD-DWLCDRCE   36 (36)
T ss_dssp             CEEEE-SS-S--EEEHHHHT-S----S--SS------HHH-
T ss_pred             CceEEeCC-CCCcCChhhCCcc----cCCCCC-cEECCcCC
Confidence            67999996 9999999999965    456652 29999884

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

Probab=96.12  E-value=0.0048  Score=49.67  Aligned_cols=42  Identities=12%  Similarity=0.295  Sum_probs=32.1

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          453 VEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       453 ~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      ++-|+..|..+.++...+-..|..+.+|+..||+.||--++.
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

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

Probab=95.97  E-value=0.0021  Score=76.07  Aligned_cols=68  Identities=22%  Similarity=0.520  Sum_probs=50.8

Q ss_pred             ccCCCCCCCcCCcccCCCCcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193          215 DSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC  294 (574)
Q Consensus       215 d~l~~~~~l~~s~l~~dg~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~  294 (574)
                      |.+....++++.+..+.  ...-++.|.+|...     ++++||. +|++.||+-|+.||+.  .+|...  |-|-.|..
T Consensus       323 Dq~l~~~s~R~e~~se~--~~~~ddhcrf~~d~-----~~~lc~E-t~prvvhlEcv~hP~~--~~~s~~--~e~evc~~  390 (1414)
T KOG1473|consen  323 DQFLTVNSLRDEIDSEG--EIEYDDHCRFCHDL-----GDLLCCE-TCPRVVHLECVFHPRF--AVPSAF--WECEVCNI  390 (1414)
T ss_pred             HHHHHHHHHHHHHhccc--ceeecccccccCcc-----cceeecc-cCCceEEeeecCCccc--cCCCcc--chhhhhhh
Confidence            34444444544443322  23446789999876     8999999 6999999999999998  789888  99999973

>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]

Probab=94.91  E-value=0.041  Score=63.22  Aligned_cols=48  Identities=25%  Similarity=0.419  Sum_probs=44.2

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhh
Q 008193          453 VEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE  503 (574)
Q Consensus       453 ~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e  503 (574)
                      +..|..+|..|.+|+..+-..+|.+.||+...|++||+|+++   ..+..+
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a---~e~sv~  615 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEA---EEMSVE  615 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhh---hhhhhc
Confidence            889999999999999999999999999999999999999999   445444

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

Probab=94.59  E-value=0.018  Score=63.61  Aligned_cols=56  Identities=32%  Similarity=0.813  Sum_probs=44.0

Q ss_pred             ccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCC-----CccccCcccchh
Q 008193          239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGD-----QGWFCKFCECKM  296 (574)
Q Consensus       239 ~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gd-----e~W~C~~C~~k~  296 (574)
                      .+|.||-...+.+.++||.||. |.-..|-.|++-. +...||.+.     +.|||..|.+..
T Consensus       120 ~iCcVClg~rs~da~ei~qCd~-CGi~VHEgCYGv~-dn~si~s~~s~~stepWfCeaC~~Gv  180 (707)
T KOG0957|consen  120 VICCVCLGQRSVDAGEILQCDK-CGINVHEGCYGVL-DNVSIPSGSSDCSTEPWFCEACLYGV  180 (707)
T ss_pred             eEEEEeecCccccccceeeccc-cCceecccccccc-cccccCCCCccCCCCchhhhhHhcCC
Confidence            3899999887777899999995 9999999999954 333566542     469999887643

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

Probab=93.27  E-value=0.046  Score=53.09  Aligned_cols=56  Identities=25%  Similarity=0.627  Sum_probs=39.9

Q ss_pred             ccccccc-CCCCCCCCccccCCCcCCcccccccCCCCCCCC----CCCCCCccccCcccchh
Q 008193          240 ICAKCKL-REAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES----IPPGDQGWFCKFCECKM  296 (574)
Q Consensus       240 ~C~vC~~-~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~----iP~gde~W~C~~C~~k~  296 (574)
                      .|.+|+. ++...-|.||.|-| |-.+||..||+|-...+.    |-+++....|..|+--.
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 34345689999998 999999999998764332    33444456788887543

>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=92.97  E-value=0.18  Score=39.88  Aligned_cols=48  Identities=17%  Similarity=0.279  Sum_probs=36.5

Q ss_pred             CCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      ||+|..||-++.-.+=..+...+     ...+||+++|++..+|..|..|+..
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            45678899999888888888776     5889999999999999999999753

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=91.46  E-value=0.05  Score=61.98  Aligned_cols=58  Identities=17%  Similarity=0.490  Sum_probs=44.2

Q ss_pred             cccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchhh
Q 008193          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKME  297 (574)
Q Consensus       236 ~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~~  297 (574)
                      ..+.+|.+|+.......+.|+.|.. |...||.+|+.-.+....+..+   |-|+.|+..-.
T Consensus        16 ~~~~mc~l~~s~G~~~ag~m~ac~~-c~~~yH~~cvt~~~~~~~l~~g---WrC~~crvCe~   73 (694)
T KOG4443|consen   16 IVCLMCPLCGSSGKGRAGRLLACSD-CGQKYHPYCVTSWAQHAVLSGG---WRCPSCRVCEA   73 (694)
T ss_pred             hhhhhhhhhccccccccCcchhhhh-hcccCCcchhhHHHhHHHhcCC---cccCCceeeee
Confidence            4567888998876666788999995 9999999999976653233333   99999987543

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

Probab=87.37  E-value=0.44  Score=53.63  Aligned_cols=53  Identities=17%  Similarity=0.289  Sum_probs=43.0

Q ss_pred             CcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193          233 SVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC  294 (574)
Q Consensus       233 ~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~  294 (574)
                      .....+++|..|...     +..|.|+ .|.+.||..|..|--.   ++.....|.|+.|..
T Consensus        55 ~~~N~d~~cfechlp-----g~vl~c~-vc~Rs~h~~c~sp~~q---~r~~s~p~~~p~p~s  107 (588)
T KOG3612|consen   55 PSSNIDPFCFECHLP-----GAVLKCI-VCHRSFHENCQSPDPQ---KRNYSVPSDKPQPYS  107 (588)
T ss_pred             cccCCCcccccccCC-----cceeeee-hhhccccccccCcchh---hccccccccCCcccc
Confidence            344567999999986     8889999 6999999999998643   666555799999974

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

Probab=86.66  E-value=0.4  Score=54.64  Aligned_cols=51  Identities=29%  Similarity=0.707  Sum_probs=42.3

Q ss_pred             cccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchhh
Q 008193          238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKME  297 (574)
Q Consensus       238 d~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~~  297 (574)
                      ...|..|..+     +++++|+. |+.+||+.|.++++.. ..+...  |.|..|-....
T Consensus        47 ~ts~~~~~~~-----gn~~~~~~-~~~s~h~~~~~~~~sp-~~~~~~--~~~~~~~~~~~   97 (613)
T KOG4299|consen   47 ATSCGICKSG-----GNLLCCDH-CPASFHLECDKPPLSP-DLKGSE--INCSRCPKGRE   97 (613)
T ss_pred             hhhcchhhhc-----CCcccccc-CccccchhccCcccCc-cccccc--ccccCCCcccc
Confidence            5679999987     88999995 9999999999999984 455555  99999977543

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=83.44  E-value=0.6  Score=37.54  Aligned_cols=35  Identities=26%  Similarity=0.710  Sum_probs=28.6

Q ss_pred             cccccccccCCCCCCCCccccCCCcCCcccccccCCC
Q 008193          238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPP  274 (574)
Q Consensus       238 d~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PP  274 (574)
                      ...|.+|+..- .+.+++|.|. .|...||-.|+...
T Consensus         5 ~~~C~~Cg~~~-~~~dDiVvCp-~CgapyHR~C~~~~   39 (54)
T PF14446_consen    5 GCKCPVCGKKF-KDGDDIVVCP-ECGAPYHRDCWEKA   39 (54)
T ss_pred             CccChhhCCcc-cCCCCEEECC-CCCCcccHHHHhhC
Confidence            46799999863 2468999999 59999999998743

>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=81.58  E-value=0.73  Score=49.68  Aligned_cols=46  Identities=30%  Similarity=0.593  Sum_probs=33.9

Q ss_pred             ccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193          239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC  294 (574)
Q Consensus       239 ~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~  294 (574)
                      +.|.+|-....  .|+.|--= .|...||..|.+|.|..    .+   =+||.|..
T Consensus       230 ~~CaIClEdY~--~GdklRiL-PC~H~FH~~CIDpWL~~----~r---~~CPvCK~  275 (348)
T KOG4628|consen  230 DTCAICLEDYE--KGDKLRIL-PCSHKFHVNCIDPWLTQ----TR---TFCPVCKR  275 (348)
T ss_pred             ceEEEeecccc--cCCeeeEe-cCCCchhhccchhhHhh----cC---ccCCCCCC
Confidence            68999998653  34444334 58899999999999872    11   37999986

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	574
1mm2_A	61	Solution Structure Of The 2nd Phd Domain From Mi2b		9e-04

>pdb|1MM2|A Chain A, Solution Structure Of The 2nd Phd Domain From Mi2b Length = 61

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 25/63 (39%), Positives = 30/63 (47%), Gaps = 11/63 (17%)
Query: 232 GSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKF 291
           GS HH    C  CK      D   +LC  TC  ++H  CL+PPL    IP G+  W C  
Sbjct: 4   GSDHHMEF-CRVCK------DGGELLCCDTCPSSYHIHCLNPPL--PEIPNGE--WLCPR 52
Query: 292 CEC 294
           C C
Sbjct: 53  CTC 55

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	574
2yt5_A	66	Metal-response element-binding transcription facto	5e-17
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	2e-16
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	8e-14
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	4e-13
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	4e-13
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-13
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	6e-13
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	8e-13
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	3e-12
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	7e-12
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	9e-12
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	1e-11
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	6e-11
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	2e-10
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	5e-10
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	6e-10
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	1e-09
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	5e-09
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	2e-08
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	2e-08
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	7e-08
3ask_A	226	E3 ubiquitin-protein ligase UHRF1; histone reader	8e-08
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	5e-07
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	2e-06
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	2e-06
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	4e-04
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	3e-06
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	4e-06
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	9e-06
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	1e-05
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	2e-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	7e-05
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	7e-05
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	1e-04
1x4i_A	70	Inhibitor of growth protein 3; structural genomics	2e-04
2g6q_A	62	Inhibitor of growth protein 2; protein-peptide com	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	3e-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	6e-04
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	8e-04
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	8e-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 = 74.5 bits (183), Expect = 5e-17
 Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 2/56 (3%)

Query: 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFC 292
              +C  C+   +   N++V+CD  C   +HQ C  P +D+  I   D+ W C+ C
Sbjct: 5   SSGVCTICQEEYSEAPNEMVICDK-CGQGYHQLCHTPHIDSSVIDS-DEKWLCRQC 58

>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 = 74.0 bits (181), Expect = 2e-16
 Identities = 15/69 (21%), Positives = 26/69 (37%), Gaps = 1/69 (1%)

Query: 229 ATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWF 288
             D       + C  C+       N +V C   C+  +HQ C  P +  + +      W+
Sbjct: 7   GADDFAMEMGLACVVCRQMTVASGNQLVECQE-CHNLYHQDCHKPQVTDKEVNDPRLVWY 65

Query: 289 CKFCECKME 297
           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 = 65.7 bits (160), Expect = 8e-14
 Identities = 22/66 (33%), Positives = 29/66 (43%), Gaps = 7/66 (10%)

Query: 230 TDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFC 289
              S+  E  +C+ C   E+   N I+ CD  CN A HQ+C   P     IP G   W C
Sbjct: 8   HMQSLIDEDAVCSICMDGESQNSNVILFCDM-CNLAVHQECYGVP----YIPEGQ--WLC 60

Query: 290 KFCECK 295
           + C   
Sbjct: 61  RHCLQS 66

>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 = 63.2 bits (154), Expect = 4e-13
 Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 11/67 (16%)

Query: 229 ATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWF 288
            + GS  HE   C+ C+         +++CD  C+  +H  CLDPPL  ++IP G   W 
Sbjct: 1   GSSGSSGHEDF-CSVCRK-----SGQLLMCDT-CSRVYHLDCLDPPL--KTIPKGM--WI 49

Query: 289 CKFCECK 295
           C  C+ +
Sbjct: 50  CPRCQDQ 56

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

 Score = 63.2 bits (154), Expect = 4e-13
 Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 11/63 (17%)

Query: 235 HHEHI-ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCE 293
           H  H   C+ C+         +++CD  C+  +H  CLDPPL  ++IP G   W C  C+
Sbjct: 1   HMIHEDFCSVCRK-----SGQLLMCDT-CSRVYHLDCLDPPL--KTIPKGM--WICPRCQ 50

Query: 294 CKM 296
            +M
Sbjct: 51  DQM 53

>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 = 71.0 bits (173), Expect = 6e-13
 Identities = 93/623 (14%), Positives = 200/623 (32%), Gaps = 163/623 (26%)

Query: 20  PKKDSGSELIASLKFKKGSKISK---SKKLRS-----KSRCQSKTVNSTLLKRTVAESHS 71
               SG+  +      K  ++ +    + LR       S  +++    +++ R   E   
Sbjct: 58  KDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRD 117

Query: 72  KGAGDDFARSK-SISQKNLHIKIDRKGSKNWASSKHKGKNSALVISKGNGEVVDGDGETK 130
           +   D+   +K ++S+   ++K+               + + L +      ++DG   + 
Sbjct: 118 RLYNDNQVFAKYNVSRLQPYLKL---------------RQALLELRPAKNVLIDGVLGSG 162

Query: 131 K-------LRKGRSKKRRKEKVE-LDEASRLQRRTRYLLIKMKLEQNL---IDAYSGEGW 179
           K           + + +   K+  L+   +       +L  +   Q L   ID       
Sbjct: 163 KTWVALDVCLSYKVQCKMDFKIFWLN--LKNCNSPETVLEML---QKLLYQIDPNWTSRS 217

Query: 180 KGHSREKIRPEKELQRAKKQILKCKIGIRDAIRQLDSLSSVGCIEGSVIATDGSVHHEHI 239
              S  K+R    +Q   +++LK K      +  L ++ +         A +        
Sbjct: 218 DHSSNIKLRIH-SIQAELRRLLKSKPYENCLL-VLLNVQNAKAWN----AFNL------- 264

Query: 240 ICAKCKL----REAFPDNDIVLCDGTCNCA--FHQKCLDPPLDTESIPPGDQGWFCKFCE 293
               CK+    R      D +    T + +   H   L P  + +S+         K+ +
Sbjct: 265 ---SCKILLTTRFK-QVTDFLSAATTTHISLDHHSMTLTPD-EVKSL-------LLKYLD 312

Query: 294 CKMEII--ESMNAH------IGTSFSVN----SNWQDIFKEEAAFPDGCSALLNQEEEWP 341
           C+ + +  E +  +      I  S         NW+ +  ++        + LN  E   
Sbjct: 313 CRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDK--LTTIIESSLNVLEP-- 368

Query: 342 SDDSEDDDYNPERREN--SCSISRAGTDDD---PSSSTSLSWFSDSETFSES-MSEDEDW 395
                      E R+     S+           P+   SL WF   ++     +++   +
Sbjct: 369 ----------AEYRKMFDRLSVFP----PSAHIPTILLSLIWFDVIKSDVMVVVNKLHKY 414

Query: 396 GPAKRRRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEK 455
              +++ KE       S+ ++Y            E+K KL +      + HR   +    
Sbjct: 415 SLVEKQPKESTI----SIPSIY-----------LELKVKLEN----EYALHRSIVDHYNI 455

Query: 456 LRQVFAENELPSRIVKEN---------LSK-ELSLEPEKVNKWFKNARYLALKARKVESA 505
            +   +++ +P  +  +          L   E           F + R+L  K R   +A
Sbjct: 456 PKTFDSDDLIPPYL--DQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTA 513

Query: 506 RQVSGS------------PRISKESSLETEKKNADVLTLKNSLEETLICSPKSLKKIHPK 553
              SGS            P I   +  + E+    +L     +EE LICS       +  
Sbjct: 514 WNASGSILNTLQQLKFYKPYICD-NDPKYERLVNAILDFLPKIEENLICSK------YTD 566

Query: 554 RIQ------NQSAVAAASRKISR 570
            ++      +++    A +++ R
Sbjct: 567 LLRIALMAEDEAIFEEAHKQVQR 589

>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 = 62.8 bits (153), Expect = 6e-13
 Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 10/56 (17%)

Query: 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK 295
            C  CK        +++ CD  C  ++H  CL+PPL    IP G+  W C  C C 
Sbjct: 11  FCRVCKD-----GGELLCCDT-CPSSYHIHCLNPPL--PEIPNGE--WLCPRCTCP 56

>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 = 63.5 bits (154), Expect = 8e-13
 Identities = 23/72 (31%), Positives = 31/72 (43%), Gaps = 7/72 (9%)

Query: 224 EGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPG 283
            G    +  S+  E  +C+ C   E+   N I+ CD  CN A HQ+C   P     IP G
Sbjct: 11  TGGSSGSSQSLIDEDAVCSICMDGESQNSNVILFCDM-CNLAVHQECYGVP----YIPEG 65

Query: 284 DQGWFCKFCECK 295
              W C+ C   
Sbjct: 66  Q--WLCRHCLQS 75

>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 = 60.9 bits (148), Expect = 3e-12
 Identities = 22/65 (33%), Positives = 30/65 (46%), Gaps = 11/65 (16%)

Query: 232 GSVHHEHI-ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCK 290
           G++  ++   CA C+        +++ CDG C  AFH  CL PPL    IP G   W C 
Sbjct: 1   GAMAQKNEDECAVCRD-----GGELICCDG-CPRAFHLACLSPPLR--EIPSGT--WRCS 50

Query: 291 FCECK 295
            C   
Sbjct: 51  SCLQA 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 = 60.7 bits (147), Expect = 7e-12
 Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 11/79 (13%)

Query: 224 EGSVIATDGSVHHEHI-ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPP 282
            GS I  +     +   IC  C+        D+V+C+  C   FH  C  P L  + +P 
Sbjct: 10  HGSDIIDEFGTLDDSATICRVCQK-----PGDLVMCNQ-CEFCFHLDCHLPAL--QDVPG 61

Query: 283 GDQGWFCKFCECKMEIIES 301
            +  W C  C    ++ E 
Sbjct: 62  EE--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 = 59.4 bits (144), Expect = 9e-12
 Identities = 20/55 (36%), Positives = 26/55 (47%), Gaps = 10/55 (18%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK 295
           C  C+        +I+LCD  C  A+H  CLDP +  E  P G   W C  CE +
Sbjct: 14  CEVCQQ-----GGEIILCDT-CPRAYHMVCLDPDM--EKAPEGK--WSCPHCEKE 58

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

 Score = 58.5 bits (142), Expect = 1e-11
 Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 7/53 (13%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCE 293
           C  C+ +    D+ ++LCD  CN AFH  CL P L    +P G+  W C  C+
Sbjct: 3   CKVCRKKGE--DDKLILCDE-CNKAFHLFCLRPALY--EVPDGE--WQCPACQ 48

>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 = 57.5 bits (139), Expect = 6e-11
 Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 6/53 (11%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCE 293
           C  C  +     N  +LCD  CN A+H  CL+PPLD   +P  +  W+C  C+
Sbjct: 29  CRVCGGKHE--PNMQLLCDE-CNVAYHIYCLNPPLD--KVPEEEY-WYCPSCK 75

>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 = 56.5 bits (136), Expect = 2e-10
 Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 7/59 (11%)

Query: 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK 295
           +  IC  C   +   D+ ++ CDG C+  +H  CL PPL    IP G   W C  C   
Sbjct: 15  DSYICQVCSRGD--EDDKLLFCDG-CDDNYHIFCLLPPLP--EIPRGI--WRCPKCILA 66

>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 = 54.8 bits (132), Expect = 5e-10
 Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 6/53 (11%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCE 293
           C  C  R+    +  ++CD  C+ AFH  CLDPPL   S+P  D+ W+C  C 
Sbjct: 21  CHLCGGRQD--PDKQLMCDE-CDMAFHIYCLDPPLS--SVPSEDE-WYCPECR 67

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

 Score = 54.9 bits (132), Expect = 6e-10
 Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 6/53 (11%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCE 293
           C  C  R+    +  ++CD  C+ AFH  CLDPPL   S+P  D+ W+C  C 
Sbjct: 29  CHLCGGRQD--PDKQLMCDE-CDMAFHIYCLDPPLS--SVPSEDE-WYCPECR 75

>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 = 55.1 bits (132), Expect = 1e-09
 Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 7/61 (11%)

Query: 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM 296
           E   C  C   E   D+ ++ CD  C+  +H  CL+PP+     P G   W C  C   +
Sbjct: 57  ECKSCILCGTSEN--DDQLLFCDD-CDRGYHMYCLNPPVA--EPPEGS--WSCHLCWELL 109

Query: 297 E 297
           +
Sbjct: 110 K 110

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

 Score = 53.1 bits (127), Expect = 5e-09
 Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 6/60 (10%)

Query: 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK 295
            E   C+ C+  +    ++++ CD  C+  FH +C DPPL    +P G   W C+ C  +
Sbjct: 59  IECKTCSSCR-DQGKNADNMLFCDS-CDRGFHMECCDPPLT--RMPKGM--WICQICRPR 112

>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 = 50.5 bits (120), Expect = 2e-08
 Identities = 14/54 (25%), Positives = 19/54 (35%), Gaps = 3/54 (5%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKC--LDPPLDTESIPPGDQGWFCKFC 292
           C  C   E   D D +LC+ +C   FH+ C  +               W C  C
Sbjct: 11  CGICT-NEVNDDQDAILCEASCQKWFHRICTGMTETAYGLLTAEASAVWGCDTC 63

>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 = 51.1 bits (121), Expect = 2e-08
 Identities = 16/67 (23%), Positives = 24/67 (35%), Gaps = 3/67 (4%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKC--LDPPLDTESIPPGDQGWFCKFCECKMEI 298
           C  C+  E   D D +LC+ +C   FH++C  +               W C  C    E 
Sbjct: 6   CGACR-SEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTKEG 64

Query: 299 IESMNAH 305
             S +  
Sbjct: 65  SGSGSGS 71

>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 = 51.8 bits (123), Expect = 7e-08
 Identities = 26/145 (17%), Positives = 42/145 (28%), Gaps = 15/145 (10%)

Query: 240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKMEII 299
           IC  C+        D+V+C+  C   FH  C  P L  + +P  +  W C  C    ++ 
Sbjct: 4   ICRVCQK-----PGDLVMCN-QCEFCFHLDCHLPAL--QDVPGEE--WSCSLCHVLPDLK 53

Query: 300 ESMNAHIGTSFSVNSNWQDIFKEEAAFPDG-CSALLNQEEEW----PSDDSEDDDYNPER 354
           E   +              +        +    AL   E        + DS      P  
Sbjct: 54  EEDGSLSLDGADSTGVVAKLSPANQRKCERVLLALFCHEPCRPLHQLATDSTFSLDQPGG 113

Query: 355 RENSCSISRAGTDDDPSSSTSLSWF 379
             +   I     +      +S   F
Sbjct: 114 TLDLTLIRARLQEKLSPPYSSPQEF 138

>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 = 52.4 bits (125), Expect = 8e-08
 Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 6/53 (11%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCE 293
           C  C  R+    +  ++CD  C+ AFH  CLDPPL   S+P  D+ W+C  C 
Sbjct: 177 CHLCGGRQD--PDKQLMCDE-CDMAFHIYCLDPPLS--SVPSEDE-WYCPECR 223

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

 Score = 49.1 bits (116), Expect = 5e-07
 Identities = 20/112 (17%), Positives = 40/112 (35%), Gaps = 2/112 (1%)

Query: 384 TFSESMSEDEDWGPAKRRRKEKESDAVNSLMTLYGSEEKYSKVKTAEVKKK--LPSNAKI 441
           T S+ +   + W   K  R+             +              +++         
Sbjct: 38  TLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPEFQRMSALRLAACKRKEQEHGKDRGNTP 97

Query: 442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 493
           ++            L  +F EN+ PS+ ++  +S++L LE   V+ +F NAR
Sbjct: 98  KKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 149

>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 = 46.3 bits (109), Expect = 2e-06
 Identities = 14/60 (23%), Positives = 24/60 (40%), Gaps = 11/60 (18%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIP----PGDQGWFCKFCECKM 296
           C  C         +++ CD  C+ AF +KC+   L    +       +Q W+C  C  + 
Sbjct: 60  CRWCAE-----GGNLICCD-FCHNAFCKKCILRNLGRRELSTIMDENNQ-WYCYICHPEP 112

>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 = 46.1 bits (109), Expect = 2e-06
 Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 7/56 (12%)

Query: 237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFC 292
           E  +C  CK      D+ +++CD  C+  +H  CL P +   S+P     W CK C
Sbjct: 53  ECKVCQNCKQSGE--DSKMLVCDT-CDKGYHTFCLQPVMK--SVPTNG--WKCKNC 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 = 39.2 bits (91), Expect = 4e-04
 Identities = 17/69 (24%), Positives = 21/69 (30%), Gaps = 10/69 (14%)

Query: 232 GSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCK- 290
           GS       CA C         D   C   C   +H  CLD  +     P    GW C  
Sbjct: 1   GSSGSSGANCAVCDSPGD--LLDQFFCTT-CGQHYHGMCLDIAVT----PLKRAGWQCPE 53

Query: 291 --FCECKME 297
              C+   +
Sbjct: 54  CKVCQNCKQ 62

>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: 437 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA 496
           S A I +  ++     +  L+  F  N+ P +   E+L+K   L   +V KWF + RY  
Sbjct: 6   SGASIYK--NKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRY-- 61

Query: 497 LKARKVESARQVSGS 511
              R ++ +R    S
Sbjct: 62  -HCRNLKGSRSGPSS 75

>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 = 4e-06
 Identities = 19/74 (25%), Positives = 27/74 (36%)

Query: 420 EEKYSKVKTAEVKKKLPSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELS 479
           EE  S   +     K+ +  + R+    +       L   F +   PS      L+  L 
Sbjct: 78  EETDSSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQ 137

Query: 480 LEPEKVNKWFKNAR 493
           LE E V  WF N R
Sbjct: 138 LEKEVVRVWFCNRR 151

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

 Score = 44.8 bits (105), Expect = 9e-06
 Identities = 13/59 (22%), Positives = 23/59 (38%), Gaps = 9/59 (15%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQ---GWFCKFCECKM 296
           C  C         +++ CD  C+ AF +KC+   L  + +         W+C  C  + 
Sbjct: 66  CRWCAE-----GGNLICCD-FCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPEP 118

>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 = 42.5 bits (100), Expect = 1e-05
 Identities = 15/64 (23%), Positives = 25/64 (39%), Gaps = 11/64 (17%)

Query: 236 HEHIICAKCKLREAFPDND--IVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCE 293
           ++  IC  C      PD+   ++ CD  C+  +H  C+               WFC  C 
Sbjct: 16  NQIWICPGCNK----PDDGSPMIGCDD-CDDWYHWPCVGIMA--APPEEMQ--WFCPKCA 66

Query: 294 CKME 297
            K++
Sbjct: 67  NKIK 70

>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 = 2e-05
 Identities = 11/56 (19%), Positives = 21/56 (37%)

Query: 439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494
           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: 445 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES 504
           F       +  L+  F  + + +      L  +  L   +++ WF   +       +   
Sbjct: 15  FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKME 74

Query: 505 ARQVSGSPRISKES 518
             + +        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 = 7e-05
 Identities = 15/74 (20%), Positives = 28/74 (37%), Gaps = 2/74 (2%)

Query: 445 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES 504
           F       V+ L   F ++  P++   + L  E  L   +++ WF   R   L+    ++
Sbjct: 17  FKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERR--KLRDSMEQA 74

Query: 505 ARQVSGSPRISKES 518
                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 = 7e-05
 Identities = 15/69 (21%), Positives = 26/69 (37%), Gaps = 1/69 (1%)

Query: 442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 501
              +    P  +  L   FA+N LP     + L  E  +   +++ WF   R     A +
Sbjct: 8   PTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKV-NAEE 66

Query: 502 VESARQVSG 510
            + +   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 = 1e-04
 Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 4/66 (6%)

Query: 437 SNAKIRRSFHRMPPNAVEKLRQVFAE-NELPSRIVKENLSKELSLEPEKVNKWFKNARYL 495
           S +   RS  ++   A+  L+    +    P +     LS +L L    + K+F+N RY 
Sbjct: 3   SGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRY- 61

Query: 496 ALKARK 501
               + 
Sbjct: 62  --HVKH 65

>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 = 39.1 bits (91), Expect = 2e-04
 Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 10/49 (20%)

Query: 252 DNDIVLCDGTCNCA---FHQKCLDPPLDTESIPPGDQGWFCKFCECKME 297
             ++V CD   +C    FH  C+         P G   W+C  C   M+
Sbjct: 16  YGEMVGCDN-QDCPIEWFHYGCVGL----TEAPKGK--WYCPQCTAAMK 57

>2g6q_A Inhibitor of growth protein 2; protein-peptide complex, gene regulation, apoptosis; HET: M3L; 2.00A {Mus musculus} Length = 62

 Score = 38.7 bits (90), Expect = 2e-04
 Identities = 12/71 (16%), Positives = 21/71 (29%), Gaps = 11/71 (15%)

Query: 229 ATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNC--AFHQKCLDPPLDTESIPPGDQG 286
            ++ ++         C         +++ CD        FH  C+         P G   
Sbjct: 1   GSEFAIDPNEPTYCLCNQVS---YGEMIGCDNEQCPIEWFHFSCVS----LTYKPKGK-- 51

Query: 287 WFCKFCECKME 297
           W+C  C    E
Sbjct: 52  WYCPKCRGDNE 62

>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 = 38.5 bits (90), Expect = 3e-04
 Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 3/68 (4%)

Query: 440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 499
           K  R    +    +  LR  +A N  P  ++KE L +   L P  +  WF+N R    K 
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKR---CKD 58

Query: 500 RKVESARQ 507
           +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 = 3e-04
 Identities = 14/57 (24%), Positives = 29/57 (50%)

Query: 437 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 493
              + +R    + P  +E L Q +  +  P+R + ++++ E+ L+   V  WF+N R
Sbjct: 13  EPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTR 69

>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: 446 HRMPPNAVEKLRQVFAENEL---PSRIVKENLSKELSLEPEKVNKWFKNAR 493
           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: 419 SEEKYSKVKTAEVKKKLPSNA-KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKE 477
           +   +      EV  + P+          +  P  +  L+  F   + PS    + L+KE
Sbjct: 2   AHHHHHHSSGLEVLFQGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKE 61

Query: 478 LSLEPEKVNKWFKNARY 494
             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 = 37.3 bits (87), Expect = 6e-04
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 447 RMPPNAVEKLRQVFAENEL---PSRIVKENLSKELSLEPEKVNKWFKNAR 493
             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 = 6e-04
 Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 5/60 (8%)

Query: 437 SNAKIRRSFHRMPPNAVEKLRQVFAENEL---PSRIVKENLSKELSLEPEKVNKWFKNAR 493
           S+  I      M   A E L + F  +     PS   KE L+K+  +   +V+ WF N R
Sbjct: 1   SSGHIEGR--HMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKR 58

>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70

 Score = 37.3 bits (87), Expect = 8e-04
 Identities = 22/67 (32%), Positives = 28/67 (41%), Gaps = 3/67 (4%)

Query: 437 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA 496
           S +  R S  R     +  L+  F  N  P     E LS  L+L    +  WF+NAR   
Sbjct: 3   SGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQ-- 60

Query: 497 LKARKVE 503
            KARK  
Sbjct: 61  -KARKSG 66

>2kgg_A Histone demethylase jarid1A; PHD finger, histone modification, leukemia, alternative splicing, chromatin regulator, developmental protein; NMR {Homo sapiens} PDB: 2kgi_A* 3gl6_A* Length = 52

 Score = 36.8 bits (85), Expect = 8e-04
 Identities = 17/55 (30%), Positives = 23/55 (41%), Gaps = 7/55 (12%)

Query: 240 ICA--KCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFC 292
           +CA   C+        D V CDG C+  FHQ C+   +  E     D  + C  C
Sbjct: 2   VCAAQNCQRPCK-DKVDWVQCDGGCDEWFHQVCVG--VSPEMAENED--YICINC 51

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	574
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.74
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.74
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.73
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.73
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.73
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.73
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.73
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.72
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.72
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.72
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.72
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.72
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.72
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.71
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.71
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.71
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.71
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.71
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.71
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.71
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.7
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.7
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.7
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.7
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.7
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.7
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.7
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.69
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.69
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.69
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.69
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.69
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.69
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.68
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.68
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.68
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.68
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.68
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.68
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.67
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.67
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.67
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.67
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.67
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.67
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.66
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.66
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.66
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.66
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.65
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.65
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.65
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.65
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.65
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.65
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.62
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.62
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.61
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.61
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.6
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.58
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.58
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.58
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.57
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.57
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.57
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.57
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.56
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.55
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.55
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.54
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.5
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.46
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	99.38
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.38
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	99.37
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.36
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	99.33
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.33
2yt5_A	66	Metal-response element-binding transcription facto	99.3
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	99.29
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	99.29
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	99.27
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	99.26
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	99.26
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	99.26
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	99.25
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	99.23
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	99.23
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	99.2
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	99.18
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	99.15
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	99.14
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.14
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	99.13
3ask_A	226	E3 ubiquitin-protein ligase UHRF1; histone reader	99.08
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	99.07
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	99.05
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	99.04
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	99.02
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	99.01
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	98.89
4gne_A	107	Histone-lysine N-methyltransferase NSD3; zinc fing	98.74
2vnf_A	60	ING 4, P29ING4, inhibitor of growth protein 4; ace	98.64
1weu_A	91	Inhibitor of growth family, member 4; structural g	98.63
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	98.58
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	98.57
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	98.56
2jmi_A	90	Protein YNG1, ING1 homolog 1; PHD, histone, recogn	98.52
2g6q_A	62	Inhibitor of growth protein 2; protein-peptide com	98.48
3c6w_A	59	P28ING5, inhibitor of growth protein 5; chromatin,	98.47
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	98.25
1x4i_A	70	Inhibitor of growth protein 3; structural genomics	98.25
1we9_A	64	PHD finger family protein; structural genomics, PH	98.24
2rsd_A	68	E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant	98.13
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	98.11
1wee_A	72	PHD finger family protein; structural genomics, PH	98.09
1wew_A	78	DNA-binding family protein; structural genomics, P	98.02
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.01
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	97.93
1wem_A	76	Death associated transcription factor 1; structura	97.93
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	97.85
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	97.72
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	97.72
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	97.69
3kqi_A	75	GRC5, PHD finger protein 2; metal-binding, zinc-fi	97.66
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	97.61
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	97.58
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	97.56
3o7a_A	52	PHD finger protein 13 variant; PHF13, zinc finger,	97.55
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	97.26
3pur_A	528	Lysine-specific demethylase 7 homolog; oxidoreduct	96.98
3kv5_D	488	JMJC domain-containing histone demethylation prote	96.92
3kv4_A	447	PHD finger protein 8; epigenetics, histone CODE, c	96.16
4bbq_A	117	Lysine-specific demethylase 2A; oxidoreductase, ub	95.58
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	94.46
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	94.45
4gne_A	107	Histone-lysine N-methyltransferase NSD3; zinc fing	93.88
3a1b_A	159	DNA (cytosine-5)-methyltransferase 3A, histone H3;	86.67
2pv0_B	386	DNA (cytosine-5)-methyltransferase 3-like; DNMT3L,	83.59
3rsn_A	177	SET1/ASH2 histone methyltransferase complex subun;	80.49

>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=2.2e-18  Score=140.51  Aligned_cols=60  Identities=30%  Similarity=0.463  Sum_probs=55.2

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHH
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  498 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k  498 (574)
                      ...+|+|+.||.+|+.+||.+|..++||+..+|++||.+|||++.||++||||||++.+|
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr   64 (70)
T 2dmu_A            5 SSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRR   64 (70)
T ss_dssp             TSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccc
Confidence            445778899999999999999999999999999999999999999999999999994433

>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=99.74  E-value=1.7e-18  Score=141.27  Aligned_cols=57  Identities=19%  Similarity=0.350  Sum_probs=54.1

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  495 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~  495 (574)
                      ...+|+|++||.+|+.+||.+|..++||+..+|.+||.+|||++.||+|||||||++
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k   61 (70)
T 2cra_A            5 SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVK   61 (70)
T ss_dssp             CCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHH
Confidence            456778899999999999999999999999999999999999999999999999993

>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=4.8e-18  Score=141.79  Aligned_cols=64  Identities=19%  Similarity=0.250  Sum_probs=57.5

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhh
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV  502 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~  502 (574)
                      ...+|+|+.||.+|+.+||.+|..++||+..+|++||.+|||++.||+|||||||++.+|....
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (80)
T 2dmq_A            5 SSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLR   68 (80)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHH
Confidence            4567888999999999999999999999999999999999999999999999999955554433

>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=2.2e-18  Score=140.41  Aligned_cols=58  Identities=31%  Similarity=0.386  Sum_probs=54.6

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA  496 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~  496 (574)
                      .+.+|+|++||.+|+.+||.+|..++||+..++++||.+|||++.||++||||||++.
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~   62 (70)
T 2da2_A            5 SSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKA   62 (70)
T ss_dssp             CCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHH
Confidence            4567788999999999999999999999999999999999999999999999999943

>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=3.5e-18  Score=139.44  Aligned_cols=60  Identities=22%  Similarity=0.312  Sum_probs=55.0

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHH
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  498 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k  498 (574)
                      ...+++|++||.+|+.+||.+|..++||+..+|.+||.+|||++.||++||||||++.++
T Consensus         5 ~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr   64 (70)
T 2e1o_A            5 SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR   64 (70)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCC
Confidence            455677899999999999999999999999999999999999999999999999994433

>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=99.73  E-value=2.2e-18  Score=140.43  Aligned_cols=59  Identities=22%  Similarity=0.418  Sum_probs=55.0

Q ss_pred             ccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193          438 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA  496 (574)
Q Consensus       438 ~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~  496 (574)
                      ..+.+|+|++||.+|+.+||.+|..++||+..++.+||.+|||++.||++||||||++.
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~   62 (70)
T 2da1_A            4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKE   62 (70)
T ss_dssp             SCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHH
Confidence            34567888999999999999999999999999999999999999999999999999943

>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=6.1e-18  Score=141.43  Aligned_cols=61  Identities=23%  Similarity=0.440  Sum_probs=55.9

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHh
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA  499 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~  499 (574)
                      .+.+|+|++||.+|+.+||.+|..++||+..+|++||.+|||++.||+|||||||++.+|.
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~   65 (80)
T 2dms_A            5 SSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQ   65 (80)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHH
Confidence            4567888999999999999999999999999999999999999999999999999944443

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

Probab=99.72  E-value=5.6e-18  Score=141.81  Aligned_cols=64  Identities=20%  Similarity=0.412  Sum_probs=57.5

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhh
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV  502 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~  502 (574)
                      ...+|+|+.||.+|+.+||.+|..++||+..+|.+||..|||++.||+|||||||++.+|..+.
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~   68 (80)
T 2cue_A            5 SSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL   68 (80)
T ss_dssp             CSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhh
Confidence            4557788999999999999999999999999999999999999999999999999955554443

>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=99.72  E-value=3.1e-18  Score=143.39  Aligned_cols=59  Identities=24%  Similarity=0.295  Sum_probs=55.1

Q ss_pred             ccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193          438 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA  496 (574)
Q Consensus       438 ~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~  496 (574)
                      ..+.+|+|+.||.+|+.+||.+|..++||+..+|++||..|||++.||+|||||||++.
T Consensus        14 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~   72 (80)
T 2dmt_A           14 AKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKW   72 (80)
T ss_dssp             CCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHh
Confidence            35567888999999999999999999999999999999999999999999999999933

>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=7.8e-18  Score=139.96  Aligned_cols=62  Identities=26%  Similarity=0.411  Sum_probs=56.2

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  500 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~  500 (574)
                      .+.+|+|+.||..|+.+||.+|..++||+..+|.+||..|||++.||+|||||||++.++..
T Consensus         7 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~   68 (77)
T 1nk2_P            7 NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ   68 (77)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhh
Confidence            45677889999999999999999999999999999999999999999999999999444433

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

Probab=99.72  E-value=2.3e-18  Score=140.54  Aligned_cols=58  Identities=19%  Similarity=0.300  Sum_probs=54.5

Q ss_pred             ccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193          438 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  495 (574)
Q Consensus       438 ~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~  495 (574)
                      +...+|+|+.||.+|+.+||.+|..++||+..+|++||.+|||++.||++||||||++
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   61 (70)
T 2djn_A            4 GSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSK   61 (70)
T ss_dssp             CCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhh
Confidence            3456788899999999999999999999999999999999999999999999999993

>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=99.72  E-value=2.8e-18  Score=142.90  Aligned_cols=59  Identities=24%  Similarity=0.429  Sum_probs=55.1

Q ss_pred             ccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193          438 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA  496 (574)
Q Consensus       438 ~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~  496 (574)
                      +.+.+|+|+.||.+|+.+||.+|..++||+..+|++||.+|||++.||+|||||||++.
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~   72 (80)
T 2da3_A           14 PQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARE   72 (80)
T ss_dssp             CCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhH
Confidence            35667888999999999999999999999999999999999999999999999999933

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

Probab=99.72  E-value=6.4e-18  Score=132.72  Aligned_cols=55  Identities=25%  Similarity=0.382  Sum_probs=52.2

Q ss_pred             CCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193          442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA  496 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~  496 (574)
                      +|+|+.||.+|+.+||.+|..++||+..++.+||..|||++.||++||||||++.
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~   55 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKA   55 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhh
Confidence            4678999999999999999999999999999999999999999999999999943

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

Probab=99.71  E-value=6.1e-18  Score=133.98  Aligned_cols=57  Identities=23%  Similarity=0.400  Sum_probs=52.9

Q ss_pred             CCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHH
Q 008193          442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  498 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k  498 (574)
                      +|+|+.||.+|+.+||.+|..++||+..++.+||.+|||++.||++||||||++.+|
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   58 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR   58 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHhHhhc
Confidence            567899999999999999999999999999999999999999999999999995444

>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=99.71  E-value=5.2e-18  Score=134.81  Aligned_cols=55  Identities=27%  Similarity=0.485  Sum_probs=50.1

Q ss_pred             cCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193          441 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  495 (574)
Q Consensus       441 ~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~  495 (574)
                      .+|+|+.||.+|+.+||.+|..|+||+..+|.+||..|||++.||++||||||++
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   57 (61)
T 2hdd_A            3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAK   57 (61)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhccc
Confidence            4677899999999999999999999999999999999999999999999999993

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

Probab=99.71  E-value=7.5e-18  Score=134.85  Aligned_cols=56  Identities=23%  Similarity=0.300  Sum_probs=51.9

Q ss_pred             cCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193          441 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA  496 (574)
Q Consensus       441 ~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~  496 (574)
                      .+|+|+.||..|+.+||.+|..++||+..+|.+||..|||++.||++||||||++.
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~   58 (63)
T 2h1k_A            3 NKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKW   58 (63)
T ss_dssp             --CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhh
Confidence            46778999999999999999999999999999999999999999999999999943

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

Probab=99.71  E-value=5e-18  Score=142.94  Aligned_cols=59  Identities=22%  Similarity=0.313  Sum_probs=55.3

Q ss_pred             ccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193          438 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA  496 (574)
Q Consensus       438 ~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~  496 (574)
                      ..+.+|+|+.||..|+.+||.+|..++||+..+|.+||..|||++.||+|||||||++.
T Consensus        19 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~   77 (84)
T 2kt0_A           19 PVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKS   77 (84)
T ss_dssp             CSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence            45667889999999999999999999999999999999999999999999999999943

>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=99.71  E-value=7e-18  Score=141.89  Aligned_cols=56  Identities=11%  Similarity=0.214  Sum_probs=53.8

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAE----NELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~----~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      .+.+|+|+.||.+|+.+||.+|..    ++||+..+|++||.+|||++.||+|||||||+
T Consensus        15 ~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRa   74 (80)
T 1wh5_A           15 GIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKH   74 (80)
T ss_dssp             CCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSS
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCc
Confidence            456788899999999999999999    99999999999999999999999999999999

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

Probab=99.71  E-value=1.1e-17  Score=135.85  Aligned_cols=58  Identities=26%  Similarity=0.425  Sum_probs=53.8

Q ss_pred             cCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHH
Q 008193          441 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  498 (574)
Q Consensus       441 ~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k  498 (574)
                      ++|+|+.||..|+.+||.+|..++||+..+|.+||..|||++.||++||||||++.++
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr   59 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKR   59 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhh
Confidence            4678899999999999999999999999999999999999999999999999994433

>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=99.71  E-value=6.5e-18  Score=137.39  Aligned_cols=60  Identities=22%  Similarity=0.300  Sum_probs=54.7

Q ss_pred             cCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193          441 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  500 (574)
Q Consensus       441 ~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~  500 (574)
                      ++|.|+.||.+|+.+||.+|..++||+..+|.+||..|||++.||+|||||||++.+|..
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   61 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN   61 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhc
Confidence            367789999999999999999999999999999999999999999999999999444433

>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=99.70  E-value=1.7e-17  Score=140.16  Aligned_cols=65  Identities=25%  Similarity=0.342  Sum_probs=57.5

Q ss_pred             ccccCCCccCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhh
Q 008193          438 NAKIRRSFHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV  502 (574)
Q Consensus       438 ~~~~kr~r~r~t~~Q~~~Le~~F~~---~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~  502 (574)
                      +.+.+++|++||.+|+.+||.+|.+   |+||+..+|++||.+|||++.||+|||||+|++.++....
T Consensus         4 ~~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~~   71 (83)
T 2dmn_A            4 GSSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQ   71 (83)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHTC
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHHH
Confidence            3556778899999999999999998   5999999999999999999999999999999966554433

>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=99.70  E-value=1.2e-17  Score=140.06  Aligned_cols=62  Identities=24%  Similarity=0.466  Sum_probs=55.6

Q ss_pred             ccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHh
Q 008193          438 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA  499 (574)
Q Consensus       438 ~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~  499 (574)
                      ..+.+|+|+.||..|+.+||.+|..++||+..+|.+||.+|||++.||++||||||++.+|.
T Consensus        15 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~   76 (81)
T 1fjl_A           15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ   76 (81)
T ss_dssp             --CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhh
Confidence            35567888999999999999999999999999999999999999999999999999954443

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

Probab=99.70  E-value=1.4e-17  Score=135.25  Aligned_cols=60  Identities=25%  Similarity=0.341  Sum_probs=54.9

Q ss_pred             cCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193          441 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  500 (574)
Q Consensus       441 ~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~  500 (574)
                      .+|+|+.||.+|+.+||.+|..++||+..+|.+||..|||++.||+|||||||++.++..
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~   61 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQS   61 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHh
Confidence            367789999999999999999999999999999999999999999999999999544443

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

Probab=99.70  E-value=7.5e-18  Score=134.30  Aligned_cols=55  Identities=22%  Similarity=0.312  Sum_probs=49.2

Q ss_pred             cCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193          441 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  495 (574)
Q Consensus       441 ~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~  495 (574)
                      .+|+|+.||.+|+.+||.+|..++||+..+|.+||..|||++.||++||||||++
T Consensus         3 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k   57 (62)
T 2vi6_A            3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMK   57 (62)
T ss_dssp             -----CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcc
Confidence            4678899999999999999999999999999999999999999999999999993

>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=99.70  E-value=8e-18  Score=135.71  Aligned_cols=55  Identities=27%  Similarity=0.486  Sum_probs=52.8

Q ss_pred             cCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193          441 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  495 (574)
Q Consensus       441 ~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~  495 (574)
                      .+|+|+.||.+|+.+||.+|..++||+..++++||..|||++.||++||||||++
T Consensus         3 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k   57 (66)
T 1bw5_A            3 TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCK   57 (66)
T ss_dssp             CSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHH
Confidence            4678899999999999999999999999999999999999999999999999993

>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=99.70  E-value=2.2e-17  Score=137.23  Aligned_cols=62  Identities=21%  Similarity=0.269  Sum_probs=56.2

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  500 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~  500 (574)
                      ...+|+|+.||..|+.+||.+|..++||+..+|++||..|||++.||+|||||||++.+|..
T Consensus        11 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   72 (77)
T 1puf_A           11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKIN   72 (77)
T ss_dssp             CTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhh
Confidence            44567889999999999999999999999999999999999999999999999999554443

>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=99.70  E-value=2.1e-17  Score=135.77  Aligned_cols=61  Identities=23%  Similarity=0.366  Sum_probs=55.4

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHh
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA  499 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~---~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~  499 (574)
                      .+.+++|+.||.+|+.+||.+|..   ++||+..+|++||.+|||++.||++||||||++.++.
T Consensus         5 ~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~   68 (73)
T 1x2n_A            5 SSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQS   68 (73)
T ss_dssp             SSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhcccc
Confidence            455677899999999999999987   9999999999999999999999999999999955443

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

Probab=99.69  E-value=2e-17  Score=142.63  Aligned_cols=64  Identities=17%  Similarity=0.303  Sum_probs=57.7

Q ss_pred             ccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhh
Q 008193          438 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  501 (574)
Q Consensus       438 ~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~  501 (574)
                      +++.+|+|+.||.+|+.+||.+|..++||+..+|.+||..|||++.||+|||||||++.++...
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~   77 (93)
T 3a01_A           14 PPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTA   77 (93)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhH
Confidence            4567788999999999999999999999999999999999999999999999999995444433

>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=99.69  E-value=1.2e-17  Score=132.51  Aligned_cols=55  Identities=27%  Similarity=0.433  Sum_probs=46.8

Q ss_pred             ccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       440 ~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      +.+|+|++||.+|+.+||.+|..++||+..++.+||.+|||++.||++||||||+
T Consensus         4 k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~   58 (61)
T 1akh_A            4 KSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRM   58 (61)
T ss_dssp             --------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHh
Confidence            4567889999999999999999999999999999999999999999999999999

>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=99.69  E-value=1.2e-17  Score=140.73  Aligned_cols=56  Identities=18%  Similarity=0.328  Sum_probs=53.0

Q ss_pred             ccccCCCccCCCHHHHHHHHHHHHh-----CCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          438 NAKIRRSFHRMPPNAVEKLRQVFAE-----NELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       438 ~~~~kr~r~r~t~~Q~~~Le~~F~~-----~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      ..+.+|.|+.||.+|+.+|| .|..     ++||+..+|++||.+|||++.||+|||||||+
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~   74 (80)
T 1wh7_A           14 GGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKN   74 (80)
T ss_dssp             CCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSC
T ss_pred             CCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCccccccccccc
Confidence            35667888999999999999 8999     99999999999999999999999999999999

>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=99.69  E-value=9.4e-18  Score=136.21  Aligned_cols=58  Identities=26%  Similarity=0.408  Sum_probs=54.0

Q ss_pred             cCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHH
Q 008193          441 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  498 (574)
Q Consensus       441 ~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k  498 (574)
                      .+|+|+.||..|+.+||.+|..++||+..++.+||..|||++.||++||||||++.+|
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk   60 (68)
T 1yz8_P            3 QRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK   60 (68)
T ss_dssp             SSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHH
Confidence            4678899999999999999999999999999999999999999999999999994433

>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=99.69  E-value=3.3e-17  Score=135.73  Aligned_cols=56  Identities=21%  Similarity=0.430  Sum_probs=51.4

Q ss_pred             CCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHH
Q 008193          443 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  498 (574)
Q Consensus       443 r~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k  498 (574)
                      ++|++||.+|+.+||.+|..++||+..+|.+||.+|||++.||+|||||||++.++
T Consensus         9 ~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk   64 (75)
T 2da5_A            9 TKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNA   64 (75)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHH
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHH
Confidence            34578999999999999999999999999999999999999999999999994433

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

Probab=99.69  E-value=3.2e-17  Score=135.06  Aligned_cols=56  Identities=20%  Similarity=0.340  Sum_probs=53.5

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      .+.+|+|++||..|+.+||.+|..++||+..+|.+||..|||++.||++||||||+
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~   60 (73)
T 2l7z_A            5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRV   60 (73)
T ss_dssp             SCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhH
Confidence            44577889999999999999999999999999999999999999999999999999

>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=99.68  E-value=2.6e-17  Score=134.35  Aligned_cols=56  Identities=25%  Similarity=0.382  Sum_probs=54.1

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAE-NELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~-~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      ...+|+|+.|+.+|+.+|+.+|+. ++||+...|++||.+|||++++|+|||||+|+
T Consensus         5 ~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~   61 (71)
T 1wi3_A            5 SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRY   61 (71)
T ss_dssp             CCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhcccee
Confidence            466889999999999999999999 99999999999999999999999999999999

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

Probab=99.68  E-value=1.9e-17  Score=131.20  Aligned_cols=55  Identities=24%  Similarity=0.460  Sum_probs=49.1

Q ss_pred             CccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHH
Q 008193          444 SFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  498 (574)
Q Consensus       444 ~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k  498 (574)
                      +|++||.+|+.+||.+|..++||+..+|.+||.+|||++.||++||||||++.+|
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk   56 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK   56 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC-
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHh
Confidence            3589999999999999999999999999999999999999999999999994433

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

Probab=99.68  E-value=3.7e-17  Score=134.37  Aligned_cols=56  Identities=29%  Similarity=0.514  Sum_probs=53.7

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      .+.+|.|+.||..|+.+||.+|..++||+..++.+||..|||++.||++||||||+
T Consensus         7 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~   62 (75)
T 2m0c_A            7 GKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRA   62 (75)
T ss_dssp             SCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHH
Confidence            45677889999999999999999999999999999999999999999999999999

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

Probab=99.68  E-value=2.3e-17  Score=128.97  Aligned_cols=54  Identities=26%  Similarity=0.427  Sum_probs=52.1

Q ss_pred             cCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          441 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       441 ~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      ++|+|+.|+..|+.+||.+|..++||+..++.+||..|||++.||++||||||+
T Consensus         2 ~rr~Rt~~t~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~   55 (58)
T 3rkq_A            2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRY   55 (58)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCCCCCcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhhc
Confidence            457789999999999999999999999999999999999999999999999999

>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=99.68  E-value=2.4e-17  Score=138.50  Aligned_cols=60  Identities=23%  Similarity=0.335  Sum_probs=51.3

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHH
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  498 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k  498 (574)
                      ...+|.|+.||.+|+.+||.+|..++||+..+|++||..|||++.||+|||||||++.+|
T Consensus        18 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk   77 (81)
T 1b8i_A           18 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKK   77 (81)
T ss_dssp             ------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhh
Confidence            345778899999999999999999999999999999999999999999999999994433

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

Probab=99.68  E-value=1.8e-17  Score=138.62  Aligned_cols=58  Identities=17%  Similarity=0.248  Sum_probs=54.4

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhC----CCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAEN----ELPSRIVKENLSKELSLEPEKVNKWFKNARYLA  496 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~----~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~  496 (574)
                      .+.+|.|+.||.+|+.+||.+|..+    +||+..+|++||.+|||++.||+|||||||++.
T Consensus         6 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~   67 (80)
T 2da4_A            6 SGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKY   67 (80)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHH
Confidence            4567788999999999999999999    999999999999999999999999999999933

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

Probab=99.67  E-value=3.6e-17  Score=132.23  Aligned_cols=53  Identities=34%  Similarity=0.577  Sum_probs=51.7

Q ss_pred             CCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      +|+|+.||++|+.+||.+|..++||+..++.+||.+|||++.||++||||||+
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~   54 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRA   54 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHH
Confidence            57789999999999999999999999999999999999999999999999999

>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=99.67  E-value=5.7e-17  Score=135.53  Aligned_cols=57  Identities=23%  Similarity=0.385  Sum_probs=51.8

Q ss_pred             ccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhh
Q 008193          445 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKV  502 (574)
Q Consensus       445 r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~  502 (574)
                      +.+||.+|+.+||.+|..|+||+..+|++||.+|||++.||+|||||||+ ++|+...
T Consensus         7 r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~-k~Kk~~l   63 (76)
T 2ecc_A            7 GKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRY-ALKHGQL   63 (76)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHH-HHHHTCC
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHH-HHHHHHH
Confidence            35799999999999999999999999999999999999999999999999 4454433

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

Probab=99.67  E-value=3.1e-17  Score=139.60  Aligned_cols=59  Identities=20%  Similarity=0.296  Sum_probs=51.8

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHH
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL  497 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~  497 (574)
                      ...+|+|+.||..|+.+||.+|..++||+..+|.+||..|||++.||+|||||||++.+
T Consensus        26 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~k   84 (88)
T 2r5y_A           26 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK   84 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhH
Confidence            45577889999999999999999999999999999999999999999999999999443

>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=99.67  E-value=4.7e-17  Score=133.69  Aligned_cols=59  Identities=32%  Similarity=0.447  Sum_probs=54.2

Q ss_pred             CCCccCCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193          442 RRSFHRMPPNAVEKLRQVF---AENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  500 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F---~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~  500 (574)
                      +|+|++||.+|+.+||.+|   ..++||+..+|.+||..|||++.||++||||||++.++..
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~   63 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccccc
Confidence            5678999999999999999   8999999999999999999999999999999999554443

>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=99.67  E-value=4.1e-17  Score=141.35  Aligned_cols=64  Identities=23%  Similarity=0.333  Sum_probs=53.8

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhh
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVE  503 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e  503 (574)
                      ...+++|+.||.+|+.+||.+|..++||+..+|.+||..|||++.||+|||||||++ .|+...+
T Consensus        32 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k-~kk~~~~   95 (97)
T 1b72_A           32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMK-QKKRERE   95 (97)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH-HHHHHTC
T ss_pred             CCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHH-HhHHhcc
Confidence            345677899999999999999999999999999999999999999999999999994 4444333

>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=8e-17  Score=139.02  Aligned_cols=64  Identities=20%  Similarity=0.326  Sum_probs=57.6

Q ss_pred             ccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcC---------------CChhhHHHhhcccccHHHHhhh
Q 008193          438 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELS---------------LEPEKVNKWFKNARYLALKARK  501 (574)
Q Consensus       438 ~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~Lg---------------L~~~qV~vWFQNrR~~~~k~~~  501 (574)
                      ..+.+|.|+.|++.|+.+||.+|..++||+..+|++||.+||               |++.||++||||||++.++..+
T Consensus         4 ~~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~   82 (95)
T 2cuf_A            4 GSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRAN   82 (95)
T ss_dssp             SSCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhh
Confidence            356678889999999999999999999999999999999999               9999999999999995544443

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

Probab=99.66  E-value=5.6e-17  Score=126.98  Aligned_cols=51  Identities=22%  Similarity=0.369  Sum_probs=47.6

Q ss_pred             cCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193          446 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA  496 (574)
Q Consensus       446 ~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~  496 (574)
                      +.||.+|+.+||.+|..++||+..+|.+||..|||++.||++||||||++.
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~   52 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKW   52 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhh
Confidence            579999999999999999999999999999999999999999999999943

>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=99.66  E-value=9e-17  Score=131.79  Aligned_cols=56  Identities=25%  Similarity=0.306  Sum_probs=51.7

Q ss_pred             CCccCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHH
Q 008193          443 RSFHRMPPNAVEKLRQVFAE-NELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  498 (574)
Q Consensus       443 r~r~r~t~~Q~~~Le~~F~~-~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k  498 (574)
                      +.|++||.+|+.+||.+|.. ++||+..+|++||.+|||++.||++||||||++.+|
T Consensus         3 k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk   59 (72)
T 1uhs_A            3 EGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRR   59 (72)
T ss_dssp             CCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhh
Confidence            45689999999999999996 999999999999999999999999999999994433

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

Probab=99.66  E-value=1.1e-16  Score=131.76  Aligned_cols=57  Identities=23%  Similarity=0.266  Sum_probs=52.2

Q ss_pred             CCCccCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHH
Q 008193          442 RRSFHRMPPNAVEKLRQVFA-ENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  498 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F~-~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k  498 (574)
                      .++|++||.+|+.+||.+|. .++||+..+|.+||.+|||++.||++||||||++.+|
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk   60 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRR   60 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            35678999999999999999 5999999999999999999999999999999994433

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

Probab=99.66  E-value=3.8e-17  Score=130.86  Aligned_cols=54  Identities=31%  Similarity=0.450  Sum_probs=51.5

Q ss_pred             CCCccCCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193          442 RRSFHRMPPNAVEKLRQVF---AENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  495 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F---~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~  495 (574)
                      +++|+.||.+|+.+||.+|   ..++||+..++++||.+|||++.||++||||+|++
T Consensus         4 rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r   60 (64)
T 1du6_A            4 HIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR   60 (64)
T ss_dssp             CCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            5667899999999999999   89999999999999999999999999999999993

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

Probab=99.65  E-value=9.5e-17  Score=133.07  Aligned_cols=51  Identities=27%  Similarity=0.537  Sum_probs=49.7

Q ss_pred             CccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          444 SFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       444 ~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      .|++||.+|+.+||.+|..++||+..+|++||.+|||++.||++||||||+
T Consensus        11 ~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~   61 (76)
T 2dn0_A           11 YKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRY   61 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_pred             CCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhH
Confidence            468999999999999999999999999999999999999999999999999

>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=99.65  E-value=6.8e-17  Score=136.86  Aligned_cols=60  Identities=32%  Similarity=0.434  Sum_probs=54.4

Q ss_pred             CCCccCCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhh
Q 008193          442 RRSFHRMPPNAVEKLRQVF---AENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK  501 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F---~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~  501 (574)
                      ||+|++|+.+|+.+||.+|   ..++||+..+|++||.+|||++.||++||||||++.++...
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~   64 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG   64 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGG
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhccc
Confidence            5678999999999999999   89999999999999999999999999999999996555443

>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=99.65  E-value=9.9e-17  Score=126.85  Aligned_cols=51  Identities=31%  Similarity=0.364  Sum_probs=49.3

Q ss_pred             ccCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193          445 FHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARYL  495 (574)
Q Consensus       445 r~r~t~~Q~~~Le~~F~~---~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~  495 (574)
                      +++||.+|+.+||.+|..   ++||+..+|.+||.+|||++.||++||||||++
T Consensus         2 r~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r   55 (60)
T 1k61_A            2 GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRK   55 (60)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             cCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHcc
Confidence            478999999999999999   999999999999999999999999999999993

>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=2.2e-16  Score=135.63  Aligned_cols=49  Identities=12%  Similarity=0.303  Sum_probs=48.2

Q ss_pred             cCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          446 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       446 ~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      .+||.+|+.+||.+|..|+||+..+|++||..|||+++||+|||||||+
T Consensus        16 k~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~   64 (89)
T 2ecb_A           16 KEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKK   64 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccch
Confidence            4899999999999999999999999999999999999999999999999

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

Probab=99.65  E-value=1.4e-16  Score=130.96  Aligned_cols=53  Identities=21%  Similarity=0.377  Sum_probs=51.3

Q ss_pred             CCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      ++.|+.||.+|+.+||.+|..++||+..+|++||..|||++.||++||||||+
T Consensus         7 ~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~   59 (74)
T 2ly9_A            7 FGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRY   59 (74)
T ss_dssp             CCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_pred             CCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhH
Confidence            56679999999999999999999999999999999999999999999999999

>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=99.65  E-value=9.5e-17  Score=135.43  Aligned_cols=54  Identities=28%  Similarity=0.301  Sum_probs=50.2

Q ss_pred             CCccCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193          443 RSFHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARYLA  496 (574)
Q Consensus       443 r~r~r~t~~Q~~~Le~~F~~---~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~  496 (574)
                      +++++||.+|+.+||.+|..   ++||+..+|.+||..|||++.||++||||||++.
T Consensus         4 krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~   60 (83)
T 1le8_B            4 YRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKE   60 (83)
T ss_dssp             -CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHccc
Confidence            44577999999999999999   9999999999999999999999999999999944

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

Probab=99.62  E-value=2.2e-16  Score=136.58  Aligned_cols=60  Identities=25%  Similarity=0.466  Sum_probs=52.7

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHh
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA  499 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~  499 (574)
                      ...+|.|++||..|+.+||.+|..++||+..+|.+||..|||++.||++||||||+ ++|+
T Consensus        23 ~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~-k~kk   82 (96)
T 3nar_A           23 SGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRY-AWKN   82 (96)
T ss_dssp             ----CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHH-HHTT
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhh-Hhhh
Confidence            34556789999999999999999999999999999999999999999999999999 4443

>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=99.62  E-value=3.6e-16  Score=132.75  Aligned_cols=56  Identities=29%  Similarity=0.322  Sum_probs=52.6

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~---~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      ...+++|++||.+|+.+||.+|..   ++||+..+|++||.+|||++.||++||||||+
T Consensus        25 ~~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~   83 (87)
T 1mnm_C           25 STKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRR   83 (87)
T ss_dssp             ESSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHh
Confidence            344566899999999999999999   99999999999999999999999999999999

>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=99.61  E-value=7.2e-16  Score=131.92  Aligned_cols=52  Identities=23%  Similarity=0.485  Sum_probs=49.2

Q ss_pred             CccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193          444 SFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  495 (574)
Q Consensus       444 ~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~  495 (574)
                      ++.+||.+|+.+||.+|..++||+..+|++||.+|||++.||+|||||||++
T Consensus        16 k~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k   67 (89)
T 2dmp_A           16 KFKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKL   67 (89)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             ccccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHH
Confidence            3456999999999999999999999999999999999999999999999993

>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.61  E-value=1.5e-16  Score=131.18  Aligned_cols=52  Identities=23%  Similarity=0.394  Sum_probs=49.6

Q ss_pred             CCccCCCHHHHHHHHHHH-HhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          443 RSFHRMPPNAVEKLRQVF-AENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       443 r~r~r~t~~Q~~~Le~~F-~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      +.+.+++.+|+.+||.+| ..++||+..+|++||.+|||+++||+|||||||+
T Consensus        10 k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~   62 (72)
T 2cqx_A           10 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRN   62 (72)
T ss_dssp             CCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhccc
Confidence            445689999999999999 9999999999999999999999999999999999

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

Probab=99.60  E-value=5.4e-16  Score=126.14  Aligned_cols=52  Identities=19%  Similarity=0.426  Sum_probs=48.7

Q ss_pred             CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193          448 MPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  500 (574)
Q Consensus       448 ~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~  500 (574)
                      -|.+|+.+||..|..++||+..+|++||..|||+++||++||||||+ ++|+.
T Consensus        11 ~~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~-k~Kkg   62 (66)
T 3nau_A           11 KTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRY-RCQRG   62 (66)
T ss_dssp             CCHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHH-HHHHH
T ss_pred             hhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchh-hhhcc
Confidence            57899999999999999999999999999999999999999999999 55543

>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=99.58  E-value=7.5e-16  Score=143.00  Aligned_cols=57  Identities=30%  Similarity=0.412  Sum_probs=51.7

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  495 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~  495 (574)
                      .+.+|+|+.||..|+.+||.+|..++||+..+|.+||..|||+++||+|||||||++
T Consensus        85 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k  141 (146)
T 1au7_A           85 ERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQR  141 (146)
T ss_dssp             ----CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhh
Confidence            456778899999999999999999999999999999999999999999999999993

>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=99.58  E-value=2.2e-15  Score=132.36  Aligned_cols=62  Identities=23%  Similarity=0.318  Sum_probs=56.1

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHc---------------------CCChhhHHHhhcccccHHH
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKEL---------------------SLEPEKVNKWFKNARYLAL  497 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~L---------------------gL~~~qV~vWFQNrR~~~~  497 (574)
                      .+.||.|+.|++.|+.+||.+|..++||+..+|++||.+|                     +|++.+|+|||||||++..
T Consensus         4 ~~~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k~k   83 (102)
T 2da6_A            4 GSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEEA   83 (102)
T ss_dssp             CCSCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHHHH
Confidence            4567888999999999999999999999999999999999                     7999999999999999544


Q ss_pred             Hhh
Q 008193          498 KAR  500 (574)
Q Consensus       498 k~~  500 (574)
                      ++.
T Consensus        84 r~~   86 (102)
T 2da6_A           84 FRQ   86 (102)
T ss_dssp             HHH
T ss_pred             Hhh
Confidence            433

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

Probab=99.58  E-value=7.1e-16  Score=145.85  Aligned_cols=60  Identities=25%  Similarity=0.308  Sum_probs=48.6

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHH
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  498 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k  498 (574)
                      .+.+|+|++|+..|+.+||.+|..++||+..+|.+||..|||+++||+|||||||++.+|
T Consensus        97 ~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr  156 (164)
T 2xsd_C           97 GRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKR  156 (164)
T ss_dssp             ---------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTB
T ss_pred             ccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhh
Confidence            456778899999999999999999999999999999999999999999999999994433

>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=99.57  E-value=1.4e-15  Score=141.58  Aligned_cols=57  Identities=33%  Similarity=0.547  Sum_probs=54.2

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  495 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~  495 (574)
                      .+.+|+|+.|+..|+.+||.+|..++||+..+|.+||.+|||++.||+|||||||++
T Consensus        91 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k  147 (151)
T 3d1n_I           91 SKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQT  147 (151)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhc
Confidence            466778899999999999999999999999999999999999999999999999993

>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=99.57  E-value=1.1e-15  Score=143.83  Aligned_cols=57  Identities=25%  Similarity=0.403  Sum_probs=51.0

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  495 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~  495 (574)
                      .+.||+|+.||..|+.+||.+|..++||+..+|.+||.+|||++.||+|||||||++
T Consensus        99 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k  155 (160)
T 1e3o_C           99 SRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQK  155 (160)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhh
Confidence            466788899999999999999999999999999999999999999999999999993

>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=99.57  E-value=1.4e-15  Score=123.56  Aligned_cols=54  Identities=28%  Similarity=0.401  Sum_probs=48.8

Q ss_pred             CCCHHHHHHHHHHHH---hCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193          447 RMPPNAVEKLRQVFA---ENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  500 (574)
Q Consensus       447 r~t~~Q~~~Le~~F~---~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~  500 (574)
                      +||.+|+.+|+.+|.   .||||+..+|.+||.+|||++.||++||||+|++.+|..
T Consensus         4 ~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~   60 (67)
T 3k2a_A            4 IFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPM   60 (67)
T ss_dssp             --CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC
T ss_pred             cCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHH
Confidence            699999999999999   999999999999999999999999999999999555443

>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=1.3e-15  Score=122.91  Aligned_cols=49  Identities=22%  Similarity=0.355  Sum_probs=47.4

Q ss_pred             cCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          446 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       446 ~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      ..++.+|+.+||.+|..++||+..+|.+||.+|||+++||+|||||||+
T Consensus         8 ~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRa   56 (64)
T 2e19_A            8 QPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQA   56 (64)
T ss_dssp             CCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccC
Confidence            4578999999999999999999999999999999999999999999999

>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.56  E-value=2.4e-15  Score=123.40  Aligned_cols=49  Identities=31%  Similarity=0.532  Sum_probs=47.8

Q ss_pred             cCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          446 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       446 ~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      ..+|..|+.+||.+|..++||+..+|.+||..|||+++||+|||||||+
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRa   57 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRY   57 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhh
Confidence            4689999999999999999999999999999999999999999999999

>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A

Probab=99.55  E-value=1.5e-15  Score=132.80  Aligned_cols=56  Identities=30%  Similarity=0.466  Sum_probs=49.5

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHH------------------cC---CChhhHHHhhccccc
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKE------------------LS---LEPEKVNKWFKNARY  494 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~------------------Lg---L~~~qV~vWFQNrR~  494 (574)
                      .+.+|.|+.|++.|+.+||.+|..++||+..+|++||.+                  ||   |++.||+|||||||+
T Consensus         7 ~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~   83 (99)
T 1lfb_A            7 KKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRK   83 (99)
T ss_dssp             ------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHH
Confidence            456788899999999999999999999999999999999                  99   999999999999999

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

Probab=99.55  E-value=1.6e-15  Score=142.69  Aligned_cols=57  Identities=26%  Similarity=0.374  Sum_probs=50.9

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  495 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~  495 (574)
                      .+.||+|+.||..|+.+||.+|..++||+..+|++||.+|||++.||+|||||||++
T Consensus        95 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r  151 (164)
T 2d5v_A           95 NTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRR  151 (164)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhcc
Confidence            455778899999999999999999999999999999999999999999999999993

>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=99.54  E-value=1.8e-15  Score=122.51  Aligned_cols=47  Identities=28%  Similarity=0.468  Sum_probs=44.0

Q ss_pred             CCHHHHHHHHHHH-HhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          448 MPPNAVEKLRQVF-AENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       448 ~t~~Q~~~Le~~F-~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      -.+.|+.+||.+| ..+.||+..+|.+||++|||+++||+|||||||+
T Consensus         7 ~~~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~   54 (64)
T 1x2m_A            7 GTAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRN   54 (64)
T ss_dssp             CSSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence            3456899999999 6799999999999999999999999999999999

>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=99.50  E-value=6.7e-15  Score=137.79  Aligned_cols=57  Identities=23%  Similarity=0.334  Sum_probs=53.9

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  495 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~  495 (574)
                      .+.+|+|+.|+..|+.+||.+|..++||+..+|.+||..|||+++||+|||||||++
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k  150 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQK  150 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             cCCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeecccccccc
Confidence            356678899999999999999999999999999999999999999999999999993

>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens}

Probab=99.46  E-value=7.8e-14  Score=119.78  Aligned_cols=59  Identities=34%  Similarity=0.436  Sum_probs=53.3

Q ss_pred             cCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhhhhhc
Q 008193          446 HRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARKVES  504 (574)
Q Consensus       446 ~r~t~~Q~~~Le~~F~~---~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~~~e~  504 (574)
                      +-|+.+++.+|+.||.+   +|||+..+|++||.+|||++.||++||||+|++.++......
T Consensus        10 ~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~~~~   71 (89)
T 2lk2_A           10 HMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRKD   71 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHHHhc
Confidence            57999999999999998   999999999999999999999999999999997766654443

>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=99.38  E-value=7.2e-14  Score=119.57  Aligned_cols=62  Identities=24%  Similarity=0.637  Sum_probs=51.2

Q ss_pred             cccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCC--CCCCCCCccccCcccchhhh
Q 008193          234 VHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTE--SIPPGDQGWFCKFCECKMEI  298 (574)
Q Consensus       234 ~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~--~iP~gde~W~C~~C~~k~~~  298 (574)
                      ..+++.+|.+|+.++...++.||+||+ |+++||++||+|||..+  .+|.++  |||+.|......
T Consensus        12 ~~e~~~~C~vC~~~~~~~~~~ll~CD~-C~~~yH~~Cl~Ppl~~~~~~~p~g~--W~C~~C~~~~~~   75 (88)
T 1wev_A           12 AMEMGLACVVCRQMTVASGNQLVECQE-CHNLYHQDCHKPQVTDKEVNDPRLV--WYCARCTRQMKR   75 (88)
T ss_dssp             HHHHCCSCSSSCCCCCCTTCCEEECSS-SCCEEETTTSSSCCCHHHHHCTTCC--CCCHHHHHHHCC
T ss_pred             cCCCCCcCCCCCCCCCCCCCceEECCC-CCCeEcCccCCCcccccccCCCCCC--eeCccccchhhh
Confidence            345678999999987655689999996 99999999999999721  289998  999999876543

>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=99.38  E-value=7.2e-14  Score=135.60  Aligned_cols=58  Identities=28%  Similarity=0.427  Sum_probs=51.3

Q ss_pred             CccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcC---------------------CChhhHHHhhccccc
Q 008193          437 SNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELS---------------------LEPEKVNKWFKNARY  494 (574)
Q Consensus       437 ~~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~Lg---------------------L~~~qV~vWFQNrR~  494 (574)
                      ...+.||.|+.|++.|+.+||.+|..++||+..+|++||..||                     |++.||++||||||+
T Consensus       111 ~~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~  189 (194)
T 1ic8_A          111 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRK  189 (194)
T ss_dssp             ------CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHH
T ss_pred             ccccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhh
Confidence            3456678899999999999999999999999999999999999                     999999999999999

>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=2.9e-13  Score=116.05  Aligned_cols=57  Identities=30%  Similarity=0.825  Sum_probs=50.0

Q ss_pred             CCCCcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193          230 TDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM  296 (574)
Q Consensus       230 ~dg~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~  296 (574)
                      .+.+...++++|.+|+.+     ++||+||+ |+++||++|+.|||.  .+|.|+  |||+.|....
T Consensus        17 ~~~~~d~n~~~C~vC~~~-----g~LL~CD~-C~~~fH~~Cl~PpL~--~~P~g~--W~C~~C~~~~   73 (88)
T 1fp0_A           17 EFGTLDDSATICRVCQKP-----GDLVMCNQ-CEFCFHLDCHLPALQ--DVPGEE--WSCSLCHVLP   73 (88)
T ss_dssp             CCCSSSSSSSCCSSSCSS-----SCCEECTT-SSCEECTTSSSTTCC--CCCSSS--CCCCSCCCCC
T ss_pred             cccccCCCCCcCcCcCCC-----CCEEECCC-CCCceecccCCCCCC--CCcCCC--cCCccccCCC
Confidence            345667788999999986     78999996 999999999999998  799998  9999998654

>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=99.36  E-value=4e-13  Score=110.28  Aligned_cols=45  Identities=22%  Similarity=0.353  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          450 PNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       450 ~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      ++|+.+|+.+|..|++|+.+++.+||..|||+.++|+|||||||+
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            689999999999999999999999999999999999999999998

>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=99.33  E-value=6.8e-13  Score=106.12  Aligned_cols=52  Identities=38%  Similarity=1.072  Sum_probs=45.7

Q ss_pred             ccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM  296 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~  296 (574)
                      +.++.+|.+|+.+     ++||+||+ |+++||++|++|||.  .+|.++  |||+.|..+.
T Consensus         6 d~~~~~C~vC~~~-----g~ll~Cd~-C~~~fH~~Cl~ppl~--~~p~g~--W~C~~C~~~~   57 (61)
T 1mm2_A            6 DHHMEFCRVCKDG-----GELLCCDT-CPSSYHIHCLNPPLP--EIPNGE--WLCPRCTCPA   57 (61)
T ss_dssp             CSSCSSCTTTCCC-----SSCBCCSS-SCCCBCSSSSSSCCS--SCCSSC--CCCTTTTTTC
T ss_pred             cCCCCcCCCCCCC-----CCEEEcCC-CCHHHcccccCCCcC--cCCCCc--cCChhhcCch
Confidence            3457899999975     79999996 999999999999998  799998  9999998653

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens}

Probab=99.33  E-value=7e-13  Score=130.69  Aligned_cols=57  Identities=30%  Similarity=0.494  Sum_probs=52.3

Q ss_pred             ccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcC---------------------CChhhHHHhhccccc
Q 008193          438 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELS---------------------LEPEKVNKWFKNARY  494 (574)
Q Consensus       438 ~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~Lg---------------------L~~~qV~vWFQNrR~  494 (574)
                      ..+.||.|+.|++.|+.+||.+|..|+||+..+|++||.+||                     |++.||++||||||+
T Consensus       139 ~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~  216 (221)
T 2h8r_A          139 NKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRK  216 (221)
T ss_dssp             ---CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHT
T ss_pred             cCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhh
Confidence            356678889999999999999999999999999999999998                     899999999999998

>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=99.30  E-value=2.3e-13  Score=109.79  Aligned_cols=58  Identities=28%  Similarity=0.733  Sum_probs=48.3

Q ss_pred             ccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCC-CCCCCccccCcccch
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESI-PPGDQGWFCKFCECK  295 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~i-P~gde~W~C~~C~~k  295 (574)
                      +.++.+|.+|+.++..+++.||+||+ |+++||++||+|||....+ |.++  |||+.|...
T Consensus         3 ~~~~~~C~vC~~~~~~~~~~ll~Cd~-C~~~~H~~C~~p~l~~~~~~p~~~--W~C~~C~~~   61 (66)
T 2yt5_A            3 SGSSGVCTICQEEYSEAPNEMVICDK-CGQGYHQLCHTPHIDSSVIDSDEK--WLCRQCVFA   61 (66)
T ss_dssp             CCCCCCBSSSCCCCCBTTBCEEECSS-SCCEEETTTSSSCCCHHHHHSSCC--CCCHHHHHT
T ss_pred             CCCCCCCCCCCCCCCCCCCCEEECCC-CChHHHhhhCCCcccccccCCCCC--EECCCCcCc
Confidence            34678999999986556799999996 9999999999999873224 7888  999999754

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

Probab=99.29  E-value=7.9e-13  Score=107.21  Aligned_cols=51  Identities=41%  Similarity=0.976  Sum_probs=45.3

Q ss_pred             ccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      ..++++|.+|+.+     ++||+||+ |+++||++||+|||.  .+|.++  |||+.|...
T Consensus         5 ~~~~~~C~vC~~~-----g~ll~CD~-C~~~fH~~Cl~ppl~--~~P~g~--W~C~~C~~~   55 (66)
T 1xwh_A            5 QKNEDECAVCRDG-----GELICCDG-CPRAFHLACLSPPLR--EIPSGT--WRCSSCLQA   55 (66)
T ss_dssp             CSCCCSBSSSSCC-----SSCEECSS-CCCEECTTTSSSCCS--SCCSSC--CCCHHHHHT
T ss_pred             CCCCCCCccCCCC-----CCEEEcCC-CChhhcccccCCCcC--cCCCCC--eECccccCc
Confidence            3467899999976     78999996 999999999999998  799988  999999754

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

Probab=99.29  E-value=1.3e-12  Score=104.57  Aligned_cols=52  Identities=37%  Similarity=0.914  Sum_probs=45.8

Q ss_pred             CcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193          233 SVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC  294 (574)
Q Consensus       233 ~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~  294 (574)
                      ....++.+|.+|+.+     ++||+||+ |+++||++|++||+.  .+|.++  |||+.|..
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-----GEIILCDT-CPRAYHMVCLDPDME--KAPEGK--WSCPHCEK   57 (61)
T ss_dssp             CSSCCCSSCTTTSCC-----SSEEECSS-SSCEEEHHHHCTTCC--SCCCSS--CCCTTGGG
T ss_pred             ccCCCCCCCccCCCC-----CcEEECCC-CChhhhhhccCCCCC--CCCCCc--eECccccc
Confidence            345667899999985     79999995 999999999999998  799998  99999974

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

Probab=99.27  E-value=1.2e-12  Score=104.18  Aligned_cols=51  Identities=37%  Similarity=1.028  Sum_probs=45.2

Q ss_pred             cccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM  296 (574)
Q Consensus       236 ~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~  296 (574)
                      .++++|.+|+.+     ++||+||+ |+++||++|++|||.  .+|.++  |||+.|....
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-CSRVYHLDCLDPPLK--TIPKGM--WICPRCQDQM   53 (60)
T ss_dssp             CCCSSCTTTCCC-----SSCEECSS-SSCEECGGGSSSCCS--SCCCSC--CCCHHHHHHH
T ss_pred             CCCCCCcCCCCC-----CcEEEcCC-CCcCEECCcCCCCcC--CCCCCc--eEChhccChh
Confidence            356899999986     79999996 999999999999998  799988  9999997654

>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=99.26  E-value=1.2e-12  Score=113.01  Aligned_cols=56  Identities=36%  Similarity=0.865  Sum_probs=48.5

Q ss_pred             CcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          233 SVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       233 ~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      +...++.+|.+|+..+  +.+.||+||+ |+++||++||+|||.  .+|.++  |||+.|...
T Consensus        11 ~~~~~~~~C~vC~~~~--~~~~ll~CD~-C~~~~H~~Cl~Ppl~--~~P~g~--W~C~~C~~~   66 (92)
T 2e6r_A           11 AQFIDSYICQVCSRGD--EDDKLLFCDG-CDDNYHIFCLLPPLP--EIPRGI--WRCPKCILA   66 (92)
T ss_dssp             CCCCCCCCCSSSCCSG--GGGGCEECTT-TCCEECSSSSSSCCS--SCCSSC--CCCHHHHHH
T ss_pred             hhccCCCCCccCCCcC--CCCCEEEcCC-CCchhccccCCCCcc--cCCCCC--cCCccCcCc
Confidence            4566778999999874  3468999996 999999999999998  799998  999999764

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

Probab=99.26  E-value=1.7e-12  Score=101.92  Aligned_cols=50  Identities=36%  Similarity=1.014  Sum_probs=44.3

Q ss_pred             ccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC  294 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~  294 (574)
                      ..++++|.+|+..     ++||+||+ |+++||++|++|||.  .+|.++  |||+.|..
T Consensus         6 ~~~~~~C~vC~~~-----g~ll~Cd~-C~~~~H~~Cl~ppl~--~~p~g~--W~C~~C~~   55 (56)
T 2yql_A            6 SGHEDFCSVCRKS-----GQLLMCDT-CSRVYHLDCLDPPLK--TIPKGM--WICPRCQD   55 (56)
T ss_dssp             CSSCCSCSSSCCS-----SCCEECSS-SSCEECSSSSSSCCC--SCCCSS--CCCHHHHC
T ss_pred             CCCCCCCccCCCC-----CeEEEcCC-CCcceECccCCCCcC--CCCCCc--eEChhhhC
Confidence            3457899999986     79999995 999999999999998  799988  99999963

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=99.26  E-value=2.1e-12  Score=105.06  Aligned_cols=50  Identities=28%  Similarity=0.558  Sum_probs=43.8

Q ss_pred             ccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC  294 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~  294 (574)
                      ......|.+|+.+     ++||+||+ |+++||++||+|||.  .+|.++  |||+.|..
T Consensus         9 ~~~~~~C~vC~~~-----~~ll~Cd~-C~~~~H~~Cl~P~l~--~~P~g~--W~C~~C~~   58 (66)
T 2lri_C            9 LAPGARCGVCGDG-----TDVLRCTH-CAAAFHWRCHFPAGT--SRPGTG--LRCRSCSG   58 (66)
T ss_dssp             CCTTCCCTTTSCC-----TTCEECSS-SCCEECHHHHCTTTC--CCCSSS--CCCTTTTT
T ss_pred             CCCCCCcCCCCCC-----CeEEECCC-CCCceecccCCCccC--cCCCCC--EECccccC
Confidence            3445679999865     78999995 999999999999998  799998  99999974

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

Probab=99.25  E-value=1.9e-12  Score=99.51  Aligned_cols=48  Identities=42%  Similarity=1.043  Sum_probs=42.7

Q ss_pred             cccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193          240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC  294 (574)
Q Consensus       240 ~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~  294 (574)
                      +|.+|+..+  +++.||+||+ |+++||++|++|||.  .+|.++  |||+.|..
T Consensus         2 ~C~vC~~~~--~~~~ll~Cd~-C~~~~H~~Cl~p~l~--~~P~g~--W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKG--EDDKLILCDE-CNKAFHLFCLRPALY--EVPDGE--WQCPACQP   49 (51)
T ss_dssp             CCTTTCCSS--CCSCCEECTT-TCCEECHHHHCTTCC--SCCSSC--CSCTTTSC
T ss_pred             CCCCCCCCC--CCCCEEECCC-CChhhCcccCCCCcC--CCCCCc--EECcCccc
Confidence            699999874  3578999996 999999999999998  799988  99999974

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

Probab=99.23  E-value=1.9e-12  Score=106.73  Aligned_cols=55  Identities=38%  Similarity=0.839  Sum_probs=47.4

Q ss_pred             ccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM  296 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~  296 (574)
                      ..++.+|.+|+.+++.+++.||+||+ |+++||++|++|+    .+|.|+  |||+.|....
T Consensus        13 ~~~~~~C~vC~~~~s~~~~~ll~CD~-C~~~~H~~Cl~~~----~vP~g~--W~C~~C~~~~   67 (71)
T 2ku3_A           13 IDEDAVCSICMDGESQNSNVILFCDM-CNLAVHQECYGVP----YIPEGQ--WLCRHCLQSR   67 (71)
T ss_dssp             CCSSCSCSSSCCCCCCSSSCEEECSS-SCCEEEHHHHTCS----SCCSSC--CCCHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCCEEECCC-CCCccccccCCCC----cCCCCC--cCCccCcCcC
Confidence            45678999999987666789999996 9999999999998    389998  9999998653

>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=105.29  Aligned_cols=55  Identities=38%  Similarity=0.904  Sum_probs=46.4

Q ss_pred             CCcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCC-CCccccCcccc
Q 008193          232 GSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPG-DQGWFCKFCEC  294 (574)
Q Consensus       232 g~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~g-de~W~C~~C~~  294 (574)
                      .|...+. +|.+|+..+  +++.||+||+ |+++||++||+|||.  .+|.| +  |||+.|..
T Consensus        21 ~w~C~~c-~C~vC~~~~--~~~~ll~CD~-C~~~yH~~Cl~Ppl~--~~P~g~~--W~C~~C~~   76 (77)
T 2e6s_A           21 EKKCHSC-SCRVCGGKH--EPNMQLLCDE-CNVAYHIYCLNPPLD--KVPEEEY--WYCPSCKT   76 (77)
T ss_dssp             SSCCSSS-SCSSSCCCC--CSTTEEECSS-SCCEEETTSSSSCCS--SCCCSSC--CCCTTTCC
T ss_pred             CeECCCC-CCcCcCCcC--CCCCEEEcCC-CCccccccccCCCcc--CCCCCCC--cCCcCccC
Confidence            3555555 899999864  4589999996 999999999999998  79998 7  99999963

>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=99.20  E-value=7.3e-12  Score=102.93  Aligned_cols=55  Identities=36%  Similarity=0.929  Sum_probs=45.8

Q ss_pred             CCcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCC-CCccccCcccc
Q 008193          232 GSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPG-DQGWFCKFCEC  294 (574)
Q Consensus       232 g~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~g-de~W~C~~C~~  294 (574)
                      .|..... +|.+|+..+  +++.||+||+ |+++||++||+|||.  .+|.| +  |||+.|..
T Consensus        13 ~w~C~~C-~C~~C~~~~--~~~~ll~CD~-C~~~yH~~Cl~Ppl~--~~P~g~~--W~C~~C~~   68 (70)
T 3asl_A           13 NRLCRVC-ACHLCGGRQ--DPDKQLMCDE-CDMAFHIYCLDPPLS--SVPSEDE--WYCPECRN   68 (70)
T ss_dssp             TSCCTTT-SBTTTCCCS--CGGGEEECTT-TCCEEEGGGSSSCCS--SCCSSSC--CCCTTTSC
T ss_pred             CeECCCC-CCcCCCCcC--CCCCEEEcCC-CCCceecccCCCCcC--CCCCCCC--cCCcCccC
Confidence            3455555 777888764  4589999996 999999999999998  79998 7  99999974

>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=3.3e-12  Score=109.34  Aligned_cols=55  Identities=38%  Similarity=0.850  Sum_probs=47.0

Q ss_pred             ccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM  296 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~  296 (574)
                      ..++.+|.+|+.+++.+++.||+||+ |+.+||++|++|++    +|.|+  |||+.|....
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----IPEGQ--WLCRHCLQSR   76 (88)
T ss_dssp             CCCCCCCSSCCSSSSCSEEEEEECSS-SCCCCCHHHHTCSS----CCSSC--CCCHHHHHHT
T ss_pred             CCCCCcCCcCCCCCCCCCCCEEECCC-CCchhhcccCCCCc----cCCCc--eECccccCcc
Confidence            35678999999986556689999996 99999999999983    78888  9999998654

>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=99.15  E-value=9.6e-12  Score=110.86  Aligned_cols=77  Identities=26%  Similarity=0.632  Sum_probs=60.9

Q ss_pred             hhccCCCCCCCcCC-----cccCCCCcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCcc
Q 008193          213 QLDSLSSVGCIEGS-----VIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGW  287 (574)
Q Consensus       213 ~~d~l~~~~~l~~s-----~l~~dg~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W  287 (574)
                      .+...+|..++...     .+....|...+..+|.+|+..+  +++.||+||+ |+++||++||+|||.  .+|.|+  |
T Consensus        28 ~C~~~~H~~Cl~~~~~~~~~~~~~~W~C~~C~~C~~C~~~~--~~~~ll~Cd~-C~~~yH~~Cl~ppl~--~~P~g~--W  100 (114)
T 2kwj_A           28 DCGRSGHPTCLQFTLNMTEAVKTYKWQCIECKSCILCGTSE--NDDQLLFCDD-CDRGYHMYCLNPPVA--EPPEGS--W  100 (114)
T ss_dssp             SSCCEECTTTTTCCHHHHHHHHHTTCCCGGGCCCTTTTCCT--TTTTEEECSS-SCCEEETTTSSSCCS--SCCSSC--C
T ss_pred             CCCCccchhhCCChhhhhhccCCCccCccccCccCcccccC--CCCceEEcCC-CCccccccccCCCcc--CCCCCC--e
Confidence            34555677777643     3445567778888899998864  4689999996 999999999999998  799998  9


Q ss_pred             ccCcccchh
Q 008193          288 FCKFCECKM  296 (574)
Q Consensus       288 ~C~~C~~k~  296 (574)
                      ||+.|....
T Consensus       101 ~C~~C~~~~  109 (114)
T 2kwj_A          101 SCHLCWELL  109 (114)
T ss_dssp             CCHHHHHHH
T ss_pred             ECccccchh
Confidence            999997543

>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=99.14  E-value=1.6e-11  Score=117.17  Aligned_cols=50  Identities=32%  Similarity=0.883  Sum_probs=44.8

Q ss_pred             cccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       236 ~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      .++++|.+|+.+     |+||+||+ |+++||++|++|||.  .+|.|+  |+|+.|...
T Consensus         2 ~~~~~C~~C~~~-----g~ll~Cd~-C~~~~H~~C~~p~l~--~~p~~~--W~C~~C~~~   51 (184)
T 3o36_A            2 PNEDWCAVCQNG-----GELLCCEK-CPKVFHLSCHVPTLT--NFPSGE--WICTFCRDL   51 (184)
T ss_dssp             CSCSSCTTTCCC-----SSCEECSS-SSCEECTTTSSSCCS--SCCSSC--CCCTTTSCS
T ss_pred             CCCCccccCCCC-----CeeeecCC-CCcccCccccCCCCC--CCCCCC--EECccccCc
Confidence            356899999976     78999996 999999999999998  799998  999999854

>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=99.14  E-value=1.6e-11  Score=127.38  Aligned_cols=52  Identities=29%  Similarity=0.444  Sum_probs=49.6

Q ss_pred             CCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          443 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       443 r~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      +.+..|+..|+..||..|..++||+..+|++||.+|||+++||+|||||||+
T Consensus       367 ~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~  418 (421)
T 1mh3_A          367 AAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRM  418 (421)
T ss_dssp             HHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHC
T ss_pred             hhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhccc
Confidence            3456899999999999999999999999999999999999999999999998

>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=99.13  E-value=1.4e-11  Score=119.83  Aligned_cols=51  Identities=37%  Similarity=0.877  Sum_probs=45.5

Q ss_pred             ccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      +.++++|.+|+.+     |+||+||+ |+++||++|++|||.  .+|.|+  |+|+.|...
T Consensus         4 d~~~~~C~~C~~~-----g~ll~Cd~-C~~~~H~~Cl~p~l~--~~p~~~--W~C~~C~~~   54 (207)
T 3u5n_A            4 DPNEDWCAVCQNG-----GDLLCCEK-CPKVFHLTCHVPTLL--SFPSGD--WICTFCRDI   54 (207)
T ss_dssp             CSSCSSBTTTCCC-----EEEEECSS-SSCEECTTTSSSCCS--SCCSSC--CCCTTTSCS
T ss_pred             CCCCCCCCCCCCC-----CceEEcCC-CCCccCCccCCCCCC--CCCCCC--EEeCceeCc
Confidence            3467899999976     78999996 999999999999998  799998  999999864

>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=99.08  E-value=4.9e-11  Score=117.96  Aligned_cols=54  Identities=37%  Similarity=0.944  Sum_probs=41.8

Q ss_pred             CcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCC-CCccccCcccc
Q 008193          233 SVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPG-DQGWFCKFCEC  294 (574)
Q Consensus       233 ~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~g-de~W~C~~C~~  294 (574)
                      +.+..+ .|.+|+..+  +++.||+||+ |+++||++||+|||.  .+|.| +  |||+.|..
T Consensus       170 w~C~~c-~C~vC~~~~--~~~~lL~CD~-C~~~yH~~CL~PPL~--~vP~G~~--W~Cp~C~~  224 (226)
T 3ask_A          170 RLCRVC-ACHLCGGRQ--DPDKQLMCDE-CDMAFHIYCLDPPLS--SVPSEDE--WYCPECRN  224 (226)
T ss_dssp             SCCTTT-SCSSSCCCC--C--CCEECSS-SCCEECSCC--CCCC--SCCSSSC--CCCGGGC-
T ss_pred             EecCCC-CCcCCCCCC--CCCCeEEcCC-CCcceeCccCCCCcc--cCCCCCC--CCCcCCcC
Confidence            444444 899999864  4589999996 999999999999998  79998 7  99999974

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

Probab=99.07  E-value=5.8e-11  Score=99.39  Aligned_cols=56  Identities=38%  Similarity=0.920  Sum_probs=45.3

Q ss_pred             CCcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193          232 GSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC  294 (574)
Q Consensus       232 g~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~  294 (574)
                      .|..... .|.+|+..+  +++.||+||+ |+++||++||+|||.  .+|.++ .|||+.|..
T Consensus        21 ~W~C~~C-~C~vC~~~~--d~~~ll~CD~-C~~~yH~~Cl~PpL~--~~P~g~-~W~C~~C~~   76 (77)
T 3shb_A           21 NRLCRVC-ACHLCGGRQ--DPDKQLMCDE-CDMAFHIYCLDPPLS--SVPSED-EWYCPECRN   76 (77)
T ss_dssp             TSCCTTT-SBTTTCCCS--CGGGEEECTT-TCCEEETTTSSSCCS--SCCSSS-CCCCTTTC-
T ss_pred             CCCCCCC-cCCccCCCC--CCcceeEeCC-CCCccCcccCCCccc--CCCCCC-ceECcCccc
Confidence            3555666 678888764  4578999996 999999999999998  799874 499999973

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

Probab=99.05  E-value=9.9e-11  Score=103.93  Aligned_cols=62  Identities=29%  Similarity=0.815  Sum_probs=52.0

Q ss_pred             ccCCCCcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          228 IATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       228 l~~dg~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      +....|...+..+|.+|+.... +++.||+||+ |+++||++||+|||.  .+|.++  |||+.|..+
T Consensus        51 ~~~~~W~C~~C~~C~vC~~~~~-~~~~ll~Cd~-C~~~yH~~Cl~p~l~--~~P~~~--W~C~~C~~k  112 (112)
T 3v43_A           51 VKALRWQCIECKTCSSCRDQGK-NADNMLFCDS-CDRGFHMECCDPPLT--RMPKGM--WICQICRPR  112 (112)
T ss_dssp             HHTSCCCCTTTCCBTTTCCCCC-TTCCCEECTT-TCCEECGGGCSSCCS--SCCSSC--CCCTTTSCC
T ss_pred             hhccccccccCCccccccCcCC-CccceEEcCC-CCCeeecccCCCCCC--CCCCCC--eECCCCCCc
Confidence            3456788888889999997532 4578999996 999999999999998  799998  999999753

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

Probab=99.04  E-value=8.3e-11  Score=113.39  Aligned_cols=48  Identities=33%  Similarity=0.953  Sum_probs=43.6

Q ss_pred             cccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       238 d~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      +++|.+|+.+     |+||+||+ |+++||++|+.||+.  .+|.|+  |+|+.|...
T Consensus         2 ~~~C~~C~~~-----g~ll~Cd~-C~~~~H~~Cl~p~l~--~~p~g~--W~C~~C~~~   49 (189)
T 2ro1_A            2 ATICRVCQKP-----GDLVMCNQ-CEFCFHLDCHLPALQ--DVPGEE--WSCSLCHVL   49 (189)
T ss_dssp             CCCBTTTCCC-----SSCCCCTT-TCCBCCSTTSTTCCS--SCCCTT--CCTTTTSCS
T ss_pred             CCcCccCCCC-----CceeECCC-CCchhccccCCCCcc--cCCCCC--CCCcCccCC
Confidence            4689999976     78999996 999999999999998  799998  999999865

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

Probab=99.02  E-value=9.2e-11  Score=96.84  Aligned_cols=55  Identities=24%  Similarity=0.614  Sum_probs=45.5

Q ss_pred             ccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM  296 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~  296 (574)
                      ..+..+|.+|+..+  +++.||+||+ |+.+||+.|+++++.  .+|.++  |||+.|..+.
T Consensus        15 ~~~~~~C~~C~~~~--~~~~mi~CD~-C~~wfH~~Cv~~~~~--~~~~~~--w~C~~C~~~~   69 (75)
T 2k16_A           15 GNQIWICPGCNKPD--DGSPMIGCDD-CDDWYHWPCVGIMAA--PPEEMQ--WFCPKCANKI   69 (75)
T ss_dssp             SCEEECBTTTTBCC--SSCCEEECSS-SSSEEEHHHHTCSSC--CCSSSC--CCCTTTHHHH
T ss_pred             CCCCcCCCCCCCCC--CCCCEEEcCC-CCcccccccCCCCcc--CCCCCC--EEChhccCch
Confidence            45678899999975  3457999996 999999999999987  567677  9999998653

>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=99.01  E-value=1.6e-10  Score=102.03  Aligned_cols=75  Identities=28%  Similarity=0.664  Sum_probs=58.7

Q ss_pred             hccCCCCCCCcCCc--ccCCCCcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCc
Q 008193          214 LDSLSSVGCIEGSV--IATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKF  291 (574)
Q Consensus       214 ~d~l~~~~~l~~s~--l~~dg~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~  291 (574)
                      +...+|..++...+  +....|...+..+|.+|+...  ++..||+||+ |+++||++||+|||.  .+|.++  |||+.
T Consensus        28 C~~~~H~~Cl~~~~~~~~~~~W~C~~C~~C~~C~~~~--~~~~ll~Cd~-C~~~yH~~Cl~ppl~--~~P~g~--W~C~~  100 (111)
T 2ysm_A           28 CGQHYHGMCLDIAVTPLKRAGWQCPECKVCQNCKQSG--EDSKMLVCDT-CDKGYHTFCLQPVMK--SVPTNG--WKCKN  100 (111)
T ss_dssp             SCCEECTTTTTCCCCTTTSTTCCCTTTCCCTTTCCCS--CCTTEEECSS-SCCEEEGGGSSSCCS--SCCSSC--CCCHH
T ss_pred             CCCCcChHHhCCccccccccCccCCcCCcccccCccC--CCCCeeECCC-CCcHHhHHhcCCccc--cCCCCC--cCCcC
Confidence            44556666665433  234678888888899999874  3467999995 999999999999998  799988  99999


Q ss_pred             ccch
Q 008193          292 CECK  295 (574)
Q Consensus       292 C~~k  295 (574)
                      |...
T Consensus       101 C~~c  104 (111)
T 2ysm_A          101 CRIC  104 (111)
T ss_dssp             HHCC
T ss_pred             CcCc
Confidence            9754

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=98.89  E-value=1e-09  Score=95.57  Aligned_cols=56  Identities=27%  Similarity=0.660  Sum_probs=43.9

Q ss_pred             CCCcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          231 DGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       231 dg~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      ++....+.+.| +|+..+  +++.||+||+ |+.+||+.|++|++.  .+|+ .  |||+.|..+
T Consensus        21 dg~~~~d~vrC-iC~~~~--~~~~mi~Cd~-C~~w~H~~C~~~~~~--~~p~-~--w~C~~C~~~   76 (98)
T 2lv9_A           21 DGSYGTDVTRC-ICGFTH--DDGYMICCDK-CSVWQHIDCMGIDRQ--HIPD-T--YLCERCQPR   76 (98)
T ss_dssp             TCCCCCCBCCC-TTSCCS--CSSCEEEBTT-TCBEEETTTTTCCTT--SCCS-S--BCCTTTSSS
T ss_pred             cCCCCCCCEEe-ECCCcc--CCCcEEEcCC-CCCcCcCcCCCCCcc--CCCC-C--EECCCCcCC
Confidence            34444445667 898875  4689999995 999999999999987  6774 4  999999754

>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=98.74  E-value=3.8e-09  Score=93.56  Aligned_cols=49  Identities=33%  Similarity=0.859  Sum_probs=42.7

Q ss_pred             ccccccccccccCCCCCCCCccccC--CCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCD--GTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCD--g~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      ..++++|.+|+.+     |+||+||  + |+++||++||+  |.  .+|.|+  |||+.|.+.
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--LT--QPPYGK--WECPWHQCD   62 (107)
T ss_dssp             CSSCSSCTTTCCC-----SEEEECCSTT-CCCEECTGGGT--CS--SCCSSC--CCCGGGBCT
T ss_pred             CCCCCCCCcCCCC-----CcEeEECCCC-CCcccccccCc--CC--cCCCCC--EECCCCCCC
Confidence            4567899999965     8999999  6 99999999999  55  799998  999999754

>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=98.64  E-value=5.3e-09  Score=83.35  Aligned_cols=50  Identities=30%  Similarity=0.734  Sum_probs=38.3

Q ss_pred             ccccccccccccCCCCCCCCccccCCCcC---CcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDGTCN---CAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~C~---rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      ..+..+| +|+..+   .+.||+|| .|+   .+||+.|++  |.  .+|.+.  |||+.|..+
T Consensus         7 ~~e~~~C-~C~~~~---~g~mi~CD-~cdC~~~wfH~~Cvg--l~--~~p~g~--w~C~~C~~~   59 (60)
T 2vnf_A            7 PNEPTYC-LCHQVS---YGEMIGCD-NPDCSIEWFHFACVG--LT--TKPRGK--WFCPRCSQE   59 (60)
T ss_dssp             --CCEET-TTTEEC---CSEEEECS-CTTCSSCEEETGGGT--CS--SCCSSC--CCCHHHHC-
T ss_pred             CCCCCEE-ECCCcC---CCCEEEeC-CCCCCCceEehhcCC--CC--cCCCCC--EECcCccCc
Confidence            3456778 899873   47899999 555   799999999  44  678887  999999754

>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=98.63  E-value=4.1e-08  Score=84.59  Aligned_cols=50  Identities=30%  Similarity=0.781  Sum_probs=39.7

Q ss_pred             ccccccccccccCCCCCCCCccccCCC--cC-CcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDGT--CN-CAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~--C~-rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      ..+..+| +|+..+   .+.||+|| .  |+ .+||+.|++.  .  .+|.+.  |||+.|...
T Consensus        33 ~~e~~yC-iC~~~~---~g~MI~CD-~~dC~~~WfH~~CVgl--~--~~p~g~--W~Cp~C~~~   85 (91)
T 1weu_A           33 PNEPTYC-LCHQVS---YGEMIGCD-NPDCSIEWFHFACVGL--T--TKPRGK--WFCPRCSQE   85 (91)
T ss_dssp             SCCCBCS-TTCCBC---CSCCCCCS-CSSCSCCCCCSTTTTC--S--SCCCSS--CCCTTTCCC
T ss_pred             CCCCcEE-ECCCCC---CCCEeEec-CCCCCCCCEecccCCc--C--cCCCCC--EECcCccCc
Confidence            4456788 999874   47899999 5  55 6999999994  4  577777  999999764

>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=98.58  E-value=3.5e-08  Score=81.24  Aligned_cols=50  Identities=32%  Similarity=0.822  Sum_probs=39.9

Q ss_pred             ccccccccccccCCCCCCCCccccCCC--cC-CcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDGT--CN-CAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~--C~-rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      ..+..+| +|+..+   .+.||+|| .  |+ .+||+.|++  |.  .+|.+.  |||+.|...
T Consensus        13 ~~~~~~C-~C~~~~---~g~MI~CD-~~~C~~~wfH~~Cvg--l~--~~p~g~--w~Cp~C~~~   65 (71)
T 1wen_A           13 PNEPTYC-LCHQVS---YGEMIGCD-NPDCSIEWFHFACVG--LT--TKPRGK--WFCPRCSQE   65 (71)
T ss_dssp             TTSCCCS-TTCCCS---CSSEECCS-CSSCSCCCEETTTTT--CS--SCCSSC--CCCTTTSSC
T ss_pred             CCCCCEE-ECCCCC---CCCEeEee-CCCCCCccEecccCC--cC--cCCCCC--EECCCCCcc
Confidence            3456788 799874   47899999 6  66 699999999  44  578787  999999764

>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=98.57  E-value=4e-08  Score=86.59  Aligned_cols=55  Identities=24%  Similarity=0.537  Sum_probs=44.8

Q ss_pred             cccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          234 VHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       234 ~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      ...++++|.+|+.+.  +.++||+|++ |++.||++|++|++.  .++.+.  |+|+.|..-
T Consensus         3 ~~~~~~~C~~C~~~g--~~~~ll~C~~-C~~~~H~~Cl~~~~~--~~~~~~--W~C~~C~~C   57 (111)
T 2ysm_A            3 SGSSGANCAVCDSPG--DLLDQFFCTT-CGQHYHGMCLDIAVT--PLKRAG--WQCPECKVC   57 (111)
T ss_dssp             CCCCCSCBTTTCCCC--CTTTSEECSS-SCCEECTTTTTCCCC--TTTSTT--CCCTTTCCC
T ss_pred             CCCCCCCCcCCCCCC--CCcCCeECCC-CCCCcChHHhCCccc--cccccC--ccCCcCCcc
Confidence            355788999999874  2256799995 999999999999986  577777  999999643

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

Probab=98.56  E-value=8.6e-09  Score=95.51  Aligned_cols=54  Identities=24%  Similarity=0.622  Sum_probs=44.7

Q ss_pred             ccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCC---C--CCCCCCccccCcccchh
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTE---S--IPPGDQGWFCKFCECKM  296 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~---~--iP~gde~W~C~~C~~k~  296 (574)
                      +..+++|.+|+.+     |+||+|| .|+++||..|+.|||...   .  .|.++  |+|+.|....
T Consensus        60 Dg~~d~C~vC~~G-----G~LlcCD-~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~--W~C~~C~~~p  118 (142)
T 2lbm_A           60 DGMDEQCRWCAEG-----GNLICCD-FCHNAFCKKCILRNLGRKELSTIMDENNQ--WYCYICHPEP  118 (142)
T ss_dssp             TSCBCSCSSSCCC-----SSEEECS-SSCCEEEHHHHHHHTCHHHHHHHHTSTTC--CCCTTTCCCT
T ss_pred             CCCCCeecccCCC-----CcEEeCC-CCCCeeeHhhcCCCCChhhhhhcccCCCC--CEeecccCcc
Confidence            3457899999987     8999999 599999999999998621   1  37787  9999998653

>2jmi_A Protein YNG1, ING1 homolog 1; PHD, histone, recognition, yeast, protein binding; NMR {Saccharomyces cerevisiae} PDB: 2jmj_A*

Probab=98.52  E-value=3.9e-08  Score=84.57  Aligned_cols=48  Identities=29%  Similarity=0.765  Sum_probs=38.0

Q ss_pred             ccccccccccccCCCCCCCCccccCCCcC---CcccccccCCCCCCCCCCCCCCccccCc-cc
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDGTCN---CAFHQKCLDPPLDTESIPPGDQGWFCKF-CE  293 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~C~---rafH~~Cl~PPL~~~~iP~gde~W~C~~-C~  293 (574)
                      ..+..+| +|+..+   .+.||+||+ |+   .+||+.|++.  .  .+|.+.  |||+. |.
T Consensus        23 ~~~~~yC-iC~~~~---~g~MI~CD~-c~C~~eWfH~~CVgl--~--~~p~~~--W~Cp~cC~   74 (90)
T 2jmi_A           23 NQEEVYC-FCRNVS---YGPMVACDN-PACPFEWFHYGCVGL--K--QAPKGK--WYCSKDCK   74 (90)
T ss_dssp             -CCSCCS-TTTCCC---SSSEECCCS-SSCSCSCEETTTSSC--S--SCTTSC--CCSSHHHH
T ss_pred             CCCCcEE-EeCCCC---CCCEEEecC-CCCccccCcCccCCC--C--cCCCCC--ccCChhhc
Confidence            3456788 899863   478999995 77   8999999994  3  567777  99999 86

>2g6q_A Inhibitor of growth protein 2; protein-peptide complex, gene regulation, apoptosis; HET: M3L; 2.00A {Mus musculus}

Probab=98.48  E-value=2.5e-08  Score=80.03  Aligned_cols=49  Identities=27%  Similarity=0.677  Sum_probs=38.3

Q ss_pred             cccccccccccCCCCCCCCccccCCCcC---CcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          236 HEHIICAKCKLREAFPDNDIVLCDGTCN---CAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       236 ~ed~~C~vC~~~~~~~~g~lLlCDg~C~---rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      .+..+| +|+..+   .+.||.|| .|+   .+||+.|++..    .+|.+.  |||+.|..+
T Consensus         9 ~e~~yC-~C~~~~---~g~MI~CD-~c~C~~~WfH~~Cvgl~----~~p~~~--w~Cp~C~~~   60 (62)
T 2g6q_A            9 NEPTYC-LCNQVS---YGEMIGCD-NEQCPIEWFHFSCVSLT----YKPKGK--WYCPKCRGD   60 (62)
T ss_dssp             -CCEET-TTTEEC---CSEEEECS-CTTCSSCEEETGGGTCS----SCCSSC--CCCHHHHTC
T ss_pred             CCCcEE-ECCCCC---CCCeeeee-CCCCCcccEecccCCcC----cCCCCC--EECcCcccC
Confidence            445788 899863   47899999 555   99999999943    467777  999999754

>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=98.47  E-value=2.9e-08  Score=78.89  Aligned_cols=49  Identities=35%  Similarity=0.853  Sum_probs=38.6

Q ss_pred             cccccccccccCCCCCCCCccccCCC--cC-CcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          236 HEHIICAKCKLREAFPDNDIVLCDGT--CN-CAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       236 ~ed~~C~vC~~~~~~~~g~lLlCDg~--C~-rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      .+..+| +|+..+   .+.||.|| .  |+ .+||+.|++  |.  .+|.+.  |||+.|..+
T Consensus         7 ~e~~yC-~C~~~~---~g~mi~CD-~~~C~~~wfH~~Cvg--l~--~~p~~~--w~Cp~C~~~   58 (59)
T 3c6w_A            7 NEPTYC-LCHQVS---YGEMIGCD-NPDCPIEWFHFACVD--LT--TKPKGK--WFCPRCVQE   58 (59)
T ss_dssp             -CCEET-TTTEEC---CSEEEECS-CTTCSSCEEETGGGT--CS--SCCSSC--CCCHHHHCC
T ss_pred             CCCcEE-ECCCCC---CCCeeEee-CCCCCCCCEecccCC--cc--cCCCCC--EECcCccCc
Confidence            355778 899873   47899999 6  66 699999999  44  577787  999999753

>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=98.25  E-value=7.2e-08  Score=88.01  Aligned_cols=54  Identities=26%  Similarity=0.647  Sum_probs=43.5

Q ss_pred             ccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCC---CC--CCCCCccccCcccchh
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTE---SI--PPGDQGWFCKFCECKM  296 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~---~i--P~gde~W~C~~C~~k~  296 (574)
                      +..+.+|.+|+.+     |+||+||. |+++||..|+.|++...   .+  |.+.  |+|..|..+.
T Consensus        54 Dg~~~~C~vC~dG-----G~LlcCd~-Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~--W~C~~C~~~p  112 (129)
T 3ql9_A           54 DGMDEQCRWCAEG-----GNLICCDF-CHNAFCKKCILRNLGRRELSTIMDENNQ--WYCYICHPEP  112 (129)
T ss_dssp             TSCBSSCTTTCCC-----SEEEECSS-SSCEEEHHHHHHHTCHHHHHHHTCTTSC--CCCTTTCCGG
T ss_pred             CCCCCcCeecCCC-----CeeEecCC-CchhhhHHHhCCCcchhHHHHhccCCCC--eEcCCcCCHH
Confidence            3456789999987     89999995 99999999999986411   23  6676  9999998764

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

Probab=98.25  E-value=2.6e-07  Score=75.86  Aligned_cols=50  Identities=28%  Similarity=0.686  Sum_probs=39.0

Q ss_pred             cccccccccccCCCCCCCCccccCCCcC---CcccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193          236 HEHIICAKCKLREAFPDNDIVLCDGTCN---CAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM  296 (574)
Q Consensus       236 ~ed~~C~vC~~~~~~~~g~lLlCDg~C~---rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~  296 (574)
                      .+..+|. |+..+   .+.||.||+ |+   .+||+.|++..    ..|.+.  |||+.|....
T Consensus         4 ~~~~yC~-C~~~~---~g~MI~CD~-cdC~~~WfH~~Cvgl~----~~p~~~--w~Cp~C~~~~   56 (70)
T 1x4i_A            4 GSSGYCI-CNQVS---YGEMVGCDN-QDCPIEWFHYGCVGLT----EAPKGK--WYCPQCTAAM   56 (70)
T ss_dssp             SCCCCST-TSCCC---CSSEECCSC-TTCSCCCEEHHHHTCS----SCCSSC--CCCHHHHHHH
T ss_pred             CCCeEEE-cCCCC---CCCEeEeCC-CCCCccCCcccccccC----cCCCCC--EECCCCCccc
Confidence            3456784 98873   479999995 75   79999999954    467776  9999998654

>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=98.24  E-value=2.9e-07  Score=73.54  Aligned_cols=55  Identities=25%  Similarity=0.437  Sum_probs=41.4

Q ss_pred             cccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCC-CCCCccccCcccchh
Q 008193          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIP-PGDQGWFCKFCECKM  296 (574)
Q Consensus       236 ~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP-~gde~W~C~~C~~k~  296 (574)
                      .+..+|.+|+..+. +++.||.||. |..+||..|++....  .+. ...  |+|+.|..+.
T Consensus         4 ~e~~~C~~C~~~~~-~~~~mI~Cd~-C~~WfH~~Cvgl~~~--~~~~~~~--~~C~~C~~k~   59 (64)
T 1we9_A            4 GSSGQCGACGESYA-ADEFWICCDL-CEMWFHGKCVKITPA--RAEHIKQ--YKCPSCSNKS   59 (64)
T ss_dssp             SSCCCCSSSCCCCC-SSSCEEECSS-SCCEEETTTTTCCTT--GGGGCSS--CCCHHHHTTT
T ss_pred             CCCCCCCCCCCccC-CCCCEEEccC-CCCCCCccccCcChh--HhcCCCc--EECCCCcCcC
Confidence            45678999998742 3578999995 999999999996543  222 133  9999998654

>2rsd_A E3 SUMO-protein ligase SIZ1; E3 SUMO ligase, plant homeodomain (PHD), histone binding; NMR {Oryza sativa japonica group}

Probab=98.13  E-value=1.2e-06  Score=71.18  Aligned_cols=55  Identities=20%  Similarity=0.665  Sum_probs=38.6

Q ss_pred             ccccccccccccCCCCCCCCccccCC-CcCCcccccccCCCCCC---CCCCCCCCccccCcccch
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDG-TCNCAFHQKCLDPPLDT---ESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg-~C~rafH~~Cl~PPL~~---~~iP~gde~W~C~~C~~k  295 (574)
                      +++..+| +|+..+  +++.||.||+ .|..+||..|++..-..   ..+|+   .|||+.|+..
T Consensus         7 ~e~~v~C-~C~~~~--~~g~mI~CD~~~C~~W~H~~Cvgi~~~~~~~~~~p~---~~~C~~Cr~~   65 (68)
T 2rsd_A            7 PEAKVRC-ICSSTM--VNDSMIQCEDQRCQVWQHLNCVLIPDKPGESAEVPP---VFYCELCRLS   65 (68)
T ss_dssp             SSCEECC-TTCCCS--CCSCEEECSCTTTCEEEETTTSCCCSSTTSCCCCCS---SCCCHHHHHH
T ss_pred             CCCCEEe-ECCCCc--CCCCEEEECCCCCCCeEchhhCCCCcccccccCCCC---cEECcCccCc
Confidence            3445677 798764  4589999993 39999999999854321   12332   3999999754

>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=98.11  E-value=1.1e-06  Score=71.71  Aligned_cols=51  Identities=18%  Similarity=0.509  Sum_probs=39.7

Q ss_pred             ccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC  294 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~  294 (574)
                      ..+..+| +|+..+  +++.||.||. |..+||..|++....  .+| +.  |+|+.|..
T Consensus        16 ~~~~~~C-iC~~~~--~~~~MIqCd~-C~~WfH~~Cvgi~~~--~~~-~~--~~C~~C~~   66 (68)
T 3o70_A           16 FQGLVTC-FCMKPF--AGRPMIECNE-CHTWIHLSCAKIRKS--NVP-EV--FVCQKCRD   66 (68)
T ss_dssp             TTTCCCS-TTCCCC--TTCCEEECTT-TCCEEETTTTTCCTT--SCC-SS--CCCHHHHT
T ss_pred             CCCceEe-ECCCcC--CCCCEEECCC-CCccccccccCcCcc--cCC-Cc--EECCCCCC
Confidence            4456788 999874  3457999995 999999999997654  455 34  99999963

>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=98.09  E-value=1.2e-06  Score=71.78  Aligned_cols=52  Identities=25%  Similarity=0.687  Sum_probs=38.7

Q ss_pred             cccccccccccCCCCCCC-CccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          236 HEHIICAKCKLREAFPDN-DIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       236 ~ed~~C~vC~~~~~~~~g-~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      ....+| +|+..+  +++ .||.||. |..+||..|++..... .+| ..  |+|+.|..+
T Consensus        14 ~~~~~C-~C~~~~--~~g~~mI~Cd~-C~~W~H~~Cvg~~~~~-~~~-~~--~~C~~C~~~   66 (72)
T 1wee_A           14 NWKVDC-KCGTKD--DDGERMLACDG-CGVWHHTRCIGINNAD-ALP-SK--FLCFRCIEL   66 (72)
T ss_dssp             SSEECC-TTCCCS--CCSSCEEECSS-SCEEEETTTTTCCTTS-CCC-SC--CCCHHHHHH
T ss_pred             CcceEe-eCCCcc--CCCCcEEECCC-CCCccCCeeeccCccc-cCC-Cc--EECCCccCC
Confidence            445789 699874  234 6999995 9999999999976432 344 44  999999754

>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=98.02  E-value=1.7e-06  Score=72.07  Aligned_cols=57  Identities=19%  Similarity=0.548  Sum_probs=40.3

Q ss_pred             ccccccccccccCCCCCCCCccccC--CCcCCcccccccCCCCCCCC-CCCCCCccccCcccch
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCD--GTCNCAFHQKCLDPPLDTES-IPPGDQGWFCKFCECK  295 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCD--g~C~rafH~~Cl~PPL~~~~-iP~gde~W~C~~C~~k  295 (574)
                      ..+..+| +|+..+  +++.||.||  . |..+||..|++.+-.... .+.....|||+.|...
T Consensus        13 ~~~~~~C-iC~~~~--~~g~MI~CD~~~-C~~W~H~~CVgi~~~~~~~~~~~~~~~~C~~C~~~   72 (78)
T 1wew_A           13 PEIKVRC-VCGNSL--ETDSMIQCEDPR-CHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLT   72 (78)
T ss_dssp             CCCCCCC-SSCCCC--CCSCEEECSSTT-TCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHC
T ss_pred             CCCCEEe-ECCCcC--CCCCEEEECCcc-CCccccCEEEccccccccccccCCCCEECCCCCcc
Confidence            3456788 899974  458999999  7 999999999996543210 0111124999999754

>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=98.01  E-value=6.4e-07  Score=65.01  Aligned_cols=20  Identities=30%  Similarity=0.664  Sum_probs=16.0

Q ss_pred             hhHHHhhcccccHHHHhhhhh
Q 008193          483 EKVNKWFKNARYLALKARKVE  503 (574)
Q Consensus       483 ~qV~vWFQNrR~~~~k~~~~e  503 (574)
                      +||+|||||||+ ++|++..+
T Consensus         1 rQVkIWFQNRRa-K~Kk~~~~   20 (37)
T 2nzz_A            1 RQIKIWFQNRRM-KWKKRVFN   20 (37)
T ss_dssp             CCTTTTTTCSHH-HHTSSHHH
T ss_pred             CCceeccHHHHH-HHHHHhHH
Confidence            589999999999 55665554

>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=97.93  E-value=6.8e-07  Score=84.16  Aligned_cols=55  Identities=20%  Similarity=0.515  Sum_probs=39.7

Q ss_pred             cccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM  296 (574)
Q Consensus       236 ~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~  296 (574)
                      .+..+| +|+..+. +++.||.||+ |+.+||..|++..... ..+.+.  |+|+.|....
T Consensus         6 ~~~~~C-~C~~~~~-~~~~mi~Cd~-C~~WfH~~Cv~~~~~~-~~~~~~--~~C~~C~~~~   60 (174)
T 2ri7_A            6 DTKLYC-ICKTPED-ESKFYIGCDR-CQNWYHGRCVGILQSE-AELIDE--YVCPQCQSTE   60 (174)
T ss_dssp             -CCEET-TTTEECC-TTSCEEECTT-TCCEEEHHHHTCCHHH-HTTCSS--CCCHHHHHHH
T ss_pred             CCCcEe-eCCCCCC-CCCCEeECCC-CCchhChhhcCCchhh-ccCccC--eecCCCcchh
Confidence            456789 9998742 3577999995 9999999999864321 112344  9999998654

>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=97.93  E-value=8.7e-07  Score=73.22  Aligned_cols=54  Identities=20%  Similarity=0.553  Sum_probs=38.1

Q ss_pred             cccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCC-C--CCCCCccccCcccch
Q 008193          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTES-I--PPGDQGWFCKFCECK  295 (574)
Q Consensus       236 ~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~-i--P~gde~W~C~~C~~k  295 (574)
                      .+..+| +|+..+  +++.||.||. |..+||..|++....... +  +...  |+|+.|...
T Consensus        14 ~~~~~C-~C~~~~--~~~~MI~Cd~-C~~WfH~~Cvgl~~~~~~~l~~~~~~--~~C~~C~~~   70 (76)
T 1wem_A           14 PNALYC-ICRQPH--NNRFMICCDR-CEEWFHGDCVGISEARGRLLERNGED--YICPNCTIL   70 (76)
T ss_dssp             TTCCCS-TTCCCC--CSSCEEECSS-SCCEEEHHHHSCCHHHHHHHHHHTCC--CCCHHHHHH
T ss_pred             CCCCEE-ECCCcc--CCCCEEEeCC-CCCcEeCeEEccchhhhhhccCCCCe--EECcCCcCc
Confidence            335678 899875  3468999995 999999999996432000 0  1234  999999754

>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=97.85  E-value=2.3e-06  Score=76.09  Aligned_cols=54  Identities=24%  Similarity=0.508  Sum_probs=40.3

Q ss_pred             ccccccccCCC-----CCCCCccccCCCcCCcccccccCCCCCC-CCCCCCCCccccCcccch
Q 008193          239 IICAKCKLREA-----FPDNDIVLCDGTCNCAFHQKCLDPPLDT-ESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       239 ~~C~vC~~~~~-----~~~g~lLlCDg~C~rafH~~Cl~PPL~~-~~iP~gde~W~C~~C~~k  295 (574)
                      ++|.+|..+..     .+.++||+|++ |++.||++||++++.. ..+|.+.  |+|+.|..-
T Consensus         2 ~~C~~C~~~~~~n~k~g~~~~Li~C~~-C~~~~H~~Cl~~~~~~~~~~~~~~--W~C~~C~~C   61 (114)
T 2kwj_A            2 SYCDFCLGGSNMNKKSGRPEELVSCAD-CGRSGHPTCLQFTLNMTEAVKTYK--WQCIECKSC   61 (114)
T ss_dssp             CCCSSSCCBTTBCTTTCCCCCCEECSS-SCCEECTTTTTCCHHHHHHHHHTT--CCCGGGCCC
T ss_pred             CcCccCCCCccccccCCCCCCCeEeCC-CCCccchhhCCChhhhhhccCCCc--cCccccCcc
Confidence            57999987642     13469999996 9999999999987421 1356677  999999643

>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=97.72  E-value=6.3e-06  Score=68.65  Aligned_cols=52  Identities=19%  Similarity=0.436  Sum_probs=37.9

Q ss_pred             ccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCC-CCCCccccCcccch
Q 008193          237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIP-PGDQGWFCKFCECK  295 (574)
Q Consensus       237 ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP-~gde~W~C~~C~~k  295 (574)
                      +..+| +|+..+. +++.||.||. |..+||..|++....  ... ..  .|+|+.|...
T Consensus        11 ~~~~C-~C~~~~d-~~~~MIqCd~-C~~WfH~~Cvgl~~~--~~~~~~--~~~C~~C~~~   63 (79)
T 1wep_A           11 VPVYC-LCRQPYN-VNHFMIECGL-CQDWFHGSCVGIEEE--NAVDID--IYHCPDCEAV   63 (79)
T ss_dssp             CCCCS-TTSCSCC-SSSCEEEBTT-TCCEEEHHHHTCCHH--HHTTCS--BBCCTTTTTT
T ss_pred             CccEE-EcCCccC-CCCceEEcCC-CCCcEEeeecCcccc--cccCCC--eEECCCcccc
Confidence            34667 9998742 3578999995 999999999995433  121 13  4999999854

>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=97.72  E-value=5.9e-06  Score=72.70  Aligned_cols=55  Identities=24%  Similarity=0.594  Sum_probs=39.9

Q ss_pred             cccccccccCCCCCCCCccccC-CCcCCcccccccCCCCCC-CC---CCCCCCccccCcccchh
Q 008193          238 HIICAKCKLREAFPDNDIVLCD-GTCNCAFHQKCLDPPLDT-ES---IPPGDQGWFCKFCECKM  296 (574)
Q Consensus       238 d~~C~vC~~~~~~~~g~lLlCD-g~C~rafH~~Cl~PPL~~-~~---iP~gde~W~C~~C~~k~  296 (574)
                      ...|.+|+.... +++.||.|| + |..+||..|++..... ..   -|.+.  |+|+.|....
T Consensus         3 ~~~C~iC~~p~~-~~~~mi~Cdd~-C~~WfH~~CVglt~~~~~~i~~~~~~~--~~Cp~C~~~~   62 (105)
T 2xb1_A            3 VYPCGACRSEVN-DDQDAILCEAS-CQKWFHRECTGMTESAYGLLTTEASAV--WACDLCLKTK   62 (105)
T ss_dssp             CCBCTTTCSBCC-TTSCEEECTTT-TCCEEEGGGTTCCHHHHHHHHHCTTEE--ECCHHHHHTT
T ss_pred             cCCCCCCCCccC-CCCCEEEecCC-cccccccccCCcCHHHHHhhccCCCCC--EECccccCcC
Confidence            467999999753 357899998 6 9999999999954210 00   24444  9999998654

>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=97.69  E-value=2.4e-06  Score=69.20  Aligned_cols=54  Identities=24%  Similarity=0.543  Sum_probs=38.0

Q ss_pred             cccccccccccCCCCCCCCccccC-CCcCCcccccccCCCCCCC----CCCCCCCccccCccc
Q 008193          236 HEHIICAKCKLREAFPDNDIVLCD-GTCNCAFHQKCLDPPLDTE----SIPPGDQGWFCKFCE  293 (574)
Q Consensus       236 ~ed~~C~vC~~~~~~~~g~lLlCD-g~C~rafH~~Cl~PPL~~~----~iP~gde~W~C~~C~  293 (574)
                      +....|.+|+.... ++..||.|| + |..+||..|++......    .-|.+.  |+|+.|.
T Consensus         6 ~~~~~C~~C~~p~~-~~~~mI~CD~~-C~~WfH~~Cvglt~~~~~~l~~e~~~~--w~C~~C~   64 (65)
T 2vpb_A            6 DPVYPCGICTNEVN-DDQDAILCEAS-CQKWFHRICTGMTETAYGLLTAEASAV--WGCDTCM   64 (65)
T ss_dssp             ---CBCTTTCSBCC-TTSCEEEBTTT-TCCEEEHHHHTCCHHHHHHHHHCTTEE--ECCHHHH
T ss_pred             CCcCcCccCCCccC-CCCCeEecccC-ccccCchhccCCCHHHHHHhhccCCCc--EECcCcc
Confidence            44578999999753 456899999 7 99999999998542100    024444  9999995

>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=97.66  E-value=6.9e-06  Score=67.82  Aligned_cols=53  Identities=26%  Similarity=0.578  Sum_probs=37.8

Q ss_pred             ccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       237 ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      +..+| +|+..+. +++.||.||. |..+||..|++....  .++..+ .|+|+.|...
T Consensus         9 ~~~yC-iC~~~~~-~~~~MI~Cd~-C~~WfH~~Cvg~~~~--~~~~~~-~~~C~~C~~~   61 (75)
T 3kqi_A            9 VPVYC-VCRLPYD-VTRFMIECDA-CKDWFHGSCVGVEEE--EAPDID-IYHCPNCEKT   61 (75)
T ss_dssp             CCEET-TTTEECC-TTSCEEECTT-TCCEEEHHHHTCCTT--TGGGBS-SCCCHHHHHH
T ss_pred             CeeEE-ECCCcCC-CCCCEEEcCC-CCCCEeccccccccc--ccCCCC-EEECCCCccc
Confidence            34566 8988641 3578999995 999999999996543  333222 3999999754

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

Probab=97.61  E-value=4.7e-06  Score=73.78  Aligned_cols=55  Identities=22%  Similarity=0.469  Sum_probs=40.2

Q ss_pred             cccccccccCCC----CCCCCccccCCCcCCcccccccCC--CCCCCCCCCCCCccccCcccchh
Q 008193          238 HIICAKCKLREA----FPDNDIVLCDGTCNCAFHQKCLDP--PLDTESIPPGDQGWFCKFCECKM  296 (574)
Q Consensus       238 d~~C~vC~~~~~----~~~g~lLlCDg~C~rafH~~Cl~P--PL~~~~iP~gde~W~C~~C~~k~  296 (574)
                      ..+|.+|.....    ...++||.|++ |++.||++||++  ++. ..++.++  |+|+.|..-.
T Consensus         5 ~~~C~~C~~~~~~~~~g~~~~Ll~C~~-C~~~~H~~Cl~~~~~~~-~~~~~~~--W~C~~C~~C~   65 (112)
T 3v43_A            5 IPICSFCLGTKEQNREKKPEELISCAD-CGNSGHPSCLKFSPELT-VRVKALR--WQCIECKTCS   65 (112)
T ss_dssp             CSSBTTTCCCTTCCTTSCCCCCEECTT-TCCEECHHHHTCCHHHH-HHHHTSC--CCCTTTCCBT
T ss_pred             CccccccCCchhhCcCCCchhceEhhh-cCCCCCCchhcCCHHHH-HHhhccc--cccccCCccc
Confidence            467889977531    13468999996 999999999974  232 1466777  9999997443

>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=8.8e-06  Score=62.72  Aligned_cols=48  Identities=29%  Similarity=0.616  Sum_probs=34.6

Q ss_pred             cccccccCCCCCCCCccccC-CCcCCcccccccCCCCCCCCCCCCCCccccCccc
Q 008193          240 ICAKCKLREAFPDNDIVLCD-GTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCE  293 (574)
Q Consensus       240 ~C~vC~~~~~~~~g~lLlCD-g~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~  293 (574)
                      .|.+|+..+. ++..||.|| + |..+||..|++....  ......  |+|+.|.
T Consensus         4 ~cc~C~~p~~-~~~~mI~Cd~~-C~~WfH~~Cvgl~~~--~~~~~~--~~C~~C~   52 (52)
T 2kgg_A            4 AAQNCQRPCK-DKVDWVQCDGG-CDEWFHQVCVGVSPE--MAENED--YICINCA   52 (52)
T ss_dssp             SCTTCCCCCC-TTCCEEECTTT-TCCEEETTTTTCCHH--HHHHSC--CCCSCC-
T ss_pred             cCCCCcCccC-CCCcEEEeCCC-CCccCcccccCCCcc--ccCCCC--EECCCCC
Confidence            4778888752 356799999 7 999999999995432  111244  9999994

>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=97.56  E-value=3.2e-05  Score=65.54  Aligned_cols=54  Identities=22%  Similarity=0.760  Sum_probs=39.2

Q ss_pred             cccccccccccCCCCCCCCccccCCCcCCcccccccCCC--------CCCCCCCCCCCccccCccc
Q 008193          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPP--------LDTESIPPGDQGWFCKFCE  293 (574)
Q Consensus       236 ~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PP--------L~~~~iP~gde~W~C~~C~  293 (574)
                      ..+..|.||..-.   .+.++-|. .|.+.||..||.++        +.....-..+.+|.|+.|.
T Consensus        13 ~~D~~C~VC~~~t---~~~l~pCR-vC~RvfH~~CL~r~gy~~~~~a~e~~l~A~T~~GWSC~~Ce   74 (89)
T 1wil_A           13 VNDEMCDVCEVWT---AESLFPCR-VCTRVFHDGCLRRMGYIQGDSAAEVTEMAHTETGWSCHYCD   74 (89)
T ss_dssp             CCSCCCTTTCCCC---SSCCSSCS-SSSSCCCHHHHHHHTSCCCCCCCSCSCCCSSSSSCCCTTTC
T ss_pred             CCCcccCcccccc---ccceeccc-cccccccHhhcccccccccHHHHHHHHccCCCCCccccccc
Confidence            4678999999863   47899999 79999999999875        1110111223459999995

>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=97.55  E-value=2.2e-05  Score=60.37  Aligned_cols=46  Identities=20%  Similarity=0.599  Sum_probs=35.5

Q ss_pred             ccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCccc
Q 008193          239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCE  293 (574)
Q Consensus       239 ~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~  293 (574)
                      .+| +|+..+  +++.||.||. |..+||..|++....  .+| +.  |+|+.|.
T Consensus         5 ~~C-~C~~~~--~~~~MI~Cd~-C~~W~H~~Cvgi~~~--~~~-~~--~~C~~C~   50 (52)
T 3o7a_A            5 VTC-FCMKPF--AGRPMIECNE-CHTWIHLSCAKIRKS--NVP-EV--FVCQKCR   50 (52)
T ss_dssp             BCS-TTCCBC--TTCCEEECTT-TCCEEETTTTTCCGG--GCC-SS--CCCHHHH
T ss_pred             eEE-EeCCcC--CCCCEEEcCC-CCccccccccCCCcc--cCC-Cc--EECcCCC
Confidence            345 688764  3569999995 999999999997644  455 33  9999996

>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=97.26  E-value=0.0001  Score=70.81  Aligned_cols=56  Identities=20%  Similarity=0.476  Sum_probs=38.2

Q ss_pred             ccccccccCCCCCC--CCccccCCCcCCcccccccCCCCCC----CCCCCCCCccccCcccchh
Q 008193          239 IICAKCKLREAFPD--NDIVLCDGTCNCAFHQKCLDPPLDT----ESIPPGDQGWFCKFCECKM  296 (574)
Q Consensus       239 ~~C~vC~~~~~~~~--g~lLlCDg~C~rafH~~Cl~PPL~~----~~iP~gde~W~C~~C~~k~  296 (574)
                      .+|.+|+..+..++  ..||.||+ |..+||..|++..-..    ..+|+. ..|+|+.|....
T Consensus         3 ~~CpiC~k~Y~~~~~~~~MIqCd~-C~~W~H~~Cvgi~~~~~e~~~~~pe~-~~y~Cp~C~~~~   64 (183)
T 3lqh_A            3 NFCPLCDKCYDDDDYESKMMQCGK-CDRWVHSKCENLSDEMYEILSNLPES-VAYTCVNCTERH   64 (183)
T ss_dssp             CBCTTTCCBCTTCCTTCCEEECTT-TCCEEEGGGSSCCHHHHHHHHHSHHH-HCCCCTTTCCSS
T ss_pred             CcCCCCcCccCCcccCCCeEECCC-CCcccchhccccCHHHHHHhhcCCCC-CeeECcCCCCCC
Confidence            47999999864322  34999995 9999999999853200    012321 139999998754

>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=96.98  E-value=0.0002  Score=78.56  Aligned_cols=40  Identities=23%  Similarity=0.404  Sum_probs=29.3

Q ss_pred             CCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          252 DNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       252 ~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      +..||.||+ |+.+||..|++..-.  .... ...|+||.|...
T Consensus        55 ~~~mI~CD~-C~~WfH~~CVgi~~~--~a~~-~~~y~Cp~C~~~   94 (528)
T 3pur_A           55 DFQWIGCDS-CQTWYHFLCSGLEQF--EYYL-YEKFFCPKCVPH   94 (528)
T ss_dssp             TTSEEECTT-TCCEEEGGGTTCCGG--GTTT-EEECCCTTTHHH
T ss_pred             CCCEEECCC-CCcCCCCcCCCCChh--HhcC-CCeEECcCCcCC
Confidence            467999995 999999999995532  1111 124999999864

>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=96.92  E-value=8.5e-05  Score=81.06  Aligned_cols=55  Identities=18%  Similarity=0.391  Sum_probs=38.3

Q ss_pred             cccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM  296 (574)
Q Consensus       236 ~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~  296 (574)
                      .+..+| +|+..+. +++.||.||. |..+||..|++..-.  .... ...|+|+.|....
T Consensus        35 ~~~~yC-~C~~~~d-~~~~MIqCd~-C~~WfH~~Cvgl~~~--~~~~-~~~~~C~~C~~~~   89 (488)
T 3kv5_D           35 PPPVYC-VCRQPYD-VNRFMIECDI-CKDWFHGSCVGVEEH--HAVD-IDLYHCPNCAVLH   89 (488)
T ss_dssp             CCCEET-TTTEECC-TTSCEEEBTT-TCCEEEHHHHTCCGG--GGGG-EEEBCCHHHHHHH
T ss_pred             CCCeEE-eCCCcCC-CCCCeEEccC-CCCceeeeecCcCcc--cccC-CCEEECCCCcCCc
Confidence            334566 9998641 2588999995 999999999985432  2211 1249999998643

>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=96.16  E-value=0.00036  Score=75.42  Aligned_cols=51  Identities=22%  Similarity=0.452  Sum_probs=36.1

Q ss_pred             cccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       240 ~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      .+++|+..+. +++.||.||. |..+||..|++..-.  ..+.. ..|+|+.|...
T Consensus         6 ~yCiC~~~~d-~~~~MIqCD~-C~~WfH~~CVgi~~~--~~~~~-~~y~C~~C~~~   56 (447)
T 3kv4_A            6 VYCLCRLPYD-VTRFMIECDM-CQDWFHGSCVGVEEE--KAADI-DLYHCPNCEVL   56 (447)
T ss_dssp             EETTTTEECC-TTSCEEECTT-TCCEEEHHHHTCCHH--HHTTE-EECCCHHHHHH
T ss_pred             eEEeCCCcCC-CCCCeEEcCC-CCcccccccCCcCcc--cccCC-CEEECCCCccc
Confidence            3458988641 3588999995 999999999985432  12111 24999999764

>4bbq_A Lysine-specific demethylase 2A; oxidoreductase, ubiquitin, ligase, ubiquitination, demethyla ZF-CXXC DNA binding domain, CPG island, chromatin; 2.24A {Homo sapiens}

Probab=95.58  E-value=0.0035  Score=55.12  Aligned_cols=40  Identities=23%  Similarity=0.511  Sum_probs=28.8

Q ss_pred             CCccccCCCcCCcccccccCCCCCCCCCCCC--CCccccCcccch
Q 008193          253 NDIVLCDGTCNCAFHQKCLDPPLDTESIPPG--DQGWFCKFCECK  295 (574)
Q Consensus       253 g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~g--de~W~C~~C~~k  295 (574)
                      ..||.|+ .|+.+||..|++++..  .++..  .+.|+|+.|...
T Consensus        73 ~~m~~C~-~C~~~~H~~C~~~~~~--~~~~~~~~~~~~C~~C~~~  114 (117)
T 4bbq_A           73 KKLMECC-ICNEIVHPGCLQMDGE--GLLNEELPNCWECPKCYQE  114 (117)
T ss_dssp             GSCEEET-TTCCEECGGGCCSCCC--CEECSSSSSEEECTTTC--
T ss_pred             cceEEee-ecCCeEECCCCCCCcc--ccccccCCCCeECCCCcCC
Confidence            4588999 5999999999998754  23221  124999999854

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=94.46  E-value=0.009  Score=52.45  Aligned_cols=40  Identities=20%  Similarity=0.551  Sum_probs=28.0

Q ss_pred             CccccCCCcCCcccccccCCCCC----CCCCCCCCCccccCcccch
Q 008193          254 DIVLCDGTCNCAFHQKCLDPPLD----TESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       254 ~lLlCDg~C~rafH~~Cl~PPL~----~~~iP~gde~W~C~~C~~k  295 (574)
                      .||.||. |..|||..|.+..-.    ...+|... .|.|+.|...
T Consensus         1 ~mi~c~~-c~~w~H~~c~~~~~~~~~~l~~lp~~~-~~~c~~C~~~   44 (140)
T 2ku7_A            1 SMMQCGK-CDRWVHSKCENLSDEMYEILSNLPESV-AYTCVNCTER   44 (140)
T ss_dssp             CCCCCSC-CSSCHHHHHCCCCHHHHHHHHSSCTTT-TCCSSCCTTT
T ss_pred             Ccccccc-CCCccCCcccccCHHHHHHHhhccccc-eeeCcccccc
Confidence            3899995 999999999874310    01455332 4999999754

>2ys9_A Homeobox and leucine zipper protein homez; homeodomain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.45  E-value=0.033  Score=45.67  Aligned_cols=49  Identities=20%  Similarity=0.327  Sum_probs=43.1

Q ss_pred             cCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          446 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       446 ~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      ...++.-.+.|+.+|..+..+..+.-+.|+.+.+|+..||+.||--|-.
T Consensus        11 ~~~~p~~~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~k~~   59 (70)
T 2ys9_A           11 IPPPPPDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSRLP   59 (70)
T ss_dssp             CCCCCCCCHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHHHSC
T ss_pred             CCCCCCcchHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHhccc
Confidence            3456667789999999999999999999999999999999999965443

>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=93.88  E-value=0.032  Score=49.18  Aligned_cols=64  Identities=14%  Similarity=0.257  Sum_probs=38.7

Q ss_pred             hccCCCCCCCcCCcccCCCCcccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCcccc
Q 008193          214 LDSLSSVGCIEGSVIATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFC  289 (574)
Q Consensus       214 ~d~l~~~~~l~~s~l~~dg~~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C  289 (574)
                      ++...|..++.-..+....|....+ .|.+|+..      ..+.|. .|+.+||..|+.+.|.  ..+.+.  |+|
T Consensus        35 Cp~~fH~~Cl~L~~~P~g~W~Cp~c-~C~~C~k~------~~~~C~-~Cp~sfC~~c~~g~l~--~~~~~~--~~c   98 (107)
T 4gne_A           35 CPKAYHLLCLNLTQPPYGKWECPWH-QCDECSSA------AVSFCE-FCPHSFCKDHEKGALV--PSALEG--RLC   98 (107)
T ss_dssp             CCCEECTGGGTCSSCCSSCCCCGGG-BCTTTCSB------CCEECS-SSSCEECTTTCTTSCE--ECTTTT--CEE
T ss_pred             CCcccccccCcCCcCCCCCEECCCC-CCCcCCCC------CCcCcC-CCCcchhhhccCCcce--ecCCCC--cee
Confidence            3445566666532232222333322 24455554      237899 5999999999999997  345444  998

>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=86.67  E-value=0.13  Score=48.44  Aligned_cols=55  Identities=20%  Similarity=0.547  Sum_probs=39.3

Q ss_pred             ccccccccccCCCCCCCCccccCC-CcCCcccccccCCCCCCCCCC--CCCCccccCcccchh
Q 008193          237 EHIICAKCKLREAFPDNDIVLCDG-TCNCAFHQKCLDPPLDTESIP--PGDQGWFCKFCECKM  296 (574)
Q Consensus       237 ed~~C~vC~~~~~~~~g~lLlCDg-~C~rafH~~Cl~PPL~~~~iP--~gde~W~C~~C~~k~  296 (574)
                      .+.+|.+|+.+     +.||+||. .|.+.|-..|+.--+....+-  ...++|.|-.|...+
T Consensus        78 ~~~yC~wC~~G-----g~l~~Cdn~~C~r~FC~~CI~~nvG~~~~~~i~~~d~W~Cy~C~P~~  135 (159)
T 3a1b_A           78 YQSYCTICCGG-----REVLMCGNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKG  135 (159)
T ss_dssp             SBSSCTTTSCC-----SEEEECSSTTTCCEEEHHHHHHHTCTTHHHHHHTSSSCCCTTTCSSC
T ss_pred             CcceeeEecCC-----CeEEeeCCCCCCCchhHHHHHHhcCHhHHHHHhccCCCEEEecCCcc
Confidence            36799999987     89999992 399999999987554421111  112359999998654

>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=83.59  E-value=0.15  Score=54.14  Aligned_cols=54  Identities=17%  Similarity=0.539  Sum_probs=39.5

Q ss_pred             ccccccccccCCCCCCCCccccC--CCcCCcccccccCCCCCCCCCC--CCCCccccCcccchh
Q 008193          237 EHIICAKCKLREAFPDNDIVLCD--GTCNCAFHQKCLDPPLDTESIP--PGDQGWFCKFCECKM  296 (574)
Q Consensus       237 ed~~C~vC~~~~~~~~g~lLlCD--g~C~rafH~~Cl~PPL~~~~iP--~gde~W~C~~C~~k~  296 (574)
                      .+.+|..|+.+     +++|+||  . |.++|-..|+.--+....+-  .....|.|-.|....
T Consensus        92 ~~~yCr~C~~G-----g~l~~Cdn~~-C~r~FC~~Ci~~n~g~~~~~~i~~~d~W~Cf~C~p~p  149 (386)
T 2pv0_B           92 YQSYCSICCSG-----ETLLICGNPD-CTRCYCFECVDSLVGPGTSGKVHAMSNWVCYLCLPSS  149 (386)
T ss_dssp             SBCSCTTTCCC-----SSCEECCSTT-CCCEECHHHHHHHTCTTHHHHHHHCSSCCCTTTSSCC
T ss_pred             CcccceEcCCC-----CeEEEeCCCC-CCcchHHHHHHHhcChhHHHHhhccCCceEEEcCCcc
Confidence            46789999987     8999999  6 99999999987555321111  112359999998764

>3rsn_A SET1/ASH2 histone methyltransferase complex subun; PHD domain, winged helix domain, binding, transcription; 2.10A {Homo sapiens} PDB: 3s32_A

Probab=80.49  E-value=1  Score=42.96  Aligned_cols=50  Identities=12%  Similarity=0.278  Sum_probs=32.2

Q ss_pred             ccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCC-CCCCccccCcccch
Q 008193          243 KCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIP-PGDQGWFCKFCECK  295 (574)
Q Consensus       243 vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP-~gde~W~C~~C~~k  295 (574)
                      .|+.... -.-.||.|+. |.++||..|+..+... -+| ...-...|..|...
T Consensus         9 YCG~~~~-~~~~mLqC~~-C~qWFH~~Cl~~~~~~-~lp~~~fY~F~C~~C~~~   59 (177)
T 3rsn_A            9 DEENGRQ-LGEVELQCGI-CTKWFTADTFGIDTSS-CLPFMTNYSFHCNVCHHS   59 (177)
T ss_dssp             --CTTCC-TTSCEEECTT-TCCEEEGGGGTCCCTT-CCTTCCSEEEECTTTSTT
T ss_pred             EcCCCCC-CCceeEeecc-ccceecHHHhcccccC-ccccceeEEEEccccCCC
Confidence            4665321 2356999995 9999999999866542 344 22224669999763

---

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	574
d1weva_	88	g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus mu	3e-11
d1fp0a1	70	g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-	2e-10
d1f62a_	51	g.50.1.2 (A:) Williams-Beuren syndrome transcripti	1e-09
d1mm2a_	61	g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens	4e-08
d1we9a_	64	g.50.1.2 (A:) PHD finger protein At5g26210 {Thale	3e-07
d1weea_	72	g.50.1.2 (A:) PHD finger protein At1g33420 {Thale	1e-06
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
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	7e-06
d1wema_	76	g.50.1.2 (A:) Death associated transcription facto	3e-05
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	8e-05
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	9e-05
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	2e-04
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	3e-04
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	3e-04
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	3e-04
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	3e-04
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	3e-04
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	5e-04
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	6e-04
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	6e-04
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	8e-04
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	8e-04
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	0.001
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	0.003
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	0.004

>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 = 57.9 bits (139), Expect = 3e-11
 Identities = 15/69 (21%), Positives = 26/69 (37%), Gaps = 1/69 (1%)

Query: 229 ATDGSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWF 288
             D       + C  C+       N +V C   C+  +HQ C  P +  + +      W+
Sbjct: 7   GADDFAMEMGLACVVCRQMTVASGNQLVECQE-CHNLYHQDCHKPQVTDKEVNDPRLVWY 65

Query: 289 CKFCECKME 297
           C  C  +M+
Sbjct: 66  CARCTRQMK 74

>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 = 54.6 bits (131), Expect = 2e-10
 Identities = 18/70 (25%), Positives = 28/70 (40%), Gaps = 10/70 (14%)

Query: 232 GSVHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKF 291
           G++     IC  C+        D+V+C+  C   FH  C  P L    +P  +  W C  
Sbjct: 1   GTLDDSATICRVCQK-----PGDLVMCNQ-CEFCFHLDCHLPALQ--DVPGEE--WSCSL 50

Query: 292 CECKMEIIES 301
           C    ++ E 
Sbjct: 51  CHVLPDLKEE 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 = 51.9 bits (124), Expect = 1e-09
 Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 7/53 (13%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCE 293
           C  C+ +    D+ ++LCD  CN AFH  CL P L    +P G+  W C  C+
Sbjct: 3   CKVCRKKG--EDDKLILCDE-CNKAFHLFCLRPALYE--VPDGE--WQCPACQ 48

>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 = 48.0 bits (114), Expect = 4e-08
 Identities = 20/61 (32%), Positives = 27/61 (44%), Gaps = 10/61 (16%)

Query: 236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK 295
           H    C  CK        +++ CD  C  ++H  CL+PPL    IP G+  W C  C C 
Sbjct: 7   HHMEFCRVCKD-----GGELLCCDT-CPSSYHIHCLNPPLPE--IPNGE--WLCPRCTCP 56

Query: 296 M 296
            
Sbjct: 57  A 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 = 45.8 bits (108), Expect = 3e-07
 Identities = 15/55 (27%), Positives = 18/55 (32%), Gaps = 5/55 (9%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK 295
           C  C    A  D   + CD  C   FH KC+             Q + C  C  K
Sbjct: 9   CGACGESYA-ADEFWICCDL-CEMWFHGKCVKITP--ARAEHIKQ-YKCPSCSNK 58

>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 = 44.3 bits (104), Expect = 1e-06
 Identities = 10/55 (18%), Positives = 15/55 (27%), Gaps = 4/55 (7%)

Query: 241 CAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK 295
              CK      D + +L    C    H +C+          P    + C  C   
Sbjct: 16  KVDCKCGTKDDDGERMLACDGCGVWHHTRCIGINN--ADALPSK--FLCFRCIEL 66

>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: 442 RRSFHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNAR 493
           +     +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: 446 HRMPPNAVEKLRQVFAENEL---PSRIVKENLSKELSLEPEKVNKWFKNAR 493
           HR     V  L   FA+N           ENL K  SL   ++  W  N R
Sbjct: 3   HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR 53

>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 = 7e-06
 Identities = 8/63 (12%), Positives = 17/63 (26%), Gaps = 4/63 (6%)

Query: 436 PSNAKIRRSFHRMPPNAVEKLRQVFAE----NELPSRIVKENLSKELSLEPEKVNKWFKN 491
            S    +R   +      EK+           +    +  E    E  +  + +  W  N
Sbjct: 12  SSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHN 71

Query: 492 ARY 494
            + 
Sbjct: 72  NKN 74

>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 = 40.4 bits (94), Expect = 3e-05
 Identities = 11/55 (20%), Positives = 18/55 (32%), Gaps = 6/55 (10%)

Query: 244 CKLREAFPDNDIVLCDGTCNCAFHQKCL---DPPLDTESIPPGDQGWFCKFCECK 295
           C  R+   +  ++ CD  C   FH  C+   +           D  + C  C   
Sbjct: 19  CICRQPHNNRFMICCDR-CEEWFHGDCVGISEARGRLLERNGED--YICPNCTIL 70

>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 = 38.3 bits (89), Expect = 8e-05
 Identities = 15/41 (36%), Positives = 25/41 (60%)

Query: 453 VEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 493
              L  +F EN+ PS+ ++  +S++L LE   V+ +F NAR
Sbjct: 10  RRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>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 = 38.6 bits (90), Expect = 9e-05
 Identities = 14/66 (21%), Positives = 28/66 (42%)

Query: 442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 501
           +R+        +E L + F     P    +E L+ ++ L   ++  WF N R    +  K
Sbjct: 2   QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 61

Query: 502 VESARQ 507
           + + 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 = 37.9 bits (88), Expect = 2e-04
 Identities = 16/54 (29%), Positives = 24/54 (44%)

Query: 440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 493
           K  R    +    +  LR  +A N  P  ++KE L +   L P  +  WF+N R
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKR 55

>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: 453 VEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494
           + +L++ F EN   +   ++ LS EL L   ++  WF+NAR 
Sbjct: 11  LARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARA 52

>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: 440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 499
           K R+           +L + F +    S   +E+L+  + L P +V  WF+N RY   K 
Sbjct: 8   KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRY---KT 64

Query: 500 RKVESARQVSGSP 512
           ++ ++ +   G P
Sbjct: 65  KRAQNEKGYEGHP 77

>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 = 3e-04
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 3/49 (6%)

Query: 453 VEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 501
             +L + F  N   +R  +  ++  LSL   ++  WF+N R    K +K
Sbjct: 9   TLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRM---KWKK 54

>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: 446 HRMPPNAVEKLRQVFA-ENELPSRIVKENLSKELSLEPEKVNKWFKNAR 493
           +++ PN    L +VF    + P     + LSK+L     K+  WF++ R
Sbjct: 8   NKVEPNDT--LEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRR 54

>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 = 3e-04
 Identities = 15/72 (20%), Positives = 29/72 (40%), Gaps = 3/72 (4%)

Query: 436 PSNAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL 495
                 R+       +   +L + F  N   +R  +  +++ L+L   +V  WF+N R  
Sbjct: 8   LHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRM- 66

Query: 496 ALKARKVESARQ 507
             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 = 5e-04
 Identities = 15/48 (31%), Positives = 23/48 (47%)

Query: 447 RMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY 494
            + 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 = 36.4 bits (84), Expect = 6e-04
 Identities = 15/62 (24%), Positives = 28/62 (45%)

Query: 440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA 499
           K RRS      + +++L + F   + P    +E L++  +L   ++  WF+N R    K 
Sbjct: 1   KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 60

Query: 500 RK 501
             
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 = 36.4 bits (84), Expect = 6e-04
 Identities = 18/66 (27%), Positives = 33/66 (50%)

Query: 442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 501
           R+         V +L + F + +  S   +E+L+  + L P +V  WF+N RY   +  K
Sbjct: 3   RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62

Query: 502 VESARQ 507
            ++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 = 35.7 bits (82), Expect = 8e-04
 Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 3/62 (4%)

Query: 442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKARK 501
           RR         +++L   F  N  P    +E ++   +L   +V  WFKN R    K RK
Sbjct: 2   RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRA---KWRK 58

Query: 502 VE 503
            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 = 35.6 bits (82), Expect = 8e-04
 Identities = 13/52 (25%), Positives = 23/52 (44%)

Query: 442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 493
           +    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: 450 PNAVEKLRQVFAE-NELPSRIVKENLSKELSLEPEKVNKWFKNAR 493
           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 = 0.001
 Identities = 20/69 (28%), Positives = 28/69 (40%), Gaps = 6/69 (8%)

Query: 442 RRSFHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK 498
           RR        A E L + F     N  PS   KE L+K+  +   +V+ WF N R    +
Sbjct: 2   RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRI---R 58

Query: 499 ARKVESARQ 507
            +K     Q
Sbjct: 59  YKKNIGKFQ 67

>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 = 34.1 bits (78), Expect = 0.003
 Identities = 11/41 (26%), Positives = 21/41 (51%)

Query: 453 VEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 493
           + +L + F +    SR  +  L+ +L+L    +  WF+N R
Sbjct: 11  LGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRR 51

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 58

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]

 Score = 33.7 bits (77), Expect = 0.004
 Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 3/54 (5%)

Query: 440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR 493
           K R +       A + L + F E+  PS      +++EL+LE E V  WF N R
Sbjct: 1   KRRTTIS---IAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRR 51

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	574
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.78
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.78
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.78
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.78
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.77
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.77
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.77
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.76
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.76
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.76
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.76
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.74
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.73
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.72
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.72
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.72
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.72
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.71
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.7
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.7
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.7
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.67
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.67
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.66
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.65
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.65
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.63
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.6
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.6
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.58
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.57
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.52
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	99.18
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	99.1
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	99.09
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	98.94
d1weea_	72	PHD finger protein At1g33420 {Thale cress (Arabido	98.4
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	98.36
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	98.33
d2pnxa1	51	Inhibitor of growth protein 4, Ing4 {Homo sapiens	98.31
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	97.99
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	97.93
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	97.86
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	95.98
d1hlva1	66	DNA-binding domain of centromere binding protein B	88.44
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	87.0
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	82.63

>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=99.78  E-value=3.4e-20  Score=145.62  Aligned_cols=53  Identities=21%  Similarity=0.410  Sum_probs=51.5

Q ss_pred             CCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      ||+|+.||++|+.+||.+|..|+||+..+|++||..|||++.||+|||||||+
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~   54 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRV   54 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhh
Confidence            56789999999999999999999999999999999999999999999999999

>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=99.78  E-value=5.1e-20  Score=141.94  Aligned_cols=52  Identities=29%  Similarity=0.533  Sum_probs=50.6

Q ss_pred             CCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          443 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       443 r~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      |+|+.||++|+.+||..|..|+||+..+|.+||..|||++.||+|||||||+
T Consensus         1 R~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~lgL~~~qV~vWFqNrRa   52 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARA   52 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChHHhhhcccccCC
Confidence            5679999999999999999999999999999999999999999999999998

>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=99.78  E-value=8.1e-20  Score=142.84  Aligned_cols=54  Identities=24%  Similarity=0.385  Sum_probs=51.7

Q ss_pred             CCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193          442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  495 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~  495 (574)
                      |+.|++||++|+.+||.+|..|+||+..++++||.+|||++.||+|||||||++
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k   54 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAK   54 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhh
Confidence            467799999999999999999999999999999999999999999999999993

>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=99.78  E-value=9.4e-20  Score=142.81  Aligned_cols=54  Identities=24%  Similarity=0.374  Sum_probs=51.8

Q ss_pred             CCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193          442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  495 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~  495 (574)
                      ||+|+.||++|+.+||..|..|+||+..+|++||..|||++.||+|||||||++
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k   54 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAK   54 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhH
Confidence            467899999999999999999999999999999999999999999999999993

>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=99.77  E-value=1e-19  Score=141.93  Aligned_cols=53  Identities=21%  Similarity=0.284  Sum_probs=50.5

Q ss_pred             ccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHH
Q 008193          445 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL  497 (574)
Q Consensus       445 r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~  497 (574)
                      |+.||++|+.+||.+|..|+||+..+|++||..|||+++||+|||||||++.+
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~k   53 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK   53 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhh
Confidence            58999999999999999999999999999999999999999999999999443

>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=99.77  E-value=2.1e-19  Score=148.65  Aligned_cols=61  Identities=21%  Similarity=0.276  Sum_probs=55.6

Q ss_pred             ccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193          440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  500 (574)
Q Consensus       440 ~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~  500 (574)
                      ..+|+|++||++|+.+||.+|..|+||+..+|++||..|||++.||+|||||||++.++..
T Consensus        12 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~   72 (77)
T d1pufa_          12 STRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKIN   72 (77)
T ss_dssp             TTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHH
Confidence            4467789999999999999999999999999999999999999999999999999554443

>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=99.77  E-value=1.7e-19  Score=141.04  Aligned_cols=54  Identities=22%  Similarity=0.389  Sum_probs=51.4

Q ss_pred             CCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193          443 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA  496 (574)
Q Consensus       443 r~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~  496 (574)
                      |.|+.||++|+++||.+|..++||+..+|++||.+|||++.||+|||||||++.
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~   54 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKD   54 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhh
Confidence            467999999999999999999999999999999999999999999999999943

>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=99.76  E-value=1.3e-19  Score=149.82  Aligned_cols=58  Identities=26%  Similarity=0.405  Sum_probs=54.6

Q ss_pred             ccccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193          438 NAKIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  495 (574)
Q Consensus       438 ~~~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~  495 (574)
                      +.+.+|+|++||++|+.+||.+|..|+||+..+|++||..|||++.||+|||||||++
T Consensus         6 p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k   63 (77)
T d1vnda_           6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYK   63 (77)
T ss_dssp             SSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHH
Confidence            3556778899999999999999999999999999999999999999999999999993

>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=99.76  E-value=2.3e-19  Score=143.74  Aligned_cols=58  Identities=24%  Similarity=0.480  Sum_probs=54.4

Q ss_pred             cCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHH
Q 008193          441 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  498 (574)
Q Consensus       441 ~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k  498 (574)
                      .||+|++||++|+.+||.+|..|+||+..++.+||.+|||++.||++||||+|++.++
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk   59 (65)
T d1fjla_           2 QRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK   59 (65)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHh
Confidence            5778899999999999999999999999999999999999999999999999995444

>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=99.76  E-value=2.3e-19  Score=144.97  Aligned_cols=58  Identities=26%  Similarity=0.425  Sum_probs=54.1

Q ss_pred             cCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHH
Q 008193          441 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  498 (574)
Q Consensus       441 ~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k  498 (574)
                      +||+|+.||+.|+.+||.+|..|+||+..+|.+||..|||++.||+|||||+|++.++
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk   59 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKR   59 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhh
Confidence            3678899999999999999999999999999999999999999999999999994433

>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=99.76  E-value=2.4e-19  Score=144.45  Aligned_cols=57  Identities=26%  Similarity=0.376  Sum_probs=53.2

Q ss_pred             CCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHH
Q 008193          442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  498 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k  498 (574)
                      ||+|++||++|+.+||.+|..|+||+..+|.+||..|||++.||+|||||||++.++
T Consensus         2 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk   58 (67)
T d1zq3p1           2 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKI   58 (67)
T ss_dssp             SCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhh
Confidence            467899999999999999999999999999999999999999999999999994443

>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=99.74  E-value=6.6e-19  Score=142.25  Aligned_cols=59  Identities=20%  Similarity=0.437  Sum_probs=54.4

Q ss_pred             CCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHhh
Q 008193          442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKAR  500 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~~  500 (574)
                      +|+|+.||++|+.+||.+|..|+||+..+|++||.+|||++.||++||||+|++.++..
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~   60 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREE   60 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhh
Confidence            56789999999999999999999999999999999999999999999999999554443

>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=99.73  E-value=9.5e-19  Score=140.53  Aligned_cols=56  Identities=29%  Similarity=0.497  Sum_probs=53.3

Q ss_pred             ccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193          440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  495 (574)
Q Consensus       440 ~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~  495 (574)
                      +.+|+|++||++|+++||.+|..|+||+..++++||.+|||++.||++||||+|++
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k   57 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCK   57 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHH
Confidence            35788899999999999999999999999999999999999999999999999993

>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=99.72  E-value=6.6e-19  Score=138.82  Aligned_cols=55  Identities=25%  Similarity=0.436  Sum_probs=52.4

Q ss_pred             CCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193          442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLA  496 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~  496 (574)
                      ||+|++||++|+.+||.+|..|+||+..++.+||.+|||++.||++||||+|++.
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~   56 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKW   56 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHH
Confidence            5678999999999999999999999999999999999999999999999999943

>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=99.72  E-value=1.4e-18  Score=146.98  Aligned_cols=59  Identities=22%  Similarity=0.314  Sum_probs=52.1

Q ss_pred             ccCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHH
Q 008193          440 KIRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALK  498 (574)
Q Consensus       440 ~~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k  498 (574)
                      ..+|.|+.||++|+.+||.+|..|+||+..+|++||..|||+++||+|||||||++.+|
T Consensus        26 ~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk   84 (88)
T d1b72a_          26 SPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK   84 (88)
T ss_dssp             ----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHH
Confidence            34677899999999999999999999999999999999999999999999999994433

>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=99.72  E-value=1.3e-18  Score=141.39  Aligned_cols=56  Identities=25%  Similarity=0.336  Sum_probs=52.1

Q ss_pred             ccCCCccCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193          440 KIRRSFHRMPPNAVEKLRQVFA-ENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  495 (574)
Q Consensus       440 ~~kr~r~r~t~~Q~~~Le~~F~-~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~  495 (574)
                      ..+|+|++||++|+++||.+|. .|+||+.+++++||.+|||+++||++||||+|++
T Consensus         6 ~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k   62 (71)
T d1wi3a_           6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYH   62 (71)
T ss_dssp             CCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhh
Confidence            3467789999999999999997 4999999999999999999999999999999993

>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=99.72  E-value=3.5e-18  Score=139.49  Aligned_cols=55  Identities=25%  Similarity=0.308  Sum_probs=51.0

Q ss_pred             CCCccCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHcCCChhhHHHhhcccccHH
Q 008193          442 RRSFHRMPPNAVEKLRQVFAE-NELPSRIVKENLSKELSLEPEKVNKWFKNARYLA  496 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F~~-~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~  496 (574)
                      ++.|++||++|+++||..|.. |+||+..+|++||.+|||+++||+|||||||++.
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~   57 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEW   57 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence            356789999999999999985 7899999999999999999999999999999943

>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=99.71  E-value=2e-18  Score=132.94  Aligned_cols=50  Identities=30%  Similarity=0.458  Sum_probs=49.0

Q ss_pred             ccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          445 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       445 r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      |++||++|+.+||.+|..|+||+..++.+||.+|||++.||++||||||+
T Consensus         1 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~   50 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRM   50 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhh
Confidence            57899999999999999999999999999999999999999999999999

>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=99.70  E-value=3.2e-18  Score=134.12  Aligned_cols=52  Identities=31%  Similarity=0.432  Sum_probs=50.5

Q ss_pred             CCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          443 RSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       443 r~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      |+|+.|+++|+.+||.+|..|+||+..++.+||.+|||++.||++||||+|+
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~   52 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQ   52 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhH
Confidence            4579999999999999999999999999999999999999999999999999

>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=99.70  E-value=2.3e-18  Score=130.82  Aligned_cols=50  Identities=30%  Similarity=0.436  Sum_probs=49.0

Q ss_pred             CccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccc
Q 008193          444 SFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNAR  493 (574)
Q Consensus       444 ~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR  493 (574)
                      ||+.||++|+.+||.+|..|+||+..++.+||.+|||+++||++||||||
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            57999999999999999999999999999999999999999999999998

>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=99.70  E-value=2.7e-18  Score=138.33  Aligned_cols=54  Identities=24%  Similarity=0.334  Sum_probs=52.2

Q ss_pred             cCCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          441 IRRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       441 ~kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      ++|+|++|+++|+.+|+.+|..|+||+..++++||.+|||++.||++||||+|+
T Consensus         8 ~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~   61 (67)
T d1ocpa_           8 RKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQ   61 (67)
T ss_dssp             SSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHS
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHH
Confidence            467789999999999999999999999999999999999999999999999999

>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=1.6e-17  Score=138.58  Aligned_cols=57  Identities=23%  Similarity=0.385  Sum_probs=52.2

Q ss_pred             CCCccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcC---------------CChhhHHHhhcccccHHHH
Q 008193          442 RRSFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELS---------------LEPEKVNKWFKNARYLALK  498 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~Lg---------------L~~~qV~vWFQNrR~~~~k  498 (574)
                      ||.|+.||++|+.+||.+|..|+||+..+|++||..||               |++.+|+|||||||++.+|
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk   72 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKR   72 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHH
Confidence            46779999999999999999999999999999999875               9999999999999994444

>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=99.67  E-value=1.4e-17  Score=129.97  Aligned_cols=52  Identities=25%  Similarity=0.386  Sum_probs=50.1

Q ss_pred             CccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193          444 SFHRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYL  495 (574)
Q Consensus       444 ~r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~  495 (574)
                      +|+.|+++|+.+||.+|..|+||+..++++||.+|||++.||++||||+|++
T Consensus         1 kRT~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k   52 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQK   52 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            3689999999999999999999999999999999999999999999999993

>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=99.66  E-value=4e-17  Score=135.54  Aligned_cols=56  Identities=13%  Similarity=0.236  Sum_probs=52.8

Q ss_pred             cccCCCccCCCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          439 AKIRRSFHRMPPNAVEKLRQVFAE----NELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       439 ~~~kr~r~r~t~~Q~~~Le~~F~~----~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      .++||+|++||++|+++|+.+|+.    ++||+..++++||++|||++.||+|||||+|+
T Consensus        15 ~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~   74 (80)
T d1wh7a_          15 GTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKN   74 (80)
T ss_dssp             CCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSC
T ss_pred             cCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcC
Confidence            456778999999999999999986    89999999999999999999999999999998

>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=99.65  E-value=5e-17  Score=132.60  Aligned_cols=56  Identities=32%  Similarity=0.462  Sum_probs=51.8

Q ss_pred             CCCccCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHH
Q 008193          442 RRSFHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL  497 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F~~---~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~  497 (574)
                      ||+|+.||++|+++||.+|.+   ||||+..+|++||.+|||++.||++||||+|++.+
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k   60 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK   60 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhc
Confidence            566789999999999999985   89999999999999999999999999999999544

>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=99.65  E-value=8.1e-17  Score=132.36  Aligned_cols=49  Identities=12%  Similarity=0.303  Sum_probs=47.4

Q ss_pred             cCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          446 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       446 ~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      .++|++|+.+||.+|..|+||+..+|++||.+|||+++||++||||||+
T Consensus         9 k~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~   57 (76)
T d2ecba1           9 KEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKK   57 (76)
T ss_dssp             CCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHH
Confidence            3579999999999999999999999999999999999999999999998

>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=99.63  E-value=1.8e-16  Score=130.27  Aligned_cols=53  Identities=25%  Similarity=0.432  Sum_probs=49.6

Q ss_pred             cCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHHHh
Q 008193          446 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARYLALKA  499 (574)
Q Consensus       446 ~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~k~  499 (574)
                      .+||++|+.+||.+|..|+||+..++++||.+|||++.||++||||+|+ ++|.
T Consensus         8 ~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~-k~k~   60 (76)
T d2ecca1           8 KRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRY-ALKH   60 (76)
T ss_dssp             CCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHH-HHHH
T ss_pred             CCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHH-HHHh
Confidence            4799999999999999999999999999999999999999999999999 4443

>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=99.60  E-value=3e-16  Score=123.47  Aligned_cols=49  Identities=33%  Similarity=0.428  Sum_probs=46.8

Q ss_pred             cCCCHHHHHHHHHHHHhC---CCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          446 HRMPPNAVEKLRQVFAEN---ELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       446 ~r~t~~Q~~~Le~~F~~~---~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      .+||++|+.+|+.+|..|   |||+.+++++||.+|||++.||++||||+|+
T Consensus         3 ~Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~   54 (60)
T d1k61a_           3 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRR   54 (60)
T ss_dssp             CSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcc
Confidence            469999999999999875   7999999999999999999999999999998

>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=99.60  E-value=4.8e-16  Score=123.13  Aligned_cols=56  Identities=25%  Similarity=0.403  Sum_probs=51.0

Q ss_pred             CCCccCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHcCCChhhHHHhhcccccHHH
Q 008193          442 RRSFHRMPPNAVEKLRQVFAE---NELPSRIVKENLSKELSLEPEKVNKWFKNARYLAL  497 (574)
Q Consensus       442 kr~r~r~t~~Q~~~Le~~F~~---~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~~~  497 (574)
                      +++|+.||++|+.+|+.+|..   ||||+..++.+||.++||+..||++||||+|++.+
T Consensus         3 krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R~l   61 (62)
T d1x2na1           3 KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRIL   61 (62)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhc
Confidence            345678999999999999985   89999999999999999999999999999998543

>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=99.58  E-value=2.4e-16  Score=120.79  Aligned_cols=46  Identities=26%  Similarity=0.510  Sum_probs=44.1

Q ss_pred             CHHHHHHHHHHHHh-CCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          449 PPNAVEKLRQVFAE-NELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       449 t~~Q~~~Le~~F~~-~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      |++|+.+||.+|.. ++||+..++++||.+|||+++||++||||||+
T Consensus         1 T~~q~~iLE~~F~~~~~~P~~~~~~~LA~~~~ls~~qV~~WFqNrR~   47 (52)
T d1x2ma1           1 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRN   47 (52)
T ss_dssp             SSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHH
T ss_pred             ChhHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhc
Confidence            57899999999987 79999999999999999999999999999999

>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=99.57  E-value=3.1e-16  Score=129.66  Aligned_cols=53  Identities=25%  Similarity=0.382  Sum_probs=49.5

Q ss_pred             ccCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcC---------------------CChhhHHHhhcccccHHH
Q 008193          445 FHRMPPNAVEKLRQVFAENELPSRIVKENLSKELS---------------------LEPEKVNKWFKNARYLAL  497 (574)
Q Consensus       445 r~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~Lg---------------------L~~~qV~vWFQNrR~~~~  497 (574)
                      |++||++|+++||.+|..|+||+..+|++||++||                     |++.+|++||||||++.+
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~k   74 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEA   74 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTS
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999999999994                     999999999999999443

>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=99.52  E-value=1.4e-15  Score=119.39  Aligned_cols=52  Identities=23%  Similarity=0.374  Sum_probs=48.3

Q ss_pred             CccCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHcCCChhhHHHhhcccccH
Q 008193          444 SFHRMPPNAVEKLRQVFAE-NELPSRIVKENLSKELSLEPEKVNKWFKNARYL  495 (574)
Q Consensus       444 ~r~r~t~~Q~~~Le~~F~~-~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~~  495 (574)
                      .+++++.+|..+||.+|.. ++||+..++++||++|||+++||++||||||++
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            4578999999999999975 799999999999999999999999999999993

>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=99.18  E-value=5.9e-12  Score=101.24  Aligned_cols=53  Identities=30%  Similarity=0.866  Sum_probs=44.9

Q ss_pred             cccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193          234 VHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM  296 (574)
Q Consensus       234 ~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~  296 (574)
                      .+....+|.+|+.+     ++||+||+ |+++||++|++|||.  .+|.++  |+|+.|....
T Consensus         3 ~Dd~c~~C~~C~~~-----~~ll~Cd~-C~~~~H~~C~~p~l~--~~p~~~--W~C~~C~~~~   55 (70)
T d1fp0a1           3 LDDSATICRVCQKP-----GDLVMCNQ-CEFCFHLDCHLPALQ--DVPGEE--WSCSLCHVLP   55 (70)
T ss_dssp             SSSSSSCCSSSCSS-----SCCEECTT-SSCEECTTSSSTTCC--CCCSSS--CCCCSCCCCC
T ss_pred             cCCCCCCCCCCCCc-----CEEEECCC-CChhhccccCCCCcC--cCCCCC--EECcCCcCcC
Confidence            34567788888865     78999996 999999999999998  789888  9999997543

>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=99.10  E-value=2.4e-11  Score=95.04  Aligned_cols=51  Identities=39%  Similarity=1.091  Sum_probs=43.8

Q ss_pred             cccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193          236 HEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM  296 (574)
Q Consensus       236 ~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~  296 (574)
                      .++++|.+|+..     ++||+||+ |+++||+.|++|++.  .+|.+.  |||+.|..+.
T Consensus         7 ~~~~~C~~C~~~-----g~lv~Cd~-C~~~~H~~C~~~~~~--~~~~~~--W~C~~C~~~~   57 (61)
T d1mm2a_           7 HHMEFCRVCKDG-----GELLCCDT-CPSSYHIHCLNPPLP--EIPNGE--WLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC-----SSCBCCSS-SCCCBCSSSSSSCCS--SCCSSC--CCCTTTTTTC
T ss_pred             CCcCCCcCCCCC-----CeEEEeCC-CCccCchhhcCCCcC--cCCCCc--EECCCCcCcc
Confidence            456789999865     78999995 999999999999987  688877  9999998653

>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=99.09  E-value=1.5e-11  Score=92.64  Aligned_cols=48  Identities=42%  Similarity=1.043  Sum_probs=41.9

Q ss_pred             cccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193          240 ICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC  294 (574)
Q Consensus       240 ~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~  294 (574)
                      .|.+|+..+  +++.||+||+ |+.+||++|++||+.  .+|.++  |||+.|..
T Consensus         2 ~C~vC~~~~--~~~~~i~Cd~-C~~~~H~~C~~p~~~--~~p~~~--W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKG--EDDKLILCDE-CNKAFHLFCLRPALY--EVPDGE--WQCPACQP   49 (51)
T ss_dssp             CCTTTCCSS--CCSCCEECTT-TCCEECHHHHCTTCC--SCCSSC--CSCTTTSC
T ss_pred             CCcCcCCCC--CCCCEEEcCC-CCCCCCCCCCCCCCC--cCCCCC--EECcCCcC
Confidence            488898865  4578999996 999999999999998  789887  99999975

>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=98.94  E-value=9.1e-11  Score=97.58  Aligned_cols=59  Identities=24%  Similarity=0.652  Sum_probs=46.2

Q ss_pred             cccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCC--CCCCCCCccccCcccch
Q 008193          234 VHHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTE--SIPPGDQGWFCKFCECK  295 (574)
Q Consensus       234 ~~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~--~iP~gde~W~C~~C~~k  295 (574)
                      ..+...+|.+|+.....+.+.||+||+ |..+||+.|++|++...  .+|.++  |||+.|...
T Consensus        12 ~~~~~~~C~iC~~~~~~~~~~~v~Cd~-C~~~~H~~C~~p~~~~~~~~~~~~~--W~C~~C~~~   72 (88)
T d1weva_          12 AMEMGLACVVCRQMTVASGNQLVECQE-CHNLYHQDCHKPQVTDKEVNDPRLV--WYCARCTRQ   72 (88)
T ss_dssp             HHHHCCSCSSSCCCCCCTTCCEEECSS-SCCEEETTTSSSCCCHHHHHCTTCC--CCCHHHHHH
T ss_pred             cCcCcCCccCCCCccCCCCCeEEEcCC-CCCccccccCCCcccccccccCCCe--EECcccCch
Confidence            345567899999876555678999996 99999999999997521  256666  999999754

>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=98.40  E-value=5.2e-08  Score=77.79  Aligned_cols=51  Identities=24%  Similarity=0.637  Sum_probs=39.3

Q ss_pred             ccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccchh
Q 008193          239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECKM  296 (574)
Q Consensus       239 ~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k~  296 (574)
                      ..| +|+..+. +...||.||. |.++||+.|++++..  .+|.++  |+|+.|+...
T Consensus        17 ~~C-~C~~~~~-~~~~mv~Cd~-C~~w~H~~C~g~~~~--~~~~~~--~~C~~C~~~~   67 (72)
T d1weea_          17 VDC-KCGTKDD-DGERMLACDG-CGVWHHTRCIGINNA--DALPSK--FLCFRCIELS   67 (72)
T ss_dssp             ECC-TTCCCSC-CSSCEEECSS-SCEEEETTTTTCCTT--SCCCSC--CCCHHHHHHC
T ss_pred             EEe-eCCCCcC-CCCeEEEeCC-CCCcCchhhcCCccc--cCCCCc--EECcCCcCcC
Confidence            346 7887542 3356999995 999999999998866  567677  9999998653

>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=98.36  E-value=4.4e-08  Score=76.51  Aligned_cols=53  Identities=26%  Similarity=0.481  Sum_probs=40.7

Q ss_pred             ccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCC-CCCccccCcccch
Q 008193          237 EHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPP-GDQGWFCKFCECK  295 (574)
Q Consensus       237 ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~-gde~W~C~~C~~k  295 (574)
                      ....|.+|+..+. ++..||.||+ |..+||+.|++++..  .++. ..  |+|+.|..+
T Consensus         5 ~~~~C~~C~~~~~-~~~~~I~Cd~-C~~w~H~~C~~~~~~--~~~~~~~--w~C~~C~~~   58 (64)
T d1we9a_           5 SSGQCGACGESYA-ADEFWICCDL-CEMWFHGKCVKITPA--RAEHIKQ--YKCPSCSNK   58 (64)
T ss_dssp             SCCCCSSSCCCCC-SSSCEEECSS-SCCEEETTTTTCCTT--GGGGCSS--CCCHHHHTT
T ss_pred             CCCcCcCcCCCCC-CCCCEEEcCC-CCccCCcccCCcChH--HCCCCCe--EECcCCcCc
Confidence            4568999998642 2356899995 999999999998766  3443 34  999999854

>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=98.33  E-value=1.8e-07  Score=75.06  Aligned_cols=49  Identities=31%  Similarity=0.802  Sum_probs=35.8

Q ss_pred             cccccccccccCCCCCCCCccccCC-CcC-CcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193          236 HEHIICAKCKLREAFPDNDIVLCDG-TCN-CAFHQKCLDPPLDTESIPPGDQGWFCKFCEC  294 (574)
Q Consensus       236 ~ed~~C~vC~~~~~~~~g~lLlCDg-~C~-rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~  294 (574)
                      .+..+| +|+..+   +++||+|+. .|. .+||+.|+.  |.  .+|.++  |||+.|..
T Consensus        14 ~e~~~C-iC~~~~---~~~~i~c~~~~C~~~wfH~~Cvg--l~--~~p~~~--w~C~~C~~   64 (71)
T d1wesa_          14 NEPTYC-LCNQVS---YGEMIGCDNEQCPIEWFHFSCVS--LT--YKPKGK--WYCPKCRG   64 (71)
T ss_dssp             SSCCCS-TTCCCC---CSSEECCSCTTCSCCCEETTTTT--CS--SCCSSC--CCCTTTSS
T ss_pred             CCCCEE-EeCCCC---CCCEEEEECCCCCCcCccCccCC--CC--cCCCCc--EECcCCcc
Confidence            344677 899863   456666641 376 589999996  55  688888  99999974

>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=98.31  E-value=5.9e-08  Score=73.08  Aligned_cols=46  Identities=30%  Similarity=0.793  Sum_probs=35.8

Q ss_pred             ccccccccCCCCCCCCccccCC-Cc-CCcccccccCCCCCCCCCCCCCCccccCcccc
Q 008193          239 IICAKCKLREAFPDNDIVLCDG-TC-NCAFHQKCLDPPLDTESIPPGDQGWFCKFCEC  294 (574)
Q Consensus       239 ~~C~vC~~~~~~~~g~lLlCDg-~C-~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~  294 (574)
                      .+| +|+..+   +++||.||. .| ..+||+.|++.  .  .+|.++  |||+.|..
T Consensus         3 ~yC-~C~~~~---~~~mi~Cd~~~C~~~WfH~~Cvgl--~--~~p~~~--w~C~~C~~   50 (51)
T d2pnxa1           3 TYC-LCHQVS---YGEMIGCDNPDCSIEWFHFACVGL--T--TKPRGK--WFCPRCSQ   50 (51)
T ss_dssp             EET-TTTEEC---CSEEEECSCTTCSSCEEEGGGGTC--S--SCCSSC--CCCHHHHC
T ss_pred             cEE-EcCCCC---CCCEEEEecCCCCCCCEeCCccCC--C--cCCCCc--EECcCCCC
Confidence            578 799863   567999983 24 57899999984  4  578887  99999974

>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=97.99  E-value=7.1e-07  Score=72.48  Aligned_cols=51  Identities=20%  Similarity=0.453  Sum_probs=37.4

Q ss_pred             ccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          239 IICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       239 ~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      .+| +|+..+. +++.||.||. |..+||..|+++...  .++.. ..|+|+.|...
T Consensus        13 v~C-iC~~~~~-~~~~mI~Cd~-C~~W~H~~C~g~~~~--~~~~~-~~~~C~~C~~~   63 (79)
T d1wepa_          13 VYC-LCRQPYN-VNHFMIECGL-CQDWFHGSCVGIEEE--NAVDI-DIYHCPDCEAV   63 (79)
T ss_dssp             CCS-TTSCSCC-SSSCEEEBTT-TCCEEEHHHHTCCHH--HHTTC-SBBCCTTTTTT
T ss_pred             eEe-ECCCccC-CCCcEEECCC-CCCcEeccccCcchh--cCCCC-CEEECccCcCC
Confidence            456 8998643 2456999995 999999999997644  33432 24999999753

>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=97.93  E-value=2.3e-07  Score=74.29  Aligned_cols=54  Identities=20%  Similarity=0.539  Sum_probs=38.1

Q ss_pred             ccccccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCC---CCCCCCCccccCcccc
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTE---SIPPGDQGWFCKFCEC  294 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~---~iP~gde~W~C~~C~~  294 (574)
                      +.+..+| +|+..+  +++.||.||. |..+||+.|++.+....   ..+...  |+|+.|..
T Consensus        13 d~~~~~C-iC~~~~--~~~~mi~Cd~-C~~w~H~~Cvg~~~~~~~~~~~~~~~--w~C~~C~~   69 (76)
T d1wema_          13 DPNALYC-ICRQPH--NNRFMICCDR-CEEWFHGDCVGISEARGRLLERNGED--YICPNCTI   69 (76)
T ss_dssp             CTTCCCS-TTCCCC--CSSCEEECSS-SCCEEEHHHHSCCHHHHHHHHHHTCC--CCCHHHHH
T ss_pred             CCCcCEE-ECCCcc--CCCeEEEECC-CCCcCCccccCCCcccccccCCCCCc--EECCCCcC
Confidence            3456778 899874  4567999995 99999999997442100   122344  99999964

>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=97.86  E-value=2.9e-06  Score=68.59  Aligned_cols=58  Identities=19%  Similarity=0.543  Sum_probs=37.3

Q ss_pred             ccccccccccccCCCCCCCCccccCC-CcCCcccccccCCCCCCC-CCCCCCCccccCcccch
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDG-TCNCAFHQKCLDPPLDTE-SIPPGDQGWFCKFCECK  295 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg-~C~rafH~~Cl~PPL~~~-~iP~gde~W~C~~C~~k  295 (574)
                      ..+..+| +|+..+  +++.||+|+. .|..+||+.|++.+-... ..+.....|+|+.|...
T Consensus        13 ~~~~~~C-~C~~~~--~~~~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~   72 (78)
T d1wewa_          13 PEIKVRC-VCGNSL--ETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLT   72 (78)
T ss_dssp             CCCCCCC-SSCCCC--CCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHC
T ss_pred             CCCccEe-ECCCcc--CCCcEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCc
Confidence            3445778 899875  3467888861 399999999997431100 11221224999999753

>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=95.98  E-value=0.004  Score=50.55  Aligned_cols=56  Identities=21%  Similarity=0.712  Sum_probs=39.9

Q ss_pred             ccccccccccccCCCCCCCCccccCCCcCCcccccccCCC--------CCCCCCCCCCCccccCcccc
Q 008193          235 HHEHIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPP--------LDTESIPPGDQGWFCKFCEC  294 (574)
Q Consensus       235 ~~ed~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PP--------L~~~~iP~gde~W~C~~C~~  294 (574)
                      ..++..|.+|...   ..+.++-|- .|.+.||-.||.--        +........+.+|.|..|..
T Consensus        12 v~~D~mC~vC~v~---t~~~l~pCR-vCtRv~H~~CL~r~gyl~~e~a~e~~e~A~T~~GWSC~~C~n   75 (89)
T d1wila_          12 VVNDEMCDVCEVW---TAESLFPCR-VCTRVFHDGCLRRMGYIQGDSAAEVTEMAHTETGWSCHYCDN   75 (89)
T ss_dssp             CCCSCCCTTTCCC---CSSCCSSCS-SSSSCCCHHHHHHHTSCCCCCCCSCSCCCSSSSSCCCTTTCC
T ss_pred             CCcCccccccCcc---cccceecce-eecchhhHHHHHHhcccccHHHHHHHHhhcCCCCcchhhhcc
Confidence            4567899999776   347888999 79999999998421        11112334455799999974

>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=88.44  E-value=0.37  Score=37.10  Aligned_cols=46  Identities=17%  Similarity=0.291  Sum_probs=40.2

Q ss_pred             cCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCChhhHHHhhccccc
Q 008193          446 HRMPPNAVEKLRQVFAENELPSRIVKENLSKELSLEPEKVNKWFKNARY  494 (574)
Q Consensus       446 ~r~t~~Q~~~Le~~F~~~~yPs~~~r~~LA~~LgL~~~qV~vWFQNrR~  494 (574)
                      ..||-++.-.+=..|..++..+   +.+||+++|++..+|..|..|+..
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            4699998888888899988766   567999999999999999999876

>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=87.00  E-value=0.028  Score=41.93  Aligned_cols=51  Identities=20%  Similarity=0.408  Sum_probs=34.0

Q ss_pred             cccccccccccCCCCCCCCcc--ccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          236 HEHIICAKCKLREAFPDNDIV--LCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       236 ~ed~~C~vC~~~~~~~~g~lL--lCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      ++..+|.+|.....  +..+.  .|.| |...||..||.-.+..    .+.  +.||.|+..
T Consensus         4 ed~~~C~IC~~~~~--~~~~~~c~c~~-c~h~~H~~Cl~~W~~~----~~~--~~CP~Cr~~   56 (60)
T d1vyxa_           4 EDVPVCWICNEELG--NERFRACGCTG-ELENVHRSCLSTWLTI----SRN--TACQICGVV   56 (60)
T ss_dssp             CSCCEETTTTEECS--CCCCCSCCCSS-GGGSCCHHHHHHHHHH----HTC--SBCTTTCCB
T ss_pred             CCCCCCccCCccCC--CceeEecccCC-CCCEEcHHHHHHHHhh----CCC--CCCcccCCe
Confidence            34578999987532  22233  3555 7899999999976531    133  679999864

>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=82.63  E-value=0.3  Score=35.75  Aligned_cols=48  Identities=23%  Similarity=0.526  Sum_probs=33.9

Q ss_pred             cccccccccCCCCCCCCccccCCCcCCcccccccCCCCCCCCCCCCCCccccCcccch
Q 008193          238 HIICAKCKLREAFPDNDIVLCDGTCNCAFHQKCLDPPLDTESIPPGDQGWFCKFCECK  295 (574)
Q Consensus       238 d~~C~vC~~~~~~~~g~lLlCDg~C~rafH~~Cl~PPL~~~~iP~gde~W~C~~C~~k  295 (574)
                      +..|.+|..... .++.++.+.. |...||..|+...+..      .  -.||.|+..
T Consensus         5 ~~~C~ICl~~~~-~~~~~~~l~~-C~H~Fh~~Ci~~Wl~~------~--~~CP~CR~~   52 (55)
T d1iyma_           5 GVECAVCLAELE-DGEEARFLPR-CGHGFHAECVDMWLGS------H--STCPLCRLT   52 (55)
T ss_dssp             SCCCTTTCCCCC-TTSCCEECSS-SCCEECTTHHHHTTTT------C--CSCSSSCCC
T ss_pred             CCCCeEECcccc-CCCEEEEeCC-CCCcccHHHHHHHHHh------C--CcCCCCCCE
Confidence            456999998643 2344555663 9999999999988762      1  249999854