Citrus Sinensis ID: 017477

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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-
Protein Sequence
MDITPTNNNTLNTNTNSKSPETDTTDNHQTGATRIHSAKPLTFTNGVLKRHQPQPQHHQRHHHHHHHHPIVVTYKECLKNHAASIGGHALDGCGEFMPSPTATPSDPTSLKCAACGCHRNFHRREPDQDHHLPHVPTTATTATIEYQPHHRHHPPPPVTQPPSRRSPSSASPPPISSSYYPSAPHMLLALSGNLQQSSAAAAVPQENHHISNNHHHNNNNIMMSNSGGSSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVVWMHNNKSTFAKRDLNGAGGSGSGSAGGGIGRINLDDDNTGNDNINNSKSGDGDDQDEEEGINNNNNGVRNLNHQFGSATESAAHVANANGGSSSSS
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccHHHHHHHHHHHEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccEEEEEHHHHHHHHHHccccccccccccccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEcccccHHHHHHHHHHHHHHcccEccccHHHHHHHHHHHHEEHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccEEEEEEccccccccc
Coil and Loop (DISEMBL)
mditptnnntlntntnskspetdttdnhqtgatrihsakpltftngvlkrhqpqpqhhqrhhhhhhhhpIVVTYKECLKNHAAsigghaldgcgefmpsptatpsdptslkcaacgchrnfhrrepdqdhhlphvpttattatieyqphhrhhppppvtqppsrrspssaspppisssyypsapHMLLALSGnlqqssaaaavpqenhhisnnhhhnnnnimmsnsggssggrkrfRTKFSQSQKEKMFEFAERVGwkmqkrddDLVHEFCNEVVWMHNnkstfakrdlngaggsgsgsagggigrinldddntgndninnsksgdgddqdeeeginnnnngvrnlnhqfgsatESAAHVananggsssss
Flexible Loop (DISEMBL)
mditptnnntlntntnskspetdTTDNHQTGATRIHSAKPLTFTNGVLKRHQPQPQHHQRHHHHHHHHPIVVTYKECLKNHAASIGGHALDGCGEFMPSPTATPSDPTSLKCAACGCHRNFHrrepdqdhhlphVPTTATTATIEYQPHHRHHPPPPVTQPPSRRSPSSASPPPISSSYYPSAPHMLLALSGNLQQSSAAAAVPQENHHISNNHHHNNNNIMMSNSGGSSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVVWMHNNKSTFAKRDLNGAGGSGSGSAGGGIGRINLDDDNTGNDNINNsksgdgddqdEEEGINNNNNGVRNLNHQFGSATESAAHVANanggsssss
Low Complexity Region (SEG)
MDItptnnntlntntnSKSPETDTTDNHQTGATRIHSAKPLTFTNGVLKrhqpqpqhhqrhhhhhhhhpIVVTYKECLKNHAASIGGHALDGCGEFMpsptatpsdptsLKCAACGCHRNFHRREPDQDHHLPHVPTTATTATIEYQphhrhhppppvtqppsrrspssaspppisssyypsaphMLLALSGNLQQSSAAAAVPQEnhhisnnhhhnnnnimmsnsggssggRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVVWMHNNKSTFAKRDLNgaggsgsgsagggigRInldddntgndninnSKSgdgddqdeeeginnnnngVRNLNHQFGSATEsaahvananggsssss
Disordered region (IsUnstruct)
*********************************************************************IVVTYKECLKNHAASIGGHALDGCGEF**************KCAACGCHRNF*******************************************************************************************************************************FEFAERVGWKMQKRDDDLVHEFCNEVVWMHNNKS*****************************************************************************************
Disordered Region (DISOPRED)
***********************************************************************VTYKECLKNHAASIGGHALDGCGEFMPS****PSDPTSLKCAACGCHRNFHRREP*********************************************************************************************************************QKEKMFEFAERVGWKMQKRDDDLVHEFCNEVVWMHNNK******************************************************************************************
Disordered Region (DISEMBL)
MDITPTNNNTLNTNTN**************GATRIHSAKPLTFTNGVLK********************IVVTYKECLKNHAASIGGHALDGCGEFMPS**********LKCAACGCHRNFHRREPDQDHHLPHVPTTATTATIEY*****************************SSSYYPSAPHMLLALSGNLQ*********QENHHISNNHHHNNNNIMMSN********************EKMFEFAERVGWKMQKRDDDLVHEFCNEVVWMHNNKSTFAKRDLNG********AGGGIGRINLDDDNTGNDNINNSK**********EGINNNNNGVRNLNHQFGSATESAAHV***********
Disordered Region (DISPRO)
*************************************AKPLTFTNGVL******************HHPIVVTYKECLKNHAASIGGHALDGCGEFMPSPTATPSDPTSLKCAACGCHRNFHRREPDQDHHLPHVPTTATTATIEYQPHHRHHPPPPVTQPPSRRSPSSASPPPISSSYYPSAPHMLLA*********************************************RFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVVWMHNNKSTF***************************************************INNNNNGVRNLNHQFGSATESAAHVANA********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDITPTNNNTLNTNTNSKSPETDTTDNHQTGATRIHSAKPLTFTNGVLKRHQPQPQHHQRHHHHHHHHPIVVTYKECLKNHAASIGGHALDGCGEFMPSPTATPSDPTSLKCAACGCHRNFHRREPDQDHHLPHVPTTATTATIEYQPHHRHHPPPPVTQPPSRRSPSSASPPPISSSYYPSAPHMLLALSGNLQQSSAAAAVPQENHHISNNHHHNNNNIMMSNSGGSSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVVWMHNNKSTFAKRDLNGAGGSGSGSAGGGIGRINLDDDNTGNDNINNSKSGDGDDQDEEEGINNNNNGVRNLNHQFGSATESAAHVANANGGSSSSS
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	371	2.2.26 [Sep-21-2011]
Q9SEZ1	242	Transcription factor HB29	no	no	0.485	0.743	0.443	4e-43
Q9SB61	220	ZF-HD homeobox protein At	no	no	0.444	0.75	0.388	3e-31
Q9FKP8	279	ZF-HD homeobox protein At	no	no	0.455	0.605	0.369	3e-30

>sp|Q9SEZ1|HB29_ARATH Transcription factor HB29 OS=Arabidopsis thaliana GN=HB29 PE=1 SV=1

 Score =  175 bits (444), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 102/230 (44%), Positives = 127/230 (55%), Gaps = 50/230 (21%)

Query: 72  VTYKECLKNHAASIGGHALDGCGEFMPSPTATPSDPTSLKCAACGCHRNFHRREPDQDHH 131
           V YKECLKNHAA++GGHALDGCGEFMPSPTAT +DP+SL+CAACGCHRNFHRR+P ++ +
Sbjct: 29  VCYKECLKNHAANLGGHALDGCGEFMPSPTATSTDPSSLRCAACGCHRNFHRRDPSENLN 88

Query: 132 LPHVPTTATTATIEYQPHHRHHPPPPVTQPPSRRSPSSASPPPISSSYYPSAP--HMLLA 189
               P  ++ +  E               PPSR   S     P+  SYY SAP  H++L+
Sbjct: 89  FLTAPPISSPSGTE--------------SPPSRHVSS-----PVPCSYYTSAPPHHVILS 129

Query: 190 LSGNLQQSSAAAAVPQENHHISNNHHHNNNNIMMSNSGGSSGGRKRFRTKFSQSQKEKMF 249
           LS      S                   +  ++ S +      RKR RTKF+  QK KM 
Sbjct: 130 LSSGFPGPS-----------------DQDPTVVRSENSSRGAMRKRTRTKFTPEQKIKMR 172

Query: 250 EFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRDLNG 291
            FAE+ GWK+   D+  V EFCNEV        VWMHNNK +     LNG
Sbjct: 173 AFAEKAGWKINGCDEKSVREFCNEVGIERGVLKVWMHNNKYSL----LNG 218

Transcription factor involved in the up-regulation of several stress-inducible genes. Acts as a transcriptional activator by interacting with MED25 and NAC proteins. Involved in increased drought tolerance.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9SB61|Y4466_ARATH ZF-HD homeobox protein At4g24660 OS=Arabidopsis thaliana GN=At4g24660 PE=1 SV=1

 Score =  136 bits (342), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 87/224 (38%), Positives = 108/224 (48%), Gaps = 59/224 (26%)

Query: 72  VTYKECLKNHAASIGGHALDGCGEFMPSPTATPSDPTSLKCAACGCHRNFHRREPDQDHH 131
           + Y+ECLKNHA +IGGHA+DGC EFMPS      D  +LKCAACGCHRNFHR+E      
Sbjct: 47  IRYRECLKNHAVNIGGHAVDGCCEFMPSGEDGTLD--ALKCAACGCHRNFHRKE------ 98

Query: 132 LPHVPTTATTATIEYQPHHRHHPPPPVTQPPSRRSPSSASPPPISSSYYPSAPHMLLALS 191
                T +        P + + PP P  QPP                             
Sbjct: 99  -----TESIGGRAHRVPTYYNRPPQP-HQPP----------------------------- 123

Query: 192 GNLQQSSAAAAVPQENHHISNNHHHNNNNIMMSNSGGSSGGRKRFRTKFSQSQKEKMFEF 251
           G L  +S AA               + +    SN   S G  KRFRTKF+  QKEKM  F
Sbjct: 124 GYLHLTSPAAP--------YRPPAASGDEEDTSNPSSSGGTTKRFRTKFTAEQKEKMLAF 175

Query: 252 AERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKR 287
           AER+GW++QK DD  V +FC E         +WMHNNK++  K+
Sbjct: 176 AERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSLGKK 219

Putative transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FKP8|Y5541_ARATH ZF-HD homeobox protein At5g65410 OS=Arabidopsis thaliana GN=At5g65410 PE=1 SV=1

 Score =  133 bits (334), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 82/222 (36%), Positives = 108/222 (48%), Gaps = 53/222 (23%)

Query: 74  YKECLKNHAASIGGHALDGCGEFMPSPTATPSDPTSLKCAACGCHRNFHRREPDQDHHLP 133
           ++ECLKN A +IGGHA+DGCGEFMP+      D  +LKCAACGCHRNFHR+E      LP
Sbjct: 75  FRECLKNQAVNIGGHAVDGCGEFMPAGIEGTID--ALKCAACGCHRNFHRKE------LP 126

Query: 134 HVPTTATTATIEYQPHHRHHPPPPVTQPPSRRSPSSASPPPISSSYYPSAPHMLLALSGN 193
           +             P   +  P PV          S  PPP                S  
Sbjct: 127 YFHHAPPQHQPPPPPPGFYRLPAPV----------SYRPPP----------------SQA 160

Query: 194 LQQSSAAAAVPQENHHISNNHHHNNNNIMMSNSGGSSGG-RKRFRTKFSQSQKEKMFEFA 252
                A     +E           + + M ++S  + GG RKR RTKF+  QKE+M   A
Sbjct: 161 PPLQLALPPPQRER----------SEDPMETSSAEAGGGIRKRHRTKFTAEQKERMLALA 210

Query: 253 ERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAK 286
           ER+GW++Q++DD+++  FC E         VW+HNNK T  K
Sbjct: 211 ERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHTLGK 252


  Database: swissprot
    Posted date:  Mar 23, 2013  2:32 AM
  Number of letters in database: 191,569,459
  Number of sequences in database:  539,616
  
Lambda     K      H
   0.311    0.126    0.388 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 163,382,465
Number of Sequences: 539616
Number of extensions: 8081213
Number of successful extensions: 157323
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 940
Number of HSP's successfully gapped in prelim test: 793
Number of HSP's that attempted gapping in prelim test: 63727
Number of HSP's gapped (non-prelim): 56890
length of query: 371
length of database: 191,569,459
effective HSP length: 119
effective length of query: 252
effective length of database: 127,355,155
effective search space: 32093499060
effective search space used: 32093499060
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 62 (28.5 bits)

Putative transcription factor.

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	371
225452813	341	PREDICTED: ZF-HD homeobox protein At4g24	0.641	0.697	0.600	2e-64
357501809	341	ZF-HD homeobox protein [Medicago truncat	0.668	0.727	0.559	1e-63
255586792	335	conserved hypothetical protein [Ricinus	0.698	0.773	0.557	2e-60
224077726	241	predicted protein [Populus trichocarpa]	0.617	0.950	0.651	1e-59
224141391	243	predicted protein [Populus trichocarpa]	0.617	0.942	0.632	3e-58
449459474	298	PREDICTED: transcription factor HB29-lik	0.676	0.842	0.56	3e-58
449522934	307	PREDICTED: transcription factor HB29-lik	0.692	0.837	0.573	2e-57
164562231	302	zinc finger-homeodomain protein 1, parti	0.668	0.821	0.577	1e-54
356550836	331	PREDICTED: ZF-HD homeobox protein At4g24	0.595	0.667	0.503	5e-54
356568656	338	PREDICTED: ZF-HD homeobox protein At4g24	0.681	0.748	0.543	3e-53

>gi|225452813|ref|XP_002283533.1| PREDICTED: ZF-HD homeobox protein At4g24660-like [Vitis vinifera]

 Score =  252 bits (644), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 170/283 (60%), Positives = 187/283 (66%), Gaps = 45/283 (15%)

Query: 18  KSPETDTTDNHQTGATRIHSAKPLTFTNGVLKRHQPQPQHHQRHHHHHHHHPIVVTYKEC 77
           KSPE +T        T+I   K L+ TNGVLKRHQ    HH  H        +VV YKEC
Sbjct: 25  KSPEAETET-----PTQIQPRKGLSLTNGVLKRHQQHHHHHHHHFAAPQ---VVVAYKEC 76

Query: 78  LKNHAASIGGHALDGCGEFMPSPTATPSDPTSLKCAACGCHRNFHRREPDQDHHLPHVPT 137
           LKNHAAS+GGHALDGCGEFMPSPTAT +DPTSLKCAACGCHRNFHRREPD          
Sbjct: 77  LKNHAASLGGHALDGCGEFMPSPTATSADPTSLKCAACGCHRNFHRREPDDP-------- 128

Query: 138 TATTATIEYQPHHRHHPPPPVTQPPSRRSPSSASPPPISSSYYPSAPHMLLALSGNLQQS 197
             TT  IEYQPHHRH    P   PP  RSP+S SPPPISSSYYPSAPHMLLALS  +   
Sbjct: 129 PPTTHVIEYQPHHRHQ---PPPPPPRPRSPNSPSPPPISSSYYPSAPHMLLALSAGI--- 182

Query: 198 SAAAAVPQENHHISNNHHHNNNNIMMSNSGGSSGGRKRFRTKFSQSQKEKMFEFAERVGW 257
              +  P+    IS            S+    + GRKRFRTKFSQ QKEKMFEFAERVGW
Sbjct: 183 ---SGPPENAPPIS------------SSPASGANGRKRFRTKFSQGQKEKMFEFAERVGW 227

Query: 258 KMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRDLNGA 292
           KMQKRD++LV EFCNEV        VWMHNNK+TF KRD+NG+
Sbjct: 228 KMQKRDEELVAEFCNEVGVDKGVLKVWMHNNKNTFGKRDVNGS 270

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357501809|ref|XP_003621193.1| ZF-HD homeobox protein [Medicago truncatula] gi|124359224|gb|ABN05735.1| Homeobox domain, ZF-HD class; ZF-HD homeobox protein Cys/His-rich dimerisation region; Homeodomain-like [Medicago truncatula] gi|124360958|gb|ABN08930.1| Homeobox domain, ZF-HD class; ZF-HD homeobox protein Cys/His-rich dimerisation region; Homeodomain-like [Medicago truncatula] gi|355496208|gb|AES77411.1| ZF-HD homeobox protein [Medicago truncatula]

 Score =  249 bits (637), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 161/288 (55%), Positives = 190/288 (65%), Gaps = 40/288 (13%)

Query: 10  TLNTNTNSKSPETDTTDNHQTGATRIHSAKPLT-FTNGVLKRHQPQPQHHQRHHHHHHHH 68
           T +T T +KSPE        T      +   ++ F+NGVLKR      H   H++H    
Sbjct: 27  TASTTTLTKSPEQQHETETPTTKFTTSTTPKISPFSNGVLKRFHHHHHHFNHHNNHQP-- 84

Query: 69  PIVVTYKECLKNHAASIGGHALDGCGEFMPSPTATPSDPTSLKCAACGCHRNFHRREPDQ 128
              +TYKECLKNHAA++GGHALDGCGEFM SPTATP+DPTSLKCAACGCHRNFHRREP++
Sbjct: 85  --TITYKECLKNHAANLGGHALDGCGEFMTSPTATPTDPTSLKCAACGCHRNFHRREPEE 142

Query: 129 DHHLPHVPTTATTATIEYQPHHRHHPPPPVTQPPSRRSPSSASPPPISSSYYPSAPHMLL 188
                  P   TT  IEYQPHHRH P PP   P S RSP+S+SPPPISSSYYPSAPHMLL
Sbjct: 143 -------PPLTTTHVIEYQPHHRHQPLPP--PPFSHRSPNSSSPPPISSSYYPSAPHMLL 193

Query: 189 ALSGNLQQSSAAAAVPQENHHISNNHHHNNNNIMMSNSGGSSGGRKRFRTKFSQSQKEKM 248
           ALS  L ++ AA                  N  M+ NS  S+  RKRFRTKF+Q QK+KM
Sbjct: 194 ALSAALPENVAAP-----------------NQTMLMNS-HSNNSRKRFRTKFTQDQKDKM 235

Query: 249 FEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD 288
            +FAE+VGWKMQK+DD+ VHEFCNE+        VWMHNNK+T AKR+
Sbjct: 236 LKFAEKVGWKMQKKDDEFVHEFCNEIGVDRSVLKVWMHNNKNTLAKRE 283

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255586792|ref|XP_002534012.1| conserved hypothetical protein [Ricinus communis] gi|223525985|gb|EEF28370.1| conserved hypothetical protein [Ricinus communis]

 Score =  239 bits (609), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 171/307 (55%), Positives = 195/307 (63%), Gaps = 48/307 (15%)

Query: 18  KSPETDTTDNHQTGATRIHSAKPLTFTNGVLKRHQPQPQHHQRHHHHHHHHPIVVTYKEC 77
           KSP+ +T        TRI   KPL+FTNGVLKRH     HH          P+V+TYKEC
Sbjct: 27  KSPDQETET-----PTRIQPPKPLSFTNGVLKRHHHHHHHHHHLSAPP---PVVITYKEC 78

Query: 78  LKNHAASIGGHALDGCGEFMPSPTATPSDPTSLKCAACGCHRNFHRREPDQDHHLPHVPT 137
           LKNHAA++GGHALDGCGEFMPSPTAT +DPTSLKCAACGCHRNFHRREP+      H   
Sbjct: 79  LKNHAATLGGHALDGCGEFMPSPTATHTDPTSLKCAACGCHRNFHRREPEDSPPPHHPHP 138

Query: 138 TA----TTATIEYQPHHRHHPPPPVTQPPSRRSPSSASPPPISSSYYPSAPHMLLALSGN 193
                 TT TIEYQPHHRHHPPPP  Q        +++ PP  SS YPSAPHMLLALSG 
Sbjct: 139 HHHPVNTTTTIEYQPHHRHHPPPPPPQAAQPYRSPNSASPPPISSSYPSAPHMLLALSGG 198

Query: 194 LQQSSAAAAVPQENHHISNNHHHNNNNIMMSNSGGSSGGRKRFRTKFSQSQKEKMFEFAE 253
           + +                     N+ + +   GG S GRKRFRTKFSQ+QKE+M EFAE
Sbjct: 199 VNE---------------------NSGLHIGGGGGGSSGRKRFRTKFSQTQKERMHEFAE 237

Query: 254 RVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRDLNGAGGSGSGSAGGGIG 305
           RVGWKMQKRD++LV EFCNEV        VWMHNNK+TFA+RD NG  G+        I 
Sbjct: 238 RVGWKMQKRDEELVQEFCNEVGVDKGVLKVWMHNNKNTFARRDANGHNGN-------SID 290

Query: 306 RINLDDD 312
           R NLD D
Sbjct: 291 RSNLDQD 297

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224077726|ref|XP_002305381.1| predicted protein [Populus trichocarpa] gi|222848345|gb|EEE85892.1| predicted protein [Populus trichocarpa]

 Score =  236 bits (603), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 172/264 (65%), Positives = 191/264 (72%), Gaps = 35/264 (13%)

Query: 33  TRIHSAKPLTFTNGVLKRHQPQPQHHQRHHHHHHHHPIVVTYKECLKNHAASIGGHALDG 92
           TRI   KPL+FTNGVLKRH     HH   H+H    P+V+TYKECLKNHAA+IGGHALDG
Sbjct: 5   TRIPQTKPLSFTNGVLKRHH---PHHHHLHNHFAPPPVVITYKECLKNHAATIGGHALDG 61

Query: 93  CGEFMPSPTATPSDPTSLKCAACGCHRNFHRREPDQDHHLPHVPTTATTATIEYQPHHRH 152
           CGEFMPSPTAT +DPTSLKCAACGCHRNFHRREP+     PH  TTA T TIEYQPHHRH
Sbjct: 62  CGEFMPSPTATHTDPTSLKCAACGCHRNFHRREPEDSP--PH--TTAIT-TIEYQPHHRH 116

Query: 153 HPPPPVTQPPSRRSPSSASPPPISSSYYPSAPHMLLALSGNLQQSSAAAAVPQENHHISN 212
           HPPPP   P   RSP+SASPPPISSSYYPSAPHMLLALSG +                  
Sbjct: 117 HPPPPQAHPQHNRSPNSASPPPISSSYYPSAPHMLLALSGGV------------------ 158

Query: 213 NHHHNNNNIMMSNSGGSSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCN 272
           +  + N NI      GSS  RKRFRTKFSQSQKE+M +FAE+VGWKMQKRD+DLV EFCN
Sbjct: 159 SGLNENVNINAPPRAGSS-PRKRFRTKFSQSQKERMHQFAEKVGWKMQKRDEDLVQEFCN 217

Query: 273 EV--------VWMHNNKSTFAKRD 288
           EV        VWMHNNK++F K++
Sbjct: 218 EVGVDRSALKVWMHNNKNSFGKKE 241

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224141391|ref|XP_002324056.1| predicted protein [Populus trichocarpa] gi|222867058|gb|EEF04189.1| predicted protein [Populus trichocarpa]

 Score =  231 bits (590), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 167/264 (63%), Positives = 187/264 (70%), Gaps = 35/264 (13%)

Query: 34  RIHSAKPLTFTNGVLKRHQPQPQHHQRHHHHHHHHPIVVTYKECLKNHAASIGGHALDGC 93
           RIH  KPL+FTNGVLKRH P   HH  HHHH    PIV+ YKECLKNHAA+IGGHALDGC
Sbjct: 6   RIHDTKPLSFTNGVLKRHPPH--HHHHHHHHFSPSPIVIAYKECLKNHAATIGGHALDGC 63

Query: 94  GEFMPSPTATPSDPTSLKCAACGCHRNFHRREPDQDHHLPHVPTTATTATIEYQPHHRHH 153
           GEFMPSP AT ++PTSLKCAACGCHRNFHRREP+        P TATT TI+YQ HHRHH
Sbjct: 64  GEFMPSPIATHTNPTSLKCAACGCHRNFHRREPEDSP-----PHTATTTTIQYQSHHRHH 118

Query: 154 PPPPVTQPPSRR-SPSSASPPPISSSYYPSAPHMLLALSGNLQQSSAAAAVPQENHHISN 212
           P PP    P    SP+SASPPPISSSYYPS PHMLLALSG +                  
Sbjct: 119 PLPPPQAQPLHNGSPNSASPPPISSSYYPSGPHMLLALSGGV------------------ 160

Query: 213 NHHHNNNNIMMSNSGGSSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCN 272
           +  + N NI +    GSS  RKRFRTKFSQSQKE+M++FAERVGWKMQKRD+DLV EFCN
Sbjct: 161 SGLNENANINVPPPVGSS-PRKRFRTKFSQSQKERMYQFAERVGWKMQKRDEDLVQEFCN 219

Query: 273 EV--------VWMHNNKSTFAKRD 288
           EV        VWMHNNK++  K++
Sbjct: 220 EVGVDRGVLKVWMHNNKNSLGKKE 243

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449459474|ref|XP_004147471.1| PREDICTED: transcription factor HB29-like [Cucumis sativus] gi|449509241|ref|XP_004163533.1| PREDICTED: transcription factor HB29-like [Cucumis sativus]

 Score =  231 bits (590), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 168/300 (56%), Positives = 199/300 (66%), Gaps = 49/300 (16%)

Query: 1   MDITP---TNNNTLNTNTNS-KSPETDTTDNHQTGATRIHSAKPLTFTNGVLKRHQPQPQ 56
           MD+TP   T   T++T   + KSPE ++    +T      + K   FTNGVLKRH     
Sbjct: 1   MDLTPAISTAAATISTGGGAVKSPELES----ETPIKIQPTTKSHPFTNGVLKRH----- 51

Query: 57  HHQRHHHHHHHHPIVVTYKECLKNHAASIGGHALDGCGEFMPSPTATPSDPTSLKCAACG 116
                 HH    P  V YKECLKNHAAS+GGHALDGCGEFMPSPTAT +DPTSLKCAACG
Sbjct: 52  ------HHTAPPPPQVVYKECLKNHAASLGGHALDGCGEFMPSPTATATDPTSLKCAACG 105

Query: 117 CHRNFHRREPDQDHHLPHVPTTATTATIEYQPHHRHHPPPPVTQPPSRRSPSSASPPPIS 176
           CHRNFHRREPD       + T  TT  IEYQPHHRHHPPPP T   + RSPSSASPPPIS
Sbjct: 106 CHRNFHRREPDDP-----IATPTTTHVIEYQPHHRHHPPPPSTAAAAHRSPSSASPPPIS 160

Query: 177 SSYYPSAPHMLLALSGNLQQSSAAAAVPQENHHISNNHHHNNNNIMMSNSGGSSGGRKRF 236
           SSYYPSAPHMLLALSG L +++                HH     +++ S  S   RKRF
Sbjct: 161 SSYYPSAPHMLLALSGVLPENAGGGG----------GFHHT----ILTPSPNS---RKRF 203

Query: 237 RTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD 288
           RTKF+Q+QKE+M+EFAE+VGWK+QKRD+D++ EFC++V        VWMHNNK+T  K+D
Sbjct: 204 RTKFTQNQKERMYEFAEKVGWKIQKRDEDMIQEFCSDVGVDRGVLKVWMHNNKNTLGKKD 263

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449522934|ref|XP_004168480.1| PREDICTED: transcription factor HB29-like [Cucumis sativus]

 Score =  229 bits (584), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 172/300 (57%), Positives = 195/300 (65%), Gaps = 43/300 (14%)

Query: 1   MDITPTNNNTLNTNTNSKSPETDTTDNHQTGATRIHSAKPLTFTNGVLKRHQPQPQHHQR 60
           MD+ P    T + NT S  P++DT        T+I    P +FTNGVLKRH     HH R
Sbjct: 1   MDLAPAPITTSSNNTKSPDPDSDT-------PTKI----PPSFTNGVLKRHHHNHHHHHR 49

Query: 61  HHHHHHHHPIVVTYKECLKNHAASIGGHALDGCGEFMPSPTATPSDPTSLKCAACGCHRN 120
                    +VV+YKECLKNHAA++G HALDGCGEFMPSP+ATPSDPTSL+CAACGCHRN
Sbjct: 50  PPSST----VVVSYKECLKNHAATLGAHALDGCGEFMPSPSATPSDPTSLRCAACGCHRN 105

Query: 121 FHRREPDQDHHLPHVPTTATTATIEYQPHHRHHPPPPVTQPPSRRSPSSASPPPISSSYY 180
           FHRR+P+       +  TA T  IEYQPHHRHHPPPP       RSP+SASPPPISSSYY
Sbjct: 106 FHRRDPEDPISTLAI-NTAPTHVIEYQPHHRHHPPPPPLA--GNRSPNSASPPPISSSYY 162

Query: 181 PSAPHMLLALSGNLQQSSAAAAVPQENHHISNNHHHNNNNIMMSNSGGSSGGRKRFRTKF 240
           PSAPHMLLALS  L      +  P ENH   NN          S    S   RKRFRTKF
Sbjct: 163 PSAPHMLLALSAGL------SGRPPENHTQGNN----------SVPTVSPNTRKRFRTKF 206

Query: 241 SQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKR-DLNG 291
           S  QKEKM +FAERVGWKMQKRD+DLV +FCN+V        VWMHNNK+T  K+ D NG
Sbjct: 207 SNEQKEKMLDFAERVGWKMQKRDEDLVRDFCNQVGVERGVLKVWMHNNKNTMGKKPDSNG 266

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|164562231|gb|ABY61030.1| zinc finger-homeodomain protein 1, partial [Cucumis sativus]

 Score =  219 bits (559), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 168/291 (57%), Positives = 190/291 (65%), Gaps = 43/291 (14%)

Query: 10  TLNTNTNSKSPETDTTDNHQTGATRIHSAKPLTFTNGVLKRHQPQPQHHQRHHHHHHHHP 69
           T + NT S  P++DT        T+I    P +FTNGVLKRH     HH R         
Sbjct: 5   TSSNNTKSPDPDSDT-------PTKI----PPSFTNGVLKRHHHNHHHHHRPPSST---- 49

Query: 70  IVVTYKECLKNHAASIGGHALDGCGEFMPSPTATPSDPTSLKCAACGCHRNFHRREPDQD 129
           +VV+YKECLKNHAA++G HAL GCGEFMPSP+ATPSDPTSL+CAACGCHRNFHRR+P+  
Sbjct: 50  VVVSYKECLKNHAATLGAHALYGCGEFMPSPSATPSDPTSLRCAACGCHRNFHRRDPEDP 109

Query: 130 HHLPHVPTTATTATIEYQPHHRHHPPPPVTQPPSRRSPSSASPPPISSSYYPSAPHMLLA 189
                +  TA T  IEYQPHHRHHPPPP       RSP+SASPPPISSSYYPSAPHMLLA
Sbjct: 110 ISTLAI-NTAPTHVIEYQPHHRHHPPPPPLA--GNRSPNSASPPPISSSYYPSAPHMLLA 166

Query: 190 LSGNLQQSSAAAAVPQENHHISNNHHHNNNNIMMSNSGGSSGGRKRFRTKFSQSQKEKMF 249
           LS  L      +  P ENH   NN          S    S   RKRFRTKFS  QKEKM 
Sbjct: 167 LSAGL------SGRPPENHTQGNN----------SVPTVSPNTRKRFRTKFSNEQKEKML 210

Query: 250 EFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKR-DLNG 291
           +FAERVGWKMQKRD+DLV +FCN+V        VWMHNNK+T  K+ D NG
Sbjct: 211 DFAERVGWKMQKRDEDLVRDFCNQVGVERGVLKVWMHNNKNTMGKKPDSNG 261

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356550836|ref|XP_003543789.1| PREDICTED: ZF-HD homeobox protein At4g24660-like [Glycine max]

 Score =  218 bits (554), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 146/290 (50%), Positives = 168/290 (57%), Gaps = 69/290 (23%)

Query: 18  KSPETDTTDNHQTGATRIH-----SAKPLTFTNGVLKRHQPQPQHHQRHHHHHHHHPIVV 72
           KSPE D         TRIH     + KP++F+NGVLKRH             H +H   V
Sbjct: 16  KSPEPDIET-----MTRIHQNPNPNPKPVSFSNGVLKRH-------------HVNHRAAV 57

Query: 73  TYKECLKNHAASIGGHALDGCGEFMPSPTATPSDPTSLKCAACGCHRNFHRREPDQDHHL 132
            YKECLKNH AS+GGHALDGCGEFMPSP AT  DP+S+KCAACGCHRNFHRREP++    
Sbjct: 58  VYKECLKNHVASLGGHALDGCGEFMPSPAATADDPSSIKCAACGCHRNFHRREPEESPIS 117

Query: 133 PHVPTTATTATIEYQPHHRHHPPPPVTQPPSRRSPSSASPPPISSSYYPSAPHMLLALSG 192
           P     AT   +EY+PHH           P     S  S  P   S YPSAPHMLLALSG
Sbjct: 118 P-----ATHHVLEYRPHH--------RHHPPPPHRSPNSASPPPISSYPSAPHMLLALSG 164

Query: 193 NLQQSSAA--AAVPQENHHISNNHHHNNNNIMMSNSGGSSGGRKRFRTKFSQSQKEKMFE 250
               S A    A P   HH                       RKRFRTKF+Q QKEKM E
Sbjct: 165 GAGLSVAPENTAAPAPPHH----------------------SRKRFRTKFTQEQKEKMHE 202

Query: 251 FAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD-LNG 291
           FA++VGWKMQ+RD+++V EFCNE+        VWMHNNK+TFAK+D LNG
Sbjct: 203 FADKVGWKMQRRDEEMVMEFCNEIGVDRGVLKVWMHNNKNTFAKKDNLNG 252

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356568656|ref|XP_003552526.1| PREDICTED: ZF-HD homeobox protein At4g24660-like [Glycine max]

 Score =  215 bits (547), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 167/307 (54%), Positives = 195/307 (63%), Gaps = 54/307 (17%)

Query: 41  LTFTNGVLKRHQPQPQHHQRHHHHHHHHPIVVTYKECLKNHAASIGGHALDGCGEFMPSP 100
           L+F+NGVLKRH     HH          P VVTYKECLKNHAA++GG ALDGCGEFMPSP
Sbjct: 44  LSFSNGVLKRHHHHHLHHPM--------PAVVTYKECLKNHAANLGGLALDGCGEFMPSP 95

Query: 101 TATPSDPTSLKCAACGCHRNFHRREPDQDHHLPHVPTTATTATIEYQPHHRHHPPPPVTQ 160
           TAT +DP+S+KCAACGCHRNFHRREP+     P + T+ TT  IEYQPHHRHHPPPP+  
Sbjct: 96  TATAADPSSIKCAACGCHRNFHRREPED----PPI-TSNTTHVIEYQPHHRHHPPPPLHA 150

Query: 161 PPSRRSPSSASPPPISSSYYPSAPHMLLALSGNLQQSSAAAAVPQENHHISNNHHHNNNN 220
             + RSP+SASPPPISSSYYPSAPHMLLALS  L     + A P                
Sbjct: 151 AAAARSPNSASPPPISSSYYPSAPHMLLALSAGLAAPPESTAAP---------------- 194

Query: 221 IMMSNSGGSSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV------ 274
                   ++  RKRFRTKFSQ QKEKM +FAE+VGWK+QKRD+DL+HEFCNEV      
Sbjct: 195 -------SAALSRKRFRTKFSQEQKEKMHKFAEKVGWKIQKRDEDLIHEFCNEVGVDRSV 247

Query: 275 --VWMHNNKSTFAKRDLNGAGGSGSGSAGGGIGRINLDDDNTGNDNINNSKSGDGDDQDE 332
             VWMHNNK+TFAK+D N    +           IN+   N  N +I +    +G D   
Sbjct: 248 LKVWMHNNKNTFAKKDNNIVISND----------INITTSNNINTSIIDDNDANGGDVKV 297

Query: 333 EEGINNN 339
            E  NNN
Sbjct: 298 FENPNNN 304

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	371
TAIR|locus:2095157	312	HB34 "AT3G28920" [Arabidopsis	0.307	0.365	0.496	7.1e-49
TAIR|locus:2167052	334	HB23 "AT5G39760" [Arabidopsis	0.312	0.347	0.441	2e-47
TAIR|locus:2150871	271	HB30 "AT5G15210" [Arabidopsis	0.226	0.309	0.521	1.1e-41
TAIR|locus:2026734	242	ZFHD1 "AT1G69600" [Arabidopsis	0.194	0.297	0.561	1.9e-33
TAIR|locus:2065304	310	HB21 "homeobox protein 21" [Ar	0.150	0.180	0.568	8.9e-33
TAIR|locus:2121989	220	HB22 "AT4G24660" [Arabidopsis	0.172	0.290	0.567	1.3e-32
TAIR|locus:2168240	279	HB25 "AT5G65410" [Arabidopsis	0.164	0.218	0.584	2.1e-32
TAIR|locus:2062141	262	HB24 "AT2G18350" [Arabidopsis	0.153	0.217	0.553	2.6e-32
TAIR|locus:2012602	312	HB31 "AT1G14440" [Arabidopsis	0.142	0.169	0.581	3.3e-31
TAIR|locus:2025121	309	HB33 "AT1G75240" [Arabidopsis	0.145	0.174	0.607	6.1e-30

TAIR|locus:2095157 HB34 "AT3G28920" [Arabidopsis thaliana (taxid:3702)]

 Score = 297 (109.6 bits), Expect = 7.1e-49, Sum P(3) = 7.1e-49
 Identities = 66/133 (49%), Positives = 79/133 (59%)

Query:    18 KSPETDTTDNHQTGATRIHSAKPLTFTNGVLKXXXXXXXXXXXXXXXXXXXXIVVTYKEC 77
             KSPE ++    +T  TRI  AKP++F+NG++K                      VTYKEC
Sbjct:    12 KSPEPES----ET-PTRIQPAKPISFSNGIIKRHHHHHHNNNK-----------VTYKEC 55

Query:    78 LKNHAASIGGHALDGCGEFMXXXXXXXXXXXXLKCAACGCHRNFHRREPDQDHHLPH--- 134
             LKNHAA+IGGHALDGCGEFM            LKCAACGCHRNFHRRE D    +P    
Sbjct:    56 LKNHAAAIGGHALDGCGEFMPSPSSTPSDPTSLKCAACGCHRNFHRRETDDSSAVPPPSL 115

Query:   135 VPTTATTATIEYQ 147
             +P++ TTA IEYQ
Sbjct:   116 LPSSTTTAAIEYQ 128

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

GO:0005634 "nucleus" evidence=ISM

GO:0003677 "DNA binding" evidence=ISS

TAIR|locus:2167052 HB23 "AT5G39760" [Arabidopsis thaliana (taxid:3702)]

 Score = 286 (105.7 bits), Expect = 2.0e-47, Sum P(2) = 2.0e-47
 Identities = 57/129 (44%), Positives = 75/129 (58%)

Query:    19 SPETDTTDNHQTGATRIHSAKPLTFTNGVLKXXXXXXXXXXXXXXXXXXXXIVVTYKECL 78
             +P   + +      TRI  AKP++F+NG++K                    ++ TYKECL
Sbjct:    13 TPTPKSPEPESETPTRIQPAKPISFSNGIIKRHHHHHHP------------LLFTYKECL 60

Query:    79 KNHAASIGGHALDGCGEFMXXXXXXXXXXXXLKCAACGCHRNFHRREPDQDHHLPHVPTT 138
             KNHAA++GGHALDGCGEFM            LKCAACGCHRNFHRR+PD ++    +P  
Sbjct:    61 KNHAAALGGHALDGCGEFMPSPSSISSDPTSLKCAACGCHRNFHRRDPDNNNDSSQIPPP 120

Query:   139 ATTATIEYQ 147
              +TA +EYQ
Sbjct:   121 PSTA-VEYQ 128

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

GO:0005634 "nucleus" evidence=ISM

GO:0003677 "DNA binding" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2150871 HB30 "AT5G15210" [Arabidopsis thaliana (taxid:3702)]

 Score = 235 (87.8 bits), Expect = 1.1e-41, Sum P(3) = 1.1e-41
 Identities = 49/94 (52%), Positives = 52/94 (55%)

Query:    34 RIHSAKPLTFTNGVLKXXXXXXXXXXXXXXXXXXXXIVVTYKECLKNHAASIGGHALDGC 93
             RI  AKP++F+NG                        V TYKECLKNHAA IGGHALDGC
Sbjct:    26 RIQPAKPISFSNG----------KRCHHHHLASEAVAVATYKECLKNHAAGIGGHALDGC 75

Query:    94 GEFMXXXXXXXXXXXXLKCAACGCHRNFHRREPD 127
             GEFM            L CAACGCHRNFHRRE D
Sbjct:    76 GEFMPSPSFNSNDPASLTCAACGCHRNFHRREED 109

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

GO:0005634 "nucleus" evidence=ISM

GO:0003677 "DNA binding" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2026734 ZFHD1 "AT1G69600" [Arabidopsis thaliana (taxid:3702)]

 Score = 232 (86.7 bits), Expect = 1.9e-33, Sum P(2) = 1.9e-33
 Identities = 41/73 (56%), Positives = 51/73 (69%)

Query:    72 VTYKECLKNHAASIGGHALDGCGEFMXXXXXXXXXXXXLKCAACGCHRNFHRREPDQD-H 130
             V YKECLKNHAA++GGHALDGCGEFM            L+CAACGCHRNFHRR+P ++ +
Sbjct:    29 VCYKECLKNHAANLGGHALDGCGEFMPSPTATSTDPSSLRCAACGCHRNFHRRDPSENLN 88

Query:   131 HLPHVPTTATTAT 143
              L   P ++ + T
Sbjct:    89 FLTAPPISSPSGT 101

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

GO:0005634 "nucleus" evidence=ISM

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

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0009410 "response to xenobiotic stimulus" evidence=RCA

GO:0048522 "positive regulation of cellular process" evidence=RCA

TAIR|locus:2065304 HB21 "homeobox protein 21" [Arabidopsis thaliana (taxid:3702)]

 Score = 191 (72.3 bits), Expect = 8.9e-33, Sum P(2) = 8.9e-33
 Identities = 33/58 (56%), Positives = 41/58 (70%)

Query:    70 IVVTYKECLKNHAASIGGHALDGCGEFMXXXXXXXXXXXXLKCAACGCHRNFHRREPD 127
             +V+ YKECLKNHAA++GG+A+DGCGEFM            L C+ C CHRNFHRRE +
Sbjct:    83 VVIKYKECLKNHAATMGGNAIDGCGEFMPSGEEGSIEA--LTCSVCNCHRNFHRRETE 138

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

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0003677 "DNA binding" evidence=ISS

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

TAIR|locus:2121989 HB22 "AT4G24660" [Arabidopsis thaliana (taxid:3702)]

 Score = 198 (74.8 bits), Expect = 1.3e-32, Sum P(2) = 1.3e-32
 Identities = 38/67 (56%), Positives = 44/67 (65%)

Query:    72 VTYKECLKNHAASIGGHALDGCGEFMXXXXXXXXXXXXLKCAACGCHRNFHRREPDQDHH 131
             + Y+ECLKNHA +IGGHA+DGC EFM            LKCAACGCHRNFHR+E +    
Sbjct:    47 IRYRECLKNHAVNIGGHAVDGCCEFMPSGEDGTLDA--LKCAACGCHRNFHRKETESIGG 104

Query:   132 LPH-VPT 137
               H VPT
Sbjct:   105 RAHRVPT 111

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

GO:0005634 "nucleus" evidence=ISM

GO:0003677 "DNA binding" evidence=ISS

GO:0009793 "embryo development ending in seed dormancy" evidence=RCA;IMP

GO:0005515 "protein binding" evidence=IPI

GO:0009686 "gibberellin biosynthetic process" evidence=RCA

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

GO:0009740 "gibberellic acid mediated signaling pathway" evidence=RCA

GO:0009845 "seed germination" evidence=RCA

GO:0010162 "seed dormancy process" evidence=RCA

GO:0048608 "reproductive structure development" evidence=RCA

TAIR|locus:2168240 HB25 "AT5G65410" [Arabidopsis thaliana (taxid:3702)]

 Score = 203 (76.5 bits), Expect = 2.1e-32, Sum P(2) = 2.1e-32
 Identities = 38/65 (58%), Positives = 43/65 (66%)

Query:    74 YKECLKNHAASIGGHALDGCGEFMXXXXXXXXXXXXLKCAACGCHRNFHRREPDQDHHLP 133
             ++ECLKN A +IGGHA+DGCGEFM            LKCAACGCHRNFHR+E    HH P
Sbjct:    75 FRECLKNQAVNIGGHAVDGCGEFMPAGIEGTIDA--LKCAACGCHRNFHRKELPYFHHAP 132

Query:   134 --HVP 136
               H P
Sbjct:   133 PQHQP 137

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

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2062141 HB24 "AT2G18350" [Arabidopsis thaliana (taxid:3702)]

 Score = 193 (73.0 bits), Expect = 2.6e-32, Sum P(2) = 2.6e-32
 Identities = 36/65 (55%), Positives = 46/65 (70%)

Query:   233 RKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTF 284
             +KRFRTKF++ QKEKM EFAE++GW+M K +DD V+ FC E+        VWMHNNK   
Sbjct:   198 KKRFRTKFNEEQKEKMMEFAEKIGWRMTKLEDDEVNRFCREIKVKRQVFKVWMHNNKQAA 257

Query:   285 AKRDL 289
              K+DL
Sbjct:   258 KKKDL 262

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

GO:0005634 "nucleus" evidence=ISM

GO:0003677 "DNA binding" evidence=ISS

TAIR|locus:2012602 HB31 "AT1G14440" [Arabidopsis thaliana (taxid:3702)]

 Score = 182 (69.1 bits), Expect = 3.3e-31, Sum P(2) = 3.3e-31
 Identities = 32/55 (58%), Positives = 39/55 (70%)

Query:    71 VVTYKECLKNHAASIGGHALDGCGEFMXXXXXXXXXXXXLKCAACGCHRNFHRRE 125
             ++ YKECLKNHAA++GG+A DGCGEFM            L C+AC CHRNFHR+E
Sbjct:    87 MIKYKECLKNHAAAMGGNATDGCGEFMPSGEDGSIEA--LTCSACNCHRNFHRKE 139

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

GO:0005634 "nucleus" evidence=ISM

TAIR|locus:2025121 HB33 "AT1G75240" [Arabidopsis thaliana (taxid:3702)]

 Score = 185 (70.2 bits), Expect = 6.1e-30, Sum P(2) = 6.1e-30
 Identities = 34/56 (60%), Positives = 38/56 (67%)

Query:    72 VTYKECLKNHAASIGGHALDGCGEFMXXXXXXXXXXXXLKCAACGCHRNFHRREPD 127
             V Y+ECLKNHAAS+GG   DGCGEFM            L+CAAC CHRNFHR+E D
Sbjct:    74 VRYRECLKNHAASVGGSVHDGCGEFMPSGEEGTIEA--LRCAACDCHRNFHRKEMD 127

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

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0003677 "DNA binding" evidence=IPI

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

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

GO:0010103 "stomatal complex morphogenesis" evidence=RCA

---

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: GSVIVG00020963001 SubName- Full=Chromosome chr14 scaffold_21, whole genome shotgun sequence; (323 aa) (Vitis vinifera)

Predicted Functional Partners:

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

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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	371
pfam04770	60	pfam04770, ZF-HD_dimer, ZF-HD protein dimerisation	1e-31
TIGR01566	53	TIGR01566, ZF_HD_prot_N, ZF-HD homeobox protein Cy	1e-24
TIGR01565	58	TIGR01565, homeo_ZF_HD, homeobox domain, ZF-HD cla	1e-19

>gnl|CDD|218256 pfam04770, ZF-HD_dimer, ZF-HD protein dimerisation region

 Score =  113 bits (285), Expect = 1e-31
 Identities = 44/59 (74%), Positives = 47/59 (79%), Gaps = 2/59 (3%)

Query: 69  PIVVTYKECLKNHAASIGGHALDGCGEFMPSPTATPSDPTSLKCAACGCHRNFHRREPD 127
              V Y+ECLKNHAASIGGHA+DGCGEFMPS       P SLKCAACGCHRNFHRREP+
Sbjct: 1   GSGVRYRECLKNHAASIGGHAVDGCGEFMPSGEE--GTPDSLKCAACGCHRNFHRREPE 57

This family of proteins has are plant transcription factors, and have been named ZF-HD for zinc finger homeodomain proteins, on the basis of similarity to proteins of known structure. This region is thought to be involved in the formation of homo and heterodimers, and may form a zinc finger. Length = 60

>gnl|CDD|130629 TIGR01566, ZF_HD_prot_N, ZF-HD homeobox protein Cys/His-rich dimerization domain

 Score = 94.9 bits (236), Expect = 1e-24
 Identities = 44/54 (81%), Positives = 45/54 (83%), Gaps = 1/54 (1%)

Query: 73  TYKECLKNHAASIGGHALDGCGEFMPSPTATPSDPTSLKCAACGCHRNFHRREP 126
            YKECLKNHAASIGGHALDGCGEFMPS      DP SL CAACGCHRNFHR+EP
Sbjct: 1   LYKECLKNHAASIGGHALDGCGEFMPSSGEE-GDPESLTCAACGCHRNFHRKEP 53

This model describes a 54-residue domain found in the N-terminal region of plant proteins, the vast majority of which contain a ZF-HD class homeobox domain toward the C-terminus. The region between the two domains typically is rich in low complexity sequence. The companion ZF-HD homeobox domain is described in model TIGR01565. Length = 53

>gnl|CDD|130628 TIGR01565, homeo_ZF_HD, homeobox domain, ZF-HD class

 Score = 81.1 bits (200), Expect = 1e-19
 Identities = 29/57 (50%), Positives = 39/57 (68%), Gaps = 8/57 (14%)

Query: 233 RKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNK 281
           +KR RTKF+  QKEKM +FAE++GWK++ +  + V EFC E+        VWMHNNK
Sbjct: 1   KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57

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. Length = 58

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	371
TIGR01566	53	ZF_HD_prot_N ZF-HD homeobox protein Cys/His-rich d	100.0
PF04770	60	ZF-HD_dimer: ZF-HD protein dimerisation region; In	99.97
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.88
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	96.49
KOG0843	197	consensus Transcription factor EMX1 and related HO	95.99
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	92.0
KOG0494	332	consensus Transcription factor CHX10 and related H	91.25
KOG0493	342	consensus Transcription factor Engrailed, contains	91.11
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	89.52
PRK11470	200	hypothetical protein; Provisional	87.18
PF12651	44	RHH_3: Ribbon-helix-helix domain	83.03
PF05572	154	Peptidase_M43: Pregnancy-associated plasma protein	81.44
KOG0485	268	consensus Transcription factor NKX-5.1/HMX1, conta	81.37

>TIGR01566 ZF_HD_prot_N ZF-HD homeobox protein Cys/His-rich dimerization domain

Probab=100.00  E-value=4.6e-34  Score=213.51  Aligned_cols=50  Identities=84%  Similarity=1.519  Sum_probs=45.5

Q ss_pred             HHHhhhhhhccCCccccCcccccc-CCCCCCCCCCcccccccCccccccccCC
Q 017477           75 KECLKNHAASIGGHALDGCGEFMP-SPTATPSDPTSLKCAACGCHRNFHRREP  126 (371)
Q Consensus        75 RECLKNHAAsIGGHAvDGCGEFMP-SGeeGt~dp~ALKCAACGCHRNFHRKE~  126 (371)
                      ..-||||||+|||||||||||||| +|++++  +++||||||||||||||||+
T Consensus         3 ~EC~kNHAa~~Gg~a~DGCgEFmps~g~~~~--~~al~CaACgCHRnFHRre~   53 (53)
T TIGR01566         3 KECLKNHAASIGGHALDGCGEFMPSSGEEGD--PESLTCAACGCHRNFHRKEP   53 (53)
T ss_pred             HHHHHhhHHHhCCcccccccccccCCCCCCC--CcceeeeecCcccccccCCC
Confidence            467999999999999999999999 677665  67999999999999999995

This model describes a 54-residue domain found in the N-terminal region of plant proteins, the vast majority of which contain a ZF-HD class homeobox domain toward the C-terminus. The region between the two domains typically is rich in low complexity sequence. The companion ZF-HD homeobox domain is described in model TIGR01565.

>PF04770 ZF-HD_dimer: ZF-HD protein dimerisation region; InterPro: IPR006456 The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many transcription factors

Probab=99.97  E-value=5.5e-33  Score=213.39  Aligned_cols=55  Identities=76%  Similarity=1.414  Sum_probs=50.0

Q ss_pred             eehHHHhhhhhhccCCccccCccccccC-CCCCCCCCCcccccccCccccccccCCCC
Q 017477           72 VTYKECLKNHAASIGGHALDGCGEFMPS-PTATPSDPTSLKCAACGCHRNFHRREPDQ  128 (371)
Q Consensus        72 VrYRECLKNHAAsIGGHAvDGCGEFMPS-GeeGt~dp~ALKCAACGCHRNFHRKE~eg  128 (371)
                      .....-||||||+||||||||||||||+ |+||+  +++|+||||||||||||||+++
T Consensus         4 v~Y~EC~kNHAa~~Gg~a~DGCgEFm~~~g~eg~--~~al~CaACgCHRnFHRre~~~   59 (60)
T PF04770_consen    4 VRYRECLKNHAASIGGHAVDGCGEFMPSPGEEGT--PEALKCAACGCHRNFHRREVEG   59 (60)
T ss_pred             eeHHHHHhhHhHhhCCcccccccccccCCCCCCC--cccceecccCcchhcccCCcCC
Confidence            4567889999999999999999999999 88865  6799999999999999999865

HD-containing proteins are found in diverse organisms such as humans, Drosophila, nematode worms, and plants, where they play important roles in development. Zinc-finger-homeodomain (ZF- HD) subfamily proteins have only been identified in plants, and likely play plant specific roles. ZF-HD proteins are expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development []. The ZF-HD class of homeodomain proteins may also be involved in the photosynthesis-related mesophyll-specific gene expression of phosphoenolpyruvate carboxylase in C4 species [] and in pathogen signaling and plant defense mechanisms []. These proteins share three domains of high sequence similarity: the homeodomain (II) located at the carboxy-terminus, and two other segments (Ia and Ib) located in the amino-terminal part. These N-terminal domains contain five conserved cysteine residues and at least three conserved histidine residues whose spacing ressembles zinc-binding domains involved in dimerization of transcription factors. Although the two domains contain at least eight potential zinc-binding amino-acids, the unique spacing of the conserved cysteine and histidine residues within domain Ib suggests that both domains form one rather than two zinc finger structures. The two conserved motifs Ia and Ib constitute a dimerization domain which is sufficient for the formation of homo- and heterodimers []. This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in IPR006455 from INTERPRO.

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.88  E-value=1.5e-23  Score=160.31  Aligned_cols=50  Identities=58%  Similarity=1.090  Sum_probs=48.9

Q ss_pred             CCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCc
Q 017477          233 RKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKS  282 (371)
Q Consensus       233 KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKh  282 (371)
                      |||+||+||+|||++|.+|+|++||||||.|+.+|++||.+|        |||||||+
T Consensus         1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k~   58 (58)
T TIGR01565         1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNKK   58 (58)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCCC
Confidence            699999999999999999999999999999999999999999        99999995

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.

>PF00046 Homeobox: Homeobox domain not present here

Probab=96.49  E-value=0.00061  Score=49.82  Aligned_cols=46  Identities=24%  Similarity=0.435  Sum_probs=38.5

Q ss_pred             CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcC
Q 017477          234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKST  283 (371)
Q Consensus       234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKht  283 (371)
                      ||.||+||.+|.+.|.++-++    -+.-+.+++++.+.++        +|+.|.+..
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~----~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k   54 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQE----NPYPSKEEREELAKELGLTERQVKNWFQNRRRK   54 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHH----SSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHH----hccccccccccccccccccccccccCHHHhHHH
Confidence            789999999999999999885    4567777888888877        999987643

; 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=95.99  E-value=0.0028  Score=59.43  Aligned_cols=60  Identities=22%  Similarity=0.359  Sum_probs=44.7

Q ss_pred             CCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHh---ccc-eeeecCCcCCCCCCCCC
Q 017477          232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFC---NEV-VWMHNNKSTFAKRDLNG  291 (371)
Q Consensus       232 ~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC---~EI-VWMHNNKhtl~Kk~~~~  291 (371)
                      .-||.||-||.||-.|+-..-|+-+|-.-...+.+-+..-   .+| ||+-|..-..+|+....
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~  164 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED  164 (197)
T ss_pred             CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence            4599999999999999988888887776655555444432   223 99999988777766543

>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=92.00  E-value=0.099  Score=37.66  Aligned_cols=49  Identities=22%  Similarity=0.449  Sum_probs=40.8

Q ss_pred             CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCC
Q 017477          234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAK  286 (371)
Q Consensus       234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~K  286 (371)
                      |+.|+.||.+|.+.|.++=++    -..-+.+++++.+.++        +|+-|.+...++
T Consensus         1 ~~~r~~~~~~~~~~Le~~f~~----~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~   57 (59)
T cd00086           1 RRKRTRFTPEQLEELEKEFEK----NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR   57 (59)
T ss_pred             CCCCCcCCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence            567899999999999998888    5577888999999987        899887765443

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

Probab=91.25  E-value=0.12  Score=51.34  Aligned_cols=55  Identities=24%  Similarity=0.508  Sum_probs=31.8

Q ss_pred             CCCccccCCCHHHHHHHHH-HHHHhCCcccCCCHHHHHHHh----ccc-eeeecCCcCCCCCC
Q 017477          232 GRKRFRTKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFC----NEV-VWMHNNKSTFAKRD  288 (371)
Q Consensus       232 ~KKRFRTKFTqEQKEKMl~-FAEKLGWRIQK~DE~~VqqFC----~EI-VWMHNNKhtl~Kk~  288 (371)
                      +|+||||.||+-|-|++.. |-|. -+-=.+-. +++..|-    .+| ||+-|.+-...|+.
T Consensus       140 kRRh~RTiFT~~Qle~LEkaFkea-HYPDv~Ar-e~la~ktelpEDRIqVWfQNRRAKWRk~E  200 (332)
T KOG0494|consen  140 KRRHFRTIFTSYQLEELEKAFKEA-HYPDVYAR-EMLADKTELPEDRIQVWFQNRRAKWRKTE  200 (332)
T ss_pred             ccccccchhhHHHHHHHHHHHhhc-cCccHHHH-HHHhhhccCchhhhhHHhhhhhHHhhhhh
Confidence            4567899999999887643 4332 11111111 1111111    123 99999998888875

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

Probab=91.11  E-value=0.14  Score=50.86  Aligned_cols=51  Identities=27%  Similarity=0.506  Sum_probs=36.2

Q ss_pred             CCccccCCCHHHHHHHH-HHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          233 RKRFRTKFSQSQKEKMF-EFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       233 KKRFRTKFTqEQKEKMl-~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      .||-||-||.||-+|+. ||-|--     -.-|.--|+..+|+        +|+-|-+-.++|--
T Consensus       246 eKRPRTAFtaeQL~RLK~EF~enR-----YlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT  305 (342)
T KOG0493|consen  246 EKRPRTAFTAEQLQRLKAEFQENR-----YLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST  305 (342)
T ss_pred             hcCccccccHHHHHHHHHHHhhhh-----hHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence            38999999999999986 565532     23455566777776        99998766555543

>smart00389 HOX Homeodomain

Probab=89.52  E-value=0.33  Score=34.84  Aligned_cols=45  Identities=22%  Similarity=0.389  Sum_probs=34.3

Q ss_pred             CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCc
Q 017477          234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKS  282 (371)
Q Consensus       234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKh  282 (371)
                      ||-||.||++|.+.|.++=++--    .-+.+++++-..++        .|+.|.+.
T Consensus         1 ~k~r~~~~~~~~~~L~~~f~~~~----~P~~~~~~~la~~~~l~~~qV~~WF~nrR~   53 (56)
T smart00389        1 RRKRTSFTPEQLEELEKEFQKNP----YPSREEREELAAKLGLSERQVKVWFQNRRA   53 (56)
T ss_pred             CCCCCcCCHHHHHHHHHHHHhCC----CCCHHHHHHHHHHHCcCHHHHHHhHHHHhh
Confidence            56788999999999988776554    45666777776666        89988764

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

>PRK11470 hypothetical protein; Provisional

Probab=87.18  E-value=0.28  Score=46.30  Aligned_cols=41  Identities=20%  Similarity=0.406  Sum_probs=33.7

Q ss_pred             CCccccCCCHHHHHHHHHHHHHh-----CCcccCCCHHHHHHHhcccee
Q 017477          233 RKRFRTKFSQSQKEKMFEFAERV-----GWKMQKRDDDLVHEFCNEVVW  276 (371)
Q Consensus       233 KKRFRTKFTqEQKEKMl~FAEKL-----GWRIQK~DE~~VqqFC~EIVW  276 (371)
                      -+|.++.+|.+|+++|.++|++.     .|+..-.|+   ..||+|.||
T Consensus        78 v~Rl~~~l~~~~~~~~~~~A~~~lGkpYD~~F~~~d~---~~YCSElV~  123 (200)
T PRK11470         78 IKRLDAGLTEQQKQRIVEQVPSRLRKLYHTGFKYESS---RQFCSKFVF  123 (200)
T ss_pred             EEEecCCCCHHHHHHHHHHHHHHcCCCCCCccCCCCC---ceehHHHHH
Confidence            48999999999999999999984     566555454   579999977

>PF12651 RHH_3: Ribbon-helix-helix domain

Probab=83.03  E-value=0.91  Score=33.08  Aligned_cols=41  Identities=24%  Similarity=0.374  Sum_probs=36.0

Q ss_pred             CCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhc
Q 017477          232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCN  272 (371)
Q Consensus       232 ~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~  272 (371)
                      .||||-+.+..|+-+|+.++|++.|-.+-+-=+.+|+.|=.
T Consensus         1 ~r~r~t~~l~~el~~~L~~ls~~t~i~~S~Ll~eAle~~l~   41 (44)
T PF12651_consen    1 NRKRFTFSLDKELYEKLKELSEETGIPKSKLLREALEDYLE   41 (44)
T ss_pred             CceEEEEecCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            37999999999999999999999998888877778887743

>PF05572 Peptidase_M43: Pregnancy-associated plasma protein-A; InterPro: IPR008754 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families

Probab=81.44  E-value=0.95  Score=40.53  Aligned_cols=18  Identities=22%  Similarity=0.235  Sum_probs=13.5

Q ss_pred             cccCCCHHHHHHHHHHHH
Q 017477          236 FRTKFSQSQKEKMFEFAE  253 (371)
Q Consensus       236 FRTKFTqEQKEKMl~FAE  253 (371)
                      -++.||+.||+||+++-|
T Consensus       137 c~~~FT~gQ~~RM~~~l~  154 (154)
T PF05572_consen  137 CMNMFTPGQVARMRAVLE  154 (154)
T ss_dssp             G--B-BHHHHHHHHHHHH
T ss_pred             cccccCHHHHHHHHHHhC
Confidence            689999999999998865

Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase M43 (cytophagalysin family, clan MA(M)), subfamily M43. The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The type example of this family is the pregnancy-associated plasma protein A (PAPP-A), which cleaves insulin-like growth factor (IGF) binding protein-4 (IGFBP-4), causing a dramatic reduction in its affinity for IGF-I and -II. Through this mechanism, PAPP-A is a regulator of IGF bioactivity in several systems, including the Homo sapiens ovary and the cardiovascular system [, , , ].; PDB: 3LUN_A 3LUM_B 2J83_A 2CKI_A.

>KOG0485 consensus Transcription factor NKX-5

Probab=81.37  E-value=0.54  Score=45.84  Aligned_cols=54  Identities=26%  Similarity=0.460  Sum_probs=36.8

Q ss_pred             CCCCCCccccCCCHHHH---H------HHHHHHHHhCCcccCCCHHHHHHHhccc-eeeecCCcCCCCCC
Q 017477          229 SSGGRKRFRTKFSQSQK---E------KMFEFAERVGWKMQKRDDDLVHEFCNEV-VWMHNNKSTFAKRD  288 (371)
Q Consensus       229 ~s~~KKRFRTKFTqEQK---E------KMl~FAEKLGWRIQK~DE~~VqqFC~EI-VWMHNNKhtl~Kk~  288 (371)
                      +...|||-||-|+.-|-   |      |-|.-|||.|---+-|=      -=-+| +|+-|.+++++++-
T Consensus       100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqL------TETQVKIWFQNRRnKwKRq~  163 (268)
T KOG0485|consen  100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQL------TETQVKIWFQNRRNKWKRQY  163 (268)
T ss_pred             cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhh------hhhhhhhhhhhhhHHHHHHH
Confidence            45679999999999874   3      33455777775433221      11345 99999999888874

1/HMX1, contains HOX domain [Transcription]

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Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	371
1wh7_A	80	Solution Structure Of Homeobox Domain Of Arabidopsi		3e-12
1wh5_A	80	Solution Structure Of Homeobox Domain Of Arabidopsi		2e-11

>pdb|1WH7|A Chain A, Solution Structure Of Homeobox Domain Of Arabidopsis Thaliana Hypothetical Protein F22k18.140 Length = 80

Iteration: 1
 Score = 69.3 bits (168), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 32/58 (55%), Positives = 40/58 (68%), Gaps = 8/58 (13%)
Query: 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKST 283
           KRFRTKF+  QKEKM  FAER+GW++QK DD  V +FC E         +WMHNNK++
Sbjct: 18  KRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNS 75

>pdb|1WH5|A Chain A, Solution Structure Of Homeobox Domain Of Arabidopsisthaliana Zinc Finger Homeobox Family Protein Length = 80

Iteration: 1
 Score = 67.0 bits (162), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 39/57 (68%), Gaps = 8/57 (14%)
Query: 233 RKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNK 281
           RKR RTKF+  QKE+M   AER+GW++Q++DD+++  FC E         VW+HNNK
Sbjct: 17  RKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNK 73
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	371
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	6e-27
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	4e-26

>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 Length = 80

 Score =  101 bits (252), Expect = 6e-27
 Identities = 36/72 (50%), Positives = 44/72 (61%), Gaps = 8/72 (11%)

Query: 224 SNSGGSSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------V 275
           SN   S G  KRFRTKF+  QKEKM  FAER+GW++QK DD  V +FC E         +
Sbjct: 8   SNPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKI 67

Query: 276 WMHNNKSTFAKR 287
           WMHNNK++    
Sbjct: 68  WMHNNKNSGPSS 79

>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 Length = 80

 Score = 99.3 bits (247), Expect = 4e-26
 Identities = 30/73 (41%), Positives = 44/73 (60%), Gaps = 8/73 (10%)

Query: 223 MSNSGGSSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV-------- 274
            S++    G RKR RTKF+  QKE+M   AER+GW++Q++DD+++  FC E         
Sbjct: 7   GSSAEAGGGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLK 66

Query: 275 VWMHNNKSTFAKR 287
           VW+HNNK +    
Sbjct: 67  VWLHNNKHSGPSS 79

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	371
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.51
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.33
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	98.16
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	98.15
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	98.03
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	97.34
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	97.31
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	96.6
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	96.56
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	96.55
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	96.53
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	96.5
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	96.34
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	96.28
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	96.15
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	96.02
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	95.89
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	95.87
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	95.83
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	95.78
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	95.77
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	95.76
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	95.54
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	95.31
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	95.29
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	95.13
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	95.1
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	95.07
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	95.01
1e3o_C	160	Octamer-binding transcription factor 1; transcript	95.01
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	94.98
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	94.97
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	94.95
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	94.95
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	94.81
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	94.8
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	94.65
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	94.55
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	94.43
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	94.36
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	94.28
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	94.14
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	94.09
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	94.07
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	94.06
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	93.99
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	93.67
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	93.57
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	93.51
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	93.47
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	93.42
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	93.23
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	92.34
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	92.24
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	92.06
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	90.93
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	89.86
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	89.48
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	89.35
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	86.76
1lfb_A	99	Liver transcription factor (LFB1); transcription r	86.33
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	86.27
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	85.36
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	84.77
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	83.93
1uhs_A	72	HOP, homeodomain only protein; structural genomics	83.38
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	80.42

>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=99.51  E-value=1.8e-14  Score=114.12  Aligned_cols=58  Identities=59%  Similarity=1.041  Sum_probs=54.2

Q ss_pred             CCCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCC
Q 017477          229 SSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAK  286 (371)
Q Consensus       229 ~s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~K  286 (371)
                      ....+||.||+||.+|++.|.+|++++||+.++.|..+.+++|.+|        |||+|++..+++
T Consensus        13 ~~~~~rR~Rt~ft~~Ql~~Le~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           13 SGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            4456899999999999999999999999999999999999999999        999999987765

>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=99.33  E-value=1.1e-12  Score=103.39  Aligned_cols=57  Identities=51%  Similarity=1.029  Sum_probs=53.3

Q ss_pred             CCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCC
Q 017477          230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAK  286 (371)
Q Consensus       230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~K  286 (371)
                      ...+||.||+||.+|++.|..+.+++|||.++.|..+.+++|.+|        |||+|++..+++
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           14 GGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            456899999999999999999999999999999999999999999        999999987654

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

Probab=98.16  E-value=2.2e-07  Score=72.09  Aligned_cols=58  Identities=16%  Similarity=0.264  Sum_probs=52.3

Q ss_pred             CCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCC
Q 017477          230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKR  287 (371)
Q Consensus       230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk  287 (371)
                      ...+||.||.||.+|++.|..+-++-+|..+..+..+.++++.++        ||+.|......|.
T Consensus         5 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~   70 (80)
T 2da4_A            5 SSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLM   70 (80)
T ss_dssp             CCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhc
Confidence            456799999999999999999999999999999999999999999        9999998766554

>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=98.15  E-value=4.6e-07  Score=70.01  Aligned_cols=56  Identities=23%  Similarity=0.437  Sum_probs=47.1

Q ss_pred             CCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCCC
Q 017477          230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRDL  289 (371)
Q Consensus       230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~~  289 (371)
                      ...+||.||.||.+|++.|..+-++    -+..+..+++++|.++        ||+.|.....+|+..
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (80)
T 2dmq_A            4 GSSGKRMRTSFKHHQLRTMKSYFAI----NHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLL   67 (80)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHH----cCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHH
Confidence            3457999999999999999877654    4678999999999999        999999987777643

>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=98.03  E-value=1.8e-06  Score=66.43  Aligned_cols=56  Identities=21%  Similarity=0.350  Sum_probs=46.3

Q ss_pred             CCCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          229 SSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       229 ~s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      ....+||.||.||.||++.|..+-++    -+..+..+++++|.++        ||+.|.....+|+.
T Consensus        13 ~~~~~rr~Rt~ft~~Ql~~Le~~f~~----~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   76 (80)
T 2da3_A           13 EPQRDKRLRTTITPEQLEILYQKYLL----DSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSG   76 (80)
T ss_dssp             CCCCCTTCCSSCCTTTHHHHHHHHHH----CSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh----cCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhc
Confidence            34568999999999999998666554    4788999999999998        99999988776654

>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=97.34  E-value=0.00014  Score=57.51  Aligned_cols=51  Identities=24%  Similarity=0.362  Sum_probs=44.6

Q ss_pred             CCCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCc
Q 017477          229 SSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKS  282 (371)
Q Consensus       229 ~s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKh  282 (371)
                      +...+||.||.||.||-..|..|=+.|+=   +-|++++++...++        ||+-|-.-
T Consensus         3 ~~~~~kR~RT~~s~eQL~~Lqs~f~~~~~---yPd~~~r~~La~~tGL~~~~IqVWFQNrR~   61 (71)
T 1wi3_A            3 SGSSGPRSRTKISLEALGILQSFIHDVGL---YPDQEAIHTLSAQLDLPKHTIIKFFQNQRY   61 (71)
T ss_dssp             CCCCCCCCCCCCCSHHHHHHHHHHHHHCS---CCCHHHHHHHHHHSCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHhcCC---CCCHHHHHHHHHHhCCCHHHHHHhhcccee
Confidence            34568999999999999999999999874   67999999999998        99988654

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

Probab=97.31  E-value=0.00019  Score=55.47  Aligned_cols=57  Identities=18%  Similarity=0.317  Sum_probs=43.9

Q ss_pred             CCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCCCCC
Q 017477          231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRDLNG  291 (371)
Q Consensus       231 ~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~~~~  291 (371)
                      ..+||.||.||.+|.+.|..+=++    -+.-+..+.++.+.++        ||+-|-.....|+....
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~~   69 (80)
T 2dms_A            5 SSGRRERTTFTRAQLDVLEALFAK----TRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQ   69 (80)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHc----cCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHcc
Confidence            457999999999999988776655    3456777777777777        99999888777665433

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

Probab=96.60  E-value=0.00074  Score=50.76  Aligned_cols=54  Identities=20%  Similarity=0.412  Sum_probs=41.4

Q ss_pred             CCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       231 ~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      ..+||.||.||.+|.+.|..+=++    -+.-+..+.++.+.++        ||+-|-.....|+.
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~----~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~   66 (70)
T 2dmu_A            5 SSGRRHRTIFTDEQLEALENLFQE----TKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSG   66 (70)
T ss_dssp             TSSCCCCCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHc----cCCCCHHHHHHHHHHHCCCHHHeehccccccccccccC
Confidence            457999999999999988776665    4556777777777777        99999876655543

>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=96.56  E-value=0.0018  Score=50.01  Aligned_cols=55  Identities=16%  Similarity=0.228  Sum_probs=40.8

Q ss_pred             CCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      ...+||.||.||.+|.+.|..+=++    -+..+..+..+.+.++        ||+-|-....+|..
T Consensus        14 ~~~~rr~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   76 (80)
T 2dmt_A           14 AKKGRRSRTVFTELQLMGLEKRFEK----QKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSG   76 (80)
T ss_dssp             CCCCCCSCCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHh----cCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhccc
Confidence            3457899999999999988766554    3456666777776666        99999877666554

>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=96.55  E-value=0.0014  Score=49.15  Aligned_cols=55  Identities=22%  Similarity=0.378  Sum_probs=42.5

Q ss_pred             CCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      ...+||.||.||.+|.+.|..+=++    -+..+..+.++.+.++        ||+-|-....+|+.
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~----~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2da2_A            4 GSSGRSSRTRFTDYQLRVLQDFFDA----NAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSG   66 (70)
T ss_dssp             SCCSCCCCCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHc----CCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhcc
Confidence            3467999999999999988776655    3567777788887777        99999877665554

>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=96.53  E-value=0.0021  Score=48.34  Aligned_cols=55  Identities=13%  Similarity=0.195  Sum_probs=42.6

Q ss_pred             CCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      ...+||.||.||.+|.+.|..+=++    -+..+..+..+.+.++        ||+-|-....+|..
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~   66 (70)
T 2cra_A            4 GSSGRKKRIPYSKGQLRELEREYAA----NKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSG   66 (70)
T ss_dssp             SCCCCCSCCCSCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHh----cCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccC
Confidence            3457999999999999988766654    3567777777777777        99999887666654

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

Probab=96.50  E-value=0.0015  Score=49.16  Aligned_cols=55  Identities=18%  Similarity=0.242  Sum_probs=42.1

Q ss_pred             CCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      ...+||.||.||.+|.+.|..+=++    -+.-+..+.++.+.++        ||+-|-....+|..
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2djn_A            4 GSSGRKPRTIYSSFQLAALQRRFQK----TQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSG   66 (70)
T ss_dssp             CCCCCCSSCSSCHHHHHHHHHHHTT----CSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHcC----CCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccC
Confidence            3457999999999999988765543    4566777788887777        99999887766654

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

Probab=96.34  E-value=0.006  Score=47.19  Aligned_cols=55  Identities=18%  Similarity=0.253  Sum_probs=41.3

Q ss_pred             CCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      ...+||.||.||.+|.+.|..+-++    -+.-+..+..+.+.++        ||+-|-....+|+.
T Consensus        19 ~~~~rr~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   81 (84)
T 2kt0_A           19 PVKKQKTRTVFSSTQLCVLNDRFQR----QKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQ   81 (84)
T ss_dssp             CSCSCCCSSCCCHHHHHHHHHHHHH----SSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHh
Confidence            4567999999999999988665553    3456666666766666        99999887766654

>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=96.28  E-value=0.0038  Score=46.97  Aligned_cols=54  Identities=13%  Similarity=0.225  Sum_probs=40.4

Q ss_pred             CCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCC
Q 017477          230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKR  287 (371)
Q Consensus       230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk  287 (371)
                      ...+||-||.||.+|.+.|..+=++    -+..+..+.++.+.++        ||+-|-....+|.
T Consensus         4 ~~~~~r~R~~ft~~q~~~Le~~F~~----~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~   65 (70)
T 2e1o_A            4 GSSGKGGQVRFSNDQTIELEKKFET----QKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRS   65 (70)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHc----CCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCC
Confidence            3457889999999999988776654    3556777777777777        9999876554443

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

Probab=96.15  E-value=0.003  Score=48.73  Aligned_cols=53  Identities=25%  Similarity=0.377  Sum_probs=39.6

Q ss_pred             CCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCC
Q 017477          231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKR  287 (371)
Q Consensus       231 ~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk  287 (371)
                      ..+||.||.||.+|.+.|..+-++    -+..+..+..+.+.++        ||+-|-....+|+
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   65 (80)
T 2cue_A            5 SSGQRNRTSFTQEQIEALEKEFER----THYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE   65 (80)
T ss_dssp             CSSCCCCCCSCHHHHHHHHHHHTT----CSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCHHHHHHHHHHHhc----cCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHH
Confidence            457999999999999888665442    3456677777777776        9999987665554

>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=96.02  E-value=0.0021  Score=48.21  Aligned_cols=54  Identities=15%  Similarity=0.286  Sum_probs=39.4

Q ss_pred             CCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       231 ~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      ..+||-||.||.+|.+.|..+=++-    +.-+..+.++.+.++        ||+-|-.....|+.
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~----~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2da1_A            5 SSGKRPRTRITDDQLRVLRQYFDIN----NSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSG   66 (70)
T ss_dssp             CCCCSCSCCCCHHHHHHHHHHHHHC----SSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHC----CCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhc
Confidence            4579999999999999887666542    445556666666666        99999876555543

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

Probab=95.89  E-value=0.0026  Score=50.73  Aligned_cols=58  Identities=17%  Similarity=0.283  Sum_probs=38.2

Q ss_pred             CCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHH---HHHHHhc-----------------c--c-eeeecCCcCCCC
Q 017477          230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDD---LVHEFCN-----------------E--V-VWMHNNKSTFAK  286 (371)
Q Consensus       230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~---~VqqFC~-----------------E--I-VWMHNNKhtl~K  286 (371)
                      ...+||.||+||.+|.+.|..+=++    -+.-+..   ++.+-|.                 +  | ||+-|-....+|
T Consensus         4 ~~~~rr~R~~ft~~ql~~Le~~F~~----~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr   79 (95)
T 2cuf_A            4 GSSGRGSRFTWRKECLAVMESYFNE----NQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKR   79 (95)
T ss_dssp             SSCCCCCSCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhc----CCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHH
Confidence            3457999999999999998777666    2334433   3333333                 1  2 999998877666


Q ss_pred             CCCCC
Q 017477          287 RDLNG  291 (371)
Q Consensus       287 k~~~~  291 (371)
                      +....
T Consensus        80 ~~~~~   84 (95)
T 2cuf_A           80 RANIA   84 (95)
T ss_dssp             HHHCC
T ss_pred             Hhhcc
Confidence            65433

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

Probab=95.87  E-value=0.0042  Score=44.37  Aligned_cols=46  Identities=20%  Similarity=0.347  Sum_probs=34.3

Q ss_pred             CCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCC
Q 017477          232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNK  281 (371)
Q Consensus       232 ~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNK  281 (371)
                      ++||.||.||.+|.+.+..+-+    +-+..+..+..+.+.++        ||+.|..
T Consensus         1 g~rr~Rt~~t~~q~~~Le~~F~----~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR   54 (58)
T 3rkq_A            1 GRRKPRVLFSQAQVYELERRFK----QQRYLSAPERDQLASVLKLTSTQVKIWFQNRR   54 (58)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHT----TCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CcCCCCCCcCHHHHHHHHHHHH----HcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhh
Confidence            4789999999999998877644    22446666777777666        9998754

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

Probab=95.83  E-value=0.0074  Score=46.13  Aligned_cols=53  Identities=13%  Similarity=0.093  Sum_probs=39.6

Q ss_pred             CCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCCC
Q 017477          233 RKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRDL  289 (371)
Q Consensus       233 KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~~  289 (371)
                      .++.||+||.+|.+.|..+=++    -+..+..+.++.+.++        ||+-|-....+|+..
T Consensus         8 ~~~~R~~ft~~Ql~~Le~~F~~----~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~   68 (76)
T 2dn0_A            8 ASIYKNKKSHEQLSALKGSFCR----NQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKG   68 (76)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHH----SSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCS
T ss_pred             CCCCCccCCHHHHHHHHHHHhc----CCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhcc
Confidence            4667999999999988766554    3456666777777766        999998877666543

>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=95.78  E-value=0.0055  Score=47.95  Aligned_cols=57  Identities=5%  Similarity=0.122  Sum_probs=42.8

Q ss_pred             CCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCC
Q 017477          230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKR  287 (371)
Q Consensus       230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk  287 (371)
                      ...+||-||.||.+|++.|.++-+. -+.=..-++++-++.+.++        ||+-|-....+|+
T Consensus         4 ~~~~rk~R~~~s~~q~~~L~~~f~~-~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~   68 (83)
T 2dmn_A            4 GSSGKKRKGNLPAESVKILRDWMYK-HRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPD   68 (83)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHH-TTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHH-hccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHH
Confidence            3467999999999999999876543 2233557778888888777        9999987665544

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

Probab=95.77  E-value=0.0052  Score=46.26  Aligned_cols=55  Identities=24%  Similarity=0.431  Sum_probs=42.2

Q ss_pred             CCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCCC
Q 017477          231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRDL  289 (371)
Q Consensus       231 ~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~~  289 (371)
                      ..+||-||.||.+|.+.|..+-++-    +..+..+..+.+.++        ||+-|......|+.-
T Consensus         7 ~~~rr~Rt~ft~~q~~~Le~~F~~~----~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r   69 (75)
T 2m0c_A            7 GKKRRNRTTFTSYQLEELEKVFQKT----HYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRER   69 (75)
T ss_dssp             SCCCSCSCSSCHHHHHHHHHHHHHC----SSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhc----CCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHh
Confidence            4578999999999999988766543    346667777777776        999998877666643

>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=95.76  E-value=0.0045  Score=45.92  Aligned_cols=53  Identities=19%  Similarity=0.292  Sum_probs=41.2

Q ss_pred             CCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       232 ~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      .+||-||.||.+|.+.+..+=++    -+..+..+.++.+.++        ||+-|-....+|+.
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~----~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   62 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAA----NPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHH----CSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhc----CCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHHh
Confidence            46999999999999988776665    3567777777777777        99999877665553

>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=95.54  E-value=0.013  Score=44.90  Aligned_cols=53  Identities=9%  Similarity=0.233  Sum_probs=39.2

Q ss_pred             CCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCC
Q 017477          230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAK  286 (371)
Q Consensus       230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~K  286 (371)
                      ...+||-||.||.+|.+.|..+=++    -+.-+..+..+.+.++        ||+-|-....+|
T Consensus         6 ~~~~rr~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr   66 (77)
T 1nk2_P            6 PNKKRKRRVLFTKAQTYELERRFRQ----QRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR   66 (77)
T ss_dssp             SCCCCCCCCCCCHHHHHHHHHHHHH----CSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHhh----cCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhh
Confidence            3457889999999999988766554    3456667777777776        999987655444

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

Probab=95.31  E-value=0.0047  Score=49.37  Aligned_cols=56  Identities=13%  Similarity=0.154  Sum_probs=37.9

Q ss_pred             CCCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          229 SSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       229 ~s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      +....+|.||+||.+|.+.+..+=++    -+..+..+..+.+.++        ||+-|.....+|..
T Consensus        21 ~~~~~~r~Rt~ft~~Ql~~Le~~F~~----~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   84 (96)
T 3nar_A           21 PKSGSTGKICKKTPEQLHMLKSAFVR----TQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGN   84 (96)
T ss_dssp             ------CCSSSSCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTC
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHH----cCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhc
Confidence            34456889999999999998776553    3456667777777666        99999887666543

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

Probab=95.29  E-value=0.017  Score=46.04  Aligned_cols=56  Identities=14%  Similarity=0.286  Sum_probs=42.3

Q ss_pred             CCCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          229 SSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       229 ~s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      ....+||-||.||.+|.+.+..+=++-    +.-+..+..+.+.++        ||+-|-....+|+.
T Consensus        13 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~----~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~   76 (93)
T 3a01_A           13 TPPKRKKPRTSFTRIQVAELEKRFHKQ----KYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQT   76 (93)
T ss_dssp             CCCCCCCCCCCCCHHHHHHHHHHHHHC----SCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCcCCCHHHHHHHHHHHHcC----CCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhh
Confidence            345679999999999999887666553    557777777777777        99999876655543

>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=95.13  E-value=0.0087  Score=43.52  Aligned_cols=45  Identities=18%  Similarity=0.250  Sum_probs=29.5

Q ss_pred             CCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecC
Q 017477          232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNN  280 (371)
Q Consensus       232 ~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNN  280 (371)
                      .+||-||.||.+|.+.|..+-++-    +..+..+.++.+.++        ||+-|-
T Consensus         4 k~rr~Rt~ft~~q~~~Le~~f~~~----~yp~~~~r~~La~~~~l~~~qV~~WFqNr   56 (61)
T 1akh_A            4 KSPKGKSSISPQARAFLEEVFRRK----QSLNSKEKEEVAKKCGITPLQVRVWFINK   56 (61)
T ss_dssp             --------CCHHHHHHHHHHHHHC----SSCCHHHHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhC----CCcCHHHHHHHHHHHCcCHHHHHHHHHHH
Confidence            468999999999999987776654    567778888888777        998774

>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=95.10  E-value=0.0052  Score=47.71  Aligned_cols=53  Identities=17%  Similarity=0.270  Sum_probs=34.4

Q ss_pred             CCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCC
Q 017477          231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKR  287 (371)
Q Consensus       231 ~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk  287 (371)
                      ..+||.||.||.+|.+.|..+=++    -+.-+..+..+.+.++        ||+-|-....+|.
T Consensus        18 ~~~rr~Rt~ft~~Ql~~Le~~F~~----~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   78 (81)
T 1b8i_A           18 GLRRRGRQTYTRYQTLELEKEFHT----NHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE   78 (81)
T ss_dssp             ------CCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCcccCHHHHHHHHHHHhc----CCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhh
Confidence            357999999999999988766554    3456666777776666        9999876654443

>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=95.07  E-value=0.014  Score=45.03  Aligned_cols=51  Identities=29%  Similarity=0.400  Sum_probs=37.1

Q ss_pred             CCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCC
Q 017477          231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFA  285 (371)
Q Consensus       231 ~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~  285 (371)
                      ..+||.||.||.+|.+.|..+=++    -+.-+..+..+.+.++        ||+-|-....+
T Consensus        16 ~~~rr~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~r   74 (81)
T 1fjl_A           16 RKQRRSRTTFSASQLDELERAFER----TQYPDIYTREELAQRTNLTEARIQVWFQNRRARLR   74 (81)
T ss_dssp             -CCCCCCCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHH----cCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhh
Confidence            457899999999999988766554    3456667777777666        99988665433

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

Probab=95.01  E-value=0.0083  Score=43.97  Aligned_cols=52  Identities=17%  Similarity=0.306  Sum_probs=31.7

Q ss_pred             CCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCC
Q 017477          232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKR  287 (371)
Q Consensus       232 ~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk  287 (371)
                      .+||-||.||.+|.+.|..+=++    -+..+..+..+.+.++        ||+-|-....+|+
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~----~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQK----QKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHH----CSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            46899999999999888665543    2345556666666555        9998876655443

>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=95.01  E-value=0.0068  Score=52.68  Aligned_cols=53  Identities=15%  Similarity=0.238  Sum_probs=36.3

Q ss_pred             CCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCC
Q 017477          231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKR  287 (371)
Q Consensus       231 ~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk  287 (371)
                      ..+||.||.||.+|++.|..+-++    -++-+..+..+.+.++        ||+-|.....+|+
T Consensus        99 ~~~rr~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C           99 SRRRKKRTSIETNIRVALEKSFME----NQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCcCccccCHHHHHHHHHHHhh----cCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            467999999999999988766555    3456666777776666        9999987655553

>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=94.98  E-value=0.0095  Score=44.70  Aligned_cols=53  Identities=17%  Similarity=0.240  Sum_probs=37.7

Q ss_pred             CCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       232 ~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      .+||.||.||.+|.+.|..+=++-    +..+..+..+.+.++        ||+-|-.....|+.
T Consensus         1 ~~rr~Rt~ft~~Q~~~Le~~F~~~----~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   61 (68)
T 1ahd_P            1 MRKRGRQTYTRYQTLELEKEFHFN----RYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN   61 (68)
T ss_dssp             CCSCTTCCCCHHHHHHHHHHHHHC----SSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCcCHHHHHHHHHHHccC----CCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhc
Confidence            379999999999999887665543    345555555555555        99999876655544

>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=94.97  E-value=0.0057  Score=44.73  Aligned_cols=47  Identities=21%  Similarity=0.371  Sum_probs=30.2

Q ss_pred             CCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCc
Q 017477          232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKS  282 (371)
Q Consensus       232 ~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKh  282 (371)
                      .+||.||.||.+|.+.|..+=++    -+.-+..+..+.+.++        ||+-|-..
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~   56 (61)
T 2hdd_A            2 AEKRPRTAFSSEQLARLKREFNE----NRYLTERRRQQLSSELGLNEAQIKIWFKNKRA   56 (61)
T ss_dssp             -----CCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHc----cCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcc
Confidence            36999999999999888665553    2455666666666665        89887654

>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=94.95  E-value=0.0048  Score=46.15  Aligned_cols=53  Identities=25%  Similarity=0.401  Sum_probs=34.6

Q ss_pred             CCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       232 ~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      .+||.||.||.+|.+.|..+=++    -+..+..+..+.+.++        ||+-|-.....|+.
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~   62 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQR----NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE   62 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTT----CSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHc----cCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHh
Confidence            47999999999999988665443    2233333444444444        99988766554443

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

Probab=94.95  E-value=0.014  Score=42.93  Aligned_cols=49  Identities=16%  Similarity=0.208  Sum_probs=32.9

Q ss_pred             CCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCC
Q 017477          232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTF  284 (371)
Q Consensus       232 ~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl  284 (371)
                      ++||-||.||.+|.+.|..+=++    -+..+..+..+.+.++        ||+-|-....
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~   58 (63)
T 2h1k_A            2 SNKRTRTAYTRAQLLELEKEFLF----NKYISRPRRVELAVMLNLTERHIKIWFQNRRMKW   58 (63)
T ss_dssp             ---CCCCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCHHHHHHHHHHHhc----CCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhh
Confidence            46899999999999888665553    2445666666666666        8988765433

>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=94.81  E-value=0.011  Score=50.69  Aligned_cols=52  Identities=21%  Similarity=0.435  Sum_probs=38.8

Q ss_pred             CCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCC
Q 017477          230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFA  285 (371)
Q Consensus       230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~  285 (371)
                      ...+||.||.||.+|++.+..+=++    -++-+..+..+.+.++        ||+-|.....+
T Consensus        90 ~~~~rr~Rt~ft~~q~~~Le~~F~~----~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~K  149 (151)
T 3d1n_I           90 PSKKRKRRTSFTPQAIEALNAYFEK----NPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLK  149 (151)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCcccCHHHHHHHHHHHHh----cCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccC
Confidence            3467889999999999988766655    3456677777777766        99988765443

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

Probab=94.80  E-value=0.019  Score=41.27  Aligned_cols=44  Identities=20%  Similarity=0.298  Sum_probs=33.6

Q ss_pred             CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCC
Q 017477          234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNK  281 (371)
Q Consensus       234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNK  281 (371)
                      ||.||.||.+|.+.|..+=++    -+.-+..+..+.+.++        ||+-|-.
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR   52 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQ----KQYLSIAERAEFSSSLSLTETQVKIWFQNRR   52 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHH----CSCCCHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhc----CCCcCHHHHHHHHHHHCcCHHHhhhhhhHhh
Confidence            688999999999988766554    3456777777777777        8987754

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

Probab=94.65  E-value=0.014  Score=43.68  Aligned_cols=50  Identities=16%  Similarity=0.291  Sum_probs=35.4

Q ss_pred             CCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCC
Q 017477          233 RKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAK  286 (371)
Q Consensus       233 KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~K  286 (371)
                      +||.||.||.+|.+.|..+-++    -+..+..+..+.+.++        ||+-|-....+|
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk   59 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQ----GRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKI   59 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTT----CSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCcCHHHHHHHHHHHhc----CCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHH
Confidence            5899999999999888655433    3455666666666666        999887654433

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

Probab=94.55  E-value=0.02  Score=41.59  Aligned_cols=45  Identities=20%  Similarity=0.371  Sum_probs=32.3

Q ss_pred             CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCc
Q 017477          234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKS  282 (371)
Q Consensus       234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKh  282 (371)
                      ||.||.||.+|.+.+..+=++    -+.-+..+..+.+.++        ||+-|-..
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~   54 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEFYK----ENYVSRPRRCELAAQLNLPESTIKVWFQNRRM   54 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHH----CSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHH----cCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHh
Confidence            789999999999888765554    2455666666666666        89887543

>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=94.43  E-value=0.038  Score=41.64  Aligned_cols=56  Identities=11%  Similarity=0.139  Sum_probs=40.6

Q ss_pred             CCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCC
Q 017477          231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKR  287 (371)
Q Consensus       231 ~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk  287 (371)
                      ..+||.||.||.+|.+.|..+-++- +.-..-+.++.++.+.++        ||+-|-....+|+
T Consensus         5 ~~~rr~R~~~~~~q~~~Le~~f~~~-~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~   68 (73)
T 1x2n_A            5 SSGKNKRGVLPKHATNVMRSWLFQH-IGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQS   68 (73)
T ss_dssp             SSSCCSSCCCCHHHHHHHHHHHHHT-TTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHh-CCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhcccc
Confidence            4578999999999999987765541 233456777778887777        9998876544443

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

Probab=94.36  E-value=0.026  Score=42.83  Aligned_cols=52  Identities=12%  Similarity=0.174  Sum_probs=39.1

Q ss_pred             CCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCC
Q 017477          232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKR  287 (371)
Q Consensus       232 ~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk  287 (371)
                      .+||.||.||.+|.+.|..+=++    -+..+..+..+.+.++        ||+-|-....+|.
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   65 (73)
T 2l7z_A            6 EGRKKRVPYTKVQLKELEREYAT----NKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKV   65 (73)
T ss_dssp             CCCCCCCCSCHHHHHHHHHHHHH----TSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhh----CCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHH
Confidence            46899999999999988766555    3456677777777666        9999987655554

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

Probab=94.28  E-value=0.031  Score=41.05  Aligned_cols=54  Identities=11%  Similarity=0.196  Sum_probs=39.8

Q ss_pred             CCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCC
Q 017477          232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAK  286 (371)
Q Consensus       232 ~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~K  286 (371)
                      ..||-||.||.+|.+.|..+-.. ...-+.-+.++.++.+.++        ||+-|-.....|
T Consensus         2 ~~rr~R~~ft~~q~~~Le~~f~~-~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A            2 SGHIEGRHMNKQATEILNEYFYS-HLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             CCCCCCCSSTTTHHHHHHHHHHH-TTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHH-cccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            35889999999999998876521 1234567778888888877        999887765544

>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=94.14  E-value=0.047  Score=41.72  Aligned_cols=48  Identities=13%  Similarity=0.151  Sum_probs=34.7

Q ss_pred             CCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCc
Q 017477          231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKS  282 (371)
Q Consensus       231 ~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKh  282 (371)
                      ..+||.||.||.+|.+.|..+=++    -+.-+..+..+.+.++        ||+-|-..
T Consensus        11 ~~~rr~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~   66 (77)
T 1puf_A           11 RSTRKKRCPYTKHQTLELEKEFLF----NMYLTRDRRYEVARLLNLTERQVKIWFQNRRM   66 (77)
T ss_dssp             CTTSCCCCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhc----cCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            456899999999999888665543    3456666666666665        99888654

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

Probab=94.09  E-value=0.012  Score=43.77  Aligned_cols=51  Identities=20%  Similarity=0.399  Sum_probs=38.5

Q ss_pred             CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      ||-||.||.+|.+.+..+=++    -+..+..+.++.+.++        ||+-|-....+|+.
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~----~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~   60 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRV----NCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSH   60 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTT----CSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSC
T ss_pred             cCCCCCCCHHHHHHHHHHHHh----cCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhc
Confidence            789999999999888766543    4456777777777776        99999876655544

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

Probab=94.07  E-value=0.029  Score=41.93  Aligned_cols=52  Identities=15%  Similarity=0.275  Sum_probs=37.2

Q ss_pred             CCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCC
Q 017477          232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKR  287 (371)
Q Consensus       232 ~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk  287 (371)
                      .+||-||.||.+|.+.+..+=++    -+..+..+..+.+.++        ||+-|-....+|.
T Consensus         1 ~~rr~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~   60 (68)
T 1ftt_A            1 MRRKRRVLFSQAQVYELERRFKQ----QKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ   60 (68)
T ss_dssp             CCSSSCSSCCHHHHHHHHHHHHH----SSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCccCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhh
Confidence            36899999999999888666553    2345666666666666        9999876555444

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

Probab=94.06  E-value=0.011  Score=46.24  Aligned_cols=52  Identities=19%  Similarity=0.288  Sum_probs=33.9

Q ss_pred             CCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCC
Q 017477          231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAK  286 (371)
Q Consensus       231 ~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~K  286 (371)
                      ..+||.||.||.+|.+.|..+=+    +-+.-+..+..+.+.++        ||+-|-....+|
T Consensus        26 ~~~rr~Rt~ft~~Ql~~Le~~F~----~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk   85 (88)
T 2r5y_A           26 GETKRQRTSYTRYQTLELEKEFH----FNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK   85 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHT----TCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCcCHHHHHHHHHHHh----ccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHh
Confidence            34699999999999988865544    23456666677776666        999887654444

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

Probab=93.99  E-value=0.02  Score=49.46  Aligned_cols=54  Identities=11%  Similarity=0.195  Sum_probs=37.6

Q ss_pred             CCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       231 ~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      ..+||.||.||.+|++.+..+-++-    +.-+..+.++.+.++        ||+-|-....+|..
T Consensus        95 ~~~rr~Rt~ft~~q~~~Le~~F~~~----~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~  156 (164)
T 2d5v_A           95 NTPKKPRLVFTDVQRRTLHAIFKEN----KRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKW  156 (164)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHHC----SSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC-
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHhcC----CCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccC
Confidence            4569999999999999887666554    567777777777766        99999887655554

>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=93.67  E-value=0.025  Score=48.63  Aligned_cols=54  Identities=17%  Similarity=0.295  Sum_probs=34.4

Q ss_pred             CCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCC
Q 017477          230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKR  287 (371)
Q Consensus       230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk  287 (371)
                      ...+||-||.||.+|++.+..+=++    -++-+..+..+.+.++        ||+-|.....+|+
T Consensus        84 ~~~~rr~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           84 NERKRKRRTTISIAAKDALERHFGE----HSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCcCccHHHHHHHHHHHHH----cCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            3457889999999999887655444    3345555555555555        9999987655554

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

Probab=93.57  E-value=0.019  Score=50.37  Aligned_cols=55  Identities=15%  Similarity=0.271  Sum_probs=33.0

Q ss_pred             CCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      ...+||.||.||.+|++.|..+=++    -++-+..+..+.+.++        ||+-|.....+|+.
T Consensus        96 ~~~~rr~Rt~ft~~Ql~~LE~~F~~----~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~  158 (164)
T 2xsd_C           96 QGRKRKKRTSIEVGVKGALESHFLK----CPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMT  158 (164)
T ss_dssp             ----------CCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSC
T ss_pred             cccCCCCceeccHHHHHHHHHHHhc----CCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhcc
Confidence            3467889999999999988666554    3456666666666666        99999887666655

>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=93.51  E-value=0.059  Score=41.12  Aligned_cols=52  Identities=8%  Similarity=0.075  Sum_probs=38.1

Q ss_pred             CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCCC
Q 017477          234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRDL  289 (371)
Q Consensus       234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~~  289 (371)
                      .+.|++||.+|.+.+..+=++    -+.-+..+..+.+.++        ||+-|-....+|+..
T Consensus         8 ~~kr~~~t~~Ql~~Le~~F~~----~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (75)
T 2da5_A            8 PTKYKERAPEQLRALESSFAQ----NPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEET   67 (75)
T ss_dssp             SCCCCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSC
T ss_pred             CCCCccCCHHHHHHHHHHHhc----cCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhh
Confidence            345678999999888766555    3456777777777776        999998877666653

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

Probab=93.47  E-value=0.051  Score=40.92  Aligned_cols=52  Identities=12%  Similarity=0.096  Sum_probs=39.9

Q ss_pred             CCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          233 RKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       233 KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      .++-||.||.+|.+.+..+=++    -+..+..+.++.+.++        ||+-|.....+|+.
T Consensus         6 ~~~~Rt~ft~~Ql~~Le~~F~~----~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   65 (74)
T 2ly9_A            6 SFGIRAKKTKEQLAELKVSYLK----NQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSK   65 (74)
T ss_dssp             CCCTTCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTT
T ss_pred             CCCCCcCCCHHHHHHHHHHHHH----cCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhC
Confidence            3789999999999998776554    2456677777777776        99999887666654

>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=93.42  E-value=0.046  Score=42.40  Aligned_cols=55  Identities=16%  Similarity=0.294  Sum_probs=40.4

Q ss_pred             CCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          233 RKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       233 KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      .||.||.||.+|++.|..+-. ...+-+.-+.++.++.+.++        ||+-|-....+|+.
T Consensus         1 ~rr~R~~ft~~q~~~Le~~f~-~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~   63 (87)
T 1b72_B            1 ARRKRRNFNKQATEILNEYFY-SHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (87)
T ss_dssp             --CCCCCCCHHHHHHHHHHHH-TTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCG
T ss_pred             CCCCCCCCCHHHHHHHHHHHH-HhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhcc
Confidence            379999999999999887652 12244567888888888887        99999876655543

>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=93.23  E-value=0.03  Score=44.66  Aligned_cols=53  Identities=19%  Similarity=0.266  Sum_probs=34.0

Q ss_pred             CCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCC
Q 017477          231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKR  287 (371)
Q Consensus       231 ~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk  287 (371)
                      ..+||.||.||.+|.+.+..+=++    -+.-+..+..+.+.++        ||+-|-....+|+
T Consensus        32 ~~~rr~Rt~ft~~Ql~~Le~~F~~----~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   92 (97)
T 1b72_A           32 GSPSGLRTNFTTRQLTELEKEFHF----NKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKR   92 (97)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTT----CSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCcCHHHHHHHHHHHhc----cCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHH
Confidence            457899999999999887655443    3456666666666666        9998876554443

>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=92.34  E-value=0.094  Score=39.44  Aligned_cols=55  Identities=16%  Similarity=0.299  Sum_probs=40.5

Q ss_pred             CCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          233 RKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       233 KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      .||.||.||.+|++.|..+-.. ..+-+.-+.++.++.+.++        ||+-|-.....|+.
T Consensus         1 ~rr~R~~ft~~q~~~Le~~f~~-~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~   63 (73)
T 1puf_B            1 ARRKRRNFNKQATEILNEYFYS-HLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHH-TTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCcCCHHHHHHHHHHHHH-hccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccccc
Confidence            3799999999999998776521 1234567778888888877        99998776554443

>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=92.24  E-value=0.084  Score=41.63  Aligned_cols=53  Identities=9%  Similarity=0.092  Sum_probs=42.4

Q ss_pred             ccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCCCCC
Q 017477          235 RFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRDLNG  291 (371)
Q Consensus       235 RFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~~~~  291 (371)
                      +-|+|||.||.+.|...=++    =+..+.++.++...++        ||+-|.....+|....-
T Consensus         5 ~~r~kfT~~Ql~~Le~~F~~----~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~l~w   65 (76)
T 2ecc_A            5 SSGKRKTKEQLAILKSFFLQ----CQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLKW   65 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCCSS
T ss_pred             CCCCCCCHHHHHHHHHHHHH----CCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHHHHH
Confidence            45678999999999876663    3789999999999888        99999887776665543

>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=92.06  E-value=0.11  Score=40.52  Aligned_cols=49  Identities=8%  Similarity=0.192  Sum_probs=36.3

Q ss_pred             CCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCC
Q 017477          232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNK  281 (371)
Q Consensus       232 ~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNK  281 (371)
                      .++|-||.||.+|++.|..+-++ .|.-+.-+..+.++.+.++        ||+-|-.
T Consensus        26 ~~~k~r~~ft~~q~~~Le~~f~~-~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR   82 (87)
T 1mnm_C           26 TKPYRGHRFTKENVRILESWFAK-NIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR   82 (87)
T ss_dssp             SSCCTTCCCCHHHHHHHHHHHHH-TTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHH-hCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence            45666999999999998766542 3334567788888888877        9987753

>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=90.93  E-value=0.034  Score=48.15  Aligned_cols=50  Identities=22%  Similarity=0.286  Sum_probs=36.3

Q ss_pred             CCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCC
Q 017477          231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTF  284 (371)
Q Consensus       231 ~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl  284 (371)
                      ..+||.||.||.+|++.+..+-+    +-+..+..+..+.+.++        ||+-|.....
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~----~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~  151 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFL----KSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKG  151 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTT----TCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCcccCHHHHHHHHHHHc----cCCCCCHHHHHHHHHHcCCChhheeeccccccccc
Confidence            46789999999999998865432    23445666777777666        9999876543

>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=89.86  E-value=0.09  Score=43.70  Aligned_cols=58  Identities=26%  Similarity=0.440  Sum_probs=37.7

Q ss_pred             CCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhc-------------------------cc-eeeecCCcC
Q 017477          230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCN-------------------------EV-VWMHNNKST  283 (371)
Q Consensus       230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~-------------------------EI-VWMHNNKht  283 (371)
                      +..+||-||+||.+|...|..+=++-= ...+.+-+++.+-|+                         .| ||+-|-+..
T Consensus         3 ~~~~Rr~Rt~ft~~ql~~Le~~F~~~~-yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k   81 (102)
T 2da6_A            3 SGSSGRNRFKWGPASQQILYQAYDRQK-NPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKE   81 (102)
T ss_dssp             TCCSCCCCCCCCHHHHHHHHHHHTTCS-SCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHcCCC-CCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHH
Confidence            456899999999999998865543322 222223345555663                         12 999998876


Q ss_pred             CCCCC
Q 017477          284 FAKRD  288 (371)
Q Consensus       284 l~Kk~  288 (371)
                      .+++.
T Consensus        82 ~kr~~   86 (102)
T 2da6_A           82 EAFRQ   86 (102)
T ss_dssp             HHHHH
T ss_pred             HHHhh
Confidence            66554

>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=89.48  E-value=0.43  Score=37.65  Aligned_cols=47  Identities=9%  Similarity=0.078  Sum_probs=34.0

Q ss_pred             cCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       238 TKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      .+||.+|.+.|..+=++-    +..+..+.++.+.++        ||+-|-.....++.
T Consensus        18 k~~t~~Ql~~Le~~F~~~----~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~   72 (89)
T 2dmp_A           18 KEKTQGQVKILEDSFLKS----SFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSME   72 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHC----SSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSC
T ss_pred             ccCCHHHHHHHHHHHccC----CCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHh
Confidence            459999998887665553    456777777777776        99999876554444

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

Probab=89.35  E-value=0.094  Score=38.02  Aligned_cols=46  Identities=22%  Similarity=0.339  Sum_probs=31.0

Q ss_pred             ccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCC
Q 017477          237 RTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAK  286 (371)
Q Consensus       237 RTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~K  286 (371)
                      ||.||.+|.+.|..+=++    -+.-+..+.++.+.++        ||+-|-....+|
T Consensus         3 Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk   56 (60)
T 3a02_A            3 HMTFTSFQLEELEKAFSR----THYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK   56 (60)
T ss_dssp             --CCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC-
T ss_pred             CcccCHHHHHHHHHHHHc----CCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHh
Confidence            799999999988766554    2346666677777666        999887655444

>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=86.76  E-value=0.42  Score=37.02  Aligned_cols=54  Identities=6%  Similarity=0.119  Sum_probs=37.8

Q ss_pred             CCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCC
Q 017477          233 RKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKR  287 (371)
Q Consensus       233 KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk  287 (371)
                      |++-||.||.+|.+.|..+-++ .+.-..-+..+.++.+.++        ||+-|-.....|.
T Consensus         2 K~krr~rft~~q~~~Le~~f~~-h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~   63 (83)
T 1le8_B            2 KPYRGHRFTKENVRILESWFAK-NIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTI   63 (83)
T ss_dssp             ---CCCCCCHHHHHHHHHHHHH-TSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCCCHHHHHHHHHHHHh-hCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHcccccc
Confidence            4556777999999998776553 2334567788888888877        9999987655444

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

Probab=86.33  E-value=0.24  Score=40.40  Aligned_cols=54  Identities=26%  Similarity=0.431  Sum_probs=30.8

Q ss_pred             CCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHH---HHHHHhcc--------------------c------eeeecCC
Q 017477          231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDD---LVHEFCNE--------------------V------VWMHNNK  281 (371)
Q Consensus       231 ~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~---~VqqFC~E--------------------I------VWMHNNK  281 (371)
                      ..+||.||.||.+|.+.+..+=++    -+.-|..   ++.+-|++                    |      ||+-|-.
T Consensus         7 ~k~rr~Rt~ft~~Ql~~LE~~F~~----~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR   82 (99)
T 1lfb_A            7 KKGRRNRFKWGPASQQILFQAYER----QKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRR   82 (99)
T ss_dssp             ------CCCCCHHHHHHHHHHHTT----CSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCcCcCHHHHHHHHHHHhc----CCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHH
Confidence            357999999999999888654433    3344443   33334331                    4      9999987


Q ss_pred             cCCCCCC
Q 017477          282 STFAKRD  288 (371)
Q Consensus       282 htl~Kk~  288 (371)
                      ...++|.
T Consensus        83 ~k~k~k~   89 (99)
T 1lfb_A           83 KEEAFRH   89 (99)
T ss_dssp             HTTSCCC
T ss_pred             HHHHHhc
Confidence            7665554

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

Probab=86.27  E-value=0.2  Score=46.65  Aligned_cols=42  Identities=19%  Similarity=0.316  Sum_probs=26.8

Q ss_pred             CCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhc
Q 017477          230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCN  272 (371)
Q Consensus       230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~  272 (371)
                      ...+||.||+||.+|...|..+=++--+ ..+..-+++.+-|+
T Consensus       139 ~~k~RR~R~~ft~~ql~~Le~~F~~~~Y-P~~~~ReeLA~~~n  180 (221)
T 2h8r_A          139 NKKMRRNRFKWGPASQQILYQAYDRQKN-PSKEEREALVEECN  180 (221)
T ss_dssp             ---CCCCCCCCCHHHHHHHHHHHHHCSS-CCHHHHHHHHHHHH
T ss_pred             cCCCCCCCcCCCHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHC
Confidence            3457999999999999999887765111 11112256677776

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

Probab=85.36  E-value=0.23  Score=37.49  Aligned_cols=52  Identities=12%  Similarity=0.160  Sum_probs=37.9

Q ss_pred             CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      ++-||.||.+|.+.|..+=++.   -+.-+..+..+.+.++        ||+-|......|+.
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~---~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~   62 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKV---NKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   62 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHT---TSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHhc---CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhc
Confidence            4668999999999887665431   2346667777777776        99999887666554

>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=84.77  E-value=0.61  Score=33.55  Aligned_cols=44  Identities=9%  Similarity=0.244  Sum_probs=33.2

Q ss_pred             ccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCC
Q 017477          237 RTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNK  281 (371)
Q Consensus       237 RTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNK  281 (371)
                      ||.||.+|.+.|..+-++ .+.-..-+.++.++.+.++        ||+-|-.
T Consensus         2 r~~ft~~q~~~Le~~f~~-~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR   53 (60)
T 1k61_A            2 GHRFTKENVRILESWFAK-NIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR   53 (60)
T ss_dssp             CCSCCHHHHHHHHHHHHH-TTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_pred             cCcCCHHHHHHHHHHHHH-cCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence            799999999998776653 2224567778888888877        9988754

>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=83.93  E-value=0.5  Score=42.82  Aligned_cols=41  Identities=22%  Similarity=0.319  Sum_probs=25.2

Q ss_pred             CCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhc
Q 017477          231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCN  272 (371)
Q Consensus       231 ~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~  272 (371)
                      ..+||.||+||.+|.+.|..+=++--+==.... +++.+-|+
T Consensus       113 ~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~R-e~la~~~~  153 (194)
T 1ic8_A          113 KKGRRNRFKWGPASQQILFQAYERQKNPSKEER-ETLVEECN  153 (194)
T ss_dssp             ----CCCCCCCHHHHHHHHHHHHHHCCCCTTTT-HHHHHHHH
T ss_pred             ccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHH-HHHHHHhC
Confidence            456899999999999999877777554322223 34444454

>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=83.38  E-value=0.32  Score=36.44  Aligned_cols=52  Identities=12%  Similarity=0.182  Sum_probs=38.0

Q ss_pred             CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      .|-||.||.+|.+.|..+-++.   -+..+..+.++.+.++        ||+-|-....+|+.
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~---~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~   61 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKV---NKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSS---CSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHcc---CCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhc
Confidence            3568999999999887765431   2456677777777777        99999887666654

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

Probab=80.42  E-value=1.9  Score=34.53  Aligned_cols=50  Identities=12%  Similarity=0.227  Sum_probs=35.2

Q ss_pred             CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      ++|| +||.+|.+.+...=++    =+.-+..+..+...++        ||+-|......|+.
T Consensus        13 ~k~k-~~t~~Ql~~Le~~F~~----~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~   70 (89)
T 2ecb_A           13 QKFK-EKTAEQLRVLQASFLN----SSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE   70 (89)
T ss_dssp             CCCC-CCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCC
T ss_pred             hhhc-cCCHHHHHHHHHHHHh----cCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHH
Confidence            4555 9999998887544333    3457777778877776        99999876555543

---

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	371
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	1e-09

>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 = 52.3 bits (125), Expect = 1e-09
 Identities = 36/72 (50%), Positives = 44/72 (61%), Gaps = 8/72 (11%)

Query: 224 SNSGGSSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------V 275
           SN   S G  KRFRTKF+  QKEKM  FAER+GW++QK DD  V +FC E         +
Sbjct: 8   SNPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKI 67

Query: 276 WMHNNKSTFAKR 287
           WMHNNK++    
Sbjct: 68  WMHNNKNSGPSS 79

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	371
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.57
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	97.9
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	97.03
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	96.76
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	96.76
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	96.44
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	96.07
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	95.9
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	95.65
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	95.59
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	95.5
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	95.42
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	95.41
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	95.34
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	95.25
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	95.02
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	94.85
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	94.66
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	94.23
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	93.96
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	93.88
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	93.78
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	93.2
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	92.22
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	91.13
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	87.3
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	86.47
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	81.12

>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=99.57  E-value=1e-15  Score=119.60  Aligned_cols=58  Identities=59%  Similarity=1.041  Sum_probs=53.8

Q ss_pred             CCCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCC
Q 017477          229 SSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAK  286 (371)
Q Consensus       229 ~s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~K  286 (371)
                      ....+||.||.||.||++.|.+|.|+++|+.++.|+++++++|.+|        |||+|++++.++
T Consensus        13 ~~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          13 SGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            3456799999999999999999999999999999999999999999        999999987665

>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=97.90  E-value=2.7e-06  Score=63.83  Aligned_cols=54  Identities=20%  Similarity=0.324  Sum_probs=44.0

Q ss_pred             CCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCC
Q 017477          231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKR  287 (371)
Q Consensus       231 ~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk  287 (371)
                      ++.||.||+||.||++.|.++-+++.+   .-+.++.++.+.++        ||++|.+...+|.
T Consensus         5 ~~~~r~R~~~t~~Q~~~Le~~F~~~~~---~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk~   66 (71)
T d1wi3a_           5 SSGPRSRTKISLEALGILQSFIHDVGL---YPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS   66 (71)
T ss_dssp             CCCCCCCCCCCSHHHHHHHHHHHHHCS---CCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCSS
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHHhcC---CCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhccc
Confidence            345899999999999999987766544   46778888888888        9999999876654

>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=97.03  E-value=0.00033  Score=53.25  Aligned_cols=55  Identities=9%  Similarity=0.227  Sum_probs=44.2

Q ss_pred             CCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      ...+||-||.||.+|++.|..+=+.    =+.-+....++.+.++        ||+.|-....+|+.
T Consensus         6 p~k~rr~Rt~ft~~Q~~~Le~~F~~----~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   68 (77)
T d1vnda_           6 PNKKRKRRVLFTKAQTYELERRFRQ----QRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ   68 (77)
T ss_dssp             SSSSCSSCCCCCTTHHHHHHHHHHH----CSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHH----CCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHh
Confidence            3467889999999999999887665    3457788888888888        99999887666554

>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=96.76  E-value=0.00032  Score=52.10  Aligned_cols=52  Identities=19%  Similarity=0.283  Sum_probs=41.8

Q ss_pred             CCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCC
Q 017477          231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAK  286 (371)
Q Consensus       231 ~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~K  286 (371)
                      ..+||.||.||.+|++.+..+=++    =..-+.++.++.+.++        ||+.|-....+|
T Consensus         6 ~~~rr~Rt~~t~~q~~~Le~~F~~----n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk   65 (67)
T d1ocpa_           6 QARKRKRTSIENRVRWSLETMFLK----CPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR   65 (67)
T ss_dssp             CCSSSCCSSCCHHHHHHHHHHHSS----CSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSS
T ss_pred             hccCCCCCCCCHHHHHHHHHHHHH----ccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhc
Confidence            357899999999999999877653    3457778888888888        999998776554

>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=96.76  E-value=0.00027  Score=52.21  Aligned_cols=53  Identities=19%  Similarity=0.292  Sum_probs=43.3

Q ss_pred             CCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       232 ~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      .+||.||.||.||++.|.++=+.-    ..-+.++.++.+.++        ||+.|-....+|+.
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n----~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~~   62 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAAN----PRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHC----SCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHC----CCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHHH
Confidence            469999999999999998877643    347788888999888        99999887665554

>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=96.44  E-value=0.00068  Score=49.76  Aligned_cols=50  Identities=30%  Similarity=0.414  Sum_probs=38.8

Q ss_pred             CCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCC
Q 017477          232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFA  285 (371)
Q Consensus       232 ~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~  285 (371)
                      .+||.||.||.+|++.|.+.=+.    =..-+..+.++.+.++        ||+.|.....+
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~----n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~k   58 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFER----TQYPDIYTREELAQRTNLTEARIQVWFQNRRARLR   58 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHH----cCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHH
Confidence            36999999999999999876553    2467777888888877        99999765433

>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=96.07  E-value=0.0013  Score=47.43  Aligned_cols=47  Identities=13%  Similarity=0.208  Sum_probs=37.1

Q ss_pred             CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCC
Q 017477          234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTF  284 (371)
Q Consensus       234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl  284 (371)
                      ||-||.||.+|.+.|.++=+.    -..-+.++.++.+.++        ||+.|-....
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~   56 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAA----NKFITKDKRRKISAATSLSERQITIWFQNRRVKE   56 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCHHHHHHHHHHHhh----cCCCCHHHHHHHHHHcCCCHHHeeecccchhhhc
Confidence            677999999999998775554    3567788888888888        9999976543

>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=95.90  E-value=0.0023  Score=47.33  Aligned_cols=53  Identities=15%  Similarity=0.268  Sum_probs=40.9

Q ss_pred             CCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       232 ~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      .|||-||.||.+|++-|.++=+.    =..-+....++.+.++        ||+.|.....+|..
T Consensus         1 ~krr~Rt~ft~~Ql~~Le~~F~~----~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~   61 (68)
T d1ftta_           1 MRRKRRVLFSQAQVYELERRFKQ----QKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA   61 (68)
T ss_dssp             CCSSSCSSCCHHHHHHHHHHHHH----SSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHH----CCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhcc
Confidence            37999999999999998876553    3456777777777777        99999877665543

>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=95.65  E-value=0.00098  Score=47.74  Aligned_cols=46  Identities=20%  Similarity=0.312  Sum_probs=36.3

Q ss_pred             ccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCC
Q 017477          235 RFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTF  284 (371)
Q Consensus       235 RFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl  284 (371)
                      |.||.||++|++.|..+=++-    ..-+..+.++-+.++        ||+.|..-..
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~----~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~   54 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKE----NYVSRPRRCELAAQLNLPESTIKVWFQNRRMKD   54 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHC----SCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHC----CCCCHHHHHHHHHHhCCChhHhhhcchhhhhhh
Confidence            789999999999998776643    336777888888887        9999976433

>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=95.59  E-value=0.0013  Score=47.14  Aligned_cols=46  Identities=20%  Similarity=0.294  Sum_probs=36.8

Q ss_pred             CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcC
Q 017477          234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKST  283 (371)
Q Consensus       234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKht  283 (371)
                      ||-||.||++|++.|..+=++    =..-+.+..++.+.++        ||+.|....
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~----~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k   54 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQ----KQYLSIAERAEFSSSLSLTETQVKIWFQNRRAK   54 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHH----CSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHH----CCCCCHHHHHHHHHHhCCChhheeecCcchHhH
Confidence            678999999999999876664    3556778888888887        999986543

>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=95.50  E-value=0.0025  Score=49.45  Aligned_cols=52  Identities=17%  Similarity=0.240  Sum_probs=36.0

Q ss_pred             CCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCC
Q 017477          231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAK  286 (371)
Q Consensus       231 ~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~K  286 (371)
                      ..+||.||.||.+|.+.|.++=+    +=..-+.++.++.+.++        ||+.|.....+|
T Consensus        25 ~~~kr~Rt~ft~~Ql~~Le~~F~----~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk   84 (88)
T d1b72a_          25 GSPSGLRTNFTTRQLTELEKEFH----FNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK   84 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHT----TCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCCCHHHHHHHHHHHH----hCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHH
Confidence            34689999999999998876554    23456777888888877        999987654443

>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=95.42  E-value=0.0052  Score=46.51  Aligned_cols=50  Identities=12%  Similarity=0.156  Sum_probs=36.2

Q ss_pred             CCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCC
Q 017477          231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTF  284 (371)
Q Consensus       231 ~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl  284 (371)
                      ..+||.||.||++|.+-+..+=+.    =..-+....++.+.+|        ||+.|-...+
T Consensus        11 ~~~rr~Rt~ft~~Ql~~Le~~F~~----~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~   68 (77)
T d1pufa_          11 RSTRKKRCPYTKHQTLELEKEFLF----NMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKM   68 (77)
T ss_dssp             CTTSCCCCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCCCHHHHHHHHHHHHH----CCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHH
Confidence            456899999999999988876664    2356666666666666        9999865433

>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=95.41  E-value=0.0041  Score=43.71  Aligned_cols=42  Identities=21%  Similarity=0.348  Sum_probs=34.3

Q ss_pred             ccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecC
Q 017477          235 RFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNN  280 (371)
Q Consensus       235 RFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNN  280 (371)
                      |.||.||.+|.+.|.++=++    -+.-+.++.++.+.++        ||+.|.
T Consensus         1 R~Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~LA~~lgL~~~qV~vWFqNr   50 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREFNE----NRYLTERRRQQLSSELGLNEAQIKIWFQNA   50 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHHH----CCCCCHHHHHHHHHHhCCChHHhhhccccc
Confidence            67999999999999876654    3467778888888888        999884

>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=95.34  E-value=0.0041  Score=44.33  Aligned_cols=44  Identities=16%  Similarity=0.219  Sum_probs=35.0

Q ss_pred             CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCC
Q 017477          234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNK  281 (371)
Q Consensus       234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNK  281 (371)
                      ||-||.||.+|.+.|..+=++-    ..-+.++.++.+.++        ||+.|-.
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~~n----~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR   52 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFETQ----KYLSPPERKRLAKMLQLSERQVKTWFQNRR   52 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHC----SSCCHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHhC----CCCCHHHHHHHHHHhCCCHHHhhHhhhhhh
Confidence            7889999999999998776642    346777888888877        9998854

>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=95.25  E-value=0.0016  Score=46.80  Aligned_cols=45  Identities=24%  Similarity=0.357  Sum_probs=33.5

Q ss_pred             CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCc
Q 017477          234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKS  282 (371)
Q Consensus       234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKh  282 (371)
                      ||.||.||.||++.|.++=++    -..-+..+.++.+.++        ||+.|..-
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~----~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~   54 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQR----NRYPDMSTREEIAVWTNLTEARVRVWFKNRRA   54 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHTT----CSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHH----cCCCChHHHHHHHHHHCCChHHHHHHhHHHHH
Confidence            789999999999999876543    3445666666666666        99988653

>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=95.02  E-value=0.0041  Score=45.86  Aligned_cols=45  Identities=29%  Similarity=0.403  Sum_probs=36.1

Q ss_pred             CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCc
Q 017477          234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKS  282 (371)
Q Consensus       234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKh  282 (371)
                      ||-||.||.+|.+.+.++=++-    +.-+....++...++        ||+.|..-
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n----~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~   54 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERT----HYPDVFARERLAAKIDLPEARIQVWFSNRRA   54 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTC----SSCCHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHc----CCCCHHHHHHHHHHhCcChhheeecCcchhH
Confidence            6789999999999988766543    667778888888877        89988654

>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=94.85  E-value=0.0046  Score=44.23  Aligned_cols=48  Identities=19%  Similarity=0.314  Sum_probs=39.1

Q ss_pred             ccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCC
Q 017477          235 RFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAK  286 (371)
Q Consensus       235 RFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~K  286 (371)
                      |-||.||.+|++-|..+=++    =+.-+.+++++.+.++        ||+.|-....+|
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~----~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr   56 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGE----HSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR   56 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCHHHHHHHHHHHHH----ccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHh
Confidence            56999999999999876665    4678889999999998        999997654443

>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=94.66  E-value=0.0061  Score=42.06  Aligned_cols=40  Identities=13%  Similarity=0.296  Sum_probs=32.9

Q ss_pred             ccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecC
Q 017477          237 RTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNN  280 (371)
Q Consensus       237 RTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNN  280 (371)
                      ||.||.+|++.|.++=+    +=..-|.++.++.+.++        ||+.|-
T Consensus         2 Rt~ft~~Q~~~Le~~F~----~n~~P~~~~~~~LA~~l~l~~~~V~~WFqNr   49 (50)
T d1s7ea1           2 RLVFTDVQRRTLHAIFK----ENKRPSKELQITISQQLGLELSTVSNFFMNA   49 (50)
T ss_dssp             CSCCCHHHHHHHHHHTT----SSCSSTHHHHHHHHTTSCSSSHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHH----HCCCCCHHHHHHHHHHHCcCHHHhhhcCCcC
Confidence            89999999999987433    33567888999999998        999885

>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=94.23  E-value=0.0083  Score=44.03  Aligned_cols=49  Identities=16%  Similarity=0.303  Sum_probs=34.3

Q ss_pred             CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCC
Q 017477          234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAK  286 (371)
Q Consensus       234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~K  286 (371)
                      ||.||.||.+|.+-|..+=++    =..-+.++-++.+.++        ||+.|....++|
T Consensus         2 rr~Rt~ft~~Ql~~Le~~F~~----~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk   58 (67)
T d1zq3p1           2 RRTRTTFTSSQIAELEQHFLQ----GRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKI   58 (67)
T ss_dssp             SCCSCCCCHHHHHHHHHHHTT----CSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHH----CCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhh
Confidence            677999999999988765443    2345555556666655        999997665544

>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=93.96  E-value=0.017  Score=43.00  Aligned_cols=51  Identities=10%  Similarity=0.117  Sum_probs=39.9

Q ss_pred             ccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCCC
Q 017477          235 RFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRDL  289 (371)
Q Consensus       235 RFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~~  289 (371)
                      +.|++||.||++.|.+.=++    =+.-+++++++.+.++        ||+-|....+++...
T Consensus         5 s~~~r~T~eQ~~~Le~~F~~----n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~~~   63 (76)
T d2ecca1           5 SSGKRKTKEQLAILKSFFLQ----CQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQL   63 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCHHHHHHHHHHHHH----cCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhchH
Confidence            44567899999999654433    3678899999999999        999999887766543

>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=93.88  E-value=0.017  Score=42.61  Aligned_cols=54  Identities=17%  Similarity=0.304  Sum_probs=41.6

Q ss_pred             CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      ||-||.||.||++.|.++-+.- +.=-.-++++.++.+.++        ||+-|.....++..
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~-~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~   63 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSH-LSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHT-TTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHh-cCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccc
Confidence            6679999999999999876632 333347788888888887        99999987655443

>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=93.78  E-value=0.022  Score=41.10  Aligned_cols=47  Identities=13%  Similarity=0.166  Sum_probs=36.0

Q ss_pred             CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCC
Q 017477          234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNK  281 (371)
Q Consensus       234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNK  281 (371)
                      ||.||+|+.||++-|.++-+. -+.=..-++++.++.+.++        +|+-|..
T Consensus         3 krkR~~~~~~~~~iL~~wf~~-~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R   57 (62)
T d1x2na1           3 KNKRGVLPKHATNVMRSWLFQ-HIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINAR   57 (62)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHH-TTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHH-hccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHH
Confidence            677899999999999986652 2222356788888888887        9998864

>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=93.20  E-value=0.023  Score=39.76  Aligned_cols=41  Identities=17%  Similarity=0.319  Sum_probs=33.6

Q ss_pred             ccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCC
Q 017477          237 RTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNK  281 (371)
Q Consensus       237 RTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNK  281 (371)
                      ||.||+||++.+.++=+.    =+.-+..+.++-+.++        ||+.|-.
T Consensus         1 Rt~~s~~q~~~Le~~F~~----~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR   49 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRR----KQSLNSKEKEEVAKKCGITPLQVRVWFINKR   49 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHH----CSCCCHHHHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHHCCCHHHHHHHHHhhh
Confidence            899999999999665543    2678889999999988        9998854

>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=92.22  E-value=0.0092  Score=42.76  Aligned_cols=47  Identities=13%  Similarity=0.227  Sum_probs=35.5

Q ss_pred             ccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCC
Q 017477          237 RTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKR  287 (371)
Q Consensus       237 RTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk  287 (371)
                      ||.||.+|.+.|..+=++    =+.-+..+.++.+.++        ||+.|.....+|+
T Consensus         1 Rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk~   55 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   55 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTT----CSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCcCCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhhc
Confidence            899999999988665432    3567777888888877        9999987655443

>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=91.13  E-value=0.056  Score=40.25  Aligned_cols=50  Identities=16%  Similarity=0.306  Sum_probs=39.8

Q ss_pred             CccccCCCHHHHHHHH-HHHHHhCCcccC-CCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477          234 KRFRTKFSQSQKEKMF-EFAERVGWKMQK-RDDDLVHEFCNEV--------VWMHNNKSTFAKRD  288 (371)
Q Consensus       234 KRFRTKFTqEQKEKMl-~FAEKLGWRIQK-~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~  288 (371)
                      +|-||.||++|.+-|. .|.     +..+ -+....++.+.++        ||+-|..-.++|..
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~-----~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~   61 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFN-----KVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHH-----SSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHH-----HccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhcc
Confidence            6889999999999995 574     3444 6888889999888        99999887665543

>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=87.30  E-value=0.026  Score=42.60  Aligned_cols=21  Identities=10%  Similarity=0.083  Sum_probs=16.6

Q ss_pred             CccccCCCHHHHHHHHHHHHH
Q 017477          234 KRFRTKFSQSQKEKMFEFAER  254 (371)
Q Consensus       234 KRFRTKFTqEQKEKMl~FAEK  254 (371)
                      .|.||.||.+|.+-|..+=++
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~   21 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNE   21 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHh
Confidence            478999999999888765543

>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=86.47  E-value=0.11  Score=36.67  Aligned_cols=47  Identities=15%  Similarity=0.217  Sum_probs=37.2

Q ss_pred             cccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCC
Q 017477          236 FRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAK  286 (371)
Q Consensus       236 FRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~K  286 (371)
                      .||-|+.+||+-|..+=++    =+.-+.++.++-+.++        ||+.|.....+|
T Consensus         1 kRT~~~~~q~~~Le~~F~~----~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk   55 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFME----NQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR   55 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTS
T ss_pred             CCCCCCHHHHHHHHHHHHh----cCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHc
Confidence            3899999999988776664    3678888999998888        999997654433

>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=81.12  E-value=0.61  Score=34.19  Aligned_cols=43  Identities=12%  Similarity=0.105  Sum_probs=34.3

Q ss_pred             CCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCC
Q 017477          240 FSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAK  286 (371)
Q Consensus       240 FTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~K  286 (371)
                      +|.||.+.+.++=++    =+.-+.++.++.+.++        ||+.|.....++
T Consensus        11 ~T~~Q~~~Le~~F~~----~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~   61 (76)
T d2ecba1          11 KTAEQLRVLQASFLN----SSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKAL   61 (76)
T ss_dssp             CCHHHHHHHHHHHHH----CSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHS
T ss_pred             CCHHHHHHHHHHHHH----CCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHH
Confidence            599999999886665    3578889999999988        999997754333