Psyllid ID: psy8538

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60----
Protein Sequence
MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIVSFLEKVHGDGRNSSR
Secondary Structure (PSIPRED)
cccccEEccHHHHHHHHHHHHHHHcccccEEEccccccccccccHHHHHHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
cccEEEEccEEEEHHHHHHHHHHccccHHccccccccccEcccccEEEEEHHHHHccccccccc
Coil and Loop (DISEMBL)
MDSLEFHYSRYITIRRKAELANslglserqvrcphhqlttvnnNTAIIVSFLEKvhgdgrnssr
Flexible Loop (DISEMBL)
MDSLEFHYSRYITIRRKAELANSLGLSERQVRCphhqlttvnnntAIIVSFlekvhgdgrnssr
Low Complexity Region (SEG)
MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIVSFLEKVHGDGRNSSR
Disordered region (IsUnstruct)
*****FHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIVSFLEKV*********
Disordered Region (DISOPRED)
*DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLT*************************
Disordered Region (DISEMBL)
MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIVSFLEKV*********
Disordered Region (DISPRO)
**SLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIVSFLEKVH********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIVSFLEKVHGDGRNSSR
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	64	2.2.26 [Sep-21-2011]
Q04649	313	Homeobox protein CDX-2 OS	N/A	N/A	0.437	0.089	0.892	4e-08
Q99626	313	Homeobox protein CDX-2 OS	yes	N/A	0.437	0.089	0.892	6e-08
Q91622	263	Homeobox protein CDX-1 OS	N/A	N/A	0.437	0.106	0.857	9e-08
P46692	248	Homeobox protein CHOX-CAD	no	N/A	0.437	0.112	0.857	2e-07
Q9DEB6	260	Homeobox protein CDX-1 OS	no	N/A	0.437	0.107	0.857	2e-07
A2T7H5	265	Homeobox protein CDX-1 OS	N/A	N/A	0.437	0.105	0.821	2e-07
P18111	268	Homeobox protein CDX-1 OS	yes	N/A	0.437	0.104	0.821	2e-07
P47902	265	Homeobox protein CDX-1 OS	no	N/A	0.437	0.105	0.821	2e-07
P43241	311	Homeobox protein CDX-2 OS	no	N/A	0.437	0.090	0.821	5e-07
Q05095	123	Homeobox protein CDX-1 (F	no	N/A	0.437	0.227	0.821	6e-07

>sp|Q04649|CDX2_MESAU Homeobox protein CDX-2 OS=Mesocricetus auratus GN=CDX2 PE=2 SV=1

 Score = 56.6 bits (135), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 25/28 (89%), Positives = 27/28 (96%)

Query: 5   EFHYSRYITIRRKAELANSLGLSERQVR 32
           EFHYSRYITIRRKAELA +LGLSERQV+
Sbjct: 203 EFHYSRYITIRRKAELAATLGLSERQVK 230

Involved in the transcriptional regulation of multiple genes expressed in the intestinal epithelium. Important in broad range of functions from early differentiation to maintenance of the intestinal epithelial lining of both the small and large intestine.
Mesocricetus auratus (taxid: 10036)

>sp|Q99626|CDX2_HUMAN Homeobox protein CDX-2 OS=Homo sapiens GN=CDX2 PE=1 SV=3

 Score = 56.2 bits (134), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 25/28 (89%), Positives = 27/28 (96%)

Query: 5   EFHYSRYITIRRKAELANSLGLSERQVR 32
           EFHYSRYITIRRKAELA +LGLSERQV+
Sbjct: 204 EFHYSRYITIRRKAELAATLGLSERQVK 231

Involved in the transcriptional regulation of multiple genes expressed in the intestinal epithelium. Important in broad range of functions from early differentiation to maintenance of the intestinal epithelial lining of both the small and large intestine.

Homo sapiens (taxid: 9606)

>sp|Q91622|CDX1_XENLA Homeobox protein CDX-1 OS=Xenopus laevis GN=cdx1 PE=2 SV=1

 Score = 55.5 bits (132), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 24/28 (85%), Positives = 27/28 (96%)

Query: 5   EFHYSRYITIRRKAELANSLGLSERQVR 32
           EFHYSRYITIRRKAELA +LGL+ERQV+
Sbjct: 168 EFHYSRYITIRRKAELAAALGLTERQVK 195

Xenopus laevis (taxid: 8355)

>sp|P46692|HMD1_CHICK Homeobox protein CHOX-CAD OS=Gallus gallus GN=CHOX-CAD1 PE=2 SV=1

 Score = 54.7 bits (130), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 24/28 (85%), Positives = 27/28 (96%)

Query: 5   EFHYSRYITIRRKAELANSLGLSERQVR 32
           EFHYSRYITIRRKAELA +LGL+ERQV+
Sbjct: 155 EFHYSRYITIRRKAELAAALGLTERQVK 182

May play an important role during the early steps of organogenesis.

Gallus gallus (taxid: 9031)

>sp|Q9DEB6|CDX1_CHICK Homeobox protein CDX-1 OS=Gallus gallus GN=CDX1 PE=2 SV=2

 Score = 54.7 bits (130), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 24/28 (85%), Positives = 27/28 (96%)

Query: 5   EFHYSRYITIRRKAELANSLGLSERQVR 32
           EFHYSRYITIRRKAELA +LGL+ERQV+
Sbjct: 167 EFHYSRYITIRRKAELAAALGLTERQVK 194

Gallus gallus (taxid: 9031)

>sp|A2T7H5|CDX1_PONPY Homeobox protein CDX-1 OS=Pongo pygmaeus GN=CDX1 PE=3 SV=1

 Score = 54.3 bits (129), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 23/28 (82%), Positives = 27/28 (96%)

Query: 5   EFHYSRYITIRRKAELANSLGLSERQVR 32
           EFHYSRYITIRRK+ELA +LGL+ERQV+
Sbjct: 172 EFHYSRYITIRRKSELAANLGLTERQVK 199

Could play a role in the terminal differentiation of the intestine.

Pongo pygmaeus (taxid: 9600)

>sp|P18111|CDX1_MOUSE Homeobox protein CDX-1 OS=Mus musculus GN=Cdx1 PE=2 SV=2

 Score = 54.3 bits (129), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 23/28 (82%), Positives = 27/28 (96%)

Query: 5   EFHYSRYITIRRKAELANSLGLSERQVR 32
           EFHYSRYITIRRK+ELA +LGL+ERQV+
Sbjct: 172 EFHYSRYITIRRKSELAANLGLTERQVK 199

Could play a role in the terminal differentiation of the intestine.

Mus musculus (taxid: 10090)

>sp|P47902|CDX1_HUMAN Homeobox protein CDX-1 OS=Homo sapiens GN=CDX1 PE=2 SV=2

 Score = 54.3 bits (129), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 23/28 (82%), Positives = 27/28 (96%)

Query: 5   EFHYSRYITIRRKAELANSLGLSERQVR 32
           EFHYSRYITIRRK+ELA +LGL+ERQV+
Sbjct: 172 EFHYSRYITIRRKSELAANLGLTERQVK 199

Could play a role in the terminal differentiation of the intestine.

Homo sapiens (taxid: 9606)

>sp|P43241|CDX2_MOUSE Homeobox protein CDX-2 OS=Mus musculus GN=Cdx2 PE=1 SV=1

 Score = 53.1 bits (126), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 23/28 (82%), Positives = 27/28 (96%)

Query: 5   EFHYSRYITIRRKAELANSLGLSERQVR 32
           EFH+SRYITIRRK+ELA +LGLSERQV+
Sbjct: 203 EFHFSRYITIRRKSELAATLGLSERQVK 230

Involved in the transcriptional regulation of multiple genes expressed in the intestinal epithelium. Important in broad range of functions from early differentiation to maintenance of the intestinal epithelial lining of both the small and large intestine.

Mus musculus (taxid: 10090)

>sp|Q05095|CDX1_RAT Homeobox protein CDX-1 (Fragment) OS=Rattus norvegicus GN=Cdx1 PE=2 SV=1

 Score = 52.8 bits (125), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 23/28 (82%), Positives = 27/28 (96%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          EFHYSRYITIRRK+ELA +LGL+ERQV+
Sbjct: 23 EFHYSRYITIRRKSELAANLGLTERQVK 50

Could play a role in the terminal differentiation of the intestine.

Rattus norvegicus (taxid: 10116)

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	64
45383526	276	homeobox protein CDX-2 [Gallus gallus] g	0.437	0.101	0.928	4e-07
255755665	313	homeodomain transcription factor [Balano	0.437	0.089	0.892	1e-06
449484370	271	PREDICTED: LOW QUALITY PROTEIN: homeobox	0.437	0.103	0.892	1e-06
259013416	358	caudal homeobox protein [Saccoglossus ko	0.437	0.078	0.892	1e-06
270006390	112	caudal-2 [Tribolium castaneum]	0.437	0.25	0.928	2e-06
329665001	306	homeobox protein CDX-2 [Bos taurus]	0.437	0.091	0.892	2e-06
395520819	298	PREDICTED: homeobox protein CDX-2 [Sarco	0.437	0.093	0.892	2e-06
344284496	310	PREDICTED: homeobox protein CDX-2-like [	0.437	0.090	0.892	2e-06
194221805	309	PREDICTED: LOW QUALITY PROTEIN: homeobox	0.437	0.090	0.892	2e-06
126327413	302	PREDICTED: homeobox protein CDX-2-like [	0.437	0.092	0.892	2e-06

>gi|45383526|ref|NP_989642.1| homeobox protein CDX-2 [Gallus gallus] gi|1737445|gb|AAB38964.1| homeobox protein [Gallus gallus]

 Score = 58.9 bits (141), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 26/28 (92%), Positives = 28/28 (100%)

Query: 5   EFHYSRYITIRRKAELANSLGLSERQVR 32
           EFHYSRYITIRRKAELA+SLGLSERQV+
Sbjct: 196 EFHYSRYITIRRKAELASSLGLSERQVK 223

Source: Gallus gallus

Species: Gallus gallus

Genus: Gallus

Family: Phasianidae

Order: Galliformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|255755665|dbj|BAH96558.1| homeodomain transcription factor [Balanoglossus simodensis]

 Score = 57.4 bits (137), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/28 (89%), Positives = 27/28 (96%)

Query: 5   EFHYSRYITIRRKAELANSLGLSERQVR 32
           EFHYSRYITIRRKAELA +LGLSERQV+
Sbjct: 193 EFHYSRYITIRRKAELAQALGLSERQVK 220

Source: Balanoglossus simodensis

Species: Balanoglossus simodensis

Genus: Balanoglossus

Family: Ptychoderidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|449484370|ref|XP_004175127.1| PREDICTED: LOW QUALITY PROTEIN: homeobox protein CDX-2 [Taeniopygia guttata]

 Score = 57.4 bits (137), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 25/28 (89%), Positives = 28/28 (100%)

Query: 5   EFHYSRYITIRRKAELANSLGLSERQVR 32
           EFHYSRYITIRRKAELA++LGLSERQV+
Sbjct: 191 EFHYSRYITIRRKAELASNLGLSERQVK 218

Source: Taeniopygia guttata

Species: Taeniopygia guttata

Genus: Taeniopygia

Family: Estrildidae

Order: Passeriformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|259013416|ref|NP_001158415.1| caudal homeobox protein [Saccoglossus kowalevskii] gi|196123799|gb|ACG70188.1| caudal homeobox protein [Saccoglossus kowalevskii]

 Score = 57.0 bits (136), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/28 (89%), Positives = 28/28 (100%)

Query: 5   EFHYSRYITIRRKAELANSLGLSERQVR 32
           EFHYSRYITIRRKAELA++LGLSERQV+
Sbjct: 182 EFHYSRYITIRRKAELAHALGLSERQVK 209

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|270006390|gb|EFA02838.1| caudal-2 [Tribolium castaneum]

 Score = 57.0 bits (136), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/28 (92%), Positives = 28/28 (100%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          EF+YSRYITIRRKAELANSLGLSERQV+
Sbjct: 30 EFYYSRYITIRRKAELANSLGLSERQVK 57

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|329665001|ref|NP_001193228.1| homeobox protein CDX-2 [Bos taurus]

 Score = 56.6 bits (135), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/28 (89%), Positives = 27/28 (96%)

Query: 5   EFHYSRYITIRRKAELANSLGLSERQVR 32
           EFHYSRYITIRRKAELA +LGLSERQV+
Sbjct: 204 EFHYSRYITIRRKAELAATLGLSERQVK 231

Source: Bos taurus

Species: Bos taurus

Genus: Bos

Family: Bovidae

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|395520819|ref|XP_003764520.1| PREDICTED: homeobox protein CDX-2 [Sarcophilus harrisii]

 Score = 56.6 bits (135), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/28 (89%), Positives = 27/28 (96%)

Query: 5   EFHYSRYITIRRKAELANSLGLSERQVR 32
           EFHYSRYITIRRKAELA +LGLSERQV+
Sbjct: 195 EFHYSRYITIRRKAELAATLGLSERQVK 222

Source: Sarcophilus harrisii

Species: Sarcophilus harrisii

Genus: Sarcophilus

Family: Dasyuridae

Order: Dasyuromorphia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|344284496|ref|XP_003414002.1| PREDICTED: homeobox protein CDX-2-like [Loxodonta africana]

 Score = 56.6 bits (135), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/28 (89%), Positives = 27/28 (96%)

Query: 5   EFHYSRYITIRRKAELANSLGLSERQVR 32
           EFHYSRYITIRRKAELA +LGLSERQV+
Sbjct: 204 EFHYSRYITIRRKAELAATLGLSERQVK 231

Source: Loxodonta africana

Species: Loxodonta africana

Genus: Loxodonta

Family: Elephantidae

Order: Proboscidea

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|194221805|ref|XP_001915543.1| PREDICTED: LOW QUALITY PROTEIN: homeobox protein CDX-2-like [Equus caballus]

 Score = 56.6 bits (135), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/28 (89%), Positives = 27/28 (96%)

Query: 5   EFHYSRYITIRRKAELANSLGLSERQVR 32
           EFHYSRYITIRRKAELA +LGLSERQV+
Sbjct: 196 EFHYSRYITIRRKAELAATLGLSERQVK 223

Source: Equus caballus

Species: Equus caballus

Genus: Equus

Family: Equidae

Order: Perissodactyla

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|126327413|ref|XP_001367105.1| PREDICTED: homeobox protein CDX-2-like [Monodelphis domestica]

 Score = 56.6 bits (135), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/28 (89%), Positives = 27/28 (96%)

Query: 5   EFHYSRYITIRRKAELANSLGLSERQVR 32
           EFHYSRYITIRRKAELA +LGLSERQV+
Sbjct: 195 EFHYSRYITIRRKAELAATLGLSERQVK 222

Source: Monodelphis domestica

Species: Monodelphis domestica

Genus: Monodelphis

Family: Didelphidae

Order: Didelphimorphia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

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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	64
UNIPROTKB|F1P2M4	274	CDX2 "Uncharacterized protein"	0.437	0.102	0.928	2.8e-08
UNIPROTKB|F1MJX0	142	CDX2 "Uncharacterized protein"	0.437	0.197	0.892	4.2e-08
UNIPROTKB|H0YJ33	156	CDX2 "Homeobox protein CDX-2"	0.437	0.179	0.892	4.2e-08
UNIPROTKB|F1M7G8	239	Cdx2 "Protein Cdx2" [Rattus no	0.437	0.117	0.892	8.7e-08
UNIPROTKB|F6R243	117	CDX1 "Homeobox protein CDX-1"	0.437	0.239	0.857	8.7e-08
UNIPROTKB|F1RSU9	311	CDX2 "Uncharacterized protein"	0.437	0.090	0.892	1.8e-07
UNIPROTKB|Q99626	313	CDX2 "Homeobox protein CDX-2"	0.437	0.089	0.892	1.8e-07
UNIPROTKB|E2RI97	314	CDX2 "Uncharacterized protein"	0.437	0.089	0.892	1.8e-07
UNIPROTKB|F1MCF6	118	CDX1 "Uncharacterized protein"	0.437	0.237	0.821	1.8e-07
RGD|621233	123	Cdx1 "caudal type homeo box 1"	0.437	0.227	0.821	1.8e-07

UNIPROTKB|F1P2M4 CDX2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 131 (51.2 bits), Expect = 2.8e-08, P = 2.8e-08
 Identities = 26/28 (92%), Positives = 28/28 (100%)

Query:     5 EFHYSRYITIRRKAELANSLGLSERQVR 32
             EFHYSRYITIRRKAELA+SLGLSERQV+
Sbjct:   196 EFHYSRYITIRRKAELASSLGLSERQVK 223

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IEA

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

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

GO:0000794 "condensed nuclear chromosome" evidence=IEA

GO:0001568 "blood vessel development" evidence=IEA

GO:0001829 "trophectodermal cell differentiation" evidence=IEA

GO:0003714 "transcription corepressor activity" evidence=IEA

GO:0008333 "endosome to lysosome transport" evidence=IEA

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

GO:0017053 "transcriptional repressor complex" evidence=IEA

GO:0035019 "somatic stem cell maintenance" evidence=IEA

GO:0045197 "establishment or maintenance of epithelial cell apical/basal polarity" evidence=IEA

GO:0045597 "positive regulation of cell differentiation" evidence=IEA

GO:0060711 "labyrinthine layer development" evidence=IEA

UNIPROTKB|F1MJX0 CDX2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 125 (49.1 bits), Expect = 4.2e-08, P = 4.2e-08
 Identities = 25/28 (89%), Positives = 27/28 (96%)

Query:     5 EFHYSRYITIRRKAELANSLGLSERQVR 32
             EFHYSRYITIRRKAELA +LGLSERQV+
Sbjct:    40 EFHYSRYITIRRKAELAATLGLSERQVK 67

GO:0060711 "labyrinthine layer development" evidence=IEA

GO:0045597 "positive regulation of cell differentiation" evidence=IEA

GO:0045197 "establishment or maintenance of epithelial cell apical/basal polarity" evidence=IEA

GO:0035019 "somatic stem cell maintenance" evidence=IEA

GO:0017053 "transcriptional repressor complex" evidence=IEA

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

GO:0008333 "endosome to lysosome transport" evidence=IEA

GO:0003714 "transcription corepressor activity" evidence=IEA

GO:0001829 "trophectodermal cell differentiation" evidence=IEA

GO:0001568 "blood vessel development" evidence=IEA

GO:0000794 "condensed nuclear chromosome" evidence=IEA

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

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

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IEA

UNIPROTKB|H0YJ33 CDX2 "Homeobox protein CDX-2" [Homo sapiens (taxid:9606)]

 Score = 125 (49.1 bits), Expect = 4.2e-08, P = 4.2e-08
 Identities = 25/28 (89%), Positives = 27/28 (96%)

Query:     5 EFHYSRYITIRRKAELANSLGLSERQVR 32
             EFHYSRYITIRRKAELA +LGLSERQV+
Sbjct:    47 EFHYSRYITIRRKAELAATLGLSERQVK 74

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|F1M7G8 Cdx2 "Protein Cdx2" [Rattus norvegicus (taxid:10116)]

 Score = 125 (49.1 bits), Expect = 8.7e-08, P = 8.7e-08
 Identities = 25/28 (89%), Positives = 27/28 (96%)

Query:     5 EFHYSRYITIRRKAELANSLGLSERQVR 32
             EFHYSRYITIRRKAELA +LGLSERQV+
Sbjct:   132 EFHYSRYITIRRKAELAATLGLSERQVK 159

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

UNIPROTKB|F6R243 CDX1 "Homeobox protein CDX-1" [Gallus gallus (taxid:9031)]

 Score = 122 (48.0 bits), Expect = 8.7e-08, P = 8.7e-08
 Identities = 24/28 (85%), Positives = 27/28 (96%)

Query:     5 EFHYSRYITIRRKAELANSLGLSERQVR 32
             EFHYSRYITIRRKAELA +LGL+ERQV+
Sbjct:    24 EFHYSRYITIRRKAELAAALGLTERQVK 51

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0060349 "bone morphogenesis" evidence=IEA

UNIPROTKB|F1RSU9 CDX2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 125 (49.1 bits), Expect = 1.8e-07, P = 1.8e-07
 Identities = 25/28 (89%), Positives = 27/28 (96%)

Query:     5 EFHYSRYITIRRKAELANSLGLSERQVR 32
             EFHYSRYITIRRKAELA +LGLSERQV+
Sbjct:   204 EFHYSRYITIRRKAELAATLGLSERQVK 231

GO:0060711 "labyrinthine layer development" evidence=IEA

GO:0045597 "positive regulation of cell differentiation" evidence=IEA

GO:0045197 "establishment or maintenance of epithelial cell apical/basal polarity" evidence=IEA

GO:0035019 "somatic stem cell maintenance" evidence=IEA

GO:0017053 "transcriptional repressor complex" evidence=IEA

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

GO:0008333 "endosome to lysosome transport" evidence=IEA

GO:0003714 "transcription corepressor activity" evidence=IEA

GO:0001829 "trophectodermal cell differentiation" evidence=IEA

GO:0001568 "blood vessel development" evidence=IEA

GO:0000794 "condensed nuclear chromosome" evidence=IEA

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

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

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IEA

UNIPROTKB|Q99626 CDX2 "Homeobox protein CDX-2" [Homo sapiens (taxid:9606)]

 Score = 125 (49.1 bits), Expect = 1.8e-07, P = 1.8e-07
 Identities = 25/28 (89%), Positives = 27/28 (96%)

Query:     5 EFHYSRYITIRRKAELANSLGLSERQVR 32
             EFHYSRYITIRRKAELA +LGLSERQV+
Sbjct:   204 EFHYSRYITIRRKAELAATLGLSERQVK 231

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IEA

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

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

GO:0000794 "condensed nuclear chromosome" evidence=IEA

GO:0001568 "blood vessel development" evidence=IEA

GO:0001829 "trophectodermal cell differentiation" evidence=IEA

GO:0003714 "transcription corepressor activity" evidence=IEA

GO:0008333 "endosome to lysosome transport" evidence=IEA

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

GO:0017053 "transcriptional repressor complex" evidence=IEA

GO:0035019 "somatic stem cell maintenance" evidence=IEA

GO:0045197 "establishment or maintenance of epithelial cell apical/basal polarity" evidence=IEA

GO:0045597 "positive regulation of cell differentiation" evidence=IEA

GO:0060711 "labyrinthine layer development" evidence=IEA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0009887 "organ morphogenesis" evidence=TAS

UNIPROTKB|E2RI97 CDX2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 125 (49.1 bits), Expect = 1.8e-07, P = 1.8e-07
 Identities = 25/28 (89%), Positives = 27/28 (96%)

Query:     5 EFHYSRYITIRRKAELANSLGLSERQVR 32
             EFHYSRYITIRRKAELA +LGLSERQV+
Sbjct:   204 EFHYSRYITIRRKAELAATLGLSERQVK 231

GO:0060711 "labyrinthine layer development" evidence=IEA

GO:0045597 "positive regulation of cell differentiation" evidence=IEA

GO:0045197 "establishment or maintenance of epithelial cell apical/basal polarity" evidence=IEA

GO:0035019 "somatic stem cell maintenance" evidence=IEA

GO:0017053 "transcriptional repressor complex" evidence=IEA

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

GO:0008333 "endosome to lysosome transport" evidence=IEA

GO:0003714 "transcription corepressor activity" evidence=IEA

GO:0001829 "trophectodermal cell differentiation" evidence=IEA

GO:0001568 "blood vessel development" evidence=IEA

GO:0000794 "condensed nuclear chromosome" evidence=IEA

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

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

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IEA

UNIPROTKB|F1MCF6 CDX1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 119 (46.9 bits), Expect = 1.8e-07, P = 1.8e-07
 Identities = 23/28 (82%), Positives = 27/28 (96%)

Query:     5 EFHYSRYITIRRKAELANSLGLSERQVR 32
             EFHYSRYITIRRK+ELA +LGL+ERQV+
Sbjct:    25 EFHYSRYITIRRKSELAANLGLTERQVK 52

GO:0005634 "nucleus" evidence=IEA

GO:0060349 "bone morphogenesis" evidence=IEA

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

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

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

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IEA

RGD|621233 Cdx1 "caudal type homeo box 1" [Rattus norvegicus (taxid:10116)]

 Score = 119 (46.9 bits), Expect = 1.8e-07, P = 1.8e-07
 Identities = 23/28 (82%), Positives = 27/28 (96%)

Query:     5 EFHYSRYITIRRKAELANSLGLSERQVR 32
             EFHYSRYITIRRK+ELA +LGL+ERQV+
Sbjct:    23 EFHYSRYITIRRKSELAANLGLTERQVK 50

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007389 "pattern specification process" evidence=ISO

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

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

GO:0060349 "bone morphogenesis" evidence=IEA;ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q99626	CDX2_HUMAN	No assigned EC number	0.8928	0.4375	0.0894	yes	N/A
P18111	CDX1_MOUSE	No assigned EC number	0.8214	0.4375	0.1044	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	64
pfam00046	57	pfam00046, Homeobox, Homeobox domain	5e-06
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	2e-05
smart00389	57	smart00389, HOX, Homeodomain	3e-05

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

 Score = 38.6 bits (91), Expect = 5e-06
 Identities = 14/28 (50%), Positives = 19/28 (67%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          EF  +RY +   + ELA  LGL+ERQV+
Sbjct: 18 EFEKNRYPSAEEREELAKKLGLTERQVK 45

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 = 37.2 bits (87), Expect = 2e-05
 Identities = 13/28 (46%), Positives = 18/28 (64%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          EF  + Y +   + ELA  LGL+ERQV+
Sbjct: 18 EFEKNPYPSREEREELAKELGLTERQVK 45

Length = 59

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 36.8 bits (86), Expect = 3e-05
 Identities = 14/28 (50%), Positives = 18/28 (64%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          EF  + Y +   + ELA  LGLSERQV+
Sbjct: 19 EFQKNPYPSREEREELAKKLGLSERQVK 46

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	64
KOG0848|consensus	317		99.71
KOG0487|consensus	308		99.7
KOG0842|consensus	307		99.7
KOG0488|consensus	309		99.7
KOG0489|consensus	261		99.69
KOG0843|consensus	197		99.67
KOG0484|consensus	125		99.61
KOG0485|consensus	268		99.61
KOG0850|consensus	245		99.59
KOG0492|consensus	246		99.56
KOG0483|consensus	198		99.55
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.5
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.47
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.47
COG5576	156	Homeodomain-containing transcription factor [Trans	99.47
KOG2251|consensus	228		99.43
KOG0494|consensus	332		99.42
KOG0491|consensus	194		99.39
KOG0844|consensus	408		99.37
KOG0493|consensus	342		99.33
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.31
KOG3802|consensus	398		99.24
KOG0847|consensus	288		99.23
KOG4577|consensus	383		99.19
KOG0486|consensus	351		99.14
KOG0775|consensus	304		99.12
KOG0490|consensus	235		99.1
KOG0849|consensus	354		98.83
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.69
KOG1168|consensus	385		98.62
KOG0774|consensus	334		98.12
KOG0490|consensus	235		97.79
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	97.33
KOG2252|consensus	558		97.06
KOG0773|consensus	342		96.92
KOG1146|consensus	1406		96.73
KOG3623|consensus	1007		94.54
PF10668	60	Phage_terminase: Phage terminase small subunit; In	86.57
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	81.81

>KOG0848|consensus

Probab=99.71  E-value=2.3e-18  Score=113.20  Aligned_cols=48  Identities=48%  Similarity=0.562  Sum_probs=45.1

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHHH
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIV   49 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~   49 (64)
                      ||++|+.++|+++..+.+||.-|+|+|+||+|||||||+|+|+..+..
T Consensus       214 LEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk  261 (317)
T KOG0848|consen  214 LEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK  261 (317)
T ss_pred             hhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence            899999999999999999999999999999999999999999885544

>KOG0487|consensus

Probab=99.70  E-value=1.7e-18  Score=115.41  Aligned_cols=51  Identities=25%  Similarity=0.309  Sum_probs=46.5

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHHHHHH
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIVSFL   52 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~~~~   52 (64)
                      ||++|..|.|++.+.|.+|++.|+|+++||+|||||||-|+|++.+.....
T Consensus       250 LEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r~~  300 (308)
T KOG0487|consen  250 LEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENRLK  300 (308)
T ss_pred             HHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhhcc
Confidence            899999999999999999999999999999999999999999885544443

>KOG0842|consensus

Probab=99.70  E-value=5.3e-18  Score=113.03  Aligned_cols=51  Identities=24%  Similarity=0.230  Sum_probs=46.1

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHHHHHHH
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIVSFLE   53 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~~~~~   53 (64)
                      ||+.|...+|++..+|++||..|+||++||+|||||||.|.||. ...+..+
T Consensus       168 LERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~-~~dk~~~  218 (307)
T KOG0842|consen  168 LERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQ-QKDKALE  218 (307)
T ss_pred             HHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhh-hhhhhhh
Confidence            89999999999999999999999999999999999999999998 4444433

>KOG0488|consensus

Probab=99.70  E-value=3.9e-18  Score=113.84  Aligned_cols=58  Identities=24%  Similarity=0.277  Sum_probs=49.8

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHHHHHHHHhcCCCCC
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIVSFLEKVHGDGRN   61 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~~~~~~~~~~g~~   61 (64)
                      ||+.|++..|++..+|++||..|||+..||++||||||+|+|+.. . ...+.....|+.
T Consensus       187 LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~-a-~g~~~~~~~~~~  244 (309)
T KOG0488|consen  187 LEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQT-A-EGGELLYQAGNS  244 (309)
T ss_pred             HHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHH-H-hhhccccccccc
Confidence            899999999999999999999999999999999999999999993 2 355555555544

>KOG0489|consensus

Probab=99.69  E-value=9.6e-19  Score=114.32  Aligned_cols=51  Identities=27%  Similarity=0.368  Sum_probs=46.6

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHHHHHH
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIVSFL   52 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~~~~   52 (64)
                      ||++|+.|+|++...|.+||..|+|+|+||+|||||||.|+|+..+.....
T Consensus       174 LEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~  224 (261)
T KOG0489|consen  174 LEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ  224 (261)
T ss_pred             hhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence            899999999999999999999999999999999999999999885555443

>KOG0843|consensus

Probab=99.67  E-value=1.8e-17  Score=103.82  Aligned_cols=48  Identities=25%  Similarity=0.221  Sum_probs=44.9

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHHH
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIV   49 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~   49 (64)
                      ||.+|..++|....+|+.||..|+|++.||+|||||||+|.|+.....
T Consensus       117 LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~  164 (197)
T KOG0843|consen  117 LEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED  164 (197)
T ss_pred             HHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence            899999999999999999999999999999999999999999885443

>KOG0484|consensus

Probab=99.61  E-value=7e-17  Score=94.09  Aligned_cols=55  Identities=15%  Similarity=0.073  Sum_probs=49.7

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHHHHHHHHhc
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIVSFLEKVH   56 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~~~~~~~~   56 (64)
                      ||+.|...+||++..|++||.+++|++..|||||||||++-+++.+.+.......
T Consensus        32 LErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~~~~~   86 (125)
T KOG0484|consen   32 LERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAKMAAK   86 (125)
T ss_pred             HHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHHhhhh
Confidence            7999999999999999999999999999999999999999998877776655544

>KOG0485|consensus

Probab=99.61  E-value=6e-17  Score=104.27  Aligned_cols=45  Identities=27%  Similarity=0.285  Sum_probs=43.7

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      +||.+|...+|++..+|..||.+|.|+++||+|||||||+|+||.
T Consensus       118 qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq  162 (268)
T KOG0485|consen  118 QLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQ  162 (268)
T ss_pred             HHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHH
Confidence            489999999999999999999999999999999999999999998

>KOG0850|consensus

Probab=99.59  E-value=1.8e-16  Score=102.29  Aligned_cols=47  Identities=26%  Similarity=0.346  Sum_probs=43.4

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHH
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAI   47 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~   47 (64)
                      ||.+.|+.++|+--.+|.+||..|||+.+||+|||||||.|-|+..+
T Consensus       136 aL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k  182 (245)
T KOG0850|consen  136 ALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK  182 (245)
T ss_pred             HHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence            57889999999999999999999999999999999999999886633

>KOG0492|consensus

Probab=99.56  E-value=6.1e-16  Score=98.95  Aligned_cols=45  Identities=24%  Similarity=0.330  Sum_probs=43.3

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||+-|...+|++++++.+++..|.|+++||+|||||||++.||.
T Consensus       158 aLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRl  202 (246)
T KOG0492|consen  158 ALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRL  202 (246)
T ss_pred             HHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHH
Confidence            389999999999999999999999999999999999999999987

>KOG0483|consensus

Probab=99.55  E-value=1.5e-15  Score=96.43  Aligned_cols=48  Identities=23%  Similarity=0.238  Sum_probs=44.5

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHH
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAII   48 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~   48 (64)
                      +||..|..+.++.+..+..||+.|||.++||.|||||||+++|.....
T Consensus        64 ~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE  111 (198)
T KOG0483|consen   64 FLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLE  111 (198)
T ss_pred             HhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhh
Confidence            589999999999999999999999999999999999999999977433

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.50  E-value=4.8e-16  Score=80.57  Aligned_cols=43  Identities=28%  Similarity=0.325  Sum_probs=40.6

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccc
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNN   44 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~   44 (64)
                      ||..|..++||+..++..||..+||+..+|++||+|+|.++|+
T Consensus        15 L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen   15 LEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             HHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence            8899999999999999999999999999999999999987763

; 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 ....

>smart00389 HOX Homeodomain

Probab=99.47  E-value=5.9e-15  Score=75.84  Aligned_cols=43  Identities=33%  Similarity=0.341  Sum_probs=40.0

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCccccc
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNN   43 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k   43 (64)
                      .||..|..++||+..++..||..+||+..+|+.||+|+|.+.+
T Consensus        14 ~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~   56 (56)
T smart00389       14 ELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK   56 (56)
T ss_pred             HHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence            3889999999999999999999999999999999999997653

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=99.47  E-value=4.3e-15  Score=76.77  Aligned_cols=45  Identities=29%  Similarity=0.333  Sum_probs=41.6

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||..|..++||+..++..||..+||++.+|++||+|+|.+.++.
T Consensus        14 ~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~   58 (59)
T cd00086          14 ELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS   58 (59)
T ss_pred             HHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence            388999999999999999999999999999999999999877653

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.47  E-value=1.1e-14  Score=89.59  Aligned_cols=44  Identities=14%  Similarity=0.150  Sum_probs=41.9

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      |+..|..++||+...+..|+..++|+++.|+|||||+|++.|..
T Consensus        66 L~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~  109 (156)
T COG5576          66 LEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKK  109 (156)
T ss_pred             HHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHh
Confidence            78999999999999999999999999999999999999988765

>KOG2251|consensus

Probab=99.43  E-value=6.8e-14  Score=89.83  Aligned_cols=47  Identities=19%  Similarity=0.134  Sum_probs=44.1

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHH
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAII   48 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~   48 (64)
                      ||..|..+.||+...+++||.+|+|++.+|+|||.|||+|.++...-
T Consensus        52 Le~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q   98 (228)
T KOG2251|consen   52 LEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ   98 (228)
T ss_pred             HHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence            78999999999999999999999999999999999999999987443

>KOG0494|consensus

Probab=99.42  E-value=3.3e-14  Score=93.63  Aligned_cols=48  Identities=15%  Similarity=0.099  Sum_probs=45.0

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHHH
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIV   49 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~   49 (64)
                      ||+.|...+||+...|+-||.++.|++..|+|||||||+|+++.++..
T Consensus       156 LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w  203 (332)
T KOG0494|consen  156 LEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW  203 (332)
T ss_pred             HHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence            799999999999999999999999999999999999999999886544

>KOG0491|consensus

Probab=99.39  E-value=2.7e-14  Score=88.77  Aligned_cols=47  Identities=28%  Similarity=0.322  Sum_probs=43.7

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHH
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAII   48 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~   48 (64)
                      ||+.|+..+|++..++.+||..|+|+++||+.||||||.|.|+..+.
T Consensus       115 l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~  161 (194)
T KOG0491|consen  115 LEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRN  161 (194)
T ss_pred             cHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhc
Confidence            79999999999999999999999999999999999999998887333

>KOG0844|consensus

Probab=99.37  E-value=1.2e-13  Score=92.68  Aligned_cols=47  Identities=21%  Similarity=0.306  Sum_probs=44.1

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHHH
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIV   49 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~   49 (64)
                      ||++|-+..|.+...|-+||..|+|++..|+|||||||.|+||+ +++
T Consensus       196 LEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQ-Rla  242 (408)
T KOG0844|consen  196 LEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQ-RLA  242 (408)
T ss_pred             HHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhh-hhh
Confidence            89999999999999999999999999999999999999999998 543

>KOG0493|consensus

Probab=99.33  E-value=2.1e-13  Score=89.99  Aligned_cols=44  Identities=32%  Similarity=0.453  Sum_probs=40.9

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      |..+|+.++|++...|.+||.+|+|.+.||+|||||+|+|-|+.
T Consensus       261 LK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs  304 (342)
T KOG0493|consen  261 LKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS  304 (342)
T ss_pred             HHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence            56789999999999999999999999999999999999987754

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.31  E-value=1.3e-12  Score=69.05  Aligned_cols=38  Identities=8%  Similarity=0.016  Sum_probs=36.4

Q ss_pred             chhhhccCCC----CCHHHHHHHHHHhCCCCCcccccccCCc
Q psy8538           2 DSLEFHYSRY----ITIRRKAELANSLGLSERQVRCPHHQLT   39 (64)
Q Consensus         2 ~e~~F~~~~~----p~~~~r~~La~~l~l~~~qV~vWFqNrR   39 (64)
                      ||..|..++|    |+...+.+||..+||++.+|+|||||.+
T Consensus        16 Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565        16 MRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             HHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            7889999999    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.

>KOG3802|consensus

Probab=99.24  E-value=4.2e-12  Score=87.00  Aligned_cols=47  Identities=17%  Similarity=0.051  Sum_probs=44.5

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHH
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAI   47 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~   47 (64)
                      .||+.|..|+.|+..++..||.+|+|-...|+|||+|||.++||...
T Consensus       308 aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  308 ALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             HHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            38999999999999999999999999999999999999999999844

>KOG0847|consensus

Probab=99.23  E-value=1.1e-12  Score=84.88  Aligned_cols=45  Identities=22%  Similarity=0.281  Sum_probs=42.6

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||..|....|+-.+++.+||..+|+++.||+|||||||+++++.
T Consensus       181 ~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKk  225 (288)
T KOG0847|consen  181 QLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKK  225 (288)
T ss_pred             hhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhh
Confidence            378999999999999999999999999999999999999999876

>KOG4577|consensus

Probab=99.19  E-value=4.4e-12  Score=84.77  Aligned_cols=47  Identities=13%  Similarity=0.049  Sum_probs=42.4

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHH
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAII   48 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~   48 (64)
                      |...|...+.|..+.|++|+.++||..+.|||||||||+|+||.++-
T Consensus       182 LK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD  228 (383)
T KOG4577|consen  182 LKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD  228 (383)
T ss_pred             HHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence            45678889999999999999999999999999999999999988443

>KOG0486|consensus

Probab=99.14  E-value=2.5e-11  Score=81.48  Aligned_cols=56  Identities=20%  Similarity=0.172  Sum_probs=49.2

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHHHHHHHHhcCC
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIVSFLEKVHGD   58 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~~~~~~~~~~   58 (64)
                      ||..|++++||+...|+++|.-++|++..|.|||.|||+++++.++-.. .|.+.++
T Consensus       127 le~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~-ae~~k~~  182 (351)
T KOG0486|consen  127 LEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ-AELAKGG  182 (351)
T ss_pred             HHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH-HHhhhcC
Confidence            6888999999999999999999999999999999999999998866655 5555444

>KOG0775|consensus

Probab=99.12  E-value=2.3e-11  Score=80.47  Aligned_cols=43  Identities=23%  Similarity=0.157  Sum_probs=40.1

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccc
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNN   44 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~   44 (64)
                      |...|..++||+..++.+||+.+||+..||-.||.|||.++|.
T Consensus       191 LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa  233 (304)
T KOG0775|consen  191 LREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA  233 (304)
T ss_pred             HHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence            5667899999999999999999999999999999999998883

>KOG0490|consensus

Probab=99.10  E-value=1.8e-11  Score=77.11  Aligned_cols=46  Identities=13%  Similarity=-0.031  Sum_probs=43.5

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchH
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTA   46 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~   46 (64)
                      +||+.|...+||+...++.||..+++++..|+|||||+|+++++..
T Consensus        74 ~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~  119 (235)
T KOG0490|consen   74 ELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE  119 (235)
T ss_pred             HHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence            5899999999999999999999999999999999999999999774

>KOG0849|consensus

Probab=98.83  E-value=7.8e-10  Score=75.19  Aligned_cols=46  Identities=20%  Similarity=0.156  Sum_probs=43.2

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchH
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTA   46 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~   46 (64)
                      +||+.|..++||+...|+.||.++++++..|+|||+|+|++.++..
T Consensus       190 ~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~  235 (354)
T KOG0849|consen  190 ALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH  235 (354)
T ss_pred             HHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence            5899999999999999999999999999999999999999888773

>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=98.69  E-value=8.9e-10  Score=54.21  Aligned_cols=32  Identities=28%  Similarity=0.291  Sum_probs=27.2

Q ss_pred             cCCCCCHHHHHHHHHHhCCCCCcccccccCCc
Q psy8538           8 YSRYITIRRKAELANSLGLSERQVRCPHHQLT   39 (64)
Q Consensus         8 ~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR   39 (64)
                      .++||+..++..||..+||+..||..||-|-|
T Consensus         7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaR   38 (40)
T PF05920_consen    7 HNPYPSKEEKEELAKQTGLSRKQISNWFINAR   38 (40)
T ss_dssp             TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhH
Confidence            47899999999999999999999999999976

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

>KOG1168|consensus

Probab=98.62  E-value=1.4e-08  Score=68.21  Aligned_cols=47  Identities=15%  Similarity=0.021  Sum_probs=43.5

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHH
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAII   48 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~   48 (64)
                      ||.+|...+.|+.+....+|.+|+|....|+|||.|.|.|.||++..
T Consensus       324 LEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~S  370 (385)
T KOG1168|consen  324 LEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRS  370 (385)
T ss_pred             HHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhh
Confidence            78999999999999999999999999999999999999999987443

>KOG0774|consensus

Probab=98.12  E-value=2.2e-06  Score=57.11  Aligned_cols=44  Identities=18%  Similarity=0.061  Sum_probs=37.6

Q ss_pred             chhhh---ccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEF---HYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F---~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      |...|   ..++||+...+++||+++|++..||..||.|.|-+-|+.
T Consensus       203 LneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~  249 (334)
T KOG0774|consen  203 LNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN  249 (334)
T ss_pred             HHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence            44556   468999999999999999999999999999998766544

>KOG0490|consensus

Probab=97.79  E-value=7.3e-06  Score=51.54  Aligned_cols=44  Identities=18%  Similarity=0.144  Sum_probs=39.6

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ++..|..+.+|+...+..|+..+|+++..|++||||++.+.++.
T Consensus       168 ~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~  211 (235)
T KOG0490|consen  168 LETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKH  211 (235)
T ss_pred             hhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhh
Confidence            35568889999999999999999999999999999999888765

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

Probab=97.33  E-value=2.4e-05  Score=41.00  Aligned_cols=39  Identities=15%  Similarity=0.010  Sum_probs=28.9

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcc
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTT   40 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~   40 (64)
                      |+..|...+++...+...|+.+.+|+..||+.||--+..
T Consensus        13 L~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~   51 (56)
T PF11569_consen   13 LEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ   51 (56)
T ss_dssp             HHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred             HHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence            788899889998899999999999999999999976653

>KOG2252|consensus

Probab=97.06  E-value=0.00021  Score=51.29  Aligned_cols=40  Identities=10%  Similarity=-0.022  Sum_probs=36.6

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCccc
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTV   41 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~   41 (64)
                      |-.+|+.+++|+.+....|+.+|+|....|..||-|-|.+
T Consensus       435 L~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRR  474 (558)
T KOG2252|consen  435 LQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRR  474 (558)
T ss_pred             HHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhh
Confidence            5678999999999999999999999999999999997644

>KOG0773|consensus

Probab=96.92  E-value=0.00044  Score=46.45  Aligned_cols=37  Identities=24%  Similarity=0.081  Sum_probs=32.4

Q ss_pred             CCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           9 SRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         9 ~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .+||+..++..||.++||+..||..||-|.|-+....
T Consensus       264 ~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p  300 (342)
T KOG0773|consen  264 HPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKP  300 (342)
T ss_pred             CCCCcchhccccchhcCCCcccCCchhhhcccccCCc
Confidence            5899999999999999999999999999977655433

>KOG1146|consensus

Probab=96.73  E-value=0.00061  Score=53.03  Aligned_cols=41  Identities=15%  Similarity=0.233  Sum_probs=36.4

Q ss_pred             hhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           5 EFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         5 ~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .|....||...+.+.|...++++.+.|++||||-|.+.+..
T Consensus       921 ~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~  961 (1406)
T KOG1146|consen  921 CYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKA  961 (1406)
T ss_pred             HHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhh
Confidence            45667788888888999999999999999999999988876

>KOG3623|consensus

Probab=94.54  E-value=0.0093  Score=44.82  Aligned_cols=44  Identities=9%  Similarity=0.038  Sum_probs=39.2

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      |...|..|..|+..+-..+|.+.||+..-|+.||++.++.+...
T Consensus       571 lkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv  614 (1007)
T KOG3623|consen  571 LKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSV  614 (1007)
T ss_pred             HHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhh
Confidence            45578999999999999999999999999999999998766655

>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes

Probab=86.57  E-value=0.21  Score=26.35  Aligned_cols=18  Identities=33%  Similarity=0.453  Sum_probs=16.1

Q ss_pred             HHHHHHHhCCCCCccccc
Q psy8538          17 KAELANSLGLSERQVRCP   34 (64)
Q Consensus        17 r~~La~~l~l~~~qV~vW   34 (64)
                      -..+|.+||+++.+|..|
T Consensus        25 lkdIA~~Lgvs~~tIr~W   42 (60)
T PF10668_consen   25 LKDIAEKLGVSESTIRKW   42 (60)
T ss_pred             HHHHHHHHCCCHHHHHHH
Confidence            346899999999999999

Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].

>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=81.81  E-value=0.43  Score=24.17  Aligned_cols=24  Identities=21%  Similarity=0.293  Sum_probs=18.2

Q ss_pred             HHHHHHHHhCCCCCcccccccCCc
Q psy8538          16 RKAELANSLGLSERQVRCPHHQLT   39 (64)
Q Consensus        16 ~r~~La~~l~l~~~qV~vWFqNrR   39 (64)
                      ....||..+|++..+|..|..|+.
T Consensus        24 s~~~ia~~fgv~~sTv~~I~K~k~   47 (53)
T PF04218_consen   24 SKRDIAREFGVSRSTVSTILKNKD   47 (53)
T ss_dssp             -HHHHHHHHT--CCHHHHHHHCHH
T ss_pred             CHHHHHHHhCCCHHHHHHHHHhHH
Confidence            356899999999999999988864

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	64
1ftz_A	70	Nuclear Magnetic Resonance Solution Structure Of Th		6e-05
2r5y_A	88	Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO		5e-04
1san_A	62	The Des(1-6)antennapedia Homeodomain: Comparison Of		6e-04
9ant_A	62	Antennapedia Homeodomain-Dna Complex Length = 62		7e-04
1ahd_P	68	Determination Of The Nmr Solution Structure Of An A		8e-04

>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 = 42.4 bits (98), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 17/29 (58%), Positives = 25/29 (86%)
Query: 5  EFHYSRYITIRRKAELANSLGLSERQVRC 33
          EFH++RYIT RR+ ++AN+L LSERQ++ 
Sbjct: 21 EFHFNRYITRRRRIDIANALSLSERQIKI 49

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

Iteration: 1
 Score = 39.3 bits (90), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 15/29 (51%), Positives = 25/29 (86%)
Query: 5  EFHYSRYITIRRKAELANSLGLSERQVRC 33
          EFH++RY+T RR+ E+A++L L+ERQ++ 
Sbjct: 46 EFHFNRYLTRRRRIEIAHALSLTERQIKI 74

>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 = 38.9 bits (89), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 15/29 (51%), Positives = 25/29 (86%)
Query: 5  EFHYSRYITIRRKAELANSLGLSERQVRC 33
          EFH++RY+T RR+ E+A++L L+ERQ++ 
Sbjct: 14 EFHFNRYLTRRRRIEIAHALSLTERQIKI 42

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

Iteration: 1
 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 15/29 (51%), Positives = 25/29 (86%)
Query: 5  EFHYSRYITIRRKAELANSLGLSERQVRC 33
          EFH++RY+T RR+ E+A++L L+ERQ++ 
Sbjct: 21 EFHFNRYLTRRRRIEIAHALSLTERQIKI 49

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

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 15/29 (51%), Positives = 25/29 (86%)
Query: 5  EFHYSRYITIRRKAELANSLGLSERQVRC 33
          EFH++RY+T RR+ E+A++L L+ERQ++ 
Sbjct: 20 EFHFNRYLTRRRRIEIAHALSLTERQIKI 48

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	64
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	8e-10
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	3e-09
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	3e-09
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	1e-08
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	2e-08
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	2e-08
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	2e-08
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	3e-08
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	4e-08
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	4e-08
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	5e-08
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	7e-08
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	8e-08
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	1e-07
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	3e-07
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	4e-07
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	5e-07
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	1e-06
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	2e-06
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	2e-06
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	4e-06
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	1e-05
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	1e-05
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	1e-04

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

 Score = 48.7 bits (116), Expect = 8e-10
 Identities = 15/28 (53%), Positives = 25/28 (89%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          EFH++RY+T RR+ E+A++L L+ERQ++
Sbjct: 46 EFHFNRYLTRRRRIEIAHALSLTERQIK 73

>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 = 47.6 bits (113), Expect = 3e-09
 Identities = 12/28 (42%), Positives = 22/28 (78%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          EFH+++Y++  R+ E+A +L L+E QV+
Sbjct: 52 EFHFNKYLSRARRVEIAATLELNETQVK 79

>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 = 47.1 bits (112), Expect = 3e-09
 Identities = 14/28 (50%), Positives = 23/28 (82%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          EFH + Y+T RR+ E+A++L L+ERQ++
Sbjct: 38 EFHTNHYLTRRRRIEMAHALSLTERQIK 65

>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 = 45.4 bits (108), Expect = 1e-08
 Identities = 13/28 (46%), Positives = 23/28 (82%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          EF+ +RY+T RR+ +L++ LGL+E Q++
Sbjct: 21 EFNENRYLTERRRQQLSSELGLNEAQIK 48

>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 = 45.1 bits (107), Expect = 2e-08
 Identities = 11/28 (39%), Positives = 17/28 (60%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          +F   +Y++   +  LA  L LSERQV+
Sbjct: 25 KFETQKYLSPPERKRLAKMLQLSERQVK 52

>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 = 44.7 bits (106), Expect = 2e-08
 Identities = 15/28 (53%), Positives = 25/28 (89%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          EFH++RY+T RR+ E+A++L L+ERQ++
Sbjct: 20 EFHFNRYLTRRRRIEIAHALSLTERQIK 47

>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 = 44.8 bits (106), Expect = 2e-08
 Identities = 11/27 (40%), Positives = 17/27 (62%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQV 31
           F   +Y++   + +LA SLGLS+ QV
Sbjct: 35 RFEKQKYLSTPDRIDLAESLGLSQLQV 61

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

 Score = 43.9 bits (104), Expect = 3e-08
 Identities = 12/28 (42%), Positives = 20/28 (71%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          EF +++YI+  R+ ELA  L L+ER ++
Sbjct: 21 EFLFNKYISRPRRVELAVMLNLTERHIK 48

>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 = 43.9 bits (104), Expect = 4e-08
 Identities = 11/28 (39%), Positives = 15/28 (53%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
           F   RY+T  R A+L+  L L   QV+
Sbjct: 20 HFLQGRYLTAPRLADLSAKLALGTAQVK 47

>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 = 43.3 bits (103), Expect = 4e-08
 Identities = 8/28 (28%), Positives = 14/28 (50%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
           F   + +  + K E+A   G++  QVR
Sbjct: 23 VFRRKQSLNSKEKEEVAKKCGITPLQVR 50

>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 = 43.7 bits (103), Expect = 5e-08
 Identities = 13/28 (46%), Positives = 20/28 (71%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          EF ++ Y+T  R+ E+A  L L+ERQV+
Sbjct: 31 EFLFNMYLTRDRRYEVARLLNLTERQVK 58

>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 = 43.1 bits (102), Expect = 7e-08
 Identities = 10/28 (35%), Positives = 16/28 (57%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          EF+   Y++  R+ ELA  L L E  ++
Sbjct: 19 EFYKENYVSRPRRCELAAQLNLPESTIK 46

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

 Score = 43.2 bits (102), Expect = 8e-08
 Identities = 12/27 (44%), Positives = 19/27 (70%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQV 31
           F  ++Y+ +  +AELA SLGL++ QV
Sbjct: 25 RFQKTQYLALPERAELAASLGLTQTQV 51

>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 = 42.5 bits (100), Expect = 1e-07
 Identities = 8/28 (28%), Positives = 19/28 (67%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          E+  +++IT  ++ +++ +  LSERQ+ 
Sbjct: 25 EYAANKFITKDKRRKISAATSLSERQIT 52

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

 Score = 42.2 bits (99), Expect = 3e-07
 Identities = 9/27 (33%), Positives = 15/27 (55%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQV 31
           FH  +Y+    +A LA  L +++ QV
Sbjct: 35 RFHKQKYLASAERAALARGLKMTDAQV 61

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

 Score = 41.4 bits (97), Expect = 4e-07
 Identities = 9/28 (32%), Positives = 18/28 (64%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          E+  +++IT  ++  ++ +  LSERQV 
Sbjct: 25 EYATNKFITKDKRRRISATTNLSERQVT 52

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

 Score = 40.7 bits (96), Expect = 5e-07
 Identities = 11/27 (40%), Positives = 19/27 (70%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQV 31
          +F   +Y++I  +AE ++SL L+E QV
Sbjct: 18 KFRQKQYLSIAERAEFSSSLSLTETQV 44

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

 Score = 39.6 bits (93), Expect = 1e-06
 Identities = 9/27 (33%), Positives = 18/27 (66%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQV 31
           F   +Y+++++  EL++ L LS +QV
Sbjct: 21 RFQKQKYLSLQQMQELSSILNLSYKQV 47

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

 Score = 40.2 bits (94), Expect = 2e-06
 Identities = 10/27 (37%), Positives = 18/27 (66%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQV 31
           F   +Y+++++  EL+N L LS +QV
Sbjct: 40 RFQRQKYLSLQQMQELSNILNLSYKQV 66

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

 Score = 39.3 bits (92), Expect = 2e-06
 Identities = 10/27 (37%), Positives = 18/27 (66%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQV 31
          +F + +Y++   +A LA +L L+E QV
Sbjct: 22 KFSHQKYLSAPERAHLAKNLKLTETQV 48

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

 Score = 38.4 bits (90), Expect = 4e-06
 Identities = 8/27 (29%), Positives = 15/27 (55%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQV 31
           F   +Y+    +A LA +L +++ QV
Sbjct: 15 RFLRQKYLASAERAALAKALRMTDAQV 41

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

 Score = 37.2 bits (87), Expect = 1e-05
 Identities = 9/27 (33%), Positives = 15/27 (55%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQV 31
           F   RY++   + +LA+ L L+  QV
Sbjct: 20 RFKQQRYLSAPERDQLASVLKLTSTQV 46

>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 = 37.8 bits (88), Expect = 1e-05
 Identities = 8/27 (29%), Positives = 14/27 (51%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQV 31
           F   RY++   +  LA+ + L+  QV
Sbjct: 27 RFRQQRYLSAPEREHLASLIRLTPTQV 53

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

 Score = 35.0 bits (81), Expect = 1e-04
 Identities = 7/27 (25%), Positives = 14/27 (51%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQV 31
           F   +Y++   +  LA+ + L+  QV
Sbjct: 20 RFKQQKYLSAPEREHLASMIHLTPTQV 46

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	64
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.78
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.75
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.74
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.73
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.73
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.73
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.72
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.72
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.72
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.71
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.71
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.71
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.71
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.71
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.71
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.7
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.7
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.7
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.7
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.69
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.69
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.69
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.69
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.69
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.69
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.69
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.69
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.68
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.68
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.68
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.68
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.68
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.68
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.68
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.68
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.67
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.67
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.67
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.67
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.67
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.67
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.66
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.66
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.66
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.66
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.66
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.66
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.66
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.66
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.65
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.65
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.65
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.65
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.64
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.63
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.63
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.62
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.62
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.61
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.61
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.59
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.59
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.58
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.58
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.57
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.57
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.57
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.57
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.56
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.55
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.52
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.52
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.48
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.46
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.41
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.29
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.19
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.92
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	96.21

>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=99.78  E-value=6.8e-21  Score=101.61  Aligned_cols=45  Identities=13%  Similarity=0.105  Sum_probs=42.3

Q ss_pred             Cchhhh-ccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEF-HYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F-~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||..| ..++||+..++.+||.+|||+++||+|||||||+++|+.
T Consensus        14 ~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~~   59 (64)
T 1x2m_A           14 ILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPS   59 (64)
T ss_dssp             HHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCCS
T ss_pred             HHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCCC
Confidence            389999 679999999999999999999999999999999999976

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

Probab=99.75  E-value=1.3e-20  Score=106.03  Aligned_cols=45  Identities=13%  Similarity=0.059  Sum_probs=42.4

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchH
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTA   46 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~   46 (64)
                      ||..|..++||+..++.+||..|||+++||+|||||||++.++..
T Consensus        26 Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~   70 (89)
T 2ecb_A           26 LQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE   70 (89)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHH
Confidence            899999999999999999999999999999999999999887653

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

Probab=99.74  E-value=2.5e-19  Score=98.25  Aligned_cols=49  Identities=14%  Similarity=0.154  Sum_probs=44.7

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHHH
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAIIV   49 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~~   49 (64)
                      .||..|..++||+..++..||..+||++.+|+|||||||+++|+.....
T Consensus        21 ~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~   69 (80)
T 2cue_A           21 ALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLR   69 (80)
T ss_dssp             HHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhh
Confidence            3899999999999999999999999999999999999999999774433

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

Probab=99.73  E-value=8.4e-20  Score=100.09  Aligned_cols=45  Identities=20%  Similarity=0.189  Sum_probs=42.8

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        21 ~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~   65 (80)
T 2dms_A           21 VLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQ   65 (80)
T ss_dssp             HHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHT
T ss_pred             HHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHH
Confidence            389999999999999999999999999999999999999998876

>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=8.7e-20  Score=94.30  Aligned_cols=44  Identities=20%  Similarity=0.252  Sum_probs=42.0

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        12 Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~   55 (56)
T 3a03_A           12 LERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ   55 (56)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhhccc
Confidence            89999999999999999999999999999999999999988864

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

Probab=99.73  E-value=2e-19  Score=95.54  Aligned_cols=45  Identities=9%  Similarity=0.059  Sum_probs=42.3

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||..|..++||+..++..||..+||++++|+|||||||++.++.
T Consensus        17 ~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~~   61 (64)
T 2e19_A           17 LLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISV   61 (64)
T ss_dssp             HHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSCS
T ss_pred             HHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCCC
Confidence            389999999999999999999999999999999999999988763

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

Probab=99.72  E-value=1.4e-19  Score=98.00  Aligned_cols=45  Identities=18%  Similarity=0.276  Sum_probs=42.8

Q ss_pred             Cchhhh-ccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEF-HYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F-~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||..| ..++||+..++.+||..+||++++|+|||||||+++|+.
T Consensus        22 ~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~   67 (72)
T 2cqx_A           22 TLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPS   67 (72)
T ss_dssp             HHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCC
Confidence            389999 999999999999999999999999999999999999876

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

Probab=99.72  E-value=2e-19  Score=96.97  Aligned_cols=44  Identities=23%  Similarity=0.298  Sum_probs=42.6

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++++|+|||||||+++|+.
T Consensus        19 LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~   62 (69)
T 2l9r_A           19 LERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRK   62 (69)
T ss_dssp             HHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCS
T ss_pred             HHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhh
Confidence            89999999999999999999999999999999999999999876

>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=99.72  E-value=1.9e-19  Score=98.54  Aligned_cols=44  Identities=14%  Similarity=0.109  Sum_probs=42.4

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        22 Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   65 (80)
T 2dmq_A           22 MKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRN   65 (80)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHH
Confidence            89999999999999999999999999999999999999999876

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

Probab=99.71  E-value=3.9e-19  Score=93.29  Aligned_cols=44  Identities=20%  Similarity=0.252  Sum_probs=42.2

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        18 Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A           18 LKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             HHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             HHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            89999999999999999999999999999999999999999864

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

Probab=99.71  E-value=2.1e-19  Score=93.81  Aligned_cols=45  Identities=18%  Similarity=0.235  Sum_probs=41.1

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchH
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTA   46 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~   46 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||++.|+..
T Consensus        14 Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~   58 (60)
T 3a02_A           14 LEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE   58 (60)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC---
T ss_pred             HHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhc
Confidence            899999999999999999999999999999999999999988763

>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=99.71  E-value=6.6e-20  Score=102.65  Aligned_cols=45  Identities=16%  Similarity=0.090  Sum_probs=42.6

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchH
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTA   46 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~   46 (64)
                      ||..|..++||+..++..||..+||++.+|+|||||||+++++..
T Consensus        28 Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~   72 (89)
T 2dmp_A           28 LEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSME   72 (89)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSC
T ss_pred             HHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHh
Confidence            899999999999999999999999999999999999999887763

>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=99.71  E-value=3.8e-19  Score=95.35  Aligned_cols=44  Identities=18%  Similarity=0.289  Sum_probs=42.7

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        22 Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~   65 (70)
T 2cra_A           22 LEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKS   65 (70)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSS
T ss_pred             HHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhccc
Confidence            89999999999999999999999999999999999999999976

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

Probab=99.71  E-value=2.2e-19  Score=93.00  Aligned_cols=43  Identities=26%  Similarity=0.378  Sum_probs=41.3

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccc
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNN   44 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~   44 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|+
T Consensus        15 Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A           15 LERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             HHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            8999999999999999999999999999999999999998875

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

Probab=99.71  E-value=2.7e-19  Score=93.68  Aligned_cols=43  Identities=30%  Similarity=0.437  Sum_probs=41.3

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccc
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNN   44 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~   44 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|+
T Consensus        18 Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A           18 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            8999999999999999999999999999999999999998875

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

Probab=99.70  E-value=3.1e-19  Score=95.61  Aligned_cols=45  Identities=11%  Similarity=0.017  Sum_probs=42.3

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||..|..++||+..++.+||..+||++++|++||||||++.|+.
T Consensus        18 ~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg   62 (66)
T 3nau_A           18 HLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRG   62 (66)
T ss_dssp             HHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhcc
Confidence            389999999999999999999999999999999999999888754

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

Probab=99.70  E-value=4.1e-19  Score=93.57  Aligned_cols=44  Identities=27%  Similarity=0.376  Sum_probs=42.0

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        18 Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   61 (63)
T 2h1k_A           18 LEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE   61 (63)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhh
Confidence            89999999999999999999999999999999999999988864

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

Probab=99.70  E-value=7.8e-19  Score=94.13  Aligned_cols=45  Identities=27%  Similarity=0.395  Sum_probs=43.0

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        21 ~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   65 (70)
T 2djn_A           21 ALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKS   65 (70)
T ss_dssp             HHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSS
T ss_pred             HHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhccc
Confidence            389999999999999999999999999999999999999999876

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

Probab=99.70  E-value=6.2e-19  Score=90.95  Aligned_cols=42  Identities=21%  Similarity=0.279  Sum_probs=40.0

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCccccc
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNN   43 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k   43 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|
T Consensus        17 Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~k   58 (58)
T 3rkq_A           17 LERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK   58 (58)
T ss_dssp             HHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhhccCC
Confidence            799999999999999999999999999999999999998764

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

Probab=99.69  E-value=4.5e-19  Score=96.36  Aligned_cols=45  Identities=9%  Similarity=-0.006  Sum_probs=42.7

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        21 ~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~   65 (75)
T 2da5_A           21 ALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAE   65 (75)
T ss_dssp             HHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHS
T ss_pred             HHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHh
Confidence            389999999999999999999999999999999999999988876

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

Probab=99.69  E-value=9.3e-19  Score=94.63  Aligned_cols=44  Identities=20%  Similarity=0.280  Sum_probs=42.4

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        22 Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   65 (73)
T 2l7z_A           22 LEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKV   65 (73)
T ss_dssp             HHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHH
Confidence            89999999999999999999999999999999999999998876

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

Probab=99.69  E-value=5.3e-19  Score=92.28  Aligned_cols=44  Identities=23%  Similarity=0.314  Sum_probs=41.8

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        16 Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (60)
T 1jgg_A           16 LEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   59 (60)
T ss_dssp             HHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHhHhhcc
Confidence            89999999999999999999999999999999999999988764

>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=99.69  E-value=7.6e-19  Score=96.31  Aligned_cols=44  Identities=25%  Similarity=0.314  Sum_probs=42.5

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|+|||||||+++|+.
T Consensus        32 Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~   75 (80)
T 2dmt_A           32 LEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKS   75 (80)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcc
Confidence            89999999999999999999999999999999999999998876

>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=99.69  E-value=4.7e-19  Score=96.54  Aligned_cols=45  Identities=18%  Similarity=0.223  Sum_probs=42.8

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||..|..++||+..++..||..+||++.+|+|||||||+++|+.
T Consensus        23 ~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~   67 (77)
T 1nk2_P           23 ELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRA   67 (77)
T ss_dssp             HHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhh
Confidence            389999999999999999999999999999999999999998876

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

Probab=99.69  E-value=1.3e-18  Score=95.93  Aligned_cols=44  Identities=23%  Similarity=0.302  Sum_probs=42.5

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|+|||||||+++|+.
T Consensus        37 Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~   80 (84)
T 2kt0_A           37 LNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRW   80 (84)
T ss_dssp             HHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSC
T ss_pred             HHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999999999999999999999999999876

>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=99.69  E-value=1e-18  Score=95.20  Aligned_cols=45  Identities=29%  Similarity=0.336  Sum_probs=43.0

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchH
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTA   46 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~   46 (64)
                      ||..|..++||+..++..||..+||++.+|+|||||||+++|+..
T Consensus        28 Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   72 (77)
T 1puf_A           28 LEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKIN   72 (77)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhh
Confidence            899999999999999999999999999999999999999998763

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

Probab=99.69  E-value=7e-19  Score=94.23  Aligned_cols=45  Identities=16%  Similarity=0.168  Sum_probs=42.6

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        21 ~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~   65 (70)
T 2dmu_A           21 ALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRS   65 (70)
T ss_dssp             HHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehcccccccccccc
Confidence            389999999999999999999999999999999999999988865

>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=99.68  E-value=9.1e-19  Score=93.70  Aligned_cols=44  Identities=16%  Similarity=0.075  Sum_probs=42.3

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        22 Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   65 (70)
T 2da2_A           22 LQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKS   65 (70)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCC
T ss_pred             HHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhc
Confidence            89999999999999999999999999999999999999998875

>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=99.68  E-value=8.4e-19  Score=94.00  Aligned_cols=44  Identities=25%  Similarity=0.295  Sum_probs=42.3

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        22 Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~   65 (70)
T 2e1o_A           22 LEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRS   65 (70)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCC
Confidence            89999999999999999999999999999999999999998876

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

Probab=99.68  E-value=1.3e-18  Score=92.32  Aligned_cols=44  Identities=16%  Similarity=0.085  Sum_probs=42.4

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        18 Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   61 (66)
T 1bw5_A           18 LRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR   61 (66)
T ss_dssp             HHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSC
T ss_pred             HHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHH
Confidence            89999999999999999999999999999999999999998876

>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=99.68  E-value=9.6e-19  Score=94.21  Aligned_cols=45  Identities=16%  Similarity=0.079  Sum_probs=42.4

Q ss_pred             Cchhhhcc-CCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHY-SRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~-~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||..|.. ++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        15 ~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~   60 (72)
T 1uhs_A           15 ILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS   60 (72)
T ss_dssp             HHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhh
Confidence            38999996 9999999999999999999999999999999998876

>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=99.68  E-value=8.8e-19  Score=96.10  Aligned_cols=45  Identities=9%  Similarity=-0.009  Sum_probs=42.5

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||..|..++||+..++.+||..+||++.||+|||||+|++.|+.
T Consensus        17 ~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~   61 (76)
T 2ecc_A           17 ILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             HHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHH
Confidence            389999999999999999999999999999999999999988765

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

Probab=99.68  E-value=1.4e-18  Score=92.71  Aligned_cols=44  Identities=25%  Similarity=0.261  Sum_probs=42.3

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        17 Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~   60 (68)
T 1zq3_P           17 LEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQ   60 (68)
T ss_dssp             HHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHH
Confidence            89999999999999999999999999999999999999988876

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

Probab=99.68  E-value=3.1e-19  Score=96.47  Aligned_cols=44  Identities=16%  Similarity=0.062  Sum_probs=41.9

Q ss_pred             chhhhcc-CCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHY-SRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~-~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|.. ++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        17 Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~   61 (73)
T 2hi3_A           17 LEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS   61 (73)
T ss_dssp             HHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence            8999994 9999999999999999999999999999999998876

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

Probab=99.68  E-value=1.5e-18  Score=90.60  Aligned_cols=42  Identities=19%  Similarity=0.170  Sum_probs=39.6

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCccccc
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNN   43 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k   43 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|
T Consensus        20 Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A           20 LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            899999999999999999999999999999999999998764

>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=99.67  E-value=3.2e-18  Score=94.26  Aligned_cols=44  Identities=5%  Similarity=-0.079  Sum_probs=41.6

Q ss_pred             chhhhcc----CCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHY----SRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~----~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..    ++||+..++.+||..+||++.+|+|||||||++.+..
T Consensus        32 Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~~   79 (80)
T 1wh5_A           32 MLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPSS   79 (80)
T ss_dssp             HHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSCC
T ss_pred             HHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCCC
Confidence            7889998    9999999999999999999999999999999998753

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

Probab=99.67  E-value=1.2e-18  Score=92.98  Aligned_cols=44  Identities=16%  Similarity=0.206  Sum_probs=42.3

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        17 Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~   60 (68)
T 1ftt_A           17 LERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ   60 (68)
T ss_dssp             HHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhh
Confidence            89999999999999999999999999999999999999988876

>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=99.67  E-value=7.3e-19  Score=93.93  Aligned_cols=44  Identities=34%  Similarity=0.532  Sum_probs=42.3

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        17 Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~   60 (68)
T 1ahd_P           17 LEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   60 (68)
T ss_dssp             HHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHh
Confidence            89999999999999999999999999999999999999988866

>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=99.67  E-value=1.6e-18  Score=94.57  Aligned_cols=44  Identities=14%  Similarity=0.139  Sum_probs=42.2

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        32 Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   75 (80)
T 2da3_A           32 LYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKS   75 (80)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhh
Confidence            89999999999999999999999999999999999999988875

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

Probab=99.67  E-value=2.5e-18  Score=92.79  Aligned_cols=44  Identities=9%  Similarity=0.093  Sum_probs=42.4

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||++.|+.
T Consensus        21 Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   64 (74)
T 2ly9_A           21 LKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNS   64 (74)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTT
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhh
Confidence            89999999999999999999999999999999999999998876

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

Probab=99.67  E-value=6.1e-18  Score=89.09  Aligned_cols=43  Identities=21%  Similarity=0.106  Sum_probs=41.1

Q ss_pred             chhhh---ccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccc
Q psy8538           2 DSLEF---HYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNN   44 (64)
Q Consensus         2 ~e~~F---~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~   44 (64)
                      ||..|   ..++||+..++..||..+||++.||++||||+|++.|+
T Consensus        18 Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A           18 LNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             HHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             HHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            78899   89999999999999999999999999999999999875

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

Probab=99.66  E-value=2.3e-18  Score=91.55  Aligned_cols=44  Identities=16%  Similarity=0.101  Sum_probs=42.2

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        16 Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (67)
T 2k40_A           16 LENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRS   59 (67)
T ss_dssp             HHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCS
T ss_pred             HHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHh
Confidence            89999999999999999999999999999999999999988876

>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=99.66  E-value=2.4e-18  Score=94.45  Aligned_cols=45  Identities=18%  Similarity=0.202  Sum_probs=42.8

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchH
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTA   46 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~   46 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||++.|+..
T Consensus        33 Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~   77 (81)
T 1fjl_A           33 LERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH   77 (81)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhc
Confidence            899999999999999999999999999999999999999988763

>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=99.66  E-value=1.1e-18  Score=93.37  Aligned_cols=44  Identities=11%  Similarity=0.105  Sum_probs=42.3

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        22 Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   65 (70)
T 2da1_A           22 LRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQS   65 (70)
T ss_dssp             HHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhh
Confidence            89999999999999999999999999999999999999988876

>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=99.66  E-value=2.2e-18  Score=94.76  Aligned_cols=44  Identities=32%  Similarity=0.452  Sum_probs=42.3

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|+|||||||+++|+.
T Consensus        35 Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   78 (81)
T 1b8i_A           35 LEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE   78 (81)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhh
Confidence            89999999999999999999999999999999999999998875

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

Probab=99.66  E-value=2.1e-18  Score=93.73  Aligned_cols=45  Identities=20%  Similarity=0.104  Sum_probs=42.9

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        22 ~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~   66 (76)
T 2dn0_A           22 ALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNL   66 (76)
T ss_dssp             HHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSC
T ss_pred             HHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHh
Confidence            389999999999999999999999999999999999999999876

>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=99.66  E-value=2.3e-18  Score=89.77  Aligned_cols=45  Identities=13%  Similarity=0.096  Sum_probs=41.9

Q ss_pred             Cchhhhcc---CCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHY---SRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~---~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||..|..   ++||+..++..||..+||++.||++||||+|+++|+.
T Consensus        12 ~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A           12 ILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             HHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            37899999   9999999999999999999999999999999988764

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

Probab=99.66  E-value=1.3e-18  Score=97.93  Aligned_cols=46  Identities=22%  Similarity=0.286  Sum_probs=43.4

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHH
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAI   47 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~   47 (64)
                      ||..|..++||+..++..||..+||++.+|+|||||||+++|+...
T Consensus        32 Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~   77 (93)
T 3a01_A           32 LEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTA   77 (93)
T ss_dssp             HHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhH
Confidence            8999999999999999999999999999999999999999987743

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

Probab=99.66  E-value=3.1e-18  Score=95.27  Aligned_cols=44  Identities=34%  Similarity=0.532  Sum_probs=42.2

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|+|||||||+++|+.
T Consensus        43 Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~   86 (88)
T 2r5y_A           43 LEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   86 (88)
T ss_dssp             HHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhh
Confidence            89999999999999999999999999999999999999988865

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

Probab=99.65  E-value=4.1e-18  Score=91.92  Aligned_cols=44  Identities=16%  Similarity=0.146  Sum_probs=42.2

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        24 Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~   67 (75)
T 2m0c_A           24 LEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKR   67 (75)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHH
Confidence            89999999999999999999999999999999999999988875

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

Probab=99.65  E-value=8.6e-18  Score=93.10  Aligned_cols=44  Identities=20%  Similarity=0.107  Sum_probs=42.1

Q ss_pred             chhhh---ccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEF---HYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F---~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|   ..++||+..++..||..+||++.||++||||+|++.|+.
T Consensus        16 Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~   62 (87)
T 1b72_B           16 LNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN   62 (87)
T ss_dssp             HHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhc
Confidence            78899   899999999999999999999999999999999998877

>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=99.65  E-value=1.2e-17  Score=92.01  Aligned_cols=43  Identities=7%  Similarity=-0.002  Sum_probs=40.2

Q ss_pred             chhhhcc-----CCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHY-----SRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~-----~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      || .|..     ++||+...+.+||..+||++.+|+|||||||++.+..
T Consensus        32 Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~s   79 (80)
T 1wh7_A           32 ML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPSS   79 (80)
T ss_dssp             HH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCCC
T ss_pred             HH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCCC
Confidence            67 7988     9999999999999999999999999999999998753

>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=99.65  E-value=4.8e-18  Score=96.02  Aligned_cols=44  Identities=27%  Similarity=0.451  Sum_probs=42.3

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|+|||||||+++|+.
T Consensus        49 Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   92 (97)
T 1b72_A           49 LEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKR   92 (97)
T ss_dssp             HHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHH
Confidence            89999999999999999999999999999999999999998866

>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=99.64  E-value=1.3e-18  Score=92.81  Aligned_cols=44  Identities=20%  Similarity=0.209  Sum_probs=42.2

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        18 Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~   61 (68)
T 1yz8_P           18 LEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   61 (68)
T ss_dssp             HHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHH
Confidence            89999999999999999999999999999999999999988865

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

Probab=99.63  E-value=8e-18  Score=92.89  Aligned_cols=47  Identities=15%  Similarity=0.120  Sum_probs=43.5

Q ss_pred             Cchhhhcc---CCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHH
Q psy8538           1 MDSLEFHY---SRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAI   47 (64)
Q Consensus         1 ~~e~~F~~---~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~   47 (64)
                      .||..|..   ++||+..++..||..+||++.||++||||||++.|+...
T Consensus        16 ~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~~   65 (83)
T 1le8_B           16 ILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITI   65 (83)
T ss_dssp             HHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSCC
T ss_pred             HHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHcccccccc
Confidence            38899998   999999999999999999999999999999999988743

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

Probab=99.63  E-value=1e-17  Score=94.59  Aligned_cols=44  Identities=14%  Similarity=0.082  Sum_probs=42.5

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||||++.|+.
T Consensus        40 Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~   83 (96)
T 3nar_A           40 LKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNG   83 (96)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhh
Confidence            89999999999999999999999999999999999999998876

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

Probab=99.62  E-value=9.8e-18  Score=94.44  Aligned_cols=46  Identities=15%  Similarity=0.114  Sum_probs=43.2

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhC---------------CCCCcccccccCCcccccchH
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLG---------------LSERQVRCPHHQLTTVNNNTA   46 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~---------------l~~~qV~vWFqNrR~~~k~~~   46 (64)
                      .||..|..++||+..++..||..++               |++.+|++||||||+++|+..
T Consensus        21 ~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~   81 (95)
T 2cuf_A           21 VMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRA   81 (95)
T ss_dssp             HHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHh
Confidence            3899999999999999999999999               999999999999999998773

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

Probab=99.62  E-value=3.7e-18  Score=93.47  Aligned_cols=44  Identities=9%  Similarity=-0.070  Sum_probs=41.9

Q ss_pred             chhhhccC----CCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYS----RYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~----~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..+    +||+..++..||..+||++.+|+|||||||++.|+.
T Consensus        23 Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~   70 (80)
T 2da4_A           23 LKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLM   70 (80)
T ss_dssp             HHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhc
Confidence            89999999    999999999999999999999999999999988864

>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=99.61  E-value=2.1e-17  Score=89.01  Aligned_cols=44  Identities=20%  Similarity=0.107  Sum_probs=41.7

Q ss_pred             chhhh---ccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEF---HYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F---~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|   ..++||+..++..||..+||++.||++||||+|++.|+.
T Consensus        16 Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~   62 (73)
T 1puf_B           16 LNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN   62 (73)
T ss_dssp             HHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcccc
Confidence            78899   899999999999999999999999999999999988766

>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=99.61  E-value=2e-17  Score=89.15  Aligned_cols=44  Identities=16%  Similarity=-0.038  Sum_probs=40.9

Q ss_pred             chhhhcc---CCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHY---SRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~---~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..   ++||+..++..||..+||++.||++||||+|++.++.
T Consensus        22 Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~   68 (73)
T 1x2n_A           22 MRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQS   68 (73)
T ss_dssp             HHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhcccc
Confidence            7888965   9999999999999999999999999999999888765

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

Probab=99.59  E-value=8.9e-17  Score=92.25  Aligned_cols=61  Identities=8%  Similarity=0.023  Sum_probs=48.7

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHh---------------------CCCCCcccccccCCcccccchHHHHHHHHHhcCCC
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSL---------------------GLSERQVRCPHHQLTTVNNNTAIIVSFLEKVHGDG   59 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l---------------------~l~~~qV~vWFqNrR~~~k~~~~~~~~~~~~~~~g   59 (64)
                      .||..|..++||+...+.+||..+                     +|++.+|++||||||+++++.....  .....+..
T Consensus        20 ~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k~kr~~~~~--~~~~~~~~   97 (102)
T 2da6_A           20 ILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEEAFRQKLA--MDAYSSNS   97 (102)
T ss_dssp             HHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHHHHHHHHHH--HSSSSSSC
T ss_pred             HHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHHHHHhhHhh--hccccCCC
Confidence            389999999999999999999999                     7999999999999999998774433  33333444


Q ss_pred             CCCC
Q psy8538          60 RNSS   63 (64)
Q Consensus        60 ~~ss   63 (64)
                      .+||
T Consensus        98 ~~~~  101 (102)
T 2da6_A           98 GPSS  101 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            4443

>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=99.59  E-value=3.3e-17  Score=87.44  Aligned_cols=44  Identities=18%  Similarity=0.035  Sum_probs=41.4

Q ss_pred             chhhhc---cCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFH---YSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~---~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      |+..|.   .++||+..++..||..+||++.||++||||+|++.++.
T Consensus        13 L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~   59 (67)
T 3k2a_A           13 MRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQP   59 (67)
T ss_dssp             HHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHH
Confidence            788888   99999999999999999999999999999999988776

>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=99.58  E-value=5.7e-17  Score=89.98  Aligned_cols=42  Identities=14%  Similarity=0.084  Sum_probs=40.1

Q ss_pred             chhhhcc---CCCCCHHHHHHHHHHhCCCCCcccccccCCccccc
Q psy8538           2 DSLEFHY---SRYITIRRKAELANSLGLSERQVRCPHHQLTTVNN   43 (64)
Q Consensus         2 ~e~~F~~---~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k   43 (64)
                      ||..|..   ++||+..++..||..+||++.||++||||||+++|
T Consensus        42 Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k   86 (87)
T 1mnm_C           42 LESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK   86 (87)
T ss_dssp             HHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcc
Confidence            7899999   99999999999999999999999999999998776

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

Probab=99.58  E-value=7.2e-17  Score=97.02  Aligned_cols=44  Identities=14%  Similarity=0.051  Sum_probs=42.3

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|+|||||||+++|+.
T Consensus       102 Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A          102 LERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            89999999999999999999999999999999999999999875

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

Probab=99.57  E-value=7.5e-17  Score=98.03  Aligned_cols=44  Identities=11%  Similarity=0.046  Sum_probs=42.3

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|+|||||||+++|+.
T Consensus       116 Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C          116 LEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             HHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            89999999999999999999999999999999999999998874

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

Probab=99.57  E-value=8.1e-17  Score=98.45  Aligned_cols=45  Identities=18%  Similarity=0.075  Sum_probs=43.2

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchH
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTA   46 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~   46 (64)
                      ||..|..++||+..++..||..+||++.+|+|||||||+++|+..
T Consensus       114 LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~  158 (164)
T 2xsd_C          114 LESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMT  158 (164)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSC
T ss_pred             HHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhcc
Confidence            899999999999999999999999999999999999999999873

>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=99.57  E-value=6.7e-17  Score=89.27  Aligned_cols=44  Identities=14%  Similarity=-0.123  Sum_probs=39.8

Q ss_pred             chhhhcc---CCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHY---SRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~---~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..   ++||+..++..||..+||++.||++||||+|++.++.
T Consensus        22 L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~   68 (83)
T 2dmn_A           22 LRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPD   68 (83)
T ss_dssp             HHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHH
T ss_pred             HHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHH
Confidence            6777765   6999999999999999999999999999999888765

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

Probab=99.57  E-value=9.1e-17  Score=96.76  Aligned_cols=43  Identities=19%  Similarity=0.086  Sum_probs=41.5

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccc
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNN   44 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~   44 (64)
                      ||..|..++||+..++..||..+||++.+|+|||||||+++|+
T Consensus       108 Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I          108 LNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            8999999999999999999999999999999999999998886

>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=99.56  E-value=1.3e-16  Score=96.64  Aligned_cols=44  Identities=20%  Similarity=0.188  Sum_probs=41.6

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|+|||||||+++|+.
T Consensus       111 Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A          111 LETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             HHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            78999999999999999999999999999999999999998874

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

Probab=99.55  E-value=1.7e-16  Score=90.49  Aligned_cols=49  Identities=10%  Similarity=0.066  Sum_probs=43.1

Q ss_pred             CchhhhccCCCCCHHHHHHHHHH------------------hC---CCCCcccccccCCcccccchHHHH
Q psy8538           1 MDSLEFHYSRYITIRRKAELANS------------------LG---LSERQVRCPHHQLTTVNNNTAIIV   49 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~------------------l~---l~~~qV~vWFqNrR~~~k~~~~~~   49 (64)
                      +||..|..++||+...+.+||..                  +|   |++.+|++||||||+++++....+
T Consensus        23 ~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k~k~k~~~~   92 (99)
T 1lfb_A           23 ILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFRHKLA   92 (99)
T ss_dssp             HHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCCC---
T ss_pred             HHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHHHHHhchhh
Confidence            38999999999999999999999                  88   999999999999999988774433

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

Probab=99.52  E-value=5.7e-16  Score=94.09  Aligned_cols=44  Identities=11%  Similarity=0.035  Sum_probs=42.5

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+...+..||..+||++.+|+|||||||++.|+.
T Consensus       112 Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~  155 (164)
T 2d5v_A          112 LHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDK  155 (164)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC
T ss_pred             HHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhcccccc
Confidence            89999999999999999999999999999999999999998876

>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=99.52  E-value=6.7e-16  Score=83.19  Aligned_cols=39  Identities=13%  Similarity=0.004  Sum_probs=37.3

Q ss_pred             chhhhcc-CCCCCHHHHHHHHHHhCCCCCcccccccCCcc
Q psy8538           2 DSLEFHY-SRYITIRRKAELANSLGLSERQVRCPHHQLTT   40 (64)
Q Consensus         2 ~e~~F~~-~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~   40 (64)
                      |+..|.. ++||+...+..||.++||++++|+|||||+|-
T Consensus        22 Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~   61 (71)
T 1wi3_A           22 LQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRY   61 (71)
T ss_dssp             HHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhcccee
Confidence            7888998 99999999999999999999999999999985

>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=99.48  E-value=2.7e-15  Score=98.83  Aligned_cols=42  Identities=19%  Similarity=0.180  Sum_probs=40.3

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCccccc
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNN   43 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k   43 (64)
                      ||+.|+.++||+..+|.+||.++||+++||++||||||.+.|
T Consensus       380 Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             HHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            789999999999999999999999999999999999998875

>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=99.46  E-value=2.9e-15  Score=80.90  Aligned_cols=40  Identities=10%  Similarity=0.019  Sum_probs=38.2

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcc
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTT   40 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~   40 (64)
                      +||..|..+++|+..++..||..+||+.+.|+|||||||+
T Consensus        19 ~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa   58 (71)
T 2da7_A           19 VLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKV   58 (71)
T ss_dssp             HHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhccc
Confidence            3889999999999999999999999999999999999995

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

Probab=99.41  E-value=8.1e-15  Score=82.32  Aligned_cols=44  Identities=18%  Similarity=-0.105  Sum_probs=38.6

Q ss_pred             chhhhcc---CCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHY---SRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~---~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      |+..|..   ++||+..++..||..+||++.||++||+|+|.+.++.
T Consensus        20 L~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~   66 (89)
T 2lk2_A           20 LRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPD   66 (89)
T ss_dssp             HHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhH
Confidence            4555644   8999999999999999999999999999999877765

>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=99.29  E-value=2.9e-14  Score=89.29  Aligned_cols=43  Identities=7%  Similarity=-0.033  Sum_probs=40.3

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhC---------------------CCCCcccccccCCcccccc
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLG---------------------LSERQVRCPHHQLTTVNNN   44 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~---------------------l~~~qV~vWFqNrR~~~k~   44 (64)
                      ||..|..++||+...|.+||..++                     |++.+|++||||||++++.
T Consensus       130 Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~~k~  193 (194)
T 1ic8_A          130 LFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAF  193 (194)
T ss_dssp             HHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHHCC-
T ss_pred             HHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhhhhc
Confidence            799999999999999999999999                     9999999999999987763

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

Probab=99.19  E-value=1.1e-12  Score=83.60  Aligned_cols=42  Identities=7%  Similarity=-0.001  Sum_probs=38.9

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhC---------------------CCCCcccccccCCccccc
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLG---------------------LSERQVRCPHHQLTTVNN   43 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~---------------------l~~~qV~vWFqNrR~~~k   43 (64)
                      ||..|..++||+...|.+||..+|                     |++.+|++||||||+.+.
T Consensus       157 Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~~~~  219 (221)
T 2h8r_A          157 LYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEEA  219 (221)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhhhhh
Confidence            789999999999999999999988                     899999999999997653

>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=98.92  E-value=1.4e-10  Score=55.60  Aligned_cols=20  Identities=10%  Similarity=0.008  Sum_probs=17.6

Q ss_pred             CcccccccCCcccccchHHH
Q psy8538          29 RQVRCPHHQLTTVNNNTAII   48 (64)
Q Consensus        29 ~qV~vWFqNrR~~~k~~~~~   48 (64)
                      +||+|||||||++.|+....
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~   20 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFN   20 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHH
T ss_pred             CCceeccHHHHHHHHHHhHH
Confidence            58999999999999998554

>2ys9_A Homeobox and leucine zipper protein homez; homeodomain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.21  E-value=0.00066  Score=36.23  Aligned_cols=37  Identities=14%  Similarity=-0.032  Sum_probs=33.4

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCC
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQL   38 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNr   38 (64)
                      |+..|.....+...+...|+.+..|+..||+.||--+
T Consensus        21 L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~k   57 (70)
T 2ys9_A           21 LERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSR   57 (70)
T ss_dssp             HHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHhc
Confidence            6788998999999999999999999999999999543

---

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	64
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	3e-05
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	4e-05
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	4e-05
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	8e-05
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	1e-04
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	1e-04
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	2e-04
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	5e-04
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	6e-04
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	8e-04
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	0.002
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	0.002
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	0.003

>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 = 35.1 bits (81), Expect = 3e-05
 Identities = 15/28 (53%), Positives = 25/28 (89%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          EFH++RY+T RR+ E+A++L L+ERQ++
Sbjct: 15 EFHFNRYLTRRRRIEIAHALSLTERQIK 42

>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 = 34.7 bits (80), Expect = 4e-05
 Identities = 4/26 (15%), Positives = 11/26 (42%)

Query: 7  HYSRYITIRRKAELANSLGLSERQVR 32
            +++   +R   L+  L    R ++
Sbjct: 14 AITKHPDEKRLEGLSKQLDWDVRSIQ 39

>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 = 35.2 bits (81), Expect = 4e-05
 Identities = 7/28 (25%), Positives = 14/28 (50%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          EF  + Y  +  +  LA  + L E +++
Sbjct: 19 EFERTHYPDVFARERLAAKIDLPEARIQ 46

>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 = 34.4 bits (79), Expect = 8e-05
 Identities = 13/28 (46%), Positives = 20/28 (71%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          EF ++ Y+T  R+ E+A  L L+ERQV+
Sbjct: 31 EFLFNMYLTRDRRYEVARLLNLTERQVK 58

>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 = 33.6 bits (77), Expect = 1e-04
 Identities = 7/27 (25%), Positives = 14/27 (51%)

Query: 7  HYSRYITIRRKAELANSLGLSERQVRC 33
            ++Y   +R   L+  L  S R+++C
Sbjct: 22 SVTKYPDEKRLKGLSKQLDWSVRKIQC 48

>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 = 33.3 bits (76), Expect = 1e-04
 Identities = 5/28 (17%), Positives = 11/28 (39%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
           F  ++  +   +  ++  LGL    V 
Sbjct: 16 IFKENKRPSKELQITISQQLGLELSTVS 43

>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 = 33.2 bits (76), Expect = 2e-04
 Identities = 7/28 (25%), Positives = 11/28 (39%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          +     Y T   K ++A    L+  QV 
Sbjct: 23 QHIGHPYPTEDEKKQIAAQTNLTLLQVN 50

>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 = 32.1 bits (73), Expect = 5e-04
 Identities = 11/28 (39%), Positives = 17/28 (60%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          +F   +Y++   +  LA  L LSERQV+
Sbjct: 18 KFETQKYLSPPERKRLAKMLQLSERQVK 45

>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 = 31.8 bits (72), Expect = 6e-04
 Identities = 13/28 (46%), Positives = 23/28 (82%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          EF+ +RY+T RR+ +L++ LGL+E Q++
Sbjct: 17 EFNENRYLTERRRQQLSSELGLNEAQIK 44

>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 = 31.4 bits (71), Expect = 8e-04
 Identities = 8/28 (28%), Positives = 19/28 (67%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
          E+  +++IT  ++ +++ +  LSERQ+ 
Sbjct: 19 EYAANKFITKDKRRKISAATSLSERQIT 46

>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 = 30.6 bits (69), Expect = 0.002
 Identities = 7/28 (25%), Positives = 11/28 (39%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
           +  +       K +L    GLS R +R
Sbjct: 21 CYAANPRPDALMKEQLVEMTGLSPRVIR 48

>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 = 30.3 bits (68), Expect = 0.002
 Identities = 6/28 (21%), Positives = 10/28 (35%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
           F      + +    +A  L L +  VR
Sbjct: 17 HFGEHSKPSSQEIMRMAEELNLEKEVVR 44

>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 = 30.3 bits (68), Expect = 0.003
 Identities = 8/28 (28%), Positives = 12/28 (42%)

Query: 5  EFHYSRYITIRRKAELANSLGLSERQVR 32
              + Y +   K ELA   G++  QV 
Sbjct: 22 SHLSNPYPSEEAKEELAKKCGITVSQVS 49

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	64
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.78
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.78
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.76
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.76
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.75
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.75
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.74
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.73
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.73
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.72
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.72
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.71
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.7
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.7
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.7
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.7
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.7
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.69
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.69
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.69
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.69
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.67
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.66
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.66
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.66
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.63
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.62
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.58
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.51
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.51
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.5
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.38

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=3e-21  Score=99.97  Aligned_cols=43  Identities=19%  Similarity=0.285  Sum_probs=41.5

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccc
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNN   44 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~   44 (64)
                      ||..|..++||+..++..||..+||++.+|+|||||||+++|+
T Consensus        16 Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1          16 LEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             HHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            8999999999999999999999999999999999999999874

>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=99.78  E-value=2.7e-21  Score=99.57  Aligned_cols=45  Identities=33%  Similarity=0.505  Sum_probs=42.3

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||..|..++||+...+.+||..+||++++|+|||||||++.|+.
T Consensus        11 ~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk~   55 (56)
T d9anta_          11 ELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   55 (56)
T ss_dssp             HHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhhc
Confidence            389999999999999999999999999999999999999988764

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=5.4e-21  Score=98.79  Aligned_cols=44  Identities=25%  Similarity=0.364  Sum_probs=41.8

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccc
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNN   44 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~   44 (64)
                      .||..|..++||+..++..||..+||++.+|++||||+|++.|+
T Consensus        14 ~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_          14 ALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             HHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            38999999999999999999999999999999999999998875

>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=99.76  E-value=1.1e-20  Score=96.20  Aligned_cols=41  Identities=32%  Similarity=0.467  Sum_probs=39.2

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCccc
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTV   41 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~   41 (64)
                      +||..|..++||+..++.+||..+||++.+|+|||||||+|
T Consensus        13 ~Le~~F~~~~yp~~~~r~~LA~~lgL~~~qV~vWFqNrRaK   53 (53)
T d1p7ia_          13 RLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK   53 (53)
T ss_dssp             HHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHhCCChHHhhhcccccCCC
Confidence            48999999999999999999999999999999999999975

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.75  E-value=1e-20  Score=97.55  Aligned_cols=44  Identities=23%  Similarity=0.301  Sum_probs=41.7

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccc
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNN   44 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~   44 (64)
                      .||..|..++||+..++.+||..+||++.+|+|||||+|++.|+
T Consensus        13 ~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk   56 (57)
T d1jgga_          13 RLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR   56 (57)
T ss_dssp             HHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhc
Confidence            38999999999999999999999999999999999999998774

>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=99.75  E-value=1.4e-20  Score=96.96  Aligned_cols=44  Identities=25%  Similarity=0.269  Sum_probs=41.3

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccc
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNN   44 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~   44 (64)
                      .||..|..++||+..++..||..+||++.+|+|||||||++.|+
T Consensus        14 ~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k~kk   57 (57)
T d2e1oa1          14 ELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR   57 (57)
T ss_dssp             HHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhhccC
Confidence            38999999999999999999999999999999999999988763

>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=99.74  E-value=2.7e-20  Score=94.44  Aligned_cols=44  Identities=14%  Similarity=0.089  Sum_probs=41.2

Q ss_pred             Cchhhhcc-CCCCCHHHHHHHHHHhCCCCCcccccccCCcccccc
Q psy8538           1 MDSLEFHY-SRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNN   44 (64)
Q Consensus         1 ~~e~~F~~-~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~   44 (64)
                      +||..|.. ++||+..++..||..+||++++|++||||||+++|+
T Consensus         7 iLE~~F~~~~~~P~~~~~~~LA~~~~ls~~qV~~WFqNrR~k~k~   51 (52)
T d1x2ma1           7 ILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   51 (52)
T ss_dssp             HHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccCc
Confidence            48999976 789999999999999999999999999999999886

>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=99.73  E-value=4.8e-20  Score=97.64  Aligned_cols=45  Identities=24%  Similarity=0.240  Sum_probs=42.7

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||..|..++||+..++..||..+||++.+|+|||||||++.|+.
T Consensus        15 ~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~   59 (67)
T d1zq3p1          15 ELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQ   59 (67)
T ss_dssp             HHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhh
Confidence            389999999999999999999999999999999999999988865

>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=8.5e-20  Score=92.80  Aligned_cols=43  Identities=19%  Similarity=0.188  Sum_probs=40.9

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCccccc
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNN   43 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k   43 (64)
                      +||..|..++||+..++..||..+||++.+|++||||+|++.|
T Consensus        11 ~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~K   53 (53)
T d1le8a_          11 FLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   53 (53)
T ss_dssp             HHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhccC
Confidence            4899999999999999999999999999999999999998875

>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=99.72  E-value=2.3e-19  Score=97.24  Aligned_cols=45  Identities=18%  Similarity=0.223  Sum_probs=42.9

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      +||..|..++||+..++..||..+||++.+|+|||||+|++.|+.
T Consensus        23 ~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   67 (77)
T d1vnda_          23 ELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRA   67 (77)
T ss_dssp             HHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSS
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHH
Confidence            389999999999999999999999999999999999999998865

>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=99.72  E-value=9e-20  Score=98.89  Aligned_cols=45  Identities=29%  Similarity=0.336  Sum_probs=43.0

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchH
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTA   46 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~   46 (64)
                      ||..|..++||+..++..||..+||++.+|+|||||||++.|+..
T Consensus        28 Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~   72 (77)
T d1pufa_          28 LEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKIN   72 (77)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHH
Confidence            899999999999999999999999999999999999999998763

>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=99.71  E-value=9.6e-20  Score=98.38  Aligned_cols=44  Identities=14%  Similarity=0.060  Sum_probs=41.0

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||+|++.+..
T Consensus        19 Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~   62 (76)
T d2ecba1          19 LQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALK   62 (76)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHH
Confidence            89999999999999999999999999999999999999766544

>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=99.70  E-value=1.8e-19  Score=94.84  Aligned_cols=45  Identities=18%  Similarity=0.193  Sum_probs=42.8

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||..|..++||+..++..||..+||++.+|++||||+|+++|+.
T Consensus        16 ~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~   60 (65)
T d1fjla_          16 ELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ   60 (65)
T ss_dssp             HHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhc
Confidence            389999999999999999999999999999999999999998876

>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=99.70  E-value=3.2e-19  Score=94.63  Aligned_cols=47  Identities=15%  Similarity=0.180  Sum_probs=43.9

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccchHHH
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNTAII   48 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~~~~   48 (64)
                      ||..|..++||+...+..||..+||++.+|++||||+|++.|+....
T Consensus        16 Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~   62 (68)
T d2cuea1          16 LEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL   62 (68)
T ss_dssp             HHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhhh
Confidence            89999999999999999999999999999999999999999876444

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeodomain-only protein, Hop
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.70  E-value=2e-19  Score=96.44  Aligned_cols=45  Identities=16%  Similarity=0.079  Sum_probs=41.5

Q ss_pred             Cchhhhcc-CCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHY-SRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~-~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||..|.. ++||+...+..||..+||++++|+|||||||++.|+.
T Consensus        15 ~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~   60 (72)
T d1uhsa_          15 ILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS   60 (72)
T ss_dssp             HHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhc
Confidence            38899985 7899999999999999999999999999999998865

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.70  E-value=2.7e-19  Score=92.35  Aligned_cols=45  Identities=13%  Similarity=0.045  Sum_probs=42.7

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      +||..|..++||+..++..||..+||++.+|++||||+|++.|+.
T Consensus        13 ~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr~   57 (58)
T d1au7a1          13 ALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV   57 (58)
T ss_dssp             HHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             HHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHhc
Confidence            389999999999999999999999999999999999999998865

>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=99.70  E-value=1.7e-19  Score=93.47  Aligned_cols=44  Identities=18%  Similarity=0.252  Sum_probs=40.6

Q ss_pred             Cchhhhcc-CCCCCHHHHHHHHHHhCCCCCcccccccCCcccccc
Q psy8538           1 MDSLEFHY-SRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNN   44 (64)
Q Consensus         1 ~~e~~F~~-~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~   44 (64)
                      +||..|.. ++||+..++..||..+||++++|++||||||+++|+
T Consensus        15 iLE~~F~~~~~yPs~~~~~~LA~~lgls~~qV~~WFqNrR~k~rp   59 (59)
T d2cqxa1          15 TLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKP   59 (59)
T ss_dssp             HHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccCc
Confidence            48999975 689999999999999999999999999999998874

>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=99.69  E-value=1.6e-19  Score=95.90  Aligned_cols=45  Identities=16%  Similarity=0.186  Sum_probs=42.4

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      +||..|..++||+...+..||..+||++.+|++||||+|++.|+.
T Consensus        16 ~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~   60 (68)
T d1ftta_          16 ELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ   60 (68)
T ss_dssp             HHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhc
Confidence            489999999999999999999999999999999999999888765

>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=99.69  E-value=2.5e-19  Score=92.23  Aligned_cols=45  Identities=11%  Similarity=0.040  Sum_probs=42.5

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      +||..|..++||+..++..||..+||++.+|++||||+|++.|+.
T Consensus        12 ~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk~   56 (57)
T d1e3oc1          12 ALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI   56 (57)
T ss_dssp             HHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             HHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHcc
Confidence            489999999999999999999999999999999999999988864

>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=99.69  E-value=3.2e-19  Score=98.76  Aligned_cols=44  Identities=27%  Similarity=0.451  Sum_probs=42.4

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++++|+|||||+|++.|+.
T Consensus        42 Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~   85 (88)
T d1b72a_          42 LEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKR   85 (88)
T ss_dssp             HHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHh
Confidence            89999999999999999999999999999999999999998865

>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=99.69  E-value=7.1e-19  Score=93.11  Aligned_cols=44  Identities=18%  Similarity=0.163  Sum_probs=42.3

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||+|++.|+.
T Consensus        23 Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_          23 LETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             HHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             HHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            89999999999999999999999999999999999999999864

>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=99.67  E-value=8.3e-19  Score=92.55  Aligned_cols=44  Identities=16%  Similarity=0.085  Sum_probs=42.2

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||+|+++|+.
T Consensus        18 Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~   61 (66)
T d1bw5a_          18 LRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR   61 (66)
T ss_dssp             HHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSC
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHH
Confidence            78999999999999999999999999999999999999988875

>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=99.66  E-value=2.3e-19  Score=93.14  Aligned_cols=45  Identities=20%  Similarity=0.197  Sum_probs=42.1

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||..|..++||+..++..||..+||++.+|++||||+|++.|+.
T Consensus        15 ~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1          15 QLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             HHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            389999999999999999999999999999999999999988754

>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=99.66  E-value=2.6e-19  Score=97.90  Aligned_cols=51  Identities=16%  Similarity=0.126  Sum_probs=45.0

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhC---------------CCCCcccccccCCcccccchHHHHHH
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLG---------------LSERQVRCPHHQLTTVNNNTAIIVSF   51 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~---------------l~~~qV~vWFqNrR~~~k~~~~~~~~   51 (64)
                      +||..|..++||+..++.+||..+|               |++.+|++||||||++.|+....+.+
T Consensus        14 ~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~~a~~   79 (82)
T d2cufa1          14 VMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANIAAI   79 (82)
T ss_dssp             HHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHCCCC
T ss_pred             HHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhhHHHh
Confidence            4899999999999999999999875               99999999999999999887555443

>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=99.66  E-value=3.6e-18  Score=85.63  Aligned_cols=39  Identities=13%  Similarity=0.051  Sum_probs=37.6

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCc
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLT   39 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR   39 (64)
                      .||..|..++||+..++..||..+||++.+|++||||+|
T Consensus        12 ~Le~~F~~n~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1          12 TLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             HHHHHTTSSCSSTHHHHHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhhcCCcCc
Confidence            389999999999999999999999999999999999997

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-leucine zipper protein Homez
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=3.2e-18  Score=92.26  Aligned_cols=44  Identities=9%  Similarity=-0.028  Sum_probs=41.7

Q ss_pred             chhhhccCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFHYSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|..++||+..++..||..+||++.+|++||||+|++.|+.
T Consensus        18 Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~   61 (76)
T d2ecca1          18 LKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             HHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhc
Confidence            88999999999999999999999999999999999999887754

>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=99.62  E-value=7.7e-18  Score=89.70  Aligned_cols=45  Identities=11%  Similarity=0.030  Sum_probs=41.3

Q ss_pred             Cchhhhc-cCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           1 MDSLEFH-YSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~-~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      .||..|. .++||+..++..||..+||++.+|++||||+|++.|+.
T Consensus        21 ~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk~   66 (71)
T d1wi3a_          21 ILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS   66 (71)
T ss_dssp             HHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCSS
T ss_pred             HHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhccc
Confidence            3889997 58999999999999999999999999999999988864

>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=99.58  E-value=1.9e-17  Score=89.83  Aligned_cols=45  Identities=7%  Similarity=-0.014  Sum_probs=41.9

Q ss_pred             CchhhhccCCCCCHHHHHHHHHHhC---------------------CCCCcccccccCCcccccch
Q psy8538           1 MDSLEFHYSRYITIRRKAELANSLG---------------------LSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         1 ~~e~~F~~~~~p~~~~r~~La~~l~---------------------l~~~qV~vWFqNrR~~~k~~   45 (64)
                      +||..|..++||+..++..||.++|                     |++.+|++||||||.++|+.
T Consensus        11 ~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr~   76 (78)
T d1lfba_          11 ILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFR   76 (78)
T ss_dssp             HHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCC
T ss_pred             HHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHHh
Confidence            4899999999999999999999995                     89999999999999998875

>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=99.51  E-value=1.9e-16  Score=81.89  Aligned_cols=44  Identities=14%  Similarity=0.103  Sum_probs=38.6

Q ss_pred             Cchhhhcc---CCCCCHHHHHHHHHHhCCCCCcccccccCCcccccc
Q psy8538           1 MDSLEFHY---SRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNN   44 (64)
Q Consensus         1 ~~e~~F~~---~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~   44 (64)
                      +||..|..   ++||+..++..||..+||++.||++||||+|.+.|.
T Consensus        12 ~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_          12 ILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             HHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            37788854   579999999999999999999999999999976653

>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=99.51  E-value=2e-16  Score=84.47  Aligned_cols=44  Identities=20%  Similarity=0.105  Sum_probs=40.0

Q ss_pred             chhhhc---cCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccch
Q psy8538           2 DSLEFH---YSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNNT   45 (64)
Q Consensus         2 ~e~~F~---~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~~   45 (64)
                      ||..|.   .++||+..++..||..+||++.||++||||+|++.|+.
T Consensus        16 Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~   62 (73)
T d1pufb_          16 LNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN   62 (73)
T ss_dssp             HHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhccc
Confidence            788885   58899999999999999999999999999999887754

>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=99.50  E-value=6.8e-16  Score=83.75  Aligned_cols=43  Identities=5%  Similarity=-0.109  Sum_probs=37.7

Q ss_pred             chhhhc----cCCCCCHHHHHHHHHHhCCCCCcccccccCCcccccc
Q psy8538           2 DSLEFH----YSRYITIRRKAELANSLGLSERQVRCPHHQLTTVNNN   44 (64)
Q Consensus         2 ~e~~F~----~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~~~k~   44 (64)
                      |+..|.    .++||+..++.+||..+||++.+|+|||||+|...|.
T Consensus        32 L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          32 MLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             HHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             HHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            555554    5899999999999999999999999999999987764

>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=99.38  E-value=9.7e-15  Score=75.80  Aligned_cols=39  Identities=18%  Similarity=-0.015  Sum_probs=35.4

Q ss_pred             chhhhc---cCCCCCHHHHHHHHHHhCCCCCcccccccCCcc
Q psy8538           2 DSLEFH---YSRYITIRRKAELANSLGLSERQVRCPHHQLTT   40 (64)
Q Consensus         2 ~e~~F~---~~~~p~~~~r~~La~~l~l~~~qV~vWFqNrR~   40 (64)
                      |+..|.   .++||+..++..||..+||+..||++||+|+|.
T Consensus        17 L~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~   58 (62)
T d1x2na1          17 MRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARR   58 (62)
T ss_dssp             HHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHH
Confidence            677775   478999999999999999999999999999984