Psyllid ID: psy17007

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-----
Protein Sequence
MAAYLSYPSPYLHKSDSFYITPQGLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFYVI
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccHHHHHHHHHHccccccHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHcccHHHHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHccccHHHHEEEc
Coil and Loop (DISEMBL)
maaylsypspylhksdsfyitpqglpfgslfstsphelgskhcrrrkartvfsdhqltGLEKRFEAQRYLSTPERVELATALQLSETQVKTWfqnrlpfgslfstsphelgskhcrrrkartvfsdhqltGLEKRFEAQRYLSTPERVELATALQLSETQLFYVI
Flexible Loop (DISEMBL)
maaylsypspylHKSDSFYITPQGLPFGSLFSTSPHELGSKHCRRRKARtvfsdhqltglekRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARtvfsdhqltglekRFEAQRYLSTPERVELAtalqlsetqlfyvi
Low Complexity Region (SEG)
MAAYLSYPSPYLHKSDSFYITPQGLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFYVI
Disordered region (IsUnstruct)
**********YLHKSDSFYITPQGLPFGSLF******************TVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS*****************TVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY**
Disordered Region (DISOPRED)
****************************************************SDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELG*******************************************QLSETQLFYV*
Disordered Region (DISEMBL)
MAAYLSYPSPYLHKSDSFYITPQGLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFYVI
Disordered Region (DISPRO)
************************************************RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS**************************************STPERVELATALQLSETQLFYVI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAAYLSYPSPYLHKSDSFYITPQGLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFYVI
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	165	2.2.26 [Sep-21-2011]
Q6RFL5	233	Brain-specific homeobox p	yes	N/A	0.575	0.407	0.653	7e-29
Q3C1V8	233	Brain-specific homeobox p	yes	N/A	0.563	0.399	0.66	2e-28
Q810B3	232	Brain-specific homeobox p	yes	N/A	0.515	0.366	0.719	2e-28
Q6R3Q6	227	Brain-specific homeobox p	yes	N/A	0.436	0.317	0.794	1e-25
Q04787	429	Brain-specific homeobox p	yes	N/A	0.339	0.130	0.910	3e-24
Q9HBU1	254	Homeobox protein BarH-lik	no	N/A	0.678	0.440	0.420	6e-18
Q9ER42	254	Homeobox protein BarH-lik	no	N/A	0.678	0.440	0.420	5e-17
Q9W6D8	207	Homeobox protein BarH-lik	no	N/A	0.678	0.541	0.420	9e-17
Q9DED6	247	Homeobox protein BarH-lik	no	N/A	0.690	0.461	0.424	2e-16
Q503F2	248	Homeobox protein BarH-lik	no	N/A	0.575	0.383	0.449	5e-15

>sp|Q6RFL5|BSH_CHICK Brain-specific homeobox protein homolog OS=Gallus gallus GN=BSX PE=2 SV=1

 Score =  126 bits (316), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 66/101 (65%), Positives = 74/101 (73%), Gaps = 6/101 (5%)

Query: 2   AAYLSYPSPYLHKSD-----SFYITPQGLPFGSLFSTSPH-ELGSKHCRRRKARTVFSDH 55
           A    +P P LHK +      +++T  G+P  +LF    H EL  KHCRRRKARTVFSD 
Sbjct: 63  ALLAPHPHPALHKPEHHHHHPYFLTTSGVPVPALFPHHAHAELPGKHCRRRKARTVFSDS 122

Query: 56  QLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
           QL+GLEKRFE QRYLSTPERVELATAL LSETQVKTWFQNR
Sbjct: 123 QLSGLEKRFEIQRYLSTPERVELATALSLSETQVKTWFQNR 163

DNA binding protein that function as transcriptional activator (By similarity). May play a role in the determination and function of cell types in the brain.
Gallus gallus (taxid: 9031)

>sp|Q3C1V8|BSH_HUMAN Brain-specific homeobox protein homolog OS=Homo sapiens GN=BSX PE=2 SV=2

 Score =  124 bits (312), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 66/100 (66%), Positives = 75/100 (75%), Gaps = 7/100 (7%)

Query: 1   MAAYLSYPSPYLHKSD---SFYITPQGLPFGSLFSTSPH-ELGSKHCRRRKARTVFSDHQ 56
           +A +  +P   LHK D    +++T  G+P  +LF    H EL  KHCRRRKARTVFSD Q
Sbjct: 65  LAPHAHHP---LHKGDHHHPYFLTTSGMPVPALFPHPQHAELPGKHCRRRKARTVFSDSQ 121

Query: 57  LTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
           L+GLEKRFE QRYLSTPERVELATAL LSETQVKTWFQNR
Sbjct: 122 LSGLEKRFEIQRYLSTPERVELATALSLSETQVKTWFQNR 161

DNA binding protein that function as transcriptional activator. Is essentiel for normal postnatal growth and nursing. Is an essential factor for neuronal neuropeptide Y and agouti-related peptide function and locomotory behavior in the control of energy balance.

Homo sapiens (taxid: 9606)

>sp|Q810B3|BSH_MOUSE Brain-specific homeobox protein homolog OS=Mus musculus GN=Bsx PE=1 SV=1

 Score =  124 bits (312), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 64/89 (71%), Positives = 70/89 (78%), Gaps = 4/89 (4%)

Query: 12  LHKSD---SFYITPQGLPFGSLFSTSPH-ELGSKHCRRRKARTVFSDHQLTGLEKRFEAQ 67
           LHK D    +++T  G+P  +LF    H EL  KHCRRRKARTVFSD QL+GLEKRFE Q
Sbjct: 73  LHKGDHHHPYFLTTSGMPVPALFPHPQHAELPGKHCRRRKARTVFSDSQLSGLEKRFEIQ 132

Query: 68  RYLSTPERVELATALQLSETQVKTWFQNR 96
           RYLSTPERVELATAL LSETQVKTWFQNR
Sbjct: 133 RYLSTPERVELATALSLSETQVKTWFQNR 161

DNA binding protein that function as transcriptional activator. Is essentiel for normal postnatal growth and nursing. Is an essential factor for neuronal neuropeptide Y and agouti-related peptide function and locomotory behavior in the control of energy balance.

Mus musculus (taxid: 10090)

>sp|Q6R3Q6|BSH_DANRE Brain-specific homeobox protein homolog OS=Danio rerio GN=bsx PE=2 SV=1

 Score =  115 bits (288), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 58/73 (79%), Positives = 61/73 (83%), Gaps = 1/73 (1%)

Query: 24  GLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQ 83
           G+   +LF   P EL  KHCRRRKARTVFSD QL+GLEKRFE QRYLSTPERVELATAL 
Sbjct: 85  GMQMPALFQHHP-ELPGKHCRRRKARTVFSDSQLSGLEKRFEIQRYLSTPERVELATALS 143

Query: 84  LSETQVKTWFQNR 96
           LSETQVKTWFQNR
Sbjct: 144 LSETQVKTWFQNR 156

DNA binding protein that function as transcriptional activator (By similarity). May play a role in the determination and function of cell types in the brain.

Danio rerio (taxid: 7955)

>sp|Q04787|BSH_DROME Brain-specific homeobox protein OS=Drosophila melanogaster GN=bsh PE=2 SV=5

 Score =  110 bits (276), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 51/56 (91%), Positives = 53/56 (94%)

Query: 41  KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
           +HCRRRKARTVFSD QL+GLEKRFE QRYLSTPERVELATAL LSETQVKTWFQNR
Sbjct: 270 RHCRRRKARTVFSDPQLSGLEKRFEGQRYLSTPERVELATALGLSETQVKTWFQNR 325

DNA binding protein that function as transcriptional activator (By similarity). May play a role in the determination and function of cell types in the brain.

Drosophila melanogaster (taxid: 7227)

>sp|Q9HBU1|BARX1_HUMAN Homeobox protein BarH-like 1 OS=Homo sapiens GN=BARX1 PE=1 SV=2

 Score = 90.1 bits (222), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 53/126 (42%), Positives = 75/126 (59%), Gaps = 14/126 (11%)

Query: 28  GSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSET 87
           G L +  P E G+K  + R++RTVF++ QL GLEKRFE Q+YLSTP+R++LA +L LS+ 
Sbjct: 125 GKLEAAGPGEPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQL 184

Query: 88  QVKTWFQNR--------LPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQ 139
           QVKTW+QNR        L  G L S       +K   R K  ++ +  QLT  E+  +A+
Sbjct: 185 QVKTWYQNRRMKWKKIVLQGGGLESP------TKPKGRPKKNSIPTSEQLTEQERAKDAE 238

Query: 140 RYLSTP 145
           +    P
Sbjct: 239 KPAEVP 244

Transcription factor, which is involved in craniofacial development, in odontogenesis and in stomach organogenesis. May have a role in the differentiation of molars from incisors. Plays a role in suppressing endodermal Wnt activity (By similarity). Binds to a regulatory module of the NCAM promoter.

Homo sapiens (taxid: 9606)

>sp|Q9ER42|BARX1_MOUSE Homeobox protein BarH-like 1 OS=Mus musculus GN=Barx1 PE=2 SV=1

 Score = 87.0 bits (214), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 53/126 (42%), Positives = 74/126 (58%), Gaps = 14/126 (11%)

Query: 28  GSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSET 87
           G L +    E G+K  + R++RTVF++ QL GLEKRFE Q+YLSTP+R++LA +L LS+ 
Sbjct: 125 GKLEAAGSGEPGAKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQL 184

Query: 88  QVKTWFQNR--------LPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQ 139
           QVKTW+QNR        L  G L S       +K   R K  ++ +  QLT  E+  E +
Sbjct: 185 QVKTWYQNRRMKWKKIVLQGGGLESP------TKPKGRPKKNSIPTSEQLTEQERAKETE 238

Query: 140 RYLSTP 145
           +   TP
Sbjct: 239 KPAETP 244

Transcription factor, which is involved in craniofacial development, in odontogenesis and in stomach organogenesis. May have a role in the differentiation of molars from incisors. Plays a role in suppressing endodermal Wnt activity. Binds to a regulatory module of the NCAM promoter.

Mus musculus (taxid: 10090)

>sp|Q9W6D8|BARX1_CHICK Homeobox protein BarH-like 1 (Fragment) OS=Gallus gallus GN=BARX1 PE=2 SV=1

 Score = 86.3 bits (212), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 53/126 (42%), Positives = 74/126 (58%), Gaps = 14/126 (11%)

Query: 28  GSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSET 87
           G L +    E GSK  + R++RTVF++ QL GLEKRFE Q+YLSTP+R++LA +L LS+ 
Sbjct: 78  GKLEAAGSGEPGSKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQL 137

Query: 88  QVKTWFQNR--------LPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQ 139
           QVKTW+QNR        L  G L S       +K   R K  ++ S  QL+  E+  E +
Sbjct: 138 QVKTWYQNRRMKWKKIVLQGGGLESP------TKPKGRPKKNSIPSSEQLSEQERAKETE 191

Query: 140 RYLSTP 145
           +   +P
Sbjct: 192 KPPESP 197

Transcription factor, which is involved in craniofacial development, in odontogenic region definition, and in stomach organogenesis. Binds to a regulatory module of the NCAM promoter.

Gallus gallus (taxid: 9031)

>sp|Q9DED6|BAX1B_CHICK Homeobox protein BarH-like 1b OS=Gallus gallus GN=BARX1B PE=2 SV=1

 Score = 85.1 bits (209), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 56/132 (42%), Positives = 77/132 (58%), Gaps = 18/132 (13%)

Query: 28  GSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSET 87
           G L    P E GSK  + R++RTVF++ QL GLEKRFE Q+YLSTP+R++LA +L LS+ 
Sbjct: 119 GKLEPGGP-ETGSKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQL 177

Query: 88  QVKTWFQNR--------LPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQ 139
           QVKTW+QNR        L  G L S       +K   R K  ++ S  QL+  E+  +A+
Sbjct: 178 QVKTWYQNRRMKWKKIVLQGGGLESP------TKPKGRPKKNSIPSSEQLSEQERARDAE 231

Query: 140 R---YLSTPERV 148
           +    L +P  V
Sbjct: 232 KPPESLGSPAEV 243

Transcription factor which is involved with the serum response factor (SRF) in the smooth muscle cell-specific transcription of the beta-tropomyosin gene in the upper digestive organs and their attached arteries.

Gallus gallus (taxid: 9031)

>sp|Q503F2|BARX1_DANRE Homeobox protein BarH-like 1 OS=Danio rerio GN=barx1 PE=2 SV=2

 Score = 80.5 bits (197), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 49/109 (44%), Positives = 67/109 (61%), Gaps = 14/109 (12%)

Query: 40  SKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR--- 96
           SK  + R++RTVF++ QL GLEKRFE Q+YLSTP+R++LA +L LS+ QVKTW+QNR   
Sbjct: 130 SKTKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMK 189

Query: 97  -----LPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQR 140
                L  G L S       +K   R K  ++ +  QL+  E+  EA R
Sbjct: 190 WKKIVLQGGGLESP------TKPKGRPKKNSIPTSEQLSEQERTREADR 232

Transcription factor, is involved in craniofacial development, and in stomach organogenesis.

Danio rerio (taxid: 7955)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	165
193636579	286	PREDICTED: brain-specific homeobox prote	0.575	0.332	0.686	7e-32
242023322	342	brain-specific homeobox protein, putativ	0.509	0.245	0.767	1e-30
431842059	232	Brain-specific homeobox protein like pro	0.515	0.366	0.730	8e-28
126326512	233	PREDICTED: brain-specific homeobox prote	0.515	0.364	0.719	1e-27
395520088	233	PREDICTED: brain-specific homeobox prote	0.515	0.364	0.719	2e-27
45383147	233	brain-specific homeobox protein homolog	0.575	0.407	0.653	3e-27
296216447	232	PREDICTED: brain-specific homeobox prote	0.515	0.366	0.719	8e-27
426370818	232	PREDICTED: brain-specific homeobox prote	0.515	0.366	0.719	9e-27
403262508	232	PREDICTED: brain-specific homeobox prote	0.563	0.400	0.66	9e-27
332838046	233	PREDICTED: brain-specific homeobox prote	0.563	0.399	0.66	9e-27

>gi|193636579|ref|XP_001943337.1| PREDICTED: brain-specific homeobox protein homolog [Acyrthosiphon pisum]

 Score =  142 bits (357), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 70/102 (68%), Positives = 83/102 (81%), Gaps = 7/102 (6%)

Query: 2   AAYLSYPSPYLHKS---DSFYITPQGLPFGSLFSTSPH----ELGSKHCRRRKARTVFSD 54
           +AYLSYP+ Y+HK+   + F+I+PQG+PFGS++         +L S+ CRRRKARTVFSD
Sbjct: 63  SAYLSYPAHYMHKNSITEPFFISPQGVPFGSIWGARSDYGHGQLSSRLCRRRKARTVFSD 122

Query: 55  HQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
            QLTGLEKRFE QRYLSTPERVELAT L+LSETQVKTWFQNR
Sbjct: 123 QQLTGLEKRFEVQRYLSTPERVELATELRLSETQVKTWFQNR 164

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242023322|ref|XP_002432083.1| brain-specific homeobox protein, putative [Pediculus humanus corporis] gi|212517457|gb|EEB19345.1| brain-specific homeobox protein, putative [Pediculus humanus corporis]

 Score =  137 bits (345), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 66/86 (76%), Positives = 74/86 (86%), Gaps = 2/86 (2%)

Query: 11  YLHKSDSFYITPQGLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYL 70
           YLH+ + F+++  GLPFG+LF+    +L  KHCRRRKARTVFSDHQLTGLEKRFEAQRYL
Sbjct: 65  YLHEPEPFFLSTPGLPFGTLFTGL--DLTGKHCRRRKARTVFSDHQLTGLEKRFEAQRYL 122

Query: 71  STPERVELATALQLSETQVKTWFQNR 96
           STPERVELA AL LSETQVKTWFQNR
Sbjct: 123 STPERVELANALNLSETQVKTWFQNR 148

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|431842059|gb|ELK01408.1| Brain-specific homeobox protein like protein [Pteropus alecto]

 Score =  128 bits (321), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 65/89 (73%), Positives = 71/89 (79%), Gaps = 4/89 (4%)

Query: 12  LHKSD---SFYITPQGLPFGSLFSTSPH-ELGSKHCRRRKARTVFSDHQLTGLEKRFEAQ 67
           LHK D    +++T  G+P  +LF   PH EL  KHCRRRKARTVFSD QL+GLEKRFE Q
Sbjct: 73  LHKGDHHHPYFLTTSGVPVPALFPHPPHAELPGKHCRRRKARTVFSDSQLSGLEKRFEIQ 132

Query: 68  RYLSTPERVELATALQLSETQVKTWFQNR 96
           RYLSTPERVELATAL LSETQVKTWFQNR
Sbjct: 133 RYLSTPERVELATALSLSETQVKTWFQNR 161

Source: Pteropus alecto

Species: Pteropus alecto

Genus: Pteropus

Family: Pteropodidae

Order: Chiroptera

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|126326512|ref|XP_001370233.1| PREDICTED: brain-specific homeobox protein homolog [Monodelphis domestica]

 Score =  128 bits (321), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 64/89 (71%), Positives = 71/89 (79%), Gaps = 4/89 (4%)

Query: 12  LHKSD---SFYITPQGLPFGSLFSTSPH-ELGSKHCRRRKARTVFSDHQLTGLEKRFEAQ 67
           LHK D    +++T  G+P  +LF   PH +L  KHCRRRKARTVFSD QL+GLEKRFE Q
Sbjct: 73  LHKGDHHHPYFLTTSGMPVSALFPHPPHTDLPGKHCRRRKARTVFSDSQLSGLEKRFEIQ 132

Query: 68  RYLSTPERVELATALQLSETQVKTWFQNR 96
           RYLSTPERVELATAL LSETQVKTWFQNR
Sbjct: 133 RYLSTPERVELATALSLSETQVKTWFQNR 161

Source: Monodelphis domestica

Species: Monodelphis domestica

Genus: Monodelphis

Family: Didelphidae

Order: Didelphimorphia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|395520088|ref|XP_003764170.1| PREDICTED: brain-specific homeobox protein homolog [Sarcophilus harrisii]

 Score =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 64/89 (71%), Positives = 71/89 (79%), Gaps = 4/89 (4%)

Query: 12  LHKSD---SFYITPQGLPFGSLFSTSPH-ELGSKHCRRRKARTVFSDHQLTGLEKRFEAQ 67
           LHK D    +++T  G+P  +LF   PH +L  KHCRRRKARTVFSD QL+GLEKRFE Q
Sbjct: 73  LHKGDHHHPYFLTTSGVPVSALFPHPPHTDLPGKHCRRRKARTVFSDSQLSGLEKRFEIQ 132

Query: 68  RYLSTPERVELATALQLSETQVKTWFQNR 96
           RYLSTPERVELATAL LSETQVKTWFQNR
Sbjct: 133 RYLSTPERVELATALSLSETQVKTWFQNR 161

Source: Sarcophilus harrisii

Species: Sarcophilus harrisii

Genus: Sarcophilus

Family: Dasyuridae

Order: Dasyuromorphia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|45383147|ref|NP_989843.1| brain-specific homeobox protein homolog [Gallus gallus] gi|51701277|sp|Q6RFL5.1|BSH_CHICK RecName: Full=Brain-specific homeobox protein homolog gi|40737191|gb|AAR89086.1| brain-specific homeodomain protein [Gallus gallus]

 Score =  126 bits (316), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 66/101 (65%), Positives = 74/101 (73%), Gaps = 6/101 (5%)

Query: 2   AAYLSYPSPYLHKSD-----SFYITPQGLPFGSLFSTSPH-ELGSKHCRRRKARTVFSDH 55
           A    +P P LHK +      +++T  G+P  +LF    H EL  KHCRRRKARTVFSD 
Sbjct: 63  ALLAPHPHPALHKPEHHHHHPYFLTTSGVPVPALFPHHAHAELPGKHCRRRKARTVFSDS 122

Query: 56  QLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
           QL+GLEKRFE QRYLSTPERVELATAL LSETQVKTWFQNR
Sbjct: 123 QLSGLEKRFEIQRYLSTPERVELATALSLSETQVKTWFQNR 163

Source: Gallus gallus

Species: Gallus gallus

Genus: Gallus

Family: Phasianidae

Order: Galliformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|296216447|ref|XP_002754567.1| PREDICTED: brain-specific homeobox protein homolog [Callithrix jacchus]

 Score =  125 bits (313), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 64/89 (71%), Positives = 70/89 (78%), Gaps = 4/89 (4%)

Query: 12  LHKSD---SFYITPQGLPFGSLFSTSPH-ELGSKHCRRRKARTVFSDHQLTGLEKRFEAQ 67
           LHK D    +++T  G+P  +LF    H EL  KHCRRRKARTVFSD QL+GLEKRFE Q
Sbjct: 73  LHKGDHHHPYFLTTSGMPVPALFPQPQHAELPGKHCRRRKARTVFSDSQLSGLEKRFEIQ 132

Query: 68  RYLSTPERVELATALQLSETQVKTWFQNR 96
           RYLSTPERVELATAL LSETQVKTWFQNR
Sbjct: 133 RYLSTPERVELATALSLSETQVKTWFQNR 161

Source: Callithrix jacchus

Species: Callithrix jacchus

Genus: Callithrix

Family: Cebidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|426370818|ref|XP_004052355.1| PREDICTED: brain-specific homeobox protein homolog [Gorilla gorilla gorilla]

 Score =  124 bits (312), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 64/89 (71%), Positives = 70/89 (78%), Gaps = 4/89 (4%)

Query: 12  LHKSD---SFYITPQGLPFGSLFSTSPH-ELGSKHCRRRKARTVFSDHQLTGLEKRFEAQ 67
           LHK D    +++T  G+P  +LF    H EL  KHCRRRKARTVFSD QL+GLEKRFE Q
Sbjct: 73  LHKGDHHHPYFLTTSGMPVPALFPHPQHAELPGKHCRRRKARTVFSDSQLSGLEKRFEIQ 132

Query: 68  RYLSTPERVELATALQLSETQVKTWFQNR 96
           RYLSTPERVELATAL LSETQVKTWFQNR
Sbjct: 133 RYLSTPERVELATALSLSETQVKTWFQNR 161

Source: Gorilla gorilla gorilla

Species: Gorilla gorilla

Genus: Gorilla

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|403262508|ref|XP_003923628.1| PREDICTED: brain-specific homeobox protein homolog [Saimiri boliviensis boliviensis]

 Score =  124 bits (312), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 66/100 (66%), Positives = 75/100 (75%), Gaps = 7/100 (7%)

Query: 1   MAAYLSYPSPYLHKSD---SFYITPQGLPFGSLFSTSPH-ELGSKHCRRRKARTVFSDHQ 56
           +A +  +P   LHK D    +++T  G+P  +LF    H EL  KHCRRRKARTVFSD Q
Sbjct: 65  LAPHAHHP---LHKGDHHHPYFLTTSGMPVPALFPHPQHAELPGKHCRRRKARTVFSDSQ 121

Query: 57  LTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
           L+GLEKRFE QRYLSTPERVELATAL LSETQVKTWFQNR
Sbjct: 122 LSGLEKRFEIQRYLSTPERVELATALSLSETQVKTWFQNR 161

Source: Saimiri boliviensis boliviensis

Species: Saimiri boliviensis

Genus: Saimiri

Family: Cebidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|332838046|ref|XP_522208.3| PREDICTED: brain-specific homeobox protein homolog [Pan troglodytes]

 Score =  124 bits (312), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 66/100 (66%), Positives = 75/100 (75%), Gaps = 7/100 (7%)

Query: 1   MAAYLSYPSPYLHKSD---SFYITPQGLPFGSLFSTSPH-ELGSKHCRRRKARTVFSDHQ 56
           +A +  +P   LHK D    +++T  G+P  +LF    H EL  KHCRRRKARTVFSD Q
Sbjct: 65  LAPHAHHP---LHKGDHHHPYFLTTSGMPVPALFPHPQHAELPGKHCRRRKARTVFSDSQ 121

Query: 57  LTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
           L+GLEKRFE QRYLSTPERVELATAL LSETQVKTWFQNR
Sbjct: 122 LSGLEKRFEIQRYLSTPERVELATALSLSETQVKTWFQNR 161

Source: Pan troglodytes

Species: Pan troglodytes

Genus: Pan

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	165
UNIPROTKB|E2R0R6	232	BSX "Uncharacterized protein"	0.539	0.383	0.694	2.4e-28
UNIPROTKB|Q6RFL5	233	BSX "Brain-specific homeobox p	0.545	0.386	0.677	3.1e-28
UNIPROTKB|E1BAF5	232	BSX "Uncharacterized protein"	0.539	0.383	0.694	3.1e-28
UNIPROTKB|F1S9Q4	232	BSX "Uncharacterized protein"	0.539	0.383	0.694	3.1e-28
UNIPROTKB|Q3C1V8	233	BSX "Brain-specific homeobox p	0.563	0.399	0.66	5e-28
MGI|MGI:2669849	232	Bsx "brain specific homeobox"	0.515	0.366	0.719	6.4e-28
RGD|1565120	232	Bsx "brain specific homeobox"	0.515	0.366	0.696	5.7e-27
ZFIN|ZDB-GENE-040628-4	245	bsx "brain specific homeobox"	0.533	0.359	0.695	1.2e-26
FB|FBgn0000529	429	bsh "brain-specific homeobox"	0.557	0.214	0.613	9.8e-23
WB|WBGene00006380	197	tab-1 [Caenorhabditis elegans	0.327	0.274	0.851	2.7e-20

UNIPROTKB|E2R0R6 BSX "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 316 (116.3 bits), Expect = 2.4e-28, P = 2.4e-28
 Identities = 66/95 (69%), Positives = 73/95 (76%)

Query:     8 PSPY--LHKSDS---FYITPQGLPFGSLFSTSPH-ELGSKHCRRRKARTVFSDHQLTGLE 61
             P P+  LHK D    +++T  G+P  +LF    H EL  KHCRRRKARTVFSD QL+GLE
Sbjct:    67 PHPHHPLHKGDHHHPYFLTTSGMPVPALFPHPQHSELPGKHCRRRKARTVFSDSQLSGLE 126

Query:    62 KRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
             KRFE QRYLSTPERVELATAL LSETQVKTWFQNR
Sbjct:   127 KRFEIQRYLSTPERVELATALSLSETQVKTWFQNR 161

GO:0060056 "mammary gland involution" evidence=IEA

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

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

GO:0042755 "eating behavior" evidence=IEA

GO:0007626 "locomotory behavior" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

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

UNIPROTKB|Q6RFL5 BSX "Brain-specific homeobox protein homolog" [Gallus gallus (taxid:9031)]

 Score = 315 (115.9 bits), Expect = 3.1e-28, P = 3.1e-28
 Identities = 65/96 (67%), Positives = 73/96 (76%)

Query:     7 YPSPYLHKSDS-----FYITPQGLPFGSLFSTSPH-ELGSKHCRRRKARTVFSDHQLTGL 60
             +P P LHK +      +++T  G+P  +LF    H EL  KHCRRRKARTVFSD QL+GL
Sbjct:    68 HPHPALHKPEHHHHHPYFLTTSGVPVPALFPHHAHAELPGKHCRRRKARTVFSDSQLSGL 127

Query:    61 EKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
             EKRFE QRYLSTPERVELATAL LSETQVKTWFQNR
Sbjct:   128 EKRFEIQRYLSTPERVELATALSLSETQVKTWFQNR 163

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

GO:0007420 "brain development" evidence=ISS

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

GO:0005667 "transcription factor complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0007626 "locomotory behavior" evidence=IEA

GO:0042755 "eating behavior" evidence=IEA

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

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

GO:0060056 "mammary gland involution" evidence=IEA

UNIPROTKB|E1BAF5 BSX "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 315 (115.9 bits), Expect = 3.1e-28, P = 3.1e-28
 Identities = 66/95 (69%), Positives = 73/95 (76%)

Query:     8 PSPY--LHKSDS---FYITPQGLPFGSLFSTSPH-ELGSKHCRRRKARTVFSDHQLTGLE 61
             P P+  LHK D    +++T  G+P  +LF    H EL  KHCRRRKARTVFSD QL+GLE
Sbjct:    67 PHPHHPLHKGDHHHPYFLTTSGVPVPALFPHPQHPELPGKHCRRRKARTVFSDSQLSGLE 126

Query:    62 KRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
             KRFE QRYLSTPERVELATAL LSETQVKTWFQNR
Sbjct:   127 KRFEIQRYLSTPERVELATALSLSETQVKTWFQNR 161

GO:0060056 "mammary gland involution" evidence=IEA

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

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

GO:0042755 "eating behavior" evidence=IEA

GO:0007626 "locomotory behavior" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

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

UNIPROTKB|F1S9Q4 BSX "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 315 (115.9 bits), Expect = 3.1e-28, P = 3.1e-28
 Identities = 66/95 (69%), Positives = 73/95 (76%)

Query:     8 PSPY--LHKSDS---FYITPQGLPFGSLFSTSPH-ELGSKHCRRRKARTVFSDHQLTGLE 61
             P P+  LHK D    +++T  G+P  +LF    H EL  KHCRRRKARTVFSD QL+GLE
Sbjct:    67 PHPHHPLHKGDHHHPYFLTTSGVPVPALFPHPQHTELPGKHCRRRKARTVFSDSQLSGLE 126

Query:    62 KRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
             KRFE QRYLSTPERVELATAL LSETQVKTWFQNR
Sbjct:   127 KRFEIQRYLSTPERVELATALSLSETQVKTWFQNR 161

GO:0060056 "mammary gland involution" evidence=IEA

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

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

GO:0042755 "eating behavior" evidence=IEA

GO:0007626 "locomotory behavior" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

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

UNIPROTKB|Q3C1V8 BSX "Brain-specific homeobox protein homolog" [Homo sapiens (taxid:9606)]

 Score = 313 (115.2 bits), Expect = 5.0e-28, P = 5.0e-28
 Identities = 66/100 (66%), Positives = 75/100 (75%)

Query:     1 MAAYLSYPSPYLHKSDS---FYITPQGLPFGSLFSTSPH-ELGSKHCRRRKARTVFSDHQ 56
             +A +  +P   LHK D    +++T  G+P  +LF    H EL  KHCRRRKARTVFSD Q
Sbjct:    65 LAPHAHHP---LHKGDHHHPYFLTTSGMPVPALFPHPQHAELPGKHCRRRKARTVFSDSQ 121

Query:    57 LTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
             L+GLEKRFE QRYLSTPERVELATAL LSETQVKTWFQNR
Sbjct:   122 LSGLEKRFEIQRYLSTPERVELATALSLSETQVKTWFQNR 161

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

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

GO:0005667 "transcription factor complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0007626 "locomotory behavior" evidence=IEA

GO:0042755 "eating behavior" evidence=IEA

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

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

GO:0060056 "mammary gland involution" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

MGI|MGI:2669849 Bsx "brain specific homeobox" [Mus musculus (taxid:10090)]

 Score = 312 (114.9 bits), Expect = 6.4e-28, P = 6.4e-28
 Identities = 64/89 (71%), Positives = 70/89 (78%)

Query:    12 LHKSDS---FYITPQGLPFGSLFSTSPH-ELGSKHCRRRKARTVFSDHQLTGLEKRFEAQ 67
             LHK D    +++T  G+P  +LF    H EL  KHCRRRKARTVFSD QL+GLEKRFE Q
Sbjct:    73 LHKGDHHHPYFLTTSGMPVPALFPHPQHAELPGKHCRRRKARTVFSDSQLSGLEKRFEIQ 132

Query:    68 RYLSTPERVELATALQLSETQVKTWFQNR 96
             RYLSTPERVELATAL LSETQVKTWFQNR
Sbjct:   133 RYLSTPERVELATALSLSETQVKTWFQNR 161

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005667 "transcription factor complex" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

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

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

GO:0007626 "locomotory behavior" evidence=IMP

GO:0042755 "eating behavior" evidence=IMP

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

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

GO:0060056 "mammary gland involution" evidence=IMP

RGD|1565120 Bsx "brain specific homeobox" [Rattus norvegicus (taxid:10116)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 62/89 (69%), Positives = 69/89 (77%)

Query:    12 LHKSDS---FYITPQGLPFGSLFSTSPH-ELGSKHCRRRKARTVFSDHQLTGLEKRFEAQ 67
             LHK +    +++   G+P  +LF    H EL  KHCRRRKARTVFSD QL+GLEKRFE Q
Sbjct:    73 LHKGEHHHPYFLATSGMPVPALFPHPQHAELPGKHCRRRKARTVFSDSQLSGLEKRFEIQ 132

Query:    68 RYLSTPERVELATALQLSETQVKTWFQNR 96
             RYLSTPERVELATAL LSETQVKTWFQNR
Sbjct:   133 RYLSTPERVELATALSLSETQVKTWFQNR 161

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

GO:0005634 "nucleus" evidence=ISO

GO:0005667 "transcription factor complex" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

GO:0007626 "locomotory behavior" evidence=IEA;ISO

GO:0042755 "eating behavior" evidence=IEA;ISO

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

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

GO:0060056 "mammary gland involution" evidence=IEA;ISO

ZFIN|ZDB-GENE-040628-4 bsx "brain specific homeobox" [Danio rerio (taxid:7955)]

 Score = 300 (110.7 bits), Expect = 1.2e-26, P = 1.2e-26
 Identities = 64/92 (69%), Positives = 69/92 (75%)

Query:     8 PSPY--LHKSDSF-YITPQGLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRF 64
             P P+  LHK +   Y    G+   +LF   P EL  KHCRRRKARTVFSD QL+GLEKRF
Sbjct:    84 PHPHHPLHKPEHHPYFFTSGMQMPALFQHHP-ELPGKHCRRRKARTVFSDSQLSGLEKRF 142

Query:    65 EAQRYLSTPERVELATALQLSETQVKTWFQNR 96
             E QRYLSTPERVELATAL LSETQVKTWFQNR
Sbjct:   143 EIQRYLSTPERVELATALSLSETQVKTWFQNR 174

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

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0007420 "brain development" evidence=ISS

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

FB|FBgn0000529 bsh "brain-specific homeobox" [Drosophila melanogaster (taxid:7227)]

 Score = 266 (98.7 bits), Expect = 9.8e-23, P = 9.8e-23
 Identities = 65/106 (61%), Positives = 74/106 (69%)

Query:     4 YLSYPSPYLHKS-DSFYITPQGLPFGSLFSTSPH-----ELGS-------KHCRRRKART 50
             YLS PS   +KS D ++++   L  G+ F  +P       LG        +HCRRRKART
Sbjct:   221 YLS-PSSGTYKSVDPYFLSQASLFGGAPFFGAPGCVPELALGLGMGVNALRHCRRRKART 279

Query:    51 VFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
             VFSD QL+GLEKRFE QRYLSTPERVELATAL LSETQVKTWFQNR
Sbjct:   280 VFSDPQLSGLEKRFEGQRYLSTPERVELATALGLSETQVKTWFQNR 325

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

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

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

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

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

WB|WBGene00006380 tab-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 240 (89.5 bits), Expect = 2.7e-20, P = 2.7e-20
 Identities = 46/54 (85%), Positives = 49/54 (90%)

Query:    43 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
             C RRKARTVFSD QL GLE+RFE+QRYLSTPER+ELA AL LSETQVKTWFQNR
Sbjct:   118 CSRRKARTVFSDQQLQGLERRFESQRYLSTPERIELANALNLSETQVKTWFQNR 171

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

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

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

GO:0005634 "nucleus" evidence=IEA

---

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)
Q6RFL5	BSH_CHICK	No assigned EC number	0.6534	0.5757	0.4077	yes	N/A
Q810B3	BSH_MOUSE	No assigned EC number	0.7191	0.5151	0.3663	yes	N/A
Q3C1V8	BSH_HUMAN	No assigned EC number	0.66	0.5636	0.3991	yes	N/A
Q6R3Q6	BSH_DANRE	No assigned EC number	0.7945	0.4363	0.3171	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	165
pfam00046	57	pfam00046, Homeobox, Homeobox domain	2e-20
smart00389	57	smart00389, HOX, Homeodomain	1e-17
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	1e-16
pfam00046	57	pfam00046, Homeobox, Homeobox domain	1e-12
smart00389	57	smart00389, HOX, Homeodomain	6e-10
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	4e-09
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	1e-07

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

 Score = 79.1 bits (196), Expect = 2e-20
 Identities = 30/51 (58%), Positives = 33/51 (64%)

Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          R+ RT F+  QL  LEK FE  RY S  ER ELA  L L+E QVK WFQNR
Sbjct: 1  RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNR 51

Length = 57

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 71.5 bits (176), Expect = 1e-17
 Identities = 29/52 (55%), Positives = 33/52 (63%)

Query: 45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          +R+ RT F+  QL  LEK F+   Y S  ER ELA  L LSE QVK WFQNR
Sbjct: 1  KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNR 52

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

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

 Score = 69.2 bits (170), Expect = 1e-16
 Identities = 29/51 (56%), Positives = 32/51 (62%)

Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          R+ RT F+  QL  LEK FE   Y S  ER ELA  L L+E QVK WFQNR
Sbjct: 1  RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNR 51

Length = 59

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

 Score = 59.0 bits (144), Expect = 1e-12
 Identities = 23/46 (50%), Positives = 27/46 (58%)

Query: 118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163
           R+ RT F+  QL  LEK FE  RY S  ER ELA  L L+E Q+  
Sbjct: 1   RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKV 46

Length = 57

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 51.9 bits (125), Expect = 6e-10
 Identities = 22/44 (50%), Positives = 26/44 (59%)

Query: 117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           +R+ RT F+  QL  LEK F+   Y S  ER ELA  L LSE Q
Sbjct: 1   KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQ 44

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

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

 Score = 49.9 bits (120), Expect = 4e-09
 Identities = 22/43 (51%), Positives = 25/43 (58%)

Query: 118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           R+ RT F+  QL  LEK FE   Y S  ER ELA  L L+E Q
Sbjct: 1   RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQ 43

Length = 59

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

 Score = 48.2 bits (115), Expect = 1e-07
 Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 29  SLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 88
           S       + GS   + ++ RT  +D QL  LE+ FE   Y S+  R++L+  L +    
Sbjct: 37  SEMKLERKQDGSSPPKSKRRRT--TDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKS 94

Query: 89  VKTWFQNR 96
           V+ WFQN+
Sbjct: 95  VQIWFQNK 102

Length = 156

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	165
KOG2251|consensus	228		99.75
KOG0488|consensus	309		99.75
KOG0484|consensus	125		99.73
KOG0487|consensus	308		99.73
KOG0843|consensus	197		99.72
KOG0842|consensus	307		99.71
KOG0850|consensus	245		99.7
KOG0489|consensus	261		99.7
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.67
KOG0490|consensus	235		99.66
KOG0492|consensus	246		99.66
KOG0494|consensus	332		99.66
KOG0848|consensus	317		99.65
KOG0485|consensus	268		99.63
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.63
KOG3802|consensus	398		99.61
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.58
KOG0493|consensus	342		99.56
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.55
KOG0844|consensus	408		99.48
KOG0491|consensus	194		99.47
KOG0483|consensus	198		99.47
KOG4577|consensus	383		99.46
KOG0486|consensus	351		99.45
COG5576	156	Homeodomain-containing transcription factor [Trans	99.43
KOG0847|consensus	288		99.37
KOG1168|consensus	385		99.16
KOG0849|consensus	354		99.11
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	98.97
KOG0488|consensus	309		98.92
KOG0775|consensus	304		98.9
KOG0484|consensus	125		98.81
KOG0489|consensus	261		98.78
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	98.74
KOG0843|consensus	197		98.72
KOG2251|consensus	228		98.72
KOG0487|consensus	308		98.72
KOG0848|consensus	317		98.69
KOG0842|consensus	307		98.69
KOG0850|consensus	245		98.68
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.59
KOG0774|consensus	334		98.59
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	98.57
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	98.51
KOG2252|consensus	558		98.46
KOG0492|consensus	246		98.45
KOG0493|consensus	342		98.43
KOG0491|consensus	194		98.36
KOG0485|consensus	268		98.34
KOG0494|consensus	332		98.25
KOG0490|consensus	235		97.95
KOG1146|consensus	1406		97.83
KOG0849|consensus	354		97.73
KOG0486|consensus	351		97.73
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	97.68
KOG0844|consensus	408		97.65
COG5576	156	Homeodomain-containing transcription factor [Trans	97.5
KOG0483|consensus	198		97.46
KOG3623|consensus	1007		96.96
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	96.96
KOG3802|consensus	398		96.8
KOG0847|consensus	288		96.71
KOG0773|consensus	342		96.69
KOG4577|consensus	383		96.22
KOG2252|consensus	558		96.1
KOG0774|consensus	334		96.0
KOG0775|consensus	304		95.09
KOG1146|consensus	1406		94.97
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	94.58
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	92.38
COG3413	215	Predicted DNA binding protein [General function pr	85.17
KOG1168|consensus	385		84.98
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	84.84
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	84.27
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	84.24
cd04764	67	HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding dom	83.31
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	81.19
cd01104	68	HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain	80.93
cd04763	68	HTH_MlrA-like Helix-Turn-Helix DNA binding domain	80.77

>KOG2251|consensus

Probab=99.75  E-value=3.7e-18  Score=125.75  Aligned_cols=68  Identities=34%  Similarity=0.459  Sum_probs=63.5

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCC
Q psy17007         39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTS  106 (165)
Q Consensus        39 ~~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~  106 (165)
                      ....+|.||.||+|+..|+++||.+|.++.||++..+++||.+|+|.+.+|+|||.|||+|+++....
T Consensus        31 ~~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q   98 (228)
T KOG2251|consen   31 SSGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ   98 (228)
T ss_pred             CccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence            36778999999999999999999999999999999999999999999999999999999999876543

>KOG0488|consensus

Probab=99.75  E-value=1e-18  Score=137.64  Aligned_cols=70  Identities=53%  Similarity=0.725  Sum_probs=64.0

Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCC
Q psy17007         37 ELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTS  106 (165)
Q Consensus        37 ~~~~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~  106 (165)
                      ......+|.|+.||.||..|+..||+.|+..+|++..+|.+||..|||+..||++||||||+|+|+....
T Consensus       164 ~~~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~  233 (309)
T KOG0488|consen  164 YQRSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE  233 (309)
T ss_pred             cccCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence            3455668889999999999999999999999999999999999999999999999999999999875544

>KOG0484|consensus

Probab=99.73  E-value=6.9e-19  Score=114.90  Aligned_cols=62  Identities=34%  Similarity=0.535  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      ..+|+||-||+||..||.+||..|.+..||++-.|++||.++.|++..|++||||||+|.+.
T Consensus        13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRK   74 (125)
T KOG0484|consen   13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRK   74 (125)
T ss_pred             HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHH
Confidence            45788999999999999999999999999999999999999999999999999999999764

>KOG0487|consensus

Probab=99.73  E-value=1.3e-18  Score=135.32  Aligned_cols=65  Identities=38%  Similarity=0.557  Sum_probs=61.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST  105 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~  105 (165)
                      ..++.|++|+.||+.|+.+||+.|.-|.|++.+.|.+|+..|+|+++||+|||||||.|+|++..
T Consensus       231 ~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r  295 (308)
T KOG0487|consen  231 SARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR  295 (308)
T ss_pred             cccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence            34788999999999999999999999999999999999999999999999999999999987663

>KOG0843|consensus

Probab=99.72  E-value=1.2e-17  Score=119.39  Aligned_cols=63  Identities=44%  Similarity=0.656  Sum_probs=59.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCC
Q psy17007         44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTS  106 (165)
Q Consensus        44 ~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~  106 (165)
                      +.+|.||.|+.+|+..||..|+.+.|....+|+.||..|+|++.||+|||||||.|.|+....
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e  163 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE  163 (197)
T ss_pred             CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence            778999999999999999999999999999999999999999999999999999999876544

>KOG0842|consensus

Probab=99.71  E-value=1.4e-17  Score=129.67  Aligned_cols=67  Identities=46%  Similarity=0.674  Sum_probs=61.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCC
Q psy17007         42 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPH  108 (165)
Q Consensus        42 ~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~  108 (165)
                      ..++||.|..||..|+-+||..|....|++..||+.||..|+||..||||||||||.|.||......
T Consensus       150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~  216 (307)
T KOG0842|consen  150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKA  216 (307)
T ss_pred             cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhh
Confidence            4566777888999999999999999999999999999999999999999999999999998665543

>KOG0850|consensus

Probab=99.70  E-value=1.8e-17  Score=122.70  Aligned_cols=69  Identities=43%  Similarity=0.655  Sum_probs=64.3

Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007         37 ELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST  105 (165)
Q Consensus        37 ~~~~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~  105 (165)
                      ..+++.+|.|+.||.|+.-||..|...|++++|+-..||.+||..|||+..||+|||||||.|.|....
T Consensus       114 ~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k  182 (245)
T KOG0850|consen  114 RPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK  182 (245)
T ss_pred             ccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence            358889999999999999999999999999999999999999999999999999999999999876443

>KOG0489|consensus

Probab=99.70  E-value=4.5e-18  Score=131.72  Aligned_cols=67  Identities=37%  Similarity=0.558  Sum_probs=61.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCC
Q psy17007         42 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPH  108 (165)
Q Consensus        42 ~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~  108 (165)
                      .++.||.||.||..|+.+||+.|.-|.|+++..|.+||..|+|+++||+|||||||+|+|+......
T Consensus       156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~  222 (261)
T KOG0489|consen  156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS  222 (261)
T ss_pred             cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence            3567999999999999999999999999999999999999999999999999999999987554443

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.67  E-value=2.8e-17  Score=98.93  Aligned_cols=56  Identities=46%  Similarity=0.652  Sum_probs=53.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcc
Q psy17007         46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGS  101 (165)
Q Consensus        46 rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~  101 (165)
                      |+.|+.||.+|+..|+..|..++||+..+++.||..+||+..+|++||+|+|.+.+
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k   56 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEK   56 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhC
Confidence            57789999999999999999999999999999999999999999999999998764

; 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 ....

>KOG0490|consensus

Probab=99.66  E-value=1.2e-16  Score=121.61  Aligned_cols=122  Identities=32%  Similarity=0.357  Sum_probs=104.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC--CCCcc---------
Q psy17007         42 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST--SPHEL---------  110 (165)
Q Consensus        42 ~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~--~~~~~---------  110 (165)
                      ..++++.|+.|+..|+++|+..|+.++||+...++.||..+++++..|++||||+|++.+....  .....         
T Consensus        57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~~~~~~~~~~~~~~~~~  136 (235)
T KOG0490|consen   57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEERPLPEGENLPDLSGTAP  136 (235)
T ss_pred             hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhccccccccCCCCCCCCC
Confidence            5678899999999999999999999999999999999999999999999999999999875441  11100         


Q ss_pred             ----------CccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        111 ----------GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       111 ----------~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                                .....+.++.++.+...|+..+...|..+.+|+...+..|+..+|+++..|+-
T Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~  199 (235)
T KOG0490|consen  137 PSASRDKLDKGPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQV  199 (235)
T ss_pred             ccccccccccCCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhh
Confidence                      11123556678899999999999999999999999999999999999987763

>KOG0492|consensus

Probab=99.66  E-value=4.6e-17  Score=118.78  Aligned_cols=64  Identities=47%  Similarity=0.748  Sum_probs=59.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS  104 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~  104 (165)
                      +.+-+|+.|+.||..||..||..|.+.+|+++.+|.+++..|.|++.||+|||||||+|.|+.+
T Consensus       140 Khk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ  203 (246)
T KOG0492|consen  140 KHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ  203 (246)
T ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence            4455678899999999999999999999999999999999999999999999999999998754

>KOG0494|consensus

Probab=99.66  E-value=1.5e-16  Score=119.58  Aligned_cols=65  Identities=34%  Similarity=0.456  Sum_probs=58.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCC
Q psy17007         44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPH  108 (165)
Q Consensus        44 ~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~  108 (165)
                      ++|+.||.||..|++.||+.|++..||+..-|+.||.++.|.+++|+|||||||+|+++......
T Consensus       140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg  204 (332)
T KOG0494|consen  140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWG  204 (332)
T ss_pred             ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcC
Confidence            34445999999999999999999999999999999999999999999999999999987655443

>KOG0848|consensus

Probab=99.65  E-value=8.8e-17  Score=121.35  Aligned_cols=58  Identities=47%  Similarity=0.659  Sum_probs=54.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007         47 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS  104 (165)
Q Consensus        47 r~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~  104 (165)
                      +.|.+||+.|..+||+.|..+.|+++..+.+||..|||+++||+|||||||+|+++..
T Consensus       201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~n  258 (317)
T KOG0848|consen  201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDN  258 (317)
T ss_pred             ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHH
Confidence            5688999999999999999999999999999999999999999999999999997543

>KOG0485|consensus

Probab=99.63  E-value=2.5e-16  Score=115.71  Aligned_cols=63  Identities=52%  Similarity=0.679  Sum_probs=59.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007         43 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST  105 (165)
Q Consensus        43 ~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~  105 (165)
                      .++|+.||+|+..|+..||..|+...|++..+|..||..|.|++.||+|||||||.|+|+...
T Consensus       102 ~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a  164 (268)
T KOG0485|consen  102 DRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA  164 (268)
T ss_pred             cccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence            477888999999999999999999999999999999999999999999999999999987543

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.63  E-value=8.6e-16  Score=91.80  Aligned_cols=52  Identities=19%  Similarity=0.323  Sum_probs=50.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCC----CCHHHHHHHHHHhccchhhhhhhhccCC
Q psy17007         46 RKARTVFSDHQLTGLEKRFEAQRY----LSTPERVELATALQLSETQVKTWFQNRL   97 (165)
Q Consensus        46 rr~R~~~s~~q~~~Le~~f~~~~~----p~~~~~~~la~~l~l~~~~V~~WF~nrr   97 (165)
                      +|.||.||.+|++.|+..|..+.|    |+..++++||..+||++.+|++||+|.+
T Consensus         2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            788999999999999999999999    9999999999999999999999999964

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=99.61  E-value=5.9e-16  Score=123.07  Aligned_cols=64  Identities=30%  Similarity=0.401  Sum_probs=61.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007         42 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST  105 (165)
Q Consensus        42 ~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~  105 (165)
                      ..|+||+||.|....+..||.+|.+|+.|+.+++..||.+|+|..++|+|||||||.|+||...
T Consensus       291 ~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  291 QSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             cccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            3478899999999999999999999999999999999999999999999999999999999877

>smart00389 HOX Homeodomain

Probab=99.58  E-value=3.1e-15  Score=89.53  Aligned_cols=54  Identities=52%  Similarity=0.682  Sum_probs=51.4

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCc
Q psy17007         47 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFG  100 (165)
Q Consensus        47 r~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~  100 (165)
                      +.|+.|+.+|+..|+..|..++||+..++..||..+||+..+|+.||+|+|++.
T Consensus         2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~   55 (56)
T smart00389        2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKW   55 (56)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhcc
Confidence            567789999999999999999999999999999999999999999999999875

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

>KOG0493|consensus

Probab=99.56  E-value=5e-15  Score=111.61  Aligned_cols=64  Identities=38%  Similarity=0.595  Sum_probs=58.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCC
Q psy17007         45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPH  108 (165)
Q Consensus        45 ~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~  108 (165)
                      -+|.||.||.+||..|...|+.+.|++...|..||.+|+|.+.||+|||||+|+|-|....+..
T Consensus       246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn  309 (342)
T KOG0493|consen  246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKN  309 (342)
T ss_pred             hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCC
Confidence            3577999999999999999999999999999999999999999999999999999987555443

>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=99.55  E-value=7.5e-15  Score=88.61  Aligned_cols=56  Identities=50%  Similarity=0.640  Sum_probs=52.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         47 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        47 r~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      +.+..|+.+++..|+.+|..++||+..++..||..+||+..+|++||+|+|.+.+.
T Consensus         2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~   57 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR   57 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence            46789999999999999999999999999999999999999999999999988754

>KOG0844|consensus

Probab=99.48  E-value=1.8e-14  Score=110.79  Aligned_cols=64  Identities=44%  Similarity=0.629  Sum_probs=59.8

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         40 SKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        40 ~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      +.+..-||.||.||.+|+..||+.|-+.+|-+...|.+||..|+|.+..|++||||||.|+|+.
T Consensus       176 sa~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQ  239 (408)
T KOG0844|consen  176 SADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQ  239 (408)
T ss_pred             CccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhh
Confidence            4455678999999999999999999999999999999999999999999999999999999874

>KOG0491|consensus

Probab=99.47  E-value=7.7e-15  Score=103.58  Aligned_cols=65  Identities=72%  Similarity=0.936  Sum_probs=59.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCC
Q psy17007         44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPH  108 (165)
Q Consensus        44 ~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~  108 (165)
                      +.++.|++|+..|+..|++.|+...|.+-.++.+||..|+|++.||+.||||||.|.|+......
T Consensus        99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~  163 (194)
T KOG0491|consen   99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ  163 (194)
T ss_pred             HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence            45677999999999999999999999999999999999999999999999999999987654443

>KOG0483|consensus

Probab=99.47  E-value=1.1e-13  Score=102.30  Aligned_cols=62  Identities=29%  Similarity=0.389  Sum_probs=56.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCC
Q psy17007         45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTS  106 (165)
Q Consensus        45 ~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~  106 (165)
                      ..+++.+|+.+|+..||..|....+.....+..||..|||..+||.+|||||||++|..+..
T Consensus        50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE  111 (198)
T KOG0483|consen   50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLE  111 (198)
T ss_pred             cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhh
Confidence            44556689999999999999999999999999999999999999999999999999875543

>KOG4577|consensus

Probab=99.46  E-value=1.4e-14  Score=110.61  Aligned_cols=99  Identities=18%  Similarity=0.258  Sum_probs=81.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccch
Q psy17007         11 YLHKSDSFYITPQGLPFGSLFSTSPHELG----SKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSE   86 (165)
Q Consensus        11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~   86 (165)
                      .+.+.+.||++.....+.-.+..+.....    ..+...+|.||++|..||+-|...|...+.|-...|+.|+.++||.-
T Consensus       129 ~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~~l~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDM  208 (383)
T KOG4577|consen  129 QLATGDEFYLMEDARLVCKDDYETAKQKHCNELEGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDM  208 (383)
T ss_pred             ccccCCeeEEeccceeehhhhHHHHHhccccccccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcce
Confidence            45677888888877776655544433221    23445688999999999999999999999999999999999999999


Q ss_pred             hhhhhhhccCCCCccccCCCCCc
Q psy17007         87 TQVKTWFQNRLPFGSLFSTSPHE  109 (165)
Q Consensus        87 ~~V~~WF~nrr~~~~~~~~~~~~  109 (165)
                      +.||+||||||+|+|+..+..+.
T Consensus       209 RVVQVWFQNRRAKEKRLKKDAGR  231 (383)
T KOG4577|consen  209 RVVQVWFQNRRAKEKRLKKDAGR  231 (383)
T ss_pred             eehhhhhhhhhHHHHhhhhhcch
Confidence            99999999999999987766653

>KOG0486|consensus

Probab=99.45  E-value=5.4e-14  Score=108.54  Aligned_cols=65  Identities=32%  Similarity=0.524  Sum_probs=60.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCC
Q psy17007         44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPH  108 (165)
Q Consensus        44 ~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~  108 (165)
                      |+||.|+.|+.+|+.+||..|..+.||+...|++||.-++|++..|++||.|||+|++..+....
T Consensus       111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~  175 (351)
T KOG0486|consen  111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ  175 (351)
T ss_pred             hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence            78899999999999999999999999999999999999999999999999999999976554443

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.43  E-value=9.3e-14  Score=99.35  Aligned_cols=65  Identities=28%  Similarity=0.419  Sum_probs=58.3

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCC
Q psy17007         42 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTS  106 (165)
Q Consensus        42 ~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~  106 (165)
                      .+..+++|.+-+.+|+.+|+..|..++||+...+..|+..++|+++-|++||||+|++.+.....
T Consensus        48 s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~  112 (156)
T COG5576          48 SSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG  112 (156)
T ss_pred             CCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence            34556777888999999999999999999999999999999999999999999999999765444

>KOG0847|consensus

Probab=99.37  E-value=9.3e-13  Score=97.16  Aligned_cols=67  Identities=36%  Similarity=0.622  Sum_probs=61.4

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007         39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST  105 (165)
Q Consensus        39 ~~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~  105 (165)
                      ..++++++..|.+|+..|+..|+..|+..+|+-..++.+||..+|+++.+|+|||||||.|++....
T Consensus       161 ~~kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA  227 (288)
T KOG0847|consen  161 PNLNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA  227 (288)
T ss_pred             cCcCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence            4466778888999999999999999999999999999999999999999999999999999976543

>KOG1168|consensus

Probab=99.16  E-value=6e-12  Score=96.42  Aligned_cols=65  Identities=23%  Similarity=0.318  Sum_probs=59.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCC
Q psy17007         43 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSP  107 (165)
Q Consensus        43 ~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~  107 (165)
                      ..++|+||.+..-+...||++|...+.|+.+.+..||++|+|..+.|++||||+|.|.|++..+.
T Consensus       307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa  371 (385)
T KOG1168|consen  307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSA  371 (385)
T ss_pred             cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhh
Confidence            34678899999999999999999999999999999999999999999999999999998865443

>KOG0849|consensus

Probab=99.11  E-value=1.2e-10  Score=93.86  Aligned_cols=67  Identities=33%  Similarity=0.361  Sum_probs=61.5

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007         38 LGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS  104 (165)
Q Consensus        38 ~~~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~  104 (165)
                      .+..+++.+|.|++|+..|+..|++.|..++||++..|+.||.++++++..|++||+|+|++.++..
T Consensus       169 ~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~  235 (354)
T KOG0849|consen  169 GYALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH  235 (354)
T ss_pred             cccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence            3556677888899999999999999999999999999999999999999999999999999887654

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=98.97  E-value=4.1e-10  Score=67.33  Aligned_cols=46  Identities=15%  Similarity=0.187  Sum_probs=43.9

Q ss_pred             ccccccccccchhhhhhhccccCC----CCHHHHHHHHHHcCCChhhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRFEAQRY----LSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F~~~~y----p~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ++.||.||.+|+..|+..|+.+.|    |+..++++||..|||++.+||-
T Consensus         2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKV   51 (58)
T TIGR01565         2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKV   51 (58)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeee
Confidence            567999999999999999999999    9999999999999999999985

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.

>KOG0488|consensus

Probab=98.92  E-value=7.6e-10  Score=87.58  Aligned_cols=49  Identities=57%  Similarity=0.843  Sum_probs=46.9

Q ss_pred             ccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007        114 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLF  162 (165)
Q Consensus       114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq  162 (165)
                      +.+.++.||.||+.|+.+||+.|++-+|++..+|.+||..||||.+|||
T Consensus       169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVK  217 (309)
T KOG0488|consen  169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVK  217 (309)
T ss_pred             CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHH
Confidence            4677889999999999999999999999999999999999999999998

>KOG0775|consensus

Probab=98.90  E-value=1.4e-09  Score=83.00  Aligned_cols=47  Identities=34%  Similarity=0.429  Sum_probs=44.2

Q ss_pred             HHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcc
Q psy17007         55 HQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGS  101 (165)
Q Consensus        55 ~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~  101 (165)
                      .-...|.++|..++||+..++.+||..+||+..||-+||.|||.+++
T Consensus       186 kSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR  232 (304)
T KOG0775|consen  186 KSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR  232 (304)
T ss_pred             hhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence            34579999999999999999999999999999999999999999987

>KOG0484|consensus

Probab=98.81  E-value=1.1e-09  Score=71.97  Aligned_cols=51  Identities=29%  Similarity=0.477  Sum_probs=47.6

Q ss_pred             cccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        113 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       113 ~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ..+++++-|+.||..|+.+||+.|..++||++-.|++||..|+|+++.||-
T Consensus        13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQV   63 (125)
T KOG0484|consen   13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQV   63 (125)
T ss_pred             HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHH
Confidence            356778899999999999999999999999999999999999999999984

>KOG0489|consensus

Probab=98.78  E-value=4.1e-09  Score=81.84  Aligned_cols=68  Identities=31%  Similarity=0.544  Sum_probs=54.9

Q ss_pred             hhhhhhccCCCCccccCCCCCccCccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007         88 QVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus        88 ~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      +|.-|+.....-        ..........+|.|+.||..|+.+||+.|+.|+|++...|.+||..|.|+|+|||=
T Consensus       138 ~~~p~~~~~~~~--------~~~~~~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKI  205 (261)
T KOG0489|consen  138 QIYPWMKSTANY--------LSSSETGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKI  205 (261)
T ss_pred             ccccchhhhhcc--------cccccccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHH
Confidence            677787654322        12222333467889999999999999999999999999999999999999999983

>PF00046 Homeobox: Homeobox domain not present here

Probab=98.74  E-value=6.1e-09  Score=62.25  Aligned_cols=45  Identities=42%  Similarity=0.530  Sum_probs=42.9

Q ss_pred             cccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        119 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       119 r~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      +.++.||.+|+..|+..|..++||+..+++.||..+||+..+|+.
T Consensus         2 r~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~   46 (57)
T PF00046_consen    2 RKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKN   46 (57)
T ss_dssp             SSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHHHHhcccccccccccccccccccccccc
Confidence            568899999999999999999999999999999999999999975

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

>KOG0843|consensus

Probab=98.72  E-value=6.5e-09  Score=74.84  Aligned_cols=48  Identities=44%  Similarity=0.621  Sum_probs=45.6

Q ss_pred             ccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       116 ~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      +.++.||.||.+|+..||.+|+.++|....+|++||..|+|++.|||-
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkv  148 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKV  148 (197)
T ss_pred             CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhh
Confidence            567789999999999999999999999999999999999999999984

>KOG2251|consensus

Probab=98.72  E-value=6.7e-09  Score=77.07  Aligned_cols=52  Identities=35%  Similarity=0.430  Sum_probs=49.3

Q ss_pred             ccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        112 SKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       112 ~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ..+++.+|.||.|+-.|+++||..|.+++||+...|++||.+|+|.+.+||-
T Consensus        32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqV   83 (228)
T KOG2251|consen   32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQV   83 (228)
T ss_pred             ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhh
Confidence            6677889999999999999999999999999999999999999999999984

>KOG0487|consensus

Probab=98.72  E-value=4.7e-09  Score=82.28  Aligned_cols=53  Identities=36%  Similarity=0.493  Sum_probs=49.1

Q ss_pred             cCccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007        110 LGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLF  162 (165)
Q Consensus       110 ~~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq  162 (165)
                      ........|++|+.+|..|+.+||+.|..|.|++.+.|.+|+..|+||++|||
T Consensus       228 ~~~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVK  280 (308)
T KOG0487|consen  228 NASSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVK  280 (308)
T ss_pred             ccccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhhee
Confidence            33455788999999999999999999999999999999999999999999998

>KOG0848|consensus

Probab=98.69  E-value=8.5e-09  Score=78.47  Aligned_cols=52  Identities=40%  Similarity=0.563  Sum_probs=47.2

Q ss_pred             ccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        112 SKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       112 ~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .+.+...+.|.++|++|+.+||+.|..++|+++..+.+||.-|||+|+|||-
T Consensus       194 ~KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKI  245 (317)
T KOG0848|consen  194 VKTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKI  245 (317)
T ss_pred             ceeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhH
Confidence            3445566889999999999999999999999999999999999999999983

>KOG0842|consensus

Probab=98.69  E-value=9.7e-09  Score=80.48  Aligned_cols=49  Identities=49%  Similarity=0.752  Sum_probs=46.3

Q ss_pred             ccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007        114 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLF  162 (165)
Q Consensus       114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq  162 (165)
                      ..+.|+.|.-||..|+.+||+.|...+|++..||++||..|+||+.|||
T Consensus       150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVK  198 (307)
T KOG0842|consen  150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVK  198 (307)
T ss_pred             cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchhee
Confidence            5567778889999999999999999999999999999999999999998

>KOG0850|consensus

Probab=98.68  E-value=1e-08  Score=76.51  Aligned_cols=53  Identities=43%  Similarity=0.673  Sum_probs=48.6

Q ss_pred             CccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        111 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       111 ~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ..+..+-|+.||.|+..||..|.+.|++++|+...||++||.+||||-.|||-
T Consensus       116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKI  168 (245)
T KOG0850|consen  116 NGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKI  168 (245)
T ss_pred             CCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhh
Confidence            34556678889999999999999999999999999999999999999999983

>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=98.59  E-value=1.1e-08  Score=56.68  Aligned_cols=33  Identities=36%  Similarity=0.514  Sum_probs=27.9

Q ss_pred             hcCCCCHHHHHHHHHHhccchhhhhhhhccCCC
Q psy17007         66 AQRYLSTPERVELATALQLSETQVKTWFQNRLP   98 (165)
Q Consensus        66 ~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~   98 (165)
                      .++||+.++++.||..+||+..||..||-|.|.
T Consensus         7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRr   39 (40)
T PF05920_consen    7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARR   39 (40)
T ss_dssp             TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHc
Confidence            479999999999999999999999999999774

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

>KOG0774|consensus

Probab=98.59  E-value=4e-08  Score=74.62  Aligned_cols=57  Identities=28%  Similarity=0.384  Sum_probs=52.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHH---hcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcc
Q psy17007         45 RRKARTVFSDHQLTGLEKRFE---AQRYLSTPERVELATALQLSETQVKTWFQNRLPFGS  101 (165)
Q Consensus        45 ~rr~R~~~s~~q~~~Le~~f~---~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~  101 (165)
                      .+|+|..|++.-.++|.++|-   .++||+.+.+++||.++|++..||-.||.|+|-+.+
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIryk  247 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYK  247 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehh
Confidence            367888999999999999996   689999999999999999999999999999987654

>smart00389 HOX Homeodomain

Probab=98.57  E-value=5.5e-08  Score=57.70  Aligned_cols=45  Identities=47%  Similarity=0.579  Sum_probs=41.9

Q ss_pred             cccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        119 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       119 r~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      +.++.|+.+|+..|+..|+.++||+..++..||..+||+..||+.
T Consensus         2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~   46 (56)
T smart00389        2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKV   46 (56)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence            356779999999999999999999999999999999999999975

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=98.51  E-value=9.8e-08  Score=57.10  Aligned_cols=45  Identities=47%  Similarity=0.583  Sum_probs=42.1

Q ss_pred             cccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        119 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       119 r~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      +.+..++.+|+..|+..|..++||+..+++.||..+||+..||+.
T Consensus         2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~   46 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKI   46 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence            356789999999999999999999999999999999999999974

>KOG2252|consensus

Probab=98.46  E-value=2.2e-07  Score=77.24  Aligned_cols=58  Identities=24%  Similarity=0.303  Sum_probs=54.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCc
Q psy17007         43 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFG  100 (165)
Q Consensus        43 ~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~  100 (165)
                      -+.++.|.+||+.|...|...|+.+++|+.+..+.|+..|||....|.+||-|-|.+.
T Consensus       418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            3456779999999999999999999999999999999999999999999999988775

>KOG0492|consensus

Probab=98.45  E-value=7.7e-08  Score=70.83  Aligned_cols=50  Identities=44%  Similarity=0.696  Sum_probs=46.5

Q ss_pred             ccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        114 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ....|+.|+.||..|+..||+.|...+|+++++|.+++..|.||+.|||-
T Consensus       141 hk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKI  190 (246)
T KOG0492|consen  141 HKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKI  190 (246)
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheeh
Confidence            34567889999999999999999999999999999999999999999983

>KOG0493|consensus

Probab=98.43  E-value=1.7e-07  Score=71.35  Aligned_cols=76  Identities=29%  Similarity=0.373  Sum_probs=55.9

Q ss_pred             hhhhhhccCCCCccccCCCCCccC----ccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007         88 QVKTWFQNRLPFGSLFSTSPHELG----SKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus        88 ~V~~WF~nrr~~~~~~~~~~~~~~----~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ..-.|.-..|..++..........    ......++.||-||.+|+..|...|..|+|++...|.+||.+|||.+.|||-
T Consensus       213 mwPAWVycTRYSDRPSsGPR~Rk~kkkk~~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKI  292 (342)
T KOG0493|consen  213 MWPAWVYCTRYSDRPSSGPRHRKPKKKKSSSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKI  292 (342)
T ss_pred             ccceeeeeecccCCCCCCcccccccccCCccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhH
Confidence            344676666665544332222111    1222345779999999999999999999999999999999999999999984

>KOG0491|consensus

Probab=98.36  E-value=1.5e-07  Score=66.91  Aligned_cols=50  Identities=82%  Similarity=1.118  Sum_probs=47.3

Q ss_pred             ccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        114 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .|+.++.|++|++.|+..|++.|+.-+|++..++.+||..|+|++.|||-
T Consensus        97 ~~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKT  146 (194)
T KOG0491|consen   97 HCRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKT  146 (194)
T ss_pred             HHHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHH
Confidence            56778899999999999999999999999999999999999999999984

>KOG0485|consensus

Probab=98.34  E-value=1.6e-07  Score=69.70  Aligned_cols=48  Identities=54%  Similarity=0.745  Sum_probs=45.1

Q ss_pred             ccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       116 ~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      +.++.||+|+..|+..||..|+..+|++..+|..||.+|.|||.|||-
T Consensus       103 RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKI  150 (268)
T KOG0485|consen  103 RKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKI  150 (268)
T ss_pred             ccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhh
Confidence            556779999999999999999999999999999999999999999983

>KOG0494|consensus

Probab=98.25  E-value=6.7e-07  Score=68.03  Aligned_cols=50  Identities=32%  Similarity=0.459  Sum_probs=44.6

Q ss_pred             cccccc-ccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        114 HCRRRK-ARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       114 ~~~~rr-~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      +++.|| .||.||..|+.+||++|...+||+...|+-||..++|.+++||-
T Consensus       137 kk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqV  187 (332)
T KOG0494|consen  137 KKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQV  187 (332)
T ss_pred             cccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhH
Confidence            343444 49999999999999999999999999999999999999999874

>KOG0490|consensus

Probab=97.95  E-value=5.3e-06  Score=62.97  Aligned_cols=67  Identities=33%  Similarity=0.462  Sum_probs=60.3

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007         39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST  105 (165)
Q Consensus        39 ~~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~  105 (165)
                      .....+.++.|+.+...|+..+...|..+++|+...++.|+..+|++...|++||+|+|.+.+....
T Consensus       147 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  147 GPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             CCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            4445677888999999999999999999999999999999999999999999999999999976443

>KOG1146|consensus

Probab=97.83  E-value=5.3e-05  Score=68.91  Aligned_cols=60  Identities=32%  Similarity=0.343  Sum_probs=55.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        44 ~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      .++..|+.+++.|+..+...|....+|...+.+.|...+++..+.|++||+|-|.+.+..
T Consensus       902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~  961 (1406)
T KOG1146|consen  902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKA  961 (1406)
T ss_pred             hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhh
Confidence            456789999999999999999999999999999999999999999999999999998653

>KOG0849|consensus

Probab=97.73  E-value=3.1e-05  Score=62.71  Aligned_cols=50  Identities=32%  Similarity=0.381  Sum_probs=45.6

Q ss_pred             ccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        114 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ....++.|+.|+..|+..|++.|++++||+...|+.||.++|+++..|+-
T Consensus       173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqv  222 (354)
T KOG0849|consen  173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQV  222 (354)
T ss_pred             cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHH
Confidence            34566778999999999999999999999999999999999999998873

>KOG0486|consensus

Probab=97.73  E-value=1e-05  Score=63.24  Aligned_cols=47  Identities=34%  Similarity=0.540  Sum_probs=44.6

Q ss_pred             ccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007        116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLF  162 (165)
Q Consensus       116 ~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq  162 (165)
                      ++++-|+.||..|+.+||..|.+|+||+...|++||.-+.|++..|.
T Consensus       111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvr  157 (351)
T KOG0486|consen  111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVR  157 (351)
T ss_pred             hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhh
Confidence            67788999999999999999999999999999999999999999875

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

Probab=97.68  E-value=3e-05  Score=45.70  Aligned_cols=43  Identities=26%  Similarity=0.475  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCC
Q psy17007         56 QLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLP   98 (165)
Q Consensus        56 q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~   98 (165)
                      .+..|+.+|....++...+...|+.+.+|+..||+.||..+..
T Consensus         9 d~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~   51 (56)
T PF11569_consen    9 DIQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ   51 (56)
T ss_dssp             --HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred             chHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence            3567999999999999999999999999999999999987644

>KOG0844|consensus

Probab=97.65  E-value=9.3e-06  Score=63.25  Aligned_cols=48  Identities=44%  Similarity=0.652  Sum_probs=44.8

Q ss_pred             ccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       116 ~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .-++.||-||.+|+-.||+.|.+..|.+.+.|++||..|+|.+..||-
T Consensus       180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKV  227 (408)
T KOG0844|consen  180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKV  227 (408)
T ss_pred             HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeeh
Confidence            446889999999999999999999999999999999999999998874

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=97.50  E-value=0.00011  Score=52.78  Aligned_cols=48  Identities=27%  Similarity=0.382  Sum_probs=43.2

Q ss_pred             ccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       116 ~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ...+.+.+-|.+|+..|++.|+.++||+..+|..|+..++|++.-||-
T Consensus        50 ~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqI   97 (156)
T COG5576          50 PPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQI   97 (156)
T ss_pred             cCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhh
Confidence            345567788999999999999999999999999999999999988873

>KOG0483|consensus

Probab=97.46  E-value=0.00011  Score=54.74  Aligned_cols=45  Identities=27%  Similarity=0.384  Sum_probs=41.9

Q ss_pred             ccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLF  162 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq  162 (165)
                      ..++.+||.+|...||+.|+.+.++....+..||..|||..+||.
T Consensus        51 ~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVa   95 (198)
T KOG0483|consen   51 KGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVA   95 (198)
T ss_pred             ccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHH
Confidence            445677999999999999999999999999999999999999996

>KOG3623|consensus

Probab=96.96  E-value=0.0015  Score=56.66  Aligned_cols=52  Identities=21%  Similarity=0.261  Sum_probs=47.0

Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCC
Q psy17007         57 LTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPH  108 (165)
Q Consensus        57 ~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~  108 (165)
                      +..|..+|..|..|+.++...+|..+||+.+.|+.||+++++.....+..+.
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps  619 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPS  619 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCcc
Confidence            7899999999999999999999999999999999999999999876654443

>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=96.96  E-value=0.00074  Score=37.26  Aligned_cols=26  Identities=35%  Similarity=0.339  Sum_probs=21.0

Q ss_pred             ccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        138 AQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       138 ~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .++||+.++++.||..+||+..||.-
T Consensus         7 ~nPYPs~~ek~~L~~~tgls~~Qi~~   32 (40)
T PF05920_consen    7 HNPYPSKEEKEELAKQTGLSRKQISN   32 (40)
T ss_dssp             TSGS--HHHHHHHHHHHTS-HHHHHH
T ss_pred             CCCCCCHHHHHHHHHHcCCCHHHHHH
Confidence            47999999999999999999999964

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

>KOG3802|consensus

Probab=96.80  E-value=0.0023  Score=51.95  Aligned_cols=47  Identities=30%  Similarity=0.332  Sum_probs=44.4

Q ss_pred             ccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007        116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLF  162 (165)
Q Consensus       116 ~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq  162 (165)
                      +.|++||-++...+..||+.|.+|+.|+..|.-.||.+|+|.++.|.
T Consensus       293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVR  339 (398)
T KOG3802|consen  293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVR  339 (398)
T ss_pred             cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEE
Confidence            77889999999999999999999999999999999999999998774

>KOG0847|consensus

Probab=96.71  E-value=0.0008  Score=50.35  Aligned_cols=44  Identities=36%  Similarity=0.690  Sum_probs=41.1

Q ss_pred             ccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        120 ARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       120 ~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .+-.|+..|+..|++.|+..+|+..+++.+||..+|+++.||+-
T Consensus       170 srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkV  213 (288)
T KOG0847|consen  170 SRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKV  213 (288)
T ss_pred             cCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHH
Confidence            45679999999999999999999999999999999999999974

>KOG0773|consensus

Probab=96.69  E-value=0.0019  Score=52.14  Aligned_cols=57  Identities=23%  Similarity=0.253  Sum_probs=48.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcc
Q psy17007         45 RRKARTVFSDHQLTGLEKRFEA---QRYLSTPERVELATALQLSETQVKTWFQNRLPFGS  101 (165)
Q Consensus        45 ~rr~R~~~s~~q~~~Le~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~  101 (165)
                      ..|.+..+......+|+.+...   .+||+..+...|+..+||+..||.+||-|.|.+..
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w  298 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLW  298 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccC
Confidence            4455668899999999987543   58999999999999999999999999999887764

>KOG4577|consensus

Probab=96.22  E-value=0.0028  Score=49.40  Aligned_cols=48  Identities=17%  Similarity=0.241  Sum_probs=44.2

Q ss_pred             ccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       116 ~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ..++.||.+|..|++.|..++...+-|..+.|++|+.++||.-+.||-
T Consensus       166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQV  213 (383)
T KOG4577|consen  166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQV  213 (383)
T ss_pred             ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhh
Confidence            456789999999999999999999999999999999999999988873

>KOG2252|consensus

Probab=96.10  E-value=0.0088  Score=50.44  Aligned_cols=50  Identities=22%  Similarity=0.304  Sum_probs=44.7

Q ss_pred             cccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhhc
Q psy17007        115 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFYV  164 (165)
Q Consensus       115 ~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~~  164 (165)
                      ...++.|.+||+.|...|...|..+++|+.+..+.|+.+|||....|.-|
T Consensus       418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~Nf  467 (558)
T KOG2252|consen  418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINF  467 (558)
T ss_pred             ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHH
Confidence            34556699999999999999999999999999999999999999887643

>KOG0774|consensus

Probab=96.00  E-value=0.0049  Score=47.39  Aligned_cols=46  Identities=26%  Similarity=0.332  Sum_probs=41.3

Q ss_pred             cccccccccccchhhhhhhcc---ccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007        117 RRKARTVFSDHQLTGLEKRFE---AQRYLSTPERVELATALQLSETQLF  162 (165)
Q Consensus       117 ~rr~rt~ft~~Q~~~Le~~F~---~~~yp~~~~r~~La~~lgl~~~qVq  162 (165)
                      .+|+|..|+..-.+.|...|.   .|+||+.+++++||+++|++..||-
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvs  236 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVS  236 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhc
Confidence            457788899999999999995   6999999999999999999999874

>KOG0775|consensus

Probab=95.09  E-value=0.018  Score=44.66  Aligned_cols=37  Identities=30%  Similarity=0.294  Sum_probs=33.2

Q ss_pred             ccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007        126 DHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLF  162 (165)
Q Consensus       126 ~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq  162 (165)
                      +.-+..|.+.|..++||+..++.+||..+||+..||-
T Consensus       185 ekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVs  221 (304)
T KOG0775|consen  185 EKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVS  221 (304)
T ss_pred             HhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhh
Confidence            3446789999999999999999999999999999983

>KOG1146|consensus

Probab=94.97  E-value=0.11  Score=48.24  Aligned_cols=119  Identities=19%  Similarity=0.113  Sum_probs=95.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCC--------------
Q psy17007         43 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPH--------------  108 (165)
Q Consensus        43 ~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~--------------  108 (165)
                      -+.++.+..+-.++...|-.+|-.+..|+......|......+.+++.+||.|-+.+.+... ..+              
T Consensus       703 ~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~-v~g~~~~c~l~~y~t~~  781 (1406)
T KOG1146|consen  703 PRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ-VPGDVPSCKLKPYATNT  781 (1406)
T ss_pred             cccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc-ccCCCCcceeccccccc
Confidence            34567788888999999999999999999999999999999999999999999765432211 000              


Q ss_pred             --------------------------------------------------------------------------------
Q psy17007        109 --------------------------------------------------------------------------------  108 (165)
Q Consensus       109 --------------------------------------------------------------------------------  108 (165)
                                                                                                      
T Consensus       782 kanfqlh~Ktdkh~qk~~~~~hikegg~a~~~~t~~la~~~~P~~l~cn~cd~~Tns~~~L~lh~~~~~he~~~~~~ks~  861 (1406)
T KOG1146|consen  782 KANFQLHNKTDKHVQKYQLRAHIKEGGPANEYPTKTLASGPNPVHLKCNACDTPTNSPEPLLLHTPPSEHEGPEEIYKSL  861 (1406)
T ss_pred             chhhhhhcccchhhhccchhhhhhccCCccCCcchhhhcCCCccccccccccCCCCCccccccCCCCCccccccccchhH
Confidence                                                                                            


Q ss_pred             ---------------------------------ccCccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcC
Q psy17007        109 ---------------------------------ELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQ  155 (165)
Q Consensus       109 ---------------------------------~~~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lg  155 (165)
                                                       ......+..+..++.+++.|+..|...|..-.|+...+-+.|-..++
T Consensus       862 ~~l~~~ls~~~~s~~~as~~~s~~~~~~~~s~~s~~~~~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~  941 (1406)
T KOG1146|consen  862 LSLACSLSAGDLSDSSASSLASPESPGGGPSGGSGVPDGMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIG  941 (1406)
T ss_pred             HHHHHHhhccccccccccccccccCCCCCCCCCcccchhhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhccccc
Confidence                                             00000123346789999999999999999999999999999999999


Q ss_pred             CChhhhh
Q psy17007        156 LSETQLF  162 (165)
Q Consensus       156 l~~~qVq  162 (165)
                      +..+.|+
T Consensus       942 ~~~~~i~  948 (1406)
T KOG1146|consen  942 LPKRVIQ  948 (1406)
T ss_pred             CCcchhH
Confidence            9998775

>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=94.58  E-value=0.077  Score=30.95  Aligned_cols=46  Identities=20%  Similarity=0.356  Sum_probs=35.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccC
Q psy17007         46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR   96 (165)
Q Consensus        46 rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nr   96 (165)
                      ++.|..+|-++...+-..++...     ....||..+|++..+|..|..|+
T Consensus         1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k   46 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK   46 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred             CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence            46788999999888888887776     47788999999999999999885

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.

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=92.38  E-value=0.064  Score=31.39  Aligned_cols=39  Identities=23%  Similarity=0.248  Sum_probs=32.4

Q ss_pred             ccccchhhhhhhccccCC--CCHHHHHHHHHHcCCChhhhh
Q psy17007        124 FSDHQLTGLEKRFEAQRY--LSTPERVELATALQLSETQLF  162 (165)
Q Consensus       124 ft~~Q~~~Le~~F~~~~y--p~~~~r~~La~~lgl~~~qVq  162 (165)
                      +|+.|+..|..+++.+.|  |-.-.-.+||..+|++..-|.
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~   41 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVS   41 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHH
Confidence            478899999999999887  555566899999999987654

This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.

>COG3413 Predicted DNA binding protein [General function prediction only]

Probab=85.17  E-value=0.4  Score=36.07  Aligned_cols=41  Identities=22%  Similarity=0.237  Sum_probs=34.6

Q ss_pred             cccccchhhhhhhccccCC--CCHHHHHHHHHHcCCChhhhhh
Q psy17007        123 VFSDHQLTGLEKRFEAQRY--LSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       123 ~ft~~Q~~~Le~~F~~~~y--p~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .+|+.|+..|..+|..+.|  |-...-.+||+++|+++.-+..
T Consensus       155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~e  197 (215)
T COG3413         155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSE  197 (215)
T ss_pred             cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHH
Confidence            6999999999999999877  5555668999999999876543

>KOG1168|consensus

Probab=84.98  E-value=0.42  Score=37.61  Aligned_cols=47  Identities=21%  Similarity=0.264  Sum_probs=40.6

Q ss_pred             ccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007        116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLF  162 (165)
Q Consensus       116 ~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq  162 (165)
                      ..+|+||-+-..+-..||..|...+-|+.+..+.+|.+|+|.+..|.
T Consensus       308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVR  354 (385)
T KOG1168|consen  308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVR  354 (385)
T ss_pred             ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEE
Confidence            34567888888888999999999999999999999999999876553

>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition

Probab=84.84  E-value=1.8  Score=26.52  Aligned_cols=47  Identities=13%  Similarity=0.179  Sum_probs=31.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCC
Q psy17007         47 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRL   97 (165)
Q Consensus        47 r~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr   97 (165)
                      +.|..||.++...+-..+....    .....+|..+||+...+..|-..-+
T Consensus         2 ~~r~~ys~e~K~~~v~~~~~~g----~sv~~va~~~gi~~~~l~~W~~~~~   48 (76)
T PF01527_consen    2 RKRRRYSPEFKLQAVREYLESG----ESVSEVAREYGISPSTLYNWRKQYR   48 (76)
T ss_dssp             -SS----HHHHHHHHHHHHHHH----CHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCC----CceEeeecccccccccccHHHHHHh
Confidence            4567899988887777663322    3577889999999999999986543

This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.

>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=84.27  E-value=0.49  Score=27.49  Aligned_cols=41  Identities=15%  Similarity=0.263  Sum_probs=30.0

Q ss_pred             cccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhhc
Q psy17007        119 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFYV  164 (165)
Q Consensus       119 r~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~~  164 (165)
                      +.|..+|-++-..+-+.++.+.     ...+||..+|+...+|..|
T Consensus         2 rkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I   42 (53)
T PF04218_consen    2 RKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTI   42 (53)
T ss_dssp             SSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHH
Confidence            4567788888888888888886     6789999999999999765

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.

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=84.24  E-value=1.9  Score=25.15  Aligned_cols=39  Identities=26%  Similarity=0.286  Sum_probs=31.7

Q ss_pred             CCHHHHHHHHHHHHhcCC--CCHHHHHHHHHHhccchhhhh
Q psy17007         52 FSDHQLTGLEKRFEAQRY--LSTPERVELATALQLSETQVK   90 (165)
Q Consensus        52 ~s~~q~~~Le~~f~~~~~--p~~~~~~~la~~l~l~~~~V~   90 (165)
                      +|+.|.++|...+..--|  |-.....+||..+|++..-|.
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~   41 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVS   41 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHH
Confidence            578999999999887554  667778899999999886654

This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.

>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators

Probab=83.31  E-value=4.1  Score=24.38  Aligned_cols=64  Identities=14%  Similarity=0.229  Sum_probs=41.1

Q ss_pred             HHHHHHHhccchhhhhhhhccCCCCccccCCCCCccCccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHc
Q psy17007         75 RVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATAL  154 (165)
Q Consensus        75 ~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l  154 (165)
                      ..++|..+|++...++.|-++-.-..      +        +.......|+.+++..|..             ..-....
T Consensus         3 i~evA~~~gvs~~tlR~~~~~g~l~~------~--------~~~~g~R~y~~~~l~~l~~-------------i~~l~~~   55 (67)
T cd04764           3 IKEVSEIIGVKPHTLRYYEKEFNLYI------P--------RTENGRRYYTDEDIELLKK-------------IKTLLEK   55 (67)
T ss_pred             HHHHHHHHCcCHHHHHHHHHhcCCCC------C--------CCCCCceeeCHHHHHHHHH-------------HHHHHHC
Confidence            45789999999999999976421110      0        1122344588888777633             3334458


Q ss_pred             CCChhhhhhcC
Q psy17007        155 QLSETQLFYVI  165 (165)
Q Consensus       155 gl~~~qVq~~~  165 (165)
                      |++-.+|+-+|
T Consensus        56 g~~l~~i~~~l   66 (67)
T cd04764          56 GLSIKEIKEIL   66 (67)
T ss_pred             CCCHHHHHHHh
Confidence            88888887654

Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.

>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition

Probab=81.19  E-value=11  Score=25.58  Aligned_cols=87  Identities=23%  Similarity=0.261  Sum_probs=49.7

Q ss_pred             CHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCCccCccccccccccccccccchhhh
Q psy17007         53 SDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGL  132 (165)
Q Consensus        53 s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~~L  132 (165)
                      |-+-...+-.++....     ...++|..++++..-|..|++ +......... +        +.+  + .+.   ...|
T Consensus         4 S~DlR~rVl~~~~~g~-----s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~~k-~--------r~~--~-Kid---~~~L   62 (119)
T PF01710_consen    4 SLDLRQRVLAYIEKGK-----SIREAAKRFGVSRNTVYRWLK-RKETGDLEPK-P--------RGR--K-KID---RDEL   62 (119)
T ss_pred             CHHHHHHHHHHHHccc-----hHHHHHHHhCcHHHHHHHHHH-hccccccccc-c--------ccc--c-ccc---HHHH
Confidence            3344444445555433     355678999999999999998 4333211000 0        011  1 222   3456


Q ss_pred             hhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        133 EKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       133 e~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ....+.++-.+..   +||..+|++..-|-+
T Consensus        63 ~~~v~~~pd~tl~---Ela~~l~Vs~~ti~~   90 (119)
T PF01710_consen   63 KALVEENPDATLR---ELAERLGVSPSTIWR   90 (119)
T ss_pred             HHHHHHCCCcCHH---HHHHHcCCCHHHHHH
Confidence            6666666655443   567889998776644

This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].

>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA

Probab=80.93  E-value=5.6  Score=23.66  Aligned_cols=64  Identities=14%  Similarity=0.176  Sum_probs=38.9

Q ss_pred             HHHHHHHhccchhhhhhhhccCCCCccccCCCCCccCccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHc
Q psy17007         75 RVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATAL  154 (165)
Q Consensus        75 ~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l  154 (165)
                      ..++|..+|++...++.|-+.-   ..          ..+.+.......|+.+++..|..             .....+.
T Consensus         3 ~~eva~~~gvs~~tlr~w~~~~---g~----------~~~~r~~~~~r~yt~~~v~~l~~-------------i~~l~~~   56 (68)
T cd01104           3 IGAVARLTGVSPDTLRAWERRY---GL----------PAPQRTDGGHRLYSEADVARLRL-------------IRRLTSE   56 (68)
T ss_pred             HHHHHHHHCcCHHHHHHHHHhC---CC----------CCCCcCCCCCeecCHHHHHHHHH-------------HHHHHHC
Confidence            3578999999999999998531   00          00011112334588888777743             3334457


Q ss_pred             CCChhhhhhc
Q psy17007        155 QLSETQLFYV  164 (165)
Q Consensus       155 gl~~~qVq~~  164 (165)
                      |++-.+|+-+
T Consensus        57 g~~l~~i~~~   66 (68)
T cd01104          57 GVRISQAAAL   66 (68)
T ss_pred             CCCHHHHHHH
Confidence            7777776643

Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i

>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators

Probab=80.77  E-value=6  Score=23.72  Aligned_cols=63  Identities=11%  Similarity=0.128  Sum_probs=39.9

Q ss_pred             HHHHHHHhccchhhhhhhhccC-CCCccccCCCCCccCccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHH
Q psy17007         75 RVELATALQLSETQVKTWFQNR-LPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATA  153 (165)
Q Consensus        75 ~~~la~~l~l~~~~V~~WF~nr-r~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~  153 (165)
                      ..++|..+|++...++.|...- .-.              +.+.......||.+++..|..             ......
T Consensus         3 i~e~A~~~gVs~~tlr~ye~~~gl~~--------------~~r~~~g~R~yt~~di~~l~~-------------i~~l~~   55 (68)
T cd04763           3 IGEVALLTGIKPHVLRAWEREFGLLK--------------PQRSDGGHRLFNDADIDRILE-------------IKRWID   55 (68)
T ss_pred             HHHHHHHHCcCHHHHHHHHHhcCCCC--------------CCcCCCCCcccCHHHHHHHHH-------------HHHHHH
Confidence            4578999999999999997531 100              011122334688888777733             333455


Q ss_pred             cCCChhhhhhc
Q psy17007        154 LQLSETQLFYV  164 (165)
Q Consensus       154 lgl~~~qVq~~  164 (165)
                      .|++-.+|+-+
T Consensus        56 ~g~~l~~i~~~   66 (68)
T cd04763          56 NGVQVSKVKKL   66 (68)
T ss_pred             cCCCHHHHHHH
Confidence            88888877654

Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	165
2dmt_A	80	Solution Structure Of The Homeobox Domain Of Homeob		3e-16
2dmt_A	80	Solution Structure Of The Homeobox Domain Of Homeob		3e-11
3rkq_A	58	Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Lengt		2e-12
3rkq_A	58	Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Lengt		2e-07
2djn_A	70	The Solution Structure Of The Homeobox Domain Of Hu		4e-12
2djn_A	70	The Solution Structure Of The Homeobox Domain Of Hu		2e-07
2e1o_A	70	Solution Structure Of Rsgi Ruh-028, A Homeobox Doma		3e-11
2e1o_A	70	Solution Structure Of Rsgi Ruh-028, A Homeobox Doma		6e-06
1ftt_A	68	Thyroid Transcription Factor 1 Homeodomain (Rattus		2e-10
1ftt_A	68	Thyroid Transcription Factor 1 Homeodomain (Rattus		4e-06
3a01_A	93	Crystal Structure Of Aristaless And Clawless Homeod		3e-10
3a01_A	93	Crystal Structure Of Aristaless And Clawless Homeod		9e-05
2m34_A	71	Nmr Structure Of The Homeodomain Transcription Fact		5e-10
2m34_A	71	Nmr Structure Of The Homeodomain Transcription Fact		3e-05
1ig7_A	58	Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58		7e-10
1ig7_A	58	Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58		6e-05
1b72_A	97	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		9e-10
1b72_A	97	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		5e-05
1nk2_P	77	VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES		1e-09
1nk2_P	77	VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES		2e-05
2vi6_A	62	Crystal Structure Of The Nanog Homeodomain Length =		1e-09
2vi6_A	62	Crystal Structure Of The Nanog Homeodomain Length =		9e-05
1qry_A	80	Homeobox Protein Vnd (Ventral Nervous System Defect		4e-09
1qry_A	80	Homeobox Protein Vnd (Ventral Nervous System Defect		7e-05
3a03_A	56	Crystal Structure Of Hox11l1 Homeodomain Length = 5		6e-09
2kt0_A	84	Solution Structure Of Human Stem Cell Transcription		7e-09
2kt0_A	84	Solution Structure Of Human Stem Cell Transcription		4e-04
2l9r_A	69	Solution Nmr Structure Of Homeobox Domain Of Homeob		1e-08
2l9r_A	69	Solution Nmr Structure Of Homeobox Domain Of Homeob		9e-04
2h1k_A	63	Crystal Structure Of The Pdx1 Homeodomain In Comple		3e-08
1jgg_A	60	Even-Skipped Homeodomain Complexed To At-Rich Dna L		3e-08
1b8i_A	81	Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX		8e-08
9ant_A	62	Antennapedia Homeodomain-Dna Complex Length = 62		1e-07
1ahd_P	68	Determination Of The Nmr Solution Structure Of An A		1e-07
2r5y_A	88	Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO		2e-07
1hom_A	68	Determination Of The Three-Dimensional Structure Of		2e-07
1ftz_A	70	Nuclear Magnetic Resonance Solution Structure Of Th		3e-07
1hdd_C	61	Crystal Structure Of An Engrailed Homeodomain-Dna C		1e-06
3hdd_A	60	Engrailed Homeodomain Dna Complex Length = 60		1e-06
1enh_A	54	Structural Studies Of The Engrailed Homeodomain Len		1e-06
1p7i_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		1e-06
1p7j_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		1e-06
1puf_A	77	Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo		2e-06
1san_A	62	The Des(1-6)antennapedia Homeodomain: Comparison Of		2e-06
2hdd_A	61	Engrailed Homeodomain Q50k Variant Dna Complex Leng		2e-06
2hos_A	63	Phage-selected Homeodomain Bound To Unmodified Dna		3e-06
2lp0_A	60	The Solution Structure Of Homeodomain-Protein Compl		4e-06
1zq3_P	68	Nmr Solution Structure Of The Bicoid Homeodomain Bo		4e-06
1ztr_A	61	Solution Structure Of Engrailed Homeodomain L16a Mu		5e-06
1du0_A	57	Engrailed Homeodomain Q50a Variant Dna Complex Leng		5e-06
2dmu_A	70	Solution Structure Of The Homeobox Domain Of Homeob		6e-06
2cra_A	70	Solution Structure Of The Homeobox Domain Of Human		7e-06
1fjl_A	81	Homeodomain From The Drosophila Paired Protein Boun		2e-05
2m0c_A	75	Solution Nmr Structure Of Homeobox Domain Of Human		4e-05
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		2e-04
2l7f_P	68	Solution Structure Of The Pitx2 Homeodomain Length		2e-04
2dms_A	80	Solution Structure Of The Homeobox Domain Of Homeob		2e-04
3cmy_A	61	Structure Of A Homeodomain In Complex With Dna Leng		3e-04
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		6e-04
2l7z_A	73	Nmr Structure Of A13 Homedomain Length = 73		6e-04
2cue_A	80	Solution Structure Of The Homeobox Domain Of The Hu		7e-04
2ld5_A	67	Solution Nmr-Derived Complex Structure Of Hoxa13 Dn		8e-04

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

Iteration: 1
 Score = 81.3 bits (199), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 37/60 (61%), Positives = 50/60 (83%)
Query: 37 ELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          E G+K  + R++RTVF++ QL GLEKRFE Q+YLSTP+R++LA +L LS+ QVKTW+QNR
Sbjct: 9  EPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNR 68

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 30/53 (56%), Positives = 43/53 (81%)
Query: 109 ELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
           E G+K  + R++RTVF++ QL GLEKRFE Q+YLSTP+R++LA +L LS+ Q+
Sbjct: 9   EPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQV 61

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 32/52 (61%), Positives = 40/52 (76%)
Query: 45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          RRK R +FS  Q+  LE+RF+ QRYLS PER +LA+ L+L+ TQVK WFQNR
Sbjct: 2  RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNR 53

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/45 (55%), Positives = 34/45 (75%)
Query: 117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
           RRK R +FS  Q+  LE+RF+ QRYLS PER +LA+ L+L+ TQ+
Sbjct: 2   RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQV 46

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

Iteration: 1
 Score = 67.4 bits (163), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 30/58 (51%), Positives = 41/58 (70%)
Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          GS     RK RT++S  QL  L++RF+  +YL+ PER ELA +L L++TQVK WFQN+
Sbjct: 1  GSSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNK 58

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/51 (47%), Positives = 35/51 (68%)
Query: 111 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
           GS     RK RT++S  QL  L++RF+  +YL+ PER ELA +L L++TQ+
Sbjct: 1   GSSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQV 51

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 31/45 (68%), Positives = 34/45 (75%)
Query: 52 FSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          FS+ Q   LEK+FE Q+YLS PER  LA  LQLSE QVKTWFQNR
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNR 58

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 23/38 (60%), Positives = 27/38 (71%)
Query: 124 FSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
           FS+ Q   LEK+FE Q+YLS PER  LA  LQLSE Q+
Sbjct: 14  FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQV 51

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

Iteration: 1
 Score = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 29/51 (56%), Positives = 37/51 (72%)
Query: 45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQN 95
          RRK R +FS  Q+  LE+RF+ Q+YLS PER  LA+ + L+ TQVK WFQN
Sbjct: 2  RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQN 52

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 23/45 (51%), Positives = 32/45 (71%)
Query: 117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
           RRK R +FS  Q+  LE+RF+ Q+YLS PER  LA+ + L+ TQ+
Sbjct: 2   RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQV 46

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

Iteration: 1
 Score = 60.8 bits (146), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 39/53 (73%)
Query: 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          +R+K RT F+  Q+  LEKRF  Q+YL++ ER  LA  L++++ QVKTWFQNR
Sbjct: 16 KRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNR 68

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 20/46 (43%), Positives = 32/46 (69%)
Query: 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
           +R+K RT F+  Q+  LEKRF  Q+YL++ ER  LA  L++++ Q+
Sbjct: 16  KRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQV 61

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

Iteration: 1
 Score = 60.5 bits (145), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 29/51 (56%), Positives = 36/51 (70%)
Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          R+ RT F+  QL  LEK F  ++YLS  ER ++A AL+LSE QVK WFQNR
Sbjct: 8  RRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNR 58

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 22/44 (50%), Positives = 30/44 (68%)
Query: 118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
           R+ RT F+  QL  LEK F  ++YLS  ER ++A AL+LSE Q+
Sbjct: 8   RRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQV 51

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

Iteration: 1
 Score = 59.7 bits (143), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 28/51 (54%), Positives = 37/51 (72%)
Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          RK RT F+  QL  LE++F  ++YLS  ER E +++L L+ETQVK WFQNR
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNR 51

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/44 (47%), Positives = 31/44 (70%)
Query: 118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
           RK RT F+  QL  LE++F  ++YLS  ER E +++L L+ETQ+
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQV 44

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

Iteration: 1
 Score = 59.3 bits (142), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 29/48 (60%), Positives = 34/48 (70%)
Query: 49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          RT F+  QLT LEK F   +YLS   RVE+A  L+L+ETQVK WFQNR
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNR 85

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/41 (53%), Positives = 28/41 (68%)
Query: 121 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
           RT F+  QLT LEK F   +YLS   RVE+A  L+L+ETQ+
Sbjct: 38  RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQV 78

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

Iteration: 1
 Score = 59.3 bits (142), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/52 (53%), Positives = 37/52 (71%)
Query: 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQN 95
          ++RK R +F+  Q   LE+RF  QRYLS PER  LA+ ++L+ TQVK WFQN
Sbjct: 8  KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQN 59

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/46 (47%), Positives = 32/46 (69%)
Query: 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
           ++RK R +F+  Q   LE+RF  QRYLS PER  LA+ ++L+ TQ+
Sbjct: 8   KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQV 53

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/52 (53%), Positives = 37/52 (71%)
Query: 45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          ++K RTVFS  QL  L+ RF+ Q+YLS  +  EL++ L LS  QVKTWFQN+
Sbjct: 3  KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQ 54

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 21/45 (46%), Positives = 30/45 (66%)
Query: 117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
           ++K RTVFS  QL  L+ RF+ Q+YLS  +  EL++ L LS  Q+
Sbjct: 3   KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQV 47

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 27/52 (51%), Positives = 36/52 (69%)
Query: 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQN 95
          ++RK R +F+  Q   LE+RF  QRYLS PER  L + ++L+ TQVK WFQN
Sbjct: 11 KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQN 62

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 31/46 (67%)
Query: 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
           ++RK R +F+  Q   LE+RF  QRYLS PER  L + ++L+ TQ+
Sbjct: 11  KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQV 56

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 26/47 (55%), Positives = 35/47 (74%)
Query: 50 TVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          T FS  Q+  LE+RF  Q+YL++ ER  LA AL++++ QVKTWFQNR
Sbjct: 2  TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNR 48

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 36/53 (67%)
Query: 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          +++K RTVFS  QL  L  RF+ Q+YLS  +  EL+  L LS  QVKTWFQN+
Sbjct: 21 KKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQ 73

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%)
Query: 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
           +++K RTVFS  QL  L  RF+ Q+YLS  +  EL+  L LS  Q+
Sbjct: 21  KKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQV 66

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/41 (60%), Positives = 31/41 (75%)
Query: 56 QLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          Q+  LE++F  Q+YLS PER  LA  L+L+ETQVK WFQNR
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNR 55

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 18/34 (52%), Positives = 25/34 (73%)
Query: 128 QLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
           Q+  LE++F  Q+YLS PER  LA  L+L+ETQ+
Sbjct: 15  QVIELERKFSHQKYLSAPERAHLAKNLKLTETQV 48

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 25/51 (49%), Positives = 33/51 (64%)
Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          ++ RT ++  QL  LEK F   +Y+S P RVELA  L L+E  +K WFQNR
Sbjct: 4  KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNR 54

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 26/51 (50%), Positives = 32/51 (62%)
Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          R+ RT F+  QL  LEK F  + Y+S P R ELA  L L E+ +K WFQNR
Sbjct: 2  RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNR 52

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 24/52 (46%), Positives = 33/52 (63%)
Query: 45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          RR+ R  ++ +Q   LEK F    YL+   R+E+A AL L+E Q+K WFQNR
Sbjct: 20 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNR 71

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/52 (46%), Positives = 34/52 (65%)
Query: 45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          R++ R  ++ +Q   LEK F   RYL+   R+E+A AL L+E Q+K WFQNR
Sbjct: 3  RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNR 54

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/52 (46%), Positives = 34/52 (65%)
Query: 45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          R++ R  ++ +Q   LEK F   RYL+   R+E+A AL L+E Q+K WFQNR
Sbjct: 2  RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNR 53

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/51 (47%), Positives = 34/51 (66%)
Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          ++ RT ++ +Q   LEK F   RYL+   R+E+A AL L+E Q+K WFQNR
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNR 79

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/52 (46%), Positives = 34/52 (65%)
Query: 45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          R++ R  ++ +Q   LEK F   RYL+   R+E+A AL L+E Q+K WFQNR
Sbjct: 2  RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 53

>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 = 51.2 bits (121), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 22/51 (43%), Positives = 33/51 (64%)
Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          ++ R  ++ +Q   LEK F   RY++   R+++A AL LSE Q+K WFQNR
Sbjct: 4  KRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNR 54

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/51 (43%), Positives = 33/51 (64%)
Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          ++ RT FS  QL  L++ F   RYL+   R +L++ L L+E Q+K WFQN+
Sbjct: 4  KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNK 54

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/51 (43%), Positives = 33/51 (64%)
Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          ++ RT FS  QL  L++ F   RYL+   R +L++ L L+E Q+K WFQN+
Sbjct: 2  KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNK 52

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 31/48 (64%)
Query: 49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          RT FS  QL  L++ F   RYL+   R +L++ L L+E Q+K WFQN+
Sbjct: 3  RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNK 50

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/50 (44%), Positives = 32/50 (64%)
Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQN 95
          ++ RT FS  QL  L++ F   RYL+   R +L++ L L+E Q+K WFQN
Sbjct: 2  KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQN 51

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/50 (44%), Positives = 32/50 (64%)
Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQN 95
          ++ RT FS  QL  L++ F   RYL+   R +L++ L L+E Q+K WFQN
Sbjct: 2  KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQN 51

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/51 (49%), Positives = 30/51 (58%)
Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          RK R  ++ HQ   LEK F    YL+   R E+A  L L+E QVK WFQNR
Sbjct: 14 RKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNR 64

>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 = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/46 (47%), Positives = 30/46 (65%)
Query: 51 VFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
           ++ +Q   LEK F   RYL+   R+E+A AL L+E Q+K WFQNR
Sbjct: 2  TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNR 47

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 31/48 (64%)
Query: 49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          RT FS  QL  L++ F   RYL+   R +L++ L L+E Q+K WF+N+
Sbjct: 7  RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNK 54

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/50 (44%), Positives = 32/50 (64%)
Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQN 95
          ++ RT FS  QL  L++ F   RYL+   R +L++ L L+E QVK WF+N
Sbjct: 5  KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKN 54

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 24/51 (47%), Positives = 30/51 (58%)
Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          RK R  ++ +Q   LEK F    YL+   R E+A  L L+E QVK WFQNR
Sbjct: 2  RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNR 52

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 22/51 (43%), Positives = 30/51 (58%)
Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          R+ RT F+  Q+  LE+ F   RYL+ P   +L+  L L   QVK WF+NR
Sbjct: 3  RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNR 53

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 30/48 (62%)
Query: 49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          RT FS  QL   ++ F   RYL+   R +L++ L L+E Q+K WFQN+
Sbjct: 7  RTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNK 54

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 30/48 (62%)
Query: 49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          RT FS  QL  L++ F   RYL+   R +L++ L L+E Q+K WF N+
Sbjct: 3  RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANK 50

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 33/58 (56%)
Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          GS     R+ RT+F+D QL  LE  F+  +Y     R +LA  + L E +V+ WF+NR
Sbjct: 1  GSSGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNR 58

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 34/58 (58%)
Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          GS     RK R  +S  QL  LE+ + A ++++  +R +++ A  LSE Q+  WFQNR
Sbjct: 1  GSSGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNR 58

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/53 (43%), Positives = 33/53 (62%)
Query: 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          ++R++RT FS  QL  LE+ FE  +Y     R ELA    L+E +++ WFQNR
Sbjct: 17 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNR 69

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 23/57 (40%), Positives = 33/57 (57%)
Query: 40 SKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          S   ++R+ RT F+ +QL  LEK F+   Y     R +LA    L+E +V+ WFQNR
Sbjct: 4  SNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNR 60

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/53 (41%), Positives = 31/53 (58%)
Query: 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          ++R+ RT F+  QL  LEK F    Y     R ELA  + L+E +++ WFQNR
Sbjct: 5  KQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNR 57

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 29/51 (56%)
Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          R+ RT F+  QL  LE  F+  RY     R E+A    L+E +V+ WF+NR
Sbjct: 4  RRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNR 54

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 31/58 (53%)
Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          GS     R+ RT F+  QL  LE  F   RY     R E+A  + L E++V+ WF+NR
Sbjct: 1  GSSGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNR 58

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/51 (43%), Positives = 30/51 (58%)
Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          R++RT F+  QL  LE+ FE   Y     R ELA   +L+E +V+ WF NR
Sbjct: 3  RRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNR 53

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 27/48 (56%)
Query: 49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          RT F+  QL  LEK F    Y     R ELA  + L+E +++ WFQNR
Sbjct: 3  RTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNR 50

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 18/51 (35%), Positives = 29/51 (56%)
Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          RK R  ++  QL  LE+ +   ++++  +R  ++    LSE QV  WFQNR
Sbjct: 8  RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNR 58

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 21/58 (36%), Positives = 29/58 (50%)
Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          GS     ++ RT F+  Q+  LEK FE   Y     R  LA  + L E +++ WF NR
Sbjct: 1  GSSGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNR 58

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 18/51 (35%), Positives = 29/51 (56%)
Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          RK R  ++  QL  LE+ +   ++++  +R  ++    LSE QV  WFQNR
Sbjct: 2  RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNR 52

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	165
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	4e-28
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	1e-19
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	2e-27
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	4e-19
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	5e-27
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	2e-18
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	6e-27
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	6e-19
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	9e-27
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	2e-18
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	1e-26
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	2e-18
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	2e-26
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	4e-18
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	3e-26
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	6e-18
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	6e-26
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	1e-17
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	6e-26
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	7e-18
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	1e-25
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	1e-17
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	4e-24
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	1e-15
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	1e-20
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	4e-13
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	6e-20
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	1e-11
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	3e-18
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	8e-11
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	4e-18
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	7e-11
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	1e-17
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	2e-10
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	3e-17
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	3e-10
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	2e-16
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	2e-09
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	5e-16
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	7e-09
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	6e-16
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	6e-09
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	7e-16
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	7e-09
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	2e-15
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	6e-09
1e3o_C	160	Octamer-binding transcription factor 1; transcript	3e-15
1e3o_C	160	Octamer-binding transcription factor 1; transcript	4e-08
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	8e-15
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	7e-08
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	8e-15
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	1e-08
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	1e-14
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	1e-07
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	5e-14
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	2e-07
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	6e-14
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	7e-07
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	2e-13
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	9e-07
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	2e-12
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	1e-05
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	3e-12
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	5e-06
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	7e-12
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	6e-07
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	1e-11
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	2e-05
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	2e-11
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	1e-05
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	3e-11
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	2e-05
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	3e-11
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	2e-05
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	6e-11
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	1e-04
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	1e-10
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	6e-04
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	1e-10
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	1e-04
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	2e-10
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	5e-05
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	2e-10
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	5e-04
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	2e-10
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	1e-04
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	5e-10
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	4e-04
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	6e-10
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	3e-04
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	6e-10
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	2e-04
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	2e-09
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	3e-09
1uhs_A	72	HOP, homeodomain only protein; structural genomics	7e-09
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	2e-08
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	1e-07
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	3e-05
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	1e-07
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	5e-07
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	7e-07
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	7e-07
1lfb_A	99	Liver transcription factor (LFB1); transcription r	2e-05
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	4e-05

>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 = 98.7 bits (246), Expect = 4e-28
 Identities = 38/65 (58%), Positives = 52/65 (80%)

Query: 32 STSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKT 91
           +S  E G+K  + R++RTVF++ QL GLEKRFE Q+YLSTP+R++LA +L LS+ QVKT
Sbjct: 4  GSSGGEPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKT 63

Query: 92 WFQNR 96
          W+QNR
Sbjct: 64 WYQNR 68

>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 = 77.5 bits (191), Expect = 1e-19
 Identities = 31/57 (54%), Positives = 44/57 (77%)

Query: 104 STSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
            +S  E G+K  + R++RTVF++ QL GLEKRFE Q+YLSTP+R++LA +L LS+ Q
Sbjct: 4   GSSGGEPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQ 60

>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic development, complex (homeodomain/DNA); HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P* 1vnd_A 1qry_A Length = 77

 Score = 97.1 bits (242), Expect = 2e-27
 Identities = 28/58 (48%), Positives = 37/58 (63%)

Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
               ++RK R +F+  Q   LE+RF  QRYLS PER  LA+ ++L+ TQVK WFQN 
Sbjct: 3  DGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNH 60

>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 = 76.0 bits (187), Expect = 4e-19
 Identities = 22/50 (44%), Positives = 31/50 (62%)

Query: 111 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
                ++RK R +F+  Q   LE+RF  QRYLS PER  LA+ ++L+ TQ
Sbjct: 3   DGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQ 52

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

 Score = 95.4 bits (238), Expect = 5e-27
 Identities = 32/52 (61%), Positives = 40/52 (76%)

Query: 45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          RRK R +FS  Q+  LE+RF+ QRYLS PER +LA+ L+L+ TQVK WFQNR
Sbjct: 2  RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNR 53

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

 Score = 73.8 bits (182), Expect = 2e-18
 Identities = 25/44 (56%), Positives = 33/44 (75%)

Query: 117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           RRK R +FS  Q+  LE+RF+ QRYLS PER +LA+ L+L+ TQ
Sbjct: 2   RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQ 45

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

 Score = 95.5 bits (238), Expect = 6e-27
 Identities = 30/58 (51%), Positives = 41/58 (70%)

Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          GS     RK RT++S  QL  L++RF+  +YL+ PER ELA +L L++TQVK WFQN+
Sbjct: 1  GSSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNK 58

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

 Score = 75.1 bits (185), Expect = 6e-19
 Identities = 24/50 (48%), Positives = 34/50 (68%)

Query: 111 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           GS     RK RT++S  QL  L++RF+  +YL+ PER ELA +L L++TQ
Sbjct: 1   GSSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQ 50

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

 Score = 94.7 bits (236), Expect = 9e-27
 Identities = 28/53 (52%), Positives = 37/53 (69%)

Query: 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
           ++K RTVFS  QL  L+ RF+ Q+YLS  +  EL++ L LS  QVKTWFQN+
Sbjct: 2  TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQ 54

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

 Score = 73.1 bits (180), Expect = 2e-18
 Identities = 21/45 (46%), Positives = 29/45 (64%)

Query: 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
            ++K RTVFS  QL  L+ RF+ Q+YLS  +  EL++ L LS  Q
Sbjct: 2   TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQ 46

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

 Score = 95.3 bits (237), Expect = 1e-26
 Identities = 28/65 (43%), Positives = 39/65 (60%)

Query: 32 STSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKT 91
          ++   +      +++K RTVFS  QL  L  RF+ Q+YLS  +  EL+  L LS  QVKT
Sbjct: 9  NSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKT 68

Query: 92 WFQNR 96
          WFQN+
Sbjct: 69 WFQNQ 73

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

 Score = 74.1 bits (182), Expect = 2e-18
 Identities = 21/57 (36%), Positives = 31/57 (54%)

Query: 104 STSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           ++   +      +++K RTVFS  QL  L  RF+ Q+YLS  +  EL+  L LS  Q
Sbjct: 9   NSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQ 65

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

 Score = 94.0 bits (234), Expect = 2e-26
 Identities = 29/52 (55%), Positives = 37/52 (71%)

Query: 45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          RRK R +FS  Q+  LE+RF+ Q+YLS PER  LA+ + L+ TQVK WFQN 
Sbjct: 2  RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNH 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 = 72.8 bits (179), Expect = 4e-18
 Identities = 23/44 (52%), Positives = 31/44 (70%)

Query: 117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           RRK R +FS  Q+  LE+RF+ Q+YLS PER  LA+ + L+ TQ
Sbjct: 2   RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQ 45

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

 Score = 93.5 bits (233), Expect = 3e-26
 Identities = 28/51 (54%), Positives = 37/51 (72%)

Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          RK RT F+  QL  LE++F  ++YLS  ER E +++L L+ETQVK WFQNR
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNR 51

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

 Score = 71.9 bits (177), Expect = 6e-18
 Identities = 21/43 (48%), Positives = 30/43 (69%)

Query: 118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           RK RT F+  QL  LE++F  ++YLS  ER E +++L L+ETQ
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQ 43

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

 Score = 92.8 bits (231), Expect = 6e-26
 Identities = 26/53 (49%), Positives = 33/53 (62%)

Query: 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
                +  S  Q+  LE++F  Q+YLS PER  LA  L+L+ETQVK WFQNR
Sbjct: 3  HHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNR 55

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

 Score = 72.0 bits (177), Expect = 1e-17
 Identities = 19/45 (42%), Positives = 26/45 (57%)

Query: 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
                 +  S  Q+  LE++F  Q+YLS PER  LA  L+L+ETQ
Sbjct: 3   HHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQ 47

>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 = 92.9 bits (231), Expect = 6e-26
 Identities = 33/58 (56%), Positives = 38/58 (65%)

Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          GS     +  +  FS+ Q   LEK+FE Q+YLS PER  LA  LQLSE QVKTWFQNR
Sbjct: 1  GSSGSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNR 58

>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 = 72.5 bits (178), Expect = 7e-18
 Identities = 25/50 (50%), Positives = 30/50 (60%)

Query: 111 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           GS     +  +  FS+ Q   LEK+FE Q+YLS PER  LA  LQLSE Q
Sbjct: 1   GSSGSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQ 50

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

 Score = 93.0 bits (231), Expect = 1e-25
 Identities = 28/57 (49%), Positives = 39/57 (68%)

Query: 40 SKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
              +R+K RT F+  Q+  LEKRF  Q+YL++ ER  LA  L++++ QVKTWFQNR
Sbjct: 12 RTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNR 68

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

 Score = 72.2 bits (177), Expect = 1e-17
 Identities = 20/49 (40%), Positives = 31/49 (63%)

Query: 112 SKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
               +R+K RT F+  Q+  LEKRF  Q+YL++ ER  LA  L++++ Q
Sbjct: 12  RTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQ 60

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

 Score = 87.8 bits (218), Expect = 4e-24
 Identities = 26/47 (55%), Positives = 35/47 (74%)

Query: 50 TVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          T FS  Q+  LE+RF  Q+YL++ ER  LA AL++++ QVKTWFQNR
Sbjct: 2  TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNR 48

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

 Score = 65.8 bits (161), Expect = 1e-15
 Identities = 18/39 (46%), Positives = 27/39 (69%)

Query: 122 TVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           T FS  Q+  LE+RF  Q+YL++ ER  LA AL++++ Q
Sbjct: 2   TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQ 40

>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 = 79.4 bits (196), Expect = 1e-20
 Identities = 22/52 (42%), Positives = 30/52 (57%)

Query: 45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
           R+ RT F+  Q+  LE+ F   RYL+ P   +L+  L L   QVK WF+NR
Sbjct: 2  PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNR 53

>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 = 60.1 bits (146), Expect = 4e-13
 Identities = 16/44 (36%), Positives = 23/44 (52%)

Query: 117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
            R+ RT F+  Q+  LE+ F   RYL+ P   +L+  L L   Q
Sbjct: 2   PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQ 45

>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 = 77.2 bits (191), Expect = 6e-20
 Identities = 15/56 (26%), Positives = 29/56 (51%)

Query: 41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          K  +  K ++  S      LE+ F  ++ L++ E+ E+A    ++  QV+ WF N+
Sbjct: 1  KKEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINK 56

>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 = 56.0 bits (136), Expect = 1e-11
 Identities = 11/48 (22%), Positives = 23/48 (47%)

Query: 113 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           K  +  K ++  S      LE+ F  ++ L++ E+ E+A    ++  Q
Sbjct: 1   KKEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQ 48

>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 = 74.2 bits (182), Expect = 3e-18
 Identities = 29/52 (55%), Positives = 34/52 (65%)

Query: 45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
              RT F+  QLT LEK F   +YLS   RVE+A  L+L+ETQVK WFQNR
Sbjct: 34 PSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNR 85

>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 = 54.9 bits (132), Expect = 8e-11
 Identities = 22/44 (50%), Positives = 27/44 (61%)

Query: 117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
               RT F+  QLT LEK F   +YLS   RVE+A  L+L+ETQ
Sbjct: 34  PSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQ 77

>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 = 72.8 bits (179), Expect = 4e-18
 Identities = 26/51 (50%), Positives = 32/51 (62%)

Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          R+ RT F+  QL  LEK F  + Y+S P R ELA  L L E+ +K WFQNR
Sbjct: 2  RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNR 52

>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 = 53.9 bits (130), Expect = 7e-11
 Identities = 20/43 (46%), Positives = 25/43 (58%)

Query: 118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           R+ RT F+  QL  LEK F  + Y+S P R ELA  L L E+ 
Sbjct: 2   RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPEST 44

>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 = 71.6 bits (176), Expect = 1e-17
 Identities = 21/51 (41%), Positives = 33/51 (64%)

Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          ++ RT FS  QL  L++ F   RYL+   R +L++ L L+E Q+K WF+N+
Sbjct: 4  KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNK 54

>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 = 53.1 bits (128), Expect = 2e-10
 Identities = 17/43 (39%), Positives = 26/43 (60%)

Query: 118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           ++ RT FS  QL  L++ F   RYL+   R +L++ L L+E Q
Sbjct: 4   KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQ 46

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

 Score = 71.4 bits (175), Expect = 3e-17
 Identities = 24/65 (36%), Positives = 36/65 (55%)

Query: 32 STSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKT 91
                  + +   ++ RT ++ +Q   LEK F   RYL+   R+E+A AL L+E Q+K 
Sbjct: 15 VHLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKI 74

Query: 92 WFQNR 96
          WFQNR
Sbjct: 75 WFQNR 79

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

 Score = 52.9 bits (127), Expect = 3e-10
 Identities = 18/58 (31%), Positives = 30/58 (51%)

Query: 104 STSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
                   + +   ++ RT ++ +Q   LEK F   RYL+   R+E+A AL L+E Q+
Sbjct: 15  VHLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQI 72

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

 Score = 68.6 bits (168), Expect = 2e-16
 Identities = 25/52 (48%), Positives = 33/52 (63%)

Query: 45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
           ++ RT ++  QL  LEK F   +Y+S P RVELA  L L+E  +K WFQNR
Sbjct: 3  NKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNR 54

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

 Score = 50.1 bits (120), Expect = 2e-09
 Identities = 19/45 (42%), Positives = 27/45 (60%)

Query: 117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
            ++ RT ++  QL  LEK F   +Y+S P RVELA  L L+E  +
Sbjct: 3   NKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHI 47

>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 = 67.9 bits (166), Expect = 5e-16
 Identities = 24/52 (46%), Positives = 33/52 (63%)

Query: 45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          RR+ R  ++ +Q   LEK F    YL+   R+E+A AL L+E Q+K WFQNR
Sbjct: 20 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNR 71

>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 = 49.4 bits (118), Expect = 7e-09
 Identities = 18/44 (40%), Positives = 26/44 (59%)

Query: 117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           RR+ R  ++ +Q   LEK F    YL+   R+E+A AL L+E Q
Sbjct: 20  RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQ 63

>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 = 67.4 bits (165), Expect = 6e-16
 Identities = 24/52 (46%), Positives = 34/52 (65%)

Query: 45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          R++ R  ++ +Q   LEK F   RYL+   R+E+A AL L+E Q+K WFQNR
Sbjct: 2  RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNR 53

>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 = 49.0 bits (117), Expect = 6e-09
 Identities = 18/45 (40%), Positives = 28/45 (62%)

Query: 117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
           R++ R  ++ +Q   LEK F   RYL+   R+E+A AL L+E Q+
Sbjct: 2   RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQI 46

>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 = 67.2 bits (164), Expect = 7e-16
 Identities = 22/58 (37%), Positives = 34/58 (58%)

Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          GS     RK R  +S  QL  LE+ + A ++++  +R +++ A  LSE Q+  WFQNR
Sbjct: 1  GSSGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNR 58

>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 = 49.1 bits (117), Expect = 7e-09
 Identities = 17/51 (33%), Positives = 29/51 (56%)

Query: 111 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
           GS     RK R  +S  QL  LE+ + A ++++  +R +++ A  LSE Q+
Sbjct: 1   GSSGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQI 51

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

 Score = 65.8 bits (161), Expect = 2e-15
 Identities = 21/58 (36%), Positives = 29/58 (50%)

Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          GS     R +RT F+D+QL  L+  F+A  Y    E  +L+  L L    +  WFQN 
Sbjct: 1  GSSGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNA 58

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

 Score = 49.3 bits (118), Expect = 6e-09
 Identities = 17/51 (33%), Positives = 25/51 (49%)

Query: 111 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
           GS     R +RT F+D+QL  L+  F+A  Y    E  +L+  L L    +
Sbjct: 1   GSSGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVI 51

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A Length = 160

 Score = 68.1 bits (166), Expect = 3e-15
 Identities = 16/53 (30%), Positives = 26/53 (49%)

Query: 44  RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
           RRRK RT    +    LEK F   +  ++ +   +A  L + +  ++ WF NR
Sbjct: 100 RRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNR 152

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A Length = 160

 Score = 48.8 bits (116), Expect = 4e-08
 Identities = 25/101 (24%), Positives = 42/101 (41%), Gaps = 6/101 (5%)

Query: 63  RFEAQRYLSTPERVELATALQ--LSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKA 120
           RFEA   LS     +L   L+  L++ +      + L   S  ++   E  S   RRRK 
Sbjct: 49  RFEALN-LSFKNMSKLKPLLEKWLNDAEANLSSDSSLSSPSALNSPGIEGLS---RRRKK 104

Query: 121 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
           RT    +    LEK F   +  ++ +   +A  L + +  +
Sbjct: 105 RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVI 145

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

 Score = 64.5 bits (157), Expect = 8e-15
 Identities = 19/57 (33%), Positives = 30/57 (52%)

Query: 40 SKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          S     RK R  ++  QL  LE+ +   ++++  +R  ++    LSE QV  WFQNR
Sbjct: 2  SHMLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNR 58

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

 Score = 46.4 bits (110), Expect = 7e-08
 Identities = 13/50 (26%), Positives = 25/50 (50%)

Query: 112 SKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
           S     RK R  ++  QL  LE+ +   ++++  +R  ++    LSE Q+
Sbjct: 2   SHMLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQV 51

>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1 Length = 146

 Score = 66.5 bits (162), Expect = 8e-15
 Identities = 21/72 (29%), Positives = 30/72 (41%)

Query: 25  LPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQL 84
           L          +E    + R+RK RT  S      LE+ F      S+ E + +A  L L
Sbjct: 67  LEEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNL 126

Query: 85  SETQVKTWFQNR 96
            +  V+ WF NR
Sbjct: 127 EKEVVRVWFCNR 138

>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1 Length = 146

 Score = 50.0 bits (119), Expect = 1e-08
 Identities = 20/90 (22%), Positives = 32/90 (35%)

Query: 71  STPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLT 130
           +T  R E       +  ++K      L          +E    + R+RK RT  S     
Sbjct: 41  TTICRFENLQLSFKNACKLKAILSKWLEEAEQVGALYNEKVGANERKRKRRTTISIAAKD 100

Query: 131 GLEKRFEAQRYLSTPERVELATALQLSETQ 160
            LE+ F      S+ E + +A  L L +  
Sbjct: 101 ALERHFGEHSKPSSQEIMRMAEELNLEKEV 130

>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 = 64.1 bits (156), Expect = 1e-14
 Identities = 25/53 (47%), Positives = 30/53 (56%)

Query: 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
            RK R  ++ HQ   LEK F    YL+   R E+A  L L+E QVK WFQNR
Sbjct: 12 STRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNR 64

>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 = 46.0 bits (109), Expect = 1e-07
 Identities = 18/46 (39%), Positives = 24/46 (52%)

Query: 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
             RK R  ++ HQ   LEK F    YL+   R E+A  L L+E Q+
Sbjct: 12  STRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQV 57

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

 Score = 62.5 bits (152), Expect = 5e-14
 Identities = 15/65 (23%), Positives = 28/65 (43%)

Query: 32 STSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKT 91
           +S    G +  R ++ RT  +  QL  L +++      +      +A  + L +  V+ 
Sbjct: 4  GSSGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQV 63

Query: 92 WFQNR 96
          WFQN 
Sbjct: 64 WFQNT 68

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

 Score = 45.6 bits (108), Expect = 2e-07
 Identities = 10/55 (18%), Positives = 22/55 (40%)

Query: 104 STSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSE 158
            +S    G +  R ++ RT  +  QL  L +++      +      +A  + L +
Sbjct: 4   GSSGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKK 58

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

 Score = 64.7 bits (157), Expect = 6e-14
 Identities = 22/68 (32%), Positives = 29/68 (42%)

Query: 29  SLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 88
           S  S +  +  +   R+RK RT         LE  F      S  E   LA +LQL +  
Sbjct: 83  SSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEV 142

Query: 89  VKTWFQNR 96
           V+ WF NR
Sbjct: 143 VRVWFCNR 150

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

 Score = 45.8 bits (108), Expect = 7e-07
 Identities = 33/137 (24%), Positives = 52/137 (37%), Gaps = 11/137 (8%)

Query: 32  STSPHELG--SKHCRRRKARTVFSDHQLT-GLEKRFEAQRYLSTPERVELATALQLS--- 85
           + S  +L   +K  ++R+ +  F+   +   L   +      +T  R E   ALQLS   
Sbjct: 9   APSSDDLEQFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFE---ALQLSFKN 65

Query: 86  ETQVKTWFQNRL--PFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLS 143
             ++K      L     S  S +  +  +   R+RK RT         LE  F      S
Sbjct: 66  MCKLKPLLNKWLEETDSSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPS 125

Query: 144 TPERVELATALQLSETQ 160
             E   LA +LQL +  
Sbjct: 126 AHEITGLADSLQLEKEV 142

>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens} Length = 151

 Score = 63.1 bits (153), Expect = 2e-13
 Identities = 18/65 (27%), Positives = 27/65 (41%)

Query: 32  STSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKT 91
                 +G +  ++RK RT F+   +  L   FE     +  E  E+A  L      V+ 
Sbjct: 80  QNLMEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRV 139

Query: 92  WFQNR 96
           WF NR
Sbjct: 140 WFSNR 144

>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens} Length = 151

 Score = 45.0 bits (106), Expect = 9e-07
 Identities = 13/57 (22%), Positives = 21/57 (36%)

Query: 104 STSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
                 +G +  ++RK RT F+   +  L   FE     +  E  E+A  L      
Sbjct: 80  QNLMEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREV 136

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

 Score = 58.6 bits (142), Expect = 2e-12
 Identities = 13/53 (24%), Positives = 21/53 (39%)

Query: 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
               +   S  QL+ L+  F   ++    E   L     LS  +V+ WF +R
Sbjct: 7  GASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDR 59

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

 Score = 40.5 bits (95), Expect = 1e-05
 Identities = 9/45 (20%), Positives = 15/45 (33%)

Query: 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
                +   S  QL+ L+  F   ++    E   L     LS  +
Sbjct: 7   GASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTRE 51

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

 Score = 57.7 bits (140), Expect = 3e-12
 Identities = 18/59 (30%), Positives = 28/59 (47%)

Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRL 97
          GS     ++ RT  +D QL  L + F+     S  +  E+A    L +  +K WF+N L
Sbjct: 1  GSSGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTL 59

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

 Score = 41.6 bits (98), Expect = 5e-06
 Identities = 13/48 (27%), Positives = 21/48 (43%)

Query: 111 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSE 158
           GS     ++ RT  +D QL  L + F+     S  +  E+A    L +
Sbjct: 1   GSSGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQ 48

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

 Score = 57.3 bits (138), Expect = 7e-12
 Identities = 17/73 (23%), Positives = 27/73 (36%), Gaps = 15/73 (20%)

Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATAL---------------Q 83
          GS     R +R  +    L  +E  F   +Y    +R E+A A                +
Sbjct: 1  GSSGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLER 60

Query: 84 LSETQVKTWFQNR 96
          ++  +V  WF NR
Sbjct: 61 VTSLKVYNWFANR 73

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

 Score = 44.6 bits (105), Expect = 6e-07
 Identities = 12/50 (24%), Positives = 19/50 (38%)

Query: 111 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           GS     R +R  +    L  +E  F   +Y    +R E+A A      +
Sbjct: 1   GSSGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQK 50

>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A Length = 155

 Score = 58.6 bits (141), Expect = 1e-11
 Identities = 15/65 (23%), Positives = 24/65 (36%)

Query: 32  STSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKT 91
                +  +    R++ RT   +     LE  F      S  +   +A  L L +  V+ 
Sbjct: 83  LQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRV 142

Query: 92  WFQNR 96
           WF NR
Sbjct: 143 WFSNR 147

>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A Length = 155

 Score = 41.6 bits (97), Expect = 2e-05
 Identities = 18/93 (19%), Positives = 33/93 (35%), Gaps = 3/93 (3%)

Query: 67  QRYLSTPERVELATALQLS-ETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFS 125
           Q  +S  E ++L+          ++ W +      +L   S  E   +  +R+  RT   
Sbjct: 47  QTTISRFEALQLSLKNMSKLRPLLEKWVEEADNNENLQEISKSETLVQARKRK--RTSIE 104

Query: 126 DHQLTGLEKRFEAQRYLSTPERVELATALQLSE 158
           +     LE  F      S  +   +A  L L +
Sbjct: 105 NRVRWSLETMFLKSPKPSLQQITHIANQLGLEK 137

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

 Score = 55.8 bits (135), Expect = 2e-11
 Identities = 23/58 (39%), Positives = 33/58 (56%)

Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          GS     R+ RT+F+D QL  LE  F+  +Y     R +LA  + L E +V+ WF+NR
Sbjct: 1  GSSGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNR 58

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

 Score = 40.4 bits (95), Expect = 1e-05
 Identities = 18/48 (37%), Positives = 25/48 (52%)

Query: 111 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSE 158
           GS     R+ RT+F+D QL  LE  F+  +Y     R +LA  + L E
Sbjct: 1   GSSGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLRE 48

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

 Score = 55.5 bits (134), Expect = 3e-11
 Identities = 21/58 (36%), Positives = 29/58 (50%)

Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          GS     ++ RT F+  Q+  LEK FE   Y     R  LA  + L E +++ WF NR
Sbjct: 1  GSSGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNR 58

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

 Score = 40.1 bits (94), Expect = 2e-05
 Identities = 17/48 (35%), Positives = 22/48 (45%)

Query: 111 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSE 158
           GS     ++ RT F+  Q+  LEK FE   Y     R  LA  + L E
Sbjct: 1   GSSGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPE 48

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

 Score = 55.5 bits (134), Expect = 3e-11
 Identities = 23/58 (39%), Positives = 31/58 (53%)

Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          GS     R+ RT F+  QL  LE  F   RY     R E+A  + L E++V+ WF+NR
Sbjct: 1  GSSGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNR 58

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

 Score = 40.1 bits (94), Expect = 2e-05
 Identities = 18/48 (37%), Positives = 22/48 (45%)

Query: 111 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSE 158
           GS     R+ RT F+  QL  LE  F   RY     R E+A  + L E
Sbjct: 1   GSSGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPE 48

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

 Score = 54.4 bits (131), Expect = 6e-11
 Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 1/60 (1%)

Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRF-EAQRYLSTPERVELATALQLSETQVKTWFQNRL 97
          GS      ++RT  S   L  L+    +   Y        L+  L L +  +  +FQN+ 
Sbjct: 1  GSSGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQR 60

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

 Score = 37.9 bits (88), Expect = 1e-04
 Identities = 11/52 (21%), Positives = 18/52 (34%), Gaps = 1/52 (1%)

Query: 111 GSKHCRRRKARTVFSDHQLTGLEKRF-EAQRYLSTPERVELATALQLSETQL 161
           GS      ++RT  S   L  L+    +   Y        L+  L L +  +
Sbjct: 1   GSSGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTI 52

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

 Score = 54.0 bits (130), Expect = 1e-10
 Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 1/53 (1%)

Query: 46 RKARTVFSDHQLTGLEKRFE-AQRYLSTPERVELATALQLSETQVKTWFQNRL 97
           +  +  ++ Q+  LE  F    ++        +A    L+E Q + WF+ RL
Sbjct: 3  AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRL 55

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

 Score = 35.9 bits (83), Expect = 6e-04
 Identities = 8/44 (18%), Positives = 17/44 (38%), Gaps = 1/44 (2%)

Query: 118 RKARTVFSDHQLTGLEKRFE-AQRYLSTPERVELATALQLSETQ 160
            +  +  ++ Q+  LE  F    ++        +A    L+E Q
Sbjct: 3   AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQ 46

>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P 2lkx_A* 2l7m_P Length = 68

 Score = 53.5 bits (129), Expect = 1e-10
 Identities = 21/53 (39%), Positives = 30/53 (56%)

Query: 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
           +R+ RT F+  QL  LE  F+  RY     R E+A    L+E +V+ WF+NR
Sbjct: 2  SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNR 54

>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P 2lkx_A* 2l7m_P Length = 68

 Score = 37.7 bits (88), Expect = 1e-04
 Identities = 16/43 (37%), Positives = 22/43 (51%)

Query: 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSE 158
            +R+ RT F+  QL  LE  F+  RY     R E+A    L+E
Sbjct: 2   SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTE 44

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

 Score = 53.6 bits (129), Expect = 2e-10
 Identities = 16/58 (27%), Positives = 26/58 (44%)

Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          GS     ++ RT F  HQL  ++  F         +  +LA    L++  ++ WFQN 
Sbjct: 1  GSSGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNA 58

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

 Score = 39.0 bits (91), Expect = 5e-05
 Identities = 12/48 (25%), Positives = 20/48 (41%)

Query: 111 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSE 158
           GS     ++ RT F  HQL  ++  F         +  +LA    L++
Sbjct: 1   GSSGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTK 48

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

 Score = 55.6 bits (133), Expect = 2e-10
 Identities = 15/90 (16%), Positives = 31/90 (34%)

Query: 7   YPSPYLHKSDSFYITPQGLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEA 66
           +   +    +  +     L   +           +    +K R VF+D Q   L   F+ 
Sbjct: 59  FRRMWKWLQEPEFQRMSALRLAACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKE 118

Query: 67  QRYLSTPERVELATALQLSETQVKTWFQNR 96
            +  S   ++ ++  L L  + V  +F N 
Sbjct: 119 NKRPSKELQITISQQLGLELSTVSNFFMNA 148

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

 Score = 37.5 bits (86), Expect = 5e-04
 Identities = 12/67 (17%), Positives = 24/67 (35%)

Query: 94  QNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATA 153
            + L   +           +    +K R VF+D Q   L   F+  +  S   ++ ++  
Sbjct: 74  MSALRLAACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQ 133

Query: 154 LQLSETQ 160
           L L  + 
Sbjct: 134 LGLELST 140

>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription regulation; HET: DNA; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 3a01_B Length = 81

 Score = 53.1 bits (128), Expect = 2e-10
 Identities = 23/53 (43%), Positives = 33/53 (62%)

Query: 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          ++R++RT FS  QL  LE+ FE  +Y     R ELA    L+E +++ WFQNR
Sbjct: 17 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNR 69

>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription regulation; HET: DNA; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 3a01_B Length = 81

 Score = 38.1 bits (89), Expect = 1e-04
 Identities = 18/43 (41%), Positives = 25/43 (58%)

Query: 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSE 158
           ++R++RT FS  QL  LE+ FE  +Y     R ELA    L+E
Sbjct: 17  KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTE 59

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

 Score = 51.7 bits (124), Expect = 5e-10
 Identities = 9/53 (16%), Positives = 19/53 (35%)

Query: 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
                   +  Q+  L+  F   ++    E   L     L+ +++K WF + 
Sbjct: 3  HHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDH 55

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

 Score = 35.9 bits (83), Expect = 4e-04
 Identities = 6/45 (13%), Positives = 14/45 (31%)

Query: 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
                    +  Q+  L+  F   ++    E   L     L+ ++
Sbjct: 3   HHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSE 47

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

 Score = 51.5 bits (124), Expect = 6e-10
 Identities = 18/51 (35%), Positives = 26/51 (50%)

Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          R+ RT F+ +Q+  LE  F    Y       +LA  L L   +++ WFQNR
Sbjct: 2  RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNR 52

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

 Score = 36.5 bits (85), Expect = 3e-04
 Identities = 13/41 (31%), Positives = 18/41 (43%)

Query: 118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSE 158
           R+ RT F+ +Q+  LE  F    Y       +LA  L L  
Sbjct: 2   RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLEL 42

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

 Score = 51.6 bits (124), Expect = 6e-10
 Identities = 14/53 (26%), Positives = 24/53 (45%)

Query: 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          +  + RTV ++ QL  L   + A        + +L     LS   ++ WFQN+
Sbjct: 2  KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNK 54

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

 Score = 36.9 bits (86), Expect = 2e-04
 Identities = 10/43 (23%), Positives = 17/43 (39%)

Query: 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSE 158
           +  + RTV ++ QL  L   + A        + +L     LS 
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSP 44

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

 Score = 49.9 bits (120), Expect = 2e-09
 Identities = 19/48 (39%), Positives = 25/48 (52%)

Query: 49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
             F+  QL  LEK F    Y     R ELA  + L+E +++ WFQNR
Sbjct: 3  HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNR 50

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

 Score = 49.9 bits (119), Expect = 3e-09
 Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 3/58 (5%)

Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          GS    + K R      QL  LE  F         E   L +  +++  ++ +WF  R
Sbjct: 4  GSSGPTKYKERA---PEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSER 58

>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac development, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 72

 Score = 48.9 bits (117), Expect = 7e-09
 Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 1/53 (1%)

Query: 46 RKARTVFSDHQLTGLEKRFE-AQRYLSTPERVELATALQLSETQVKTWFQNRL 97
           +     ++ Q+  LE  F    ++        +A    L+E Q + WF+ RL
Sbjct: 2  SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRL 54

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

 Score = 48.4 bits (115), Expect = 2e-08
 Identities = 15/65 (23%), Positives = 25/65 (38%), Gaps = 3/65 (4%)

Query: 32 STSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKT 91
          S S         ++ K +T     Q+  LE  F    + +  E   L    +LS  ++ +
Sbjct: 3  SGSSGAYPDFAPQKFKEKT---QGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDS 59

Query: 92 WFQNR 96
          WF  R
Sbjct: 60 WFSER 64

>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 Length = 194

 Score = 48.3 bits (114), Expect = 1e-07
 Identities = 16/86 (18%), Positives = 25/86 (29%), Gaps = 21/86 (24%)

Query: 32  STSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATAL--------- 82
              P        + R+ R  +       L + +E Q+  S  ER  L             
Sbjct: 102 IEEPTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRG 161

Query: 83  ------------QLSETQVKTWFQNR 96
                        ++E +V  WF NR
Sbjct: 162 VSPSQAQGLGSNLVTEVRVYNWFANR 187

>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 Length = 194

 Score = 41.4 bits (96), Expect = 3e-05
 Identities = 20/85 (23%), Positives = 32/85 (37%), Gaps = 2/85 (2%)

Query: 70  LSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQL 129
           + T +R  L T     + +V   F +    G +   +  EL +K  RR   R  +     
Sbjct: 70  MKTQKRAALYTWYVRKQREVAQQFTHAGQGGLIEEPTGDELPTKKGRRN--RFKWGPASQ 127

Query: 130 TGLEKRFEAQRYLSTPERVELATAL 154
             L + +E Q+  S  ER  L    
Sbjct: 128 QILFQAYERQKNPSKEERETLVEEC 152

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

 Score = 46.1 bits (109), Expect = 1e-07
 Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 7/69 (10%)

Query: 28 GSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSET 87
          GS  S+ P     K   +       +  QL  L+  F     L+  E   L    +L+  
Sbjct: 1  GSSGSSGPDFTPQKFKEK-------TAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRR 53

Query: 88 QVKTWFQNR 96
          ++  WF  +
Sbjct: 54 EIDAWFTEK 62

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

 Score = 44.0 bits (104), Expect = 5e-07
 Identities = 14/60 (23%), Positives = 22/60 (36%), Gaps = 7/60 (11%)

Query: 38 LGSKHCRRRKARTVFSDHQLTGLEKRFEAQ-RYLSTPERVELATALQLSETQVKTWFQNR 96
           G K     K            LEK F +  +Y        L+  L  S  +++ WF++R
Sbjct: 7  GGIKDSPVNKV------EPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHR 60

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

 Score = 44.2 bits (103), Expect = 7e-07
 Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 4/57 (7%)

Query: 44 RRRKARTVFSDHQLTGLEKRFE----AQRYLSTPERVELATALQLSETQVKTWFQNR 96
             + RT FSD  L  L+K ++    +   +   +   +AT L +    V+TW  NR
Sbjct: 7  GALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNR 63

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

 Score = 46.2 bits (108), Expect = 7e-07
 Identities = 17/110 (15%), Positives = 28/110 (25%), Gaps = 22/110 (20%)

Query: 8   PSPYLHKSDSFYITPQGLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQ 67
                 +    +        G   S       +    RR  R  +       L + ++ Q
Sbjct: 106 DKSSQDQLLFLFPEFSQQSHGPGQSDDACSEPTNKKMRRN-RFKWGPASQQILYQAYDRQ 164

Query: 68  RYLSTPERVELATAL---------------------QLSETQVKTWFQNR 96
           +  S  ER  L                          ++E +V  WF NR
Sbjct: 165 KNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANR 214

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

 Score = 41.0 bits (95), Expect = 2e-05
 Identities = 15/74 (20%), Positives = 24/74 (32%), Gaps = 21/74 (28%)

Query: 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATAL--------------------- 82
          + R+ R  +       L + +E Q+  S  ER  L                         
Sbjct: 8  KGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSN 67

Query: 83 QLSETQVKTWFQNR 96
           ++E +V  WF NR
Sbjct: 68 LVTEVRVYNWFANR 81

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

 Score = 39.4 bits (91), Expect = 4e-05
 Identities = 12/65 (18%), Positives = 23/65 (35%)

Query: 32 STSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKT 91
               +  +            +  QL  L+  F   ++ S  E  +LA    L+ T + +
Sbjct: 12 LEVLFQGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVS 71

Query: 92 WFQNR 96
          WF + 
Sbjct: 72 WFGDT 76

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	165
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.84
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.84
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.83
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.83
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.82
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.82
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.82
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.82
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.82
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.82
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.81
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.81
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.81
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.8
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.79
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.79
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.79
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.79
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.79
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.79
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.79
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.79
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.79
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.79
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.78
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.78
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.78
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.78
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.78
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.77
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.77
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.77
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.77
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.77
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.77
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.77
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.77
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.77
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.76
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.76
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.76
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.75
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.75
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.75
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.75
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.75
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.75
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.75
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.74
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.73
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.72
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.72
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.72
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.71
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.71
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.71
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.71
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.71
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.7
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.7
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.7
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.7
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.7
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.69
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.69
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.69
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.69
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.69
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.68
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.66
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.65
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.57
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.56
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.55
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.52
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.39
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.37
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.29
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.12
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.11
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.1
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.1
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.09
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.09
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.08
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.08
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.08
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.07
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.07
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.05
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.05
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.05
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.04
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.04
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.04
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.04
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.04
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.04
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.04
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.03
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.03
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.03
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.02
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.02
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.01
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.0
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	98.99
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	98.98
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	98.97
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	98.97
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	98.96
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	98.96
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	98.96
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	98.95
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	98.94
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	98.94
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	98.94
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	98.93
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	98.93
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	98.93
1uhs_A	72	HOP, homeodomain only protein; structural genomics	98.91
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	98.9
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	98.9
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	98.89
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	98.86
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	98.86
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	98.83
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	98.83
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	98.81
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	98.81
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	98.78
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	98.76
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	98.76
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	98.74
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	98.73
2e19_A	64	Transcription factor 8; homeobox domain, structura	98.73
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	98.72
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	98.72
1lfb_A	99	Liver transcription factor (LFB1); transcription r	98.7
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	98.65
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	98.65
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	98.65
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	98.62
1e3o_C	160	Octamer-binding transcription factor 1; transcript	98.61
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	98.6
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	98.6
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	98.58
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	98.55
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	98.43
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	98.42
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.31
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	98.3
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	98.11
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	97.84
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	97.82
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	96.91
1u78_A	141	TC3 transposase, transposable element TC3 transpos	88.02
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	85.77
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	85.71
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	85.54
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	82.32
2k27_A	159	Paired box protein PAX-8; paired domain, solution	80.96

>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=99.84  E-value=3.6e-21  Score=122.89  Aligned_cols=68  Identities=54%  Similarity=0.805  Sum_probs=62.2

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCC
Q psy17007         39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTS  106 (165)
Q Consensus        39 ~~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~  106 (165)
                      +...++.++.|+.|+.+|+.+||..|..++||+..+++.||..+||++.+|++||+|||++.++...+
T Consensus        11 ~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~~s   78 (80)
T 2dmt_A           11 GTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGPS   78 (80)
T ss_dssp             CCCCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCCSC
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcccCC
Confidence            34566788999999999999999999999999999999999999999999999999999999876543

>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=99.84  E-value=3.9e-21  Score=119.75  Aligned_cols=66  Identities=32%  Similarity=0.495  Sum_probs=60.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCC
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTS  106 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~  106 (165)
                      ..++.++.|+.|+.+|+.+||..|..++||+..+++.||..+||++.+|++||+|||+++++...+
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~~   68 (70)
T 2cra_A            3 SGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGPS   68 (70)
T ss_dssp             SSCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSCTT
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccCCC
Confidence            445678899999999999999999999999999999999999999999999999999999876543

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

Probab=99.83  E-value=7.3e-21  Score=118.50  Aligned_cols=66  Identities=44%  Similarity=0.676  Sum_probs=60.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCC
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTS  106 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~  106 (165)
                      ..++.++.|+.|+.+|+.+||..|..++||+..+++.||..+||++.+|++||+|||++.++...+
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~s   68 (70)
T 2djn_A            3 SGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGPS   68 (70)
T ss_dssp             SCCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSSSS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccCCC
Confidence            445678899999999999999999999999999999999999999999999999999999876543

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

Probab=99.83  E-value=2e-20  Score=120.47  Aligned_cols=67  Identities=42%  Similarity=0.586  Sum_probs=61.4

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007         39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST  105 (165)
Q Consensus        39 ~~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~  105 (165)
                      ....++.++.|+.|+..|+.+||..|..++||+..++..||..+||++.+|++||||||++.++...
T Consensus        16 ~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k   82 (84)
T 2kt0_A           16 DKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK   82 (84)
T ss_dssp             CCCCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCC
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhh
Confidence            3445678899999999999999999999999999999999999999999999999999999987543

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

Probab=99.82  E-value=6.7e-21  Score=118.67  Aligned_cols=66  Identities=33%  Similarity=0.522  Sum_probs=60.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCC
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTS  106 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~  106 (165)
                      ..++.++.|+.|+.+|+.+||..|..++||+..+++.||..+||++.+|++||+|||++.++...+
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~~   68 (70)
T 2dmu_A            3 SGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGPS   68 (70)
T ss_dssp             STTSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTSTT
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccCCC
Confidence            345678899999999999999999999999999999999999999999999999999999875543

>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=99.82  E-value=9.3e-21  Score=118.02  Aligned_cols=67  Identities=31%  Similarity=0.389  Sum_probs=61.2

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCC
Q psy17007         40 SKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTS  106 (165)
Q Consensus        40 ~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~  106 (165)
                      +..++.++.|+.|+.+|+.+||..|..++||+..+++.||..+||++.+|++||+|||++.++...+
T Consensus         2 ~~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (70)
T 2da2_A            2 SSGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGPS   68 (70)
T ss_dssp             CCSCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCSSC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhcccc
Confidence            3456778899999999999999999999999999999999999999999999999999999875543

>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=99.82  E-value=9.1e-21  Score=121.03  Aligned_cols=68  Identities=22%  Similarity=0.274  Sum_probs=61.7

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCC
Q psy17007         39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTS  106 (165)
Q Consensus        39 ~~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~  106 (165)
                      .....+.++.|+.|+.+|+.+||..|..++||+..+++.||..+||++.+|++||+|||++.++...+
T Consensus        11 ~~~~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~   78 (80)
T 2da3_A           11 GEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSGPS   78 (80)
T ss_dssp             CCCCCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSCCC
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhccC
Confidence            33456778899999999999999999999999999999999999999999999999999999875543

>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=99.82  E-value=4.2e-20  Score=117.77  Aligned_cols=61  Identities=16%  Similarity=0.181  Sum_probs=57.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHh----cCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         42 HCRRRKARTVFSDHQLTGLEKRFEA----QRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        42 ~~~~rr~R~~~s~~q~~~Le~~f~~----~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      .++.+|.|+.||.+|+..||..|+.    ++||+..++++||..+||++.+|++||||||+|.+.
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           14 GGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            4567889999999999999999999    999999999999999999999999999999999864

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

Probab=99.82  E-value=1.9e-20  Score=119.59  Aligned_cols=68  Identities=31%  Similarity=0.433  Sum_probs=61.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCC
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPH  108 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~  108 (165)
                      ..++.++.|+.|+.+|+.+||..|..++||+..+++.||..+||++.+|++||+|||++.++......
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~~~   70 (80)
T 2dms_A            3 SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQQ   70 (80)
T ss_dssp             CCCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCSCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHccC
Confidence            44677899999999999999999999999999999999999999999999999999999987654443

>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=99.82  E-value=9.7e-21  Score=117.93  Aligned_cols=65  Identities=25%  Similarity=0.322  Sum_probs=60.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST  105 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~  105 (165)
                      ..++.++.|+.|+.+|+.+||..|..++||+..++..||..+||++.+|++||+|||++.++...
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2da1_A            3 SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGP   67 (70)
T ss_dssp             SSCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhcc
Confidence            44567899999999999999999999999999999999999999999999999999999987554

>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=99.81  E-value=6.3e-20  Score=116.82  Aligned_cols=61  Identities=15%  Similarity=0.206  Sum_probs=56.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh-----cCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEA-----QRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~-----~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      ...+.+|.||.||.+|+..|| .|..     ++||+..++++||..+||++.+|+|||||||++.+.
T Consensus        13 ~~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           13 SGGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            445678899999999999999 7999     999999999999999999999999999999999864

>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=99.81  E-value=2.1e-20  Score=116.41  Aligned_cols=64  Identities=48%  Similarity=0.636  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007         42 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST  105 (165)
Q Consensus        42 ~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~  105 (165)
                      ..+.++.|++|+.+|+.+||..|..++||+..+++.||..+||++.+|++||+|||+++++...
T Consensus         4 ~~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2e1o_A            4 GSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGP   67 (70)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCCC
Confidence            3456788999999999999999999999999999999999999999999999999999976544

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

Probab=99.81  E-value=1.9e-20  Score=113.90  Aligned_cols=60  Identities=47%  Similarity=0.659  Sum_probs=52.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        44 ~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      +.++.|+.|+..|+.+||..|..++||+..++..||..+||++.+|++||+|||++.++.
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            467889999999999999999999999999999999999999999999999999999764

>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=99.80  E-value=3.9e-20  Score=117.26  Aligned_cols=64  Identities=44%  Similarity=0.633  Sum_probs=59.3

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         40 SKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        40 ~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      +..++.++.|+.|+..|+.+||..|..++||+..++..||..+||++.+|++||+|||++.++.
T Consensus         4 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~   67 (77)
T 1nk2_P            4 GLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRA   67 (77)
T ss_dssp             CCSCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhh
Confidence            3456678889999999999999999999999999999999999999999999999999998754

>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=99.79  E-value=6e-20  Score=113.03  Aligned_cols=61  Identities=25%  Similarity=0.339  Sum_probs=57.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007         44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS  104 (165)
Q Consensus        44 ~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~  104 (165)
                      +.++.|+.||.+|+.+||..|..++||+..+++.||..+||++.+|++||+|||++.++..
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   62 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHHh
Confidence            3578899999999999999999999999999999999999999999999999999987643

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

Probab=99.79  E-value=1e-19  Score=114.11  Aligned_cols=63  Identities=29%  Similarity=0.493  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007         43 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST  105 (165)
Q Consensus        43 ~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~  105 (165)
                      .+.++.|+.|+..|+.+||..|..++||+..++..||..+||++.+|++||+|||++.++...
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   67 (73)
T 2l7z_A            5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVIN   67 (73)
T ss_dssp             SCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHhc
Confidence            456889999999999999999999999999999999999999999999999999999987543

>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=99.79  E-value=7.1e-20  Score=116.04  Aligned_cols=63  Identities=40%  Similarity=0.512  Sum_probs=58.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      ..++.++.|+.|+..|+.+||..|..++||+..+++.||..+||++.+|++||||||++.++.
T Consensus         9 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   71 (77)
T 1puf_A            9 HARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKI   71 (77)
T ss_dssp             CCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence            345678899999999999999999999999999999999999999999999999999998653

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

Probab=99.79  E-value=4.9e-20  Score=117.62  Aligned_cols=63  Identities=22%  Similarity=0.295  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007         42 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS  104 (165)
Q Consensus        42 ~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~  104 (165)
                      .++.++.|+.|+.+|+.+||..|..++||+..+++.||..+||++.+|++||+|||++.++..
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   66 (80)
T 2dmq_A            4 GSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNL   66 (80)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHH
Confidence            456788999999999999999999999999999999999999999999999999999997643

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

Probab=99.79  E-value=4.5e-20  Score=117.81  Aligned_cols=62  Identities=31%  Similarity=0.484  Sum_probs=58.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         42 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        42 ~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      .++.++.|+.|+.+|+.+||..|..++||+..++..||..+||++.+|++||+|||+++++.
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   65 (80)
T 2cue_A            4 GSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE   65 (80)
T ss_dssp             CCSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHH
Confidence            45678899999999999999999999999999999999999999999999999999998753

>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=99.79  E-value=3.9e-20  Score=112.17  Aligned_cols=60  Identities=23%  Similarity=0.349  Sum_probs=48.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcc
Q psy17007         42 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGS  101 (165)
Q Consensus        42 ~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~  101 (165)
                      .++.++.|+.|+..|+.+||..|..++||+..++..||..+||++.+|++||+|||++.+
T Consensus         2 k~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            2 KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             ----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            456788999999999999999999999999999999999999999999999999998763

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

Probab=99.79  E-value=3.5e-20  Score=113.07  Aligned_cols=60  Identities=42%  Similarity=0.629  Sum_probs=54.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        44 ~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      +.++.|+.||..|+.+||..|..++||+..++..||..+||++.+|++||+|||++.++.
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~   61 (63)
T 2h1k_A            2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE   61 (63)
T ss_dssp             ---CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhh
Confidence            357889999999999999999999999999999999999999999999999999998653

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

Probab=99.79  E-value=4.8e-20  Score=110.63  Aligned_cols=57  Identities=49%  Similarity=0.771  Sum_probs=54.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        46 rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      ++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||+|||++.++
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            577899999999999999999999999999999999999999999999999998764

>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=99.79  E-value=4.3e-20  Score=111.99  Aligned_cols=58  Identities=36%  Similarity=0.653  Sum_probs=52.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        45 ~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      .++.|+.||.+|+.+||..|..++||+..+++.||..+||++.+|++||+|||++.++
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            4788999999999999999999999999999999999999999999999999998764

>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=99.79  E-value=4.4e-20  Score=114.28  Aligned_cols=63  Identities=38%  Similarity=0.581  Sum_probs=58.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCC
Q psy17007         45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSP  107 (165)
Q Consensus        45 ~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~  107 (165)
                      .++.|+.||..|+.+||..|..++||+..++..||..+||++.+|++||+|||++.++.....
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~~~   64 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTK   64 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSCCC
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhcccc
Confidence            478899999999999999999999999999999999999999999999999999998755443

>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=99.78  E-value=8.6e-20  Score=116.72  Aligned_cols=62  Identities=39%  Similarity=0.566  Sum_probs=53.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         42 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        42 ~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      .++.++.|+.|+.+|+.+||..|..++||+..+++.||..+||++.+|++||+|||++.++.
T Consensus        17 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~   78 (81)
T 1b8i_A           17 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE   78 (81)
T ss_dssp             -------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhh
Confidence            34568899999999999999999999999999999999999999999999999999998764

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

Probab=99.78  E-value=4.4e-20  Score=117.85  Aligned_cols=64  Identities=27%  Similarity=0.330  Sum_probs=59.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhc----CCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEAQ----RYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS  104 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~----~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~  104 (165)
                      ..++.++.|+.|+.+|+.+||.+|..+    +||+..+++.||..+||++.+|++||||||++.++..
T Consensus         4 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~~   71 (80)
T 2da4_A            4 GSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMG   71 (80)
T ss_dssp             CCCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhcc
Confidence            345678899999999999999999999    9999999999999999999999999999999997643

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

Probab=99.78  E-value=1.7e-19  Score=118.16  Aligned_cols=64  Identities=44%  Similarity=0.667  Sum_probs=59.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS  104 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~  104 (165)
                      .+.+.++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||||||++.++..
T Consensus        13 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~   76 (93)
T 3a01_A           13 TPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQT   76 (93)
T ss_dssp             CCCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhh
Confidence            3456788999999999999999999999999999999999999999999999999999997644

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

Probab=99.78  E-value=2.9e-19  Score=112.61  Aligned_cols=65  Identities=34%  Similarity=0.490  Sum_probs=59.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST  105 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~  105 (165)
                      ..++.++.|+.|+..|+.+||..|..++||+..++..||..+||++.+|++||+|||++.++...
T Consensus         5 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r   69 (75)
T 2m0c_A            5 NKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRER   69 (75)
T ss_dssp             CCSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHh
Confidence            34567888999999999999999999999999999999999999999999999999999876543

>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=99.78  E-value=4.4e-19  Score=111.78  Aligned_cols=60  Identities=18%  Similarity=0.232  Sum_probs=55.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCC
Q psy17007         47 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTS  106 (165)
Q Consensus        47 r~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~  106 (165)
                      +.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||+|||++.++....
T Consensus         9 ~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~~   68 (75)
T 2da5_A            9 TKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETK   68 (75)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSCS
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhhc
Confidence            456789999999999999999999999999999999999999999999999999875543

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

Probab=99.77  E-value=2e-19  Score=111.34  Aligned_cols=61  Identities=48%  Similarity=0.695  Sum_probs=57.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007         45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST  105 (165)
Q Consensus        45 ~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~  105 (165)
                      .++.|+.||..|+.+||..|..++||+..++..||..+||++.+|++||+|||++.++...
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~   62 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK   62 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhh
Confidence            4788999999999999999999999999999999999999999999999999999976543

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

Probab=99.77  E-value=1.6e-19  Score=108.26  Aligned_cols=57  Identities=56%  Similarity=0.847  Sum_probs=53.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcc
Q psy17007         45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGS  101 (165)
Q Consensus        45 ~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~  101 (165)
                      .++.|+.|+..|+.+||..|..++||+..++..||..+||++.+|++||+|||++.+
T Consensus         2 ~rr~Rt~~t~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~k   58 (58)
T 3rkq_A            2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK   58 (58)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHC
T ss_pred             cCCCCCCcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhhccCC
Confidence            467899999999999999999999999999999999999999999999999998763

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

Probab=99.77  E-value=1.7e-19  Score=117.14  Aligned_cols=62  Identities=39%  Similarity=0.556  Sum_probs=54.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         42 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        42 ~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      +++.++.|+.|+..|+.+||..|..++||+..+++.||..+||++.+|++||+|||++.++.
T Consensus        25 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~   86 (88)
T 2r5y_A           25 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   86 (88)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhh
Confidence            45678899999999999999999999999999999999999999999999999999998764

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

Probab=99.77  E-value=1.4e-19  Score=109.39  Aligned_cols=57  Identities=46%  Similarity=0.705  Sum_probs=54.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        46 rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      ++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||+|||++.++
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   58 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR   58 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHhHhhc
Confidence            578999999999999999999999999999999999999999999999999998864

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

Probab=99.77  E-value=2e-19  Score=111.00  Aligned_cols=61  Identities=30%  Similarity=0.409  Sum_probs=57.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007         45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST  105 (165)
Q Consensus        45 ~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~  105 (165)
                      +++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||+|||++.++...
T Consensus         1 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~   61 (67)
T 2k40_A            1 GRRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR   61 (67)
T ss_dssp             CCCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCC
T ss_pred             CcCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhch
Confidence            3688999999999999999999999999999999999999999999999999999976543

>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=99.77  E-value=5.9e-20  Score=113.72  Aligned_cols=61  Identities=34%  Similarity=0.532  Sum_probs=57.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007         44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS  104 (165)
Q Consensus        44 ~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~  104 (165)
                      +.++.|+.|+..|+.+||..|..++||+..++..||..+||++.+|++||+|||++.++..
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~   62 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE   62 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHh
Confidence            4688899999999999999999999999999999999999999999999999999987644

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

Probab=99.77  E-value=1.4e-19  Score=112.06  Aligned_cols=60  Identities=38%  Similarity=0.650  Sum_probs=56.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007         45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS  104 (165)
Q Consensus        45 ~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~  104 (165)
                      .++.|+.|+..|+.+||..|..++||+..++..||..+||++.+|++||+|||++.++..
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~   61 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQS   61 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHh
Confidence            478899999999999999999999999999999999999999999999999999987643

>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=99.77  E-value=4.7e-19  Score=107.15  Aligned_cols=61  Identities=20%  Similarity=0.177  Sum_probs=56.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh-cCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcc
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEA-QRYLSTPERVELATALQLSETQVKTWFQNRLPFGS  101 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~-~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~  101 (165)
                      ..++.+|.||.|+.+|+..|+..|+. +.||+.+.++.||..+||++++|++||||+|..-+
T Consensus         3 ~~~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~~~   64 (71)
T 1wi3_A            3 SGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVK   64 (71)
T ss_dssp             CCCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCC
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceeeec
Confidence            34567899999999999999999999 99999999999999999999999999999987654

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

Probab=99.77  E-value=6.2e-19  Score=111.42  Aligned_cols=61  Identities=23%  Similarity=0.306  Sum_probs=56.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCC
Q psy17007         46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTS  106 (165)
Q Consensus        46 rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~  106 (165)
                      ...|++||.+|+.+||..|..++||+..+++.||..+||++.+|++||+|||++.++....
T Consensus         9 ~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~~   69 (76)
T 2dn0_A            9 SIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGS   69 (76)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCSS
T ss_pred             CCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhccc
Confidence            4458999999999999999999999999999999999999999999999999999875543

>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=99.76  E-value=2.1e-19  Score=114.94  Aligned_cols=62  Identities=37%  Similarity=0.550  Sum_probs=56.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      ..++.++.|+.|+..|+.+||..|..++||+..++..||..+||++.+|++||+|||++.++
T Consensus        14 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk   75 (81)
T 1fjl_A           14 LKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK   75 (81)
T ss_dssp             ---CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhh
Confidence            35677889999999999999999999999999999999999999999999999999999865

>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=99.76  E-value=3.1e-19  Score=111.65  Aligned_cols=62  Identities=21%  Similarity=0.304  Sum_probs=56.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh-cCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCC
Q psy17007         46 RKARTVFSDHQLTGLEKRFEA-QRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSP  107 (165)
Q Consensus        46 rr~R~~~s~~q~~~Le~~f~~-~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~  107 (165)
                      .+.|+.|+.+|+.+||..|.. ++||+..++..||..+||++.+|++||+|||++.++.....
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~~~~   64 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLP   64 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhccCC
Confidence            567899999999999999996 99999999999999999999999999999999998755433

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

Probab=99.76  E-value=3.5e-19  Score=117.40  Aligned_cols=63  Identities=19%  Similarity=0.137  Sum_probs=55.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      .....++.|+.|+.+|+.+||..|..++||+..+++.||..+||++.+|++||||||++.++.
T Consensus        21 ~~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~   83 (96)
T 3nar_A           21 PKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNG   83 (96)
T ss_dssp             ------CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhh
Confidence            345567889999999999999999999999999999999999999999999999999998764

>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=99.75  E-value=8.3e-19  Score=109.98  Aligned_cols=63  Identities=19%  Similarity=0.233  Sum_probs=58.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEA---QRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      ..++.++.|+.|+..|+.+|+.+|..   ++||+..+++.||..+||++.+|++||+|+|++.+..
T Consensus         3 ~~~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~   68 (73)
T 1x2n_A            3 SGSSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQS   68 (73)
T ss_dssp             CCSSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhcccc
Confidence            34567888999999999999999987   9999999999999999999999999999999998654

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

Probab=99.75  E-value=5.2e-19  Score=110.93  Aligned_cols=62  Identities=21%  Similarity=0.254  Sum_probs=56.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh-cCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCC
Q psy17007         46 RKARTVFSDHQLTGLEKRFEA-QRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSP  107 (165)
Q Consensus        46 rr~R~~~s~~q~~~Le~~f~~-~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~  107 (165)
                      ++.|+.|+.+|+.+||..|.. ++||+..++..||..+||++.+|++||+|||++.++.....
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~~~~   65 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLP   65 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhccCC
Confidence            567899999999999999995 99999999999999999999999999999999998755433

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

Probab=99.75  E-value=1.2e-18  Score=109.56  Aligned_cols=62  Identities=16%  Similarity=0.236  Sum_probs=57.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCC
Q psy17007         45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTS  106 (165)
Q Consensus        45 ~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~  106 (165)
                      .++.|+.|+.+|+.+||..|..++||+..+++.||..+||++.+|++||+|||++.++....
T Consensus         6 ~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~   67 (74)
T 2ly9_A            6 SFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKSN   67 (74)
T ss_dssp             CCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTTCS
T ss_pred             CCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhCcC
Confidence            46789999999999999999999999999999999999999999999999999999875543

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

Probab=99.75  E-value=9.4e-19  Score=107.00  Aligned_cols=59  Identities=20%  Similarity=0.228  Sum_probs=55.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHH---HhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         44 RRRKARTVFSDHQLTGLEKRF---EAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        44 ~~rr~R~~~s~~q~~~Le~~f---~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      .+++.|+.|+.+|+.+|+.+|   ..++||+..+++.||..+||++.+|++||+|+|++.++
T Consensus         2 ~~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A            2 SGHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             CCCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            357889999999999999999   89999999999999999999999999999999999864

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

Probab=99.75  E-value=4e-19  Score=107.30  Aligned_cols=56  Identities=34%  Similarity=0.495  Sum_probs=50.3

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         48 ARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        48 ~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      .|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||+|||++.++.
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~   57 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ   57 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC--
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhh
Confidence            47899999999999999999999999999999999999999999999999998764

>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=99.75  E-value=4.5e-19  Score=111.07  Aligned_cols=58  Identities=14%  Similarity=0.116  Sum_probs=53.6

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007         47 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS  104 (165)
Q Consensus        47 r~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~  104 (165)
                      ..|..||.+|+.+|+..|..++||+..+++.||..+||++.+|++||+|+|++.+...
T Consensus         5 ~~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~   62 (76)
T 2ecc_A            5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ   62 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHH
Confidence            3456799999999999999999999999999999999999999999999999987644

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

Probab=99.75  E-value=5.6e-19  Score=116.23  Aligned_cols=65  Identities=23%  Similarity=0.330  Sum_probs=60.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhc---------------cchhhhhhhhccCCCCccccCC
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQ---------------LSETQVKTWFQNRLPFGSLFST  105 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~---------------l~~~~V~~WF~nrr~~~~~~~~  105 (165)
                      ..++.++.|+.|+.+|+.+||.+|..++||+..+++.||..+|               |++.+|++||+|||+++++...
T Consensus         3 ~~~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~   82 (95)
T 2cuf_A            3 SGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRAN   82 (95)
T ss_dssp             SSSCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhh
Confidence            4567889999999999999999999999999999999999999               9999999999999999976543

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

Probab=99.74  E-value=5.2e-19  Score=105.35  Aligned_cols=53  Identities=49%  Similarity=0.718  Sum_probs=49.6

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         50 TVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        50 ~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      |.|+.+|+.+||..|..++||+..++..||..+||++.+|++||+|||++.++
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr   54 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRR   54 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhhcc
Confidence            67999999999999999999999999999999999999999999999998865

>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=99.73  E-value=6.5e-19  Score=116.33  Aligned_cols=62  Identities=47%  Similarity=0.609  Sum_probs=54.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007         43 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS  104 (165)
Q Consensus        43 ~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~  104 (165)
                      ++.++.|+.|+..|+.+||..|..++||+..++..||..+||++.+|++||||||++.++..
T Consensus        32 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   93 (97)
T 1b72_A           32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRE   93 (97)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHh
Confidence            45678899999999999999999999999999999999999999999999999999987643

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

Probab=99.72  E-value=3.5e-18  Score=112.79  Aligned_cols=64  Identities=25%  Similarity=0.316  Sum_probs=53.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHH------------------hc---cchhhhhhhhccCCCC
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATA------------------LQ---LSETQVKTWFQNRLPF   99 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~------------------l~---l~~~~V~~WF~nrr~~   99 (165)
                      ..++.++.|+.|+..|+.+||..|..++||+..++++||..                  +|   |++.+|++||+|||++
T Consensus         5 ~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k   84 (99)
T 1lfb_A            5 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE   84 (99)
T ss_dssp             --------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHH
Confidence            45677899999999999999999999999999999999999                  88   9999999999999999


Q ss_pred             ccccC
Q psy17007        100 GSLFS  104 (165)
Q Consensus       100 ~~~~~  104 (165)
                      .++..
T Consensus        85 ~k~k~   89 (99)
T 1lfb_A           85 EAFRH   89 (99)
T ss_dssp             TSCCC
T ss_pred             HHHhc
Confidence            87654

>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=99.72  E-value=3.8e-18  Score=106.95  Aligned_cols=60  Identities=25%  Similarity=0.305  Sum_probs=56.2

Q ss_pred             CCCCCCCCHHHHHHHHHHH---HhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007         46 RKARTVFSDHQLTGLEKRF---EAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST  105 (165)
Q Consensus        46 rr~R~~~s~~q~~~Le~~f---~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~  105 (165)
                      ++.|+.|+..|+.+|+.+|   ..++||+..++..||..+||++.+|++||+|+|++.+....
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~   64 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG   64 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcccccc
Confidence            6788999999999999999   89999999999999999999999999999999999976443

>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=99.72  E-value=7.9e-18  Score=108.00  Aligned_cols=62  Identities=19%  Similarity=0.164  Sum_probs=56.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         42 HCRRRKARTVFSDHQLTGLEKRFEA---QRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        42 ~~~~rr~R~~~s~~q~~~Le~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      ..+.++.|+.|+.+|+.+|+.+|..   ++||+..+++.||..+||+..||++||+|+|++.+..
T Consensus         4 ~~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~   68 (83)
T 2dmn_A            4 GSSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPD   68 (83)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHH
Confidence            4567788999999999999999988   5999999999999999999999999999999998653

>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=99.71  E-value=4.3e-18  Score=102.72  Aligned_cols=54  Identities=28%  Similarity=0.364  Sum_probs=52.0

Q ss_pred             CCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         49 RTVFSDHQLTGLEKRFEA---QRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        49 R~~~s~~q~~~Le~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      |++|+.+|+.+|+.+|..   ++||+..+++.||..+||++.+|++||+|||++.++
T Consensus         2 r~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk   58 (60)
T 1k61_A            2 GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             cCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHccccc
Confidence            689999999999999999   999999999999999999999999999999998865

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

Probab=99.71  E-value=1.5e-18  Score=108.34  Aligned_cols=60  Identities=22%  Similarity=0.258  Sum_probs=54.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHH-HhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007         45 RRKARTVFSDHQLTGLEKRF-EAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS  104 (165)
Q Consensus        45 ~rr~R~~~s~~q~~~Le~~f-~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~  104 (165)
                      +.+.+.+++.+|+.+||..| ..++||+..+++.||..+||++.+|++||||||++++...
T Consensus         8 g~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~~   68 (72)
T 2cqx_A            8 GIKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSG   68 (72)
T ss_dssp             CCCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSCC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCCC
Confidence            34566778899999999999 9999999999999999999999999999999999998654

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

Probab=99.71  E-value=3.8e-18  Score=122.69  Aligned_cols=66  Identities=30%  Similarity=0.336  Sum_probs=52.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCC
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTS  106 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~  106 (165)
                      ..++.+|.|++|+..|+.+||..|..++||+..++..||..+||++.+|++||||||+++++....
T Consensus        95 ~~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~  160 (164)
T 2xsd_C           95 AQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTPA  160 (164)
T ss_dssp             -----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC-
T ss_pred             ccccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhccCC
Confidence            346778899999999999999999999999999999999999999999999999999999876543

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

Probab=99.71  E-value=5.2e-18  Score=111.75  Aligned_cols=63  Identities=21%  Similarity=0.259  Sum_probs=58.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHh---------------------ccchhhhhhhhccCCCC
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATAL---------------------QLSETQVKTWFQNRLPF   99 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l---------------------~l~~~~V~~WF~nrr~~   99 (165)
                      ..++.+|.|+.|+..|+.+||..|..++||+..++++||..+                     +|++.+|++||+|||++
T Consensus         2 ~~~~~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k   81 (102)
T 2da6_A            2 SSGSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKE   81 (102)
T ss_dssp             TTCCSCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHH
Confidence            345678999999999999999999999999999999999999                     68999999999999999


Q ss_pred             cccc
Q psy17007        100 GSLF  103 (165)
Q Consensus       100 ~~~~  103 (165)
                      +++.
T Consensus        82 ~kr~   85 (102)
T 2da6_A           82 EAFR   85 (102)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            8653

>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=99.71  E-value=6e-18  Score=119.53  Aligned_cols=64  Identities=30%  Similarity=0.397  Sum_probs=55.1

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         40 SKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        40 ~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      +..++.++.|+.|+..|+.+||..|..++||+..++..||..+||++.+|++||||||++.++.
T Consensus        82 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           82 GANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             -------CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            3456678899999999999999999999999999999999999999999999999999998764

>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=99.70  E-value=6.1e-18  Score=109.50  Aligned_cols=59  Identities=25%  Similarity=0.335  Sum_probs=55.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcc
Q psy17007         43 CRRRKARTVFSDHQLTGLEKRFEA---QRYLSTPERVELATALQLSETQVKTWFQNRLPFGS  101 (165)
Q Consensus        43 ~~~rr~R~~~s~~q~~~Le~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~  101 (165)
                      .+.++.|++|+.+|+.+|+.+|..   ++||+..+++.||..+||++.+|++||+|||++.+
T Consensus        25 ~~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k   86 (87)
T 1mnm_C           25 STKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK   86 (87)
T ss_dssp             ESSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcc
Confidence            445667899999999999999999   99999999999999999999999999999998875

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

Probab=99.70  E-value=1.5e-17  Score=101.41  Aligned_cols=55  Identities=18%  Similarity=0.165  Sum_probs=51.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007         50 TVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS  104 (165)
Q Consensus        50 ~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~  104 (165)
                      ..++.+|+..||..|..++||+..++..||..+||++.+|++||||||+|.+...
T Consensus         8 ~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~~~   62 (64)
T 2e19_A            8 QPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISVQ   62 (64)
T ss_dssp             CCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSCSS
T ss_pred             CCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCCCC
Confidence            4567999999999999999999999999999999999999999999999987643

>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=99.70  E-value=3.8e-17  Score=106.09  Aligned_cols=57  Identities=19%  Similarity=0.309  Sum_probs=52.6

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCC
Q psy17007         51 VFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSP  107 (165)
Q Consensus        51 ~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~  107 (165)
                      .||.+|+.+||..|..++||+..+++.||..+||++.+|++||+|||++.+......
T Consensus        19 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~~~   75 (89)
T 2dmp_A           19 EKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAV   75 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCSCC
T ss_pred             cCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhHhh
Confidence            489999999999999999999999999999999999999999999999987655443

>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=99.70  E-value=6.5e-18  Score=121.10  Aligned_cols=61  Identities=26%  Similarity=0.415  Sum_probs=54.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         43 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        43 ~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      .+.+|.|+.|+..|+.+||..|..++||+..++..||..+||++.+|++||||||++.++.
T Consensus        99 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C           99 SRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            4678899999999999999999999999999999999999999999999999999998764

>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=99.70  E-value=1e-17  Score=119.07  Aligned_cols=63  Identities=27%  Similarity=0.426  Sum_probs=58.7

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         40 SKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        40 ~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      +..++.+|.|+.|+..|+.+||..|..++||+..++..||..+||++.+|++||||||++.|+
T Consensus        88 ~~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           88 GEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             SSCCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            345677889999999999999999999999999999999999999999999999999998864

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

Probab=99.69  E-value=1.9e-17  Score=102.33  Aligned_cols=56  Identities=46%  Similarity=0.658  Sum_probs=52.4

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007         50 TVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST  105 (165)
Q Consensus        50 ~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~  105 (165)
                      ..+|..|+.+||..|..++||+..++..||..+||++.+|++||||||++.++...
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~~   64 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQL   64 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSSS
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhhh
Confidence            46789999999999999999999999999999999999999999999999987553

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

Probab=99.69  E-value=2e-17  Score=106.98  Aligned_cols=54  Identities=20%  Similarity=0.297  Sum_probs=51.1

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007         51 VFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS  104 (165)
Q Consensus        51 ~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~  104 (165)
                      .||.+|+.+||..|..++||+..++..||..+||++.||++||||||++.+...
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~   70 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE   70 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCC
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHH
Confidence            789999999999999999999999999999999999999999999999886543

>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=99.69  E-value=1.7e-17  Score=106.50  Aligned_cols=59  Identities=24%  Similarity=0.308  Sum_probs=53.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007         46 RKARTVFSDHQLTGLEKRFEA---QRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS  104 (165)
Q Consensus        46 rr~R~~~s~~q~~~Le~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~  104 (165)
                      ++.|++|+.+|+.+|+.+|..   ++||+..++..||..+||+..||++||+|||++.++..
T Consensus         3 ~krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~   64 (83)
T 1le8_B            3 PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTIT   64 (83)
T ss_dssp             --CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHccccccc
Confidence            345667999999999999999   99999999999999999999999999999999997654

>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=99.69  E-value=9.7e-18  Score=108.54  Aligned_cols=59  Identities=25%  Similarity=0.316  Sum_probs=55.0

Q ss_pred             CCCCCCCCHHHHHHHHHHH---HhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007         46 RKARTVFSDHQLTGLEKRF---EAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS  104 (165)
Q Consensus        46 rr~R~~~s~~q~~~Le~~f---~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~  104 (165)
                      ++.|+.|+..|+.+|+.+|   ..++||+..+++.||..+||++.+|++||+|||++.+...
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~   63 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCG
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhcc
Confidence            6789999999999999999   8999999999999999999999999999999999987643

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

Probab=99.69  E-value=7.3e-18  Score=102.14  Aligned_cols=50  Identities=18%  Similarity=0.332  Sum_probs=48.0

Q ss_pred             CHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         53 SDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        53 s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      +.+|+.+||..|..++||+..++++||..+||++.+|++||+|||++.+.
T Consensus        12 ~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kk   61 (66)
T 3nau_A           12 TKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR   61 (66)
T ss_dssp             CHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhc
Confidence            78999999999999999999999999999999999999999999988764

>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=99.68  E-value=2.1e-17  Score=100.19  Aligned_cols=52  Identities=17%  Similarity=0.204  Sum_probs=47.3

Q ss_pred             HHHHHHHHHHH-HhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007         54 DHQLTGLEKRF-EAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST  105 (165)
Q Consensus        54 ~~q~~~Le~~f-~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~  105 (165)
                      ..|+.+||..| ..+.||+..++..||..+||+++||++||||||++++....
T Consensus         9 ~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~~~~   61 (64)
T 1x2m_A            9 AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPSGP   61 (64)
T ss_dssp             SCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCCSSC
T ss_pred             chHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCCCCC
Confidence            45899999999 57999999999999999999999999999999999986543

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

Probab=99.66  E-value=6.4e-17  Score=116.39  Aligned_cols=65  Identities=22%  Similarity=0.211  Sum_probs=54.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST  105 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~  105 (165)
                      ...+.+|.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||++.+....
T Consensus        93 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~  157 (164)
T 2d5v_A           93 RGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWL  157 (164)
T ss_dssp             -------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC--
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccCC
Confidence            44567889999999999999999999999999999999999999999999999999999976543

>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=99.65  E-value=4.1e-17  Score=116.31  Aligned_cols=61  Identities=26%  Similarity=0.327  Sum_probs=57.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         43 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        43 ~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      ++.+|.|+.|+..|+..||..|..++||+..++..||..+||++.+|++||||||++.++.
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             cCCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            4667889999999999999999999999999999999999999999999999999998763

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

Probab=99.57  E-value=9.4e-16  Score=94.34  Aligned_cols=54  Identities=20%  Similarity=0.200  Sum_probs=48.9

Q ss_pred             CCCCHHHHHHHHHHHH---hcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         50 TVFSDHQLTGLEKRFE---AQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        50 ~~~s~~q~~~Le~~f~---~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      ..|+.+|+.+|+.+|.   .++||+..+++.||..+||+..||++||+|+|++.++.
T Consensus         3 g~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~   59 (67)
T 3k2a_A            3 GIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQP   59 (67)
T ss_dssp             ---CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSC
T ss_pred             CcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHH
Confidence            3799999999999999   99999999999999999999999999999999988653

>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=99.56  E-value=7.6e-16  Score=113.04  Aligned_cols=62  Identities=24%  Similarity=0.323  Sum_probs=53.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhc---------------------cchhhhhhhhccCCCC
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQ---------------------LSETQVKTWFQNRLPF   99 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~---------------------l~~~~V~~WF~nrr~~   99 (165)
                      ..++.||.|+.|+..|+.+|+..|..++||+..+|+.||..+|                     |++.+|++||+|||++
T Consensus       111 ~~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~  190 (194)
T 1ic8_A          111 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE  190 (194)
T ss_dssp             ------CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHH
T ss_pred             ccccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhh
Confidence            4467789999999999999999999999999999999999999                     9999999999999988


Q ss_pred             ccc
Q psy17007        100 GSL  102 (165)
Q Consensus       100 ~~~  102 (165)
                      .+.
T Consensus       191 ~k~  193 (194)
T 1ic8_A          191 EAF  193 (194)
T ss_dssp             CC-
T ss_pred             hhc
Confidence            753

>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=99.55  E-value=2.4e-15  Score=91.54  Aligned_cols=47  Identities=19%  Similarity=0.395  Sum_probs=44.7

Q ss_pred             HHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCc
Q psy17007         54 DHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFG  100 (165)
Q Consensus        54 ~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~  100 (165)
                      ++|+..|+.+|..+++|+.+++..||..+||+.++|++||||||+..
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~~   60 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVYQ   60 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhccccc
Confidence            57899999999999999999999999999999999999999999754

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

Probab=99.52  E-value=8.6e-15  Score=108.66  Aligned_cols=62  Identities=23%  Similarity=0.315  Sum_probs=53.9

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhc---------------------cchhhhhhhhccCC
Q psy17007         39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQ---------------------LSETQVKTWFQNRL   97 (165)
Q Consensus        39 ~~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~---------------------l~~~~V~~WF~nrr   97 (165)
                      ....++.||.|+.|+..|+.+|+..|..++||+..+|++||..+|                     |++.+|++||+|||
T Consensus       136 ~~~~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR  215 (221)
T 2h8r_A          136 EPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRR  215 (221)
T ss_dssp             ------CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHH
T ss_pred             ccccCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhh
Confidence            445677889999999999999999999999999999999999998                     89999999999999


Q ss_pred             CCc
Q psy17007         98 PFG  100 (165)
Q Consensus        98 ~~~  100 (165)
                      +.+
T Consensus       216 ~~~  218 (221)
T 2h8r_A          216 KEE  218 (221)
T ss_dssp             TTC
T ss_pred             hhh
Confidence            876

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

Probab=99.39  E-value=1.3e-13  Score=88.52  Aligned_cols=53  Identities=23%  Similarity=0.232  Sum_probs=49.7

Q ss_pred             CCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         50 TVFSDHQLTGLEKRFEA---QRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        50 ~~~s~~q~~~Le~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      ..|+.+++.+|+.+|..   ++||+..++..||..+||++.||++||+|+|.+.+.
T Consensus        10 ~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk   65 (89)
T 2lk2_A           10 HMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLP   65 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhh
Confidence            46899999999999987   999999999999999999999999999999988753

>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=99.37  E-value=2.4e-13  Score=89.42  Aligned_cols=79  Identities=29%  Similarity=0.344  Sum_probs=51.2

Q ss_pred             HhccchhhhhhhhccCCCCccccCCCCCccCccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhh
Q psy17007         81 ALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ  160 (165)
Q Consensus        81 ~l~l~~~~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~q  160 (165)
                      .++++..+|..||++.|...+...    .........++.|+.||.+|+..||..|..++||+..++.+||..+||++.|
T Consensus         2 ~~~~~~~~~~~W~~~~r~~~~~~~----~~~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~q   77 (97)
T 1b72_A            2 EPNTPTARTFDWMKVKRNPPKTAK----VSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQ   77 (97)
T ss_dssp             ------CCCCGGGGC------------------------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHH
T ss_pred             CCCCCCcccccccccccCCCCCCC----CCCCCCCCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHH
Confidence            456778899999999887654321    1112234566789999999999999999999999999999999999999999


Q ss_pred             hhh
Q psy17007        161 LFY  163 (165)
Q Consensus       161 Vq~  163 (165)
                      |+-
T Consensus        78 V~v   80 (97)
T 1b72_A           78 VKI   80 (97)
T ss_dssp             HHH
T ss_pred             hHH
Confidence            984

>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=99.29  E-value=1.7e-12  Score=104.83  Aligned_cols=56  Identities=25%  Similarity=0.350  Sum_probs=52.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcc
Q psy17007         46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGS  101 (165)
Q Consensus        46 rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~  101 (165)
                      ++.++.++..|+..|+..|..++||+..+|++||..+||+++||++||+|||+|.|
T Consensus       366 ~~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          366 TAAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            34577899999999999999999999999999999999999999999999999874

>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=99.12  E-value=5e-11  Score=73.62  Aligned_cols=50  Identities=30%  Similarity=0.487  Sum_probs=46.1

Q ss_pred             ccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        114 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ....++.++.||.+|+..||..|..++||+..++.+||..+||++.||+-
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~   53 (70)
T 2cra_A            4 GSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITI   53 (70)
T ss_dssp             SCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhH
Confidence            34567789999999999999999999999999999999999999999974

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

Probab=99.11  E-value=7e-11  Score=72.96  Aligned_cols=50  Identities=44%  Similarity=0.713  Sum_probs=46.1

Q ss_pred             ccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        114 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ....++.++.||.+|+..||..|..++||+..++++||..+||++.||+.
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~   53 (70)
T 2djn_A            4 GSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKI   53 (70)
T ss_dssp             CCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHH
Confidence            34567789999999999999999999999999999999999999999984

>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=99.10  E-value=1e-10  Score=74.05  Aligned_cols=53  Identities=17%  Similarity=0.188  Sum_probs=48.3

Q ss_pred             CccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        111 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       111 ~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      +....+.++.|+.||.+|+..|+..|..++||+..++++||..+||++.||+.
T Consensus        11 ~~~~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~   63 (80)
T 2da3_A           11 GEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQV   63 (80)
T ss_dssp             CCCCCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHH
Confidence            34456677889999999999999999999999999999999999999999985

>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=99.10  E-value=8.2e-11  Score=74.53  Aligned_cols=53  Identities=55%  Similarity=0.850  Sum_probs=48.0

Q ss_pred             CccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        111 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       111 ~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      +....+.++.++.||.+|+.+||..|..++||+..++++||..+||++.||+-
T Consensus        11 ~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~v   63 (80)
T 2dmt_A           11 GTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKT   63 (80)
T ss_dssp             CCCCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHH
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeee
Confidence            34455677889999999999999999999999999999999999999999984

>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=99.09  E-value=8.2e-11  Score=72.62  Aligned_cols=50  Identities=30%  Similarity=0.379  Sum_probs=46.2

Q ss_pred             ccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        114 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ....++.++.||.+|+..||..|..++||+..++++||..+||++.||+.
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~   53 (70)
T 2da2_A            4 GSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVV   53 (70)
T ss_dssp             SCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHH
Confidence            34567789999999999999999999999999999999999999999984

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

Probab=99.09  E-value=6.9e-11  Score=72.98  Aligned_cols=49  Identities=33%  Similarity=0.527  Sum_probs=45.6

Q ss_pred             cccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        115 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       115 ~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ...++.++.||.+|+..||..|..++||+..++++||..+||++.||+.
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~   53 (70)
T 2dmu_A            5 SSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEV   53 (70)
T ss_dssp             TSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeeh
Confidence            3456789999999999999999999999999999999999999999984

>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=99.08  E-value=1e-10  Score=73.51  Aligned_cols=54  Identities=33%  Similarity=0.368  Sum_probs=48.2

Q ss_pred             cCccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        110 LGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       110 ~~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ........++.++.||.+|+..||..|..++||+..++.+||..+||++.||+.
T Consensus         6 ~~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~v   59 (77)
T 1puf_A            6 NWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKI   59 (77)
T ss_dssp             TSCCCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             ccccCCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHH
Confidence            334445667789999999999999999999999999999999999999999984

>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=99.08  E-value=1.3e-10  Score=73.67  Aligned_cols=50  Identities=14%  Similarity=0.048  Sum_probs=46.2

Q ss_pred             ccccccccccccccchhhhhhhccc----cCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        114 HCRRRKARTVFSDHQLTGLEKRFEA----QRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       114 ~~~~rr~rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ..+.++.|+.||.+|+..||..|+.    ++||+..++++||..|||++.|||-
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~Vkv   67 (80)
T 1wh5_A           14 GGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKV   67 (80)
T ss_dssp             CCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccC
Confidence            3456778999999999999999999    9999999999999999999999984

>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=99.08  E-value=6.6e-11  Score=73.86  Aligned_cols=44  Identities=14%  Similarity=0.148  Sum_probs=41.7

Q ss_pred             cccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007        119 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLF  162 (165)
Q Consensus       119 r~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq  162 (165)
                      ..+..||.+|+.+|++.|..++||+..++++||..+||++.||+
T Consensus         5 ~~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIk   48 (76)
T 2ecc_A            5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEII   48 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhh
Confidence            35677999999999999999999999999999999999999997

>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=99.07  E-value=1.3e-10  Score=70.27  Aligned_cols=50  Identities=18%  Similarity=0.163  Sum_probs=46.3

Q ss_pred             cccccccccccccchhhhhhhccc-cCCCCHHHHHHHHHHcCCChhhhhhc
Q psy17007        115 CRRRKARTVFSDHQLTGLEKRFEA-QRYLSTPERVELATALQLSETQLFYV  164 (165)
Q Consensus       115 ~~~rr~rt~ft~~Q~~~Le~~F~~-~~yp~~~~r~~La~~lgl~~~qVq~~  164 (165)
                      ...++.||.|+.+|+..|+.+|+. ++||+.++++.||.++||++++||-+
T Consensus         5 ~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVW   55 (71)
T 1wi3_A            5 SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKF   55 (71)
T ss_dssp             CCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHH
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHh
Confidence            356778999999999999999999 99999999999999999999999853

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

Probab=99.07  E-value=7.8e-11  Score=70.01  Aligned_cols=46  Identities=46%  Similarity=0.711  Sum_probs=43.3

Q ss_pred             ccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ++.++.||.+|+..||..|..++||+..++.+||..+||++.||+.
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~   46 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKI   46 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhh
Confidence            3568999999999999999999999999999999999999999984

>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=99.05  E-value=1.4e-10  Score=72.91  Aligned_cols=51  Identities=43%  Similarity=0.645  Sum_probs=46.7

Q ss_pred             cccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        113 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       113 ~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .+.+.++.++.||.+|+..||..|..++||+..++.+||..+||++.||+-
T Consensus         5 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~   55 (77)
T 1nk2_P            5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKI   55 (77)
T ss_dssp             CSCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHH
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHH
Confidence            345567789999999999999999999999999999999999999999974

>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=99.05  E-value=7.8e-11  Score=70.78  Aligned_cols=47  Identities=36%  Similarity=0.633  Sum_probs=41.8

Q ss_pred             cccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       117 ~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .++.++.||.+|+..||..|..++||+..++.+||..+||++.||+.
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~   49 (61)
T 2hdd_A            3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKI   49 (61)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHH
Confidence            46678999999999999999999999999999999999999999984

>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=99.05  E-value=7.4e-11  Score=72.82  Aligned_cols=50  Identities=22%  Similarity=0.238  Sum_probs=46.2

Q ss_pred             ccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        114 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ....++.++.||.+|+..||..|..++||+..++.+||..+||++.||+.
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~   53 (70)
T 2da1_A            4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKH   53 (70)
T ss_dssp             SCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHH
Confidence            34567789999999999999999999999999999999999999999974

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

Probab=99.04  E-value=9.9e-11  Score=70.77  Aligned_cols=47  Identities=40%  Similarity=0.651  Sum_probs=43.2

Q ss_pred             cccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       117 ~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .++.++.||.+|+..||..|..++||+..++.+||..+||++.||+.
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~   49 (63)
T 2h1k_A            3 NKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKI   49 (63)
T ss_dssp             --CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhH
Confidence            45678999999999999999999999999999999999999999984

>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=99.04  E-value=1.7e-10  Score=71.24  Aligned_cols=48  Identities=48%  Similarity=0.642  Sum_probs=44.7

Q ss_pred             ccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       116 ~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ..++.++.||.+|+..||..|..++||+..++.+||..+||++.||+.
T Consensus         6 ~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~   53 (70)
T 2e1o_A            6 SGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKT   53 (70)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhH
Confidence            455678999999999999999999999999999999999999999984

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

Probab=99.04  E-value=2e-10  Score=72.76  Aligned_cols=49  Identities=31%  Similarity=0.487  Sum_probs=45.5

Q ss_pred             cccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        115 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       115 ~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ...++.++.||.+|+..||..|..++||+..++.+||..+||++.||+-
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~v   53 (80)
T 2cue_A            5 SSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQV   53 (80)
T ss_dssp             CSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHH
T ss_pred             CCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhH
Confidence            3456789999999999999999999999999999999999999999974

>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=99.04  E-value=1.8e-10  Score=72.93  Aligned_cols=50  Identities=12%  Similarity=0.087  Sum_probs=45.6

Q ss_pred             cccccccccccccccchhhhhhhccc-----cCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        113 KHCRRRKARTVFSDHQLTGLEKRFEA-----QRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       113 ~~~~~rr~rt~ft~~Q~~~Le~~F~~-----~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ...+.++.|+.||.+|+..|| +|..     ++||+..++++||..|||++.|||-
T Consensus        13 ~~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkv   67 (80)
T 1wh7_A           13 SGGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKI   67 (80)
T ss_dssp             CCCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHH
T ss_pred             CCCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccc
Confidence            345567889999999999999 8999     9999999999999999999999984

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

Probab=99.04  E-value=2.4e-10  Score=72.95  Aligned_cols=52  Identities=40%  Similarity=0.523  Sum_probs=47.6

Q ss_pred             ccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        112 SKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       112 ~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ....+.++.|+.||.+|+..||..|..++||+..++..||..+||++.||+.
T Consensus        17 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~v   68 (84)
T 2kt0_A           17 KVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKT   68 (84)
T ss_dssp             CCCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHH
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHH
Confidence            3445677889999999999999999999999999999999999999999984

>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=99.04  E-value=1.2e-10  Score=71.01  Aligned_cols=48  Identities=21%  Similarity=0.248  Sum_probs=44.9

Q ss_pred             ccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       116 ~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      +.++.++.||.+|+..||..|..++||+..++++||..+||++.||+.
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~   49 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRV   49 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHH
Confidence            356789999999999999999999999999999999999999999974

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

Probab=99.04  E-value=1.7e-10  Score=73.08  Aligned_cols=49  Identities=33%  Similarity=0.421  Sum_probs=45.9

Q ss_pred             cccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        115 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       115 ~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ...++.|+.||.+|+..||..|..++||+..++++||..+||++.||+.
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~   53 (80)
T 2dms_A            5 SSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQV   53 (80)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhh
Confidence            4567789999999999999999999999999999999999999999974

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

Probab=99.03  E-value=9.8e-11  Score=70.57  Aligned_cols=47  Identities=45%  Similarity=0.606  Sum_probs=40.9

Q ss_pred             cccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       117 ~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .++.++.||.+|+..||..|..++||+..++.+||..+||++.||+.
T Consensus         3 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~   49 (62)
T 2vi6_A            3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKT   49 (62)
T ss_dssp             -----CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhH
Confidence            45678999999999999999999999999999999999999999974

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

Probab=99.03  E-value=1.2e-10  Score=69.78  Aligned_cols=46  Identities=43%  Similarity=0.653  Sum_probs=43.0

Q ss_pred             ccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ++.++.||.+|+..||..|..++||+..++.+||..+||++.||+.
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~   47 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKV   47 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHH
Confidence            4578999999999999999999999999999999999999999974

>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=99.03  E-value=1.9e-10  Score=72.83  Aligned_cols=49  Identities=22%  Similarity=0.306  Sum_probs=45.8

Q ss_pred             cccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        115 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       115 ~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ...++.++.||.+|+..||..|..++||+..++.+||..+||++.||+.
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~   53 (80)
T 2dmq_A            5 SSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQV   53 (80)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhH
Confidence            4467789999999999999999999999999999999999999999984

>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=99.02  E-value=1.1e-10  Score=70.08  Aligned_cols=48  Identities=21%  Similarity=0.264  Sum_probs=39.0

Q ss_pred             ccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       116 ~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      +.++.++.||.+|+..|+..|..++||+..++.+||..+||++.||+-
T Consensus         4 k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~   51 (61)
T 1akh_A            4 KSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRV   51 (61)
T ss_dssp             --------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHH
Confidence            456778999999999999999999999999999999999999999974

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

Probab=99.02  E-value=1.9e-10  Score=70.59  Aligned_cols=47  Identities=34%  Similarity=0.588  Sum_probs=44.2

Q ss_pred             cccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       117 ~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .++.++.||.+|+..||..|..++||+..++.+||..+||++.||+.
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~   48 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKI   48 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhH
Confidence            45678999999999999999999999999999999999999999974

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

Probab=99.01  E-value=1.7e-10  Score=71.80  Aligned_cols=49  Identities=24%  Similarity=0.464  Sum_probs=45.7

Q ss_pred             cccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        115 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       115 ~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ...++.++.||.+|+..||..|..++||+..++.+||..+||++.||+-
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~v   53 (73)
T 2l7z_A            5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTI   53 (73)
T ss_dssp             SCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHH
Confidence            4567789999999999999999999999999999999999999999974

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

Probab=99.00  E-value=2.6e-10  Score=67.62  Aligned_cols=46  Identities=52%  Similarity=0.780  Sum_probs=43.6

Q ss_pred             ccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ++.++.||.+|+..|+..|..++||+..++++||..+||++.||+.
T Consensus         3 rr~Rt~~t~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~   48 (58)
T 3rkq_A            3 RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKI   48 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCCcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHH
Confidence            5678999999999999999999999999999999999999999974

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

Probab=98.99  E-value=2.9e-10  Score=69.50  Aligned_cols=46  Identities=28%  Similarity=0.390  Sum_probs=43.6

Q ss_pred             ccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ++.++.||.+|+..|+..|..++||+..++.+||..+||++.||+.
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~   47 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQI   47 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhH
Confidence            5678999999999999999999999999999999999999999974

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

Probab=98.98  E-value=3.7e-10  Score=72.75  Aligned_cols=50  Identities=36%  Similarity=0.546  Sum_probs=42.7

Q ss_pred             ccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        114 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ....++.|+.||.+|+..||..|..++||+..++.+||..+||++.||+-
T Consensus        25 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~v   74 (88)
T 2r5y_A           25 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKI   74 (88)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHH
T ss_pred             CCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhH
Confidence            34567789999999999999999999999999999999999999999984

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

Probab=98.97  E-value=2.4e-10  Score=68.39  Aligned_cols=44  Identities=32%  Similarity=0.449  Sum_probs=39.9

Q ss_pred             ccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        120 ARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       120 ~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .|+.||.+|+..||..|..++||+..++.+||..+||++.||+.
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~   45 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQV   45 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHH
Confidence            57899999999999999999999999999999999999999974

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

Probab=98.97  E-value=3.1e-10  Score=69.65  Aligned_cols=47  Identities=49%  Similarity=0.753  Sum_probs=44.0

Q ss_pred             cccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       117 ~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .++.++.||.+|+..||..|..++||+..++.+||..+||++.+|+.
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~   48 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKI   48 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHH
Confidence            35678999999999999999999999999999999999999999974

>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=98.96  E-value=2e-10  Score=70.52  Aligned_cols=46  Identities=37%  Similarity=0.592  Sum_probs=43.7

Q ss_pred             ccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ++.++.||.+|+..||..|..++||+..++.+||..+||++.||+.
T Consensus         3 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~v   48 (68)
T 1ahd_P            3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKI   48 (68)
T ss_dssp             SCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhH
Confidence            5678999999999999999999999999999999999999999974

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

Probab=98.96  E-value=4.7e-10  Score=70.00  Aligned_cols=50  Identities=32%  Similarity=0.468  Sum_probs=45.9

Q ss_pred             ccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        114 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ..+.++.++.||.+|+..|+..|..++||+..++.+||..+||++.||+.
T Consensus         6 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~   55 (75)
T 2m0c_A            6 KGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQV   55 (75)
T ss_dssp             CSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHH
Confidence            34556789999999999999999999999999999999999999999974

>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=98.96  E-value=3.6e-10  Score=71.72  Aligned_cols=50  Identities=36%  Similarity=0.522  Sum_probs=45.5

Q ss_pred             ccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        114 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ..+.++.++.||.+|+..|+..|..++||+..++.+||..+||++.||+.
T Consensus        15 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~   64 (81)
T 1fjl_A           15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQV   64 (81)
T ss_dssp             --CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHH
Confidence            45567789999999999999999999999999999999999999999984

>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=98.95  E-value=5.3e-10  Score=69.91  Aligned_cols=46  Identities=15%  Similarity=0.115  Sum_probs=42.6

Q ss_pred             ccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ...+..||.+|+.+||..|..++||+..++.+||..+||++.||+.
T Consensus         8 ~~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~   53 (75)
T 2da5_A            8 PTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDS   53 (75)
T ss_dssp             SCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhH
Confidence            3456789999999999999999999999999999999999999984

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

Probab=98.94  E-value=6.7e-10  Score=72.29  Aligned_cols=51  Identities=39%  Similarity=0.628  Sum_probs=46.7

Q ss_pred             cccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        113 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       113 ~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ...+.++.++.||.+|+..||..|..++||+..++.+||..+||++.||+.
T Consensus        13 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~v   63 (93)
T 3a01_A           13 TPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKT   63 (93)
T ss_dssp             CCCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHH
T ss_pred             CCCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhccc
Confidence            344567789999999999999999999999999999999999999999984

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

Probab=98.94  E-value=4.2e-10  Score=70.54  Aligned_cols=47  Identities=19%  Similarity=0.176  Sum_probs=43.5

Q ss_pred             cccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       117 ~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ....++.||.+|+..||..|..++||+..++++||..+||++.||+.
T Consensus         8 ~~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~   54 (76)
T 2dn0_A            8 ASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRK   54 (76)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHH
T ss_pred             CCCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhH
Confidence            34458899999999999999999999999999999999999999984

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

Probab=98.94  E-value=2.6e-10  Score=72.17  Aligned_cols=50  Identities=22%  Similarity=0.229  Sum_probs=46.1

Q ss_pred             ccccccccccccccchhhhhhhcccc----CCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        114 HCRRRKARTVFSDHQLTGLEKRFEAQ----RYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~----~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ..+.++.|+.||.+|+..||..|+.+    +||+..++++||..+||++.||+.
T Consensus         5 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~v   58 (80)
T 2da4_A            5 SSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRT   58 (80)
T ss_dssp             CCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhH
Confidence            34567789999999999999999999    999999999999999999999984

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

Probab=98.93  E-value=4.1e-10  Score=66.44  Aligned_cols=42  Identities=43%  Similarity=0.643  Sum_probs=38.9

Q ss_pred             ccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        122 TVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       122 t~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      +.||.+|+..||..|..++||+..++.+||..+||++.||+-
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~   43 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKT   43 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhH
Confidence            579999999999999999999999999999999999999984

>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=98.93  E-value=2.1e-10  Score=70.35  Aligned_cols=47  Identities=34%  Similarity=0.512  Sum_probs=44.4

Q ss_pred             cccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       117 ~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .++.++.||.+|+..||..|..++||+..++.+||..+||++.||+.
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~   49 (68)
T 1yz8_P            3 QRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRV   49 (68)
T ss_dssp             SSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHH
Confidence            46778999999999999999999999999999999999999999974

>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=98.93  E-value=4.9e-10  Score=71.10  Aligned_cols=49  Identities=37%  Similarity=0.565  Sum_probs=41.8

Q ss_pred             cccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        115 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       115 ~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ...++.++.||.+|+..||..|..++||+..++.+||..+||++.||+.
T Consensus        18 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~v   66 (81)
T 1b8i_A           18 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKI   66 (81)
T ss_dssp             ------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHH
Confidence            3456789999999999999999999999999999999999999999974

>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=98.91  E-value=7.4e-10  Score=68.66  Aligned_cols=46  Identities=17%  Similarity=0.181  Sum_probs=42.9

Q ss_pred             ccccccccccchhhhhhhccc-cCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRFEA-QRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F~~-~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .+.++.||.+|+..||..|.. ++||+..++.+||..+||++.||+.
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~   48 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQK   48 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhH
Confidence            356889999999999999996 9999999999999999999999984

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

Probab=98.90  E-value=1.2e-09  Score=66.03  Aligned_cols=47  Identities=17%  Similarity=0.152  Sum_probs=43.9

Q ss_pred             cccccccccccchhhhhhhc---cccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        117 RRKARTVFSDHQLTGLEKRF---EAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       117 ~rr~rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .++.++.|+.+|+..|+..|   ..++||+..++.+||..+||++.||+-
T Consensus         3 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~   52 (64)
T 1du6_A            3 GHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSN   52 (64)
T ss_dssp             CCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence            45678999999999999999   999999999999999999999999974

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

Probab=98.90  E-value=8e-10  Score=68.70  Aligned_cols=46  Identities=17%  Similarity=0.114  Sum_probs=43.0

Q ss_pred             ccccccccccchhhhhhhccc-cCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRFEA-QRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F~~-~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .+.++.||.+|+..||..|.. ++||+..++.+||..+||++.||+.
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~   49 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQK   49 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence            457899999999999999995 9999999999999999999999984

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

Probab=98.89  E-value=1.1e-09  Score=68.15  Aligned_cols=47  Identities=15%  Similarity=0.172  Sum_probs=44.2

Q ss_pred             cccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       117 ~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ..+.++.||.+|+..|+..|..++||+..++++||..+||++.||+.
T Consensus         6 ~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~   52 (74)
T 2ly9_A            6 SFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKK   52 (74)
T ss_dssp             CCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHH
T ss_pred             CCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeee
Confidence            45678999999999999999999999999999999999999999974

>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=98.86  E-value=1.7e-09  Score=67.22  Aligned_cols=49  Identities=16%  Similarity=0.222  Sum_probs=44.6

Q ss_pred             cccccccccccccchhhhhhhccc---cCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        115 CRRRKARTVFSDHQLTGLEKRFEA---QRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       115 ~~~rr~rt~ft~~Q~~~Le~~F~~---~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ...++.++.|+.+|+..|+..|..   ++||+..++++||..+||++.||+-
T Consensus         5 ~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~   56 (73)
T 1x2n_A            5 SSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNN   56 (73)
T ss_dssp             SSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence            345677899999999999999976   9999999999999999999999974

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

Probab=98.86  E-value=1.2e-09  Score=71.53  Aligned_cols=51  Identities=20%  Similarity=0.140  Sum_probs=43.3

Q ss_pred             cccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        113 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       113 ~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .....++.++.||.+|+..|+..|..++||+..++++||..+||++.||+.
T Consensus        21 ~~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~v   71 (96)
T 3nar_A           21 PKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVS   71 (96)
T ss_dssp             ------CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHH
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeee
Confidence            344556788999999999999999999999999999999999999999974

>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=98.83  E-value=1.8e-09  Score=64.52  Aligned_cols=43  Identities=26%  Similarity=0.276  Sum_probs=41.0

Q ss_pred             cccccccchhhhhhhccc---cCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        121 RTVFSDHQLTGLEKRFEA---QRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       121 rt~ft~~Q~~~Le~~F~~---~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ++.||.+|+..|+..|..   ++||+..++++||..+||++.||+-
T Consensus         2 r~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~   47 (60)
T 1k61_A            2 GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKN   47 (60)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHH
T ss_pred             cCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHH
Confidence            578999999999999999   9999999999999999999999974

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

Probab=98.83  E-value=4.6e-09  Score=65.05  Aligned_cols=46  Identities=22%  Similarity=0.178  Sum_probs=42.5

Q ss_pred             ccccccccccchhhhhhhc-cccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRF-EAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F-~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .+.+..++.+|+.+||..| ..++||+..++++||..+||++.|||-
T Consensus         9 ~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqv   55 (72)
T 2cqx_A            9 IKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQC   55 (72)
T ss_dssp             CCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcch
Confidence            4556779999999999999 999999999999999999999999984

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

Probab=98.81  E-value=1.9e-09  Score=65.09  Aligned_cols=40  Identities=15%  Similarity=0.215  Sum_probs=37.8

Q ss_pred             ccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        124 FSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       124 ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      -|.+|+.+||..|..++||+..++++||..+||++.||+-
T Consensus        11 ~~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkv   50 (66)
T 3nau_A           11 KTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKK   50 (66)
T ss_dssp             CCHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHH
T ss_pred             hhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhH
Confidence            4679999999999999999999999999999999999974

>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=98.81  E-value=2.9e-09  Score=66.12  Aligned_cols=46  Identities=24%  Similarity=0.302  Sum_probs=43.3

Q ss_pred             ccccccccccchhhhhhhc---cccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRF---EAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ++.++.||.+|+..|+..|   ..++||+..++..||..+||++.||+-
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~   50 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSN   50 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHH
Confidence            4678999999999999999   999999999999999999999999974

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

Probab=98.78  E-value=5.7e-09  Score=67.16  Aligned_cols=41  Identities=20%  Similarity=0.161  Sum_probs=39.7

Q ss_pred             cccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        123 VFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       123 ~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .||.+|+.+||+.|..++||+..++.+||..+||++.||+-
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkv   57 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDA   57 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCee
Confidence            79999999999999999999999999999999999999973

>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=98.76  E-value=7.2e-09  Score=66.82  Aligned_cols=43  Identities=19%  Similarity=0.127  Sum_probs=40.3

Q ss_pred             cccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        121 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       121 rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ...||.+|+.+||..|..++||+..++++||..+||++.||+.
T Consensus        17 ~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~v   59 (89)
T 2dmp_A           17 FKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDS   59 (89)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             cccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccH
Confidence            4459999999999999999999999999999999999999984

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

Probab=98.76  E-value=3.9e-09  Score=68.89  Aligned_cols=49  Identities=20%  Similarity=0.371  Sum_probs=45.7

Q ss_pred             cccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcC---------------CChhhhhh
Q psy17007        115 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQ---------------LSETQLFY  163 (165)
Q Consensus       115 ~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lg---------------l~~~qVq~  163 (165)
                      .+.++.|+.||.+|+..||..|+.++||+..++++||..+|               |++.+|+.
T Consensus         5 ~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~   68 (95)
T 2cuf_A            5 SSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYN   68 (95)
T ss_dssp             SCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHH
Confidence            45677899999999999999999999999999999999999               99999985

>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=98.74  E-value=6.7e-09  Score=66.10  Aligned_cols=49  Identities=18%  Similarity=0.163  Sum_probs=44.3

Q ss_pred             cccccccccccccchhhhhhhccc---cCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        115 CRRRKARTVFSDHQLTGLEKRFEA---QRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       115 ~~~rr~rt~ft~~Q~~~Le~~F~~---~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ...++.++.|+.+|+..|+..|..   ++||+..++++||..+||++.||+-
T Consensus         5 ~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~   56 (83)
T 2dmn_A            5 SSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISN   56 (83)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhH
Confidence            445677899999999999999877   6999999999999999999999974

>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=98.73  E-value=6.4e-09  Score=66.69  Aligned_cols=46  Identities=24%  Similarity=0.302  Sum_probs=42.9

Q ss_pred             ccccccccccchhhhhhhc---cccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRF---EAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F---~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ++.++.|+.+|+..|+..|   ..++||+..++.+||..+||++.||+-
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~   50 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSN   50 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence            4678999999999999999   999999999999999999999999974

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

Probab=98.73  E-value=7.2e-09  Score=62.71  Aligned_cols=43  Identities=14%  Similarity=0.039  Sum_probs=39.9

Q ss_pred             cccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        121 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       121 rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ...++.+|+..||..|..++||+..++.+||..+||++.||+-
T Consensus         7 ~~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqv   49 (64)
T 2e19_A            7 GQPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKK   49 (64)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCc
Confidence            4557799999999999999999999999999999999999984

>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=98.72  E-value=9.3e-09  Score=67.52  Aligned_cols=49  Identities=16%  Similarity=0.209  Sum_probs=45.1

Q ss_pred             cccccccccccccchhhhhhhccccCCCCHHHHHHHHHHc---------------------CCChhhhhh
Q psy17007        115 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATAL---------------------QLSETQLFY  163 (165)
Q Consensus       115 ~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l---------------------gl~~~qVq~  163 (165)
                      .+.++.|+.|+..|+.+||+.|+.++||+..+|++||..+                     +|++.+|+.
T Consensus         4 ~~~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~   73 (102)
T 2da6_A            4 GSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYN   73 (102)
T ss_dssp             CCSCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHH
T ss_pred             CCCCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceee
Confidence            4567789999999999999999999999999999999999                     799999874

>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=98.72  E-value=6.9e-09  Score=66.59  Aligned_cols=49  Identities=22%  Similarity=0.236  Sum_probs=44.9

Q ss_pred             cccccccccccccchhhhhhhccc---cCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        115 CRRRKARTVFSDHQLTGLEKRFEA---QRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       115 ~~~rr~rt~ft~~Q~~~Le~~F~~---~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ...++.++.|+.+|+..|+..|..   ++||+..++.+||..+||++.||+-
T Consensus        25 ~~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~   76 (87)
T 1mnm_C           25 STKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKN   76 (87)
T ss_dssp             ESSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHH
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHH
Confidence            345566889999999999999999   9999999999999999999999974

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

Probab=98.70  E-value=8.5e-09  Score=67.70  Aligned_cols=49  Identities=22%  Similarity=0.295  Sum_probs=41.6

Q ss_pred             cccccccccccccchhhhhhhccccCCCCHHHHHHHHHH------------------cC---CChhhhhh
Q psy17007        115 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATA------------------LQ---LSETQLFY  163 (165)
Q Consensus       115 ~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~------------------lg---l~~~qVq~  163 (165)
                      .+.++.|+.||..|+..||..|+.++||+..+|++||..                  +|   |++.+|+.
T Consensus         7 ~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~v   76 (99)
T 1lfb_A            7 KKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYN   76 (99)
T ss_dssp             ------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHH
T ss_pred             CCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeee
Confidence            346778999999999999999999999999999999999                  99   99999975

>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=98.65  E-value=1.1e-08  Score=71.86  Aligned_cols=51  Identities=27%  Similarity=0.315  Sum_probs=43.5

Q ss_pred             cccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        113 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       113 ~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ...+.++.|+.||.+|+..||..|..++||+..++.+||..+||++.||+-
T Consensus        83 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~v  133 (146)
T 1au7_A           83 ANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRV  133 (146)
T ss_dssp             ------CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchh
Confidence            345567789999999999999999999999999999999999999999974

>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=98.65  E-value=1.5e-08  Score=71.55  Aligned_cols=50  Identities=24%  Similarity=0.349  Sum_probs=46.3

Q ss_pred             ccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        114 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ..+.++.|+.||.+|+..||..|..++||+..++.+||..+||++.||+-
T Consensus        90 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~v  139 (151)
T 3d1n_I           90 PSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRV  139 (151)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             CCCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHH
Confidence            34567789999999999999999999999999999999999999999974

>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=98.65  E-value=1.2e-08  Score=64.86  Aligned_cols=45  Identities=24%  Similarity=0.244  Sum_probs=41.3

Q ss_pred             cccccccccchhhhhhhccc---cCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        119 KARTVFSDHQLTGLEKRFEA---QRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       119 r~rt~ft~~Q~~~Le~~F~~---~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      +.++.|+.+|+..|+..|..   ++||+..++.+||..+||++.||+-
T Consensus         4 krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~   51 (83)
T 1le8_B            4 YRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKN   51 (83)
T ss_dssp             -CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHccc
Confidence            34667999999999999999   9999999999999999999999974

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

Probab=98.62  E-value=1.9e-08  Score=61.69  Aligned_cols=42  Identities=45%  Similarity=0.683  Sum_probs=39.5

Q ss_pred             ccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        122 TVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       122 t~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ..+|..|+.+||..|..++||+..++.+||..+||++.|||-
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqv   50 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKI   50 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHH
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheee
Confidence            357899999999999999999999999999999999999984

>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=98.61  E-value=1.6e-08  Score=72.08  Aligned_cols=49  Identities=24%  Similarity=0.315  Sum_probs=42.8

Q ss_pred             cccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        115 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       115 ~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .+.++.|+.||.+|+..||..|..++||+..++.+||..+||++.||+-
T Consensus        99 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~v  147 (160)
T 1e3o_C           99 SRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRV  147 (160)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhH
Confidence            4667889999999999999999999999999999999999999999984

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

Probab=98.60  E-value=1.8e-08  Score=71.99  Aligned_cols=50  Identities=22%  Similarity=0.261  Sum_probs=42.8

Q ss_pred             ccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        114 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ....++.|+.||.+|+..|+..|..++||+..++.+||..+||++.||+-
T Consensus        94 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~  143 (164)
T 2d5v_A           94 GNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSN  143 (164)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhh
Confidence            44567789999999999999999999999999999999999999999984

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

Probab=98.60  E-value=1.7e-08  Score=72.27  Aligned_cols=50  Identities=30%  Similarity=0.235  Sum_probs=39.0

Q ss_pred             ccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        114 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ..+.++.|+.||.+|+..||..|..++||+..++.+||..+||++.||+-
T Consensus        96 ~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~v  145 (164)
T 2xsd_C           96 QGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRV  145 (164)
T ss_dssp             ----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             cccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhh
Confidence            45667789999999999999999999999999999999999999999974

>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=98.58  E-value=3.7e-08  Score=59.37  Aligned_cols=39  Identities=15%  Similarity=0.088  Sum_probs=35.6

Q ss_pred             cccchhhhhhhc-cccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        125 SDHQLTGLEKRF-EAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       125 t~~Q~~~Le~~F-~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ...|+.+||+.| ..++||+..++.+||..+||+++|||-
T Consensus         8 ~~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkv   47 (64)
T 1x2m_A            8 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQR   47 (64)
T ss_dssp             SSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHH
T ss_pred             CchHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHH
Confidence            356799999999 679999999999999999999999984

>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=98.55  E-value=5.2e-08  Score=69.04  Aligned_cols=49  Identities=20%  Similarity=0.173  Sum_probs=45.5

Q ss_pred             cccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        115 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       115 ~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .+.++.|+.|+..|+..||..|..++||+..++.+||..+||++.||+-
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~v  142 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRV  142 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHH
T ss_pred             cCCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheee
Confidence            3566789999999999999999999999999999999999999999974

>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=98.43  E-value=1.1e-07  Score=57.93  Aligned_cols=42  Identities=17%  Similarity=0.156  Sum_probs=37.6

Q ss_pred             ccccccchhhhhhhcc---ccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        122 TVFSDHQLTGLEKRFE---AQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       122 t~ft~~Q~~~Le~~F~---~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ..|+.+|+..|+..|.   .++||+..++++||..+||++.||+-
T Consensus         3 g~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~   47 (67)
T 3k2a_A            3 GIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNN   47 (67)
T ss_dssp             ---CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhh
Confidence            3699999999999999   99999999999999999999999973

>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=98.42  E-value=5.8e-08  Score=71.11  Aligned_cols=49  Identities=20%  Similarity=0.270  Sum_probs=43.3

Q ss_pred             cccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcC---------------------CChhhhhh
Q psy17007        115 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQ---------------------LSETQLFY  163 (165)
Q Consensus       115 ~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lg---------------------l~~~qVq~  163 (165)
                      .+.++.|+.|+..|+..|++.|+.++||+..+|++||..++                     |++.+|+.
T Consensus       113 ~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~  182 (194)
T 1ic8_A          113 KKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYN  182 (194)
T ss_dssp             ----CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHH
T ss_pred             ccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccch
Confidence            45678899999999999999999999999999999999999                     99999974

>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=98.31  E-value=3.9e-08  Score=52.47  Aligned_cols=18  Identities=39%  Similarity=0.418  Sum_probs=15.6

Q ss_pred             hhhhhhhccCCCCccccC
Q psy17007         87 TQVKTWFQNRLPFGSLFS  104 (165)
Q Consensus        87 ~~V~~WF~nrr~~~~~~~  104 (165)
                      +||+|||||||+|.++..
T Consensus         1 rQVkIWFQNRRaK~Kk~~   18 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRV   18 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSH
T ss_pred             CCceeccHHHHHHHHHHh
Confidence            589999999999997654

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

Probab=98.30  E-value=2.5e-07  Score=68.65  Aligned_cols=42  Identities=19%  Similarity=0.211  Sum_probs=37.5

Q ss_pred             ccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcC
Q psy17007        114 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQ  155 (165)
Q Consensus       114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lg  155 (165)
                      ..+.++.|+.|+..|+..|++.|+.++||+..+|++||..+|
T Consensus       139 ~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n  180 (221)
T 2h8r_A          139 NKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECN  180 (221)
T ss_dssp             ---CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHH
T ss_pred             cCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHC
Confidence            456778899999999999999999999999999999999987

>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=98.11  E-value=1.6e-06  Score=52.66  Aligned_cols=37  Identities=11%  Similarity=0.173  Sum_probs=35.7

Q ss_pred             ccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007        126 DHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLF  162 (165)
Q Consensus       126 ~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq  162 (165)
                      ++|+..|+..|+.|++|+.+++..||..+||+++.||
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVr   50 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVK   50 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHH
Confidence            6889999999999999999999999999999999987

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

Probab=97.84  E-value=9e-06  Score=51.95  Aligned_cols=41  Identities=20%  Similarity=0.229  Sum_probs=37.6

Q ss_pred             cccccchhhhhhhccc---cCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        123 VFSDHQLTGLEKRFEA---QRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       123 ~ft~~Q~~~Le~~F~~---~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .|+.++...|+.-|..   ++||+..++.+||..+||++.||+-
T Consensus        11 ~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~   54 (89)
T 2lk2_A           11 MLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCN   54 (89)
T ss_dssp             CCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence            4788899999999876   9999999999999999999999973

>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=97.82  E-value=5.3e-06  Score=66.61  Aligned_cols=45  Identities=22%  Similarity=0.236  Sum_probs=42.2

Q ss_pred             cccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        119 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       119 r~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      +.++.++..|+..|++.|+.++||+..+|++||..+||+++|||-
T Consensus       367 ~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~  411 (421)
T 1mh3_A          367 AAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRV  411 (421)
T ss_dssp             HHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             hhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhH
Confidence            557789999999999999999999999999999999999999973

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

Probab=96.91  E-value=0.00089  Score=40.37  Aligned_cols=40  Identities=33%  Similarity=0.546  Sum_probs=37.5

Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccC
Q psy17007         57 LTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR   96 (165)
Q Consensus        57 ~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nr   96 (165)
                      .++|+.+|...+.+...+.+.|+.+.+|+..||+-||-.|
T Consensus        18 ~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~k   57 (70)
T 2ys9_A           18 IQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSR   57 (70)
T ss_dssp             CHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             chHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHhc
Confidence            4899999999999999999999999999999999999654

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=88.02  E-value=2.1  Score=28.19  Aligned_cols=91  Identities=12%  Similarity=0.206  Sum_probs=53.8

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCCccCccccccccccccccccch
Q psy17007         50 TVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQL  129 (165)
Q Consensus        50 ~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~  129 (165)
                      ..++.++...+...+... .    ....+|..+|++...|..|+..-+....        ..   .  ......+++++.
T Consensus         5 ~~~s~~~r~~i~~~~~~G-~----s~~~ia~~lgis~~Tv~r~~~~~~~~g~--------~~---~--~gr~~~l~~~~~   66 (141)
T 1u78_A            5 SALSDTERAQLDVMKLLN-V----SLHEMSRKISRSRHCIRVYLKDPVSYGT--------SK---R--APRRKALSVRDE   66 (141)
T ss_dssp             CCCCHHHHHHHHHHHHTT-C----CHHHHHHHHTCCHHHHHHHHHSGGGTTC--------CC---C--CCCCCSSCHHHH
T ss_pred             ccCCHHHHHHHHHHHHcC-C----CHHHHHHHHCcCHHHHHHHHHcccccCC--------cC---C--CCCCCcCCHHHH
Confidence            467888887777777533 2    2567799999999999999974322110        00   0  111234666666


Q ss_pred             hhhhhhccccCCCCHHHHHHHHHHcC--CChhhhh
Q psy17007        130 TGLEKRFEAQRYLSTPERVELATALQ--LSETQLF  162 (165)
Q Consensus       130 ~~Le~~F~~~~yp~~~~r~~La~~lg--l~~~qVq  162 (165)
                      ..+... ..++..+.   .+|+..+|  ++...|.
T Consensus        67 ~~i~~~-~~~~~~s~---~~i~~~lg~~~s~~tV~   97 (141)
T 1u78_A           67 RNVIRA-ASNSCKTA---RDIRNELQLSASKRTIL   97 (141)
T ss_dssp             HHHHHH-HHHCCCCH---HHHHHHTTCCSCHHHHH
T ss_pred             HHHHHH-HhCCCCCH---HHHHHHHCCCccHHHHH
Confidence            666555 33443333   45666777  5555554

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=85.77  E-value=1.1  Score=25.34  Aligned_cols=46  Identities=15%  Similarity=0.310  Sum_probs=31.5

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhcc
Q psy17007         49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQN   95 (165)
Q Consensus        49 R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~n   95 (165)
                      |..|+.+....+...+... .........+|..+|++...|..|...
T Consensus         3 r~~ys~efK~~~~~~~~~g-~s~~~~~~~vA~~~gIs~~tl~~W~~~   48 (59)
T 2glo_A            3 RRIFTPHFKLQVLESYRND-NDCKGNQRATARKYNIHRRQIQKWLQC   48 (59)
T ss_dssp             CCCCCHHHHHHHHHHHHHC-TTTTTCHHHHHHHTTSCHHHHHHHHTT
T ss_pred             CCcCCHHHHHHHHHHHHcC-CCcchHHHHHHHHHCcCHHHHHHHHHH
Confidence            4578998877775554433 221112567899999999999999753

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=85.71  E-value=2.5  Score=25.91  Aligned_cols=45  Identities=11%  Similarity=0.309  Sum_probs=32.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhcc
Q psy17007         46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQN   95 (165)
Q Consensus        46 rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~n   95 (165)
                      ++.+..|+.++.......+. ...    ....+|..+|++...|..|...
T Consensus        17 ~~~~~~ys~e~k~~~v~~~~-~g~----s~~~iA~~~gIs~sTl~rW~k~   61 (87)
T 2elh_A           17 KRPLRSLTPRDKIHAIQRIH-DGE----SKASVARDIGVPESTLRGWCKN   61 (87)
T ss_dssp             SSCCSSCCHHHHHHHHHHHH-HTC----CHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHH-CCC----CHHHHHHHHCcCHHHHHHHHHH
Confidence            34566899988766656664 332    2557899999999999999853

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5

Probab=85.54  E-value=5.2  Score=25.46  Aligned_cols=92  Identities=9%  Similarity=-0.028  Sum_probs=53.8

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCCccCccccccccccccccccchh
Q psy17007         51 VFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLT  130 (165)
Q Consensus        51 ~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~  130 (165)
                      .++.++...+...+.. .+ +   ...+|..+|++...|..|...-+....        ...... .......+++++..
T Consensus        17 ~~s~~~r~~i~~~~~~-g~-s---~~~ia~~lgis~~Tv~~w~~~~~~~g~--------~~~~~~-~g~~~~~l~~~~~~   82 (128)
T 1pdn_C           17 PLPNNIRLKIVEMAAD-GI-R---PCVISRQLRVSHGCVSKILNRYQETGS--------IRPGVI-GGSKPRIATPEIEN   82 (128)
T ss_dssp             CCCHHHHHHHHHHHHT-TC-C---HHHHHHHHTCCHHHHHHHHHHHHHHCC--------SSCCCC-SCCCCCSSCSTHHH
T ss_pred             cCCHHHHHHHHHHHHc-CC-C---HHHHHHHHCcCHHHHHHHHHHHHhhCC--------cccccC-CCCCCCcCCHHHHH
Confidence            5788877777766653 33 2   456899999999999999964321110        000111 11123356777777


Q ss_pred             hhhhhccccCCCCHHHHHHHHHHcCC
Q psy17007        131 GLEKRFEAQRYLSTPERVELATALQL  156 (165)
Q Consensus       131 ~Le~~F~~~~yp~~~~r~~La~~lgl  156 (165)
                      .+......++..+..+......+.|+
T Consensus        83 ~i~~~~~~~~~~s~~~i~~~l~~~g~  108 (128)
T 1pdn_C           83 RIEEYKRSSPGMFSWEIREKLIREGV  108 (128)
T ss_dssp             HHHHTTTTCTTCCHHHHHHHHHHTSS
T ss_pred             HHHHHHHhCcchHHHHHHHHHHHcCC
Confidence            78777777666665554332222275

>1hlv_A CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} SCOP: a.4.1.7 a.4.1.7 PDB: 1bw6_A

Probab=82.32  E-value=2  Score=28.14  Aligned_cols=48  Identities=15%  Similarity=0.218  Sum_probs=37.9

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCC
Q psy17007         48 ARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLP   98 (165)
Q Consensus        48 ~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~   98 (165)
                      .|..||.++...+...+..+.....   ..+|..+|++...|..|..++..
T Consensus         4 ~r~~~t~e~K~~iv~~~~~~g~~~~---~~~A~~~gvs~stl~~~~~~~~~   51 (131)
T 1hlv_A            4 KRRQLTFREKSRIIQEVEENPDLRK---GEIARRFNIPPSTLSTILKNKRA   51 (131)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSCH---HHHHHHHTCCHHHHHHHHHTHHH
T ss_pred             cceeCCHHHHHHHHHHHHHCCCCcH---HHHHHHhCCCHHHHHHHHhchhh
Confidence            5678999999888888766665533   35789999999999999977544

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens}

Probab=80.96  E-value=10  Score=25.53  Aligned_cols=85  Identities=8%  Similarity=-0.006  Sum_probs=52.2

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCCccCccccccccccccccccch
Q psy17007         50 TVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQL  129 (165)
Q Consensus        50 ~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~  129 (165)
                      ..++.++...+...+... .    ....+|..+|++...|..|...-+....        ...... ..+.+..+++++.
T Consensus        24 ~~~s~e~r~~ii~l~~~G-~----s~~~IA~~lgis~~TV~rwl~r~~~~G~--------~~~~~r-~gr~~~~~~~~~~   89 (159)
T 2k27_A           24 RPLPEVVRQRIVDLAHQG-V----RPCDISRQLRVSHGCVSKILGRYYETGS--------IRPGVI-GGSKPKVATPKVV   89 (159)
T ss_dssp             CSSCHHHHHHHHHHHHHT-C----CHHHHHHHHTCCSHHHHHHHCCSSTTSC--------CCCCCC-CCCCCCCCCTTHH
T ss_pred             CCCCHHHHHHHHHHHHcC-C----CHHHHHHHHCcCHHHHHHHHHHHHhcCC--------ccCCCC-CCCCCCCCCHHHH
Confidence            368888887777777533 2    2456799999999999999975332211        011111 1112345677777


Q ss_pred             hhhhhhccccCCCCHHHHH
Q psy17007        130 TGLEKRFEAQRYLSTPERV  148 (165)
Q Consensus       130 ~~Le~~F~~~~yp~~~~r~  148 (165)
                      ..+...+..++..+..+..
T Consensus        90 ~~I~~~~~~~~~~s~~~i~  108 (159)
T 2k27_A           90 EKIGDYKRQNPTMFAWEIR  108 (159)
T ss_dssp             HHHHHHHHHCSSSCHHHHH
T ss_pred             HHHHHHHHHCccchHHHHH
Confidence            7777777666656655443

---

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	165
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	1e-18
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	2e-11
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	8e-17
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	6e-10
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	2e-16
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	2e-09
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	4e-16
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	3e-09
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	2e-15
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	3e-08
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	4e-15
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	8e-08
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	8e-15
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	7e-08
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	8e-15
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	1e-07
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	1e-14
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	1e-07
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	1e-14
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	4e-08
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	3e-14
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	1e-07
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	9e-14
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	3e-08
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	2e-13
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	1e-06
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	3e-13
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	4e-07
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	4e-13
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	2e-06
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	6e-13
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	3e-07
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	6e-13
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	2e-07
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	7e-13
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	3e-06
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	1e-12
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	8e-06
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	2e-12
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	1e-07
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	2e-12
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	1e-05
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	3e-12
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	2e-05
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	7e-12
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	2e-05
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	1e-11
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	3e-05
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	2e-11
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	4e-07
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	4e-11
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	9e-06
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	9e-11
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	6e-04
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	3e-10
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	3e-05
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	3e-09
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	2e-05
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	2e-08
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	3e-08
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	2e-05

>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 = 73.3 bits (180), Expect = 1e-18
 Identities = 26/63 (41%), Positives = 32/63 (50%)

Query: 34 SPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWF 93
          +P          RK R  ++ HQ   LEK F    YL+   R E+A  L L+E QVK WF
Sbjct: 2  NPAANWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWF 61

Query: 94 QNR 96
          QNR
Sbjct: 62 QNR 64

>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 = 54.5 bits (131), Expect = 2e-11
 Identities = 19/55 (34%), Positives = 25/55 (45%)

Query: 106 SPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           +P          RK R  ++ HQ   LEK F    YL+   R E+A  L L+E Q
Sbjct: 2   NPAANWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQ 56

>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 = 68.3 bits (167), Expect = 8e-17
 Identities = 19/51 (37%), Positives = 27/51 (52%)

Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          ++ RT F+  Q+  LEK FE   Y     R  LA  + L E +++ WF NR
Sbjct: 2  QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNR 52

>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 = 50.6 bits (121), Expect = 6e-10
 Identities = 15/43 (34%), Positives = 21/43 (48%)

Query: 118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           ++ RT F+  Q+  LEK FE   Y     R  LA  + L E +
Sbjct: 2   QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEAR 44

>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 = 66.8 bits (163), Expect = 2e-16
 Identities = 31/51 (60%), Positives = 36/51 (70%)

Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          +  +  FS+ Q   LEK+FE Q+YLS PER  LA  LQLSE QVKTWFQNR
Sbjct: 1  KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNR 51

>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 = 48.7 bits (116), Expect = 2e-09
 Identities = 23/43 (53%), Positives = 28/43 (65%)

Query: 118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           +  +  FS+ Q   LEK+FE Q+YLS PER  LA  LQLSE Q
Sbjct: 1   KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQ 43

>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 = 66.3 bits (162), Expect = 4e-16
 Identities = 23/48 (47%), Positives = 31/48 (64%)

Query: 49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          R  ++ +Q   LEK F   RYL+   R+E+A AL L+E Q+K WFQNR
Sbjct: 1  RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNR 48

>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 = 48.2 bits (115), Expect = 3e-09
 Identities = 17/40 (42%), Positives = 24/40 (60%)

Query: 121 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           R  ++ +Q   LEK F   RYL+   R+E+A AL L+E Q
Sbjct: 1   RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQ 40

>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 = 64.5 bits (157), Expect = 2e-15
 Identities = 20/51 (39%), Positives = 32/51 (62%)

Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          RK R  +S  QL  LE+ + A ++++  +R +++ A  LSE Q+  WFQNR
Sbjct: 2  RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNR 52

>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 = 45.6 bits (108), Expect = 3e-08
 Identities = 15/43 (34%), Positives = 26/43 (60%)

Query: 118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           RK R  +S  QL  LE+ + A ++++  +R +++ A  LSE Q
Sbjct: 2   RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQ 44

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.6 bits (157), Expect = 4e-15
 Identities = 29/58 (50%), Positives = 34/58 (58%)

Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
                    RT F+  QLT LEK F   +YLS   RVE+A  L+L+ETQVK WFQNR
Sbjct: 21 EPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNR 78

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.4 bits (107), Expect = 8e-08
 Identities = 22/50 (44%), Positives = 27/50 (54%)

Query: 111 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
                     RT F+  QLT LEK F   +YLS   RVE+A  L+L+ETQ
Sbjct: 21  EPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQ 70

>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 = 63.3 bits (154), Expect = 8e-15
 Identities = 14/53 (26%), Positives = 24/53 (45%)

Query: 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          +  + RTV ++ QL  L   + A        + +L     LS   ++ WFQN+
Sbjct: 2  KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNK 54

>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 = 45.2 bits (107), Expect = 7e-08
 Identities = 10/45 (22%), Positives = 17/45 (37%)

Query: 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           +  + RTV ++ QL  L   + A        + +L     LS   
Sbjct: 2   KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRV 46

>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 = 63.0 bits (153), Expect = 8e-15
 Identities = 22/50 (44%), Positives = 31/50 (62%)

Query: 47 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          + RT FS  QL  L++ F   RYL+   R +L++ L L+E Q+K WFQN 
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNA 50

>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 = 44.1 bits (104), Expect = 1e-07
 Identities = 17/42 (40%), Positives = 25/42 (59%)

Query: 119 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           + RT FS  QL  L++ F   RYL+   R +L++ L L+E Q
Sbjct: 1   RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQ 42

>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 = 62.6 bits (152), Expect = 1e-14
 Identities = 13/48 (27%), Positives = 22/48 (45%)

Query: 49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          R VF+D Q   L   F+  +  S   ++ ++  L L  + V  +F N 
Sbjct: 2  RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNA 49

>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 = 44.1 bits (104), Expect = 1e-07
 Identities = 10/40 (25%), Positives = 18/40 (45%)

Query: 121 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           R VF+D Q   L   F+  +  S   ++ ++  L L  + 
Sbjct: 2   RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELST 41

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 65

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

 Score = 62.6 bits (152), Expect = 1e-14
 Identities = 23/53 (43%), Positives = 33/53 (62%)

Query: 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          ++R++RT FS  QL  LE+ FE  +Y     R ELA    L+E +++ WFQNR
Sbjct: 1  KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNR 53

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 65

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

 Score = 45.7 bits (108), Expect = 4e-08
 Identities = 18/45 (40%), Positives = 26/45 (57%)

Query: 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           ++R++RT FS  QL  LE+ FE  +Y     R ELA    L+E +
Sbjct: 1   KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEAR 45

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 68

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

 Score = 61.9 bits (150), Expect = 3e-14
 Identities = 29/52 (55%), Positives = 37/52 (71%)

Query: 45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          RRK R +FS  Q+  LE+RF+ Q+YLS PER  LA+ + L+ TQVK WFQN 
Sbjct: 2  RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNH 53

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 68

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

 Score = 44.5 bits (105), Expect = 1e-07
 Identities = 23/44 (52%), Positives = 31/44 (70%)

Query: 117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           RRK R +FS  Q+  LE+RF+ Q+YLS PER  LA+ + L+ TQ
Sbjct: 2   RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQ 45

>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 = 60.3 bits (146), Expect = 9e-14
 Identities = 17/50 (34%), Positives = 23/50 (46%)

Query: 47 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          K RT  S      LE+ F      S+ E + +A  L L +  V+ WF NR
Sbjct: 1  KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNR 50

>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 = 45.7 bits (108), Expect = 3e-08
 Identities = 12/43 (27%), Positives = 18/43 (41%)

Query: 119 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
           K RT  S      LE+ F      S+ E + +A  L L +  +
Sbjct: 1   KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVV 43

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 58

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

 Score = 59.5 bits (144), Expect = 2e-13
 Identities = 28/51 (54%), Positives = 37/51 (72%)

Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          RK RT F+  QL  LE++F  ++YLS  ER E +++L L+ETQVK WFQNR
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNR 51

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 58

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

 Score = 41.4 bits (97), Expect = 1e-06
 Identities = 21/43 (48%), Positives = 30/43 (69%)

Query: 118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           RK RT F+  QL  LE++F  ++YLS  ER E +++L L+ETQ
Sbjct: 1   RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQ 43

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.8 bits (142), Expect = 3e-13
 Identities = 21/51 (41%), Positives = 29/51 (56%)

Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          R+ RT F+  QL  LE  F+  RY     R E+A    L+E +V+ WF+NR
Sbjct: 2  RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNR 52

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.0 bits (101), Expect = 4e-07
 Identities = 16/43 (37%), Positives = 22/43 (51%)

Query: 118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           R+ RT F+  QL  LE  F+  RY     R E+A    L+E +
Sbjct: 2   RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEAR 44

>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 = 58.6 bits (142), Expect = 4e-13
 Identities = 12/54 (22%), Positives = 19/54 (35%), Gaps = 3/54 (5%)

Query: 46 RKARTVFSDHQLTGLEKRFEAQR---YLSTPERVELATALQLSETQVKTWFQNR 96
          +  R V   H    +           Y +  E+ ++A    L+  QV  WF N 
Sbjct: 3  KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINA 56

>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 = 40.9 bits (96), Expect = 2e-06
 Identities = 8/46 (17%), Positives = 15/46 (32%), Gaps = 3/46 (6%)

Query: 118 RKARTVFSDHQLTGLEKRFEAQR---YLSTPERVELATALQLSETQ 160
           +  R V   H    +           Y +  E+ ++A    L+  Q
Sbjct: 3   KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQ 48

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 58.9 bits (142), Expect = 6e-13
 Identities = 28/56 (50%), Positives = 37/56 (66%)

Query: 41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
             ++RK R +F+  Q   LE+RF  QRYLS PER  LA+ ++L+ TQVK WFQN 
Sbjct: 5  LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNH 60

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 43.5 bits (102), Expect = 3e-07
 Identities = 22/49 (44%), Positives = 32/49 (65%)

Query: 113 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
              ++RK R +F+  Q   LE+RF  QRYLS PER  LA+ ++L+ TQ+
Sbjct: 5   LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQV 53

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 67

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

 Score = 58.5 bits (141), Expect = 6e-13
 Identities = 15/53 (28%), Positives = 22/53 (41%)

Query: 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
           R++ RT   +     LE  F      S  +   +A  L L +  V+ WF NR
Sbjct: 7  ARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNR 59

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 67

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

 Score = 44.2 bits (104), Expect = 2e-07
 Identities = 10/46 (21%), Positives = 17/46 (36%)

Query: 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
            R++ RT   +     LE  F      S  +   +A  L L +  +
Sbjct: 7   ARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVV 52

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 53

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 58.0 bits (140), Expect = 7e-13
 Identities = 13/48 (27%), Positives = 26/48 (54%)

Query: 49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          ++  S      LE+ F  ++ L++ E+ E+A    ++  QV+ WF N+
Sbjct: 1  KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINK 48

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 53

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.3 bits (94), Expect = 3e-06
 Identities = 9/40 (22%), Positives = 20/40 (50%)

Query: 121 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           ++  S      LE+ F  ++ L++ E+ E+A    ++  Q
Sbjct: 1   KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQ 40

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 67

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

 Score = 57.6 bits (139), Expect = 1e-12
 Identities = 22/51 (43%), Positives = 30/51 (58%)

Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          R+ RT F+  Q+  LE+ F   RYL+ P   +L+  L L   QVK WF+NR
Sbjct: 2  RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNR 52

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 67

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

 Score = 39.5 bits (92), Expect = 8e-06
 Identities = 16/43 (37%), Positives = 23/43 (53%)

Query: 118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           R+ RT F+  Q+  LE+ F   RYL+ P   +L+  L L   Q
Sbjct: 2   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQ 44

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-containing protein 1, HMBOX1 (Flj21616)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.8 bits (139), Expect = 2e-12
 Identities = 14/66 (21%), Positives = 24/66 (36%), Gaps = 15/66 (22%)

Query: 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELAT---------------ALQLSETQVK 90
          R +R  +    L  +E  F   +Y    +R E+A                  +++  +V 
Sbjct: 1  RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVY 60

Query: 91 TWFQNR 96
           WF NR
Sbjct: 61 NWFANR 66

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-containing protein 1, HMBOX1 (Flj21616)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.0 bits (106), Expect = 1e-07
 Identities = 10/43 (23%), Positives = 17/43 (39%)

Query: 118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           R +R  +    L  +E  F   +Y    +R E+A A      +
Sbjct: 1   RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQK 43

>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 = 56.7 bits (137), Expect = 2e-12
 Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 1/51 (1%)

Query: 47 KARTVFSDHQLTGLEKRFEAQ-RYLSTPERVELATALQLSETQVKTWFQNR 96
          K   V        LEK F +  +Y        L+  L  S  +++ WF++R
Sbjct: 3  KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHR 53

>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 = 39.0 bits (91), Expect = 1e-05
 Identities = 10/43 (23%), Positives = 14/43 (32%), Gaps = 1/43 (2%)

Query: 119 KARTVFSDHQLTGLEKRFEAQ-RYLSTPERVELATALQLSETQ 160
           K   V        LEK F +  +Y        L+  L  S  +
Sbjct: 3   KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRK 45

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57

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

 Score = 56.1 bits (135), Expect = 3e-12
 Identities = 25/50 (50%), Positives = 31/50 (62%)

Query: 47 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          + RT F+  QL  LEK F  + Y+S P R ELA  L L E+ +K WFQNR
Sbjct: 1  RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNR 50

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57

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

 Score = 38.3 bits (89), Expect = 2e-05
 Identities = 19/42 (45%), Positives = 24/42 (57%)

Query: 119 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           + RT F+  QL  LEK F  + Y+S P R ELA  L L E+ 
Sbjct: 1   RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPEST 42

>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 = 55.7 bits (134), Expect = 7e-12
 Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 3/54 (5%)

Query: 46 RKARTVFSDHQLTGLEKRFEA---QRYLSTPERVELATALQLSETQVKTWFQNR 96
          R+ R  F+      L + F +     Y S   + ELA    ++ +QV  WF N+
Sbjct: 2  RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNK 55

>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 = 38.4 bits (89), Expect = 2e-05
 Identities = 11/46 (23%), Positives = 19/46 (41%), Gaps = 3/46 (6%)

Query: 118 RKARTVFSDHQLTGLEKRFEA---QRYLSTPERVELATALQLSETQ 160
           R+ R  F+      L + F +     Y S   + ELA    ++ +Q
Sbjct: 2   RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQ 47

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 54.8 bits (132), Expect = 1e-11
 Identities = 17/54 (31%), Positives = 20/54 (37%), Gaps = 5/54 (9%)

Query: 46 RKARTVFSDHQLTGLEKRFEAQR---YLSTPERVELATALQLSETQVKTWFQNR 96
          R  R  F+   +  LE  F       YL T     L     LS  Q+K W  NR
Sbjct: 1  RGHR--FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNR 52

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 37.8 bits (88), Expect = 3e-05
 Identities = 13/47 (27%), Positives = 16/47 (34%), Gaps = 5/47 (10%)

Query: 118 RKARTVFSDHQLTGLEKRFEAQR---YLSTPERVELATALQLSETQL 161
           R  R  F+   +  LE  F       YL T     L     LS  Q+
Sbjct: 1   RGHR--FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQI 45

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.2 bits (130), Expect = 2e-11
 Identities = 12/48 (25%), Positives = 22/48 (45%)

Query: 49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          RT    +    LEK F   +  ++ +   +A  L + +  ++ WF NR
Sbjct: 2  RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNR 49

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.0 bits (101), Expect = 4e-07
 Identities = 8/41 (19%), Positives = 17/41 (41%)

Query: 121 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQL 161
           RT    +    LEK F   +  ++ +   +A  L + +  +
Sbjct: 2   RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVI 42

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.6 bits (128), Expect = 4e-11
 Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 1/59 (1%)

Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRF-EAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          GS      ++RT  S   L  L+    +   Y        L+  L L +  +  +FQN+
Sbjct: 1  GSSGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQ 59

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 9e-06
 Identities = 11/52 (21%), Positives = 18/52 (34%), Gaps = 1/52 (1%)

Query: 111 GSKHCRRRKARTVFSDHQLTGLEKRF-EAQRYLSTPERVELATALQLSETQL 161
           GS      ++RT  S   L  L+    +   Y        L+  L L +  +
Sbjct: 1   GSSGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTI 52

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 52

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.4 bits (126), Expect = 9e-11
 Identities = 10/45 (22%), Positives = 17/45 (37%), Gaps = 1/45 (2%)

Query: 53 SDHQLTGLEKRFEAQ-RYLSTPERVELATALQLSETQVKTWFQNR 96
          +      LEK F A  ++        L+  L      ++ WF+ R
Sbjct: 1  TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQR 45

>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 = 33.9 bits (78), Expect = 6e-04
 Identities = 7/37 (18%), Positives = 11/37 (29%), Gaps = 1/37 (2%)

Query: 125 SDHQLTGLEKRFEAQ-RYLSTPERVELATALQLSETQ 160
           +      LEK F A  ++        L+  L      
Sbjct: 1   TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRS 37

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} Length = 72

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

 Score = 51.5 bits (123), Expect = 3e-10
 Identities = 11/52 (21%), Positives = 21/52 (40%), Gaps = 1/52 (1%)

Query: 46 RKARTVFSDHQLTGLEKRFEA-QRYLSTPERVELATALQLSETQVKTWFQNR 96
           +     ++ Q+  LE  F    ++        +A    L+E Q + WF+ R
Sbjct: 2  SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQR 53

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} Length = 72

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

 Score = 38.0 bits (88), Expect = 3e-05
 Identities = 8/46 (17%), Positives = 16/46 (34%), Gaps = 1/46 (2%)

Query: 118 RKARTVFSDHQLTGLEKRFEA-QRYLSTPERVELATALQLSETQLF 162
            +     ++ Q+  LE  F    ++        +A    L+E Q  
Sbjct: 2   SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQ 47

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Length = 78

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Rat (Rattus rattus) [TaxId: 10117]

 Score = 49.0 bits (116), Expect = 3e-09
 Identities = 14/69 (20%), Positives = 21/69 (30%), Gaps = 21/69 (30%)

Query: 49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATAL---------------------QLSET 87
          R  +       L + +E Q+  S  ER  L                          ++E 
Sbjct: 1  RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 88 QVKTWFQNR 96
          +V  WF NR
Sbjct: 61 RVYNWFANR 69

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Length = 78

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Rat (Rattus rattus) [TaxId: 10117]

 Score = 38.6 bits (89), Expect = 2e-05
 Identities = 9/40 (22%), Positives = 14/40 (35%)

Query: 121 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQ 160
           R  +       L + +E Q+  S  ER  L      +E  
Sbjct: 1   RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECI 40

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 80

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 47.3 bits (112), Expect = 2e-08
 Identities = 9/62 (14%), Positives = 16/62 (25%), Gaps = 4/62 (6%)

Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQR----YLSTPERVELATALQLSETQVKTWFQ 94
           S     ++ RT F+  Q   +    E               +      +    +K W  
Sbjct: 11 SSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMH 70

Query: 95 NR 96
          N 
Sbjct: 71 NN 72

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Zinc fingers and homeoboxes protein 1, ZHX1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.6 bits (110), Expect = 3e-08
 Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 3/53 (5%)

Query: 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          ++ K +T     QL  L+  F     L+  E   L    +L+  ++  WF  +
Sbjct: 6  QKFKEKT---AEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEK 55

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

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

 Score = 38.9 bits (90), Expect = 2e-05
 Identities = 10/58 (17%), Positives = 21/58 (36%), Gaps = 4/58 (6%)

Query: 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96
          GS     ++     +  QL  L+  F   ++    +  +L     L   ++  WF + 
Sbjct: 1  GSSGSSGKR----KTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDT 54

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	165
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.87
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.87
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.85
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.85
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.84
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.84
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.84
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.84
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.82
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.82
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.82
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.81
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.81
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.81
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.81
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.81
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.81
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.8
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.8
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.79
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.79
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.77
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.77
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.76
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.71
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.69
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.69
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.69
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.66
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.64
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.63
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.63
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.26
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.25
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.22
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.21
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.21
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.19
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.19
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.18
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.18
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.13
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.13
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.13
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.11
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.09
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.09
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.06
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.04
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.04
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.03
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.02
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.01
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	98.98
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	98.92
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	98.86
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	98.75
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	98.74
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	98.72
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	98.62
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	98.56
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	98.51
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	98.51
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	98.5
d1hlva1	66	DNA-binding domain of centromere binding protein B	91.21
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	87.64

>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=99.87  E-value=4.3e-23  Score=121.90  Aligned_cols=58  Identities=34%  Similarity=0.572  Sum_probs=55.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        45 ~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      +++.|++||.+|+.+||..|..++||+..+++.||..+||++.+|++||||||++.++
T Consensus         1 Grr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           1 GRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            4678999999999999999999999999999999999999999999999999998863

>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=99.87  E-value=2e-22  Score=125.77  Aligned_cols=68  Identities=41%  Similarity=0.601  Sum_probs=61.8

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCC
Q psy17007         39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTS  106 (165)
Q Consensus        39 ~~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~  106 (165)
                      ++.+.+.++.|++||.+|+.+||..|..++||+..+++.||..+||++.+|++||||+|++.++....
T Consensus         3 ~g~p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   70 (77)
T d1vnda_           3 DGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNE   70 (77)
T ss_dssp             SCCSSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSCCC
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHhhc
Confidence            34556778899999999999999999999999999999999999999999999999999999875543

>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=99.85  E-value=3.2e-22  Score=116.27  Aligned_cols=53  Identities=42%  Similarity=0.723  Sum_probs=51.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCC
Q psy17007         47 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPF   99 (165)
Q Consensus        47 r~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~   99 (165)
                      |.|+.||.+|+..||..|+.++||+..++..||..+||++.+|++||||||+|
T Consensus         1 R~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~lgL~~~qV~vWFqNrRaK   53 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK   53 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             CCCccCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChHHhhhcccccCCC
Confidence            56899999999999999999999999999999999999999999999999976

>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=99.85  E-value=2.3e-22  Score=119.08  Aligned_cols=57  Identities=49%  Similarity=0.771  Sum_probs=54.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        46 rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      ||.|++||.+|+.+||..|+.++||+..+++.||..+||++.+|++||||+|++.++
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            467899999999999999999999999999999999999999999999999998764

>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=99.84  E-value=9e-22  Score=122.61  Aligned_cols=61  Identities=41%  Similarity=0.520  Sum_probs=57.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         42 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        42 ~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      .+..++.|++||.+|+.+||..|..++||+..+++.||..+||++.+|++||||||++.++
T Consensus        10 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr   70 (77)
T d1pufa_          10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK   70 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             cCcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHH
Confidence            3445778999999999999999999999999999999999999999999999999999875

>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=99.84  E-value=4.9e-22  Score=117.13  Aligned_cols=56  Identities=55%  Similarity=0.768  Sum_probs=53.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcc
Q psy17007         46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGS  101 (165)
Q Consensus        46 rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~  101 (165)
                      +++|++||++|+.+||..|..++||+..+++.||..+||++.+|++||+|||++.+
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k~k   56 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR   56 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhhcc
Confidence            46789999999999999999999999999999999999999999999999998865

>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=99.84  E-value=4.1e-22  Score=116.55  Aligned_cols=54  Identities=43%  Similarity=0.624  Sum_probs=52.3

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        49 R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      ||.||.+|+.+||..|..++||+..++.+||..+||++++|++||||||++.++
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk   54 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK   54 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhh
Confidence            789999999999999999999999999999999999999999999999998865

>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=99.84  E-value=5.2e-22  Score=117.03  Aligned_cols=56  Identities=45%  Similarity=0.689  Sum_probs=53.6

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         47 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        47 r~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      |.|+.||++|+.+||..|..++||+..+++.||..+||++.+|++||||+|++.++
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk   56 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR   56 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhc
Confidence            57899999999999999999999999999999999999999999999999998764

>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=99.82  E-value=2.1e-21  Score=117.41  Aligned_cols=59  Identities=39%  Similarity=0.599  Sum_probs=56.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        44 ~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      +.++.|+.||.+|+.+||..|..++||+..++..||..+||++.+|++||+|+|++.++
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk   59 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK   59 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHh
Confidence            45788999999999999999999999999999999999999999999999999998865

>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=99.82  E-value=1.7e-21  Score=118.38  Aligned_cols=58  Identities=38%  Similarity=0.665  Sum_probs=55.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        46 rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      +|.|++||.+|+.+||..|+.++||+..++..||..+||++.+|++||||||++.++.
T Consensus         2 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~   59 (67)
T d1zq3p1           2 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQ   59 (67)
T ss_dssp             SCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhh
Confidence            5678999999999999999999999999999999999999999999999999998753

>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=99.82  E-value=2.3e-21  Score=119.08  Aligned_cols=63  Identities=21%  Similarity=0.294  Sum_probs=57.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHh-cCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCC
Q psy17007         45 RRKARTVFSDHQLTGLEKRFEA-QRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSP  107 (165)
Q Consensus        45 ~rr~R~~~s~~q~~~Le~~f~~-~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~  107 (165)
                      ++++|++||.+|+.+||..|.. ++||+...++.||..+||++.+|++||||||++.++...-+
T Consensus         1 g~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~~~p   64 (72)
T d1uhsa_           1 GSEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLP   64 (72)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhccCCc
Confidence            4678999999999999999986 78999999999999999999999999999999997755433

>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=99.81  E-value=5.3e-21  Score=116.44  Aligned_cols=60  Identities=48%  Similarity=0.706  Sum_probs=56.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007         45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS  104 (165)
Q Consensus        45 ~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~  104 (165)
                      +++.|++||..|+.+|+..|..++||+..++..||..+||++.+|++||+|+|++.+...
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~   61 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA   61 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhcc
Confidence            367899999999999999999999999999999999999999999999999999987644

>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=99.81  E-value=1e-20  Score=114.76  Aligned_cols=60  Identities=27%  Similarity=0.317  Sum_probs=56.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        44 ~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      .+++.|++|+.+|+..|+.+|..++||+..+++.||..+||+..+|++||+|+|++.++.
T Consensus         7 ~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_           7 ARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             CSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             ccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            346789999999999999999999999999999999999999999999999999998763

>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=99.81  E-value=3.2e-21  Score=117.53  Aligned_cols=58  Identities=33%  Similarity=0.548  Sum_probs=55.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        45 ~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      ++|.|++||.+|+.+||..|..++||+..+++.||..+||++.+|++||+|+|++.++
T Consensus         1 grR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr   58 (68)
T d2cuea1           1 GQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRR   58 (68)
T ss_dssp             SCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHh
Confidence            4678999999999999999999999999999999999999999999999999998864

>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=99.81  E-value=7.3e-21  Score=115.22  Aligned_cols=61  Identities=25%  Similarity=0.339  Sum_probs=57.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007         44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS  104 (165)
Q Consensus        44 ~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~  104 (165)
                      +.+|.|++||.+|+.+|+.+|..++||+..+++.||..+||++.+|++||+|+|++.+...
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~~   62 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHHH
Confidence            4578899999999999999999999999999999999999999999999999999987643

>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=99.81  E-value=3e-21  Score=123.18  Aligned_cols=61  Identities=48%  Similarity=0.617  Sum_probs=54.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         43 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        43 ~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      .+.++.|++||.+|+.+||..|..++||+..+++.||..+||++.+|++||||+|++.++.
T Consensus        25 ~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~   85 (88)
T d1b72a_          25 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKR   85 (88)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHh
Confidence            3457789999999999999999999999999999999999999999999999999998753

>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=99.81  E-value=1.1e-20  Score=109.68  Aligned_cols=53  Identities=25%  Similarity=0.378  Sum_probs=51.2

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcc
Q psy17007         49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGS  101 (165)
Q Consensus        49 R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~  101 (165)
                      |++||++|+.+|+..|..++||+..++..||..+||++.+|++||+|+|++.|
T Consensus         1 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~K   53 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   53 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTTC
T ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhccC
Confidence            68999999999999999999999999999999999999999999999999874

>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=99.80  E-value=1.6e-20  Score=110.95  Aligned_cols=57  Identities=30%  Similarity=0.385  Sum_probs=54.4

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         47 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        47 r~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      |.|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|+|++.++.
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr~   57 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV   57 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHhc
Confidence            568999999999999999999999999999999999999999999999999998763

>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=99.80  E-value=2.4e-20  Score=114.74  Aligned_cols=60  Identities=20%  Similarity=0.179  Sum_probs=55.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHH-hcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         43 CRRRKARTVFSDHQLTGLEKRFE-AQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        43 ~~~rr~R~~~s~~q~~~Le~~f~-~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      ..+++.|++|+++|+.+|+.+|. .++||+..+++.||..+||+..+|++||+|+|++.+.
T Consensus         5 ~~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk   65 (71)
T d1wi3a_           5 SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             CCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhcc
Confidence            44578899999999999999997 4899999999999999999999999999999999875

>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=99.79  E-value=2.6e-21  Score=115.23  Aligned_cols=57  Identities=37%  Similarity=0.579  Sum_probs=54.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        46 rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      +|.|++||++|+.+|+..|..++||+..+++.||..+||++.+|++||+|+|++.++
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   58 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK   58 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHh
Confidence            678999999999999999999999999999999999999999999999999998764

>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=99.79  E-value=1.6e-19  Score=113.36  Aligned_cols=62  Identities=15%  Similarity=0.153  Sum_probs=56.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh----cCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         41 KHCRRRKARTVFSDHQLTGLEKRFEA----QRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        41 ~~~~~rr~R~~~s~~q~~~Le~~f~~----~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      ...+.+|.|++||.+|++.|+.+|+.    ++||+..+++.||..+||+..+|++||||+|++.+.
T Consensus        13 ~~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          13 SGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            33456789999999999999999986    789999999999999999999999999999988753

>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=99.77  E-value=1e-19  Score=107.01  Aligned_cols=56  Identities=21%  Similarity=0.348  Sum_probs=53.5

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         48 ARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        48 ~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      +||+|+.+|+..||..|..++||+..++..||..+||++.+|++||+|+|++.++.
T Consensus         1 kRT~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk~   56 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI   56 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHcc
Confidence            48999999999999999999999999999999999999999999999999998764

>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=99.77  E-value=1.2e-19  Score=104.15  Aligned_cols=50  Identities=26%  Similarity=0.363  Sum_probs=48.7

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCC
Q psy17007         48 ARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRL   97 (165)
Q Consensus        48 ~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr   97 (165)
                      .|++||.+|+.+||..|..++||+..++..||..+||+..+|++||||+|
T Consensus         1 PRt~ft~~Q~~~Le~~F~~n~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1           1 PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             CCSCCCHHHHHHHHHHTTSSCSSTHHHHHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhhcCCcCc
Confidence            48999999999999999999999999999999999999999999999997

>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=99.76  E-value=1.3e-19  Score=114.32  Aligned_cols=58  Identities=26%  Similarity=0.374  Sum_probs=54.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhc---------------cchhhhhhhhccCCCCcccc
Q psy17007         46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQ---------------LSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        46 rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~---------------l~~~~V~~WF~nrr~~~~~~  103 (165)
                      |+.|++|+.+|+.+||.+|+.++||+..++++||..+|               |++.+|++||||||++.+..
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~   73 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRR   73 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHh
Confidence            57899999999999999999999999999999999886               89999999999999998763

>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=4.2e-18  Score=105.83  Aligned_cols=54  Identities=20%  Similarity=0.297  Sum_probs=50.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007         51 VFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS  104 (165)
Q Consensus        51 ~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~  104 (165)
                      .+|.+|+.+|+..|..++||+..+++.||..+||+..+|++||+|||++.+...
T Consensus        10 ~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~   63 (76)
T d2ecba1          10 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE   63 (76)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCC
T ss_pred             CCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHh
Confidence            458999999999999999999999999999999999999999999998876544

>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=99.69  E-value=6.4e-18  Score=104.23  Aligned_cols=58  Identities=26%  Similarity=0.332  Sum_probs=54.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         46 RKARTVFSDHQLTGLEKRFEA---QRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        46 rr~R~~~s~~q~~~Le~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      |+.|+.|+.+|+.+|+.+|..   ++||+..+++.||..+||+..||++||+|+|++.+..
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~   62 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN   62 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhccc
Confidence            667899999999999999984   8899999999999999999999999999999998653

>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=99.69  E-value=1.1e-17  Score=103.96  Aligned_cols=55  Identities=15%  Similarity=0.114  Sum_probs=51.5

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007         49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        49 R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~  103 (165)
                      +.++|.+|+.+|+.+|..++||+..+++.||..+||+..+|++||+|+|++.+..
T Consensus         7 ~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~   61 (76)
T d2ecca1           7 GKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhc
Confidence            3467999999999999999999999999999999999999999999999988753

>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=99.69  E-value=7.5e-18  Score=104.72  Aligned_cols=55  Identities=25%  Similarity=0.314  Sum_probs=51.8

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhc---------------------cchhhhhhhhccCCCCcccc
Q psy17007         49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQ---------------------LSETQVKTWFQNRLPFGSLF  103 (165)
Q Consensus        49 R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~---------------------l~~~~V~~WF~nrr~~~~~~  103 (165)
                      |++|+++|+.+||.+|+.++||+..+|+.||..++                     |++.+|++||+|||++.++.
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr~   76 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFR   76 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCC
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHHh
Confidence            68999999999999999999999999999999995                     88899999999999999764

>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=99.66  E-value=8.4e-18  Score=96.74  Aligned_cols=50  Identities=20%  Similarity=0.258  Sum_probs=46.3

Q ss_pred             CHHHHHHHHHHHHh-cCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         53 SDHQLTGLEKRFEA-QRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        53 s~~q~~~Le~~f~~-~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      |.+|..+||..|.. ++||+..+++.||..+||+.++|++||+|||+++|.
T Consensus         1 T~~q~~iLE~~F~~~~~~P~~~~~~~LA~~~~ls~~qV~~WFqNrR~k~k~   51 (52)
T d1x2ma1           1 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   51 (52)
T ss_dssp             SSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             ChhHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccCc
Confidence            45789999999987 689999999999999999999999999999999864

>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=99.64  E-value=6.1e-17  Score=95.97  Aligned_cols=53  Identities=28%  Similarity=0.377  Sum_probs=48.8

Q ss_pred             CCCCHHHHHHHHHHHHhc---CCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007         50 TVFSDHQLTGLEKRFEAQ---RYLSTPERVELATALQLSETQVKTWFQNRLPFGSL  102 (165)
Q Consensus        50 ~~~s~~q~~~Le~~f~~~---~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~  102 (165)
                      .+|+.+|+.+|+.+|..+   +||+..+++.||..+||+..+|++||+|+|++.+.
T Consensus         3 ~Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           3 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             CSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            359999999999999865   79999999999999999999999999999988764

>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=99.63  E-value=1.9e-17  Score=97.64  Aligned_cols=55  Identities=24%  Similarity=0.323  Sum_probs=50.4

Q ss_pred             CCCCCCCHHHHHHHHHHHHh-cCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcc
Q psy17007         47 KARTVFSDHQLTGLEKRFEA-QRYLSTPERVELATALQLSETQVKTWFQNRLPFGS  101 (165)
Q Consensus        47 r~R~~~s~~q~~~Le~~f~~-~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~  101 (165)
                      +.+++++.++..+||.+|.. ++||+..+++.||..+||++.+|++||+|||++++
T Consensus         3 k~~~~~k~~~~~iLE~~F~~~~~yPs~~~~~~LA~~lgls~~qV~~WFqNrR~k~r   58 (59)
T d2cqxa1           3 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK   58 (59)
T ss_dssp             CCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCccccHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccC
Confidence            45678888999999999986 68999999999999999999999999999998875

>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=99.63  E-value=1.2e-16  Score=95.14  Aligned_cols=55  Identities=22%  Similarity=0.341  Sum_probs=50.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhccchhhhhhhhccCCCC
Q psy17007         45 RRKARTVFSDHQLTGLEKRFEA---QRYLSTPERVELATALQLSETQVKTWFQNRLPF   99 (165)
Q Consensus        45 ~rr~R~~~s~~q~~~Le~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~   99 (165)
                      +++.|+.|+.+++.+|+.+|..   ++||+..++..||..+||+..||++||+|+|.+
T Consensus         2 ~krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R   59 (62)
T d1x2na1           2 GKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRR   59 (62)
T ss_dssp             SCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHH
Confidence            3566789999999999999985   789999999999999999999999999999865

>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=99.26  E-value=1.5e-12  Score=75.94  Aligned_cols=46  Identities=33%  Similarity=0.547  Sum_probs=43.5

Q ss_pred             ccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ++.|+.||++|+.+||..|..++||+.+++++||..+||++.||+-
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~v   47 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITI   47 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeee
Confidence            4678999999999999999999999999999999999999999973

>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=99.25  E-value=1.5e-12  Score=74.73  Aligned_cols=45  Identities=38%  Similarity=0.638  Sum_probs=42.5

Q ss_pred             cccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        119 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       119 r~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      +.|+.||++|+..||..|+.++||+..++.+||..+||++.||+-
T Consensus         1 R~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~lgL~~~qV~v   45 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKI   45 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChHHhhh
Confidence            358899999999999999999999999999999999999999973

>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=99.22  E-value=2.9e-12  Score=74.86  Aligned_cols=44  Identities=45%  Similarity=0.713  Sum_probs=42.4

Q ss_pred             cccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007        119 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLF  162 (165)
Q Consensus       119 r~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq  162 (165)
                      +.|+.||++|+.+|+..|+.++||+..++.+||..+||++.||+
T Consensus         2 r~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~   45 (58)
T d1ig7a_           2 KPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVK   45 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhee
Confidence            56889999999999999999999999999999999999999997

>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=99.21  E-value=4.1e-12  Score=76.51  Aligned_cols=46  Identities=33%  Similarity=0.526  Sum_probs=43.7

Q ss_pred             ccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ++.|+.||++|+.+|+..|..++||+..++++||..+||++.+|+.
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~   47 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQV   47 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheee
Confidence            4578999999999999999999999999999999999999999974

>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=99.21  E-value=5.6e-12  Score=77.65  Aligned_cols=53  Identities=34%  Similarity=0.394  Sum_probs=47.3

Q ss_pred             CccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        111 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       111 ~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .......++.|+.||++|+.+||..|+.++||+..++++||..|||++.||+-
T Consensus         7 ~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~i   59 (77)
T d1pufa_           7 WLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKI   59 (77)
T ss_dssp             SCCCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCccCcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhh
Confidence            33444566789999999999999999999999999999999999999999973

>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=99.19  E-value=3.9e-12  Score=74.01  Aligned_cols=45  Identities=42%  Similarity=0.633  Sum_probs=42.7

Q ss_pred             cccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        119 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       119 r~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      +.|+.||++|+.+||..|+.++||+..++++||..+||++.||+-
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~v   45 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKV   45 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhh
Confidence            468999999999999999999999999999999999999999973

>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=99.19  E-value=7.6e-12  Score=77.12  Aligned_cols=51  Identities=43%  Similarity=0.645  Sum_probs=46.5

Q ss_pred             cccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        113 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       113 ~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .+.+.++.|+.||++|+.+|+..|+.++||+..++++||..+||++.||+-
T Consensus         5 ~p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~   55 (77)
T d1vnda_           5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKI   55 (77)
T ss_dssp             CSSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhh
Confidence            345566789999999999999999999999999999999999999999973

>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=99.18  E-value=5.8e-12  Score=73.27  Aligned_cols=45  Identities=51%  Similarity=0.674  Sum_probs=42.8

Q ss_pred             cccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        119 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       119 r~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      +.|+.||++|+..||..|+.++||+.+++++||..+||++.||+-
T Consensus         2 ~~R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~   46 (57)
T d2e1oa1           2 GGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKT   46 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhH
Confidence            568899999999999999999999999999999999999999974

>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=99.18  E-value=5.8e-12  Score=72.78  Aligned_cols=43  Identities=40%  Similarity=0.587  Sum_probs=41.3

Q ss_pred             cccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        121 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       121 rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      |+.||++|+..||..|+.++||+..++.+||..|||++.+||-
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~i   43 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKI   43 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeee
Confidence            6789999999999999999999999999999999999999973

>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=99.13  E-value=1.3e-11  Score=74.31  Aligned_cols=46  Identities=48%  Similarity=0.735  Sum_probs=43.6

Q ss_pred             ccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ++.|+.||++|+.+|+..|..++||+..++.+||..+||++.+|+-
T Consensus         3 rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~   48 (68)
T d1ftta_           3 RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKI   48 (68)
T ss_dssp             SSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceee
Confidence            5678999999999999999999999999999999999999999974

>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=99.13  E-value=1.6e-11  Score=73.70  Aligned_cols=45  Identities=36%  Similarity=0.626  Sum_probs=42.9

Q ss_pred             ccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLF  162 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq  162 (165)
                      ++.|+.||++|+.+|+..|+.++||+..++.+||..|||++.+|+
T Consensus         2 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~   46 (67)
T d1zq3p1           2 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVK   46 (67)
T ss_dssp             SCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCcccee
Confidence            456899999999999999999999999999999999999999997

>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=99.13  E-value=1.4e-11  Score=73.47  Aligned_cols=46  Identities=39%  Similarity=0.567  Sum_probs=43.8

Q ss_pred             cccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007        117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLF  162 (165)
Q Consensus       117 ~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq  162 (165)
                      .++.|+.||++|+..|+..|..++||+..++++||..+||++.||+
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~   47 (65)
T d1fjla_           2 QRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQ   47 (65)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhh
Confidence            4667999999999999999999999999999999999999999997

>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=99.11  E-value=2.1e-11  Score=76.89  Aligned_cols=48  Identities=46%  Similarity=0.614  Sum_probs=42.5

Q ss_pred             ccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       116 ~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ..++.|+.||++|+.+|+..|+.++||+.+++++||..|||++.+|+-
T Consensus        26 ~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~v   73 (88)
T d1b72a_          26 SPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKI   73 (88)
T ss_dssp             ----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeee
Confidence            446779999999999999999999999999999999999999999973

>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=99.09  E-value=1.7e-11  Score=69.35  Aligned_cols=43  Identities=23%  Similarity=0.288  Sum_probs=41.4

Q ss_pred             cccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        121 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       121 rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      |+.||++|+..|+..|+.++||+.+++.+||..+||++.+|+-
T Consensus         2 Rt~ft~~Q~~~Le~~F~~n~~P~~~~~~~LA~~l~l~~~~V~~   44 (50)
T d1s7ea1           2 RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSN   44 (50)
T ss_dssp             CSCCCHHHHHHHHHHTTSSCSSTHHHHHHHHTTSCSSSHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhh
Confidence            7899999999999999999999999999999999999999973

>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=99.09  E-value=9.1e-12  Score=73.20  Aligned_cols=46  Identities=35%  Similarity=0.512  Sum_probs=43.6

Q ss_pred             ccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ++.|+.||++|+..|+..|..++||+..++..||..+||++.+|+-
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~   47 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRV   47 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHH
Confidence            5678999999999999999999999999999999999999999973

>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=99.06  E-value=4e-11  Score=71.64  Aligned_cols=48  Identities=21%  Similarity=0.248  Sum_probs=44.9

Q ss_pred             ccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       116 ~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      +..+.|+.||++|+..|+..|..|+||+..++++||..+||++.+|+.
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~   49 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRV   49 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHH
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhh
Confidence            356789999999999999999999999999999999999999999974

>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=99.04  E-value=4.9e-11  Score=68.20  Aligned_cols=43  Identities=21%  Similarity=0.256  Sum_probs=41.1

Q ss_pred             cccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        121 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       121 rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      |+.||++|+..|+..|..++||+..++.+||..+||++.||+-
T Consensus         1 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~   43 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRV   43 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHH
Confidence            5789999999999999999999999999999999999999974

>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=99.04  E-value=6.3e-11  Score=70.94  Aligned_cols=47  Identities=21%  Similarity=0.183  Sum_probs=44.2

Q ss_pred             cccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        117 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       117 ~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .++.|+.||++|+..|+..|+.++||+..++++||..+||++.+|+.
T Consensus         8 ~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~   54 (67)
T d1ocpa_           8 RKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRV   54 (67)
T ss_dssp             SSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHH
Confidence            45679999999999999999999999999999999999999999974

>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=99.03  E-value=1.1e-10  Score=70.79  Aligned_cols=48  Identities=19%  Similarity=0.168  Sum_probs=43.9

Q ss_pred             ccccccccccccchhhhhhhccc-cCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        116 RRRKARTVFSDHQLTGLEKRFEA-QRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       116 ~~rr~rt~ft~~Q~~~Le~~F~~-~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ..++.++.||++|+..|+..|+. ++||+.+++++||..+||+..||+.
T Consensus         6 ~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~   54 (71)
T d1wi3a_           6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIK   54 (71)
T ss_dssp             CCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHH
T ss_pred             CCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHH
Confidence            34567899999999999999975 8999999999999999999999985

>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=99.02  E-value=7.9e-11  Score=71.40  Aligned_cols=46  Identities=17%  Similarity=0.181  Sum_probs=42.5

Q ss_pred             ccccccccccchhhhhhhccc-cCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRFEA-QRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F~~-~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ++.++.||.+|+..|+..|.. ++||+..++++||..+||++.+|+-
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~Vqv   48 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQK   48 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHH
Confidence            457889999999999999986 7899999999999999999999973

>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=99.01  E-value=8.2e-11  Score=68.49  Aligned_cols=45  Identities=27%  Similarity=0.284  Sum_probs=42.6

Q ss_pred             cccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        119 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       119 r~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      +.|+.|+++|+..|+..|..++||+..++.+||..+||++.+|+-
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~   45 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRV   45 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHH
Confidence            468899999999999999999999999999999999999999974

>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=98.98  E-value=1.9e-10  Score=71.20  Aligned_cols=49  Identities=12%  Similarity=0.034  Sum_probs=44.1

Q ss_pred             cccccccccccccchhhhhhhccc----cCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        115 CRRRKARTVFSDHQLTGLEKRFEA----QRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       115 ~~~rr~rt~ft~~Q~~~Le~~F~~----~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .+.++.|+.||.+|+..|+..|+.    ++||+.+++++||..|||++.+|+-
T Consensus        15 ~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~v   67 (80)
T d1wh7a_          15 GTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKI   67 (80)
T ss_dssp             CCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHH
T ss_pred             cCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeee
Confidence            445678999999999999888875    8999999999999999999999984

>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=98.92  E-value=2.6e-10  Score=66.04  Aligned_cols=44  Identities=18%  Similarity=0.219  Sum_probs=41.8

Q ss_pred             ccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        120 ARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       120 ~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .|+.|+++|+..|+..|..++||+..+++.||..+||++.||+-
T Consensus         1 kRT~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~   44 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRV   44 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHH
Confidence            37899999999999999999999999999999999999999974

>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=98.86  E-value=4.1e-10  Score=70.03  Aligned_cols=45  Identities=22%  Similarity=0.423  Sum_probs=41.2

Q ss_pred             ccccccccccchhhhhhhccccCCCCHHHHHHHHHHcC---------------CChhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQ---------------LSETQLF  162 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lg---------------l~~~qVq  162 (165)
                      ++.|+.||++|+.+||..|+.++||+..++++||..+|               |++.+|+
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~   60 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVY   60 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHH
Confidence            46789999999999999999999999999999999875               8888886

>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=98.75  E-value=3.1e-09  Score=64.97  Aligned_cols=43  Identities=19%  Similarity=0.130  Sum_probs=39.7

Q ss_pred             cccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        121 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       121 rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      +..+|.+|+..|+..|..++||+..++++||..+||++.||+.
T Consensus         8 ~k~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~   50 (76)
T d2ecba1           8 FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDA   50 (76)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHH
Confidence            3346899999999999999999999999999999999999974

>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=98.74  E-value=3.1e-09  Score=65.00  Aligned_cols=44  Identities=14%  Similarity=0.135  Sum_probs=40.8

Q ss_pred             ccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        120 ARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       120 ~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .+..+|.+|+..|+..|..++||+.++++.||..+||++.||+.
T Consensus         6 ~~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~   49 (76)
T d2ecca1           6 SGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQ   49 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHH
Confidence            34568999999999999999999999999999999999999974

>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=98.72  E-value=3.6e-09  Score=64.20  Aligned_cols=45  Identities=24%  Similarity=0.320  Sum_probs=41.8

Q ss_pred             ccccccccccchhhhhhhcc---ccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRFE---AQRYLSTPERVELATALQLSETQLF  162 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F~---~~~yp~~~~r~~La~~lgl~~~qVq  162 (165)
                      ++.++.|+.+|+..|+..|.   .++||+..++++||..+||++.||+
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~   49 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVS   49 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhH
Confidence            45788999999999999997   5889999999999999999999997

>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=98.62  E-value=9.7e-09  Score=62.90  Aligned_cols=35  Identities=23%  Similarity=0.188  Sum_probs=33.2

Q ss_pred             cccccccchhhhhhhccccCCCCHHHHHHHHHHcC
Q psy17007        121 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQ  155 (165)
Q Consensus       121 rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lg  155 (165)
                      |..||+.|+..|+..|+.++||+..+|++||.+++
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln   35 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECN   35 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHH
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhc
Confidence            56899999999999999999999999999999995

>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=98.56  E-value=2.8e-08  Score=57.62  Aligned_cols=45  Identities=22%  Similarity=0.192  Sum_probs=40.5

Q ss_pred             cccccccccchhhhhhhccc-cCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        119 KARTVFSDHQLTGLEKRFEA-QRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       119 r~rt~ft~~Q~~~Le~~F~~-~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      +.+..++.++...||+.|.. ++||+..++++||..+||++.||+-
T Consensus         3 k~~~~~k~~~~~iLE~~F~~~~~yPs~~~~~~LA~~lgls~~qV~~   48 (59)
T d2cqxa1           3 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQC   48 (59)
T ss_dssp             CCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHH
T ss_pred             CCCCCCCccccHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHH
Confidence            34677889999999999986 7899999999999999999999973

>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=98.51  E-value=3.4e-08  Score=55.73  Aligned_cols=39  Identities=18%  Similarity=0.114  Sum_probs=36.0

Q ss_pred             cccchhhhhhhccc-cCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        125 SDHQLTGLEKRFEA-QRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       125 t~~Q~~~Le~~F~~-~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      |.+|...||..|.. ++||+..+++.||..+||++.||+-
T Consensus         1 T~~q~~iLE~~F~~~~~~P~~~~~~~LA~~~~ls~~qV~~   40 (52)
T d1x2ma1           1 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQR   40 (52)
T ss_dssp             SSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHH
T ss_pred             ChhHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHH
Confidence            57899999999976 7999999999999999999999974

>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=98.51  E-value=3.1e-08  Score=58.02  Aligned_cols=46  Identities=17%  Similarity=0.245  Sum_probs=41.5

Q ss_pred             ccccccccccchhhhhhhccc---cCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        118 RKARTVFSDHQLTGLEKRFEA---QRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       118 rr~rt~ft~~Q~~~Le~~F~~---~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      ++.++.|+.+++..|+.-|..   ++||+.+++..||..+||+..||+-
T Consensus         3 krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~   51 (62)
T d1x2na1           3 KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNN   51 (62)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHH
Confidence            455778999999999999974   8999999999999999999999974

>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=98.50  E-value=3e-08  Score=57.67  Aligned_cols=42  Identities=26%  Similarity=0.290  Sum_probs=38.2

Q ss_pred             ccccccchhhhhhhccc---cCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007        122 TVFSDHQLTGLEKRFEA---QRYLSTPERVELATALQLSETQLFY  163 (165)
Q Consensus       122 t~ft~~Q~~~Le~~F~~---~~yp~~~~r~~La~~lgl~~~qVq~  163 (165)
                      .+||++|+..|+..|..   ++||+.+++++||..+||+..||+-
T Consensus         3 ~Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~   47 (60)
T d1k61a_           3 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKN   47 (60)
T ss_dssp             CSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhH
Confidence            35999999999999976   4799999999999999999999974

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.21  E-value=0.26  Score=27.84  Aligned_cols=45  Identities=16%  Similarity=0.269  Sum_probs=38.0

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccC
Q psy17007         49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR   96 (165)
Q Consensus        49 R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nr   96 (165)
                      |..+|..+.-.+...++..+...   ..+||..+|+....|..|..|+
T Consensus         5 Rk~LT~~eK~~ii~~~e~g~k~s---q~eIA~~fGv~~STvs~IlKnK   49 (66)
T d1hlva1           5 RRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNK   49 (66)
T ss_dssp             SCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTH
T ss_pred             cccCCHHHHHHHHHHHHcCCcch---HHHHHHHhCCChhHHHHHHHHH
Confidence            45689999888888998887653   4568999999999999999985

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=87.64  E-value=0.54  Score=24.54  Aligned_cols=40  Identities=15%  Similarity=0.290  Sum_probs=34.1

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhc
Q psy17007         50 TVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQ   94 (165)
Q Consensus        50 ~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~   94 (165)
                      ..+|++|++.....+... .+    ...||..+|++...|..||.
T Consensus         4 ~~lt~~q~~~a~~l~~~G-~s----~~~iA~~~gVSr~TiYry~p   43 (47)
T d1ijwc_           4 RAINKHEQEQISRLLEKG-HP----RQQLAIIFGIGVSTLYRYFP   43 (47)
T ss_dssp             CSSCHHHHHHHHHHHHTT-CC----HHHHHHHHTCCHHHHHHHSC
T ss_pred             CcCCHHHHHHHHHHHHCC-CC----HHHHHHHHCcCHHHHHhhCC
Confidence            468999999999999754 33    77889999999999999984