Psyllid ID: psy16800

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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-
Protein Sequence
MDEKEERQRRGSRSRKDDENKGGVGGEVGKVGEEMKEKEEERLPGEGREGEERDFSARDVKTIGIFFCVFSLSSLRDLFPVKGEIGVTKVQIPSELSPLGVHPHPTSPSTDYTTPLTALKYPPPAALSQHQSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILIGVGEGSLMGAQGSSPNGGLYR
Secondary Structure (PSIPRED)
ccHHHHHHHHccccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccccHHHHHHHHHHHcccccEEHHHHcccHHHHHHHHHcccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHccccccccccccccccccccccccccccccHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHcHHHccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mdekeerqrrgsrsrkddenkggvggevgkvgeemkekeeerlpgegregeerdfsardvKTIGIFFCVFSlsslrdlfpvkgeigvtkvqipselsplgvhphptspstdyttpltalkypppaalsqhqsllnnsgrtnftnkQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEgiligvgegslmgaqgsspngglyr
Flexible Loop (DISEMBL)
mdekeerqrrgsrsrkddenkggvggevgkvgeemkekeeerlpgegregeerdfsardvKTIGIFFCVFSLSSLRDLFPVKGEIGVTKVQIpselsplgvhphptsPSTDYTTPLTALKYPPPAALSQHQSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIAsvlqlnetqvkiwfqnrrmkqkkrIKEGiligvgegslmgaqgsspngglyr
Low Complexity Region (SEG)
MDEKEERQRRGSRSRKDDenkggvggevgkvgeemkekeeerlpgegregeerDFSARDVKTIGIFFCVFSLSSLRDLFPVKGEIGVTKVQIPSELSPLGVHPHPTSPSTDYTTPLTALKYPPPAALSQHQSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILIGVGEGSLMGAQGSSPNGGLYR
Disordered region (IsUnstruct)
**********************************************************DVKTIGIFFCVFSLSSLRDLFPVKGEIGVTKVQI*****************************************************QLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILIGVG******************
Disordered Region (DISOPRED)
**********************************************************************************************************************************************TNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRR**********************************
Disordered Region (DISEMBL)
**********************GVGGEVGKVGE********************DFSARDVKTIGIFFCVFSLSSLRDLFPVKGEIGVTKVQIPSELSPLGVHPHPTSPSTDYTTPLTALKYPPPAALSQHQSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILIGVGEGSLMGAQ**********
Disordered Region (DISPRO)
*********************************************************************************************************************ALK****************SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRI***************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDEKEERQRRGSRSRKDDENKGGVGGEVGKVGEEMKEKEEERLPGEGREGEERDFSARDVKTIGIFFCVFSLSSLRDLFPVKGEIGVTKVQIPSELSPLGVHPHPTSPSTDYTTPLTALKYPPPAALSQHQSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILIGVGEGSLMGAQGSSPNGGLYR
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	221	2.2.26 [Sep-21-2011]
P10105	635	Homeotic protein labial O	yes	N/A	0.276	0.096	0.901	1e-28
Q08821	240	Homeobox protein Hox-A1 (	N/A	N/A	0.289	0.266	0.875	8e-28
Q1KL10	325	Homeobox protein Hox-A1a	N/A	N/A	0.289	0.196	0.875	2e-27
P49639	335	Homeobox protein Hox-A1 O	yes	N/A	0.289	0.191	0.875	4e-27
P09022	331	Homeobox protein Hox-A1 O	yes	N/A	0.289	0.193	0.875	5e-27
Q08820	300	Homeobox protein Hox-D1 O	N/A	N/A	0.452	0.333	0.603	6e-27
Q01822	327	Homeobox protein Hox-D1 O	no	N/A	0.524	0.354	0.515	6e-27
Q9IA19	326	Homeobox protein Hox-A1 O	N/A	N/A	0.285	0.193	0.873	1e-26
Q28IU6	301	Homeobox protein Hox-D1 O	no	N/A	0.452	0.332	0.603	2e-26
Q98SI1	329	Homeobox protein Hox-A1a	yes	N/A	0.289	0.194	0.859	2e-26

>sp|P10105|LAB_DROME Homeotic protein labial OS=Drosophila melanogaster GN=lab PE=1 SV=2

 Score =  126 bits (316), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 55/61 (90%), Positives = 60/61 (98%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGI 198
           RTNFTNKQLTELEKEFHFN+YLTRARRIEIA+ LQLNETQVKIWFQNRRMKQKKR+KEG+
Sbjct: 511 RTNFTNKQLTELEKEFHFNRYLTRARRIEIANTLQLNETQVKIWFQNRRMKQKKRVKEGL 570

Query: 199 L 199
           +
Sbjct: 571 I 571

Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Required for proper head development.
Drosophila melanogaster (taxid: 7227)

>sp|Q08821|HXA1_XENLA Homeobox protein Hox-A1 (Fragment) OS=Xenopus laevis GN=hoxa1 PE=2 SV=1

 Score =  123 bits (309), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 56/64 (87%), Positives = 60/64 (93%)

Query: 136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195
           N+ RTNFT KQLTELEKEFHFNKYLTRARR+EIA+ LQLNETQVKIWFQNRRMKQKKR K
Sbjct: 135 NTARTNFTTKQLTELEKEFHFNKYLTRARRVEIAAALQLNETQVKIWFQNRRMKQKKREK 194

Query: 196 EGIL 199
           EG+L
Sbjct: 195 EGLL 198

Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Acts on the anterior body structures.

Xenopus laevis (taxid: 8355)

>sp|Q1KL10|HXA1A_TAKRU Homeobox protein Hox-A1a OS=Takifugu rubripes GN=hoxa1a PE=3 SV=1

 Score =  122 bits (306), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 56/64 (87%), Positives = 60/64 (93%)

Query: 136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195
           N+ RTNFT KQLTELEKEFHFNKYLTRARR+EIA+ LQLNETQVKIWFQNRRMKQKKR K
Sbjct: 213 NTVRTNFTTKQLTELEKEFHFNKYLTRARRVEIAAALQLNETQVKIWFQNRRMKQKKREK 272

Query: 196 EGIL 199
           EG+L
Sbjct: 273 EGLL 276

Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.

Takifugu rubripes (taxid: 31033)

>sp|P49639|HXA1_HUMAN Homeobox protein Hox-A1 OS=Homo sapiens GN=HOXA1 PE=1 SV=2

 Score =  121 bits (303), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 56/64 (87%), Positives = 60/64 (93%)

Query: 136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195
           N+ RTNFT KQLTELEKEFHFNKYLTRARR+EIA+ LQLNETQVKIWFQNRRMKQKKR K
Sbjct: 230 NAVRTNFTTKQLTELEKEFHFNKYLTRARRVEIAASLQLNETQVKIWFQNRRMKQKKREK 289

Query: 196 EGIL 199
           EG+L
Sbjct: 290 EGLL 293

Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Acts on the anterior body structures. Seems to act in the maintenance and/or generation of hindbrain segments.

Homo sapiens (taxid: 9606)

>sp|P09022|HXA1_MOUSE Homeobox protein Hox-A1 OS=Mus musculus GN=Hoxa1 PE=1 SV=2

 Score =  121 bits (303), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 56/64 (87%), Positives = 60/64 (93%)

Query: 136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195
           N+ RTNFT KQLTELEKEFHFNKYLTRARR+EIA+ LQLNETQVKIWFQNRRMKQKKR K
Sbjct: 226 NAVRTNFTTKQLTELEKEFHFNKYLTRARRVEIAASLQLNETQVKIWFQNRRMKQKKREK 285

Query: 196 EGIL 199
           EG+L
Sbjct: 286 EGLL 289

The homeoboxless ERA-1-399 protein could act as a competitive inhibitor of the ERA-1-993 protein by competing for interaction with regulatory protein(s) while being unable to bind to DNA.

Mus musculus (taxid: 10090)

>sp|Q08820|HXD1_XENLA Homeobox protein Hox-D1 OS=Xenopus laevis GN=hoxd1 PE=2 SV=3

 Score =  120 bits (302), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 64/106 (60%), Positives = 76/106 (71%), Gaps = 6/106 (5%)

Query: 100 GVHPHPTSPSTD-YTTPLTALKY---PPPAALSQHQSLLNNSG--RTNFTNKQLTELEKE 153
           G +P P SP++D Y +    +K    PP  ++     + +     RTNFT KQLTELEKE
Sbjct: 159 GTYPKPASPASDSYVSTFDWMKVKRNPPKKSIPSEYGVTSPPCNVRTNFTTKQLTELEKE 218

Query: 154 FHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGIL 199
           FHFNKYLTRARRIEIA+ LQLN+TQVKIWFQNRRMKQKKR +EG L
Sbjct: 219 FHFNKYLTRARRIEIANSLQLNDTQVKIWFQNRRMKQKKREREGTL 264

Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Acts on the anterior body structures. Acts downstream of meis3 to pattern the hindbrain.

Xenopus laevis (taxid: 8355)

>sp|Q01822|HXD1_MOUSE Homeobox protein Hox-D1 OS=Mus musculus GN=Hoxd1 PE=2 SV=1

 Score =  120 bits (302), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 66/128 (51%), Positives = 82/128 (64%), Gaps = 12/128 (9%)

Query: 80  PVKGEIGVTKVQIPSELSPLGVHPHPTSPSTDYTTPLTALKY-------PPPAALSQHQS 132
           P  G  G  +   P+     G  P P SP++      +  ++       P  + LS++ +
Sbjct: 169 PADGHPGPFQTVSPAP----GACPKPASPTSSLPAAHSTFEWMKVKRNAPKKSKLSEYGA 224

Query: 133 LLNNSG-RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK 191
               S  RTNF+ KQLTELEKEFHFNKYLTRARRIEIA+ LQLN+TQVKIWFQNRRMKQK
Sbjct: 225 TSPPSAIRTNFSTKQLTELEKEFHFNKYLTRARRIEIANCLQLNDTQVKIWFQNRRMKQK 284

Query: 192 KRIKEGIL 199
           KR +EG+L
Sbjct: 285 KREREGLL 292

Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Acts on the anterior body structures.

Mus musculus (taxid: 10090)

>sp|Q9IA19|HXA1_HETFR Homeobox protein Hox-A1 OS=Heterodontus francisci GN=HOXA1 PE=3 SV=1

 Score =  120 bits (300), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 55/63 (87%), Positives = 59/63 (93%)

Query: 136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195
           N+ RTNFT KQLTELEKEFHFNKYLTRARR+EIA+ LQLNETQVKIWFQNRRMKQKKR K
Sbjct: 222 NTVRTNFTTKQLTELEKEFHFNKYLTRARRVEIAAALQLNETQVKIWFQNRRMKQKKREK 281

Query: 196 EGI 198
           EG+
Sbjct: 282 EGL 284

Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Acts on the anterior body structures.

Heterodontus francisci (taxid: 7792)

>sp|Q28IU6|HXD1_XENTR Homeobox protein Hox-D1 OS=Xenopus tropicalis GN=hoxd1 PE=2 SV=1

 Score =  119 bits (298), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 64/106 (60%), Positives = 77/106 (72%), Gaps = 6/106 (5%)

Query: 100 GVHPHPTSPSTD-YTTPLTALKY---PPPAALSQHQSLLN--NSGRTNFTNKQLTELEKE 153
           G +P P SP++D + +    +K    PP  +L     + +   + RTNFT KQLTELEKE
Sbjct: 162 GTYPKPASPASDTHVSTFDWMKVKRNPPKKSLQSEYGVASPPCTVRTNFTTKQLTELEKE 221

Query: 154 FHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGIL 199
           FHFNKYLTRARRIEIA+ LQLN+TQVKIWFQNRRMKQKKR +EG L
Sbjct: 222 FHFNKYLTRARRIEIANSLQLNDTQVKIWFQNRRMKQKKREREGSL 267

Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Acts on the anterior body structures. Acts downstream of meis3 to pattern the hindbrain.

Xenopus tropicalis (taxid: 8364)

>sp|Q98SI1|HXA1A_DANRE Homeobox protein Hox-A1a OS=Danio rerio GN=hoxa1a PE=2 SV=1

 Score =  119 bits (297), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 55/64 (85%), Positives = 60/64 (93%)

Query: 136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195
           N+ RTNF+ KQLTELEKEFHFNKYLTRARR+EIA+ LQLNETQVKIWFQNRRMKQKKR K
Sbjct: 226 NTVRTNFSTKQLTELEKEFHFNKYLTRARRVEIAASLQLNETQVKIWFQNRRMKQKKREK 285

Query: 196 EGIL 199
           EG+L
Sbjct: 286 EGLL 289

Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.

Danio rerio (taxid: 7955)

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	221
347972359	548	AGAP004649-PA [Anopheles gambiae str. PE	0.343	0.138	0.8	1e-29
195107210	651	GI23760 [Drosophila mojavensis] gi|19391	0.307	0.104	0.882	2e-29
195389737	643	lab [Drosophila virilis] gi|194151617|gb	0.307	0.105	0.882	2e-29
37693039	655	homeodomain transcription factor labial	0.307	0.103	0.882	2e-29
59939347	659	Dbuz\lab-PA [Drosophila buzzatii]	0.307	0.103	0.882	2e-29
350418159	474	PREDICTED: hypothetical protein LOC10074	0.298	0.139	0.909	3e-29
340727752	477	PREDICTED: hypothetical protein LOC10064	0.298	0.138	0.909	3e-29
383849613	468	PREDICTED: uncharacterized protein LOC10	0.298	0.141	0.909	3e-29
195498962	631	GE25839 [Drosophila yakuba] gi|194182848	0.294	0.103	0.907	3e-29
380028371	501	PREDICTED: uncharacterized protein LOC10	0.298	0.131	0.909	3e-29

>gi|347972359|ref|XP_001688960.2| AGAP004649-PA [Anopheles gambiae str. PEST] gi|333469402|gb|EDO63634.2| AGAP004649-PA [Anopheles gambiae str. PEST]

 Score =  135 bits (340), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 64/80 (80%), Positives = 73/80 (91%), Gaps = 4/80 (5%)

Query: 124 PAALSQHQS--LLNN--SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQV 179
           P+A+S HQS  ++NN  +GRTNFTNKQLTELEKEFHFNKYLTRARRIEIA+ L LNETQV
Sbjct: 409 PSAVSPHQSSFMINNNSTGRTNFTNKQLTELEKEFHFNKYLTRARRIEIANALHLNETQV 468

Query: 180 KIWFQNRRMKQKKRIKEGIL 199
           KIWFQNRRMKQKKR+KEG++
Sbjct: 469 KIWFQNRRMKQKKRVKEGLI 488

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195107210|ref|XP_001998208.1| GI23760 [Drosophila mojavensis] gi|193914802|gb|EDW13669.1| GI23760 [Drosophila mojavensis]

 Score =  134 bits (338), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 60/68 (88%), Positives = 65/68 (95%)

Query: 132 SLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK 191
           S  NNSGRTNFTNKQLTELEKEFHFN+YLTRARRIEIA+ LQLNETQVKIWFQNRRMKQK
Sbjct: 508 SSTNNSGRTNFTNKQLTELEKEFHFNRYLTRARRIEIANTLQLNETQVKIWFQNRRMKQK 567

Query: 192 KRIKEGIL 199
           KR+KEG++
Sbjct: 568 KRVKEGLI 575

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195389737|ref|XP_002053531.1| lab [Drosophila virilis] gi|194151617|gb|EDW67051.1| lab [Drosophila virilis]

 Score =  134 bits (338), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 60/68 (88%), Positives = 65/68 (95%)

Query: 132 SLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK 191
           S  NNSGRTNFTNKQLTELEKEFHFN+YLTRARRIEIA+ LQLNETQVKIWFQNRRMKQK
Sbjct: 506 SSTNNSGRTNFTNKQLTELEKEFHFNRYLTRARRIEIANTLQLNETQVKIWFQNRRMKQK 565

Query: 192 KRIKEGIL 199
           KR+KEG++
Sbjct: 566 KRVKEGLI 573

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|37693039|gb|AAQ98855.1| homeodomain transcription factor labial [Drosophila buzzatii]

 Score =  134 bits (338), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 60/68 (88%), Positives = 65/68 (95%)

Query: 132 SLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK 191
           S  NNSGRTNFTNKQLTELEKEFHFN+YLTRARRIEIA+ LQLNETQVKIWFQNRRMKQK
Sbjct: 514 SSTNNSGRTNFTNKQLTELEKEFHFNRYLTRARRIEIANTLQLNETQVKIWFQNRRMKQK 573

Query: 192 KRIKEGIL 199
           KR+KEG++
Sbjct: 574 KRVKEGLI 581

Source: Drosophila buzzatii

Species: Drosophila buzzatii

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|59939347|gb|AAX12439.1| Dbuz\lab-PA [Drosophila buzzatii]

 Score =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 60/68 (88%), Positives = 65/68 (95%)

Query: 132 SLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK 191
           S  NNSGRTNFTNKQLTELEKEFHFN+YLTRARRIEIA+ LQLNETQVKIWFQNRRMKQK
Sbjct: 517 SSTNNSGRTNFTNKQLTELEKEFHFNRYLTRARRIEIANTLQLNETQVKIWFQNRRMKQK 576

Query: 192 KRIKEGIL 199
           KR+KEG++
Sbjct: 577 KRVKEGLI 584

Source: Drosophila buzzatii

Species: Drosophila buzzatii

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350418159|ref|XP_003491764.1| PREDICTED: hypothetical protein LOC100744978 [Bombus impatiens]

 Score =  134 bits (337), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 60/66 (90%), Positives = 64/66 (96%)

Query: 134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
            NN+GRTNFTNKQLTELEKEFHFNKYLTRARRIEIAS LQLNETQVKIWFQNRRMKQKKR
Sbjct: 358 FNNTGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASALQLNETQVKIWFQNRRMKQKKR 417

Query: 194 IKEGIL 199
           +KEG++
Sbjct: 418 MKEGLI 423

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340727752|ref|XP_003402200.1| PREDICTED: hypothetical protein LOC100643550 [Bombus terrestris]

 Score =  134 bits (337), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 60/66 (90%), Positives = 64/66 (96%)

Query: 134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
            NN+GRTNFTNKQLTELEKEFHFNKYLTRARRIEIAS LQLNETQVKIWFQNRRMKQKKR
Sbjct: 361 FNNTGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASALQLNETQVKIWFQNRRMKQKKR 420

Query: 194 IKEGIL 199
           +KEG++
Sbjct: 421 MKEGLI 426

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383849613|ref|XP_003700439.1| PREDICTED: uncharacterized protein LOC100877608 [Megachile rotundata]

 Score =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 60/66 (90%), Positives = 64/66 (96%)

Query: 134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
            NN+GRTNFTNKQLTELEKEFHFNKYLTRARRIEIAS LQLNETQVKIWFQNRRMKQKKR
Sbjct: 352 FNNTGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASALQLNETQVKIWFQNRRMKQKKR 411

Query: 194 IKEGIL 199
           +KEG++
Sbjct: 412 MKEGLI 417

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195498962|ref|XP_002096747.1| GE25839 [Drosophila yakuba] gi|194182848|gb|EDW96459.1| GE25839 [Drosophila yakuba]

 Score =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 59/65 (90%), Positives = 64/65 (98%)

Query: 135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRI 194
           NNSGRTNFTNKQLTELEKEFHFN+YLTRARRIEIA+ LQLNETQVKIWFQNRRMKQKKR+
Sbjct: 504 NNSGRTNFTNKQLTELEKEFHFNRYLTRARRIEIANTLQLNETQVKIWFQNRRMKQKKRV 563

Query: 195 KEGIL 199
           KEG++
Sbjct: 564 KEGLI 568

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380028371|ref|XP_003697877.1| PREDICTED: uncharacterized protein LOC100865518 [Apis florea]

 Score =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 60/66 (90%), Positives = 64/66 (96%)

Query: 134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
            NN+GRTNFTNKQLTELEKEFHFNKYLTRARRIEIAS LQLNETQVKIWFQNRRMKQKKR
Sbjct: 385 FNNTGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASALQLNETQVKIWFQNRRMKQKKR 444

Query: 194 IKEGIL 199
           +KEG++
Sbjct: 445 MKEGLI 450

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

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	221
FB|FBgn0002522	635	lab "labial" [Drosophila melan	0.294	0.102	0.907	2.8e-29
UNIPROTKB|Q08820	300	hoxd1 "Homeobox protein Hox-D1	0.461	0.34	0.605	3.5e-27
UNIPROTKB|F1RZF8	327	HOXD1 "Uncharacterized protein	0.597	0.403	0.479	3.2e-26
UNIPROTKB|P49639	335	HOXA1 "Homeobox protein Hox-A1	0.479	0.316	0.577	5.2e-26
UNIPROTKB|F1NH11	307	HOXB1 "Homeobox protein Hox-B1	0.348	0.250	0.746	8.4e-26
UNIPROTKB|P31259	309	HOXB1 "Homeobox protein Hox-B1	0.348	0.249	0.746	8.4e-26
UNIPROTKB|E1B918	333	HOXA1 "Uncharacterized protein	0.479	0.318	0.568	1.1e-25
UNIPROTKB|E2R5Z1	333	HOXA1 "Uncharacterized protein	0.479	0.318	0.568	1.1e-25
UNIPROTKB|F1SHS9	336	HOXA1 "Uncharacterized protein	0.479	0.315	0.568	1.1e-25
MGI|MGI:96170	331	Hoxa1 "homeobox A1" [Mus muscu	0.479	0.320	0.568	1.1e-25

FB|FBgn0002522 lab "labial" [Drosophila melanogaster (taxid:7227)]

 Score = 317 (116.6 bits), Expect = 2.8e-29, Sum P(2) = 2.8e-29
 Identities = 59/65 (90%), Positives = 64/65 (98%)

Query:   135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRI 194
             NNSGRTNFTNKQLTELEKEFHFN+YLTRARRIEIA+ LQLNETQVKIWFQNRRMKQKKR+
Sbjct:   507 NNSGRTNFTNKQLTELEKEFHFNRYLTRARRIEIANTLQLNETQVKIWFQNRRMKQKKRV 566

Query:   195 KEGIL 199
             KEG++
Sbjct:   567 KEGLI 571

GO:0005634 "nucleus" evidence=ISS;NAS;IDA

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

GO:0046982 "protein heterodimerization activity" evidence=IPI

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

GO:0007420 "brain development" evidence=IGI;IMP

GO:0009790 "embryo development" evidence=IMP

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

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

GO:0007494 "midgut development" evidence=TAS

GO:0030154 "cell differentiation" evidence=TAS

GO:0001709 "cell fate determination" evidence=TAS

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

GO:0035284 "brain segmentation" evidence=IGI

UNIPROTKB|Q08820 hoxd1 "Homeobox protein Hox-D1" [Xenopus laevis (taxid:8355)]

 Score = 305 (112.4 bits), Expect = 3.5e-27, P = 3.5e-27
 Identities = 66/109 (60%), Positives = 79/109 (72%)

Query:    97 SPLGVHPHPTSPSTD-YTTPLTALKY---PPPAALSQHQSLLNN--SGRTNFTNKQLTEL 150
             SP G +P P SP++D Y +    +K    PP  ++     + +   + RTNFT KQLTEL
Sbjct:   157 SP-GTYPKPASPASDSYVSTFDWMKVKRNPPKKSIPSEYGVTSPPCNVRTNFTTKQLTEL 215

Query:   151 EKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGIL 199
             EKEFHFNKYLTRARRIEIA+ LQLN+TQVKIWFQNRRMKQKKR +EG L
Sbjct:   216 EKEFHFNKYLTRARRIEIANSLQLNDTQVKIWFQNRRMKQKKREREGTL 264

GO:0030902 "hindbrain development" evidence=IMP

UNIPROTKB|F1RZF8 HOXD1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 296 (109.3 bits), Expect = 3.2e-26, P = 3.2e-26
 Identities = 70/146 (47%), Positives = 91/146 (62%)

Query:    80 PVKGEIGVTKVQIPSELSPLGVHPHPTSPSTDYTTPLTALKY-------PPPAALSQHQS 132
             P  G  G  +   P+    LG +P   SP++      +  ++       P  + L+++ +
Sbjct:   169 PADGHSGAFQTASPA----LGAYPTSASPASGLPAAFSTFEWMKVKRNAPKKSKLAEYGA 224

Query:   133 LLNNSG-RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK 191
                 S  RTNF+ KQLTELEKEFHFNKYLTRARRIEIA+ LQLN+TQVKIWFQNRRMKQK
Sbjct:   225 ASPPSAIRTNFSTKQLTELEKEFHFNKYLTRARRIEIANSLQLNDTQVKIWFQNRRMKQK 284

Query:   192 KRIKEGILIGVGE-GSL-MGAQGSSP 215
             KR +EG+L+      SL +   G+SP
Sbjct:   285 KREREGLLLSATPVASLQLPLSGTSP 310

GO:0005634 "nucleus" evidence=IEA

GO:0048706 "embryonic skeletal system development" evidence=IEA

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

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

UNIPROTKB|P49639 HOXA1 "Homeobox protein Hox-A1" [Homo sapiens (taxid:9606)]

 Score = 294 (108.6 bits), Expect = 5.2e-26, P = 5.2e-26
 Identities = 67/116 (57%), Positives = 78/116 (67%)

Query:    94 SELSPLGV-HPHPT-SPSTDYTTPLTALKY------PPPAALSQHQSLLN--NSGRTNFT 143
             + LSPL   H     SP+++ ++P     +      PP          L   N+ RTNFT
Sbjct:   178 NSLSPLHASHQEACRSPASETSSPAQTFDWMKVKRNPPKTGKVGEYGYLGQPNAVRTNFT 237

Query:   144 NKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGIL 199
              KQLTELEKEFHFNKYLTRARR+EIA+ LQLNETQVKIWFQNRRMKQKKR KEG+L
Sbjct:   238 TKQLTELEKEFHFNKYLTRARRVEIAASLQLNETQVKIWFQNRRMKQKKREKEGLL 293

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

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

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

GO:0008045 "motor neuron axon guidance" evidence=IEA

GO:0009952 "anterior/posterior pattern specification" evidence=IEA

GO:0021569 "rhombomere 3 development" evidence=IEA

GO:0021570 "rhombomere 4 development" evidence=IEA

GO:0021571 "rhombomere 5 development" evidence=IEA

GO:0021612 "facial nerve structural organization" evidence=IEA

GO:0021754 "facial nucleus development" evidence=IEA

GO:0021953 "central nervous system neuron differentiation" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0050905 "neuromuscular process" evidence=IDA

GO:0007634 "optokinetic behavior" evidence=IDA

GO:0042473 "outer ear morphogenesis" evidence=IDA

GO:0007605 "sensory perception of sound" evidence=IDA

GO:0050890 "cognition" evidence=IDA

GO:0050795 "regulation of behavior" evidence=IDA

GO:0021599 "abducens nerve formation" evidence=IMP

GO:0048839 "inner ear development" evidence=IMP

GO:0090103 "cochlea morphogenesis" evidence=IMP

GO:0090102 "cochlea development" evidence=IMP

GO:0060876 "semicircular canal formation" evidence=IMP

GO:0009653 "anatomical structure morphogenesis" evidence=IMP

GO:0048702 "embryonic neurocranium morphogenesis" evidence=IMP

GO:0048844 "artery morphogenesis" evidence=IMP

GO:0060840 "artery development" evidence=IMP

GO:0007275 "multicellular organismal development" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|F1NH11 HOXB1 "Homeobox protein Hox-B1" [Gallus gallus (taxid:9031)]

 Score = 292 (107.8 bits), Expect = 8.4e-26, P = 8.4e-26
 Identities = 59/79 (74%), Positives = 64/79 (81%)

Query:   122 PPPAALSQHQSLLN--NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQV 179
             PP  A      LL   N+ RTNFT KQLTELEKEFHFNKYLTRARR+EIA+ L+LNETQV
Sbjct:   196 PPKTAKVSEYGLLGQPNTIRTNFTTKQLTELEKEFHFNKYLTRARRVEIAATLELNETQV 255

Query:   180 KIWFQNRRMKQKKRIKEGI 198
             KIWFQNRRMKQKKR KEG+
Sbjct:   256 KIWFQNRRMKQKKREKEGL 274

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

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0009952 "anterior/posterior pattern specification" evidence=IEA

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

GO:0021570 "rhombomere 4 development" evidence=IEA

GO:0021571 "rhombomere 5 development" evidence=IEA

GO:0021612 "facial nerve structural organization" evidence=IEA

GO:0021754 "facial nucleus development" evidence=IEA

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

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

GO:0048646 "anatomical structure formation involved in morphogenesis" evidence=IEA

GO:0048704 "embryonic skeletal system morphogenesis" evidence=IEA

UNIPROTKB|P31259 HOXB1 "Homeobox protein Hox-B1" [Gallus gallus (taxid:9031)]

 Score = 292 (107.8 bits), Expect = 8.4e-26, P = 8.4e-26
 Identities = 59/79 (74%), Positives = 64/79 (81%)

Query:   122 PPPAALSQHQSLLN--NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQV 179
             PP  A      LL   N+ RTNFT KQLTELEKEFHFNKYLTRARR+EIA+ L+LNETQV
Sbjct:   198 PPKTAKVSEYGLLGQPNTIRTNFTTKQLTELEKEFHFNKYLTRARRVEIAATLELNETQV 257

Query:   180 KIWFQNRRMKQKKRIKEGI 198
             KIWFQNRRMKQKKR KEG+
Sbjct:   258 KIWFQNRRMKQKKREKEGL 276

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

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|E1B918 HOXA1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 291 (107.5 bits), Expect = 1.1e-25, P = 1.1e-25
 Identities = 66/116 (56%), Positives = 78/116 (67%)

Query:    94 SELSPLGV-HPHPT-SPSTDYTTPLTALKY------PPPAALSQHQSLLN--NSGRTNFT 143
             + LSPL   H     SP+++ ++P     +      PP          +   N+ RTNFT
Sbjct:   176 NSLSPLHASHQEACRSPASETSSPAQTFDWMKVKRNPPKTGKIGEYGYVGQPNAVRTNFT 235

Query:   144 NKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGIL 199
              KQLTELEKEFHFNKYLTRARR+EIA+ LQLNETQVKIWFQNRRMKQKKR KEG+L
Sbjct:   236 TKQLTELEKEFHFNKYLTRARRVEIAASLQLNETQVKIWFQNRRMKQKKREKEGLL 291

GO:0005634 "nucleus" evidence=IEA

GO:0090103 "cochlea morphogenesis" evidence=IEA

GO:0060876 "semicircular canal formation" evidence=IEA

GO:0050905 "neuromuscular process" evidence=IEA

GO:0050890 "cognition" evidence=IEA

GO:0050795 "regulation of behavior" evidence=IEA

GO:0048844 "artery morphogenesis" evidence=IEA

GO:0048702 "embryonic neurocranium morphogenesis" evidence=IEA

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

GO:0042473 "outer ear morphogenesis" evidence=IEA

GO:0021953 "central nervous system neuron differentiation" evidence=IEA

GO:0021754 "facial nucleus development" evidence=IEA

GO:0021612 "facial nerve structural organization" evidence=IEA

GO:0021599 "abducens nerve formation" evidence=IEA

GO:0021571 "rhombomere 5 development" evidence=IEA

GO:0021570 "rhombomere 4 development" evidence=IEA

GO:0021569 "rhombomere 3 development" evidence=IEA

GO:0009952 "anterior/posterior pattern specification" evidence=IEA

GO:0008045 "motor neuron axon guidance" evidence=IEA

GO:0007634 "optokinetic behavior" evidence=IEA

GO:0007605 "sensory perception of sound" evidence=IEA

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

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

UNIPROTKB|E2R5Z1 HOXA1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 291 (107.5 bits), Expect = 1.1e-25, P = 1.1e-25
 Identities = 66/116 (56%), Positives = 78/116 (67%)

Query:    94 SELSPLGV-HPHPT-SPSTDYTTPLTALKY------PPPAALSQHQSLLN--NSGRTNFT 143
             + LSPL   H     SP+++ ++P     +      PP          +   N+ RTNFT
Sbjct:   176 NSLSPLHASHQEACRSPTSETSSPAQTFDWMKVKRNPPKTGKVGEYGYVGQPNAVRTNFT 235

Query:   144 NKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGIL 199
              KQLTELEKEFHFNKYLTRARR+EIA+ LQLNETQVKIWFQNRRMKQKKR KEG+L
Sbjct:   236 TKQLTELEKEFHFNKYLTRARRVEIAASLQLNETQVKIWFQNRRMKQKKREKEGLL 291

GO:0005634 "nucleus" evidence=IEA

GO:0090103 "cochlea morphogenesis" evidence=IEA

GO:0060876 "semicircular canal formation" evidence=IEA

GO:0050905 "neuromuscular process" evidence=IEA

GO:0050890 "cognition" evidence=IEA

GO:0050795 "regulation of behavior" evidence=IEA

GO:0048844 "artery morphogenesis" evidence=IEA

GO:0048702 "embryonic neurocranium morphogenesis" evidence=IEA

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

GO:0042473 "outer ear morphogenesis" evidence=IEA

GO:0021953 "central nervous system neuron differentiation" evidence=IEA

GO:0021754 "facial nucleus development" evidence=IEA

GO:0021612 "facial nerve structural organization" evidence=IEA

GO:0021599 "abducens nerve formation" evidence=IEA

GO:0021571 "rhombomere 5 development" evidence=IEA

GO:0021570 "rhombomere 4 development" evidence=IEA

GO:0021569 "rhombomere 3 development" evidence=IEA

GO:0009952 "anterior/posterior pattern specification" evidence=IEA

GO:0008045 "motor neuron axon guidance" evidence=IEA

GO:0007634 "optokinetic behavior" evidence=IEA

GO:0007605 "sensory perception of sound" evidence=IEA

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

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

UNIPROTKB|F1SHS9 HOXA1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 291 (107.5 bits), Expect = 1.1e-25, P = 1.1e-25
 Identities = 66/116 (56%), Positives = 78/116 (67%)

Query:    94 SELSPLGV-HPHPT-SPSTDYTTPLTALKY------PPPAALSQHQSLLN--NSGRTNFT 143
             + LSPL   H     SP+++ ++P     +      PP          +   N+ RTNFT
Sbjct:   179 NSLSPLHASHQEACRSPASETSSPAQTFDWMKVKRNPPKTGKVGEYGYVGQPNAVRTNFT 238

Query:   144 NKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGIL 199
              KQLTELEKEFHFNKYLTRARR+EIA+ LQLNETQVKIWFQNRRMKQKKR KEG+L
Sbjct:   239 TKQLTELEKEFHFNKYLTRARRVEIAASLQLNETQVKIWFQNRRMKQKKREKEGLL 294

GO:0005634 "nucleus" evidence=IEA

GO:0090103 "cochlea morphogenesis" evidence=IEA

GO:0060876 "semicircular canal formation" evidence=IEA

GO:0050905 "neuromuscular process" evidence=IEA

GO:0050890 "cognition" evidence=IEA

GO:0050795 "regulation of behavior" evidence=IEA

GO:0048844 "artery morphogenesis" evidence=IEA

GO:0048702 "embryonic neurocranium morphogenesis" evidence=IEA

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

GO:0042473 "outer ear morphogenesis" evidence=IEA

GO:0021953 "central nervous system neuron differentiation" evidence=IEA

GO:0021754 "facial nucleus development" evidence=IEA

GO:0021612 "facial nerve structural organization" evidence=IEA

GO:0021599 "abducens nerve formation" evidence=IEA

GO:0021571 "rhombomere 5 development" evidence=IEA

GO:0021570 "rhombomere 4 development" evidence=IEA

GO:0021569 "rhombomere 3 development" evidence=IEA

GO:0009952 "anterior/posterior pattern specification" evidence=IEA

GO:0008045 "motor neuron axon guidance" evidence=IEA

GO:0007634 "optokinetic behavior" evidence=IEA

GO:0007605 "sensory perception of sound" evidence=IEA

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

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

MGI|MGI:96170 Hoxa1 "homeobox A1" [Mus musculus (taxid:10090)]

 Score = 291 (107.5 bits), Expect = 1.1e-25, P = 1.1e-25
 Identities = 66/116 (56%), Positives = 78/116 (67%)

Query:    94 SELSPLGV-HPHPT-SPSTDYTTPLTALKY------PPPAALSQHQSLLN--NSGRTNFT 143
             + LSPL   H     SP+++ ++P     +      PP          +   N+ RTNFT
Sbjct:   174 NSLSPLHASHQEACRSPASETSSPAQTFDWMKVKRNPPKTGKVGEYGYVGQPNAVRTNFT 233

Query:   144 NKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGIL 199
              KQLTELEKEFHFNKYLTRARR+EIA+ LQLNETQVKIWFQNRRMKQKKR KEG+L
Sbjct:   234 TKQLTELEKEFHFNKYLTRARRVEIAASLQLNETQVKIWFQNRRMKQKKREKEGLL 289

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

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

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007399 "nervous system development" evidence=IMP

GO:0007605 "sensory perception of sound" evidence=ISO

GO:0007634 "optokinetic behavior" evidence=ISO

GO:0008045 "motor neuron axon guidance" evidence=IGI

GO:0009653 "anatomical structure morphogenesis" evidence=ISO;IGI

GO:0009952 "anterior/posterior pattern specification" evidence=IGI;IMP

GO:0021569 "rhombomere 3 development" evidence=IGI;IMP

GO:0021570 "rhombomere 4 development" evidence=IGI;IMP

GO:0021571 "rhombomere 5 development" evidence=IGI;IMP

GO:0021599 "abducens nerve formation" evidence=ISO

GO:0021612 "facial nerve structural organization" evidence=IGI

GO:0021754 "facial nucleus development" evidence=IMP

GO:0021953 "central nervous system neuron differentiation" evidence=IMP

GO:0030902 "hindbrain development" evidence=IMP

GO:0042472 "inner ear morphogenesis" evidence=IMP

GO:0042473 "outer ear morphogenesis" evidence=ISO

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

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

GO:0048646 "anatomical structure formation involved in morphogenesis" evidence=IGI

GO:0048702 "embryonic neurocranium morphogenesis" evidence=ISO

GO:0048839 "inner ear development" evidence=ISO

GO:0048844 "artery morphogenesis" evidence=ISO

GO:0050795 "regulation of behavior" evidence=ISO

GO:0050890 "cognition" evidence=ISO

GO:0050905 "neuromuscular process" evidence=ISO

GO:0060840 "artery development" evidence=ISO

GO:0060876 "semicircular canal formation" evidence=ISO

GO:0090102 "cochlea development" evidence=ISO

GO:0090103 "cochlea morphogenesis" evidence=ISO

---

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 EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	221
pfam00046	57	pfam00046, Homeobox, Homeobox domain	1e-25
smart00389	57	smart00389, HOX, Homeodomain	5e-23
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	1e-22
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	5e-06

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

 Score = 94.5 bits (236), Expect = 1e-25
 Identities = 31/54 (57%), Positives = 37/54 (68%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT FT +QL ELEKEF  N+Y +   R E+A  L L E QVK+WFQNRR K K+
Sbjct: 4   RTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57

Length = 57

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 87.3 bits (217), Expect = 5e-23
 Identities = 32/53 (60%), Positives = 38/53 (71%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK 191
           RT+FT +QL ELEKEF  N Y +R  R E+A  L L+E QVK+WFQNRR K K
Sbjct: 5   RTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

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

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

 Score = 86.5 bits (215), Expect = 1e-22
 Identities = 33/55 (60%), Positives = 37/55 (67%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
           RT FT +QL ELEKEF  N Y +R  R E+A  L L E QVKIWFQNRR K K+ 
Sbjct: 4   RTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58

Length = 59

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

 Score = 44.7 bits (106), Expect = 5e-06
 Identities = 24/56 (42%), Positives = 36/56 (64%)

Query: 137 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           S R   T++QL  LE+EF  N Y +   RI+++ +L +    V+IWFQN+R K+KK
Sbjct: 53  SKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKK 108

Length = 156

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	221
KOG0484|consensus	125		99.77
KOG0489|consensus	261		99.76
KOG0488|consensus	309		99.75
KOG0850|consensus	245		99.73
KOG0487|consensus	308		99.72
KOG0842|consensus	307		99.7
KOG0492|consensus	246		99.7
KOG2251|consensus	228		99.69
KOG0843|consensus	197		99.68
KOG0494|consensus	332		99.66
KOG0485|consensus	268		99.65
KOG0848|consensus	317		99.64
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.63
KOG0493|consensus	342		99.57
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.57
KOG0486|consensus	351		99.54
KOG0844|consensus	408		99.5
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.48
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.46
KOG0491|consensus	194		99.46
KOG3802|consensus	398		99.45
COG5576	156	Homeodomain-containing transcription factor [Trans	99.43
KOG0483|consensus	198		99.43
KOG4577|consensus	383		99.41
KOG0847|consensus	288		99.37
KOG0490|consensus	235		99.28
KOG1168|consensus	385		99.05
KOG0849|consensus	354		99.04
KOG0775|consensus	304		98.69
KOG0774|consensus	334		98.44
KOG2252|consensus	558		98.24
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.2
KOG0490|consensus	235		98.1
KOG1146|consensus	1406		98.06
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	96.23
KOG0773|consensus	342		96.07
KOG3623|consensus	1007		94.66
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	91.16

>KOG0484|consensus

Probab=99.77  E-value=1e-19  Score=138.93  Aligned_cols=68  Identities=40%  Similarity=0.557  Sum_probs=63.3

Q ss_pred             ccCCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhcc
Q psy16800        131 QSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGI  198 (221)
Q Consensus       131 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~  198 (221)
                      ..++++|.||.||..||..||+.|...+||++..|++||..++|++.+|||||||||+|.+|+.+...
T Consensus        13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~   80 (125)
T KOG0484|consen   13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAI   80 (125)
T ss_pred             HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHH
Confidence            34567889999999999999999999999999999999999999999999999999999999988643

>KOG0489|consensus

Probab=99.76  E-value=2.7e-19  Score=157.91  Aligned_cols=67  Identities=64%  Similarity=0.868  Sum_probs=63.7

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhcccc
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILI  200 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~~  200 (221)
                      ..||.||.||..|+.+||+.|+.|+|++...|.+||..|+|+|+||+|||||||+||||..+.....
T Consensus       158 ~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~  224 (261)
T KOG0489|consen  158 KSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ  224 (261)
T ss_pred             CCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence            4689999999999999999999999999999999999999999999999999999999999976655

>KOG0488|consensus

Probab=99.75  E-value=6.1e-18  Score=152.52  Aligned_cols=76  Identities=45%  Similarity=0.620  Sum_probs=68.1

Q ss_pred             cCCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccccCCCCCCC
Q psy16800        132 SLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILIGVGEGSL  207 (221)
Q Consensus       132 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~~~~~~g~~  207 (221)
                      .+++|+.||.||..||..||+.|++.+|++..+|.+||..|||+..||++||||||+||||+...+....-..+..
T Consensus       169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~~~~~~~~~  244 (309)
T KOG0488|consen  169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGELLYQAGNS  244 (309)
T ss_pred             CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhccccccccc
Confidence            3566777999999999999999999999999999999999999999999999999999999999866665555444

>KOG0850|consensus

Probab=99.73  E-value=8.5e-18  Score=144.04  Aligned_cols=71  Identities=41%  Similarity=0.531  Sum_probs=64.6

Q ss_pred             ccCCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccccC
Q psy16800        131 QSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILIG  201 (221)
Q Consensus       131 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~~~  201 (221)
                      +.++-|+.||.|+..||..|.+.|++++|+...||.+||..|||+-.||+|||||||.|.||..+.+....
T Consensus       118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~~~  188 (245)
T KOG0850|consen  118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSGPV  188 (245)
T ss_pred             CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCCcc
Confidence            34456777999999999999999999999999999999999999999999999999999999999765443

>KOG0487|consensus

Probab=99.72  E-value=3.5e-18  Score=153.03  Aligned_cols=68  Identities=50%  Similarity=0.752  Sum_probs=63.3

Q ss_pred             CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhcccc
Q psy16800        133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILI  200 (221)
Q Consensus       133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~~  200 (221)
                      +..|++|..||+.|+.+||+.|..|.|++.+.|.+|++.|+|+++||+|||||||+|.||..++....
T Consensus       233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r~~  300 (308)
T KOG0487|consen  233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENRLK  300 (308)
T ss_pred             cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhhcc
Confidence            45688899999999999999999999999999999999999999999999999999999999765444

>KOG0842|consensus

Probab=99.70  E-value=1.2e-17  Score=149.64  Aligned_cols=72  Identities=40%  Similarity=0.594  Sum_probs=65.2

Q ss_pred             cCCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccccCCC
Q psy16800        132 SLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILIGVG  203 (221)
Q Consensus       132 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~~~~~  203 (221)
                      ..++||.|..||..|+.+||+.|.+++|++..||++||..|.||+.||||||||||-|.||+.++..+.+..
T Consensus       150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~  221 (307)
T KOG0842|consen  150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALL  221 (307)
T ss_pred             cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhccc
Confidence            345677799999999999999999999999999999999999999999999999999999999986555433

>KOG0492|consensus

Probab=99.70  E-value=3.3e-17  Score=138.63  Aligned_cols=72  Identities=47%  Similarity=0.698  Sum_probs=64.1

Q ss_pred             CccccccccCCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800        124 PAALSQHQSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG  197 (221)
Q Consensus       124 ~~~~~~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g  197 (221)
                      .+.+..|.  ..|+.||.||..||..||+.|...+|+++.+|.+++..|.||+.||+|||||||+|.||.+...
T Consensus       135 ~C~LrKhk--~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae  206 (246)
T KOG0492|consen  135 TCTLRKHK--PNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAE  206 (246)
T ss_pred             cchhcccC--CCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHH
Confidence            34445444  3477899999999999999999999999999999999999999999999999999999988753

>KOG2251|consensus

Probab=99.69  E-value=7.6e-17  Score=137.51  Aligned_cols=66  Identities=36%  Similarity=0.520  Sum_probs=62.5

Q ss_pred             cCCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800        132 SLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG  197 (221)
Q Consensus       132 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g  197 (221)
                      .++.+|.||.|+..|+.+||.+|.+.+||++..|++||.+|+|.+.+|||||.|||+|+|++++..
T Consensus        34 pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   34 PRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             chhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            456789999999999999999999999999999999999999999999999999999999998863

>KOG0843|consensus

Probab=99.68  E-value=2.2e-17  Score=136.99  Aligned_cols=64  Identities=47%  Similarity=0.667  Sum_probs=61.4

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG  197 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g  197 (221)
                      +.||.||.||.+||..||..|+.++|....+|+.||..|+|++.||+|||||||.|.||...+.
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            5688899999999999999999999999999999999999999999999999999999988874

>KOG0494|consensus

Probab=99.66  E-value=8.1e-17  Score=140.21  Aligned_cols=62  Identities=40%  Similarity=0.524  Sum_probs=58.7

Q ss_pred             CCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       135 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      +|+.||.||..|+..||+.|+..+||+...|+.||..+.|.+.+|+|||||||+||||..+.
T Consensus       141 RRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~  202 (332)
T KOG0494|consen  141 RRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR  202 (332)
T ss_pred             cccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence            34449999999999999999999999999999999999999999999999999999998886

>KOG0485|consensus

Probab=99.65  E-value=5.7e-17  Score=138.07  Aligned_cols=67  Identities=43%  Similarity=0.642  Sum_probs=62.6

Q ss_pred             CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccc
Q psy16800        133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGIL  199 (221)
Q Consensus       133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~  199 (221)
                      .++|+.||+|+..|+..||..|+...|++..+|..||.+|.|++.||+|||||||.||||+......
T Consensus       102 ~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~e  168 (268)
T KOG0485|consen  102 DRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLE  168 (268)
T ss_pred             cccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhh
Confidence            3578889999999999999999999999999999999999999999999999999999999886433

>KOG0848|consensus

Probab=99.64  E-value=4.7e-16  Score=135.94  Aligned_cols=65  Identities=48%  Similarity=0.706  Sum_probs=60.1

Q ss_pred             CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800        133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG  197 (221)
Q Consensus       133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g  197 (221)
                      +.+-+-|.+||..|..+||+.|..++|.++..+.+||..|+|+|+||+|||||||+|+||..++.
T Consensus       197 RTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk  261 (317)
T KOG0848|consen  197 RTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK  261 (317)
T ss_pred             ecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence            34445588999999999999999999999999999999999999999999999999999988875

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.63  E-value=1.4e-16  Score=108.79  Aligned_cols=57  Identities=51%  Similarity=0.703  Sum_probs=55.1

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHH
Q psy16800        136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK  192 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr  192 (221)
                      |+.|+.||.+|+..|+.+|..++||+..+++.||..|+|+..+|++||+|+|+++|+
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence            577999999999999999999999999999999999999999999999999999986

; 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 ....

>KOG0493|consensus

Probab=99.57  E-value=1.7e-14  Score=125.91  Aligned_cols=61  Identities=52%  Similarity=0.774  Sum_probs=57.9

Q ss_pred             CCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       135 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      -||.||.||.+||..|+..|+.|.|++...|.+||.+|+|++.||+|||||+|+|.||..-
T Consensus       246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTg  306 (342)
T KOG0493|consen  246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTG  306 (342)
T ss_pred             hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence            4678999999999999999999999999999999999999999999999999999998654

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.57  E-value=4.3e-15  Score=103.02  Aligned_cols=52  Identities=19%  Similarity=0.318  Sum_probs=50.6

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCC----CCHHHHHHHHHHhCCCCCceeeccccch
Q psy16800        136 NSGRTNFTNKQLTELEKEFHFNKY----LTRARRIEIASVLQLNETQVKIWFQNRR  187 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~~~y----ps~~~r~~LA~~L~Lt~~qVqvWFQNRR  187 (221)
                      ||.||.||.+|+..|+.+|+.+.|    |+..++++||..|||++.+|+|||||.+
T Consensus         2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            788999999999999999999999    9999999999999999999999999975

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

>KOG0486|consensus

Probab=99.54  E-value=3.2e-15  Score=133.18  Aligned_cols=89  Identities=36%  Similarity=0.480  Sum_probs=75.9

Q ss_pred             cCCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhcc--ccCCCCCCCCC
Q psy16800        132 SLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGI--LIGVGEGSLMG  209 (221)
Q Consensus       132 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~--~~~~~~g~~~~  209 (221)
                      ..+++|.||+||..||..||..|++|.||+...|++||.-.+|++.+|+|||.|||+||+|+++..+  ..-.+-+....
T Consensus       109 i~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ae~~k~~f~~~~~  188 (351)
T KOG0486|consen  109 ISKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAELAKGGFGPQFL  188 (351)
T ss_pred             hhhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHHHHhhhcCCccccc
Confidence            3467888999999999999999999999999999999999999999999999999999999999766  33334445555


Q ss_pred             CCCCCCCCCCC
Q psy16800        210 AQGSSPNGGLY  220 (221)
Q Consensus       210 ~~~~sp~~~~~  220 (221)
                      ++-|.|.++.|
T Consensus       189 t~~~~P~~~vy  199 (351)
T KOG0486|consen  189 TGLMQPYFDVY  199 (351)
T ss_pred             ccccCchhhhc
Confidence            66777777665

>KOG0844|consensus

Probab=99.50  E-value=1.4e-14  Score=128.80  Aligned_cols=61  Identities=49%  Similarity=0.788  Sum_probs=58.8

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      ||-||.||.+||..||+.|-+.+|.+...|.+||..|+|.+..|+|||||||+|+||+...
T Consensus       182 RRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla  242 (408)
T KOG0844|consen  182 RRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA  242 (408)
T ss_pred             HHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence            7889999999999999999999999999999999999999999999999999999998765

>smart00389 HOX Homeodomain

Probab=99.48  E-value=1.9e-14  Score=97.44  Aligned_cols=55  Identities=58%  Similarity=0.820  Sum_probs=52.1

Q ss_pred             CCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHH
Q psy16800        137 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK  191 (221)
Q Consensus       137 r~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~K  191 (221)
                      +.|+.|+.+|+..|+..|..++||+..++..||..++|+..+|++||+|+|++.+
T Consensus         2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~   56 (56)
T smart00389        2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK   56 (56)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence            5678899999999999999999999999999999999999999999999998753

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

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

Probab=99.46  E-value=3.5e-14  Score=96.67  Aligned_cols=57  Identities=58%  Similarity=0.800  Sum_probs=54.0

Q ss_pred             CCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHH
Q psy16800        137 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR  193 (221)
Q Consensus       137 r~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~  193 (221)
                      +.|+.|+..|+..|+..|..++||+..++..||..+||+..+|++||+|+|++.++.
T Consensus         2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~   58 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS   58 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence            457899999999999999999999999999999999999999999999999998763

>KOG0491|consensus

Probab=99.46  E-value=9.2e-15  Score=119.96  Aligned_cols=68  Identities=46%  Similarity=0.689  Sum_probs=62.8

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccccC
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILIG  201 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~~~  201 (221)
                      .+++.||+|+..|+..|++.|+...|++..++.+||..|+|++.||+.||||||+|.||..+.....+
T Consensus        99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p~n  166 (194)
T KOG0491|consen   99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQPKN  166 (194)
T ss_pred             HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence            45667999999999999999999999999999999999999999999999999999999999865443

>KOG3802|consensus

Probab=99.45  E-value=5.5e-14  Score=128.87  Aligned_cols=62  Identities=34%  Similarity=0.413  Sum_probs=60.3

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      ++||+||.|.......||++|.+|+.|+..++..||.+|+|.+++|+|||||||+|.||...
T Consensus       293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            57888999999999999999999999999999999999999999999999999999999888

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.43  E-value=1.2e-13  Score=113.49  Aligned_cols=67  Identities=36%  Similarity=0.568  Sum_probs=61.1

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhcccc
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILI  200 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~~  200 (221)
                      ..+++|++.|..|+.+|++.|..++||+..+|..|+..|+|+++-|||||||+|++.|+....+...
T Consensus        50 ~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~~~  116 (156)
T COG5576          50 PPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQ  116 (156)
T ss_pred             cCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccchhc
Confidence            3477899999999999999999999999999999999999999999999999999999887764333

>KOG0483|consensus

Probab=99.43  E-value=4.8e-14  Score=119.81  Aligned_cols=62  Identities=35%  Similarity=0.532  Sum_probs=57.8

Q ss_pred             CCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       135 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      ..+++.+|+.+|+..||..|+.+.++....+..||.+|||.++||.||||||||+||.++.+
T Consensus        50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE  111 (198)
T KOG0483|consen   50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLE  111 (198)
T ss_pred             cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhh
Confidence            35556789999999999999999999999999999999999999999999999999988765

>KOG4577|consensus

Probab=99.41  E-value=9.3e-14  Score=122.81  Aligned_cols=70  Identities=31%  Similarity=0.400  Sum_probs=65.0

Q ss_pred             CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccccCC
Q psy16800        133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILIGV  202 (221)
Q Consensus       133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~~~~  202 (221)
                      ...||.||.+|..||+.|...|...+.|....|++|+.++||.-++|||||||||||+||.++..-.+.|
T Consensus       165 ~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RW  234 (383)
T KOG4577|consen  165 ASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRW  234 (383)
T ss_pred             cccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHH
Confidence            3569999999999999999999999999999999999999999999999999999999999998655544

>KOG0847|consensus

Probab=99.37  E-value=4.1e-13  Score=114.87  Aligned_cols=67  Identities=39%  Similarity=0.639  Sum_probs=61.3

Q ss_pred             CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccc
Q psy16800        133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGIL  199 (221)
Q Consensus       133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~  199 (221)
                      ..++..|..|+-.|+..|+..|++.+|+-.++|.+||..++|++.||+|||||||.||||++.....
T Consensus       165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEma  231 (288)
T KOG0847|consen  165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMA  231 (288)
T ss_pred             ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchh
Confidence            4455668899999999999999999999999999999999999999999999999999999876543

>KOG0490|consensus

Probab=99.28  E-value=1.9e-12  Score=110.33  Aligned_cols=63  Identities=37%  Similarity=0.499  Sum_probs=60.0

Q ss_pred             CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      ..+++.||.|+..|+.+|++.|+..+||+...++.||..+++++..|+|||||+|+||+++.+
T Consensus        58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~  120 (235)
T KOG0490|consen   58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER  120 (235)
T ss_pred             ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence            456888999999999999999999999999999999999999999999999999999999875

>KOG1168|consensus

Probab=99.05  E-value=1.1e-10  Score=103.67  Aligned_cols=64  Identities=27%  Similarity=0.397  Sum_probs=60.2

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG  197 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g  197 (221)
                      .+||+||.+..-....||++|...+.|+.+.+..||.+|+|.+.+|+|||||.|+|.||.....
T Consensus       308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa  371 (385)
T KOG1168|consen  308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSA  371 (385)
T ss_pred             ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhh
Confidence            4789999999999999999999999999999999999999999999999999999999976653

>KOG0849|consensus

Probab=99.04  E-value=1.3e-10  Score=106.94  Aligned_cols=64  Identities=33%  Similarity=0.487  Sum_probs=60.1

Q ss_pred             cCCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        132 SLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       132 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      ....+|.||.|+..|+..|++.|+.++||++..|+.||.++++++..|+|||+|||++++|...
T Consensus       173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~  236 (354)
T KOG0849|consen  173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR  236 (354)
T ss_pred             cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence            3455777999999999999999999999999999999999999999999999999999999984

>KOG0775|consensus

Probab=98.69  E-value=2.3e-08  Score=88.18  Aligned_cols=55  Identities=29%  Similarity=0.449  Sum_probs=48.8

Q ss_pred             cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        142 FTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       142 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      |...-..+|..+|..++||+..++.+||..+||+..||-+||.|||+++|-...+
T Consensus       183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~ak  237 (304)
T KOG0775|consen  183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAAAK  237 (304)
T ss_pred             hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhcccc
Confidence            4445567999999999999999999999999999999999999999999955444

>KOG0774|consensus

Probab=98.44  E-value=3.1e-07  Score=80.82  Aligned_cols=62  Identities=27%  Similarity=0.435  Sum_probs=56.6

Q ss_pred             CCCCCCcccCHHHHHHHHHHhh---hCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFH---FNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~---~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      ..+|+|..|++.-.++|..+|.   .++||+..++++||.+++++..||-.||.|+|-+.||-.-
T Consensus       187 darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~  251 (334)
T KOG0774|consen  187 DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMG  251 (334)
T ss_pred             HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhh
Confidence            3578899999999999999995   5889999999999999999999999999999999887544

>KOG2252|consensus

Probab=98.24  E-value=7.6e-07  Score=85.06  Aligned_cols=59  Identities=29%  Similarity=0.304  Sum_probs=55.1

Q ss_pred             cCCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHH
Q psy16800        132 SLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQ  190 (221)
Q Consensus       132 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~  190 (221)
                      ....|+.|.+||..|...|..+|+.+++|+.+..+.|+.+|+|....|.+||-|.|.+.
T Consensus       417 ~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  417 MLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             cccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            34567889999999999999999999999999999999999999999999999998874

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

Probab=98.20  E-value=2.8e-07  Score=59.32  Aligned_cols=34  Identities=29%  Similarity=0.540  Sum_probs=29.0

Q ss_pred             hCCCCCHHHHHHHHHHhCCCCCceeeccccchhH
Q psy16800        156 FNKYLTRARRIEIASVLQLNETQVKIWFQNRRMK  189 (221)
Q Consensus       156 ~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK  189 (221)
                      .++||+..+++.||.++||+..||..||-|.|.+
T Consensus         7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR   40 (40)
T PF05920_consen    7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR   40 (40)
T ss_dssp             TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence            4789999999999999999999999999999875

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

>KOG0490|consensus

Probab=98.10  E-value=2.2e-06  Score=72.90  Aligned_cols=63  Identities=33%  Similarity=0.461  Sum_probs=59.2

Q ss_pred             CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      ...++.|+.+...|+..|...|..+.+|+...++.|+..++++...|++||||+|++.++...
T Consensus       151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  151 KKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             cccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            345778999999999999999999999999999999999999999999999999999998766

>KOG1146|consensus

Probab=98.06  E-value=9.7e-06  Score=83.97  Aligned_cols=64  Identities=23%  Similarity=0.299  Sum_probs=60.4

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG  197 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g  197 (221)
                      .+++.|+.++..||..|..+|....|+...+.+.|-..+++..++|++||||.|+|.++....+
T Consensus       902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~  965 (1406)
T KOG1146|consen  902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG  965 (1406)
T ss_pred             hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence            4577899999999999999999999999999999999999999999999999999999988865

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

Probab=96.23  E-value=0.0011  Score=45.75  Aligned_cols=41  Identities=24%  Similarity=0.362  Sum_probs=31.0

Q ss_pred             HHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccch
Q psy16800        147 LTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRR  187 (221)
Q Consensus       147 l~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRR  187 (221)
                      +..|+.+|....++...+...|+.+.+|+..||+.||-.+.
T Consensus        10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~   50 (56)
T PF11569_consen   10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM   50 (56)
T ss_dssp             -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred             hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence            45699999999999999999999999999999999996543

>KOG0773|consensus

Probab=96.07  E-value=0.0043  Score=56.56  Aligned_cols=61  Identities=18%  Similarity=0.305  Sum_probs=50.6

Q ss_pred             CCCCCcccCHHHHHHHHHHhh---hCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        135 NNSGRTNFTNKQLTELEKEFH---FNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       135 ~rr~Rt~ft~~Ql~~Le~~F~---~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      ..|.+..+......+|+....   ..+||+..++..||.++||+..||.+||.|.|.+..+-..
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~  302 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI  302 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence            455667899999999987743   2579999999999999999999999999999987664444

>KOG3623|consensus

Probab=94.66  E-value=0.023  Score=56.74  Aligned_cols=54  Identities=19%  Similarity=0.303  Sum_probs=48.3

Q ss_pred             cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        142 FTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       142 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      |+.. +..|..+|..|..|+..+...+|.+.+|..+.|+.||+++++......+.
T Consensus       564 ~~~p-~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rs  617 (1007)
T KOG3623|consen  564 FNHP-TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERS  617 (1007)
T ss_pred             cCCc-HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccC
Confidence            4433 78999999999999999999999999999999999999999998876654

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

Probab=91.16  E-value=0.22  Score=33.59  Aligned_cols=47  Identities=17%  Similarity=0.265  Sum_probs=36.0

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccch
Q psy16800        136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRR  187 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRR  187 (221)
                      +|+|..+|-++-..+-..++...     ....||..+|++..+|..|..|+.
T Consensus         1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~   47 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD   47 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred             CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence            46789999999888888888776     467899999999999999998753

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	221
1b72_A	97	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		7e-26
2r5y_A	88	Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO		1e-16
9ant_A	62	Antennapedia Homeodomain-Dna Complex Length = 62		2e-16
1hom_A	68	Determination Of The Three-Dimensional Structure Of		2e-16
1ahd_P	68	Determination Of The Nmr Solution Structure Of An A		2e-16
1ftz_A	70	Nuclear Magnetic Resonance Solution Structure Of Th		1e-15
1b8i_A	81	Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX		2e-15
1san_A	62	The Des(1-6)antennapedia Homeodomain: Comparison Of		3e-15
2h1k_A	63	Crystal Structure Of The Pdx1 Homeodomain In Comple		1e-14
2m34_A	71	Nmr Structure Of The Homeodomain Transcription Fact		7e-14
1puf_A	77	Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo		3e-13
2lp0_A	60	The Solution Structure Of Homeodomain-Protein Compl		3e-13
1jgg_A	60	Even-Skipped Homeodomain Complexed To At-Rich Dna L		8e-11
1hdd_C	61	Crystal Structure Of An Engrailed Homeodomain-Dna C		1e-10
3hdd_A	60	Engrailed Homeodomain Dna Complex Length = 60		1e-10
1p7j_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		3e-10
1p7i_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		3e-10
2hdd_A	61	Engrailed Homeodomain Q50k Variant Dna Complex Leng		4e-10
1ig7_A	58	Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58		5e-10
1enh_A	54	Structural Studies Of The Engrailed Homeodomain Len		6e-10
1du0_A	57	Engrailed Homeodomain Q50a Variant Dna Complex Leng		7e-10
3a01_A	93	Crystal Structure Of Aristaless And Clawless Homeod		9e-10
1ztr_A	61	Solution Structure Of Engrailed Homeodomain L16a Mu		1e-09
2cra_A	70	Solution Structure Of The Homeobox Domain Of Human		2e-09
2dmt_A	80	Solution Structure Of The Homeobox Domain Of Homeob		2e-09
2hos_A	63	Phage-selected Homeodomain Bound To Unmodified Dna		4e-09
2l7z_A	73	Nmr Structure Of A13 Homedomain Length = 73		6e-09
2ld5_A	67	Solution Nmr-Derived Complex Structure Of Hoxa13 Dn		6e-09
3rkq_A	58	Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Lengt		8e-09
2e1o_A	70	Solution Structure Of Rsgi Ruh-028, A Homeobox Doma		2e-08
2djn_A	70	The Solution Structure Of The Homeobox Domain Of Hu		4e-08
2l9r_A	69	Solution Nmr Structure Of Homeobox Domain Of Homeob		4e-08
1ftt_A	68	Thyroid Transcription Factor 1 Homeodomain (Rattus		9e-08
2l7f_P	68	Solution Structure Of The Pitx2 Homeodomain Length		1e-07
1zq3_P	68	Nmr Solution Structure Of The Bicoid Homeodomain Bo		1e-07
2l7m_P	68	Solution Structure Of The Pitx2 Homeodomain R24h Mu		2e-07
1nk2_P	77	VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES		3e-07
3a03_A	56	Crystal Structure Of Hox11l1 Homeodomain Length = 5		4e-07
2p81_A	44	Engrailed Homeodomain Helix-Turn-Helix Motif Length		4e-07
1qry_A	80	Homeobox Protein Vnd (Ventral Nervous System Defect		1e-06
2vi6_A	62	Crystal Structure Of The Nanog Homeodomain Length =		1e-06
2m0c_A	75	Solution Nmr Structure Of Homeobox Domain Of Human		5e-06
2kt0_A	84	Solution Structure Of Human Stem Cell Transcription		8e-06
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		2e-05
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		2e-05
1fjl_A	81	Homeodomain From The Drosophila Paired Protein Boun		2e-05
2cue_A	80	Solution Structure Of The Homeobox Domain Of The Hu		4e-05
2dmu_A	70	Solution Structure Of The Homeobox Domain Of Homeob		5e-05
3cmy_A	61	Structure Of A Homeodomain In Complex With Dna Leng		5e-05
3a02_A	60	Crystal Structure Of Aristaless Homeodomain Length		1e-04
2dms_A	80	Solution Structure Of The Homeobox Domain Of Homeob		2e-04

>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Length = 97

Iteration: 1
 Score =  113 bits (283), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 58/95 (61%), Positives = 69/95 (72%), Gaps = 1/95 (1%)
Query: 104 HPTSPSTDYTTPLTALKYPPPAALSQHQSLLNNSG-RTNFTNKQLTELEKEFHFNKYLTR 162
            P +P+      +   + PP  A      L + SG RTNFT +QLTELEKEFHFNKYL+R
Sbjct: 2   EPNTPTARTFDWMKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSR 61
Query: 163 ARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG 197
           ARR+EIA+ L+LNETQVKIWFQNRRMKQKKR +EG
Sbjct: 62  ARRVEIAATLELNETQVKIWFQNRRMKQKKREREG 96

>pdb|2R5Y|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd Site Length = 88

Iteration: 1
 Score = 82.8 bits (203), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 44/77 (57%), Positives = 51/77 (66%), Gaps = 5/77 (6%)
Query: 121 YPPPAALSQHQSLLNNSG-----RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLN 175
           YP    +    S +N +G     RT++T  Q  ELEKEFHFN+YLTR RRIEIA  L L 
Sbjct: 9   YPWMKRVHLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLT 68
Query: 176 ETQVKIWFQNRRMKQKK 192
           E Q+KIWFQNRRMK KK
Sbjct: 69  ERQIKIWFQNRRMKWKK 85

>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex Length = 62

Iteration: 1
 Score = 82.4 bits (202), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 39/55 (70%), Positives = 42/55 (76%)
Query: 138 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           GR  +T  Q  ELEKEFHFN+YLTR RRIEIA  L L E Q+KIWFQNRRMK KK
Sbjct: 6   GRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 60

>pdb|1HOM|A Chain A, Determination Of The Three-Dimensional Structure Of The Antennapedia Homeodomain From Drosophila In Solution By 1h Nuclear Magnetic Resonance Spectroscopy Length = 68

Iteration: 1
 Score = 82.0 bits (201), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 39/59 (66%), Positives = 43/59 (72%)
Query: 134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           +   GR  +T  Q  ELEKEFHFN+YLTR RRIEIA  L L E Q+KIWFQNRRMK KK
Sbjct: 1   MRKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 59

>pdb|1AHD|P Chain P, Determination Of The Nmr Solution Structure Of An Antennapedia Homeodomain-Dna Complex Length = 68

Iteration: 1
 Score = 82.0 bits (201), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 39/55 (70%), Positives = 42/55 (76%)
Query: 138 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           GR  +T  Q  ELEKEFHFN+YLTR RRIEIA  L L E Q+KIWFQNRRMK KK
Sbjct: 5   GRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 59

>pdb|1FTZ|A Chain A, Nuclear Magnetic Resonance Solution Structure Of The Fushi Tarazu Homeodomain From Drosophila And Comparison With The Antennapedia Homeodomain Length = 70

Iteration: 1
 Score = 79.7 bits (195), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 36/54 (66%), Positives = 43/54 (79%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           R  +T  Q  ELEKEFHFN+Y+TR RRI+IA+ L L+E Q+KIWFQNRRMK KK
Sbjct: 7   RQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKK 60

>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX Length = 81

Iteration: 1
 Score = 79.0 bits (193), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 39/62 (62%), Positives = 43/62 (69%)
Query: 134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
           L   GR  +T  Q  ELEKEFH N YLTR RRIE+A  L L E Q+KIWFQNRRMK KK 
Sbjct: 19  LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE 78
Query: 194 IK 195
           I+
Sbjct: 79  IQ 80

>pdb|1SAN|A Chain A, The Des(1-6)antennapedia Homeodomain: Comparison Of The Nmr Solution Structure And The Dna Binding Affinity With The Intact Antennapedia Homeodomain Length = 62

Iteration: 1
 Score = 78.6 bits (192), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 37/51 (72%), Positives = 40/51 (78%)
Query: 142 FTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           +T  Q  ELEKEFHFN+YLTR RRIEIA  L L E Q+KIWFQNRRMK KK
Sbjct: 3   YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 53

>pdb|2H1K|A Chain A, Crystal Structure Of The Pdx1 Homeodomain In Complex With Dna Length = 63

Iteration: 1
 Score = 76.6 bits (187), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 36/58 (62%), Positives = 43/58 (74%)
Query: 135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           N   RT +T  QL ELEKEF FNKY++R RR+E+A +L L E  +KIWFQNRRMK KK
Sbjct: 3   NKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60

>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1 From Homo Sapiens Length = 71

Iteration: 1
 Score = 73.9 bits (180), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 38/59 (64%), Positives = 44/59 (74%), Gaps = 1/59 (1%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG 197
           RT FT++QL ELEKEFH  KYL+   R +IA  L+L+E QVKIWFQNRR K  KRIK G
Sbjct: 11  RTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKW-KRIKAG 68

>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To Dna Length = 77

Iteration: 1
 Score = 72.0 bits (175), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 36/54 (66%), Positives = 39/54 (72%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           R  +T  Q  ELEKEF FN YLTR RR E+A +L L E QVKIWFQNRRMK KK
Sbjct: 17  RCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70

>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex Length = 60

Iteration: 1
 Score = 71.6 bits (174), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 37/54 (68%), Positives = 39/54 (72%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           R  +T  Q  ELEKEF FN YLTR RR E+A VL L E QVKIWFQNRRMK KK
Sbjct: 5   RCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58

>pdb|1JGG|A Chain A, Even-Skipped Homeodomain Complexed To At-Rich Dna Length = 60

Iteration: 1
 Score = 63.5 bits (153), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 30/54 (55%), Positives = 39/54 (72%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT FT  QL  LEKEF+   Y++R RR E+A+ L L E+ +K+WFQNRRMK K+
Sbjct: 5   RTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 58

>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna Complex At 2.8 Angstroms Resolution: A Framework For Understanding Homeodomain-Dna Interactions Length = 61

Iteration: 1
 Score = 62.8 bits (151), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 30/54 (55%), Positives = 42/54 (77%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT F+++QL  L++EF+ N+YLT  RR +++S L LNE Q+KIWFQN+R K KK
Sbjct: 7   RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60

>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex Length = 60

Iteration: 1
 Score = 62.8 bits (151), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 30/54 (55%), Positives = 42/54 (77%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT F+++QL  L++EF+ N+YLT  RR +++S L LNE Q+KIWFQN+R K KK
Sbjct: 5   RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58

>pdb|1P7J|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52e Length = 59

Iteration: 1
 Score = 62.0 bits (149), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/54 (55%), Positives = 41/54 (75%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT F+++QL  L++EF+ N+YLT  RR +++S L LNE Q+KIWFQN R K KK
Sbjct: 5   RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58

>pdb|1P7I|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52a Length = 59

Iteration: 1
 Score = 61.6 bits (148), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/54 (55%), Positives = 41/54 (75%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT F+++QL  L++EF+ N+YLT  RR +++S L LNE Q+KIWFQN R K KK
Sbjct: 5   RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58

>pdb|2HDD|A Chain A, Engrailed Homeodomain Q50k Variant Dna Complex Length = 61

Iteration: 1
 Score = 61.2 bits (147), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 29/54 (53%), Positives = 42/54 (77%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT F+++QL  L++EF+ N+YLT  RR +++S L LNE Q+KIWF+N+R K KK
Sbjct: 7   RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58

Iteration: 1
 Score = 61.2 bits (147), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 31/54 (57%), Positives = 37/54 (68%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT FT  QL  LE++F   +YL+ A R E +S L L ETQVKIWFQNRR K K+
Sbjct: 4   RTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain Length = 54

Iteration: 1
 Score = 60.8 bits (146), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 28/51 (54%), Positives = 40/51 (78%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMK 189
           RT F+++QL  L++EF+ N+YLT  RR +++S L LNE Q+KIWFQN+R K
Sbjct: 3   RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53

>pdb|1DU0|A Chain A, Engrailed Homeodomain Q50a Variant Dna Complex Length = 57

Iteration: 1
 Score = 60.5 bits (145), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 29/54 (53%), Positives = 41/54 (75%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT F+++QL  L++EF+ N+YLT  RR +++S L LNE Q+KIWF N+R K KK
Sbjct: 3   RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56

>pdb|3A01|A Chain A, Crystal Structure Of Aristaless And Clawless Homeodomains Bo Length = 93

Iteration: 1
 Score = 60.1 bits (144), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 29/58 (50%), Positives = 38/58 (65%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196
           RT+FT  Q+ ELEK FH  KYL  A R  +A  L++ + QVK WFQNRR K +++  E
Sbjct: 21  RTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAE 78

>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant Length = 61

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 27/51 (52%), Positives = 39/51 (76%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMK 189
           RT F+++QL   ++EF+ N+YLT  RR +++S L LNE Q+KIWFQN+R K
Sbjct: 7   RTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 57

>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo Box B13 Length = 70

Iteration: 1
 Score = 58.9 bits (141), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 40/54 (74%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           R  ++  QL ELE+E+  NK++T+ +R +I++   L+E Q+ IWFQNRR+K+KK
Sbjct: 11  RIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64

>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox Protein Barh-Like 1 Length = 80

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 30/54 (55%), Positives = 36/54 (66%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT FT  QL  LEK F   KYL+   RI++A  L L++ QVK W+QNRRMK KK
Sbjct: 21  RTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKK 74

>pdb|2HOS|A Chain A, Phage-selected Homeodomain Bound To Unmodified Dna Length = 63

Iteration: 1
 Score = 57.8 bits (138), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 29/54 (53%), Positives = 40/54 (74%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT F+++QL  L++EF+ N+YLT  RR +++S L LNE QVK WF+N R K KK
Sbjct: 8   RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61

>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain Length = 73

Iteration: 1
 Score = 57.4 bits (137), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 28/56 (50%), Positives = 40/56 (71%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRI 194
           R  +T  QL ELE+E+  NK++T+ +R  I++   L+E QV IWFQNRR+K+KK I
Sbjct: 11  RVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVI 66

>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna Binding Domain Bound To Dna Length = 67

Iteration: 1
 Score = 57.4 bits (137), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 39/53 (73%)
Query: 142 FTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRI 194
           +T  QL ELE+E+  NK++T+ +R  I++   L+E QV IWFQNRR+K+KK I
Sbjct: 8   YTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVI 60

>pdb|3RKQ|A Chain A, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Length = 58

Iteration: 1
 Score = 57.0 bits (136), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 36/53 (67%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK 191
           R  F+  Q+ ELE+ F   +YL+   R ++ASVL+L  TQVKIWFQNRR K K
Sbjct: 6   RVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From Human Cdna Length = 70

Iteration: 1
 Score = 55.8 bits (133), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 27/51 (52%), Positives = 35/51 (68%)
Query: 142 FTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           F+N Q  ELEK+F   KYL+   R  +A +LQL+E QVK WFQNRR K ++
Sbjct: 14  FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64

>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human Homeobox Protein Dlx-5 Length = 70

Iteration: 1
 Score = 54.7 bits (130), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 36/54 (66%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT +++ QL  L++ F   +YL    R E+A+ L L +TQVKIWFQN+R K KK
Sbjct: 11  RTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64

>pdb|2L9R|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Homeobox Protein Nkx-3.1 From Homo Sapiens, Northeast Structural Genomics Consortium Target Hr6470a Length = 69

Iteration: 1
 Score = 54.7 bits (130), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 26/48 (54%), Positives = 34/48 (70%)
Query: 146 QLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
           Q+ ELE++F   KYL+   R  +A  L+L ETQVKIWFQNRR K K++
Sbjct: 15  QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRK 62

>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus Norvegicus) Length = 68

Iteration: 1
 Score = 53.5 bits (127), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 27/63 (42%), Positives = 38/63 (60%)
Query: 134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
           +    R  F+  Q+ ELE+ F   KYL+   R  +AS++ L  TQVKIWFQN R K K++
Sbjct: 1   MRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60
Query: 194 IKE 196
            K+
Sbjct: 61  AKD 63

>pdb|2L7F|P Chain P, Solution Structure Of The Pitx2 Homeodomain Length = 68

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/55 (49%), Positives = 37/55 (67%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
           RT+FT++QL ELE  F  N+Y   + R EIA    L E +V++WF+NRR K +KR
Sbjct: 7   RTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61

>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To The Consensus Dna Binding Site Taatcc Length = 68

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/53 (47%), Positives = 35/53 (66%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK 191
           RT FT+ Q+ ELE+ F   +YLT  R  ++++ L L   QVKIWF+NRR + K
Sbjct: 6   RTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58

>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant Length = 68

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/55 (49%), Positives = 36/55 (65%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
           RT+FT++QL ELE  F  N Y   + R EIA    L E +V++WF+NRR K +KR
Sbjct: 7   RTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61

>pdb|1NK2|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES Length = 77

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 34/54 (62%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           R  FT  Q  ELE+ F   +YL+   R  +AS+++L  TQVKIWFQN R K K+
Sbjct: 13  RVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66

>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain Length = 56

Iteration: 1
 Score = 51.2 bits (121), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 24/54 (44%), Positives = 35/54 (64%)
Query: 140 TNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
           T+F+  Q+ ELE+ F   KYL  A R  +A  L++ + QVK WFQNRR K +++
Sbjct: 2   TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif Length = 44

Iteration: 1
 Score = 51.2 bits (121), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 24/41 (58%), Positives = 32/41 (78%)
Query: 152 KEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           +EF+ N+YLT  RR +++S L LNE Q+KIWFQN+R K KK
Sbjct: 3   REFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43

>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective Protein) Length = 80

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 33/54 (61%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           R  FT  Q  ELE+ F   +YL+   R  + S+++L  TQVKIWFQN R K K+
Sbjct: 16  RVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKR 69

>pdb|2VI6|A Chain A, Crystal Structure Of The Nanog Homeodomain Length = 62

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 25/54 (46%), Positives = 35/54 (64%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT F+  QL  L+  F   KYL+  +  E++S+L L+  QVK WFQN+RMK K+
Sbjct: 7   RTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60

>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4, Northeast Structural Genomics Consortium (Nesg) Target Hr4490c Length = 75

Iteration: 1
 Score = 47.8 bits (112), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 30/73 (41%), Positives = 41/73 (56%), Gaps = 5/73 (6%)
Query: 132 SLLNNSG-----RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNR 186
           S ++N G     RT FT+ QL ELEK F    Y     R ++A    L E +V++WFQNR
Sbjct: 1   SHMSNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNR 60
Query: 187 RMKQKKRIKEGIL 199
           R K +KR + G +
Sbjct: 61  RAKWRKRERFGQM 73

>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor Nanog Homeodomain Fragment Length = 84

Iteration: 1
 Score = 47.0 bits (110), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 24/54 (44%), Positives = 35/54 (64%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT F++ QL  L   F   KYL+  +  E++++L L+  QVK WFQN+RMK K+
Sbjct: 26  RTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKR 79

>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna Length = 58

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 33/54 (61%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT FT+ QL ELEK F    Y     R E+A  + L E ++++WFQNRR K +K
Sbjct: 3   RTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56

>pdb|3A01|B Chain B, Crystal Structure Of Aristaless And Clawless Homeodomains Bo Length = 67

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 35/57 (61%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195
           RT FT+ QL ELEK F    Y     R E+A  + L E ++++WFQNRR K +K+ K
Sbjct: 10  RTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 66

>pdb|1FJL|A Chain A, Homeodomain From The Drosophila Paired Protein Bound To A Dna Oligonucleotide Length = 81

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 32/55 (58%)
Query: 138 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
            RT F+  QL ELE+ F   +Y     R E+A    L E ++++WFQNRR + +K
Sbjct: 21  SRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK 75

>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human Paired Box Protein Pax-6 Length = 80

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/57 (38%), Positives = 34/57 (59%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195
           RT+FT +Q+  LEKEF    Y     R  +A+ + L E ++++WF NRR K ++  K
Sbjct: 11  RTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 67

>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox Protein Goosecoid Length = 70

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/54 (40%), Positives = 33/54 (61%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT FT++QL  LE  F   KY     R ++A  + L E +V++WF+NRR K ++
Sbjct: 11  RTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRR 64

>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna Length = 61

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 32/55 (58%)
Query: 138 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
            RT FT +QL ELE+ F    Y     R E+A   +L E +V++WF NRR + +K
Sbjct: 5   SRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRK 59

>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain Length = 60

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 33/55 (60%)
Query: 141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195
            FT+ QL ELEK F    Y     R E+A  + L E ++++WFQNRR K +K+ K
Sbjct: 5   TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 59

>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox Protein Otx2 Length = 80

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/51 (43%), Positives = 30/51 (58%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMK 189
           RT FT  QL  LE  F   +Y     R E+A  + L E++V++WF+NRR K
Sbjct: 11  RTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAK 61

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	221
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	5e-37
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	4e-33
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	6e-33
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	1e-32
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	4e-32
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	5e-32
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	9e-31
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	1e-30
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	1e-30
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	5e-30
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	6e-30
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	3e-29
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	7e-29
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	8e-29
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	4e-28
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	6e-28
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	9e-28
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	3e-27
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	5e-27
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	6e-27
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	1e-26
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	1e-26
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	2e-26
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	3e-24
1e3o_C	160	Octamer-binding transcription factor 1; transcript	3e-20
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	3e-17
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	4e-17
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	1e-16
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	1e-16
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	2e-16
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	2e-15
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	4e-15
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	5e-15
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	9e-15
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	1e-14
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	1e-14
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	2e-14
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	4e-14
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	4e-14
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	5e-14
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	1e-13
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	1e-13
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	2e-13
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	2e-13
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	5e-13
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	6e-12
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	7e-12
1uhs_A	72	HOP, homeodomain only protein; structural genomics	9e-12
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	2e-10
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	8e-10
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	1e-09
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	4e-07
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	2e-06
1lfb_A	99	Liver transcription factor (LFB1); transcription r	4e-06
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	5e-06
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	9e-06
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	5e-05
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	6e-05
2e19_A	64	Transcription factor 8; homeobox domain, structura	2e-04
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	7e-04

>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 Length = 97

 Score =  124 bits (312), Expect = 5e-37
 Identities = 53/76 (69%), Positives = 62/76 (81%)

Query: 122 PPPAALSQHQSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKI 181
           P  A +S+      +  RTNFT +QLTELEKEFHFNKYL+RARR+EIA+ L+LNETQVKI
Sbjct: 21  PKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKI 80

Query: 182 WFQNRRMKQKKRIKEG 197
           WFQNRRMKQKKR +EG
Sbjct: 81  WFQNRRMKQKKREREG 96

>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 Length = 61

 Score =  112 bits (283), Expect = 4e-33
 Identities = 29/55 (52%), Positives = 42/55 (76%)

Query: 138 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
            RT F+++QL  L++EF+ N+YLT  RR +++S L LNE Q+KIWF+N+R K KK
Sbjct: 6   PRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA complex, transcription/DNA complex; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 Length = 60

 Score =  112 bits (282), Expect = 6e-33
 Identities = 30/56 (53%), Positives = 40/56 (71%)

Query: 138 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
            RT FT  QL  LEKEF+   Y++R RR E+A+ L L E+ +K+WFQNRRMK K++
Sbjct: 4   YRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59

>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix, helix-turn-helix; NMR {Drosophila melanogaster} SCOP: a.4.1.1 Length = 68

 Score =  112 bits (281), Expect = 1e-32
 Identities = 25/59 (42%), Positives = 37/59 (62%)

Query: 138 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196
            RT FT+ Q+ ELE+ F   +YLT  R  ++++ L L   QVKIWF+NRR + K +  +
Sbjct: 5   TRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ 63

>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A* Length = 88

 Score =  111 bits (279), Expect = 4e-32
 Identities = 40/58 (68%), Positives = 44/58 (75%)

Query: 138 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195
            RT++T  Q  ELEKEFHFN+YLTR RRIEIA  L L E Q+KIWFQNRRMK KK  K
Sbjct: 31  QRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEHK 88

>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* Length = 81

 Score =  110 bits (277), Expect = 5e-32
 Identities = 39/68 (57%), Positives = 44/68 (64%)

Query: 128 SQHQSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRR 187
               + L   GR  +T  Q  ELEKEFH N YLTR RRIE+A  L L E Q+KIWFQNRR
Sbjct: 13  IAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRR 72

Query: 188 MKQKKRIK 195
           MK KK I+
Sbjct: 73  MKLKKEIQ 80

>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 Length = 68

 Score =  107 bits (268), Expect = 9e-31
 Identities = 40/63 (63%), Positives = 44/63 (69%)

Query: 134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
           +   GR  +T  Q  ELEKEFHFN+YLTR RRIEIA  L L E Q+KIWFQNRRMK KK 
Sbjct: 1   MRKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 60

Query: 194 IKE 196
            K 
Sbjct: 61  NKT 63

>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 Length = 70

 Score =  107 bits (268), Expect = 1e-30
 Identities = 28/59 (47%), Positives = 37/59 (62%)

Query: 138 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196
           G+  F+N Q  ELEK+F   KYL+   R  +A +LQL+E QVK WFQNRR K ++    
Sbjct: 10  GQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGPS 68

>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus} Length = 63

 Score =  106 bits (267), Expect = 1e-30
 Identities = 35/55 (63%), Positives = 42/55 (76%)

Query: 138 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
            RT +T  QL ELEKEF FNKY++R RR+E+A +L L E  +KIWFQNRRMK KK
Sbjct: 6   TRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60

>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} Length = 80

 Score =  105 bits (264), Expect = 5e-30
 Identities = 30/59 (50%), Positives = 36/59 (61%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG 197
           RT FT  QL  LEK F   KYL+   RI++A  L L++ QVK W+QNRRMK KK     
Sbjct: 21  RTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGPSS 79

>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1 Length = 58

 Score =  104 bits (262), Expect = 6e-30
 Identities = 31/54 (57%), Positives = 37/54 (68%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT FT  QL  LE++F   +YL+ A R E +S L L ETQVKIWFQNRR K K+
Sbjct: 4   RTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster} Length = 93

 Score =  103 bits (259), Expect = 3e-29
 Identities = 29/60 (48%), Positives = 38/60 (63%)

Query: 138 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG 197
            RT+FT  Q+ ELEK FH  KYL  A R  +A  L++ + QVK WFQNRR K +++  E 
Sbjct: 20  PRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEE 79

>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 70

 Score =  102 bits (256), Expect = 7e-29
 Identities = 26/59 (44%), Positives = 36/59 (61%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG 197
           RT +++ QL  L++ F   +YL    R E+A+ L L +TQVKIWFQN+R K KK     
Sbjct: 11  RTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGPSS 69

>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Length = 69

 Score =  102 bits (255), Expect = 8e-29
 Identities = 27/61 (44%), Positives = 39/61 (63%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGI 198
            ++ ++ Q+ ELE++F   KYL+   R  +A  L+L ETQVKIWFQNRR K K++     
Sbjct: 8   HSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSE 67

Query: 199 L 199
           L
Sbjct: 68  L 68

>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 Length = 77

 Score =  100 bits (251), Expect = 4e-28
 Identities = 37/59 (62%), Positives = 41/59 (69%)

Query: 138 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196
            R  +T  Q  ELEKEF FN YLTR RR E+A +L L E QVKIWFQNRRMK KK  K+
Sbjct: 16  KRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD 74

>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus} Length = 62

 Score = 99.7 bits (249), Expect = 6e-28
 Identities = 25/55 (45%), Positives = 35/55 (63%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
           RT F+  QL  L+  F   KYL+  +  E++S+L L+  QVK WFQN+RMK K+ 
Sbjct: 7   RTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW 61

>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens} Length = 84

 Score = 99.9 bits (249), Expect = 9e-28
 Identities = 25/58 (43%), Positives = 36/58 (62%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196
           RT F++ QL  L   F   KYL+  +  E++++L L+  QVK WFQN+RMK K+  K 
Sbjct: 26  RTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQKN 83

>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens} Length = 56

 Score = 97.8 bits (244), Expect = 3e-27
 Identities = 24/54 (44%), Positives = 35/54 (64%)

Query: 140 TNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
           T+F+  Q+ ELE+ F   KYL  A R  +A  L++ + QVK WFQNRR K +++
Sbjct: 2   TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

>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 Length = 77

 Score = 97.9 bits (244), Expect = 5e-27
 Identities = 27/59 (45%), Positives = 35/59 (59%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG 197
           R  FT  Q  ELE+ F   +YL+   R  +AS+++L  TQVKIWFQN R K K+   E 
Sbjct: 13  RVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEK 71

>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 70

 Score = 97.6 bits (243), Expect = 6e-27
 Identities = 25/59 (42%), Positives = 40/59 (67%)

Query: 138 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196
            R  ++  QL ELE+E+  NK++T+ +R +I++   L+E Q+ IWFQNRR+K+KK    
Sbjct: 10  KRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGPS 68

>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 68

 Score = 96.6 bits (241), Expect = 1e-26
 Identities = 27/59 (45%), Positives = 37/59 (62%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG 197
           R  F+  Q+ ELE+ F   KYL+   R  +AS++ L  TQVKIWFQN R K K++ K+ 
Sbjct: 6   RVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDK 64

>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A* Length = 73

 Score = 96.8 bits (241), Expect = 1e-26
 Identities = 28/59 (47%), Positives = 41/59 (69%)

Query: 138 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196
            R  +T  QL ELE+E+  NK++T+ +R  I++   L+E QV IWFQNRR+K+KK I +
Sbjct: 10  KRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINK 68

>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens} Length = 58

 Score = 95.8 bits (239), Expect = 2e-26
 Identities = 28/53 (52%), Positives = 36/53 (67%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK 191
           R  F+  Q+ ELE+ F   +YL+   R ++ASVL+L  TQVKIWFQNRR K K
Sbjct: 6   RVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

>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* Length = 61

 Score = 89.9 bits (224), Expect = 3e-24
 Identities = 14/53 (26%), Positives = 28/53 (52%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK 191
           +++ + +    LE+ F   + L    + E+A    +   QV++WF N+RM+ K
Sbjct: 9   KSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61

>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 Length = 160

 Score = 82.7 bits (204), Expect = 3e-20
 Identities = 18/54 (33%), Positives = 27/54 (50%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT+        LEK F  N+  T      IA  L + +  +++WF NRR K+K+
Sbjct: 105 RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 158

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

 Score = 74.7 bits (183), Expect = 3e-17
 Identities = 17/59 (28%), Positives = 25/59 (42%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG 197
           RT+        LE  F      +      +A  LQL +  V++WF NRR K+K+     
Sbjct: 103 RTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTPAA 161

>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 Length = 146

 Score = 74.3 bits (182), Expect = 4e-17
 Identities = 15/54 (27%), Positives = 27/54 (50%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT  +      LE+ F  +   +    + +A  L L +  V++WF NRR ++K+
Sbjct: 91  RTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 144

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

 Score = 71.0 bits (174), Expect = 1e-16
 Identities = 18/58 (31%), Positives = 30/58 (51%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196
           RT  T +QL  L +++  +   TR     IA  + L +  V++WFQN R +++K    
Sbjct: 21  RTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSGPS 78

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

 Score = 70.5 bits (173), Expect = 1e-16
 Identities = 12/57 (21%), Positives = 28/57 (49%)

Query: 137 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
             +   +++QL+ L+  F  N++  ++    +  V  L+  +V+ WF +RR   +  
Sbjct: 10  IYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNL 66

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

 Score = 70.1 bits (172), Expect = 2e-16
 Identities = 19/58 (32%), Positives = 29/58 (50%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196
           RT FT+ QL  L+  F  N Y       +++++L L    + +WFQN R K +K    
Sbjct: 11  RTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGPS 68

>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70

 Score = 67.4 bits (165), Expect = 2e-15
 Identities = 16/59 (27%), Positives = 27/59 (45%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG 197
           RT  T+ QL  L + F  N   +  +  E+A    L +  +K WF+N   K+++     
Sbjct: 11  RTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGPSS 69

>3a02_A Homeobox protein aristaless; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.00A {Drosophila melanogaster} PDB: 3lnq_A 3cmy_A Length = 60

 Score = 66.5 bits (163), Expect = 4e-15
 Identities = 24/57 (42%), Positives = 33/57 (57%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195
              FT+ QL ELEK F    Y     R E+A  + L E ++++WFQNRR K +K+ K
Sbjct: 3   HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 59

>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant, DNA binding protein, developmental protein, disease mutation, DNA-binding; NMR {Homo sapiens} Length = 67

 Score = 66.2 bits (162), Expect = 5e-15
 Identities = 23/59 (38%), Positives = 31/59 (52%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG 197
           RT FT  Q+  LE  F  N Y       ++A  L L   +++IWFQNRR K K+  +E 
Sbjct: 5   RTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRES 63

>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 73

 Score = 65.9 bits (161), Expect = 9e-15
 Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 139 RTNFTNKQLTELEKEFH-FNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
            +  T  Q+  LE  F+  NK+        IA+   L E Q + WF+ R  + ++ 
Sbjct: 6   VSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 61

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

 Score = 65.1 bits (159), Expect = 1e-14
 Identities = 17/55 (30%), Positives = 27/55 (49%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
           RT    KQL  L   +  N       + ++  +  L+   +++WFQN+R K KKR
Sbjct: 7   RTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

>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 Length = 155

 Score = 67.4 bits (164), Expect = 1e-14
 Identities = 18/54 (33%), Positives = 28/54 (51%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT+  N+    LE  F  +   +  +   IA+ L L +  V++WF NRR K K+
Sbjct: 100 RTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKR 153

>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 Length = 68

 Score = 65.0 bits (159), Expect = 2e-14
 Identities = 26/57 (45%), Positives = 38/57 (66%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195
           RT+FT++QL +LE  F  N+Y   + R EIA    L E +V++WF+NRR K +KR +
Sbjct: 7   RTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREE 63

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

 Score = 66.8 bits (162), Expect = 4e-14
 Identities = 17/58 (29%), Positives = 26/58 (44%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196
           R  FT+ Q   L   F  NK  ++  +I I+  L L  + V  +F N R +   +  E
Sbjct: 101 RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWLE 158

>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} Length = 151

 Score = 66.2 bits (161), Expect = 4e-14
 Identities = 18/54 (33%), Positives = 25/54 (46%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT+FT + +  L   F  N   T     E+A  L  +   V++WF NRR   K 
Sbjct: 97  RTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN 150

>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 64.0 bits (156), Expect = 5e-14
 Identities = 15/57 (26%), Positives = 28/57 (49%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195
           RT+F + QL  ++  F  N         ++A    L +  +++WFQN R K ++ + 
Sbjct: 11  RTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLL 67

>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 70

 Score = 62.7 bits (153), Expect = 1e-13
 Identities = 22/57 (38%), Positives = 33/57 (57%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195
           RT FT++QL  LE  F   KY     R ++A  + L E +V++WF+NRR K ++   
Sbjct: 11  RTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP 67

>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 Length = 81

 Score = 63.2 bits (154), Expect = 1e-13
 Identities = 22/57 (38%), Positives = 33/57 (57%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195
           RT F+  QL ELE+ F   +Y     R E+A    L E ++++WFQNRR + +K+  
Sbjct: 22  RTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT 78

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

 Score = 61.7 bits (150), Expect = 2e-13
 Identities = 13/70 (18%), Positives = 29/70 (41%), Gaps = 5/70 (7%)

Query: 127 LSQHQSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNR 186
           ++ H            T +Q+  L+  F  +++   A    +  V  L  +++K WF + 
Sbjct: 1   MAHHHH-----HHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDH 55

Query: 187 RMKQKKRIKE 196
           R + ++ I  
Sbjct: 56  RYRCQRGIVH 65

>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus} Length = 80

 Score = 62.1 bits (151), Expect = 2e-13
 Identities = 22/59 (37%), Positives = 35/59 (59%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG 197
           RT FT  QL  LE  F   +Y     R E+A  + L E++V++WF+NRR K +++ ++ 
Sbjct: 11  RTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQ 69

>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 80

 Score = 61.6 bits (150), Expect = 5e-13
 Identities = 22/59 (37%), Positives = 34/59 (57%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG 197
           RT+FT +Q+  LEKEF    Y     R  +A+ + L E ++++WF NRR K ++  K  
Sbjct: 11  RTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLR 69

>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor, structural genomics, loop insertion, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 95

 Score = 58.9 bits (142), Expect = 6e-12
 Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 15/74 (20%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVL---------------QLNETQVKIWF 183
           R  +  + L  +E  F+ N+Y   A+R EIA+                 ++   +V  WF
Sbjct: 11  RFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWF 70

Query: 184 QNRRMKQKKRIKEG 197
            NRR + K+R    
Sbjct: 71  ANRRKEIKRRANIA 84

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

 Score = 57.9 bits (140), Expect = 7e-12
 Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 1/59 (1%)

Query: 139 RTNFTNKQLTELEKEFH-FNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196
           RT  + + L  L+   H    Y  +     +++ L L +  +  +FQN+R   K     
Sbjct: 11  RTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHSGPS 69

>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 Length = 72

 Score = 57.8 bits (140), Expect = 9e-12
 Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 1/56 (1%)

Query: 139 RTNFTNKQLTELEKEFH-FNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
               T  Q+  LE  F+  NK+        IA+   L E Q + WF+ R  + ++ 
Sbjct: 5   AATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60

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

 Score = 55.0 bits (132), Expect = 2e-10
 Identities = 12/50 (24%), Positives = 22/50 (44%)

Query: 143 TNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           T  Q+  LE  F  + + T+A    +    +L+  ++  WF  RR  +  
Sbjct: 21  TQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDS 70

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

 Score = 52.6 bits (126), Expect = 8e-10
 Identities = 12/54 (22%), Positives = 18/54 (33%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
                 +QL  LE  F  N          + S  ++   ++  WF  RR K   
Sbjct: 11  YKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNA 64

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

 Score = 52.7 bits (126), Expect = 1e-09
 Identities = 12/64 (18%), Positives = 27/64 (42%)

Query: 143 TNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILIGV 202
           T +QL  L+  F  +  LT      + +  +L   ++  WF  ++  +  + ++  +   
Sbjct: 19  TAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEIDES 78

Query: 203 GEGS 206
             GS
Sbjct: 79  NAGS 82

>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1 Length = 72

 Score = 45.2 bits (107), Expect = 4e-07
 Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 143 TNKQLTELEKEF-HFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
             +    LEK F    KY    R   ++  L  +  +++ WF++RR + K 
Sbjct: 16  KVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKP 66

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

 Score = 44.0 bits (103), Expect = 2e-06
 Identities = 15/86 (17%), Positives = 29/86 (33%), Gaps = 5/86 (5%)

Query: 107 SPSTDYTTPLTALKYPPPAALSQHQSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRI 166
           +    + +    + +  PA  S              T +QL  L+  F   ++ +     
Sbjct: 2   AHHHHHHSSGLEVLFQGPAPKSGSTG-----KICKKTPEQLHMLKSAFVRTQWPSPEEYD 56

Query: 167 EIASVLQLNETQVKIWFQNRRMKQKK 192
           ++A    L  T +  WF + R   K 
Sbjct: 57  KLAKESGLARTDIVSWFGDTRYAWKN 82

>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A Length = 99

 Score = 43.3 bits (101), Expect = 4e-06
 Identities = 13/78 (16%), Positives = 23/78 (29%), Gaps = 21/78 (26%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVL---------------------QLNET 177
           R  +       L + +   K  ++  R  +                          + E 
Sbjct: 13  RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 72

Query: 178 QVKIWFQNRRMKQKKRIK 195
           +V  WF NRR ++  R K
Sbjct: 73  RVYNWFANRRKEEAFRHK 90

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens} Length = 221

 Score = 45.0 bits (105), Expect = 5e-06
 Identities = 12/76 (15%), Positives = 22/76 (28%), Gaps = 21/76 (27%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVL---------------------QLNET 177
           R  +       L + +   K  ++  R  +                          + E 
Sbjct: 146 RFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEV 205

Query: 178 QVKIWFQNRRMKQKKR 193
           +V  WF NRR ++  R
Sbjct: 206 RVYNWFANRRKEEAFR 221

>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 Length = 194

 Score = 44.1 bits (103), Expect = 9e-06
 Identities = 12/76 (15%), Positives = 22/76 (28%), Gaps = 21/76 (27%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVL---------------------QLNET 177
           R  +       L + +   K  ++  R  +                          + E 
Sbjct: 119 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 178

Query: 178 QVKIWFQNRRMKQKKR 193
           +V  WF NRR ++  R
Sbjct: 179 RVYNWFANRRKEEAFR 194

>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.4.1.1 Length = 64

 Score = 39.0 bits (91), Expect = 5e-05
 Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 143 TNKQLTELEKEF-HFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           T +    LEK F    K+    R   ++  L  +   ++ WF+ RR ++K 
Sbjct: 8   TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 58

>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 Length = 76

 Score = 39.2 bits (91), Expect = 6e-05
 Identities = 12/56 (21%), Positives = 22/56 (39%)

Query: 137 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           S     T +QL  L+  F   ++  R    ++  +  L   ++  WF + R   K 
Sbjct: 5   SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH 60

>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 64

 Score = 37.3 bits (86), Expect = 2e-04
 Identities = 12/58 (20%), Positives = 21/58 (36%)

Query: 135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           + S         L+ L+  +  N   +     +IA  + L    VK WF+  +  Q  
Sbjct: 3   SGSSGQPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS 60

>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 36.5 bits (83), Expect = 7e-04
 Identities = 16/62 (25%), Positives = 29/62 (46%), Gaps = 4/62 (6%)

Query: 139 RTNFTNKQLTELEKEFH----FNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRI 194
           RT F+++ L  L+K +         + R +   +A+ L ++   V+ W  NRR K +   
Sbjct: 12  RTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMG 71

Query: 195 KE 196
            E
Sbjct: 72  IE 73

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	221
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.79
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.79
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.79
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.78
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.78
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.78
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.77
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.77
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.77
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.77
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.77
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.77
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.77
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.77
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.77
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.77
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.76
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.76
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.76
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.76
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.76
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.75
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.75
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.75
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.75
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.75
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.75
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.75
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.75
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.75
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.75
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.75
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.75
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.75
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.74
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.74
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.74
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.74
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.74
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.74
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.73
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.73
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.73
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.73
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.73
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.73
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.72
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.72
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.71
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.71
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.7
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.7
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.69
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.68
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.68
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.67
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.67
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.66
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.66
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.65
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.65
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.65
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.65
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.65
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.65
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.65
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.63
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.63
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.61
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.61
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.58
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.53
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.44
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.41
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.36
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.34
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.25
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.69
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	94.49

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

Probab=99.79  E-value=4.2e-20  Score=135.17  Aligned_cols=64  Identities=39%  Similarity=0.614  Sum_probs=60.2

Q ss_pred             CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      ...+|.||.|+..|+.+||.+|..++||+..++..||..|+|++.+|+|||||||+|+|+..+.
T Consensus        20 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k~   83 (84)
T 2kt0_A           20 VKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQKN   83 (84)
T ss_dssp             SCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhhc
Confidence            3468889999999999999999999999999999999999999999999999999999987764

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

Probab=99.79  E-value=7.3e-20  Score=132.94  Aligned_cols=65  Identities=34%  Similarity=0.502  Sum_probs=61.3

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhcc
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGI  198 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~  198 (221)
                      ..+|.|+.|+..|+.+||..|..++||+..++.+||..|+|++.+|+|||||||+|+|+..+...
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~~~   70 (80)
T 2dms_A            6 SGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQQ   70 (80)
T ss_dssp             CCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCSCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHccC
Confidence            45888999999999999999999999999999999999999999999999999999999887643

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

Probab=99.79  E-value=1e-19  Score=131.92  Aligned_cols=64  Identities=23%  Similarity=0.384  Sum_probs=60.8

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG  197 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g  197 (221)
                      ..+|.||.||..|+.+||.+|..++||+..++..||..|+|++.+|+|||||||+|+|++....
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~   69 (80)
T 2dmq_A            6 SGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQ   69 (80)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHHH
Confidence            3588899999999999999999999999999999999999999999999999999999988764

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

Probab=99.78  E-value=1.5e-19  Score=130.43  Aligned_cols=65  Identities=42%  Similarity=0.619  Sum_probs=61.1

Q ss_pred             CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800        133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG  197 (221)
Q Consensus       133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g  197 (221)
                      ...++.|+.||..|+.+||..|..++||+..++.+||..|+|++.+|+|||||||+|+|+.....
T Consensus         7 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~~   71 (77)
T 1nk2_P            7 NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEK   71 (77)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhccc
Confidence            34578899999999999999999999999999999999999999999999999999999988764

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

Probab=99.78  E-value=8.3e-20  Score=132.72  Aligned_cols=63  Identities=48%  Similarity=0.643  Sum_probs=59.3

Q ss_pred             CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      ...+|.||.||..|+.+||..|..++||+..++.+||..|+|++.+|+|||||||+|+|+...
T Consensus        15 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~~   77 (80)
T 2dmt_A           15 KKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGP   77 (80)
T ss_dssp             CCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCCS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcccC
Confidence            345788999999999999999999999999999999999999999999999999999998754

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

Probab=99.78  E-value=1.3e-19  Score=131.74  Aligned_cols=66  Identities=33%  Similarity=0.527  Sum_probs=62.0

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccc
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGIL  199 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~  199 (221)
                      ..+|.||.|+..|+.+||..|..++||+..++.+||..|+|++.+|+|||||||+|+|+..+....
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~~~   71 (80)
T 2cue_A            6 SGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQ   71 (80)
T ss_dssp             SSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhhhc
Confidence            458889999999999999999999999999999999999999999999999999999999887543

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

Probab=99.77  E-value=7.2e-20  Score=129.26  Aligned_cols=63  Identities=63%  Similarity=0.940  Sum_probs=59.9

Q ss_pred             CCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800        135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG  197 (221)
Q Consensus       135 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g  197 (221)
                      ++|.||.||..|+..||..|..++||+..++.+||..|+|++.+|+|||||||+|+|+..+..
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~~~   64 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTK   64 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSCCC
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhcccc
Confidence            478899999999999999999999999999999999999999999999999999999987654

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

Probab=99.77  E-value=1.2e-19  Score=127.98  Aligned_cols=65  Identities=42%  Similarity=0.662  Sum_probs=61.2

Q ss_pred             CCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccc
Q psy16800        135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGIL  199 (221)
Q Consensus       135 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~  199 (221)
                      +++.|+.||..|+.+||..|..++||+..++.+||..|||++.+|+|||||||+|+|+..+...+
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~~~~~   66 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDKAA   66 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSCCSS
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhhHhhh
Confidence            47889999999999999999999999999999999999999999999999999999998876543

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

Probab=99.77  E-value=1.2e-19  Score=126.07  Aligned_cols=60  Identities=60%  Similarity=0.940  Sum_probs=56.4

Q ss_pred             CCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHh
Q psy16800        135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRI  194 (221)
Q Consensus       135 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~  194 (221)
                      .+|.|+.||..|+.+||..|..++||+..++.+||..|+|++.+|+|||||||+|+|+..
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   62 (63)
T 2h1k_A            3 NKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE   62 (63)
T ss_dssp             --CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhhc
Confidence            478899999999999999999999999999999999999999999999999999999864

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

Probab=99.77  E-value=1.6e-19  Score=127.93  Aligned_cols=62  Identities=35%  Similarity=0.544  Sum_probs=59.0

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      ..+|.|+.||..|+.+||..|..++||+..++.+||..|+|++.+|+|||||||+|+|+...
T Consensus         6 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2dmu_A            6 SGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP   67 (70)
T ss_dssp             SSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTST
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccCC
Confidence            35788999999999999999999999999999999999999999999999999999998765

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

Probab=99.77  E-value=8.6e-20  Score=129.38  Aligned_cols=62  Identities=40%  Similarity=0.684  Sum_probs=58.8

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      ..++.|+.||..|+.+||..|..++||+..++.+||..|+|++.+|+|||||||+|+|+...
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (70)
T 2cra_A            6 SGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGP   67 (70)
T ss_dssp             CCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSCT
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccCC
Confidence            45788999999999999999999999999999999999999999999999999999998664

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

Probab=99.77  E-value=8.1e-20  Score=126.50  Aligned_cols=59  Identities=42%  Similarity=0.642  Sum_probs=53.1

Q ss_pred             CCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHH
Q psy16800        135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR  193 (221)
Q Consensus       135 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~  193 (221)
                      .++.||.||..|+.+||..|..++||+..++.+||..|+|++.+|+|||||||+|+|+.
T Consensus         3 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A            3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             -----CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            47889999999999999999999999999999999999999999999999999999985

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

Probab=99.77  E-value=1.8e-19  Score=122.94  Aligned_cols=57  Identities=54%  Similarity=0.800  Sum_probs=55.3

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHH
Q psy16800        136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK  192 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr  192 (221)
                      ++.|+.||..|+.+||..|..++||+..++.+||..|||++.+|++||||||+|+|+
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            477999999999999999999999999999999999999999999999999999987

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

Probab=99.77  E-value=2.4e-19  Score=126.50  Aligned_cols=63  Identities=40%  Similarity=0.659  Sum_probs=60.1

Q ss_pred             CCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800        135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG  197 (221)
Q Consensus       135 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g  197 (221)
                      .++.||.||..|+.+||..|..++||+..++..||..|+|++.+|+|||||||+|+|+.....
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~~   64 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQH   64 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhccc
Confidence            478899999999999999999999999999999999999999999999999999999988764

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

Probab=99.77  E-value=1.3e-19  Score=125.15  Aligned_cols=58  Identities=50%  Similarity=0.826  Sum_probs=53.3

Q ss_pred             CCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHH
Q psy16800        135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK  192 (221)
Q Consensus       135 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr  192 (221)
                      .+|.||.||..|+.+||..|..++||+..++.+||..|||++.+|+|||||||+|+|+
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            4788999999999999999999999999999999999999999999999999999987

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

Probab=99.77  E-value=1.2e-19  Score=131.27  Aligned_cols=62  Identities=29%  Similarity=0.393  Sum_probs=58.9

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      ..+|.||.||.+|+.+||..|..++||+..++++||..|+|++.+|+|||||||+|+|+...
T Consensus        16 ~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   77 (80)
T 2da3_A           16 RDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSGP   77 (80)
T ss_dssp             CCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhcc
Confidence            45888999999999999999999999999999999999999999999999999999998654

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

Probab=99.76  E-value=3.4e-19  Score=128.57  Aligned_cols=63  Identities=59%  Similarity=0.832  Sum_probs=60.1

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      ..++.|+.||..|+.+||..|..++||+..++.+||..|+|++.+|+|||||||+|+|+..+.
T Consensus        12 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k~   74 (77)
T 1puf_A           12 STRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             TTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhhh
Confidence            457889999999999999999999999999999999999999999999999999999998875

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

Probab=99.76  E-value=9.5e-20  Score=128.94  Aligned_cols=63  Identities=25%  Similarity=0.361  Sum_probs=59.5

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      ..++.|+.||..|+.+||..|..++||+..++.+||..|+|++.+|+|||||||+|+|+..+.
T Consensus         6 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (70)
T 2da1_A            6 SGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGPS   68 (70)
T ss_dssp             CCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhccc
Confidence            457889999999999999999999999999999999999999999999999999999987653

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

Probab=99.76  E-value=1.9e-19  Score=128.72  Aligned_cols=66  Identities=41%  Similarity=0.583  Sum_probs=61.9

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccc
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGIL  199 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~  199 (221)
                      ..++.|+.|+..|+.+||..|..++||+..++.+||..|+|++.+|+|||||||+|+|+..+.+.+
T Consensus         8 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r~~q~   73 (75)
T 2m0c_A            8 KKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRERFGQM   73 (75)
T ss_dssp             CCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCCCCSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHhhhhc
Confidence            457889999999999999999999999999999999999999999999999999999998877654

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

Probab=99.76  E-value=1.5e-19  Score=127.91  Aligned_cols=63  Identities=32%  Similarity=0.459  Sum_probs=59.2

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      ..++.|+.|+..|+.+||..|..++||+..++.+||..|+|++.+|+|||||||+|+|+....
T Consensus         6 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (70)
T 2da2_A            6 SGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGPS   68 (70)
T ss_dssp             CSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCSSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhcccc
Confidence            458889999999999999999999999999999999999999999999999999999986543

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

Probab=99.76  E-value=3.6e-19  Score=126.13  Aligned_cols=61  Identities=46%  Similarity=0.721  Sum_probs=58.4

Q ss_pred             CCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       135 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      .++.|+.||..|+.+||..|..++||+..++.+||..|+|++.+|+|||||||+|+|+...
T Consensus         7 ~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2e1o_A            7 GKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGP   67 (70)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCCC
Confidence            4778999999999999999999999999999999999999999999999999999999765

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

Probab=99.75  E-value=1.2e-19  Score=127.90  Aligned_cols=63  Identities=41%  Similarity=0.611  Sum_probs=60.3

Q ss_pred             CCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800        135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG  197 (221)
Q Consensus       135 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g  197 (221)
                      .++.|+.||..|+.+||..|..++||+..++..||..|+|++.+|+|||||||+|+|+..+.+
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~~~   65 (68)
T 1yz8_P            3 QRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEFI   65 (68)
T ss_dssp             SSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhhcc
Confidence            578899999999999999999999999999999999999999999999999999999988764

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

Probab=99.75  E-value=3e-19  Score=122.85  Aligned_cols=58  Identities=52%  Similarity=0.832  Sum_probs=55.5

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHH
Q psy16800        136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR  193 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~  193 (221)
                      +|.||.||..|+..||..|..++||+..++.+||..|||++.+|++||||||+|+|++
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   59 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHhHhhcc
Confidence            5789999999999999999999999999999999999999999999999999999985

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

Probab=99.75  E-value=4e-19  Score=127.08  Aligned_cols=63  Identities=44%  Similarity=0.725  Sum_probs=59.6

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      ..++.|+.||..|+.+||..|..++||+..++.+||..|+|++.+|+|||||||+|+|+....
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~   68 (73)
T 2l7z_A            6 EGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINK   68 (73)
T ss_dssp             CCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSSSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHhcc
Confidence            458889999999999999999999999999999999999999999999999999999987654

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

Probab=99.75  E-value=3.4e-19  Score=131.65  Aligned_cols=61  Identities=64%  Similarity=0.923  Sum_probs=55.7

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHh
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRI  194 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~  194 (221)
                      ..+|.||.||..|+.+||..|..++||+..++.+||..|+|++.+|+|||||||+|+|+..
T Consensus        27 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   87 (88)
T 2r5y_A           27 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH   87 (88)
T ss_dssp             ----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhhc
Confidence            4588899999999999999999999999999999999999999999999999999999865

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

Probab=99.75  E-value=2.2e-19  Score=130.39  Aligned_cols=64  Identities=25%  Similarity=0.325  Sum_probs=59.4

Q ss_pred             CCCCCCCcccCHHHHHHHHHHhhhC----CCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        133 LLNNSGRTNFTNKQLTELEKEFHFN----KYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~----~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      ...+|.||.||.+|+.+||.+|..+    +||+..++++||..|+|++.+|+|||||||+|+|+....
T Consensus         6 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~~~~   73 (80)
T 2da4_A            6 SGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMGIE   73 (80)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhccCC
Confidence            3458889999999999999999999    999999999999999999999999999999999986543

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

Probab=99.75  E-value=2.7e-19  Score=125.68  Aligned_cols=63  Identities=37%  Similarity=0.525  Sum_probs=59.7

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhcc
Q psy16800        136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGI  198 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~  198 (221)
                      +|.|+.||..|+.+||..|..++||+..++..||..|||++.+|++||||||+|+|+.....+
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~~~q   64 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRESQ   64 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCCTTC
T ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhchhcc
Confidence            688999999999999999999999999999999999999999999999999999999877643

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

Probab=99.75  E-value=1.8e-19  Score=127.76  Aligned_cols=62  Identities=42%  Similarity=0.611  Sum_probs=58.5

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      ..++.|+.||..|+.+||..|..++||+..++.+||..|+|++.+|+|||||||+|+|+...
T Consensus         6 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2djn_A            6 SGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGP   67 (70)
T ss_dssp             CCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccCC
Confidence            45888999999999999999999999999999999999999999999999999999988654

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

Probab=99.75  E-value=5.4e-19  Score=128.61  Aligned_cols=63  Identities=35%  Similarity=0.580  Sum_probs=59.3

Q ss_pred             CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      ...++.|+.|+..|+.+||..|..++||+..++..||..|+|++.+|+|||||||+|+|++..
T Consensus        16 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~   78 (81)
T 1fjl_A           16 RKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   78 (81)
T ss_dssp             -CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhcc
Confidence            346888999999999999999999999999999999999999999999999999999999865

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

Probab=99.75  E-value=3.8e-19  Score=129.71  Aligned_cols=62  Identities=63%  Similarity=0.945  Sum_probs=54.9

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      ..+|.||.||..|+.+||..|..++||+..++.+||..|+|++.+|+|||||||+|+|+..+
T Consensus        19 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   80 (81)
T 1b8i_A           19 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEIQ   80 (81)
T ss_dssp             -----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC-
T ss_pred             CCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhcc
Confidence            35788999999999999999999999999999999999999999999999999999998754

>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=99.75  E-value=3.3e-19  Score=130.04  Aligned_cols=59  Identities=14%  Similarity=0.167  Sum_probs=56.4

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhh----CCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHH
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHF----NKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK  192 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~----~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr  192 (221)
                      ..+|.||.||.+|+..||.+|+.    ++||+..+|++||..|+|++.+|+|||||||+|+|+
T Consensus        16 ~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           16 IRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            46888999999999999999999    999999999999999999999999999999999875

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

Probab=99.75  E-value=8.6e-19  Score=131.08  Aligned_cols=64  Identities=45%  Similarity=0.698  Sum_probs=60.7

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG  197 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g  197 (221)
                      ..++.||.||..|+..||..|..++||+..++.+||..|+|++.+|+|||||||+|+|+.....
T Consensus        16 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~   79 (93)
T 3a01_A           16 KRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEE   79 (93)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHH
Confidence            3578899999999999999999999999999999999999999999999999999999988764

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

Probab=99.75  E-value=9e-19  Score=125.14  Aligned_cols=62  Identities=24%  Similarity=0.227  Sum_probs=58.3

Q ss_pred             CCCCcccCHHHHHHHHHHhhh-CCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800        136 NSGRTNFTNKQLTELEKEFHF-NKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG  197 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~-~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g  197 (221)
                      .+.|+.||..|+.+||..|.. ++||+..++.+||..|+|++.+|+|||||||+|+|+.....
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~~~~   65 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLP   65 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhccCC
Confidence            567999999999999999995 99999999999999999999999999999999999988653

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

Probab=99.75  E-value=2.5e-19  Score=125.51  Aligned_cols=60  Identities=28%  Similarity=0.433  Sum_probs=57.5

Q ss_pred             CCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHh
Q psy16800        135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRI  194 (221)
Q Consensus       135 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~  194 (221)
                      .+|.||.||..|+..||..|..++||+..++..||..+||++.+|++||||||+|+|+..
T Consensus         3 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   62 (66)
T 1bw5_A            3 TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             CSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             CCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHHh
Confidence            578899999999999999999999999999999999999999999999999999998764

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

Probab=99.74  E-value=7.2e-19  Score=125.25  Aligned_cols=62  Identities=26%  Similarity=0.307  Sum_probs=58.1

Q ss_pred             CCCCcccCHHHHHHHHHHhhh-CCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800        136 NSGRTNFTNKQLTELEKEFHF-NKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG  197 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~-~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g  197 (221)
                      .+.|+.|+..|+.+||..|.. ++||+..++.+||..|+|++.+|+|||||||+|+|+.....
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~~~~   64 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLP   64 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhccCC
Confidence            467899999999999999996 99999999999999999999999999999999999987553

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

Probab=99.74  E-value=7.9e-19  Score=130.70  Aligned_cols=65  Identities=17%  Similarity=0.267  Sum_probs=58.4

Q ss_pred             ccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccccCCCCC
Q psy16800        141 NFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILIGVGEG  205 (221)
Q Consensus       141 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~~~~~~g  205 (221)
                      .||.+||.+||..|..++||+..+|.+||..|+|++.||+|||||||+|++++.+...+...+.+
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~~~~~~~~~~~   81 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEIDESNAG   81 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCCCCCCCCCC
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHHHhhcccCCCC
Confidence            89999999999999999999999999999999999999999999999999988776554443333

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

Probab=99.74  E-value=5.7e-19  Score=119.99  Aligned_cols=57  Identities=49%  Similarity=0.767  Sum_probs=54.7

Q ss_pred             CCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHH
Q psy16800        135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK  191 (221)
Q Consensus       135 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~K  191 (221)
                      +++.|+.|+..|+.+||..|..++||+..++.+||..|+|++.+|+|||||||+|+|
T Consensus         2 ~rr~Rt~~t~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~k   58 (58)
T 3rkq_A            2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK   58 (58)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHC
T ss_pred             cCCCCCCcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhhccCC
Confidence            477899999999999999999999999999999999999999999999999999975

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

Probab=99.74  E-value=6.2e-19  Score=132.56  Aligned_cols=64  Identities=78%  Similarity=1.130  Sum_probs=57.7

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG  197 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g  197 (221)
                      ..++.||.||..|+.+||..|..++||+..++.+||..|+|++.+|+|||||||+|+|+..+++
T Consensus        33 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~g   96 (97)
T 1b72_A           33 SPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKREREG   96 (97)
T ss_dssp             ----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHTC-
T ss_pred             CCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhccC
Confidence            3578899999999999999999999999999999999999999999999999999999988764

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

Probab=99.74  E-value=4.6e-19  Score=121.92  Aligned_cols=58  Identities=41%  Similarity=0.615  Sum_probs=50.7

Q ss_pred             CCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        138 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       138 ~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      .|+.||..|+.+||..|..++||+..++.+||..|+|++.+|++||||||+|+|+..+
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~k   59 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK   59 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC----
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhcc
Confidence            4799999999999999999999999999999999999999999999999999998764

>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=99.74  E-value=5.1e-19  Score=129.15  Aligned_cols=58  Identities=17%  Similarity=0.212  Sum_probs=55.0

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhh-----CCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHH
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHF-----NKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK  192 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~-----~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr  192 (221)
                      ..+|.||.||.+|+..|| .|..     ++||+..+|++||..|+|++.+|+|||||||+|+|+
T Consensus        16 ~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           16 TTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            458889999999999999 7999     999999999999999999999999999999999875

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

Probab=99.73  E-value=1.9e-18  Score=129.49  Aligned_cols=65  Identities=29%  Similarity=0.440  Sum_probs=61.6

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhC---------------CCCCceeeccccchhHHHHHhhhcc
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQ---------------LNETQVKIWFQNRRMKQKKRIKEGI  198 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~---------------Lt~~qVqvWFQNRRaK~Kr~~k~g~  198 (221)
                      ..+|.|+.|+..|+.+||..|..++||+..++++||..|+               |++.+|+|||||||+|+|++.+...
T Consensus         6 ~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~~~~   85 (95)
T 2cuf_A            6 SGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANIAA   85 (95)
T ss_dssp             CCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhhccC
Confidence            4588899999999999999999999999999999999999               9999999999999999999988743

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

Probab=99.73  E-value=1e-18  Score=118.76  Aligned_cols=54  Identities=44%  Similarity=0.769  Sum_probs=51.2

Q ss_pred             cccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHH
Q psy16800        140 TNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR  193 (221)
Q Consensus       140 t~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~  193 (221)
                      |.||..|+..||..|..++||+..++.+||..+||++.+|+|||||||+|+|++
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~   55 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ   55 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhhccc
Confidence            689999999999999999999999999999999999999999999999999986

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

Probab=99.73  E-value=6.2e-19  Score=126.90  Aligned_cols=64  Identities=19%  Similarity=0.300  Sum_probs=59.0

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccc
Q psy16800        136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGIL  199 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~  199 (221)
                      .+.|+.||..|+.+||..|..++||+..++++||..|+|++.+|+|||||||+|+|+..+....
T Consensus         9 ~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~~~~~   72 (76)
T 2dn0_A            9 SIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGSRSG   72 (76)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCSSSCC
T ss_pred             CCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhcccCCC
Confidence            4458999999999999999999999999999999999999999999999999999997765433

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

Probab=99.73  E-value=1.7e-18  Score=125.26  Aligned_cols=61  Identities=20%  Similarity=0.247  Sum_probs=56.9

Q ss_pred             CCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800        137 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG  197 (221)
Q Consensus       137 r~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g  197 (221)
                      ..|+.||.+|+.+|+..|..++||+..+|++||..+||++.||+|||||+|+|+|+....-
T Consensus         5 ~~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~l~w   65 (76)
T 2ecc_A            5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLKW   65 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCCSS
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHHHHH
Confidence            4467899999999999999999999999999999999999999999999999999876653

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

Probab=99.73  E-value=1.2e-18  Score=124.53  Aligned_cols=62  Identities=23%  Similarity=0.397  Sum_probs=58.8

Q ss_pred             CCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       135 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      .++.|+.||..|+.+||..|..++||+..++++||..|+|++.+|+|||||||+|+|+....
T Consensus         6 ~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~   67 (74)
T 2ly9_A            6 SFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKSN   67 (74)
T ss_dssp             CCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTTCS
T ss_pred             CCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhCcC
Confidence            36779999999999999999999999999999999999999999999999999999987665

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

Probab=99.73  E-value=1.7e-18  Score=124.52  Aligned_cols=61  Identities=20%  Similarity=0.273  Sum_probs=57.2

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      .++|+.||..|+.+||..|..++||+..++.+||..|+|++.+|+|||||||+|+|++.+.
T Consensus         8 ~~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~~   68 (75)
T 2da5_A            8 PTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETK   68 (75)
T ss_dssp             SCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSCS
T ss_pred             CCCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhhc
Confidence            3457789999999999999999999999999999999999999999999999999998765

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

Probab=99.72  E-value=9.6e-19  Score=120.48  Aligned_cols=58  Identities=26%  Similarity=0.474  Sum_probs=48.5

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHH
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK  191 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~K  191 (221)
                      ..++.|+.|+..|+.+||..|..++||+..++..||..|||++.+|+|||||||+++|
T Consensus         4 k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            4 KSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             --------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            4578899999999999999999999999999999999999999999999999999975

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

Probab=99.72  E-value=1.1e-18  Score=128.37  Aligned_cols=62  Identities=29%  Similarity=0.431  Sum_probs=58.2

Q ss_pred             CCCCcccCHHHHHHHHHHh---hhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800        136 NSGRTNFTNKQLTELEKEF---HFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG  197 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F---~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g  197 (221)
                      +|.|+.|+..|+.+|+..|   ..++||+..++.+||..|+|++.||++||||||+|+|+.....
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~   66 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKF   66 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGGG
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhccccc
Confidence            6789999999999999999   8999999999999999999999999999999999999987654

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

Probab=99.71  E-value=2.2e-18  Score=129.36  Aligned_cols=62  Identities=19%  Similarity=0.188  Sum_probs=56.8

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      ..+|.|+.||..|+.+||..|..++||+..++++||..|+|++.+|+|||||||+|+|+...
T Consensus        24 ~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~l   85 (96)
T 3nar_A           24 GSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNL   85 (96)
T ss_dssp             ---CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTCC
T ss_pred             CCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhcc
Confidence            34778999999999999999999999999999999999999999999999999999998654

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

Probab=99.71  E-value=7.6e-18  Score=128.16  Aligned_cols=69  Identities=19%  Similarity=0.215  Sum_probs=64.0

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHh---------------------CCCCCceeeccccchhHHHH
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVL---------------------QLNETQVKIWFQNRRMKQKK  192 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L---------------------~Lt~~qVqvWFQNRRaK~Kr  192 (221)
                      ..+|.|+.|+..|+.+||..|+.++||+..+|++||..|                     .|++.+|+|||||||+++|+
T Consensus         5 ~~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k~kr   84 (102)
T 2da6_A            5 SSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEEAF   84 (102)
T ss_dssp             CSCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHHHHH
Confidence            468889999999999999999999999999999999999                     79999999999999999999


Q ss_pred             HhhhccccCC
Q psy16800        193 RIKEGILIGV  202 (221)
Q Consensus       193 ~~k~g~~~~~  202 (221)
                      +++.+.....
T Consensus        85 ~~~~~~~~~~   94 (102)
T 2da6_A           85 RQKLAMDAYS   94 (102)
T ss_dssp             HHHHHHSSSS
T ss_pred             hhHhhhcccc
Confidence            9998766543

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

Probab=99.70  E-value=7.8e-18  Score=120.06  Aligned_cols=63  Identities=19%  Similarity=0.219  Sum_probs=58.9

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHF---NKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~---~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      ..++.|+.|+..|+.+|+..|..   ++||+..++++||..++|++.||+|||||+|+|+|+...+
T Consensus         6 ~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~   71 (73)
T 1x2n_A            6 SGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSGPS   71 (73)
T ss_dssp             SSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhccccccc
Confidence            45788999999999999999987   9999999999999999999999999999999999987654

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

Probab=99.70  E-value=6e-18  Score=120.64  Aligned_cols=61  Identities=30%  Similarity=0.467  Sum_probs=58.3

Q ss_pred             CCCCcccCHHHHHHHHHHh---hhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        136 NSGRTNFTNKQLTELEKEF---HFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F---~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      +|.|+.|+..|+.+|+..|   ..++||+..++..||..+||++.||+|||||+|+|+|+....
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~   65 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGK   65 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccccccc
Confidence            6789999999999999999   899999999999999999999999999999999999987765

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

Probab=99.69  E-value=2.9e-17  Score=121.83  Aligned_cols=60  Identities=20%  Similarity=0.267  Sum_probs=55.6

Q ss_pred             cccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccc
Q psy16800        140 TNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGIL  199 (221)
Q Consensus       140 t~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~  199 (221)
                      ..||..|+.+||..|..++||+..++++||..|+|++.+|+|||||||+|+|+..+....
T Consensus        18 k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~~~~~   77 (89)
T 2dmp_A           18 KEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAVLD   77 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCSCCCC
T ss_pred             ccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhHhhhc
Confidence            349999999999999999999999999999999999999999999999999988776433

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

Probab=99.68  E-value=4e-18  Score=118.55  Aligned_cols=58  Identities=24%  Similarity=0.387  Sum_probs=55.6

Q ss_pred             CCCCCcccCHHHHHHHHHHh---hhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHH
Q psy16800        135 NNSGRTNFTNKQLTELEKEF---HFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK  192 (221)
Q Consensus       135 ~rr~Rt~ft~~Ql~~Le~~F---~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr  192 (221)
                      .++.|+.|+..|+.+|+..|   ..++||+..++.+||..+||++.||++||||+|+|+|+
T Consensus         3 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A            3 GHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             CCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            47889999999999999999   89999999999999999999999999999999999876

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

Probab=99.68  E-value=1.4e-17  Score=114.35  Aligned_cols=56  Identities=30%  Similarity=0.396  Sum_probs=53.6

Q ss_pred             CCcccCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHH
Q psy16800        138 GRTNFTNKQLTELEKEFHF---NKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR  193 (221)
Q Consensus       138 ~Rt~ft~~Ql~~Le~~F~~---~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~  193 (221)
                      +|+.|+..|+.+|+..|..   ++||+..++..||..+||++.||++||||||+|+|+.
T Consensus         1 rr~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A            1 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CCCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             CcCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            3689999999999999999   9999999999999999999999999999999999874

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

Probab=99.67  E-value=5.5e-17  Score=118.81  Aligned_cols=64  Identities=14%  Similarity=0.209  Sum_probs=59.1

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHF---NKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG  197 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~---~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g  197 (221)
                      ..++.|+.|+..|+.+|+..|..   ++||+..++++||..++|++.||+|||||+|+|+++...+.
T Consensus         6 ~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~~~   72 (83)
T 2dmn_A            6 SGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQ   72 (83)
T ss_dssp             CCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHTCC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHHHh
Confidence            35788999999999999999987   59999999999999999999999999999999999877653

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

Probab=99.67  E-value=4.4e-18  Score=121.73  Aligned_cols=59  Identities=22%  Similarity=0.308  Sum_probs=55.1

Q ss_pred             CCCCcccCHHHHHHHHHHh-hhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHh
Q psy16800        136 NSGRTNFTNKQLTELEKEF-HFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRI  194 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F-~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~  194 (221)
                      .+.|..++..|+.+||..| ..++||+..++.+||..|+|++.||+|||||||+|+|+..
T Consensus         9 ~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~~   68 (72)
T 2cqx_A            9 IKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSG   68 (72)
T ss_dssp             CCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCCC
Confidence            5567788999999999999 9999999999999999999999999999999999999754

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

Probab=99.66  E-value=2.9e-17  Score=115.97  Aligned_cols=56  Identities=21%  Similarity=0.274  Sum_probs=53.9

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhh-CCCCCHHHHHHHHHHhCCCCCceeeccccchhH
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHF-NKYLTRARRIEIASVLQLNETQVKIWFQNRRMK  189 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~-~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK  189 (221)
                      ..+|.||.|+.+||..|+.+|+. +.||+...|+.||.+|||++++|+|||||+|--
T Consensus         6 ~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~   62 (71)
T 1wi3_A            6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYH   62 (71)
T ss_dssp             CCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceee
Confidence            46899999999999999999999 999999999999999999999999999999975

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

Probab=99.66  E-value=1.5e-17  Score=136.31  Aligned_cols=63  Identities=27%  Similarity=0.333  Sum_probs=53.0

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      +.+|.||.|+..|+.+||..|..++||+..+|.+||..|+|++.+|+|||||||+|+||..+.
T Consensus        98 ~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~  160 (164)
T 2xsd_C           98 RKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTPA  160 (164)
T ss_dssp             --------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC-
T ss_pred             cCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhccCC
Confidence            457889999999999999999999999999999999999999999999999999999998765

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

Probab=99.65  E-value=1.7e-17  Score=117.93  Aligned_cols=57  Identities=46%  Similarity=0.771  Sum_probs=53.8

Q ss_pred             cccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        140 TNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       140 t~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      ..+|..|+..||..|..++||+..+|.+||..|+|++.+|+|||||||+|+|+....
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~~~   65 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLS   65 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSSSS
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhhhh
Confidence            468999999999999999999999999999999999999999999999999987654

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

Probab=99.65  E-value=1.4e-17  Score=126.13  Aligned_cols=68  Identities=21%  Similarity=0.252  Sum_probs=54.7

Q ss_pred             CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHH------------------hC---CCCCceeeccccchhHHH
Q psy16800        133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASV------------------LQ---LNETQVKIWFQNRRMKQK  191 (221)
Q Consensus       133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~------------------L~---Lt~~qVqvWFQNRRaK~K  191 (221)
                      .+.+|.|+.|+..|+.+||..|..++||+..+|++||..                  |+   |++.+|+|||||||++++
T Consensus         7 ~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k~k   86 (99)
T 1lfb_A            7 KKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEA   86 (99)
T ss_dssp             ------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHHHH
Confidence            346788999999999999999999999999999999999                  88   999999999999999998


Q ss_pred             HHhhhcccc
Q psy16800        192 KRIKEGILI  200 (221)
Q Consensus       192 r~~k~g~~~  200 (221)
                      ++++.+...
T Consensus        87 ~k~~~~~~~   95 (99)
T 1lfb_A           87 FRHKLAMDT   95 (99)
T ss_dssp             CCC------
T ss_pred             Hhchhhhcc
Confidence            887765443

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

Probab=99.65  E-value=3.1e-17  Score=119.99  Aligned_cols=60  Identities=27%  Similarity=0.320  Sum_probs=55.1

Q ss_pred             CCCCcccCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        136 NSGRTNFTNKQLTELEKEFHF---NKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~---~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      ++.|++|+..|+.+|+..|..   ++||+..++.+||..+||++.||+|||||||+|+|+...
T Consensus         3 ~krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~~   65 (83)
T 1le8_B            3 PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITI   65 (83)
T ss_dssp             --CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHcccccccc
Confidence            455777999999999999999   999999999999999999999999999999999998754

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A

Probab=99.65  E-value=2.5e-17  Score=134.36  Aligned_cols=60  Identities=30%  Similarity=0.432  Sum_probs=54.9

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHH
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR  193 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~  193 (221)
                      .++|.||.|+..|+.+||..|..++||+..+|.+||..|+|++.+|+|||||||+|+||+
T Consensus       100 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C          100 RRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            458889999999999999999999999999999999999999999999999999999985

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

Probab=99.65  E-value=5.1e-17  Score=119.69  Aligned_cols=58  Identities=29%  Similarity=0.377  Sum_probs=55.2

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHhCCCCCceeeccccchhHHH
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHF---NKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK  191 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~---~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~K  191 (221)
                      .+++.|+.|+..|+.+|+..|..   ++||+..++..||..++|++.||++||||||+|+|
T Consensus        26 ~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k   86 (87)
T 1mnm_C           26 TKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK   86 (87)
T ss_dssp             SSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcc
Confidence            35667999999999999999999   99999999999999999999999999999999987

>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1

Probab=99.65  E-value=2.4e-17  Score=132.63  Aligned_cols=60  Identities=25%  Similarity=0.417  Sum_probs=55.7

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHH
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR  193 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~  193 (221)
                      .++|.||.|+..|+..||..|..++||+..++.+||..|+|++.+|+|||||||+|+||+
T Consensus        86 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           86 RKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             ---CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            457889999999999999999999999999999999999999999999999999999985

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

Probab=99.65  E-value=4.1e-17  Score=114.80  Aligned_cols=53  Identities=23%  Similarity=0.451  Sum_probs=50.5

Q ss_pred             cCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHh
Q psy16800        142 FTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRI  194 (221)
Q Consensus       142 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~  194 (221)
                      -|.+|+.+||..|..++||+..++.+||..+||++.+|++||||||+|+|+..
T Consensus        11 ~~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg~   63 (66)
T 3nau_A           11 KTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGI   63 (66)
T ss_dssp             CCHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhccC
Confidence            47899999999999999999999999999999999999999999999999754

>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens}

Probab=99.63  E-value=7.1e-17  Score=130.32  Aligned_cols=59  Identities=31%  Similarity=0.464  Sum_probs=56.7

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHH
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK  192 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr  192 (221)
                      +++|.|+.|+..|+.+||..|..++||+..++.+||..|+|++.+|+|||||||+|+||
T Consensus        92 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           92 KKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            45788999999999999999999999999999999999999999999999999999986

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

Probab=99.63  E-value=5.5e-17  Score=113.50  Aligned_cols=54  Identities=20%  Similarity=0.225  Sum_probs=50.6

Q ss_pred             CcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHH
Q psy16800        139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK  192 (221)
Q Consensus       139 Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr  192 (221)
                      +..++.+|+..||..|..++||+..+|.+||..|+|++.+|+|||||||+|.++
T Consensus         7 ~~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~   60 (64)
T 2e19_A            7 GQPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS   60 (64)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSC
T ss_pred             CCCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCC
Confidence            456679999999999999999999999999999999999999999999998765

>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.61  E-value=6.4e-17  Score=113.38  Aligned_cols=50  Identities=24%  Similarity=0.372  Sum_probs=46.5

Q ss_pred             HHHHHHHHHHh-hhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHH
Q psy16800        144 NKQLTELEKEF-HFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR  193 (221)
Q Consensus       144 ~~Ql~~Le~~F-~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~  193 (221)
                      ..|+.+||.+| ..++||+..+|.+||.+|+|+++||+|||||||+|+|+.
T Consensus         9 ~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~~   59 (64)
T 1x2m_A            9 AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPS   59 (64)
T ss_dssp             SCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCCS
T ss_pred             chHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCCC
Confidence            45899999999 579999999999999999999999999999999998864

>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A

Probab=99.61  E-value=1.3e-16  Score=129.43  Aligned_cols=60  Identities=30%  Similarity=0.405  Sum_probs=56.8

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHH
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR  193 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~  193 (221)
                      ..+|.||.|+..|+..||..|..++||+..++.+||..|+|++.+|+|||||||+|+||.
T Consensus        95 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A           95 ARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             CSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            357889999999999999999999999999999999999999999999999999999974

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

Probab=99.58  E-value=2.3e-16  Score=128.65  Aligned_cols=63  Identities=27%  Similarity=0.289  Sum_probs=54.9

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      ..+|.||.|+..|+..|+..|..++||+..++.+||..|+|++.+|+|||||||+|+|+....
T Consensus        96 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~~  158 (164)
T 2d5v_A           96 TPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWLE  158 (164)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC---
T ss_pred             CCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccCCC
Confidence            458889999999999999999999999999999999999999999999999999998886554

>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding, transcription, nucleus, phosphoprotein, DNA bindi protein; 1.95A {Homo sapiens} SCOP: a.4.1.1

Probab=99.53  E-value=2e-15  Score=106.26  Aligned_cols=57  Identities=18%  Similarity=0.246  Sum_probs=50.6

Q ss_pred             cccCHHHHHHHHHHhh---hCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        140 TNFTNKQLTELEKEFH---FNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       140 t~ft~~Ql~~Le~~F~---~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      ..|+.+|+.+|+..|.   .++||+..++.+||..++|++.||++||||+|+|+|+....
T Consensus         3 g~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~   62 (67)
T 3k2a_A            3 GIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMID   62 (67)
T ss_dssp             ---CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC--
T ss_pred             CcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHHH
Confidence            3799999999999999   99999999999999999999999999999999999987654

>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1

Probab=99.44  E-value=8.6e-15  Score=123.04  Aligned_cols=60  Identities=18%  Similarity=0.257  Sum_probs=53.7

Q ss_pred             CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhC---------------------CCCCceeeccccchhHHH
Q psy16800        133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQ---------------------LNETQVKIWFQNRRMKQK  191 (221)
Q Consensus       133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~---------------------Lt~~qVqvWFQNRRaK~K  191 (221)
                      .+.||.|+.|+..|+..|+..|..++||+..+|++||..|+                     |++.+|+|||||||++++
T Consensus       113 ~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~~k  192 (194)
T 1ic8_A          113 KKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEA  192 (194)
T ss_dssp             ----CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHHCC
T ss_pred             ccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhhhh
Confidence            35688899999999999999999999999999999999999                     999999999999999876


Q ss_pred             H
Q psy16800        192 K  192 (221)
Q Consensus       192 r  192 (221)
                      .
T Consensus       193 ~  193 (194)
T 1ic8_A          193 F  193 (194)
T ss_dssp             -
T ss_pred             c
Confidence            4

>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.41  E-value=6.1e-14  Score=99.45  Aligned_cols=46  Identities=20%  Similarity=0.387  Sum_probs=44.3

Q ss_pred             HHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhH
Q psy16800        144 NKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMK  189 (221)
Q Consensus       144 ~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK  189 (221)
                      ++|+.+|+.+|..|++|+..++..||..++|+.++|+|||||||+.
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~   59 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVY   59 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhcccc
Confidence            5789999999999999999999999999999999999999999984

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

Probab=99.36  E-value=4.9e-13  Score=99.24  Aligned_cols=58  Identities=17%  Similarity=0.216  Sum_probs=53.5

Q ss_pred             cccCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800        140 TNFTNKQLTELEKEFHF---NKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG  197 (221)
Q Consensus       140 t~ft~~Ql~~Le~~F~~---~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g  197 (221)
                      ..|+..++.+|+..|..   ++||+..++.+||..++|++.||++||||+|+|+++.....
T Consensus        10 ~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~~~   70 (89)
T 2lk2_A           10 HMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRK   70 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHHHh
Confidence            46889999999999987   89999999999999999999999999999999999877653

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

Probab=99.34  E-value=2.4e-13  Score=116.03  Aligned_cols=58  Identities=19%  Similarity=0.280  Sum_probs=53.2

Q ss_pred             CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhC---------------------CCCCceeeccccchhHH
Q psy16800        133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQ---------------------LNETQVKIWFQNRRMKQ  190 (221)
Q Consensus       133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~---------------------Lt~~qVqvWFQNRRaK~  190 (221)
                      .+.||.|+.|+..|+.+|+..|..++||+..+|++||..|+                     |++.+|++||||||++.
T Consensus       140 ~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~~~  218 (221)
T 2h8r_A          140 KKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEE  218 (221)
T ss_dssp             --CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhhhh
Confidence            45688999999999999999999999999999999999988                     89999999999999863

>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding cooperativity, maltose binding protein, MBP, sugar binding, DNA binding protein; 2.10A {Escherichia coli} SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A

Probab=99.25  E-value=9e-13  Score=118.58  Aligned_cols=56  Identities=25%  Similarity=0.446  Sum_probs=52.9

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHH
Q psy16800        136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK  191 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~K  191 (221)
                      ++.++.|+..|+..|++.|+.++||+..+|++||.+|+|+++||+|||||||+|+|
T Consensus       366 ~~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          366 TAAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            44578999999999999999999999999999999999999999999999999875

>2nzz_A Penetratin conjugated GAS (374-394) peptide; conformational analysis, G protein, GAS subunit, A2A adenosine receptor, cell-penetrating peptides; NMR {Synthetic} PDB: 2o00_A

Probab=98.69  E-value=4.4e-09  Score=65.69  Aligned_cols=21  Identities=67%  Similarity=1.056  Sum_probs=19.1

Q ss_pred             CceeeccccchhHHHHHhhhc
Q psy16800        177 TQVKIWFQNRRMKQKKRIKEG  197 (221)
Q Consensus       177 ~qVqvWFQNRRaK~Kr~~k~g  197 (221)
                      +||+|||||||+|||+.....
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~   21 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFND   21 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHH
T ss_pred             CCceeccHHHHHHHHHHhHHH
Confidence            589999999999999999874

>2ys9_A Homeobox and leucine zipper protein homez; homeodomain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.49  E-value=0.011  Score=41.41  Aligned_cols=38  Identities=21%  Similarity=0.381  Sum_probs=36.1

Q ss_pred             HHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccc
Q psy16800        147 LTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQ  184 (221)
Q Consensus       147 l~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQ  184 (221)
                      .+.|+.+|...+.+.......|+.+..|+..||+-||-
T Consensus        18 ~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa   55 (70)
T 2ys9_A           18 IQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFD   55 (70)
T ss_dssp             CHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHH
T ss_pred             chHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHH
Confidence            47899999999999999999999999999999999994

---

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	221
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	3e-24
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	1e-23
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	1e-23
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	1e-22
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	1e-21
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	8e-21
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	1e-20
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	1e-20
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	2e-20
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	7e-20
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	8e-20
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	1e-19
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	1e-19
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	3e-19
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	3e-19
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	3e-19
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	4e-19
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	5e-19
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	2e-18
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	2e-17
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	3e-17
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	3e-17
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	5e-17
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	6e-17
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	7e-17
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	8e-16
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	1e-15
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	2e-14
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	2e-14
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	6e-14
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	7e-11
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	4e-10

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 56

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Antennapedia Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

 Score = 89.1 bits (221), Expect = 3e-24
 Identities = 38/54 (70%), Positives = 41/54 (75%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           R  +T  Q  ELEKEFHFN+YLTR RRIEIA  L L E Q+KIWFQNRRMK KK
Sbjct: 1   RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 54

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 87.5 bits (217), Expect = 1e-23
 Identities = 22/58 (37%), Positives = 34/58 (58%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196
           RT+FT +Q+  LEKEF    Y     R  +A+ + L E ++++WF NRR K ++  K 
Sbjct: 5   RTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL 62

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-a9
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 88.0 bits (218), Expect = 1e-23
 Identities = 37/58 (63%), Positives = 41/58 (70%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196
           R  +T  Q  ELEKEF FN YLTR RR E+A +L L E QVKIWFQNRRMK KK  K+
Sbjct: 17  RCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD 74

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein prh
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 84.9 bits (210), Expect = 1e-22
 Identities = 28/55 (50%), Positives = 37/55 (67%)

Query: 138 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           G+  F+N Q  ELEK+F   KYL+   R  +A +LQL+E QVK WFQNRR K ++
Sbjct: 3   GQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 57

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

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]

 Score = 83.1 bits (205), Expect = 1e-21
 Identities = 52/75 (69%), Positives = 61/75 (81%)

Query: 122 PPPAALSQHQSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKI 181
           P  A +S+      +  RTNFT +QLTELEKEFHFNKYL+RARR+EIA+ L+LNETQVKI
Sbjct: 14  PKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKI 73

Query: 182 WFQNRRMKQKKRIKE 196
           WFQNRRMKQKKR +E
Sbjct: 74  WFQNRRMKQKKRERE 88

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58

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]

 Score = 79.9 bits (197), Expect = 8e-21
 Identities = 25/54 (46%), Positives = 40/54 (74%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           R  ++  QL ELE+E+  NK++T+ +R +I++   L+E Q+ IWFQNRR+K+KK
Sbjct: 5   RIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 58

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 53

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

 Score = 79.5 bits (196), Expect = 1e-20
 Identities = 28/51 (54%), Positives = 39/51 (76%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMK 189
           RT F+++QL  L++EF+ N+YLT  RR +++S L LNE Q+KIWFQN R K
Sbjct: 3   RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 66

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 79.9 bits (197), Expect = 1e-20
 Identities = 17/55 (30%), Positives = 27/55 (49%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
           RT    KQL  L   +  N       + ++  +  L+   +++WFQN+R K KKR
Sbjct: 7   RTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 78.8 bits (194), Expect = 2e-20
 Identities = 30/55 (54%), Positives = 40/55 (72%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
           RT FT  QL  LEKEF+   Y++R RR E+A+ L L E+ +K+WFQNRRMK K++
Sbjct: 3   RTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 57

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 77.7 bits (191), Expect = 7e-20
 Identities = 26/55 (47%), Positives = 37/55 (67%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
           RT+FT++QL +LE  F  N+Y   + R EIA    L E +V++WF+NRR K +KR
Sbjct: 5   RTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 59

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 53

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 77.2 bits (190), Expect = 8e-20
 Identities = 14/53 (26%), Positives = 28/53 (52%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK 191
           +++ + +    LE+ F   + L    + E+A    +   QV++WF N+RM+ K
Sbjct: 1   KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 58

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]

 Score = 77.3 bits (190), Expect = 1e-19
 Identities = 31/54 (57%), Positives = 37/54 (68%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT FT  QL  LE++F   +YL+ A R E +S L L ETQVKIWFQNRR K K+
Sbjct: 4   RTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 65

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 76.9 bits (189), Expect = 1e-19
 Identities = 22/55 (40%), Positives = 33/55 (60%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
           RT F+  QL ELE+ F   +Y     R E+A    L E ++++WFQNRR + +K+
Sbjct: 6   RTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 60

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

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]

 Score = 76.6 bits (188), Expect = 3e-19
 Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 15/70 (21%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIA---------------SVLQLNETQVKIWF 183
           R  +  + L  +E  F+ N+Y   A+R EIA                + ++   +V  WF
Sbjct: 4   RFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWF 63

Query: 184 QNRRMKQKKR 193
            NRR + K+R
Sbjct: 64  ANRRKEIKRR 73

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Thyroid transcription factor 1 homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 76.1 bits (187), Expect = 3e-19
 Identities = 27/58 (46%), Positives = 37/58 (63%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196
           R  F+  Q+ ELE+ F   KYL+   R  +AS++ L  TQVKIWFQN R K K++ K+
Sbjct: 6   RVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKD 63

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 75.7 bits (186), Expect = 3e-19
 Identities = 15/54 (27%), Positives = 27/54 (50%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT  +      LE+ F  +   +    + +A  L L +  V++WF NRR ++K+
Sbjct: 3   RTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 56

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 67

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]

 Score = 75.7 bits (186), Expect = 4e-19
 Identities = 25/58 (43%), Positives = 37/58 (63%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196
           RT FT+ Q+ ELE+ F   +YLT  R  ++++ L L   QVKIWF+NRR + K +  +
Sbjct: 5   RTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ 62

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 50

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 75.3 bits (185), Expect = 5e-19
 Identities = 16/49 (32%), Positives = 23/49 (46%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRR 187
           R  FT+ Q   L   F  NK  ++  +I I+  L L  + V  +F N R
Sbjct: 2   RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 52

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 73.6 bits (181), Expect = 2e-18
 Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 143 TNKQLTELEKEF-HFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           T +    LEK F    K+    R   ++  L  +   ++ WF+ RR ++K 
Sbjct: 1   TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 51

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Length = 62

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 71.3 bits (175), Expect = 2e-17
 Identities = 12/57 (21%), Positives = 19/57 (33%), Gaps = 3/57 (5%)

Query: 139 RTNFTNKQLTELEKEF---HFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           R          +         + Y T   + +IA+   L   QV  WF N R +  +
Sbjct: 6   RGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQ 62

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 71.0 bits (174), Expect = 3e-17
 Identities = 17/57 (29%), Positives = 23/57 (40%), Gaps = 3/57 (5%)

Query: 139 RTNFTNKQLTELEKEFHFNK---YLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
              FT + +  LE  F  N    YL       +     L+  Q+K W  NRR K+K 
Sbjct: 2   GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 71.2 bits (174), Expect = 3e-17
 Identities = 27/58 (46%), Positives = 35/58 (60%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE 196
           R  FT  Q  ELE+ F   +YL+   R  +AS+++L  TQVKIWFQN R K K+   E
Sbjct: 13  RVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNE 70

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 67

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]

 Score = 70.4 bits (172), Expect = 5e-17
 Identities = 18/55 (32%), Positives = 27/55 (49%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
           RT+  N+    LE  F      +  +   IA+ L L +  V++WF NRR K K+ 
Sbjct: 12  RTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS 66

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Length = 73

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.4 bits (172), Expect = 6e-17
 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 3/61 (4%)

Query: 139 RTNFTNKQLTELEK---EFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK 195
           R NF  +    L +       N Y +   + E+A    +  +QV  WF N+R++ KK I 
Sbjct: 5   RRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG 64

Query: 196 E 196
           +
Sbjct: 65  K 65

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 57

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]

 Score = 70.0 bits (171), Expect = 7e-17
 Identities = 18/54 (33%), Positives = 27/54 (50%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
           RT+        LEK F  N+  T      IA  L + +  +++WF NRR K+K+
Sbjct: 2   RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 55

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} Length = 72

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]

 Score = 67.3 bits (164), Expect = 8e-16
 Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 138 GRTNFTNKQLTELEKEFHF-NKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
           G    T  Q+  LE  F+  NK+        IA+   L E Q + WF+ R  + ++ 
Sbjct: 4   GAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 59

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: LAG1 longevity assurance homolog 5, LASS5
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 66.7 bits (163), Expect = 1e-15
 Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 1/54 (1%)

Query: 139 RTNFTNKQLTELEKEF-HFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK 191
                 +    LEK F    KY    R   ++  L  +  +++ WF++RR + K
Sbjct: 5   SPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]} Length = 76

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]

 Score = 64.0 bits (155), Expect = 2e-14
 Identities = 12/68 (17%), Positives = 27/68 (39%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGI 198
               T +QL  L+  F  +  LT      + +  +L   ++  WF  ++  +  + ++  
Sbjct: 8   FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKME 67

Query: 199 LIGVGEGS 206
           +     GS
Sbjct: 68  IDESNAGS 75

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

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]

 Score = 63.6 bits (154), Expect = 2e-14
 Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 1/56 (1%)

Query: 139 RTNFTNKQLTELEKEFH-FNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
           RT  + + L  L+   H    Y  +     +++ L L +  +  +FQN+R   K  
Sbjct: 11  RTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS 66

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Length = 78

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Rat (Rattus rattus) [TaxId: 10117]

 Score = 62.5 bits (151), Expect = 6e-14
 Identities = 13/78 (16%), Positives = 23/78 (29%), Gaps = 21/78 (26%)

Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVL---------------------QLNET 177
           R  +       L + +   K  ++  R  +                          + E 
Sbjct: 1   RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 178 QVKIWFQNRRMKQKKRIK 195
           +V  WF NRR ++  R K
Sbjct: 61  RVYNWFANRRKEEAFRHK 78

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]} Length = 76

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]

 Score = 54.4 bits (130), Expect = 7e-11
 Identities = 12/59 (20%), Positives = 23/59 (38%)

Query: 135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
           + S     T +QL  L+  F   ++  R    ++  +  L   ++  WF + R   K  
Sbjct: 3   SGSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG 61

>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 = 4e-10
 Identities = 9/59 (15%), Positives = 18/59 (30%), Gaps = 4/59 (6%)

Query: 139 RTNFTNKQLTELEKEFH----FNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
           RT FT +Q  ++           +        +  +   +    +KIW  N +      
Sbjct: 21  RTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPSS 79

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	221
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.82
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.82
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.81
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.81
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.81
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.81
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.81
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.8
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.79
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.79
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.79
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.79
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.79
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.78
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.77
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.75
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.74
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.74
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.74
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.73
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.71
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.71
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.69
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.69
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.67
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.65
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.64
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.62
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.59
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.55
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.53
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.51

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=7.5e-22  Score=134.39  Aligned_cols=57  Identities=44%  Similarity=0.785  Sum_probs=55.2

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHH
Q psy16800        136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK  192 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr  192 (221)
                      +|.||.||..|+.+||.+|..++||+..++++||..|||++.+|+|||||||+|+||
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            678999999999999999999999999999999999999999999999999999875

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=2.5e-21  Score=131.65  Aligned_cols=58  Identities=53%  Similarity=0.773  Sum_probs=55.7

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHH
Q psy16800        136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR  193 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~  193 (221)
                      ||.|+.||.+|+.+||.+|+.++||+..++.+||..|||++.+|+|||||+|+|+||.
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   58 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL   58 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhccC
Confidence            5679999999999999999999999999999999999999999999999999999973

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Antennapedia Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.81  E-value=2.3e-21  Score=131.06  Aligned_cols=55  Identities=69%  Similarity=1.036  Sum_probs=53.8

Q ss_pred             CcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHH
Q psy16800        139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR  193 (221)
Q Consensus       139 Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~  193 (221)
                      ||.||.+|+.+||.+|..++||+..++.+||..|||++.+|+|||||||+|+||+
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk~   55 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   55 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhhc
Confidence            7999999999999999999999999999999999999999999999999999985

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.81  E-value=3.2e-21  Score=130.76  Aligned_cols=57  Identities=53%  Similarity=0.845  Sum_probs=55.1

Q ss_pred             CCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHH
Q psy16800        137 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR  193 (221)
Q Consensus       137 r~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~  193 (221)
                      |.||.||..|+.+||.+|..++||+..++.+||..|||++.+|+|||||+|+|+||+
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk~   57 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   57 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhcC
Confidence            579999999999999999999999999999999999999999999999999999974

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein prh
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=4e-21  Score=130.28  Aligned_cols=57  Identities=49%  Similarity=0.800  Sum_probs=55.2

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHH
Q psy16800        136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK  192 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr  192 (221)
                      |+.|+.||..|+.+||.+|..++||+..++++||..|||++.||+|||||||+++||
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k~kk   57 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR   57 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhhccC
Confidence            567999999999999999999999999999999999999999999999999999986

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.81  E-value=5.8e-21  Score=133.49  Aligned_cols=62  Identities=40%  Similarity=0.674  Sum_probs=58.8

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhc
Q psy16800        136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEG  197 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g  197 (221)
                      ||.||+||..|+.+||.+|..++||+..++.+||..|||++.+|+|||||||+|+|+.....
T Consensus         2 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~~~   63 (67)
T d1zq3p1           2 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQH   63 (67)
T ss_dssp             SCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhhhc
Confidence            57799999999999999999999999999999999999999999999999999999877653

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-a9
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.81  E-value=8.3e-21  Score=136.11  Aligned_cols=63  Identities=59%  Similarity=0.832  Sum_probs=59.7

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      ..++.||.||.+|+.+||.+|..++||+..++++||..|||++.+|+|||||||+|+|+..+.
T Consensus        12 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~   74 (77)
T d1pufa_          12 STRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             TTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHH
Confidence            347889999999999999999999999999999999999999999999999999999998765

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.80  E-value=1.3e-20  Score=130.84  Aligned_cols=62  Identities=35%  Similarity=0.613  Sum_probs=59.1

Q ss_pred             CCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       135 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      +|+.||.||.+|+.+||.+|..++||+..++.+||..|||++.+|+|||||+|+|+|++...
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~~   63 (65)
T d1fjla_           2 QRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHTS   63 (65)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhcccc
Confidence            57889999999999999999999999999999999999999999999999999999987654

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.79  E-value=8.1e-21  Score=126.89  Aligned_cols=53  Identities=53%  Similarity=0.852  Sum_probs=51.5

Q ss_pred             CCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhH
Q psy16800        137 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMK  189 (221)
Q Consensus       137 r~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK  189 (221)
                      |.||.||..|+.+||..|..++||+..++.+||..|||++.+|+|||||||+|
T Consensus         1 R~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~lgL~~~qV~vWFqNrRaK   53 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK   53 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             CCCccCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChHHhhhcccccCCC
Confidence            56999999999999999999999999999999999999999999999999986

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.7e-20  Score=131.44  Aligned_cols=61  Identities=36%  Similarity=0.608  Sum_probs=58.5

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      +|.||.||.+|+.+||.+|..++||+..++++||..|+|++.+|+|||||+|+++|+..+.
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~   62 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL   62 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhhh
Confidence            6789999999999999999999999999999999999999999999999999999987664

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.3e-20  Score=138.37  Aligned_cols=61  Identities=79%  Similarity=1.142  Sum_probs=56.6

Q ss_pred             CCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       135 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      .++.|+.||..|+.+||.+|..++||+..++++||..|+|++.+|+|||||+|+|+|+..+
T Consensus        27 ~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~~   87 (88)
T d1b72a_          27 PSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   87 (88)
T ss_dssp             ---CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhcc
Confidence            4778999999999999999999999999999999999999999999999999999999865

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Thyroid transcription factor 1 homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.79  E-value=1.9e-20  Score=131.19  Aligned_cols=62  Identities=44%  Similarity=0.710  Sum_probs=58.9

Q ss_pred             CCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       135 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      +||.||.||..|+.+|+..|..++||+..++.+||..|||++.+|+|||||+|+|+|+....
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~~~   63 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKD   63 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhcccc
Confidence            47889999999999999999999999999999999999999999999999999999987654

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.79  E-value=7.9e-21  Score=136.20  Aligned_cols=64  Identities=42%  Similarity=0.635  Sum_probs=59.5

Q ss_pred             CCCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhh
Q psy16800        133 LLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKE  196 (221)
Q Consensus       133 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~  196 (221)
                      .+.++.||+||.+|+.+|+.+|..++||+..++++||..|+|++.+|+|||||||+|+|+....
T Consensus         7 ~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   70 (77)
T d1vnda_           7 NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNE   70 (77)
T ss_dssp             SSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSCCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHhhc
Confidence            4467889999999999999999999999999999999999999999999999999999876554

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeodomain-only protein, Hop
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.78  E-value=3.8e-20  Score=131.02  Aligned_cols=60  Identities=27%  Similarity=0.341  Sum_probs=56.6

Q ss_pred             CCCCcccCHHHHHHHHHHhhh-CCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        136 NSGRTNFTNKQLTELEKEFHF-NKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~-~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      ++.|+.||.+|+.+||..|.. ++||+...+++||..|||++.+|+|||||||+|+|+...
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~~   62 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   62 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhccC
Confidence            678999999999999999986 789999999999999999999999999999999998764

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=1.6e-20  Score=128.43  Aligned_cols=59  Identities=44%  Similarity=0.689  Sum_probs=56.8

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHh
Q psy16800        136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRI  194 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~  194 (221)
                      ||.||.||.+|+.+|+..|..++||+..++..||..|||++.+|++||||+|+++|+..
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~~   60 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE   60 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhcC
Confidence            68899999999999999999999999999999999999999999999999999999863

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-containing protein 1, HMBOX1 (Flj21616)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.3e-19  Score=129.82  Aligned_cols=63  Identities=30%  Similarity=0.463  Sum_probs=58.6

Q ss_pred             CCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhC---------------CCCCceeeccccchhHHHHHhhhcc
Q psy16800        136 NSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQ---------------LNETQVKIWFQNRRMKQKKRIKEGI  198 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~---------------Lt~~qVqvWFQNRRaK~Kr~~k~g~  198 (221)
                      ||.|+.|+.+|+.+||.+|..++||+..+|++||..+|               |++.+|+|||||||+|+|++...+.
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~~a~   78 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANIAA   78 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhhHHH
Confidence            57899999999999999999999999999999999875               8999999999999999999887654

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.74  E-value=1.3e-19  Score=126.15  Aligned_cols=62  Identities=27%  Similarity=0.397  Sum_probs=58.2

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      +.+|.||.||.+|+.+|+.+|..|+||+..++++||..+||++.+|++||||+|++.|+...
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~~~   63 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI   63 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCCC
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHHHH
Confidence            35889999999999999999999999999999999999999999999999999999887543

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.74  E-value=1.7e-19  Score=122.50  Aligned_cols=57  Identities=26%  Similarity=0.445  Sum_probs=54.8

Q ss_pred             CCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHH
Q psy16800        137 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR  193 (221)
Q Consensus       137 r~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~  193 (221)
                      |.||.|+.+|+.+|+..|..++||+..++.+||..|||++.+|+|||||+|+++|+.
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr~   57 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV   57 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHhc
Confidence            569999999999999999999999999999999999999999999999999999874

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-3 POU Homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=1.4e-19  Score=126.34  Aligned_cols=59  Identities=31%  Similarity=0.388  Sum_probs=56.5

Q ss_pred             CCCCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHH
Q psy16800        135 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR  193 (221)
Q Consensus       135 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~  193 (221)
                      ++|.||.|+..|+..|+.+|..++||+..++++||..+||++.+|+|||||+|+++|+.
T Consensus         8 ~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_           8 RKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             SSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            47889999999999999999999999999999999999999999999999999998864

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.73  E-value=3e-19  Score=119.22  Aligned_cols=53  Identities=26%  Similarity=0.492  Sum_probs=51.4

Q ss_pred             CcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHH
Q psy16800        139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK  191 (221)
Q Consensus       139 Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~K  191 (221)
                      ||.||++|+.+|+..|..++||+..++.+||..+||++.+|++||||+|+|.|
T Consensus         1 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~K   53 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   53 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTTC
T ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhccC
Confidence            78999999999999999999999999999999999999999999999999865

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.1e-18  Score=118.16  Aligned_cols=56  Identities=32%  Similarity=0.471  Sum_probs=54.1

Q ss_pred             CCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHH
Q psy16800        138 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR  193 (221)
Q Consensus       138 ~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~  193 (221)
                      +||.|+.+|+.+||.+|..++||+..++.+||..|||++.+|++||||+|+++|+.
T Consensus         1 kRT~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk~   56 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI   56 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHcc
Confidence            48999999999999999999999999999999999999999999999999999874

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=9.5e-19  Score=123.25  Aligned_cols=58  Identities=22%  Similarity=0.316  Sum_probs=54.9

Q ss_pred             CCCCCcccCHHHHHHHHHHhh-hCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHH
Q psy16800        135 NNSGRTNFTNKQLTELEKEFH-FNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK  192 (221)
Q Consensus       135 ~rr~Rt~ft~~Ql~~Le~~F~-~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr  192 (221)
                      .++.|++|+.+|+.+|+.+|. .++||+..++++||.+|+|++.+|++||||+|+++|+
T Consensus         7 ~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk   65 (71)
T d1wi3a_           7 GPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             CCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             CCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhcc
Confidence            478899999999999999997 5899999999999999999999999999999999876

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Zinc fingers and homeoboxes protein 1, ZHX1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=4.5e-18  Score=121.29  Aligned_cols=63  Identities=16%  Similarity=0.228  Sum_probs=55.6

Q ss_pred             CcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhhhccccC
Q psy16800        139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIKEGILIG  201 (221)
Q Consensus       139 Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k~g~~~~  201 (221)
                      +..+|.+|+.+|+.+|..++||+..++++||..|+|++.+|++||||||++.++.........
T Consensus         8 ~k~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~~~~~~~   70 (76)
T d2ecba1           8 FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEIDE   70 (76)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCCCCCC
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhHhhhccc
Confidence            334699999999999999999999999999999999999999999999999887766544443

>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=99.69  E-value=3.5e-18  Score=123.02  Aligned_cols=59  Identities=15%  Similarity=0.142  Sum_probs=54.4

Q ss_pred             CCCCCCcccCHHHHHHHHHHhhh----CCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHH
Q psy16800        134 LNNSGRTNFTNKQLTELEKEFHF----NKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK  192 (221)
Q Consensus       134 ~~rr~Rt~ft~~Ql~~Le~~F~~----~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr  192 (221)
                      .+||.||.||..|+..|+.+|+.    ++||+..++++||..|||++.+|+|||||+|++.|+
T Consensus        16 ~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          16 TTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            45788999999999999999886    899999999999999999999999999999987653

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.67  E-value=4.3e-18  Score=112.03  Aligned_cols=50  Identities=32%  Similarity=0.359  Sum_probs=48.9

Q ss_pred             CCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccch
Q psy16800        138 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRR  187 (221)
Q Consensus       138 ~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRR  187 (221)
                      +||.||.+|+.+||..|..++||+..++.+||..|||++.+|++||||+|
T Consensus         1 PRt~ft~~Q~~~Le~~F~~n~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1           1 PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             CCSCCCHHHHHHHHHHTTSSCSSTHHHHHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhhcCCcCc
Confidence            48999999999999999999999999999999999999999999999998

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-leucine zipper protein Homez
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=3.8e-17  Score=116.36  Aligned_cols=59  Identities=20%  Similarity=0.271  Sum_probs=54.5

Q ss_pred             CCCcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        137 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       137 r~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      ..+++||.+|+.+|+..|..++||+..++..||..|+|++.+|++||||+|+++|+...
T Consensus         5 s~~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~~~   63 (76)
T d2ecca1           5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQL   63 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhchH
Confidence            34567899999999999999999999999999999999999999999999999998544

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=4.4e-17  Score=115.17  Aligned_cols=60  Identities=30%  Similarity=0.466  Sum_probs=55.9

Q ss_pred             CCCCcccCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHHHhh
Q psy16800        136 NSGRTNFTNKQLTELEKEFHF---NKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKRIK  195 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~---~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr~~k  195 (221)
                      |+.|+.|+.+|+.+|+..|..   ++||+..++++||..+||++.||++||||+|+|.|+...
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~~   64 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG   64 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccch
Confidence            678999999999999999974   889999999999999999999999999999999987554

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Rat (Rattus rattus) [TaxId: 10117]

Probab=99.62  E-value=1.8e-17  Score=118.74  Aligned_cols=56  Identities=21%  Similarity=0.310  Sum_probs=52.9

Q ss_pred             CcccCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhC---------------------CCCCceeeccccchhHHHHHh
Q psy16800        139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQ---------------------LNETQVKIWFQNRRMKQKKRI  194 (221)
Q Consensus       139 Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~L~---------------------Lt~~qVqvWFQNRRaK~Kr~~  194 (221)
                      |++||+.|+.+||.+|+.++||+..+|+.||.+|+                     |++.+|++||||||+++|++.
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr~~   77 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFRH   77 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCCC
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHHhc
Confidence            68999999999999999999999999999999995                     899999999999999998764

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.59  E-value=5.8e-17  Score=107.54  Aligned_cols=50  Identities=26%  Similarity=0.371  Sum_probs=46.6

Q ss_pred             CHHHHHHHHHHhhh-CCCCCHHHHHHHHHHhCCCCCceeeccccchhHHHH
Q psy16800        143 TNKQLTELEKEFHF-NKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK  192 (221)
Q Consensus       143 t~~Ql~~Le~~F~~-~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr  192 (221)
                      |.+|..+||.+|.. ++||+..++++||..|||++++|+|||||||+++|+
T Consensus         1 T~~q~~iLE~~F~~~~~~P~~~~~~~LA~~~~ls~~qV~~WFqNrR~k~k~   51 (52)
T d1x2ma1           1 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   51 (52)
T ss_dssp             SSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             ChhHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccCc
Confidence            46799999999987 689999999999999999999999999999999874

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: LAG1 longevity assurance homolog 5, LASS5
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=2.3e-16  Score=107.23  Aligned_cols=55  Identities=24%  Similarity=0.351  Sum_probs=50.9

Q ss_pred             CCCcccCHHHHHHHHHHhhh-CCCCCHHHHHHHHHHhCCCCCceeeccccchhHHH
Q psy16800        137 SGRTNFTNKQLTELEKEFHF-NKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK  191 (221)
Q Consensus       137 r~Rt~ft~~Ql~~Le~~F~~-~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~K  191 (221)
                      +.++.++.++..+||.+|.. ++||+..++++||.+|||++.+|++||||||+++|
T Consensus         3 k~~~~~k~~~~~iLE~~F~~~~~yPs~~~~~~LA~~lgls~~qV~~WFqNrR~k~r   58 (59)
T d2cqxa1           3 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK   58 (59)
T ss_dssp             CCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCccccHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccC
Confidence            45778889999999999986 68999999999999999999999999999999976

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.53  E-value=1.5e-15  Score=103.27  Aligned_cols=53  Identities=32%  Similarity=0.446  Sum_probs=49.1

Q ss_pred             cccCHHHHHHHHHHhhhC---CCCCHHHHHHHHHHhCCCCCceeeccccchhHHHH
Q psy16800        140 TNFTNKQLTELEKEFHFN---KYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK  192 (221)
Q Consensus       140 t~ft~~Ql~~Le~~F~~~---~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~Kr  192 (221)
                      .+|+.+|+.+|+..|..+   +||+..++++||..+||++.||++||||+|+|.|+
T Consensus         3 ~Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           3 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             CSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            359999999999999765   69999999999999999999999999999998875

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=3.5e-15  Score=102.15  Aligned_cols=56  Identities=21%  Similarity=0.278  Sum_probs=52.2

Q ss_pred             CCCCcccCHHHHHHHHHHhhh---CCCCCHHHHHHHHHHhCCCCCceeeccccchhHHH
Q psy16800        136 NSGRTNFTNKQLTELEKEFHF---NKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK  191 (221)
Q Consensus       136 rr~Rt~ft~~Ql~~Le~~F~~---~~yps~~~r~~LA~~L~Lt~~qVqvWFQNRRaK~K  191 (221)
                      +++|+.|+.+++.+|+..|..   ++||+..++..||..+||+..||++||+|+|+|..
T Consensus         3 krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R~l   61 (62)
T d1x2na1           3 KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRIL   61 (62)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhc
Confidence            667899999999999999985   78999999999999999999999999999998854