Psyllid ID: psy10638

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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
Protein Sequence
MPKLINEKDKLLSPSSDLKCKKLSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQQRLAAIKQSQLNQQQENLHQQSSDQHHTSQHQYLFQQGEIA
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccHHHHHHHHHHcccccHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHcHccccccccccccccccccccccccccccccccccccccHHHHcHcc
Coil and Loop (DISEMBL)
mpklinekdkllspssdlkckklspsscssssskskrvrtiftpEQLERLEAEFERQqymvgperlYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQQRLAAIKQSQLNQQQEnlhqqssdqhHTSQHQYLFQQGEIA
Flexible Loop (DISEMBL)
mpklinekdkllspssdlkckklspsscssssskskrvrtiftpeqlERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQQRLAAIKQSQLNQQQENLHQQSSDQHHTSQHQYLFQQGEIA
Low Complexity Region (SEG)
MPKLINEkdkllspssdlkckklspsscssssskskRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQQRLAAIKqsqlnqqqenlhqqssdqhhtsqhqYLFQQGEIA
Disordered region (IsUnstruct)
***************************************************AEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQ*****************************************
Disordered Region (DISOPRED)
*****************************************FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK***************************************************
Disordered Region (DISEMBL)
********DKLLSPSSD**********************TIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQQRLAAIKQ***********************QYLFQQGEIA
Disordered Region (DISPRO)
*************PS**********************VRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ***********************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPKLINEKDKLLSPSSDLKCKKLSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQQRLAAIKQSQLNQQQENLHQQSSDQHHTSQHQYLFQQGEIA
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	140	2.2.26 [Sep-21-2011]
Q91770	233	Homeobox protein not2 OS=	N/A	N/A	0.578	0.347	0.679	7e-25
Q06615	236	Homeobox protein notochor	N/A	N/A	0.678	0.402	0.593	1e-24
Q17R00	253	Homeobox protein EMX2 OS=	yes	N/A	0.45	0.249	0.634	8e-17
Q04744	253	Homeobox protein EMX2 OS=	yes	N/A	0.45	0.249	0.634	9e-17
Q04743	252	Homeobox protein EMX2 OS=	yes	N/A	0.45	0.25	0.634	9e-17
Q9PU20	302	Ventral anterior homeobox	N/A	N/A	0.535	0.248	0.546	2e-15
Q804S6	231	Homeobox protein EMX1 OS=	no	N/A	0.45	0.272	0.603	2e-15
P18488	497	Homeotic protein empty sp	no	N/A	0.592	0.167	0.483	2e-15
Q04742	257	Homeobox protein EMX1 OS=	no	N/A	0.45	0.245	0.603	2e-15
Q04741	257	Homeobox protein EMX1 OS=	no	N/A	0.45	0.245	0.603	2e-15

>sp|Q91770|NOT2_XENLA Homeobox protein not2 OS=Xenopus laevis GN=not2 PE=2 SV=1

 Score =  112 bits (280), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 55/81 (67%), Positives = 65/81 (80%)

Query: 23  LSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVW 82
           L+P S  +   K KR+RT+FTPEQLERLE EF +QQYMVG ER+ LA TLNLTE QVKVW
Sbjct: 123 LNPLSWRTGPCKLKRIRTVFTPEQLERLEKEFLKQQYMVGTERVDLASTLNLTETQVKVW 182

Query: 83  FQNRRIKWRKQHLEFQQQRLA 103
           FQNRRIKWRKQ LE ++ +L+
Sbjct: 183 FQNRRIKWRKQSLEQKKAKLS 203

Transcriptional repressor (By similarity). Plays a fundamental role in notochord formation, acting within the mesodermal region. Acts downstream of gsc and upstream of chrd and foxa4-A/pintallavis.
Xenopus laevis (taxid: 8355)

>sp|Q06615|NOTO_XENLA Homeobox protein notochord OS=Xenopus laevis GN=noto PE=2 SV=1

 Score =  111 bits (278), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 57/96 (59%), Positives = 72/96 (75%), Gaps = 1/96 (1%)

Query: 8   KDKLLSPSSDLKCKKLSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLY 67
           K+++L P S      ++P S  +   K KR+RT+FTPEQLE+LE EF +QQYMVG ER+ 
Sbjct: 112 KERVL-PFSHCPNGAMNPLSWRTGPCKMKRIRTVFTPEQLEKLEKEFLKQQYMVGTERVD 170

Query: 68  LAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQQRLA 103
           LA TLNLTE QVKVWFQNRRIKWRKQ LE ++ +L+
Sbjct: 171 LASTLNLTETQVKVWFQNRRIKWRKQSLEQKKAKLS 206

Transcriptional repressor. Plays a fundamental role in notochord formation, acting within the mesodermal region.

Xenopus laevis (taxid: 8355)

>sp|Q17R00|EMX2_BOVIN Homeobox protein EMX2 OS=Bos taurus GN=EMX2 PE=2 SV=1

 Score = 85.5 bits (210), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 40/63 (63%), Positives = 49/63 (77%)

Query: 34  KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
           K KR+RT F+P QL RLE  FE+  Y+VG ER  LAH+L+LTE QVKVWFQNRR K+++Q
Sbjct: 154 KPKRIRTAFSPSQLLRLEHAFEKNHYVVGAERKQLAHSLSLTETQVKVWFQNRRTKFKRQ 213

Query: 94  HLE 96
            LE
Sbjct: 214 KLE 216

Transcription factor, which in cooperation with EMX2, acts to generate the boundary between the roof and archipallium in the developing brain. May function in combinations with OTX1/2 to specify cell fates in the developing central nervous system.

Bos taurus (taxid: 9913)

>sp|Q04744|EMX2_MOUSE Homeobox protein EMX2 OS=Mus musculus GN=Emx2 PE=2 SV=3

 Score = 85.5 bits (210), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 40/63 (63%), Positives = 49/63 (77%)

Query: 34  KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
           K KR+RT F+P QL RLE  FE+  Y+VG ER  LAH+L+LTE QVKVWFQNRR K+++Q
Sbjct: 154 KPKRIRTAFSPSQLLRLEHAFEKNHYVVGAERKQLAHSLSLTETQVKVWFQNRRTKFKRQ 213

Query: 94  HLE 96
            LE
Sbjct: 214 KLE 216

Transcription factor, which in cooperation with EMX2, acts to generate the boundary between the roof and archipallium in the developing brain. May function in combinations with OTX1/2 to specify cell fates in the developing central nervous system.

Mus musculus (taxid: 10090)

>sp|Q04743|EMX2_HUMAN Homeobox protein EMX2 OS=Homo sapiens GN=EMX2 PE=1 SV=2

 Score = 85.5 bits (210), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 40/63 (63%), Positives = 49/63 (77%)

Query: 34  KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
           K KR+RT F+P QL RLE  FE+  Y+VG ER  LAH+L+LTE QVKVWFQNRR K+++Q
Sbjct: 153 KPKRIRTAFSPSQLLRLEHAFEKNHYVVGAERKQLAHSLSLTETQVKVWFQNRRTKFKRQ 212

Query: 94  HLE 96
            LE
Sbjct: 213 KLE 215

Transcription factor, which in cooperation with EMX2, acts to generate the boundary between the roof and archipallium in the developing brain. May function in combinations with OTX1/2 to specify cell fates in the developing central nervous system.

Homo sapiens (taxid: 9606)

>sp|Q9PU20|VAX2A_XENLA Ventral anterior homeobox 2a OS=Xenopus laevis GN=vax2-a PE=2 SV=1

 Score = 81.3 bits (199), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 41/75 (54%), Positives = 51/75 (68%)

Query: 34  KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
           + KR RT FT EQL RLE EF+R QY+VG ER  LA  LNL+E QVKVWFQNRR K +K 
Sbjct: 104 RPKRTRTSFTAEQLYRLELEFQRCQYVVGRERTELARQLNLSETQVKVWFQNRRTKQKKD 163

Query: 94  HLEFQQQRLAAIKQS 108
                ++R ++  +S
Sbjct: 164 QSRDSEKRSSSTSES 178

Transcription factor that may function in dorsoventral specification of the forebrain. Regulates the expression of Wnt signaling antagonists including the expression of a truncated tcf7l2 isoform that cannot bind ctnnb1 and acts therefore as a potent dominant-negative Wnt antagonist. Plays a crucial role in eye development and, in particular, in the specification of the ventral optic vesicle. May be a regulator of axial polarization in the retina.

Xenopus laevis (taxid: 8355)

>sp|Q804S6|EMX1_DANRE Homeobox protein EMX1 OS=Danio rerio GN=emx1 PE=2 SV=1

 Score = 80.9 bits (198), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 38/63 (60%), Positives = 49/63 (77%)

Query: 34  KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
           K KR+RT F+P QL RLE  FE+  Y+VG ER  LA++L+L+E QVKVWFQNRR K+++Q
Sbjct: 132 KPKRIRTAFSPSQLLRLERAFEKNHYVVGAERKQLANSLSLSETQVKVWFQNRRTKYKRQ 191

Query: 94  HLE 96
            LE
Sbjct: 192 KLE 194

May function in combinations with OTX1/2 to specify cell fates in the developing central nervous system.

Danio rerio (taxid: 7955)

>sp|P18488|EMS_DROME Homeotic protein empty spiracles OS=Drosophila melanogaster GN=ems PE=2 SV=2

 Score = 80.9 bits (198), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 44/91 (48%), Positives = 54/91 (59%), Gaps = 8/91 (8%)

Query: 34  KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
           K KR+RT F+P QL +LE  FE  QY+VG ER  LA  LNL+E QVKVWFQNRR K    
Sbjct: 390 KPKRIRTAFSPSQLLKLEHAFESNQYVVGAERKALAQNLNLSETQVKVWFQNRRTK---- 445

Query: 94  HLEFQQQRLAAIKQSQLNQQQENLHQQSSDQ 124
           H   QQ+     ++      Q N+H  S D+
Sbjct: 446 HKRMQQED----EKGGEGGSQRNMHNGSGDE 472

Acts as a homeotic selector gene controlling antennal and mandibular segment identity.

Drosophila melanogaster (taxid: 7227)

>sp|Q04742|EMX1_MOUSE Homeobox protein EMX1 OS=Mus musculus GN=Emx1 PE=2 SV=2

 Score = 80.9 bits (198), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 38/63 (60%), Positives = 48/63 (76%)

Query: 34  KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
           K KR+RT F+P QL RLE  FE+  Y+VG ER  LA +L+L+E QVKVWFQNRR K+++Q
Sbjct: 158 KPKRIRTAFSPSQLLRLERAFEKNHYVVGAERKQLAGSLSLSETQVKVWFQNRRTKYKRQ 217

Query: 94  HLE 96
            LE
Sbjct: 218 KLE 220

Transcription factor, which in cooperation with EMX2, acts to generate the boundary between the roof and archipallium in the developing brain. May function in combinations with OTX1/2 to specify cell fates in the developing central nervous system.

Mus musculus (taxid: 10090)

>sp|Q04741|EMX1_HUMAN Homeobox protein EMX1 OS=Homo sapiens GN=EMX1 PE=2 SV=2

 Score = 80.9 bits (198), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 38/63 (60%), Positives = 48/63 (76%)

Query: 34  KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
           K KR+RT F+P QL RLE  FE+  Y+VG ER  LA +L+L+E QVKVWFQNRR K+++Q
Sbjct: 158 KPKRIRTAFSPSQLLRLERAFEKNHYVVGAERKQLAGSLSLSETQVKVWFQNRRTKYKRQ 217

Query: 94  HLE 96
            LE
Sbjct: 218 KLE 220

Transcription factor, which in cooperation with EMX2, acts to generate the boundary between the roof and archipallium in the developing brain. May function in combinations with OTX1/2 to specify cell fates in the developing central nervous system.

Homo sapiens (taxid: 9606)

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	140
242021601	192	Homeobox protein Hox-B1, putative [Pedic	0.642	0.468	0.833	1e-35
157136039	181	hypothetical protein AaeL_AAEL003372 [Ae	0.607	0.469	0.848	4e-34
195449994	443	GK22391 [Drosophila willistoni] gi|19416	0.642	0.203	0.811	4e-34
198453430	447	GA15009 [Drosophila pseudoobscura pseudo	0.642	0.201	0.811	5e-34
195152011	452	GL21794 [Drosophila persimilis] gi|19411	0.642	0.199	0.811	5e-34
91077424	234	PREDICTED: similar to GA15009-PA [Tribol	0.585	0.350	0.865	7e-34
194764543	448	GF23077 [Drosophila ananassae] gi|190614	0.642	0.200	0.8	1e-33
195497590	446	GE25529 [Drosophila yakuba] gi|194182266	0.642	0.201	0.8	1e-33
24647903	475	CG18599 [Drosophila melanogaster] gi|231	0.642	0.189	0.8	1e-33
195569941	467	GD19222 [Drosophila simulans] gi|1941988	0.642	0.192	0.8	1e-33

>gi|242021601|ref|XP_002431233.1| Homeobox protein Hox-B1, putative [Pediculus humanus corporis] gi|212516482|gb|EEB18495.1| Homeobox protein Hox-B1, putative [Pediculus humanus corporis]

 Score =  154 bits (389), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 75/90 (83%), Positives = 77/90 (85%)

Query: 18  LKCKKLSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEA 77
           LK K  + S       K+KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTL LTEA
Sbjct: 18  LKQKSSNESVSKKCGGKAKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLQLTEA 77

Query: 78  QVKVWFQNRRIKWRKQHLEFQQQRLAAIKQ 107
           QVKVWFQNRRIKWRKQHLE QQQRLAAIKQ
Sbjct: 78  QVKVWFQNRRIKWRKQHLEIQQQRLAAIKQ 107

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157136039|ref|XP_001656740.1| hypothetical protein AaeL_AAEL003372 [Aedes aegypti] gi|108881108|gb|EAT45333.1| AAEL003372-PA [Aedes aegypti]

 Score =  149 bits (376), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 73/86 (84%), Positives = 78/86 (90%), Gaps = 1/86 (1%)

Query: 26  SSCSSSSS-KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQ 84
           SS S+S++ KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTL LTEAQVKVWFQ
Sbjct: 11  SSLSASAALKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLQLTEAQVKVWFQ 70

Query: 85  NRRIKWRKQHLEFQQQRLAAIKQSQL 110
           NRRIKWRK HLE  QQRLA I+Q Q+
Sbjct: 71  NRRIKWRKHHLEITQQRLALIRQRQI 96

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195449994|ref|XP_002072317.1| GK22391 [Drosophila willistoni] gi|194168402|gb|EDW83303.1| GK22391 [Drosophila willistoni]

 Score =  149 bits (376), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 73/90 (81%), Positives = 77/90 (85%)

Query: 21  KKLSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVK 80
           +KL   S   SS K+KRVRTIFTPEQLE LEAEFERQQYMVGPERLYLAHTL LTEAQVK
Sbjct: 267 EKLKSDSHKKSSLKNKRVRTIFTPEQLECLEAEFERQQYMVGPERLYLAHTLKLTEAQVK 326

Query: 81  VWFQNRRIKWRKQHLEFQQQRLAAIKQSQL 110
           VWFQNRRIKWRK HLE  QQRLA I+Q+QL
Sbjct: 327 VWFQNRRIKWRKHHLELTQQRLALIRQTQL 356

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198453430|ref|XP_001359197.2| GA15009 [Drosophila pseudoobscura pseudoobscura] gi|198132355|gb|EAL28341.2| GA15009 [Drosophila pseudoobscura pseudoobscura]

 Score =  149 bits (375), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 73/90 (81%), Positives = 77/90 (85%)

Query: 21  KKLSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVK 80
           +KL   S   SS K+KRVRTIFTPEQLE LEAEFERQQYMVGPERLYLAHTL LTEAQVK
Sbjct: 276 EKLKSDSHKKSSLKNKRVRTIFTPEQLECLEAEFERQQYMVGPERLYLAHTLKLTEAQVK 335

Query: 81  VWFQNRRIKWRKQHLEFQQQRLAAIKQSQL 110
           VWFQNRRIKWRK HLE  QQRLA I+Q+QL
Sbjct: 336 VWFQNRRIKWRKHHLELTQQRLALIRQTQL 365

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195152011|ref|XP_002016932.1| GL21794 [Drosophila persimilis] gi|194111989|gb|EDW34032.1| GL21794 [Drosophila persimilis]

 Score =  149 bits (375), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 73/90 (81%), Positives = 77/90 (85%)

Query: 21  KKLSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVK 80
           +KL   S   SS K+KRVRTIFTPEQLE LEAEFERQQYMVGPERLYLAHTL LTEAQVK
Sbjct: 281 EKLKSDSHKKSSLKNKRVRTIFTPEQLECLEAEFERQQYMVGPERLYLAHTLKLTEAQVK 340

Query: 81  VWFQNRRIKWRKQHLEFQQQRLAAIKQSQL 110
           VWFQNRRIKWRK HLE  QQRLA I+Q+QL
Sbjct: 341 VWFQNRRIKWRKHHLELTQQRLALIRQTQL 370

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91077424|ref|XP_975423.1| PREDICTED: similar to GA15009-PA [Tribolium castaneum]

 Score =  148 bits (374), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 71/82 (86%), Positives = 72/82 (87%)

Query: 29  SSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRI 88
           S  S KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTL LTEAQVKVWFQNRRI
Sbjct: 135 SKKSCKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLQLTEAQVKVWFQNRRI 194

Query: 89  KWRKQHLEFQQQRLAAIKQSQL 110
           KWRK HLE   QRLA +KQ QL
Sbjct: 195 KWRKHHLELTHQRLAVLKQQQL 216

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194764543|ref|XP_001964388.1| GF23077 [Drosophila ananassae] gi|190614660|gb|EDV30184.1| GF23077 [Drosophila ananassae]

 Score =  147 bits (372), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 72/90 (80%), Positives = 77/90 (85%)

Query: 21  KKLSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVK 80
           +KL   S   S+ K+KRVRTIFTPEQLE LEAEFERQQYMVGPERLYLAHTL LTEAQVK
Sbjct: 276 EKLKSDSHKKSALKNKRVRTIFTPEQLECLEAEFERQQYMVGPERLYLAHTLKLTEAQVK 335

Query: 81  VWFQNRRIKWRKQHLEFQQQRLAAIKQSQL 110
           VWFQNRRIKWRK HLE  QQRLA I+Q+QL
Sbjct: 336 VWFQNRRIKWRKHHLELTQQRLALIRQTQL 365

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195497590|ref|XP_002096165.1| GE25529 [Drosophila yakuba] gi|194182266|gb|EDW95877.1| GE25529 [Drosophila yakuba]

 Score =  147 bits (372), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 72/90 (80%), Positives = 77/90 (85%)

Query: 21  KKLSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVK 80
           +KL   S   S+ K+KRVRTIFTPEQLE LEAEFERQQYMVGPERLYLAHTL LTEAQVK
Sbjct: 273 EKLKSESHKKSALKNKRVRTIFTPEQLECLEAEFERQQYMVGPERLYLAHTLKLTEAQVK 332

Query: 81  VWFQNRRIKWRKQHLEFQQQRLAAIKQSQL 110
           VWFQNRRIKWRK HLE  QQRLA I+Q+QL
Sbjct: 333 VWFQNRRIKWRKHHLELTQQRLALIRQTQL 362

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|24647903|ref|NP_650701.1| CG18599 [Drosophila melanogaster] gi|23171622|gb|AAF55524.2| CG18599 [Drosophila melanogaster]

 Score =  147 bits (371), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 72/90 (80%), Positives = 77/90 (85%)

Query: 21  KKLSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVK 80
           +KL   S   S+ K+KRVRTIFTPEQLE LEAEFERQQYMVGPERLYLAHTL LTEAQVK
Sbjct: 302 EKLKSDSHKKSALKNKRVRTIFTPEQLECLEAEFERQQYMVGPERLYLAHTLKLTEAQVK 361

Query: 81  VWFQNRRIKWRKQHLEFQQQRLAAIKQSQL 110
           VWFQNRRIKWRK HLE  QQRLA I+Q+QL
Sbjct: 362 VWFQNRRIKWRKHHLELTQQRLALIRQTQL 391

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195569941|ref|XP_002102967.1| GD19222 [Drosophila simulans] gi|194198894|gb|EDX12470.1| GD19222 [Drosophila simulans]

 Score =  147 bits (371), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 72/90 (80%), Positives = 77/90 (85%)

Query: 21  KKLSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVK 80
           +KL   S   S+ K+KRVRTIFTPEQLE LEAEFERQQYMVGPERLYLAHTL LTEAQVK
Sbjct: 294 EKLKSDSHKKSALKNKRVRTIFTPEQLECLEAEFERQQYMVGPERLYLAHTLKLTEAQVK 353

Query: 81  VWFQNRRIKWRKQHLEFQQQRLAAIKQSQL 110
           VWFQNRRIKWRK HLE  QQRLA I+Q+QL
Sbjct: 354 VWFQNRRIKWRKHHLELTQQRLALIRQTQL 383

Source: Drosophila simulans

Species: Drosophila simulans

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	140
FB|FBgn0038592	475	CG18599 [Drosophila melanogast	0.5	0.147	0.9	3.6e-29
UNIPROTKB|Q91770	233	not2 "Homeobox protein not2" [	0.478	0.287	0.746	2.1e-22
UNIPROTKB|Q06615	236	noto "Homeobox protein notocho	0.478	0.283	0.731	4.3e-22
UNIPROTKB|F1NJ95	168	CNOT2 "Uncharacterized protein	0.478	0.398	0.761	2.4e-21
UNIPROTKB|F1NKM9	151	CNOT2 "Uncharacterized protein	0.478	0.443	0.761	2.4e-21
ZFIN|ZDB-GENE-990415-75	241	flh "floating head" [Danio rer	0.492	0.286	0.724	4.9e-21
UNIPROTKB|Q90789	111	Cnot "Uncharacterized protein"	0.478	0.603	0.716	6.3e-21
UNIPROTKB|Q91967	171	Gnot1 "Homeodomain protein" [G	0.478	0.391	0.716	6.3e-21
UNIPROTKB|E1BT91	247	LOC100858961 "Uncharacterized	0.428	0.242	0.633	6e-16
UNIPROTKB|Q17R00	253	EMX2 "Homeobox protein EMX2" [	0.428	0.237	0.633	6e-16

FB|FBgn0038592 CG18599 [Drosophila melanogaster (taxid:7227)]

 Score = 324 (119.1 bits), Expect = 3.6e-29, P = 3.6e-29
 Identities = 63/70 (90%), Positives = 64/70 (91%)

Query:    37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE 96
             RVRTIFTPEQLE LEAEFERQQYMVGPERLYLAHTL LTEAQVKVWFQNRRIKWRK HLE
Sbjct:   318 RVRTIFTPEQLECLEAEFERQQYMVGPERLYLAHTLKLTEAQVKVWFQNRRIKWRKHHLE 377

Query:    97 FQQQRLAAIK 106
               QQRLA I+
Sbjct:   378 LTQQRLALIR 387

GO:0005634 "nucleus" evidence=IEA

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

UNIPROTKB|Q91770 not2 "Homeobox protein not2" [Xenopus laevis (taxid:8355)]

 Score = 260 (96.6 bits), Expect = 2.1e-22, P = 2.1e-22
 Identities = 50/67 (74%), Positives = 58/67 (86%)

Query:    37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE 96
             R+RT+FTPEQLERLE EF +QQYMVG ER+ LA TLNLTE QVKVWFQNRRIKWRKQ LE
Sbjct:   137 RIRTVFTPEQLERLEKEFLKQQYMVGTERVDLASTLNLTETQVKVWFQNRRIKWRKQSLE 196

Query:    97 FQQQRLA 103
              ++ +L+
Sbjct:   197 QKKAKLS 203

GO:0014028 "notochord formation" evidence=IMP

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=ISS

UNIPROTKB|Q06615 noto "Homeobox protein notochord" [Xenopus laevis (taxid:8355)]

 Score = 257 (95.5 bits), Expect = 4.3e-22, P = 4.3e-22
 Identities = 49/67 (73%), Positives = 58/67 (86%)

Query:    37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE 96
             R+RT+FTPEQLE+LE EF +QQYMVG ER+ LA TLNLTE QVKVWFQNRRIKWRKQ LE
Sbjct:   140 RIRTVFTPEQLEKLEKEFLKQQYMVGTERVDLASTLNLTETQVKVWFQNRRIKWRKQSLE 199

Query:    97 FQQQRLA 103
              ++ +L+
Sbjct:   200 QKKAKLS 206

GO:0005634 "nucleus" evidence=IC

GO:0014028 "notochord formation" evidence=IMP

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IDA

UNIPROTKB|F1NJ95 CNOT2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 250 (93.1 bits), Expect = 2.4e-21, P = 2.4e-21
 Identities = 51/67 (76%), Positives = 54/67 (80%)

Query:    37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE 96
             RVRTIFT +QL RLE EF RQQYMVG ER  LA  L+LTE QVKVWFQNRRIKWRKQ LE
Sbjct:    93 RVRTIFTSDQLARLEKEFARQQYMVGTERCLLASALHLTEEQVKVWFQNRRIKWRKQSLE 152

Query:    97 FQQQRLA 103
              QQ +LA
Sbjct:   153 QQQAKLA 159

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

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

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|F1NKM9 CNOT2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 250 (93.1 bits), Expect = 2.4e-21, P = 2.4e-21
 Identities = 51/67 (76%), Positives = 54/67 (80%)

Query:    37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE 96
             RVRTIFT +QL RLE EF RQQYMVG ER  LA  L+LTE QVKVWFQNRRIKWRKQ LE
Sbjct:    76 RVRTIFTSDQLARLEKEFARQQYMVGTERCLLASALHLTEEQVKVWFQNRRIKWRKQSLE 135

Query:    97 FQQQRLA 103
              QQ +LA
Sbjct:   136 QQQAKLA 142

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

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

GO:0005634 "nucleus" evidence=IEA

ZFIN|ZDB-GENE-990415-75 flh "floating head" [Danio rerio (taxid:7955)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 50/69 (72%), Positives = 54/69 (78%)

Query:    37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE 96
             R+RT FT +QL RLE EF RQQYMVG ER  LA  L LTEAQVKVWFQNRRIKWRKQ LE
Sbjct:   136 RMRTSFTNDQLSRLEKEFARQQYMVGSERFLLASALQLTEAQVKVWFQNRRIKWRKQSLE 195

Query:    97 FQQQRLAAI 105
              QQ +LA +
Sbjct:   196 QQQAKLAKL 204

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:0030325 "adrenal gland development" evidence=IMP

GO:0048319 "axial mesoderm morphogenesis" evidence=IGI;IMP

GO:0061371 "determination of heart left/right asymmetry" evidence=IMP

GO:0021982 "pineal gland development" evidence=IMP

GO:0035050 "embryonic heart tube development" evidence=IMP

GO:0003143 "embryonic heart tube morphogenesis" evidence=IMP

GO:2000223 "regulation of BMP signaling pathway involved in heart jogging" evidence=IMP

GO:0014028 "notochord formation" evidence=IMP

GO:0001947 "heart looping" evidence=IMP

GO:0007368 "determination of left/right symmetry" evidence=IMP

GO:0032835 "glomerulus development" evidence=IMP

GO:0003160 "endocardium morphogenesis" evidence=IMP

GO:0003140 "determination of left/right asymmetry in lateral mesoderm" evidence=IMP

UNIPROTKB|Q90789 Cnot "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 246 (91.7 bits), Expect = 6.3e-21, P = 6.3e-21
 Identities = 48/67 (71%), Positives = 56/67 (83%)

Query:    37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE 96
             RVRT+F PEQLERLE EF +QQYMVG ER+ LA TL LTE QVKVWFQNRRIKWRKQ +E
Sbjct:    18 RVRTVFKPEQLERLEQEFLKQQYMVGTERVDLAATLRLTETQVKVWFQNRRIKWRKQSME 77

Query:    97 FQQQRLA 103
              ++ +L+
Sbjct:    78 QKKAKLS 84

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0009880 "embryonic pattern specification" evidence=IEA

GO:0009953 "dorsal/ventral pattern formation" evidence=IEA

GO:0030903 "notochord development" evidence=IEA

UNIPROTKB|Q91967 Gnot1 "Homeodomain protein" [Gallus gallus (taxid:9031)]

 Score = 246 (91.7 bits), Expect = 6.3e-21, P = 6.3e-21
 Identities = 48/67 (71%), Positives = 56/67 (83%)

Query:    37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE 96
             RVRT+F PEQLERLE EF +QQYMVG ER+ LA TL LTE QVKVWFQNRRIKWRKQ +E
Sbjct:    78 RVRTVFKPEQLERLEQEFLKQQYMVGTERVDLAATLRLTETQVKVWFQNRRIKWRKQSME 137

Query:    97 FQQQRLA 103
              ++ +L+
Sbjct:   138 QKKAKLS 144

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0009880 "embryonic pattern specification" evidence=IEA

GO:0009953 "dorsal/ventral pattern formation" evidence=IEA

GO:0030903 "notochord development" evidence=IEA

UNIPROTKB|E1BT91 LOC100858961 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 199 (75.1 bits), Expect = 6.0e-16, P = 6.0e-16
 Identities = 38/60 (63%), Positives = 47/60 (78%)

Query:    37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE 96
             R+RT F+P QL RLE  FE+  Y+VG ER  LAH+L+LTE QVKVWFQNRR K+++Q LE
Sbjct:   151 RIRTAFSPSQLLRLEHAFEKNHYVVGAERKQLAHSLSLTETQVKVWFQNRRTKFKRQKLE 210

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

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0021542 "dentate gyrus development" evidence=IEA

GO:0021796 "cerebral cortex regionalization" evidence=IEA

GO:0021846 "cell proliferation in forebrain" evidence=IEA

GO:0021885 "forebrain cell migration" evidence=IEA

GO:0030182 "neuron differentiation" evidence=IEA

GO:0042493 "response to drug" evidence=IEA

GO:0072001 "renal system development" evidence=IEA

UNIPROTKB|Q17R00 EMX2 "Homeobox protein EMX2" [Bos taurus (taxid:9913)]

 Score = 199 (75.1 bits), Expect = 6.0e-16, P = 6.0e-16
 Identities = 38/60 (63%), Positives = 47/60 (78%)

Query:    37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE 96
             R+RT F+P QL RLE  FE+  Y+VG ER  LAH+L+LTE QVKVWFQNRR K+++Q LE
Sbjct:   157 RIRTAFSPSQLLRLEHAFEKNHYVVGAERKQLAHSLSLTETQVKVWFQNRRTKFKRQKLE 216

GO:0005634 "nucleus" evidence=IEA

GO:0072001 "renal system development" evidence=IEA

GO:0042493 "response to drug" evidence=IEA

GO:0030182 "neuron differentiation" evidence=IEA

GO:0021885 "forebrain cell migration" evidence=IEA

GO:0021846 "cell proliferation in forebrain" evidence=IEA

GO:0021796 "cerebral cortex regionalization" evidence=IEA

GO:0021542 "dentate gyrus development" evidence=IEA

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

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

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

---

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)
Q04743	EMX2_HUMAN	No assigned EC number	0.6349	0.45	0.25	yes	N/A
Q04744	EMX2_MOUSE	No assigned EC number	0.6349	0.45	0.2490	yes	N/A
Q17R00	EMX2_BOVIN	No assigned EC number	0.6349	0.45	0.2490	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	140
pfam00046	57	pfam00046, Homeobox, Homeobox domain	3e-23
smart00389	57	smart00389, HOX, Homeodomain	5e-19
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	2e-18
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	1e-08

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

 Score = 85.2 bits (212), Expect = 3e-23
 Identities = 36/57 (63%), Positives = 41/57 (71%)

Query: 36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          +R RT FTPEQLE LE EFE+ +Y    ER  LA  L LTE QVKVWFQNRR KW++
Sbjct: 1  RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57

Length = 57

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 74.6 bits (184), Expect = 5e-19
 Identities = 34/57 (59%), Positives = 39/57 (68%)

Query: 35 SKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR 91
           +R RT FTPEQLE LE EF++  Y    ER  LA  L L+E QVKVWFQNRR KW+
Sbjct: 1  KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

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

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

 Score = 73.0 bits (180), Expect = 2e-18
 Identities = 34/59 (57%), Positives = 39/59 (66%)

Query: 36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
          +R RT FTPEQLE LE EFE+  Y    ER  LA  L LTE QVK+WFQNRR K ++  
Sbjct: 1  RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59

Length = 59

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

 Score = 50.5 bits (121), Expect = 1e-08
 Identities = 32/73 (43%), Positives = 40/73 (54%), Gaps = 2/73 (2%)

Query: 21  KKLSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVK 80
            KL      SS  KSKR RT  T EQL  LE EFE   Y     R+ L+  LN+    V+
Sbjct: 39  MKLERKQDGSSPPKSKRRRT--TDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQ 96

Query: 81  VWFQNRRIKWRKQ 93
           +WFQN+R K +K+
Sbjct: 97  IWFQNKRAKEKKK 109

Length = 156

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	140
KOG0488|consensus	309		99.71
KOG0842|consensus	307		99.71
KOG0489|consensus	261		99.69
KOG0484|consensus	125		99.68
KOG0843|consensus	197		99.68
KOG0487|consensus	308		99.67
KOG0850|consensus	245		99.66
KOG2251|consensus	228		99.65
KOG0485|consensus	268		99.65
KOG0848|consensus	317		99.65
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.64
KOG0494|consensus	332		99.61
KOG0492|consensus	246		99.57
KOG3802|consensus	398		99.56
KOG0483|consensus	198		99.53
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.53
KOG0493|consensus	342		99.49
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.49
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.49
COG5576	156	Homeodomain-containing transcription factor [Trans	99.43
KOG0491|consensus	194		99.38
KOG0486|consensus	351		99.37
KOG4577|consensus	383		99.36
KOG0844|consensus	408		99.34
KOG0847|consensus	288		99.27
KOG1168|consensus	385		99.09
KOG0490|consensus	235		99.08
KOG0849|consensus	354		98.95
KOG0775|consensus	304		98.87
KOG0774|consensus	334		98.49
KOG2252|consensus	558		98.43
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.33
KOG0490|consensus	235		98.02
KOG1146|consensus	1406		97.43
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	97.08
KOG0773|consensus	342		96.15
KOG3623|consensus	1007		94.79
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	93.66
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	84.97

>KOG0488|consensus

Probab=99.71  E-value=1.8e-17  Score=132.76  Aligned_cols=68  Identities=47%  Similarity=0.768  Sum_probs=63.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQ   98 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~   98 (140)
                      .++|+|+.||.||..|+..||+.|++.+|++..+|+.||..|||+..+|++||||||+||||....+.
T Consensus       168 ~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~  235 (309)
T KOG0488|consen  168 TPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGG  235 (309)
T ss_pred             CCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhh
Confidence            34778889999999999999999999999999999999999999999999999999999999987643

>KOG0842|consensus

Probab=99.71  E-value=1.6e-17  Score=131.91  Aligned_cols=70  Identities=40%  Similarity=0.667  Sum_probs=64.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHHHH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQQ  100 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~~~  100 (140)
                      ...++||.|..|+..|+.+||+.|...+|++..+|+.||..|+||+.+|+|||||||-|+||..+.....
T Consensus       149 ~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~  218 (307)
T KOG0842|consen  149 GKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALE  218 (307)
T ss_pred             ccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhh
Confidence            3556777788999999999999999999999999999999999999999999999999999998766544

>KOG0489|consensus

Probab=99.69  E-value=1.3e-17  Score=130.88  Aligned_cols=68  Identities=51%  Similarity=0.811  Sum_probs=63.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHHHH
Q psy10638         33 SKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQQ  100 (140)
Q Consensus        33 ~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~~~  100 (140)
                      ++.||.||.||..|+..||+.|..|+|++...|.+||..|.|++++|+|||||||+||||..+.....
T Consensus       157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~  224 (261)
T KOG0489|consen  157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ  224 (261)
T ss_pred             CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence            45788999999999999999999999999999999999999999999999999999999988666544

>KOG0484|consensus

Probab=99.68  E-value=2.6e-17  Score=111.38  Aligned_cols=70  Identities=43%  Similarity=0.601  Sum_probs=64.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHHHH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQQ  100 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~~~  100 (140)
                      ..++.||.||.|+..|+..|++.|.+.+||++-.+++||..+.|++..|+|||||||+|+||..+.....
T Consensus        13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~   82 (125)
T KOG0484|consen   13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAK   82 (125)
T ss_pred             HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            4567889999999999999999999999999999999999999999999999999999999988655433

>KOG0843|consensus

Probab=99.68  E-value=5.1e-17  Score=119.56  Aligned_cols=65  Identities=57%  Similarity=0.865  Sum_probs=62.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHH
Q psy10638         33 SKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEF   97 (140)
Q Consensus        33 ~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~   97 (140)
                      .+.+|.||.|+.+|+..||..|+.+.|....+|+.||..|+|++.+|+|||||||.|.||...+.
T Consensus       100 ~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~  164 (197)
T KOG0843|consen  100 MRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED  164 (197)
T ss_pred             cCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence            37889999999999999999999999999999999999999999999999999999999988665

>KOG0487|consensus

Probab=99.67  E-value=8.1e-17  Score=128.00  Aligned_cols=68  Identities=44%  Similarity=0.624  Sum_probs=62.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQ   98 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~   98 (140)
                      ..++.|++|..+|+.|+..||+.|..|.|++.+.|.+|++.|+|+++||+|||||||.|+||..++.-
T Consensus       231 ~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r  298 (308)
T KOG0487|consen  231 SARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR  298 (308)
T ss_pred             cccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence            34667888999999999999999999999999999999999999999999999999999999986543

>KOG0850|consensus

Probab=99.66  E-value=2.1e-16  Score=120.20  Aligned_cols=67  Identities=43%  Similarity=0.695  Sum_probs=62.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEF   97 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~   97 (140)
                      ..+|.|+.||.++.-||..|.+.|+++.|+-..+|++||+.|||+..+|+|||||||.|.||..+.+
T Consensus       118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g  184 (245)
T KOG0850|consen  118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQG  184 (245)
T ss_pred             CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcC
Confidence            3566778899999999999999999999999999999999999999999999999999999988743

>KOG2251|consensus

Probab=99.65  E-value=1.2e-16  Score=120.88  Aligned_cols=68  Identities=49%  Similarity=0.617  Sum_probs=64.4

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHH
Q psy10638         30 SSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEF   97 (140)
Q Consensus        30 ~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~   97 (140)
                      .++++.||+||.|+-.|+.+||..|.+..||+...+++||..|+|.+.+|+|||+|||+|+|+.+...
T Consensus        32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            56788999999999999999999999999999999999999999999999999999999999988543

>KOG0485|consensus

Probab=99.65  E-value=1.5e-16  Score=120.30  Aligned_cols=68  Identities=44%  Similarity=0.729  Sum_probs=62.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQ   98 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~   98 (140)
                      +..++|+.||+|+..|+..||..|+..+|++..+|..||+.|.|++.+|+|||||||.||||+-.-..
T Consensus       100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~  167 (268)
T KOG0485|consen  100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADL  167 (268)
T ss_pred             cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhh
Confidence            44578899999999999999999999999999999999999999999999999999999999874443

>KOG0848|consensus

Probab=99.65  E-value=1.8e-16  Score=122.89  Aligned_cols=63  Identities=41%  Similarity=0.604  Sum_probs=58.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHH
Q psy10638         36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQ   98 (140)
Q Consensus        36 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~   98 (140)
                      -+=|.+++.-|+..||+.|..++|+++..+.+||..|||++++|+|||||||+|+||..++..
T Consensus       200 DKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~  262 (317)
T KOG0848|consen  200 DKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR  262 (317)
T ss_pred             cceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence            344778999999999999999999999999999999999999999999999999999887665

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.64  E-value=2.8e-16  Score=96.10  Aligned_cols=57  Identities=56%  Similarity=0.684  Sum_probs=54.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638         36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK   92 (140)
Q Consensus        36 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk   92 (140)
                      |+.|+.|+..++.+|+.+|..+++|+..+++.||..|||+..+|.+||+|+|.++||
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence            577899999999999999999999999999999999999999999999999999986

; 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 ....

>KOG0494|consensus

Probab=99.61  E-value=1.4e-15  Score=117.62  Aligned_cols=63  Identities=46%  Similarity=0.708  Sum_probs=58.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHH
Q psy10638         34 KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE   96 (140)
Q Consensus        34 ~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~   96 (140)
                      ++|+.||.|+.-|+..||+.|.+.+||+...|+.||..+.|.+.+|+|||||||+||||..+.
T Consensus       140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~  202 (332)
T KOG0494|consen  140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR  202 (332)
T ss_pred             ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence            344459999999999999999999999999999999999999999999999999999997754

>KOG0492|consensus

Probab=99.57  E-value=6e-15  Score=110.90  Aligned_cols=73  Identities=38%  Similarity=0.603  Sum_probs=63.5

Q ss_pred             CCCCCCC-CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHH
Q psy10638         26 SSCSSSS-SKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQ   98 (140)
Q Consensus        26 ~~~~~~~-~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~   98 (140)
                      ..|.... +..|++|+.|+..|+..||+.|....|.++.++.+++..|.|++.+|+|||||||+|.||-+..+.
T Consensus       134 ~~C~LrKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~  207 (246)
T KOG0492|consen  134 TTCTLRKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAEL  207 (246)
T ss_pred             ccchhcccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHH
Confidence            3344333 445678999999999999999999999999999999999999999999999999999999775544

>KOG3802|consensus

Probab=99.56  E-value=2e-15  Score=122.68  Aligned_cols=62  Identities=27%  Similarity=0.378  Sum_probs=60.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         34 KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        34 ~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      |+||+||.|....+..||.+|.+|+.|+..++..||.+|+|...+|+|||||||.|+||...
T Consensus       293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            78888999999999999999999999999999999999999999999999999999999885

>KOG0483|consensus

Probab=99.53  E-value=1.4e-14  Score=109.21  Aligned_cols=79  Identities=33%  Similarity=0.501  Sum_probs=70.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHHHHHHHHHHhhhhhHHH
Q psy10638         36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQQRLAAIKQSQLNQQQ  114 (140)
Q Consensus        36 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~~~~~~~~~~~~~~~~~  114 (140)
                      .+.+.+|+.+|+..|+..|+...+.....+..||..|||.+++|.|||||||+|||.++.+..+..++...........
T Consensus        51 ~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~~~  129 (198)
T KOG0483|consen   51 KGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSEND  129 (198)
T ss_pred             ccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhhh
Confidence            3445679999999999999999999999999999999999999999999999999999999998888877665544443

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.53  E-value=1.3e-14  Score=89.30  Aligned_cols=53  Identities=30%  Similarity=0.423  Sum_probs=50.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCC----CCHHHHhhHHHhcCCCcchhhhcccchh
Q psy10638         35 SKRVRTIFTPEQLERLEAEFERQQY----MVGPERLYLAHTLNLTEAQVKVWFQNRR   87 (140)
Q Consensus        35 ~rr~Rt~~s~~q~~~Le~~F~~~~~----p~~~~~~~La~~lgl~~~qV~vWFqNrR   87 (140)
                      ++|.||.|+++|+..|+..|+.++|    |+..+++.||..+||++++|+|||+|.+
T Consensus         1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            3788999999999999999999999    9999999999999999999999999975

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

>KOG0493|consensus

Probab=99.49  E-value=3.9e-14  Score=109.80  Aligned_cols=59  Identities=51%  Similarity=0.828  Sum_probs=56.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        36 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      ||+||.|+.+|+..|+..|..++|++...|..||.+|+|.+.+|+|||||+|+|-||-.
T Consensus       247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT  305 (342)
T KOG0493|consen  247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST  305 (342)
T ss_pred             cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence            57899999999999999999999999999999999999999999999999999999855

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

Probab=99.49  E-value=5e-14  Score=86.04  Aligned_cols=57  Identities=60%  Similarity=0.860  Sum_probs=53.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638         37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ   93 (140)
Q Consensus        37 r~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~   93 (140)
                      +.++.++..++.+|+.+|..++||+..++..||..+||+..+|.+||+|+|.+.++.
T Consensus         2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~   58 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS   58 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence            457789999999999999999999999999999999999999999999999998764

>smart00389 HOX Homeodomain

Probab=99.49  E-value=4.1e-14  Score=85.82  Aligned_cols=55  Identities=62%  Similarity=0.944  Sum_probs=51.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHH
Q psy10638         37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR   91 (140)
Q Consensus        37 r~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~k   91 (140)
                      +.|+.|+..++.+|+..|..++||+..++..||..+||+..+|.+||.|+|.+.+
T Consensus         2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~   56 (56)
T smart00389        2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK   56 (56)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence            5567899999999999999999999999999999999999999999999998753

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

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.43  E-value=2.2e-13  Score=99.51  Aligned_cols=68  Identities=38%  Similarity=0.462  Sum_probs=60.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQ   98 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~   98 (140)
                      +.+..++.|.+.+..|+.+|+..|..+++|+...+..|+..|+|+++.|++||||+|++.|+......
T Consensus        47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~  114 (156)
T COG5576          47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKV  114 (156)
T ss_pred             CCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccch
Confidence            34456666777899999999999999999999999999999999999999999999999999875543

>KOG0491|consensus

Probab=99.38  E-value=1e-13  Score=100.96  Aligned_cols=65  Identities=51%  Similarity=0.825  Sum_probs=60.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHH
Q psy10638         34 KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQ   98 (140)
Q Consensus        34 ~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~   98 (140)
                      ++++-|++|+..++..|++.|+..+|.+..++.+||..|+|++.+|+.||||||+|.||..+...
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            34567999999999999999999999999999999999999999999999999999999886554

>KOG0486|consensus

Probab=99.37  E-value=7.7e-13  Score=104.78  Aligned_cols=66  Identities=52%  Similarity=0.746  Sum_probs=62.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHH
Q psy10638         33 SKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQ   98 (140)
Q Consensus        33 ~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~   98 (140)
                      .|.||.|+.|+..|+..||..|.++.||+...+++||.-.+|++..|+|||.|||+||||+++...
T Consensus       110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~  175 (351)
T KOG0486|consen  110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ  175 (351)
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence            367889999999999999999999999999999999999999999999999999999999987665

>KOG4577|consensus

Probab=99.36  E-value=6.8e-13  Score=104.21  Aligned_cols=66  Identities=32%  Similarity=0.413  Sum_probs=61.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHH
Q psy10638         33 SKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQ   98 (140)
Q Consensus        33 ~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~   98 (140)
                      ...||+||.+++.|++.|+.+|+..+.|....|+.|+.++||..++|+|||||||+|+||-++..-
T Consensus       165 ~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAG  230 (383)
T KOG4577|consen  165 ASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAG  230 (383)
T ss_pred             cccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcc
Confidence            346789999999999999999999999999999999999999999999999999999999776554

>KOG0844|consensus

Probab=99.34  E-value=7.4e-13  Score=104.69  Aligned_cols=65  Identities=51%  Similarity=0.803  Sum_probs=60.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHH
Q psy10638         32 SSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE   96 (140)
Q Consensus        32 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~   96 (140)
                      ...-||-||.|+.+|+..||+.|-+..|.+...|.+||+.|+|.+..|+|||||||.|+||+..-
T Consensus       178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla  242 (408)
T KOG0844|consen  178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA  242 (408)
T ss_pred             cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence            34557889999999999999999999999999999999999999999999999999999998743

>KOG0847|consensus

Probab=99.27  E-value=5.5e-12  Score=95.82  Aligned_cols=64  Identities=52%  Similarity=0.896  Sum_probs=59.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      ..++++-.|..|+..++..|+..|+...|+-..++.+||..+|+++.+|+|||||||.||||+.
T Consensus       163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh  226 (288)
T KOG0847|consen  163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH  226 (288)
T ss_pred             cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence            3456666788999999999999999999999999999999999999999999999999999976

>KOG1168|consensus

Probab=99.09  E-value=3.6e-11  Score=94.66  Aligned_cols=64  Identities=31%  Similarity=0.424  Sum_probs=59.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         32 SSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        32 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      ...+||+||.+.+.....||.+|...+.|+.+.+..||..|+|...+|+|||||.|.|.||...
T Consensus       306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~  369 (385)
T KOG1168|consen  306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR  369 (385)
T ss_pred             ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence            4567788999999999999999999999999999999999999999999999999999998653

>KOG0490|consensus

Probab=99.08  E-value=5.9e-11  Score=90.45  Aligned_cols=64  Identities=39%  Similarity=0.442  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         32 SSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        32 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      ..+.++.|+.|+..++..|++.|+..+||+...++.||..+++++..|++||+|+|+++++...
T Consensus        57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~  120 (235)
T KOG0490|consen   57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER  120 (235)
T ss_pred             hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence            4567888999999999999999999999999999999999999999999999999999999874

>KOG0849|consensus

Probab=98.95  E-value=1.4e-09  Score=88.96  Aligned_cols=66  Identities=47%  Similarity=0.713  Sum_probs=61.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE   96 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~   96 (140)
                      ..++.+|.|+.|+..|+..|++.|+.++||+...++.||.+.++++..|.+||+|+|++++|....
T Consensus       172 ~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~  237 (354)
T KOG0849|consen  172 LQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD  237 (354)
T ss_pred             ccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence            355677789999999999999999999999999999999999999999999999999999998743

>KOG0775|consensus

Probab=98.87  E-value=1.8e-09  Score=84.43  Aligned_cols=52  Identities=31%  Similarity=0.399  Sum_probs=48.1

Q ss_pred             CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638         42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ   93 (140)
Q Consensus        42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~   93 (140)
                      |...-+.+|..+|..++||+..++.+||..+||+..+|-+||+|||.|+|-.
T Consensus       183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~  234 (304)
T KOG0775|consen  183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAA  234 (304)
T ss_pred             hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhc
Confidence            5566788999999999999999999999999999999999999999999943

>KOG0774|consensus

Probab=98.49  E-value=1.2e-07  Score=74.02  Aligned_cols=65  Identities=31%  Similarity=0.454  Sum_probs=57.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHH---hcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHHH
Q psy10638         35 SKRVRTIFTPEQLERLEAEFE---RQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQ   99 (140)
Q Consensus        35 ~rr~Rt~~s~~q~~~Le~~F~---~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~~   99 (140)
                      .+|+|..|+.....+|..+|-   .++||+...++.||.++|++..+|..||.|+|-+.+|..-..++
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~~e  255 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKNQE  255 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhhhh
Confidence            356778899999999999996   56799999999999999999999999999999999997655543

>KOG2252|consensus

Probab=98.43  E-value=3.2e-07  Score=77.78  Aligned_cols=60  Identities=25%  Similarity=0.280  Sum_probs=55.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKW   90 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~   90 (140)
                      .....|++|.+|+..|+..|..+|..+++|+.++...|+..|||....|.+||.|-|.|.
T Consensus       416 ~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  416 KMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             ccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            344567789999999999999999999999999999999999999999999999988775

>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=98.33  E-value=2.3e-07  Score=53.01  Aligned_cols=34  Identities=29%  Similarity=0.467  Sum_probs=28.5

Q ss_pred             hcCCCCHHHHhhHHHhcCCCcchhhhcccchhhH
Q psy10638         56 RQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK   89 (140)
Q Consensus        56 ~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k   89 (140)
                      .++||+..++..|+..+||+..+|..||-|.|.|
T Consensus         7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR   40 (40)
T PF05920_consen    7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR   40 (40)
T ss_dssp             TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence            4689999999999999999999999999998864

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

>KOG0490|consensus

Probab=98.02  E-value=6.4e-06  Score=62.63  Aligned_cols=66  Identities=42%  Similarity=0.571  Sum_probs=60.8

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         30 SSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        30 ~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      ....+.++.|+.+...++..|...|....+|+...+..|+..+|++...|.+||+|+|.+.++...
T Consensus       148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  148 PSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             CCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            345667788999999999999999999999999999999999999999999999999999998764

>KOG1146|consensus

Probab=97.43  E-value=0.00021  Score=66.16  Aligned_cols=63  Identities=30%  Similarity=0.364  Sum_probs=58.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         33 SKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        33 ~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      -.+++.|+.++..++..|...|....++...+.+.|...+++..+.|.+||+|.|.+.++...
T Consensus       901 ~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~  963 (1406)
T KOG1146|consen  901 MGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL  963 (1406)
T ss_pred             hhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence            345677899999999999999999999999999999999999999999999999999998764

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

Probab=97.08  E-value=0.0004  Score=42.29  Aligned_cols=42  Identities=19%  Similarity=0.353  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchh
Q psy10638         46 QLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRR   87 (140)
Q Consensus        46 q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR   87 (140)
                      ....|+.+|...+++...+...|....+|+..+|+.||-.+.
T Consensus         9 d~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~   50 (56)
T PF11569_consen    9 DIQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM   50 (56)
T ss_dssp             --HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred             chHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence            345699999999999999999999999999999999997654

>KOG0773|consensus

Probab=96.15  E-value=0.004  Score=50.52  Aligned_cols=63  Identities=29%  Similarity=0.361  Sum_probs=50.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHH
Q psy10638         35 SKRVRTIFTPEQLERLEAEFER---QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEF   97 (140)
Q Consensus        35 ~rr~Rt~~s~~q~~~Le~~F~~---~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~   97 (140)
                      ..|.+..+......+|+.++..   .+||+..++..|+..+||+..+|.+||-|.|-+..+-....
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~  304 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIEE  304 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchHHH
Confidence            4455667899999999977332   46899999999999999999999999999988876655433

>KOG3623|consensus

Probab=94.79  E-value=0.033  Score=49.57  Aligned_cols=48  Identities=21%  Similarity=0.227  Sum_probs=44.9

Q ss_pred             HHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         47 LERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        47 ~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      ..+|+.+|..|..|+..+...|+...||..+.|+.||.++++......
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~  615 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE  615 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence            778999999999999999999999999999999999999998887755

>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=93.66  E-value=0.15  Score=30.47  Aligned_cols=46  Identities=20%  Similarity=0.302  Sum_probs=34.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccch
Q psy10638         36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNR   86 (140)
Q Consensus        36 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNr   86 (140)
                      ++.|..+|.++...+-..++...     ....||..+|+....|..|..|+
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            46778899988888888887776     47788999999999999999874

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.

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=84.97  E-value=1.8  Score=24.84  Aligned_cols=43  Identities=14%  Similarity=0.233  Sum_probs=31.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhh
Q psy10638         41 IFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRI   88 (140)
Q Consensus        41 ~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~   88 (140)
                      .+++.+..+|...|     ........+|..+|++...|+.+...-..
T Consensus         4 ~L~~~er~vi~~~y-----~~~~t~~eIa~~lg~s~~~V~~~~~~al~   46 (50)
T PF04545_consen    4 QLPPREREVIRLRY-----FEGLTLEEIAERLGISRSTVRRILKRALK   46 (50)
T ss_dssp             TS-HHHHHHHHHHH-----TST-SHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHh-----cCCCCHHHHHHHHCCcHHHHHHHHHHHHH
Confidence            46788899999998     22334677899999999999887654333

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	140
2dmt_A	80	Solution Structure Of The Homeobox Domain Of Homeob		1e-12
2m34_A	71	Nmr Structure Of The Homeodomain Transcription Fact		1e-11
3a01_A	93	Crystal Structure Of Aristaless And Clawless Homeod		2e-11
1jgg_A	60	Even-Skipped Homeodomain Complexed To At-Rich Dna L		7e-11
3a03_A	56	Crystal Structure Of Hox11l1 Homeodomain Length = 5		9e-11
1fjl_A	81	Homeodomain From The Drosophila Paired Protein Boun		2e-10
2h1k_A	63	Crystal Structure Of The Pdx1 Homeodomain In Comple		2e-10
2r5y_A	88	Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO		3e-10
3cmy_A	61	Structure Of A Homeodomain In Complex With Dna Leng		5e-10
2l7m_P	68	Solution Structure Of The Pitx2 Homeodomain R24h Mu		1e-09
2l7f_P	68	Solution Structure Of The Pitx2 Homeodomain Length		1e-09
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		1e-09
2djn_A	70	The Solution Structure Of The Homeobox Domain Of Hu		1e-09
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		1e-09
2e1o_A	70	Solution Structure Of Rsgi Ruh-028, A Homeobox Doma		2e-09
2cue_A	80	Solution Structure Of The Homeobox Domain Of The Hu		2e-09
9ant_A	62	Antennapedia Homeodomain-Dna Complex Length = 62		4e-09
1ahd_P	68	Determination Of The Nmr Solution Structure Of An A		5e-09
2l9r_A	69	Solution Nmr Structure Of Homeobox Domain Of Homeob		7e-09
2m0c_A	75	Solution Nmr Structure Of Homeobox Domain Of Human		8e-09
1hom_A	68	Determination Of The Three-Dimensional Structure Of		8e-09
1hdd_C	61	Crystal Structure Of An Engrailed Homeodomain-Dna C		1e-08
3hdd_A	60	Engrailed Homeodomain Dna Complex Length = 60		1e-08
3rkq_A	58	Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Lengt		1e-08
1ftt_A	68	Thyroid Transcription Factor 1 Homeodomain (Rattus		1e-08
1b72_A	97	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		2e-08
1san_A	62	The Des(1-6)antennapedia Homeodomain: Comparison Of		2e-08
1ig7_A	58	Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58		3e-08
2hdd_A	61	Engrailed Homeodomain Q50k Variant Dna Complex Leng		3e-08
1p7j_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		3e-08
3a02_A	60	Crystal Structure Of Aristaless Homeodomain Length		3e-08
1enh_A	54	Structural Studies Of The Engrailed Homeodomain Len		3e-08
1p7i_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		3e-08
1ztr_A	61	Solution Structure Of Engrailed Homeodomain L16a Mu		4e-08
2dmu_A	70	Solution Structure Of The Homeobox Domain Of Homeob		5e-08
1du0_A	57	Engrailed Homeodomain Q50a Variant Dna Complex Leng		6e-08
1b8i_A	81	Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX		6e-08
1nk2_P	77	VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES		2e-07
2hos_A	63	Phage-selected Homeodomain Bound To Unmodified Dna		2e-07
1qry_A	80	Homeobox Protein Vnd (Ventral Nervous System Defect		5e-07
2kt0_A	84	Solution Structure Of Human Stem Cell Transcription		7e-07
1ftz_A	70	Nuclear Magnetic Resonance Solution Structure Of Th		9e-07
2lp0_A	60	The Solution Structure Of Homeodomain-Protein Compl		1e-06
1zq3_P	68	Nmr Solution Structure Of The Bicoid Homeodomain Bo		1e-06
2vi6_A	62	Crystal Structure Of The Nanog Homeodomain Length =		2e-06
1puf_A	77	Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo		2e-06
2ld5_A	67	Solution Nmr-Derived Complex Structure Of Hoxa13 Dn		3e-06
2l7z_A	73	Nmr Structure Of A13 Homedomain Length = 73		3e-06
2dms_A	80	Solution Structure Of The Homeobox Domain Of Homeob		2e-05
2k40_A	67	Nmr Structure Of Hesx-1 Homeodomain Double Mutant R		1e-04
2cra_A	70	Solution Structure Of The Homeobox Domain Of Human		2e-04
3d1n_I	151	Structure Of Human Brn-5 Transcription Factor In Co		2e-04
2p81_A	44	Engrailed Homeodomain Helix-Turn-Helix Motif Length		5e-04

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 30/58 (51%), Positives = 42/58 (72%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
          R RT+FT  QL  LE  FE+Q+Y+  P+R+ LA +L L++ QVK W+QNRR+KW+K  
Sbjct: 19 RSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSG 76

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

Iteration: 1
 Score = 65.1 bits (157), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 31/56 (55%), Positives = 39/56 (69%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          R RT FT EQL  LE EF  ++Y+   ER  +AH L L+E QVK+WFQNRR KW++
Sbjct: 9  RRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKR 64

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

Iteration: 1
 Score = 64.7 bits (156), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/58 (53%), Positives = 38/58 (65%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE 96
          RT FT  Q+  LE  F +Q+Y+   ER  LA  L +T+AQVK WFQNRR KWR+Q  E
Sbjct: 21 RTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAE 78

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

Iteration: 1
 Score = 62.8 bits (151), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 31/58 (53%), Positives = 40/58 (68%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
          R RT FT +QL RLE EF ++ Y+  P R  LA  LNL E+ +KVWFQNRR+K ++Q 
Sbjct: 3  RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQR 60

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

Iteration: 1
 Score = 62.4 bits (150), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 29/54 (53%), Positives = 36/54 (66%)
Query: 40 TIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          T F+  Q+  LE  F RQ+Y+   ER  LA  L +T+AQVK WFQNRR KWR+Q
Sbjct: 2  TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55

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

Iteration: 1
 Score = 61.2 bits (147), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/58 (55%), Positives = 38/58 (65%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
          R RT F+  QL+ LE  FER QY     R  LA   NLTEA+++VWFQNRR + RKQH
Sbjct: 20 RSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH 77

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

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 30/57 (52%), Positives = 39/57 (68%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          R RT +T  QL  LE EF   +Y+  P R+ LA  LNLTE  +K+WFQNRR+KW+K+
Sbjct: 5  RTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61

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

Iteration: 1
 Score = 60.5 bits (145), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 29/58 (50%), Positives = 40/58 (68%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
          R RT +T  Q   LE EF   +Y+    R+ +AH L+LTE Q+K+WFQNRR+KW+K+H
Sbjct: 30 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH 87

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

Iteration: 1
 Score = 59.7 bits (143), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 33/57 (57%), Positives = 36/57 (63%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          R RT FT EQLE LE  FER  Y     R  LA    LTEA+V+VWF NRR +WRKQ
Sbjct: 4  RSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 31/57 (54%), Positives = 39/57 (68%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          R RT FT +QL+ LEA F+R  Y     R  +A   NLTEA+V+VWF+NRR KWRK+
Sbjct: 5  RQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 31/57 (54%), Positives = 40/57 (70%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          R RT FT +QL+ LEA F+R +Y     R  +A   NLTEA+V+VWF+NRR KWRK+
Sbjct: 5  RQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 32/57 (56%), Positives = 36/57 (63%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          R RT FT  QLE LE  F R  Y     R  LA  + LTEA+++VWFQNRR KWRKQ
Sbjct: 1  RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 27/56 (48%), Positives = 38/56 (67%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
          RTI++  QL  L+  F++ QY+  PER  LA +L LT+ QVK+WFQN+R K +K  
Sbjct: 11 RTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSG 66

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 32/57 (56%), Positives = 36/57 (63%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          R RT FT  QLE LE  F R  Y     R  LA  + LTEA+++VWFQNRR KWRKQ
Sbjct: 8  RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 64

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/51 (54%), Positives = 35/51 (68%)
Query: 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          F+ +Q   LE +FE Q+Y+  PER  LA  L L+E QVK WFQNRR KWR+
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64

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

Iteration: 1
 Score = 57.8 bits (138), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 30/57 (52%), Positives = 38/57 (66%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          R RT FT EQ+E LE EFER  Y     R  LA  ++L EA+++VWF NRR KWR++
Sbjct: 9  RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE 65

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 27/58 (46%), Positives = 39/58 (67%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
          R R  +T  Q   LE EF   +Y+    R+ +AH L+LTE Q+K+WFQNRR+KW+K++
Sbjct: 5  RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 62

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 27/58 (46%), Positives = 39/58 (67%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
          R R  +T  Q   LE EF   +Y+    R+ +AH L+LTE Q+K+WFQNRR+KW+K++
Sbjct: 4  RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61

>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 = 7e-09,   Method: Compositional matrix adjust.
 Identities = 26/51 (50%), Positives = 35/51 (68%)
Query: 46 QLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE 96
          Q+  LE +F  Q+Y+  PER +LA  L LTE QVK+WFQNRR K +++ L 
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLS 65

>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 = 55.8 bits (133), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 31/56 (55%), Positives = 36/56 (64%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          R RT FT  QLE LE  F++  Y     R  LA   +LTEA+V+VWFQNRR KWRK
Sbjct: 11 RNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRK 66

>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 = 55.8 bits (133), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 27/58 (46%), Positives = 38/58 (65%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
          R R  +T  Q   LE EF   +Y+    R+ +AH L LTE Q+K+WFQNRR+KW+K++
Sbjct: 4  RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 61

>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 = 55.5 bits (132), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 27/56 (48%), Positives = 36/56 (64%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          R RT F+ EQL RL+ EF   +Y+    R  L+  L L EAQ+K+WFQN+R K +K
Sbjct: 5  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 27/56 (48%), Positives = 36/56 (64%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          R RT F+ EQL RL+ EF   +Y+    R  L+  L L EAQ+K+WFQN+R K +K
Sbjct: 3  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 26/51 (50%), Positives = 34/51 (66%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
          R +F+  Q+  LE  F++Q+Y+  PER  LA  L LT  QVK+WFQNRR K
Sbjct: 6  RVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYK 56

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/55 (45%), Positives = 38/55 (69%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          R +F+  Q+  LE  F++Q+Y+  PER +LA  ++LT  QVK+WFQN R K ++Q
Sbjct: 6  RVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/59 (49%), Positives = 38/59 (64%)
Query: 38 VRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE 96
          +RT FT  QL  LE EF   +Y+    R+ +A TL L E QVK+WFQNRR+K +K+  E
Sbjct: 37 LRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE 95

>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 = 54.7 bits (130), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 37/54 (68%)
Query: 41 IFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
           +T  Q   LE EF   +Y+    R+ +AH L+LTE Q+K+WFQNRR+KW+K++
Sbjct: 2  TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 55

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 27/54 (50%), Positives = 37/54 (68%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          RT FT  QL  LE +F ++QY+   ER   + +L+LTE QVK+WFQNRR K ++
Sbjct: 4  RTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 26/56 (46%), Positives = 36/56 (64%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          R RT F+ EQL RL+ EF   +Y+    R  L+  L L EAQ+K+WF+N+R K +K
Sbjct: 5  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 27/56 (48%), Positives = 35/56 (62%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          R RT F+ EQL RL+ EF   +Y+    R  L+  L L EAQ+K+WFQN R K +K
Sbjct: 3  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 29/52 (55%), Positives = 33/52 (63%)
Query: 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          FT  QLE LE  F R  Y     R  LA  + LTEA+++VWFQNRR KWRKQ
Sbjct: 6  FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 26/53 (49%), Positives = 34/53 (64%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
          R RT F+ EQL RL+ EF   +Y+    R  L+  L L EAQ+K+WFQN+R K
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 27/56 (48%), Positives = 35/56 (62%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          R RT F+ EQL RL+ EF   +Y+    R  L+  L L EAQ+K+WFQN R K +K
Sbjct: 3  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 26/56 (46%), Positives = 35/56 (62%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          R RT F+ EQL R + EF   +Y+    R  L+  L L EAQ+K+WFQN+R K R+
Sbjct: 5  RPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 29/57 (50%), Positives = 37/57 (64%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          R RTIFT EQLE LE  F+  +Y     R  LA  ++L E +V+VWF+NRR KWR+ 
Sbjct: 9  RHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRS 65

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 26/56 (46%), Positives = 35/56 (62%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          R RT F+ EQL RL+ EF   +Y+    R  L+  L L EAQ+K+WF N+R K +K
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 36/57 (63%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          R R  +T  Q   LE EF    Y+    R+ +AH L+LTE Q+K+WFQNRR+K +K+
Sbjct: 22 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE 78

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 34/54 (62%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          R +FT  Q   LE  F +Q+Y+  PER +LA  + LT  QVK+WFQN R K ++
Sbjct: 13 RVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/56 (48%), Positives = 34/56 (60%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          R RT F+ EQL RL+ EF   +Y+    R  L+  L L EAQVK WF+N R K +K
Sbjct: 6  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 24/54 (44%), Positives = 33/54 (61%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          R +FT  Q   LE  F +Q+Y+  PER +L   + LT  QVK+WFQN R K ++
Sbjct: 16 RVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKR 69

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 39/61 (63%), Gaps = 3/61 (4%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK---WRKQ 93
          + RT+F+  QL  L   F+RQ+Y+   +   L++ LNL+  QVK WFQN+R+K   W+K 
Sbjct: 24 KTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQKN 83
Query: 94 H 94
          +
Sbjct: 84 N 84

>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 = 48.9 bits (115), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 36/57 (63%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          R R  +T  Q   LE EF   +Y+    R+ +A+ L+L+E Q+K+WFQNRR+K +K 
Sbjct: 5  RTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKD 61

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 26/56 (46%), Positives = 33/56 (58%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
          R  +T  Q   LE EF    Y+    R  +A  LNLTE QVK+WFQNRR+K +K +
Sbjct: 5  RCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKMN 60

>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 = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 23/51 (45%), Positives = 30/51 (58%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRR 87
          R RT FT  Q+  LE  F + +Y+  P    L+  L L  AQVK+WF+NRR
Sbjct: 4  RTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRR 54

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/56 (39%), Positives = 38/56 (67%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          ++RT+F+  QL  L+  F++Q+Y+   +   L+  LNL+  QVK WFQN+R+K ++
Sbjct: 5  KMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 32/54 (59%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          R  +T  Q   LE EF    Y+    R  +A  LNLTE QVK+WFQNRR+K +K
Sbjct: 17 RCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/54 (40%), Positives = 35/54 (64%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          R  +T  QL+ LE E+   +++   +R  ++ T NL+E QV +WFQNRR+K +K
Sbjct: 5  RVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/54 (40%), Positives = 35/54 (64%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          R  +T  QL+ LE E+   +++   +R  ++ T NL+E QV +WFQNRR+K +K
Sbjct: 11 RVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/58 (46%), Positives = 37/58 (63%), Gaps = 6/58 (10%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPE---RLYLAHTLNLTEAQVKVWFQNRRIKWR 91
          R RT FT  QL+ LEA F + +Y   P+   R  +A  +NL E++V+VWF+NRR K R
Sbjct: 9  RERTTFTRAQLDVLEALFAKTRY---PDIFMREEVALKINLPESRVQVWFKNRRAKCR 63

>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L Length = 67

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 28/63 (44%), Positives = 36/63 (57%), Gaps = 2/63 (3%)
Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERL-YLAHTLNLTEAQVKVWFQNRRIKWRKQHL 95
          R RT FT  Q+E LE  F    Y  G + L  LA  LNL   ++++WFQNRR K ++ H 
Sbjct: 3  RPRTAFTQNQIEVLENVFRVNCY-PGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61
Query: 96 EFQ 98
          E Q
Sbjct: 62 ESQ 64

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 18/55 (32%), Positives = 33/55 (60%)
Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          R  ++  QL  LE E+   +++   +R  ++   +L+E Q+ +WFQNRR+K +K 
Sbjct: 11 RIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKS 65

>pdb|3D1N|I Chain I, Structure Of Human Brn-5 Transcription Factor In Complex With Corticotrophin-Releasing Hormone Gene Promoter Length = 151

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/49 (44%), Positives = 26/49 (53%)
Query: 39  RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRR 87
           RT FTP+ +E L A FE+     G E    A  LN     V+VWF NRR
Sbjct: 97  RTSFTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVRVWFSNRR 145

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 18/40 (45%), Positives = 25/40 (62%)
Query: 53 EFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          EF   +Y+    R  L+  L L EAQ+K+WFQN+R K +K
Sbjct: 4  EFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	140
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	1e-25
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	2e-23
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	3e-23
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	4e-23
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	5e-23
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	2e-22
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	3e-22
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	4e-22
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	5e-22
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	2e-21
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	3e-21
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	3e-21
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	5e-21
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	1e-20
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	2e-20
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	4e-20
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	5e-20
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	8e-20
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	9e-20
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	1e-19
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	1e-19
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	1e-19
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	2e-19
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	2e-19
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	3e-19
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	4e-19
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	5e-19
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	5e-19
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	1e-18
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	3e-18
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	4e-18
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	5e-18
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	5e-18
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	7e-18
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	1e-17
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	2e-17
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	4e-17
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	5e-17
1e3o_C	160	Octamer-binding transcription factor 1; transcript	8e-17
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	9e-17
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	6e-16
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	9e-16
1uhs_A	72	HOP, homeodomain only protein; structural genomics	2e-15
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	5e-15
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	4e-14
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	6e-14
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	1e-13
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	3e-11
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	9e-11
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	2e-10
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	1e-09
1lfb_A	99	Liver transcription factor (LFB1); transcription r	2e-09
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	1e-07
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	1e-07
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	3e-07
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	6e-07
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	2e-06
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	4e-06
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	1e-04
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	3e-04

>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 = 91.4 bits (227), Expect = 1e-25
 Identities = 32/71 (45%), Positives = 47/71 (66%)

Query: 24 SPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWF 83
          S     + + K +R RT+FT  QL  LE  FE+Q+Y+  P+R+ LA +L L++ QVK W+
Sbjct: 6  SGGEPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWY 65

Query: 84 QNRRIKWRKQH 94
          QNRR+KW+K  
Sbjct: 66 QNRRMKWKKSG 76

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

 Score = 85.9 bits (213), Expect = 2e-23
 Identities = 30/65 (46%), Positives = 43/65 (66%)

Query: 30 SSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
          SS S  ++ RTI++  QL  L+  F++ QY+  PER  LA +L LT+ QVK+WFQN+R K
Sbjct: 2  SSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSK 61

Query: 90 WRKQH 94
           +K  
Sbjct: 62 IKKSG 66

>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 = 85.6 bits (212), Expect = 3e-23
 Identities = 32/67 (47%), Positives = 40/67 (59%)

Query: 30 SSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
          SS S  K  +  F+ +Q   LE +FE Q+Y+  PER  LA  L L+E QVK WFQNRR K
Sbjct: 2  SSGSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAK 61

Query: 90 WRKQHLE 96
          WR+    
Sbjct: 62 WRRSGPS 68

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

 Score = 84.7 bits (210), Expect = 4e-23
 Identities = 29/54 (53%), Positives = 36/54 (66%)

Query: 40 TIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          T F+  Q+  LE  F RQ+Y+   ER  LA  L +T+AQVK WFQNRR KWR+Q
Sbjct: 2  TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 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 = 84.7 bits (210), Expect = 5e-23
 Identities = 26/64 (40%), Positives = 37/64 (57%)

Query: 33 SKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
                 +  +  Q+  LE +F  Q+Y+  PER +LA  L LTE QVK+WFQNRR K ++
Sbjct: 2  GHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61

Query: 93 QHLE 96
          + L 
Sbjct: 62 KQLS 65

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

 Score = 84.1 bits (208), Expect = 2e-22
 Identities = 34/87 (39%), Positives = 50/87 (57%)

Query: 21  KKLSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVK 80
           +++     + +  K K+ RT FT  Q+  LE  F +Q+Y+   ER  LA  L +T+AQVK
Sbjct: 3   RRIGHPYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVK 62

Query: 81  VWFQNRRIKWRKQHLEFQQQRLAAIKQ 107
            WFQNRR KWR+Q  E ++    A  +
Sbjct: 63  TWFQNRRTKWRRQTAEEREAERQAANR 89

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

 Score = 82.3 bits (204), Expect = 3e-22
 Identities = 27/57 (47%), Positives = 39/57 (68%)

Query: 36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          ++ RT FT  QL  LE +F ++QY+   ER   + +L+LTE QVK+WFQNRR K ++
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>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 = 82.5 bits (204), Expect = 4e-22
 Identities = 27/70 (38%), Positives = 40/70 (57%)

Query: 27 SCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNR 86
          +     +K ++ R +FT  Q   LE  F +Q+Y+  PER +LA  + LT  QVK+WFQN 
Sbjct: 1  ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNH 60

Query: 87 RIKWRKQHLE 96
          R K ++   E
Sbjct: 61 RYKTKRAQNE 70

>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 = 82.0 bits (203), Expect = 5e-22
 Identities = 26/65 (40%), Positives = 32/65 (49%)

Query: 30 SSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
          SS S  +  RT FT  QL  L+  F+   Y    E   L++ LNL    + VWFQN R K
Sbjct: 2  SSGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQK 61

Query: 90 WRKQH 94
           RK  
Sbjct: 62 ARKSG 66

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

 Score = 80.4 bits (199), Expect = 2e-21
 Identities = 22/60 (36%), Positives = 39/60 (65%)

Query: 34 KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
            +++RT+F+  QL  L+  F++Q+Y+   +   L+  LNL+  QVK WFQN+R+K ++ 
Sbjct: 2  TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW 61

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

 Score = 80.6 bits (199), Expect = 3e-21
 Identities = 24/70 (34%), Positives = 39/70 (55%)

Query: 24 SPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWF 83
                    K ++ RT+F+  QL  L   F+RQ+Y+   +   L++ LNL+  QVK WF
Sbjct: 11 VAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWF 70

Query: 84 QNRRIKWRKQ 93
          QN+R+K ++ 
Sbjct: 71 QNQRMKSKRW 80

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

 Score = 79.6 bits (197), Expect = 3e-21
 Identities = 26/56 (46%), Positives = 37/56 (66%)

Query: 36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR 91
          ++ R +F+  Q+  LE  F++Q+Y+  PER  LA  L LT  QVK+WFQNRR K +
Sbjct: 3  RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

>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 = 79.8 bits (197), Expect = 5e-21
 Identities = 24/70 (34%), Positives = 35/70 (50%)

Query: 24 SPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWF 83
          S  +      + KR+RT  TPEQLE L  ++            ++AH + L +  V+VWF
Sbjct: 6  SGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWF 65

Query: 84 QNRRIKWRKQ 93
          QN R + RK 
Sbjct: 66 QNTRARERKS 75

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

 Score = 78.5 bits (194), Expect = 1e-20
 Identities = 26/66 (39%), Positives = 43/66 (65%)

Query: 36  KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL 95
           ++ R +F+  Q+  LE  F++Q+Y+  PER +LA  ++LT  QVK+WFQN R K ++Q  
Sbjct: 3   RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62

Query: 96  EFQQQR 101
           +   Q+
Sbjct: 63  DKAAQQ 68

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

 Score = 78.2 bits (193), Expect = 2e-20
 Identities = 20/65 (30%), Positives = 30/65 (46%)

Query: 29 SSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRI 88
          SS SS +   +   + EQL  L+  F R Q+    E  +L     L+  +V+ WF +RR 
Sbjct: 2  SSGSSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRY 61

Query: 89 KWRKQ 93
            R  
Sbjct: 62 HCRNL 66

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

 Score = 77.4 bits (191), Expect = 4e-20
 Identities = 35/75 (46%), Positives = 46/75 (61%)

Query: 30  SSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
           SS S  +R RT FT EQ+E LE EFER  Y     R  LA  ++L EA+++VWF NRR K
Sbjct: 2   SSGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAK 61

Query: 90  WRKQHLEFQQQRLAA 104
           WR++     Q+R + 
Sbjct: 62  WRREEKLRNQRRQSG 76

>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 = 77.1 bits (190), Expect = 5e-20
 Identities = 25/65 (38%), Positives = 37/65 (56%)

Query: 36  KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL 95
           +R RT FT  Q+  LE  F + +Y+  P    L+  L L  AQVK+WF+NRR + + Q  
Sbjct: 3   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 62

Query: 96  EFQQQ 100
           + + Q
Sbjct: 63  QHKDQ 67

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

 Score = 76.6 bits (189), Expect = 8e-20
 Identities = 32/64 (50%), Positives = 41/64 (64%)

Query: 30 SSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
          SS S  +R RTIFT EQLE LE  F+  +Y     R  LA  ++L E +V+VWF+NRR K
Sbjct: 2  SSGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAK 61

Query: 90 WRKQ 93
          WR+ 
Sbjct: 62 WRRS 65

>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 = 76.2 bits (188), Expect = 9e-20
 Identities = 31/58 (53%), Positives = 41/58 (70%)

Query: 36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          +R RT FT +QL RLE EF ++ Y+  P R  LA  LNL E+ +KVWFQNRR+K ++Q
Sbjct: 2  RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59

>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 = 76.3 bits (188), Expect = 1e-19
 Identities = 24/75 (32%), Positives = 37/75 (49%)

Query: 30  SSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
           SS S  KR+RT F   QL  +++ F         +   LA    LT+  ++VWFQN R K
Sbjct: 2   SSGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAK 61

Query: 90  WRKQHLEFQQQRLAA 104
           +R+  L  +   ++ 
Sbjct: 62  FRRNLLRQENGGVSG 76

>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 = 75.7 bits (187), Expect = 1e-19
 Identities = 18/59 (30%), Positives = 33/59 (55%)

Query: 33 SKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR 91
           KS + ++  +P+    LE  F R+Q +   E+  +A    +T  QV+VWF N+R++ +
Sbjct: 3  EKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61

>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 = 76.9 bits (189), Expect = 1e-19
 Identities = 28/71 (39%), Positives = 38/71 (53%)

Query: 24 SPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWF 83
          +             +RT FT  QL  LE EF   +Y+    R+ +A TL L E QVK+WF
Sbjct: 23 TAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWF 82

Query: 84 QNRRIKWRKQH 94
          QNRR+K +K+ 
Sbjct: 83 QNRRMKQKKRE 93

>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 = 75.1 bits (185), Expect = 2e-19
 Identities = 27/58 (46%), Positives = 37/58 (63%)

Query: 35 SKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
           KR RT F+ EQL RL+ EF   +Y+    R  L+  L L EAQ+K+WF+N+R K +K
Sbjct: 3  EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60

>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 = 75.5 bits (186), Expect = 2e-19
 Identities = 31/75 (41%), Positives = 44/75 (58%)

Query: 30  SSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
           SS S  +R RT FT  QL+ LEA F + +Y     R  +A  +NL E++V+VWF+NRR K
Sbjct: 2   SSGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAK 61

Query: 90  WRKQHLEFQQQRLAA 104
            R+Q  + Q    + 
Sbjct: 62  CRQQQQQQQNGGQSG 76

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

 Score = 75.3 bits (185), Expect = 3e-19
 Identities = 31/75 (41%), Positives = 49/75 (65%)

Query: 20 CKKLSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQV 79
           +    +S  +++ ++KR RT +T  Q   LE EF   +Y+    R+ +AH L+LTE Q+
Sbjct: 13 KRVHLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQI 72

Query: 80 KVWFQNRRIKWRKQH 94
          K+WFQNRR+KW+K+H
Sbjct: 73 KIWFQNRRMKWKKEH 87

>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 = 74.7 bits (184), Expect = 4e-19
 Identities = 20/64 (31%), Positives = 28/64 (43%)

Query: 30 SSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
          SS S  KR RT  T +QL  L   F+        +   +A    L +  +K WF+N   K
Sbjct: 2  SSGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFK 61

Query: 90 WRKQ 93
           R+ 
Sbjct: 62 ERQS 65

>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 = 74.7 bits (184), Expect = 5e-19
 Identities = 32/68 (47%), Positives = 40/68 (58%)

Query: 26 SSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQN 85
              +   K +R RT F+  QL+ LE  FER QY     R  LA   NLTEA+++VWFQN
Sbjct: 9  EPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQN 68

Query: 86 RRIKWRKQ 93
          RR + RKQ
Sbjct: 69 RRARLRKQ 76

>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 = 74.3 bits (183), Expect = 5e-19
 Identities = 26/65 (40%), Positives = 34/65 (52%)

Query: 36  KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL 95
           +R RT FT  Q+E LE  F    Y        LA  LNL   ++++WFQNRR K ++ H 
Sbjct: 2   RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61

Query: 96  EFQQQ 100
           E Q  
Sbjct: 62  ESQFL 66

>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 = 73.5 bits (181), Expect = 1e-18
 Identities = 31/60 (51%), Positives = 42/60 (70%)

Query: 34 KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
            +R RT FT +QL++LEA F+R +Y     R  +A   NLTEA+V+VWF+NRR KWRK+
Sbjct: 2  SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61

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

 Score = 72.4 bits (178), Expect = 3e-18
 Identities = 31/61 (50%), Positives = 41/61 (67%)

Query: 34 KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
           +KR RT +T  QL  LE EF   +Y+  P R+ LA  LNLTE  +K+WFQNRR+KW+K+
Sbjct: 2  SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61

Query: 94 H 94
           
Sbjct: 62 E 62

>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 = 71.9 bits (177), Expect = 4e-18
 Identities = 29/55 (52%), Positives = 33/55 (60%)

Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
             FT  QLE LE  F R  Y     R  LA  + LTEA+++VWFQNRR KWRKQ
Sbjct: 3  HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57

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

 Score = 74.7 bits (183), Expect = 5e-18
 Identities = 24/93 (25%), Positives = 39/93 (41%), Gaps = 1/93 (1%)

Query: 1   MPKLINEKDKLLSPSSDLKCKKLSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYM 60
           M KL    +K L   +D      +     ++  + ++ RT         LE+ F +    
Sbjct: 66  MCKLKPLLNKWLE-ETDSSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKP 124

Query: 61  VGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
              E   LA +L L +  V+VWF NRR K ++ 
Sbjct: 125 SAHEITGLADSLQLEKEVVRVWFCNRRQKEKRM 157

>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 = 72.2 bits (177), Expect = 5e-18
 Identities = 26/66 (39%), Positives = 40/66 (60%)

Query: 29 SSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRI 88
          + ++   +R R  +T  Q   LE EF    Y+    R+ +AH L+LTE Q+K+WFQNRR+
Sbjct: 14 AGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRM 73

Query: 89 KWRKQH 94
          K +K+ 
Sbjct: 74 KLKKEI 79

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

 Score = 71.7 bits (176), Expect = 7e-18
 Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

Query: 35 SKRVRTIFTPEQLERLEAEFER-QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          S +  +  T +Q+E LE  F +  ++        +A    LTE Q + WF+ R  +WR+ 
Sbjct: 2  SAQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 61

>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 = 71.0 bits (174), Expect = 1e-17
 Identities = 21/65 (32%), Positives = 38/65 (58%)

Query: 30 SSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
          SS S  ++ R  ++  QL  LE E+   +++   +R  ++   +L+E Q+ +WFQNRR+K
Sbjct: 2  SSGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVK 61

Query: 90 WRKQH 94
           +K  
Sbjct: 62 EKKSG 66

>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 = 70.1 bits (172), Expect = 2e-17
 Identities = 18/65 (27%), Positives = 31/65 (47%)

Query: 34 KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          K+ RVRT+   +QL  L   +          +  L     L+   ++VWFQN+R K +K+
Sbjct: 2  KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

Query: 94 HLEFQ 98
           +  +
Sbjct: 62 SIMMK 66

>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 = 69.9 bits (171), Expect = 4e-17
 Identities = 27/76 (35%), Positives = 43/76 (56%)

Query: 24 SPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWF 83
          +P++    +  +++ R  +T  Q   LE EF    Y+    R  +A  LNLTE QVK+WF
Sbjct: 2  NPAANWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWF 61

Query: 84 QNRRIKWRKQHLEFQQ 99
          QNRR+K +K + +  +
Sbjct: 62 QNRRMKMKKINKDRAK 77

>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 = 69.4 bits (170), Expect = 5e-17
 Identities = 28/60 (46%), Positives = 40/60 (66%)

Query: 35 SKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
           KR R  +T  Q   LE EF   +Y+    R+ +AH L+LTE Q+K+WFQNRR+KW+K++
Sbjct: 2  RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61

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

 Score = 71.5 bits (175), Expect = 8e-17
 Identities = 24/92 (26%), Positives = 39/92 (42%)

Query: 1   MPKLINEKDKLLSPSSDLKCKKLSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYM 60
           + K +N+ +  LS  S L       S      S+ ++ RT         LE  F   Q  
Sbjct: 67  LEKWLNDAEANLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKP 126

Query: 61  VGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
              +   +A  LN+ +  ++VWF NRR K ++
Sbjct: 127 TSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 158

>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 = 70.8 bits (173), Expect = 9e-17
 Identities = 17/77 (22%), Positives = 34/77 (44%)

Query: 16  SDLKCKKLSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLT 75
            + +      +    ++ + ++ RT  +    + LE  F         E + +A  LNL 
Sbjct: 68  EEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLE 127

Query: 76  EAQVKVWFQNRRIKWRK 92
           +  V+VWF NRR + ++
Sbjct: 128 KEVVRVWFCNRRQREKR 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 = 68.9 bits (168), Expect = 6e-16
 Identities = 24/80 (30%), Positives = 37/80 (46%)

Query: 13  SPSSDLKCKKLSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTL 72
           +   + + ++          SK ++ RT FTP+ +E L A FE+     G E   +A  L
Sbjct: 71  AELRNQEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKEL 130

Query: 73  NLTEAQVKVWFQNRRIKWRK 92
           N     V+VWF NRR   + 
Sbjct: 131 NYDREVVRVWFSNRRQTLKN 150

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

 Score = 66.4 bits (162), Expect = 9e-16
 Identities = 23/65 (35%), Positives = 39/65 (60%)

Query: 30 SSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
          S   + ++ R  +T  QL+ LE E+   +++   +R  ++ T NL+E QV +WFQNRR+K
Sbjct: 2  SHMLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVK 61

Query: 90 WRKQH 94
           +K  
Sbjct: 62 EKKVI 66

>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 = 65.5 bits (160), Expect = 2e-15
 Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 35 SKRVRTIFTPEQLERLEAEFERQ-QYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
                  T +Q+E LE  F +  ++        +A    LTE Q + WF+ R  +WR+ 
Sbjct: 1  GSEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60

>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 = 65.0 bits (158), Expect = 5e-15
 Identities = 20/80 (25%), Positives = 33/80 (41%), Gaps = 15/80 (18%)

Query: 30 SSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLN---------------L 74
          SS S  +  R  +  E L  +E+ F   QY    +R  +A+  N               +
Sbjct: 2  SSGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERV 61

Query: 75 TEAQVKVWFQNRRIKWRKQH 94
          T  +V  WF NRR + +++ 
Sbjct: 62 TSLKVYNWFANRRKEIKRRA 81

>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 = 64.0 bits (155), Expect = 4e-14
 Identities = 23/92 (25%), Positives = 37/92 (40%), Gaps = 1/92 (1%)

Query: 1   MPKLINEKDKLLSPSSDLKCKKLSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYM 60
           M KL    +K +  + +        S   +     KR RT         LE  F +    
Sbjct: 63  MSKLRPLLEKWVEEADN-NENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKP 121

Query: 61  VGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
              +  ++A+ L L +  V+VWF NRR K ++
Sbjct: 122 SLQQITHIANQLGLEKDVVRVWFSNRRQKGKR 153

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

 Score = 61.3 bits (149), Expect = 6e-14
 Identities = 14/64 (21%), Positives = 27/64 (42%)

Query: 33 SKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          +         T EQ+  L+A F + Q+    E   L     L  +++K WF + R + ++
Sbjct: 2  AHHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR 61

Query: 93 QHLE 96
            + 
Sbjct: 62 GIVH 65

>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 = 61.0 bits (148), Expect = 1e-13
 Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 1/65 (1%)

Query: 30 SSSSKSKRVRTIFTPEQLERLEAEF-ERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRI 88
          SS S   R RT  + E L  L++   +   Y        L+  L+L +  +  +FQN+R 
Sbjct: 2  SSGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRY 61

Query: 89 KWRKQ 93
            +  
Sbjct: 62 HVKHS 66

>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 = 54.5 bits (131), Expect = 3e-11
 Identities = 18/65 (27%), Positives = 25/65 (38%)

Query: 30 SSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
          SS S          PEQL  LE+ F +    +  E   L     +T  ++  WF  RR K
Sbjct: 2  SSGSSGPTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKK 61

Query: 90 WRKQH 94
             + 
Sbjct: 62 VNAEE 66

>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 = 53.8 bits (129), Expect = 9e-11
 Identities = 14/70 (20%), Positives = 24/70 (34%)

Query: 24 SPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWF 83
          S  S  +    + +     T  Q++ LE  F +  +    E   L     L+  ++  WF
Sbjct: 2  SSGSSGAYPDFAPQKFKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWF 61

Query: 84 QNRRIKWRKQ 93
            RR      
Sbjct: 62 SERRKLRDSM 71

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

 Score = 54.5 bits (130), Expect = 2e-10
 Identities = 18/83 (21%), Positives = 32/83 (38%)

Query: 19  KCKKLSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQ 78
            CK+          +  K+ R +FT  Q   L A F+  +      ++ ++  L L  + 
Sbjct: 81  ACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELST 140

Query: 79  VKVWFQNRRIKWRKQHLEFQQQR 101
           V  +F N R +   + LE     
Sbjct: 141 VSNFFMNARRRSLDKWLEHHHHH 163

>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 = 51.2 bits (122), Expect = 1e-09
 Identities = 13/52 (25%), Positives = 20/52 (38%)

Query: 43 TPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
          T EQL  L+A F     +   E   L     LT  ++  WF  ++     + 
Sbjct: 19 TAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE 70

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

 Score = 51.0 bits (121), Expect = 2e-09
 Identities = 21/89 (23%), Positives = 32/89 (35%), Gaps = 21/89 (23%)

Query: 27 SCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLN------------- 73
          +    + K +R R  + P   + L   +ERQ+     ER  L    N             
Sbjct: 1  ARIDPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQ 60

Query: 74 --------LTEAQVKVWFQNRRIKWRKQH 94
                  +TE +V  WF NRR +   +H
Sbjct: 61 AQGLGSNLVTEVRVYNWFANRRKEEAFRH 89

>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 = 47.9 bits (113), Expect = 1e-07
 Identities = 21/95 (22%), Positives = 31/95 (32%), Gaps = 21/95 (22%)

Query: 14  PSSDLKCKKLSPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLN 73
             +        P+     + K +R R  + P   + L   +ERQ+     ER  L    N
Sbjct: 94  THAGQGGLIEEPTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECN 153

Query: 74  ---------------------LTEAQVKVWFQNRR 87
                                +TE +V  WF NRR
Sbjct: 154 RAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRR 188

>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 = 45.9 bits (108), Expect = 1e-07
 Identities = 20/77 (25%), Positives = 30/77 (38%)

Query: 24  SPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWF 83
                 +  S S       TPEQL  L++ F R Q+    E   LA    L    +  WF
Sbjct: 14  VLFQGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWF 73

Query: 84  QNRRIKWRKQHLEFQQQ 100
            + R  W+  +L++   
Sbjct: 74  GDTRYAWKNGNLKWYYY 90

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

 Score = 46.9 bits (110), Expect = 3e-07
 Identities = 19/85 (22%), Positives = 30/85 (35%), Gaps = 21/85 (24%)

Query: 24  SPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLN---------- 73
             +    ++ K +R R  + P   + L   ++RQ+     ER  L    N          
Sbjct: 131 DDACSEPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVS 190

Query: 74  -----------LTEAQVKVWFQNRR 87
                      +TE +V  WF NRR
Sbjct: 191 PSKAHGLGSNLVTEVRVYNWFANRR 215

>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 = 43.8 bits (102), Expect = 6e-07
 Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 4/72 (5%)

Query: 29 SSSSSKSKRVRTIFTPEQLERLEAEFER----QQYMVGPERLYLAHTLNLTEAQVKVWFQ 84
          SS SS + + RT F+   L  L+  ++        +   +   +A  LN+    V+ W  
Sbjct: 2  SSGSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIG 61

Query: 85 NRRIKWRKQHLE 96
          NRR K+R   +E
Sbjct: 62 NRRRKYRLMGIE 73

>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 76

 Score = 42.3 bits (99), Expect = 2e-06
 Identities = 17/64 (26%), Positives = 26/64 (40%), Gaps = 2/64 (3%)

Query: 32 SSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR 91
          SS S   R   T EQL  L++ F + Q+    +   L     L   ++  WF + R   +
Sbjct: 2  SSGSSGKR--KTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALK 59

Query: 92 KQHL 95
             L
Sbjct: 60 HGQL 63

>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 = 40.9 bits (96), Expect = 4e-06
 Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 1/65 (1%)

Query: 29 SSSSSKSKRVRTIFTPEQLERLEAEFERQ-QYMVGPERLYLAHTLNLTEAQVKVWFQNRR 87
          SS SS   +   +   E  + LE  F    +Y        L+  L+ +  +++ WF++RR
Sbjct: 2  SSGSSGGIKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRR 61

Query: 88 IKWRK 92
           + + 
Sbjct: 62 NQDKP 66

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

 Score = 37.1 bits (86), Expect = 1e-04
 Identities = 10/51 (19%), Positives = 20/51 (39%), Gaps = 1/51 (1%)

Query: 43 TPEQLERLEAEFERQ-QYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          T +    LE  F    ++        L+  L+     ++ WF+ RR + + 
Sbjct: 8  TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 58

>1wh7_A ZF-HD homeobox family protein; homeobox domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: a.4.1.1 Length = 80

 Score = 36.1 bits (83), Expect = 3e-04
 Identities = 20/73 (27%), Positives = 30/73 (41%), Gaps = 4/73 (5%)

Query: 24 SPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVG----PERLYLAHTLNLTEAQV 79
          S S+ SSS   +KR RT FT EQ E++ A  ER  + +                +    +
Sbjct: 6  SGSNPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVL 65

Query: 80 KVWFQNRRIKWRK 92
          K+W  N +     
Sbjct: 66 KIWMHNNKNSGPS 78

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	140
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.81
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.8
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.8
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.79
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.79
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.78
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.78
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.78
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.78
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.78
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.78
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.78
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.78
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.78
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.78
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.77
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.77
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.77
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.77
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.76
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.76
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.76
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.76
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.76
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.76
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.75
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.75
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.75
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.75
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.75
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.74
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.74
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.74
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.74
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.73
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.73
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.73
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.73
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.73
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.72
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.72
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.72
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.72
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.72
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.72
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.71
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.71
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.71
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.7
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.7
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.68
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.68
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.68
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.68
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.68
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.67
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.67
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.66
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.66
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.66
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.65
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.65
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.64
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.63
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.63
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.63
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.62
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.62
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.61
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.6
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.59
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.54
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.46
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.43
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.35
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.35
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.19
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.6
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	95.71
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	82.79

>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=99.81  E-value=6.4e-20  Score=119.10  Aligned_cols=66  Identities=47%  Similarity=0.857  Sum_probs=61.2

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         29 SSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        29 ~~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      +...++.++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+..
T Consensus        11 ~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   76 (80)
T 2dmt_A           11 GTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSG   76 (80)
T ss_dssp             CCCCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCC
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhccc
Confidence            334567788999999999999999999999999999999999999999999999999999999865

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

Probab=99.80  E-value=7.2e-20  Score=119.72  Aligned_cols=66  Identities=36%  Similarity=0.573  Sum_probs=61.3

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         30 SSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        30 ~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      ....+.++.|+.|+..|+.+|+.+|..++||+..++..||..|||++.+|++||+|||+++|+..+
T Consensus        17 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k   82 (84)
T 2kt0_A           17 KVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK   82 (84)
T ss_dssp             CCCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhh
Confidence            345667889999999999999999999999999999999999999999999999999999998753

>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=99.80  E-value=6.2e-20  Score=118.86  Aligned_cols=67  Identities=34%  Similarity=0.451  Sum_probs=61.8

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         28 CSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        28 ~~~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      .+....+.++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+..
T Consensus        10 ~~~~~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   76 (80)
T 2da3_A           10 GGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSG   76 (80)
T ss_dssp             CCCCCCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhc
Confidence            3345567888999999999999999999999999999999999999999999999999999999865

>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=2.2e-19  Score=116.52  Aligned_cols=66  Identities=47%  Similarity=0.705  Sum_probs=61.3

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHH
Q psy10638         32 SSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEF   97 (140)
Q Consensus        32 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~   97 (140)
                      .+..++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+..+..
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~   69 (80)
T 2cue_A            4 GSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLR   69 (80)
T ss_dssp             CCSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhh
Confidence            345778899999999999999999999999999999999999999999999999999999987543

>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=4.3e-19  Score=114.41  Aligned_cols=67  Identities=39%  Similarity=0.575  Sum_probs=62.2

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHH
Q psy10638         30 SSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE   96 (140)
Q Consensus        30 ~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~   96 (140)
                      ...++.++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+..+.
T Consensus         8 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k~   74 (77)
T 1puf_A            8 LHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             CCCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhhh
Confidence            4456678889999999999999999999999999999999999999999999999999999998754

>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=99.78  E-value=1.6e-19  Score=117.37  Aligned_cols=63  Identities=29%  Similarity=0.292  Sum_probs=58.7

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHh----cCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638         30 SSSSKSKRVRTIFTPEQLERLEAEFER----QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK   92 (140)
Q Consensus        30 ~~~~~~rr~Rt~~s~~q~~~Le~~F~~----~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk   92 (140)
                      ...++.+|.|+.|+..|+..|+..|+.    ++||+..+++.||..|||++.+|+|||+|||+|+|+
T Consensus        12 ~~~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           12 AGGGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCCCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            345678889999999999999999999    999999999999999999999999999999999874

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

Probab=99.78  E-value=3.7e-19  Score=114.68  Aligned_cols=66  Identities=41%  Similarity=0.651  Sum_probs=61.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE   96 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~   96 (140)
                      .+.+.++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+....
T Consensus         5 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~   70 (77)
T 1nk2_P            5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNE   70 (77)
T ss_dssp             CSCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhcc
Confidence            445677889999999999999999999999999999999999999999999999999999987643

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

Probab=99.78  E-value=2.1e-19  Score=113.76  Aligned_cols=64  Identities=48%  Similarity=0.742  Sum_probs=59.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      ..+..++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+..
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~   66 (70)
T 2dmu_A            3 SGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSG   66 (70)
T ss_dssp             STTSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccC
Confidence            3445778899999999999999999999999999999999999999999999999999999875

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

Probab=99.78  E-value=2.1e-19  Score=119.95  Aligned_cols=72  Identities=46%  Similarity=0.730  Sum_probs=62.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHHHHHH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQQRL  102 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~~~~~  102 (140)
                      ..++.++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+..........
T Consensus        13 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~~~~~   84 (93)
T 3a01_A           13 TPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEEREAER   84 (93)
T ss_dssp             CCCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC-----
T ss_pred             CCCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHHHHHHH
Confidence            445677889999999999999999999999999999999999999999999999999999998765544433

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

Probab=99.78  E-value=2.4e-19  Score=116.30  Aligned_cols=65  Identities=45%  Similarity=0.598  Sum_probs=60.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      ..++.++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+...
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~   67 (80)
T 2dms_A            3 SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQ   67 (80)
T ss_dssp             CCCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHH
Confidence            44567888999999999999999999999999999999999999999999999999999999763

>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=99.78  E-value=1.5e-19  Score=114.45  Aligned_cols=64  Identities=31%  Similarity=0.587  Sum_probs=60.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      ..++.++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+..
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~   66 (70)
T 2cra_A            3 SGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSG   66 (70)
T ss_dssp             SSCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccC
Confidence            4456778899999999999999999999999999999999999999999999999999999865

>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=99.78  E-value=3.9e-19  Score=115.20  Aligned_cols=64  Identities=34%  Similarity=0.507  Sum_probs=60.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         32 SSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        32 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      .++.++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+...
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (80)
T 2dmq_A            4 GSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLL   67 (80)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHH
Confidence            4557788999999999999999999999999999999999999999999999999999999763

>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=99.78  E-value=1.7e-19  Score=114.18  Aligned_cols=64  Identities=39%  Similarity=0.462  Sum_probs=60.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      ..++.++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+..
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2da2_A            3 SGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSG   66 (70)
T ss_dssp             CSCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhcc
Confidence            4556788899999999999999999999999999999999999999999999999999999865

>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=99.78  E-value=1.8e-19  Score=114.03  Aligned_cols=64  Identities=30%  Similarity=0.346  Sum_probs=60.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      ..++.++.|+.|+..|+.+|+.+|..++||+..++..||..|||++.+|++||+|||+++|+..
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2da1_A            3 SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSG   66 (70)
T ss_dssp             SSCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhc
Confidence            4456788899999999999999999999999999999999999999999999999999999865

>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=99.78  E-value=5e-19  Score=112.09  Aligned_cols=63  Identities=48%  Similarity=0.753  Sum_probs=59.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         32 SSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        32 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      .+..++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+..
T Consensus         4 ~~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~   66 (70)
T 2e1o_A            4 GSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSG   66 (70)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCC
Confidence            345667889999999999999999999999999999999999999999999999999999875

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

Probab=99.77  E-value=1.9e-19  Score=111.42  Aligned_cols=60  Identities=37%  Similarity=0.636  Sum_probs=53.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638         34 KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ   93 (140)
Q Consensus        34 ~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~   93 (140)
                      +.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+.
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            467889999999999999999999999999999999999999999999999999999985

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

Probab=99.77  E-value=3.1e-19  Score=113.07  Aligned_cols=64  Identities=45%  Similarity=0.726  Sum_probs=59.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      ..++.++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+..
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2djn_A            3 SGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSG   66 (70)
T ss_dssp             SCCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccC
Confidence            4456788899999999999999999999999999999999999999999999999999998864

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

Probab=99.77  E-value=4.6e-19  Score=110.06  Aligned_cols=61  Identities=51%  Similarity=0.858  Sum_probs=56.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         34 KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        34 ~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      ..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   62 (63)
T 2h1k_A            2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE   62 (63)
T ss_dssp             ---CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhhc
Confidence            3567899999999999999999999999999999999999999999999999999999864

>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=99.77  E-value=4.3e-19  Score=115.42  Aligned_cols=61  Identities=25%  Similarity=0.314  Sum_probs=56.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh-----cCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFER-----QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK   92 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~-----~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk   92 (140)
                      ...+.+|.||.|+..|+..|+ .|..     ++||+..+++.||..|||++.+|+|||+|||+|+|+
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            455678899999999999999 8999     999999999999999999999999999999999874

>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=6.9e-19  Score=114.38  Aligned_cols=65  Identities=51%  Similarity=0.705  Sum_probs=59.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      ..++.++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+...
T Consensus        14 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~   78 (81)
T 1fjl_A           14 LKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   78 (81)
T ss_dssp             ---CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhcc
Confidence            34567888999999999999999999999999999999999999999999999999999999764

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

Probab=99.76  E-value=4.7e-19  Score=113.30  Aligned_cols=65  Identities=49%  Similarity=0.708  Sum_probs=60.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      ..++.++.|+.|+..++.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+..+
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            34567788999999999999999999999999999999999999999999999999999998764

>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=99.76  E-value=5.3e-19  Score=111.35  Aligned_cols=62  Identities=50%  Similarity=0.763  Sum_probs=59.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         34 KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        34 ~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      +.++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+...
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~   63 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREE   63 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhh
Confidence            56788999999999999999999999999999999999999999999999999999999874

>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=99.76  E-value=6.5e-19  Score=108.68  Aligned_cols=58  Identities=47%  Similarity=0.794  Sum_probs=53.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638         35 SKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK   92 (140)
Q Consensus        35 ~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk   92 (140)
                      .++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+
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            5678999999999999999999999999999999999999999999999999999987

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

Probab=99.76  E-value=4.9e-19  Score=114.85  Aligned_cols=64  Identities=27%  Similarity=0.342  Sum_probs=60.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhc----CCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQ----QYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~----~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      ..++.++.|+.|+..|+.+|+.+|..+    +||+..++..||..|||++.+|++||+|||+|+|+..
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            456678899999999999999999999    9999999999999999999999999999999999854

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

Probab=99.76  E-value=1.2e-18  Score=106.38  Aligned_cols=57  Identities=47%  Similarity=0.736  Sum_probs=55.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638         36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK   92 (140)
Q Consensus        36 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk   92 (140)
                      ++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+
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            467899999999999999999999999999999999999999999999999999987

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

Probab=99.75  E-value=1.4e-18  Score=109.53  Aligned_cols=61  Identities=39%  Similarity=0.642  Sum_probs=58.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         35 SKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        35 ~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      .++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+...
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~   62 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD   62 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhc
Confidence            5678999999999999999999999999999999999999999999999999999999764

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

Probab=99.75  E-value=1.4e-18  Score=109.48  Aligned_cols=61  Identities=41%  Similarity=0.720  Sum_probs=58.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         35 SKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        35 ~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      +++.|+.|+..++.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+..+
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            4678999999999999999999999999999999999999999999999999999999764

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

Probab=99.75  E-value=1.6e-18  Score=110.63  Aligned_cols=63  Identities=35%  Similarity=0.582  Sum_probs=59.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         32 SSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        32 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      ..+.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   66 (73)
T 2l7z_A            4 MLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVI   66 (73)
T ss_dssp             SSCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHh
Confidence            445778899999999999999999999999999999999999999999999999999999865

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

Probab=99.75  E-value=8.3e-19  Score=115.74  Aligned_cols=64  Identities=47%  Similarity=0.833  Sum_probs=55.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      ..++.++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+..
T Consensus        24 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   87 (88)
T 2r5y_A           24 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH   87 (88)
T ss_dssp             -------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhhc
Confidence            3456778899999999999999999999999999999999999999999999999999999864

>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=99.75  E-value=1.2e-18  Score=109.86  Aligned_cols=61  Identities=46%  Similarity=0.790  Sum_probs=57.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         35 SKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        35 ~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      +++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..+
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~   62 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK   62 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhcc
Confidence            4678899999999999999999999999999999999999999999999999999999763

>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=99.74  E-value=8.4e-19  Score=109.78  Aligned_cols=61  Identities=30%  Similarity=0.449  Sum_probs=58.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         34 KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        34 ~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      +.++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
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            3678899999999999999999999999999999999999999999999999999999865

>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=99.74  E-value=1.2e-18  Score=113.45  Aligned_cols=63  Identities=41%  Similarity=0.687  Sum_probs=54.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         32 SSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        32 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      .+..++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++||..
T Consensus        17 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   79 (81)
T 1b8i_A           17 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEI   79 (81)
T ss_dssp             -------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhc
Confidence            345678899999999999999999999999999999999999999999999999999999875

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

Probab=99.74  E-value=2e-18  Score=106.13  Aligned_cols=58  Identities=53%  Similarity=0.852  Sum_probs=55.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638         36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ   93 (140)
Q Consensus        36 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~   93 (140)
                      ++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   59 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHhHhhcc
Confidence            5778999999999999999999999999999999999999999999999999999985

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

Probab=99.74  E-value=1.2e-18  Score=116.74  Aligned_cols=68  Identities=29%  Similarity=0.446  Sum_probs=57.9

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHH
Q psy10638         30 SSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEF   97 (140)
Q Consensus        30 ~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~   97 (140)
                      .+....++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+....-
T Consensus        20 ~~~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~lk~   87 (96)
T 3nar_A           20 APKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNLKW   87 (96)
T ss_dssp             -------CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTCCHH
T ss_pred             CCCCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhcccH
Confidence            34455667899999999999999999999999999999999999999999999999999999976443

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

Probab=99.73  E-value=2.3e-18  Score=105.89  Aligned_cols=58  Identities=50%  Similarity=0.706  Sum_probs=50.6

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         38 VRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        38 ~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      .|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..+
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~k   59 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK   59 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC----
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhcc
Confidence            5789999999999999999999999999999999999999999999999999998753

>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=2.1e-18  Score=115.77  Aligned_cols=65  Identities=45%  Similarity=0.685  Sum_probs=56.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHH
Q psy10638         32 SSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE   96 (140)
Q Consensus        32 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~   96 (140)
                      .+..++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+..+.
T Consensus        31 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~   95 (97)
T 1b72_A           31 LGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE   95 (97)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhcc
Confidence            35677889999999999999999999999999999999999999999999999999999998653

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

Probab=99.73  E-value=5.3e-18  Score=113.37  Aligned_cols=65  Identities=29%  Similarity=0.414  Sum_probs=61.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcC---------------CCcchhhhcccchhhHHHHHhH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLN---------------LTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lg---------------l~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      ..++.+|.|+.|+..++.+|+.+|..++||+..+++.||..||               |++.+|++||+|||+++|++..
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            4456788999999999999999999999999999999999999               9999999999999999999874

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

Probab=99.73  E-value=3.3e-18  Score=104.08  Aligned_cols=57  Identities=46%  Similarity=0.776  Sum_probs=54.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHH
Q psy10638         35 SKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR   91 (140)
Q Consensus        35 ~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~k   91 (140)
                      +++.|+.|+..++.+|+..|..++||+..++..||..+||++.+|++||+|||+++|
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            457789999999999999999999999999999999999999999999999999875

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

Probab=99.73  E-value=2.1e-18  Score=108.25  Aligned_cols=60  Identities=40%  Similarity=0.548  Sum_probs=57.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        36 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      ++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+...
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~   61 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR   61 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCC
T ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhch
Confidence            678899999999999999999999999999999999999999999999999999998764

>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=99.72  E-value=6.4e-18  Score=108.43  Aligned_cols=59  Identities=25%  Similarity=0.364  Sum_probs=55.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        37 r~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      +.|..|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++|+...
T Consensus         9 ~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (75)
T 2da5_A            9 TKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEET   67 (75)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSC
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhh
Confidence            34567999999999999999999999999999999999999999999999999998763

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

Probab=99.72  E-value=5.1e-18  Score=103.01  Aligned_cols=54  Identities=54%  Similarity=0.882  Sum_probs=51.1

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638         40 TIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ   93 (140)
Q Consensus        40 t~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~   93 (140)
                      |.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++||.
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~   55 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ   55 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhhccc
Confidence            579999999999999999999999999999999999999999999999999986

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

Probab=99.72  E-value=3.3e-18  Score=109.96  Aligned_cols=61  Identities=26%  Similarity=0.382  Sum_probs=56.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         34 KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        34 ~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      ...+.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         7 ~~~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~   67 (76)
T 2dn0_A            7 GASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLK   67 (76)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCC
T ss_pred             CCCCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhc
Confidence            3445588999999999999999999999999999999999999999999999999999865

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

Probab=99.72  E-value=3.3e-18  Score=105.36  Aligned_cols=59  Identities=31%  Similarity=0.504  Sum_probs=48.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHH
Q psy10638         33 SKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR   91 (140)
Q Consensus        33 ~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~k   91 (140)
                      .+.++.|+.|+..++.+|+..|..++||+..++..||..+||++.+|++||+|+|+++|
T Consensus         3 ~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            3 EKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             ---------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            45678899999999999999999999999999999999999999999999999999875

>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=99.72  E-value=7.5e-18  Score=107.18  Aligned_cols=59  Identities=27%  Similarity=0.450  Sum_probs=55.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh-cCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         36 KRVRTIFTPEQLERLEAEFER-QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        36 rr~Rt~~s~~q~~~Le~~F~~-~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      .+.|+.|+..|+.+|+..|.. ++||+..++..||..|||++.+|++||+|||+++|+..
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~   61 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhc
Confidence            356889999999999999996 99999999999999999999999999999999999976

>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=99.72  E-value=1.1e-17  Score=106.63  Aligned_cols=65  Identities=25%  Similarity=0.287  Sum_probs=59.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFER---QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~---~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      ..++.++.|+.|+..++.+|+.+|..   ++||+..++..||..+||++.+|++||+|+|+++++...
T Consensus         3 ~~~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~   70 (73)
T 1x2n_A            3 SGSSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSGP   70 (73)
T ss_dssp             CCSSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhcccccc
Confidence            34567788999999999999999987   999999999999999999999999999999999998753

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

Probab=99.71  E-value=1.1e-17  Score=106.71  Aligned_cols=59  Identities=27%  Similarity=0.417  Sum_probs=56.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh-cCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         36 KRVRTIFTPEQLERLEAEFER-QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        36 rr~Rt~~s~~q~~~Le~~F~~-~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      ++.|+.|+..|+.+|+..|.. ++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~   62 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   62 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhc
Confidence            466899999999999999995 99999999999999999999999999999999999976

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

Probab=99.71  E-value=1.1e-17  Score=106.73  Aligned_cols=61  Identities=28%  Similarity=0.438  Sum_probs=57.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         34 KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        34 ~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      ..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus         5 ~~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   65 (74)
T 2ly9_A            5 DSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSK   65 (74)
T ss_dssp             CCCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTT
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhC
Confidence            4567889999999999999999999999999999999999999999999999999999865

>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=99.71  E-value=1.2e-17  Score=107.40  Aligned_cols=57  Identities=21%  Similarity=0.271  Sum_probs=53.8

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         38 VRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        38 ~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      .|+.|+.+|+.+|+..|..++||+..+++.||..+||++.+|++||+|+|+++|+..
T Consensus         6 ~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~   62 (76)
T 2ecc_A            6 SGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ   62 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHH
Confidence            345699999999999999999999999999999999999999999999999999875

>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=4.4e-18  Score=123.68  Aligned_cols=62  Identities=27%  Similarity=0.419  Sum_probs=54.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638         32 SSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ   93 (140)
Q Consensus        32 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~   93 (140)
                      ..+++|.|+.|+..|+.+|+..|..++||+..++..||..+||++++|++||+|||+|+||.
T Consensus        98 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C           98 LSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            45678889999999999999999999999999999999999999999999999999999985

>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=99.70  E-value=1.6e-17  Score=103.99  Aligned_cols=59  Identities=27%  Similarity=0.293  Sum_probs=55.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh-cCCCCHHHHhhHHHhcCCCcchhhhcccchhhH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFER-QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK   89 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~-~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k   89 (140)
                      +.+.++|.||.|+.+|+.+|+..|.. ++||+...++.||..+||++++|++||||+|--
T Consensus         3 ~~~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~   62 (71)
T 1wi3_A            3 SGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYH   62 (71)
T ss_dssp             CCCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceee
Confidence            45578899999999999999999999 999999999999999999999999999999864

>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=99.68  E-value=5.5e-17  Score=109.60  Aligned_cols=65  Identities=29%  Similarity=0.313  Sum_probs=60.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhc---------------------CCCcchhhhcccchhhHH
Q psy10638         32 SSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTL---------------------NLTEAQVKVWFQNRRIKW   90 (140)
Q Consensus        32 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~l---------------------gl~~~qV~vWFqNrR~k~   90 (140)
                      .++.+|.|+.|+..++.+|+..|..++||+..+++.||..|                     +|++.+|++||+|||+++
T Consensus         3 ~~~~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k~   82 (102)
T 2da6_A            3 SGSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEE   82 (102)
T ss_dssp             TCCSCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHHH
Confidence            45678899999999999999999999999999999999999                     789999999999999999


Q ss_pred             HHHhHH
Q psy10638         91 RKQHLE   96 (140)
Q Consensus        91 kk~~~~   96 (140)
                      +++.+.
T Consensus        83 kr~~~~   88 (102)
T 2da6_A           83 AFRQKL   88 (102)
T ss_dssp             HHHHHH
T ss_pred             HHhhHh
Confidence            987644

>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=99.68  E-value=1.8e-17  Score=105.59  Aligned_cols=61  Identities=30%  Similarity=0.441  Sum_probs=57.6

Q ss_pred             CCCCCCCCHHHHHHHHHHH---HhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHH
Q psy10638         36 KRVRTIFTPEQLERLEAEF---ERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE   96 (140)
Q Consensus        36 rr~Rt~~s~~q~~~Le~~F---~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~   96 (140)
                      ++.|+.|+..++.+|+..|   ..++||+..++..||..+||++.+|++||+|+|+++|+....
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~   65 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGK   65 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccccccc
Confidence            5778999999999999999   899999999999999999999999999999999999987754

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

Probab=99.68  E-value=1.1e-17  Score=103.91  Aligned_cols=58  Identities=26%  Similarity=0.379  Sum_probs=55.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHH---HhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638         35 SKRVRTIFTPEQLERLEAEF---ERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK   92 (140)
Q Consensus        35 ~rr~Rt~~s~~q~~~Le~~F---~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk   92 (140)
                      .++.|+.|+..++.+|+..|   ..++||+..++..||..+||++.+|++||+|+|+++||
T Consensus         3 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A            3 GHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             CCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            56778999999999999999   89999999999999999999999999999999999886

>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=99.68  E-value=7.6e-17  Score=105.32  Aligned_cols=63  Identities=22%  Similarity=0.312  Sum_probs=57.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         32 SSKSKRVRTIFTPEQLERLEAEFER---QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        32 ~~~~rr~Rt~~s~~q~~~Le~~F~~---~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      ..+.++.|+.|+..++.+|+.+|..   ++||+..++..||..+||++.+|++||+|+|+|+++..
T Consensus         4 ~~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~   69 (83)
T 2dmn_A            4 GSSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDM   69 (83)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHH
Confidence            4456778899999999999999988   59999999999999999999999999999999998765

>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=99.68  E-value=4.6e-17  Score=106.95  Aligned_cols=62  Identities=31%  Similarity=0.472  Sum_probs=57.6

Q ss_pred             CCCCCCCCHHHHHHHHHHH---HhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHH
Q psy10638         36 KRVRTIFTPEQLERLEAEF---ERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEF   97 (140)
Q Consensus        36 rr~Rt~~s~~q~~~Le~~F---~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~   97 (140)
                      +|.|+.|+..++.+|+.+|   ..++||+..++..||..+||++.+|++||+|+|+++|+.....
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~   66 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKF   66 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGGG
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhccccc
Confidence            5778999999999999999   8999999999999999999999999999999999999987544

>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=99.67  E-value=2.5e-17  Score=118.14  Aligned_cols=63  Identities=27%  Similarity=0.455  Sum_probs=55.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ   93 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~   93 (140)
                      ..++++|.|+.|+..|+..|+..|..++||+..++..||..+||++++|++||+|||+|+||.
T Consensus        83 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           83 ANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             ------CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            345677889999999999999999999999999999999999999999999999999999975

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

Probab=99.67  E-value=1.3e-17  Score=121.68  Aligned_cols=66  Identities=27%  Similarity=0.340  Sum_probs=52.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE   96 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~   96 (140)
                      ..++++|.|+.|+..|+.+|+..|..++||+..++..||..+||++++|++||+|||+|+||....
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            346678889999999999999999999999999999999999999999999999999999997743

>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=99.66  E-value=8.8e-17  Score=115.70  Aligned_cols=62  Identities=39%  Similarity=0.626  Sum_probs=58.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK   92 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk   92 (140)
                      ..++++|.|+.|+..++.+|+.+|..++||+..++..||..+||++++|++||+|||+|+||
T Consensus        89 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           89 EPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             SCCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            34567788999999999999999999999999999999999999999999999999999986

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

Probab=99.66  E-value=9.5e-17  Score=98.51  Aligned_cols=55  Identities=29%  Similarity=0.387  Sum_probs=52.8

Q ss_pred             CCCCCHHHHHHHHHHHHh---cCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638         39 RTIFTPEQLERLEAEFER---QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ   93 (140)
Q Consensus        39 Rt~~s~~q~~~Le~~F~~---~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~   93 (140)
                      |+.|+..++.+|+..|..   ++||+..++..||..+||++.+|++||+|+|+++|+.
T Consensus         2 r~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A            2 GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             cCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            578999999999999999   9999999999999999999999999999999999874

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

Probab=99.66  E-value=3e-17  Score=104.64  Aligned_cols=60  Identities=18%  Similarity=0.271  Sum_probs=54.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHH-HhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         35 SKRVRTIFTPEQLERLEAEF-ERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        35 ~rr~Rt~~s~~q~~~Le~~F-~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      ..+.+..++..|+.+||..| ..++||+..++..||..|||++++|++||+|||+++|+..
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            34455667888999999999 9999999999999999999999999999999999999754

>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=99.65  E-value=1.7e-16  Score=104.95  Aligned_cols=54  Identities=22%  Similarity=0.290  Sum_probs=51.9

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         41 IFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        41 ~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      .|+..|+.+|+..|..++||+..++..||..+||++++|++||+|||+|+|+..
T Consensus        19 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~   72 (89)
T 2dmp_A           19 EKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSME   72 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSC
T ss_pred             cCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHh
Confidence            389999999999999999999999999999999999999999999999998865

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

Probab=99.65  E-value=1.8e-16  Score=104.86  Aligned_cols=54  Identities=24%  Similarity=0.320  Sum_probs=52.3

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         41 IFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        41 ~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      .|+..|+.+|+..|..++||+..++..||..|||++++|+|||+|||++++++.
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            689999999999999999999999999999999999999999999999999865

>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=99.64  E-value=1.8e-16  Score=104.24  Aligned_cols=59  Identities=29%  Similarity=0.360  Sum_probs=55.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHH
Q psy10638         33 SKSKRVRTIFTPEQLERLEAEFER---QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR   91 (140)
Q Consensus        33 ~~~rr~Rt~~s~~q~~~Le~~F~~---~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~k   91 (140)
                      .++++.|+.|+..++.+|+.+|..   ++||+..++..||..+||++.+|++||+|||+|+|
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            345566899999999999999999   99999999999999999999999999999999987

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

Probab=99.63  E-value=9.6e-17  Score=108.20  Aligned_cols=66  Identities=32%  Similarity=0.387  Sum_probs=54.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHh------------------cC---CCcchhhhcccchhhHH
Q psy10638         32 SSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHT------------------LN---LTEAQVKVWFQNRRIKW   90 (140)
Q Consensus        32 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~------------------lg---l~~~qV~vWFqNrR~k~   90 (140)
                      .++.+|.|+.|+..++.+|+..|..++||+..+++.||..                  ||   |++.+|++||+|||+++
T Consensus         6 ~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k~   85 (99)
T 1lfb_A            6 TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEE   85 (99)
T ss_dssp             -------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHHH
Confidence            4567788999999999999999999999999999999999                  88   99999999999999999


Q ss_pred             HHHhHHH
Q psy10638         91 RKQHLEF   97 (140)
Q Consensus        91 kk~~~~~   97 (140)
                      +++.+..
T Consensus        86 k~k~~~~   92 (99)
T 1lfb_A           86 AFRHKLA   92 (99)
T ss_dssp             SCCC---
T ss_pred             HHhchhh
Confidence            8877543

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

Probab=99.63  E-value=3e-16  Score=97.98  Aligned_cols=52  Identities=27%  Similarity=0.475  Sum_probs=50.1

Q ss_pred             CHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         43 TPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        43 s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      +..|+..|+..|..++||+..++..||..+||++.+|++||+|||+++|+..
T Consensus        12 ~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg~   63 (66)
T 3nau_A           12 TKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGI   63 (66)
T ss_dssp             CHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhccC
Confidence            6899999999999999999999999999999999999999999999999764

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

Probab=99.63  E-value=2.7e-16  Score=102.61  Aligned_cols=59  Identities=25%  Similarity=0.338  Sum_probs=54.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHh---cCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         37 RVRTIFTPEQLERLEAEFER---QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        37 r~Rt~~s~~q~~~Le~~F~~---~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      +.|+.|+..++.+|+.+|..   ++||+..++..||..+||++.+|++||+|+|+++|+...
T Consensus         4 krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~~   65 (83)
T 1le8_B            4 YRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITI   65 (83)
T ss_dssp             -CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHcccccccc
Confidence            44566999999999999999   999999999999999999999999999999999998753

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

Probab=99.62  E-value=2e-16  Score=100.08  Aligned_cols=55  Identities=45%  Similarity=0.762  Sum_probs=52.4

Q ss_pred             CCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         40 TIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        40 t~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      ..++..++..|+..|..++||+..++..||..|||++++|++||+|||+|+|+..
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~   63 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ   63 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSS
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhh
Confidence            4578999999999999999999999999999999999999999999999999865

>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=99.62  E-value=2.8e-16  Score=113.60  Aligned_cols=61  Identities=30%  Similarity=0.347  Sum_probs=57.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638         33 SKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ   93 (140)
Q Consensus        33 ~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~   93 (140)
                      ++++|.|+.|+..++..|+..|..++||+..++..||..+||++++|++||+|||+|+||.
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            4677889999999999999999999999999999999999999999999999999999974

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

Probab=99.61  E-value=2.9e-16  Score=97.88  Aligned_cols=52  Identities=21%  Similarity=0.176  Sum_probs=49.1

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638         41 IFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK   92 (140)
Q Consensus        41 ~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk   92 (140)
                      .+...|+..|+..|..++||+..++..||..|||++++|++||+|||+|.++
T Consensus         9 ~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~   60 (64)
T 2e19_A            9 PPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS   60 (64)
T ss_dssp             CCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSC
T ss_pred             CccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCC
Confidence            3568999999999999999999999999999999999999999999998775

>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=99.60  E-value=2e-16  Score=98.56  Aligned_cols=50  Identities=18%  Similarity=0.210  Sum_probs=46.2

Q ss_pred             HHHHHHHHHHH-HhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638         44 PEQLERLEAEF-ERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ   93 (140)
Q Consensus        44 ~~q~~~Le~~F-~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~   93 (140)
                      +.++.+||..| ..++||+..++..||..|||++++|++||||||+++|+.
T Consensus         9 ~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~~   59 (64)
T 1x2m_A            9 AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPS   59 (64)
T ss_dssp             SCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCCS
T ss_pred             chHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCCC
Confidence            34799999999 568999999999999999999999999999999999864

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

Probab=99.59  E-value=5.1e-16  Score=112.94  Aligned_cols=66  Identities=24%  Similarity=0.313  Sum_probs=55.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE   96 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~   96 (140)
                      ...+.+|.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||+|||+|+|+....
T Consensus        93 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~~  158 (164)
T 2d5v_A           93 RGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWLE  158 (164)
T ss_dssp             -------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC---
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccCCC
Confidence            345678889999999999999999999999999999999999999999999999999999987643

>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=99.54  E-value=3.8e-15  Score=93.53  Aligned_cols=59  Identities=24%  Similarity=0.280  Sum_probs=50.8

Q ss_pred             CCCCHHHHHHHHHHHH---hcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHH
Q psy10638         40 TIFTPEQLERLEAEFE---RQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQ   98 (140)
Q Consensus        40 t~~s~~q~~~Le~~F~---~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~   98 (140)
                      ..|+.+++.+|+..|.   .++||+..++..||..+||++.+|++||+|+|+|+++......
T Consensus         3 g~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~~   64 (67)
T 3k2a_A            3 GIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQS   64 (67)
T ss_dssp             ---CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC----
T ss_pred             CcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHHHHh
Confidence            3689999999999999   9999999999999999999999999999999999998765543

>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=99.46  E-value=1.6e-14  Score=107.85  Aligned_cols=61  Identities=33%  Similarity=0.405  Sum_probs=53.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcC---------------------CCcchhhhcccchhhHH
Q psy10638         32 SSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLN---------------------LTEAQVKVWFQNRRIKW   90 (140)
Q Consensus        32 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lg---------------------l~~~qV~vWFqNrR~k~   90 (140)
                      .++.||.|+.|+..++.+|+.+|..++||+..+++.||..||                     |++.+|++||+|||+++
T Consensus       112 ~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~~  191 (194)
T 1ic8_A          112 TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEE  191 (194)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHHC
T ss_pred             cccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhhh
Confidence            456788999999999999999999999999999999999999                     99999999999999987


Q ss_pred             HH
Q psy10638         91 RK   92 (140)
Q Consensus        91 kk   92 (140)
                      +.
T Consensus       192 k~  193 (194)
T 1ic8_A          192 AF  193 (194)
T ss_dssp             C-
T ss_pred             hc
Confidence            64

>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=99.43  E-value=8.5e-14  Score=87.52  Aligned_cols=46  Identities=22%  Similarity=0.381  Sum_probs=43.8

Q ss_pred             HHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhH
Q psy10638         44 PEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK   89 (140)
Q Consensus        44 ~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k   89 (140)
                      .+++..|+.+|..+++|+..++..||..+||+.++|++||||+|+.
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~   59 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVY   59 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhcccc
Confidence            4689999999999999999999999999999999999999999973

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

Probab=99.35  E-value=1.1e-12  Score=86.45  Aligned_cols=56  Identities=23%  Similarity=0.340  Sum_probs=52.0

Q ss_pred             CCCHHHHHHHHHHHHh---cCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHH
Q psy10638         41 IFTPEQLERLEAEFER---QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE   96 (140)
Q Consensus        41 ~~s~~q~~~Le~~F~~---~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~   96 (140)
                      -|+..++.+|+.+|..   ++||+..++..||..+||++.+|.+||+|+|.|.++....
T Consensus        11 ~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~~   69 (89)
T 2lk2_A           11 MLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLR   69 (89)
T ss_dssp             CCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHHH
Confidence            4889999999999987   8999999999999999999999999999999999887543

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

Probab=99.35  E-value=4.9e-13  Score=101.31  Aligned_cols=60  Identities=32%  Similarity=0.428  Sum_probs=53.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcC---------------------CCcchhhhcccchhhH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLN---------------------LTEAQVKVWFQNRRIK   89 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lg---------------------l~~~qV~vWFqNrR~k   89 (140)
                      ..++.||.|+.|+..++.+|+.+|..++||+..+++.||..||                     |++.+|++||+|||+.
T Consensus       138 ~~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~~  217 (221)
T 2h8r_A          138 TNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKE  217 (221)
T ss_dssp             ----CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHTT
T ss_pred             ccCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhhh
Confidence            4566788999999999999999999999999999999999988                     8899999999999986


Q ss_pred             H
Q psy10638         90 W   90 (140)
Q Consensus        90 ~   90 (140)
                      .
T Consensus       218 ~  218 (221)
T 2h8r_A          218 E  218 (221)
T ss_dssp             C
T ss_pred             h
Confidence            4

>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=99.19  E-value=5.6e-12  Score=101.40  Aligned_cols=55  Identities=29%  Similarity=0.490  Sum_probs=51.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHH
Q psy10638         37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR   91 (140)
Q Consensus        37 r~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~k   91 (140)
                      +.++.++..++..|+..|..++||+..+|..||..+||++++|++||+|||+|+|
T Consensus       367 ~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          367 AAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            4467899999999999999999999999999999999999999999999999875

>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=98.60  E-value=6.2e-09  Score=57.58  Aligned_cols=21  Identities=52%  Similarity=1.146  Sum_probs=18.7

Q ss_pred             chhhhcccchhhHHHHHhHHH
Q psy10638         77 AQVKVWFQNRRIKWRKQHLEF   97 (140)
Q Consensus        77 ~qV~vWFqNrR~k~kk~~~~~   97 (140)
                      ++|+|||+|||+|+||...+.
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~   21 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFND   21 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHH
T ss_pred             CCceeccHHHHHHHHHHhHHH
Confidence            589999999999999998664

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

Probab=95.71  E-value=0.0089  Score=37.08  Aligned_cols=42  Identities=24%  Similarity=0.390  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccch
Q psy10638         45 EQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNR   86 (140)
Q Consensus        45 ~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNr   86 (140)
                      .....|+.+|...+.+...+...|+.+..|+..+|+-||-.|
T Consensus        16 ~~~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~k   57 (70)
T 2ys9_A           16 PDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSR   57 (70)
T ss_dssp             CCCHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             CcchHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHhc
Confidence            345789999999999999999999999999999999999643

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=82.79  E-value=1.9  Score=24.73  Aligned_cols=45  Identities=22%  Similarity=0.366  Sum_probs=31.2

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhccc
Q psy10638         39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQ   84 (140)
Q Consensus        39 Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFq   84 (140)
                      |..|+.+....+...+... .........+|..+||+...|..|..
T Consensus         3 r~~ys~efK~~~~~~~~~g-~s~~~~~~~vA~~~gIs~~tl~~W~~   47 (59)
T 2glo_A            3 RRIFTPHFKLQVLESYRND-NDCKGNQRATARKYNIHRRQIQKWLQ   47 (59)
T ss_dssp             CCCCCHHHHHHHHHHHHHC-TTTTTCHHHHHHHTTSCHHHHHHHHT
T ss_pred             CCcCCHHHHHHHHHHHHcC-CCcchHHHHHHHHHCcCHHHHHHHHH
Confidence            4568888877665554433 22122356889999999999999964

---

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	140
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	3e-21
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	3e-20
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	3e-20
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	2e-19
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	1e-18
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	1e-18
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	1e-18
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	9e-18
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	9e-18
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	2e-17
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	2e-17
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	5e-17
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	1e-16
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	3e-16
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	3e-15
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	3e-15
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	1e-14
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	2e-14
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	2e-14
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	2e-14
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	3e-14
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	4e-14
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	6e-14
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	1e-12
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	2e-12
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	2e-12
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	3e-12
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	3e-12
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	3e-12
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	2e-11
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	2e-10
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	2e-08

>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 = 79.1 bits (195), Expect = 3e-21
 Identities = 27/76 (35%), Positives = 43/76 (56%)

Query: 24 SPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWF 83
          +P++    +  +++ R  +T  Q   LE EF    Y+    R  +A  LNLTE QVK+WF
Sbjct: 2  NPAANWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWF 61

Query: 84 QNRRIKWRKQHLEFQQ 99
          QNRR+K +K + +  +
Sbjct: 62 QNRRMKMKKINKDRAK 77

>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 = 77.0 bits (189), Expect = 3e-20
 Identities = 33/82 (40%), Positives = 45/82 (54%), Gaps = 3/82 (3%)

Query: 18 LKCKKLSPSSCSSSSS---KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNL 74
          +K K+  P +   S         +RT FT  QL  LE EF   +Y+    R+ +A TL L
Sbjct: 7  MKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLEL 66

Query: 75 TEAQVKVWFQNRRIKWRKQHLE 96
           E QVK+WFQNRR+K +K+  E
Sbjct: 67 NETQVKIWFQNRRMKQKKRERE 88

>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 = 76.4 bits (188), Expect = 3e-20
 Identities = 32/66 (48%), Positives = 42/66 (63%)

Query: 36  KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL 95
           +R RT FT EQ+E LE EFER  Y     R  LA  ++L EA+++VWF NRR KWR++  
Sbjct: 2   QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 61

Query: 96  EFQQQR 101
              Q+R
Sbjct: 62  LRNQRR 67

>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 = 74.0 bits (182), Expect = 2e-19
 Identities = 26/56 (46%), Positives = 38/56 (67%)

Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
          R  +T  Q   LE EF   +Y+    R+ +AH L+LTE Q+K+WFQNRR+KW+K++
Sbjct: 1  RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 56

>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 = 72.2 bits (177), Expect = 1e-18
 Identities = 18/57 (31%), Positives = 35/57 (61%)

Query: 36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          ++ R  ++  QL  LE E+   +++   +R  ++   +L+E Q+ +WFQNRR+K +K
Sbjct: 2  RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 58

>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 = 72.2 bits (177), Expect = 1e-18
 Identities = 18/65 (27%), Positives = 31/65 (47%)

Query: 34 KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          K+ RVRT+   +QL  L   +          +  L     L+   ++VWFQN+R K +K+
Sbjct: 2  KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

Query: 94 HLEFQ 98
           +  +
Sbjct: 62 SIMMK 66

>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 = 71.8 bits (176), Expect = 1e-18
 Identities = 29/57 (50%), Positives = 37/57 (64%)

Query: 36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          K  +  F+ +Q   LE +FE Q+Y+  PER  LA  L L+E QVK WFQNRR KWR+
Sbjct: 1  KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 57

>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 = 69.5 bits (170), Expect = 9e-18
 Identities = 26/53 (49%), Positives = 33/53 (62%)

Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
          R RT F+ EQL RL+ EF   +Y+    R  L+  L L EAQ+K+WFQN R K
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 58

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

 Score = 69.9 bits (171), Expect = 9e-18
 Identities = 27/57 (47%), Positives = 39/57 (68%)

Query: 36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          ++ RT FT  QL  LE +F ++QY+   ER   + +L+LTE QVK+WFQNRR K ++
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>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 = 69.2 bits (169), Expect = 2e-17
 Identities = 31/57 (54%), Positives = 40/57 (70%)

Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          R RT FT +QL RLE EF ++ Y+  P R  LA  LNL E+ +KVWFQNRR+K ++Q
Sbjct: 1  RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 57

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 65

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

 Score = 69.2 bits (169), Expect = 2e-17
 Identities = 33/61 (54%), Positives = 40/61 (65%)

Query: 34 KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          K +R RT F+  QL+ LE  FER QY     R  LA   NLTEA+++VWFQNRR + RKQ
Sbjct: 1  KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 60

Query: 94 H 94
          H
Sbjct: 61 H 61

>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 = 68.5 bits (167), Expect = 5e-17
 Identities = 27/70 (38%), Positives = 40/70 (57%)

Query: 27 SCSSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNR 86
          +     +K ++ R +FT  Q   LE  F +Q+Y+  PER +LA  + LT  QVK+WFQN 
Sbjct: 1  ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNH 60

Query: 87 RIKWRKQHLE 96
          R K ++   E
Sbjct: 61 RYKTKRAQNE 70

>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 = 67.3 bits (164), Expect = 1e-16
 Identities = 25/65 (38%), Positives = 37/65 (56%)

Query: 36  KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL 95
           +R RT FT  Q+  LE  F + +Y+  P    L+  L L  AQVK+WF+NRR + + Q  
Sbjct: 2   RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 61

Query: 96  EFQQQ 100
           + + Q
Sbjct: 62  QHKDQ 66

>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 = 66.1 bits (161), Expect = 3e-16
 Identities = 26/66 (39%), Positives = 43/66 (65%)

Query: 36  KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL 95
           ++ R +F+  Q+  LE  F++Q+Y+  PER +LA  ++LT  QVK+WFQN R K ++Q  
Sbjct: 3   RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62

Query: 96  EFQQQR 101
           +   Q+
Sbjct: 63  DKAAQQ 68

>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 = 63.3 bits (154), Expect = 3e-15
 Identities = 13/49 (26%), Positives = 22/49 (44%)

Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRR 87
          R +FT  Q   L A F+  +      ++ ++  L L  + V  +F N R
Sbjct: 2  RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>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 = 63.8 bits (155), Expect = 3e-15
 Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 3/69 (4%)

Query: 35  SKRVRTIFTPEQLERLEAEFE---RQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR 91
           ++R R  F  +  E L   F       Y     +  LA    +T +QV  WF N+RI+++
Sbjct: 1   ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60

Query: 92  KQHLEFQQQ 100
           K   +FQ++
Sbjct: 61  KNIGKFQEE 69

>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 = 61.8 bits (150), Expect = 1e-14
 Identities = 17/57 (29%), Positives = 27/57 (47%)

Query: 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          + RT  +    + LE  F         E + +A  LNL +  V+VWF NRR + ++ 
Sbjct: 1  KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV 57

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.5 bits (149), Expect = 2e-14
 Identities = 31/58 (53%), Positives = 42/58 (72%)

Query: 36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93
          +R RT FT +QL++LEA F+R +Y     R  +A   NLTEA+V+VWF+NRR KWRK+
Sbjct: 2  RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 59

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 53

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 61.1 bits (148), Expect = 2e-14
 Identities = 16/53 (30%), Positives = 30/53 (56%)

Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR 91
          ++  +P+    LE  F R+Q +   E+  +A    +T  QV+VWF N+R++ +
Sbjct: 1  KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 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 = 61.5 bits (149), Expect = 2e-14
 Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 36 KRVRTIFTPEQLERLEAEFER-QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
                 T +Q+E LE  F +  ++        +A    LTE Q + WF+ R  +WR+  
Sbjct: 2  SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 61

>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 = 61.6 bits (149), Expect = 3e-14
 Identities = 21/87 (24%), Positives = 35/87 (40%), Gaps = 21/87 (24%)

Query: 37  RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLN---------------LTEAQVKV 81
             R  +  E L  +E+ F   QY    +R  +A+  N               +T  +V  
Sbjct: 2   GSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYN 61

Query: 82  WFQNRRIKWRKQHLEFQQQRLAAIKQS 108
           WF NRR + ++      +  +AAI +S
Sbjct: 62  WFANRRKEIKR------RANIAAILES 82

>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 = 61.2 bits (148), Expect = 4e-14
 Identities = 21/74 (28%), Positives = 29/74 (39%), Gaps = 4/74 (5%)

Query: 24 SPSSCSSSSSKSKRVRTIFTPEQLERLEAEFERQ----QYMVGPERLYLAHTLNLTEAQV 79
          S S+ SSS   +KR RT FT EQ E++ A  ER     Q               +    +
Sbjct: 6  SGSNPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVL 65

Query: 80 KVWFQNRRIKWRKQ 93
          K+W  N +      
Sbjct: 66 KIWMHNNKNSGPSS 79

>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 = 60.5 bits (146), Expect = 6e-14
 Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 1/65 (1%)

Query: 30 SSSSKSKRVRTIFTPEQLERLEAEFER-QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRI 88
          SS S   R RT  + E L  L++       Y        L+  L+L +  +  +FQN+R 
Sbjct: 2  SSGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRY 61

Query: 89 KWRKQ 93
            +  
Sbjct: 62 HVKHS 66

>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 = 56.9 bits (137), Expect = 1e-12
 Identities = 18/64 (28%), Positives = 28/64 (43%)

Query: 30 SSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89
          +     KR RT         LE  F +       +  ++A+ L L +  V+VWF NRR K
Sbjct: 3  TLVQARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQK 62

Query: 90 WRKQ 93
           ++ 
Sbjct: 63 GKRS 66

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Length = 62

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.3 bits (136), Expect = 2e-12
 Identities = 14/60 (23%), Positives = 22/60 (36%), Gaps = 3/60 (5%)

Query: 36 KRVRTIFTPEQLERLEAEFERQQ---YMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          K  R +        + +   +     Y    E+  +A   NLT  QV  WF N R +  +
Sbjct: 3  KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQ 62

>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 = 55.9 bits (135), Expect = 2e-12
 Identities = 10/51 (19%), Positives = 20/51 (39%), Gaps = 1/51 (1%)

Query: 43 TPEQLERLEAEFERQ-QYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          T +    LE  F    ++        L+  L+     ++ WF+ RR + + 
Sbjct: 1  TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 51

>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 = 56.3 bits (135), Expect = 3e-12
 Identities = 19/77 (24%), Positives = 27/77 (35%), Gaps = 21/77 (27%)

Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLN---------------------LTEA 77
          R  + P   + L   +ERQ+     ER  L    N                     +TE 
Sbjct: 1  RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 78 QVKVWFQNRRIKWRKQH 94
          +V  WF NRR +   +H
Sbjct: 61 RVYNWFANRRKEEAFRH 77

>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 = 55.7 bits (134), Expect = 3e-12
 Identities = 16/56 (28%), Positives = 25/56 (44%)

Query: 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94
          RT         LE  F   Q     +   +A  LN+ +  ++VWF NRR K ++ +
Sbjct: 2  RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRIN 57

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 55.6 bits (134), Expect = 3e-12
 Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 3/54 (5%)

Query: 42 FTPEQLERLEAEFERQQ---YMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
          FT E +  LE+ F +     Y+       L    +L+  Q+K W  NRR K + 
Sbjct: 5  FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 59

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: LAG1 longevity assurance homolog 5, LASS5
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.6 bits (129), Expect = 2e-11
 Identities = 11/56 (19%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 37 RVRTIFTPEQLERLEAEFERQ-QYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR 91
          +   +   E  + LE  F    +Y        L+  L+ +  +++ WF++RR + +
Sbjct: 3  KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]} Length = 76

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Zinc fingers and homeoboxes protein 1, ZHX1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.3 bits (122), Expect = 2e-10
 Identities = 14/72 (19%), Positives = 25/72 (34%)

Query: 33  SKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92
             + +     T EQL  L+A F     +   E   L     LT  ++  WF  ++     
Sbjct: 2   DFTPQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKAL 61

Query: 93  QHLEFQQQRLAA 104
           +  + +     A
Sbjct: 62  KEEKMEIDESNA 73

>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 = 46.3 bits (109), Expect = 2e-08
 Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 2/70 (2%)

Query: 32  SSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR 91
           SS S   R   T EQL  L++ F + Q+    +   L     L   ++  WF + R   +
Sbjct: 2   SSGSSGKR--KTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALK 59

Query: 92  KQHLEFQQQR 101
              L++ +  
Sbjct: 60  HGQLKWFRDN 69

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	140
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.83
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.82
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.81
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.81
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.81
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.8
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.8
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.8
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.8
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.79
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.79
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.78
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.78
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.78
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.76
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.76
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.74
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.74
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.74
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.74
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.74
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.73
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.71
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.68
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.63
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.63
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.63
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.61
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.6
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.57
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.52
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.52
d1hlva1	66	DNA-binding domain of centromere binding protein B	88.45

>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=99.83  E-value=7.1e-21  Score=121.43  Aligned_cols=68  Identities=38%  Similarity=0.551  Sum_probs=61.8

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHH
Q psy10638         29 SSSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE   96 (140)
Q Consensus        29 ~~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~   96 (140)
                      ....+..++.|+.|+..|+.+|+.+|..++||+..+++.||..|||++.+|++||+|+|+++|+..+.
T Consensus         7 ~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~   74 (77)
T d1pufa_           7 WLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             SCCCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCccCcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHH
Confidence            33455567789999999999999999999999999999999999999999999999999999987654

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

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

Probab=99.82  E-value=3.9e-21  Score=116.44  Aligned_cols=57  Identities=32%  Similarity=0.634  Sum_probs=54.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638         36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK   92 (140)
Q Consensus        36 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk   92 (140)
                      ++.|+.|+..|+.+|+..|..++||+..+++.||..|||++.+|++||+|||+++||
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            577899999999999999999999999999999999999999999999999999875

>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=99.81  E-value=1e-20  Score=114.60  Aligned_cols=57  Identities=47%  Similarity=0.736  Sum_probs=55.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638         36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK   92 (140)
Q Consensus        36 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk   92 (140)
                      ||.|+.|++.|+.+|+..|..++||+..++..||..|||++.+|++||+|+|+++||
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            467899999999999999999999999999999999999999999999999999987

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=99.81  E-value=1.9e-20  Score=113.01  Aligned_cols=57  Identities=51%  Similarity=0.821  Sum_probs=54.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638         36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK   92 (140)
Q Consensus        36 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk   92 (140)
                      ++.|+.|++.|+.+|+..|..++||+..++..||..|||++.+|++||+|||+++||
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k~kk   57 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR   57 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhhccC
Confidence            467889999999999999999999999999999999999999999999999999986

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

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

Probab=99.81  E-value=1.8e-20  Score=116.65  Aligned_cols=60  Identities=40%  Similarity=0.651  Sum_probs=57.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        36 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      +|.|++|+..|+.+|+.+|..++||+..++..||..|||++++|+|||+|||+++|+...
T Consensus         2 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~   61 (67)
T d1zq3p1           2 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD   61 (67)
T ss_dssp             SCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhh
Confidence            567899999999999999999999999999999999999999999999999999998653

>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=99.80  E-value=1.9e-20  Score=113.04  Aligned_cols=57  Identities=54%  Similarity=0.851  Sum_probs=54.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638         37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ   93 (140)
Q Consensus        37 r~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~   93 (140)
                      |.|+.|++.|+..|+..|..++||+..++..||..|||++.+|++||+|+|+++||.
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk~   57 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   57 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhcC
Confidence            568999999999999999999999999999999999999999999999999999973

>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=99.80  E-value=1.5e-20  Score=112.96  Aligned_cols=55  Identities=47%  Similarity=0.855  Sum_probs=53.6

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638         39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ   93 (140)
Q Consensus        39 Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~   93 (140)
                      ||.||..|+.+|+..|..++||+..++..||..|||++++|++||||||+|+||.
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk~   55 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   55 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhhc
Confidence            6899999999999999999999999999999999999999999999999999985

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

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

Probab=99.80  E-value=3.6e-20  Score=114.60  Aligned_cols=62  Identities=53%  Similarity=0.751  Sum_probs=58.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         34 KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        34 ~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      +.++.|+.|+..|+.+|+.+|..++||+..++..||..|||++.+|++||+|+|+++|+...
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~   62 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   62 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhccc
Confidence            46788999999999999999999999999999999999999999999999999999998663

>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=99.80  E-value=1.5e-20  Score=122.71  Aligned_cols=65  Identities=43%  Similarity=0.669  Sum_probs=56.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      +..+.++.|+.|+..|+.+|+.+|..++||+..+++.||..|||++++|++||+|+|+++|+..+
T Consensus        23 ~~~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~~   87 (88)
T d1b72a_          23 GLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   87 (88)
T ss_dssp             -------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhcc
Confidence            34456788999999999999999999999999999999999999999999999999999998753

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=7.3e-20  Score=114.11  Aligned_cols=62  Identities=48%  Similarity=0.753  Sum_probs=58.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHH
Q psy10638         35 SKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE   96 (140)
Q Consensus        35 ~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~   96 (140)
                      ++|.|+.|+..|+.+|+.+|..++||+..+++.||..|||++.+|++||+|+|+++|+....
T Consensus         1 grR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~   62 (68)
T d2cuea1           1 GQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL   62 (68)
T ss_dssp             SCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhhh
Confidence            35778999999999999999999999999999999999999999999999999999986644

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.79  E-value=1.4e-20  Score=120.06  Aligned_cols=64  Identities=41%  Similarity=0.668  Sum_probs=59.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      .+.+.++.|++|+..|+.+|+.+|..++||+..+++.||..|||++++|++||+|+|+++|+..
T Consensus         5 ~p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   68 (77)
T d1vnda_           5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ   68 (77)
T ss_dssp             CSSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHh
Confidence            3456778899999999999999999999999999999999999999999999999999998754

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.78  E-value=5.3e-20  Score=109.47  Aligned_cols=53  Identities=49%  Similarity=0.809  Sum_probs=51.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhH
Q psy10638         37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK   89 (140)
Q Consensus        37 r~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k   89 (140)
                      |.|+.|+..|+..|+..|..++||+..++..||..|||++.+|++||||||+|
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            56899999999999999999999999999999999999999999999999986

>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=99.78  E-value=5.9e-20  Score=111.91  Aligned_cols=58  Identities=53%  Similarity=0.827  Sum_probs=56.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638         36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ   93 (140)
Q Consensus        36 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~   93 (140)
                      ||.|+.|+.+|+.+|+.+|..++||+..++..||..+||++.+|++||+|+|+++|+.
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            5778999999999999999999999999999999999999999999999999999986

>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=99.78  E-value=1.1e-19  Score=113.21  Aligned_cols=60  Identities=42%  Similarity=0.744  Sum_probs=57.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         35 SKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        35 ~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      +++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||+|+|+++|+..
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            467899999999999999999999999999999999999999999999999999999865

>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=99.76  E-value=3.3e-19  Score=112.19  Aligned_cols=59  Identities=27%  Similarity=0.450  Sum_probs=55.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh-cCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         36 KRVRTIFTPEQLERLEAEFER-QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        36 rr~Rt~~s~~q~~~Le~~F~~-~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      ++.|+.|+..|+.+|+..|.. ++||+...++.||..+||++++|++||+|||+++|+..
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~   61 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhcc
Confidence            567899999999999999997 67999999999999999999999999999999999864

>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=99.76  E-value=1.8e-19  Score=111.75  Aligned_cols=61  Identities=30%  Similarity=0.449  Sum_probs=58.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         34 KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        34 ~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      +.+|.|+.|+.+|+.+|+.+|..++||+..+++.||..+||++.+|++||+|+|++.|+..
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            4678899999999999999999999999999999999999999999999999999998765

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=99.74  E-value=4.1e-19  Score=110.32  Aligned_cols=60  Identities=30%  Similarity=0.323  Sum_probs=56.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638         34 KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ   93 (140)
Q Consensus        34 ~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~   93 (140)
                      .++|.|+.|+..++..|+.+|..++||+..+++.||..+||++.+|++||+|+|+++||.
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            356789999999999999999999999999999999999999999999999999998864

>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=99.74  E-value=6.6e-19  Score=104.66  Aligned_cols=53  Identities=30%  Similarity=0.531  Sum_probs=51.2

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHH
Q psy10638         39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR   91 (140)
Q Consensus        39 Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~k   91 (140)
                      |+.|+++++.+|+..|..++||+..++..||..+||++++|++||+|+|+++|
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            68899999999999999999999999999999999999999999999999875

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

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

Probab=99.74  E-value=7e-19  Score=106.38  Aligned_cols=57  Identities=30%  Similarity=0.458  Sum_probs=54.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638         37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ   93 (140)
Q Consensus        37 r~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~   93 (140)
                      |.|+.|+..++.+|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.
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            468999999999999999999999999999999999999999999999999999874

>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=99.74  E-value=7.3e-19  Score=110.36  Aligned_cols=60  Identities=23%  Similarity=0.257  Sum_probs=55.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHH-hcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638         34 KSKRVRTIFTPEQLERLEAEFE-RQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ   93 (140)
Q Consensus        34 ~~rr~Rt~~s~~q~~~Le~~F~-~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~   93 (140)
                      ..++.|+.|+.+|+.+|+.+|. .++||+..+++.||..|||++++|++||+|+|++.|+.
T Consensus         6 ~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk~   66 (71)
T d1wi3a_           6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS   66 (71)
T ss_dssp             CCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCSS
T ss_pred             CCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhccc
Confidence            3567789999999999999997 48999999999999999999999999999999998863

>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=99.74  E-value=1.3e-18  Score=111.57  Aligned_cols=63  Identities=29%  Similarity=0.300  Sum_probs=56.5

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHh----cCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638         30 SSSSKSKRVRTIFTPEQLERLEAEFER----QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK   92 (140)
Q Consensus        30 ~~~~~~rr~Rt~~s~~q~~~Le~~F~~----~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk   92 (140)
                      ....+++|.|+.|+..|+..|+.+|+.    +++|+..+++.||..|||++.+|+|||+|+|.+.++
T Consensus        12 ~~~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          12 SSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            344566788999999999999999997    789999999999999999999999999999987654

>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=99.73  E-value=1.8e-18  Score=111.41  Aligned_cols=60  Identities=28%  Similarity=0.419  Sum_probs=56.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcC---------------CCcchhhhcccchhhHHHHHhH
Q psy10638         36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLN---------------LTEAQVKVWFQNRRIKWRKQHL   95 (140)
Q Consensus        36 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lg---------------l~~~qV~vWFqNrR~k~kk~~~   95 (140)
                      ||.|+.|+..|+.+|+.+|..++||+..+++.||..+|               |++.+|++||+|||+++|++..
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~   75 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRAN   75 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhh
Confidence            57899999999999999999999999999999999875               8999999999999999999763

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=3.2e-18  Score=103.07  Aligned_cols=56  Identities=29%  Similarity=0.416  Sum_probs=53.8

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638         38 VRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ   93 (140)
Q Consensus        38 ~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~   93 (140)
                      .||.|+..++.+|+.+|..++||+..++..||..+||++.+|++||+|+|+++|+.
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            37899999999999999999999999999999999999999999999999999874

>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=99.68  E-value=9.7e-18  Score=98.36  Aligned_cols=50  Identities=26%  Similarity=0.338  Sum_probs=48.7

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchh
Q psy10638         38 VRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRR   87 (140)
Q Consensus        38 ~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR   87 (140)
                      +|+.|+..|+.+|+..|..++||+..++..||..|||++++|++||+|+|
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            58999999999999999999999999999999999999999999999987

>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=99.63  E-value=1.4e-16  Score=101.05  Aligned_cols=53  Identities=25%  Similarity=0.343  Sum_probs=50.2

Q ss_pred             CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      ++.+|+.+|+.+|..++||+..+++.||..|||++++|++||+|+|++.++..
T Consensus        11 ~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~   63 (76)
T d2ecba1          11 KTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE   63 (76)
T ss_dssp             CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCC
T ss_pred             CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHh
Confidence            58999999999999999999999999999999999999999999999887654

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

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

Probab=99.63  E-value=2.3e-16  Score=99.99  Aligned_cols=54  Identities=22%  Similarity=0.297  Sum_probs=51.6

Q ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         41 IFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        41 ~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      .++.+|+.+|+.+|..++||+..++..||..+||++.+|++||+|+|+++|+..
T Consensus         9 r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~~   62 (76)
T d2ecca1           9 RKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ   62 (76)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhch
Confidence            478999999999999999999999999999999999999999999999999854

>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=99.63  E-value=2.3e-16  Score=99.24  Aligned_cols=59  Identities=31%  Similarity=0.475  Sum_probs=54.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638         36 KRVRTIFTPEQLERLEAEFER---QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        36 rr~Rt~~s~~q~~~Le~~F~~---~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~   94 (140)
                      |+.|+.|+..++.+|+.+|..   ++||+..+++.||..+||++.+|.+||+|+|++.++..
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~   63 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccc
Confidence            567889999999999999984   78999999999999999999999999999999998755

>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=99.61  E-value=6.3e-17  Score=95.57  Aligned_cols=50  Identities=20%  Similarity=0.237  Sum_probs=46.3

Q ss_pred             CHHHHHHHHHHHHh-cCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638         43 TPEQLERLEAEFER-QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK   92 (140)
Q Consensus        43 s~~q~~~Le~~F~~-~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk   92 (140)
                      |+++..+|+.+|.. ++||+..++..||..|||++++|++||+|||+++|+
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            35688999999987 689999999999999999999999999999999875

>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=99.60  E-value=1.1e-16  Score=101.95  Aligned_cols=56  Identities=34%  Similarity=0.424  Sum_probs=52.5

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcC---------------------CCcchhhhcccchhhHHHHHh
Q psy10638         39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLN---------------------LTEAQVKVWFQNRRIKWRKQH   94 (140)
Q Consensus        39 Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lg---------------------l~~~qV~vWFqNrR~k~kk~~   94 (140)
                      |++|++.|+.+|+.+|+.++||+..+++.||..|+                     |++.+|.+||+|||+++|++.
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr~~   77 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFRH   77 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCCC
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHHhc
Confidence            67899999999999999999999999999999995                     888999999999999998764

>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=99.57  E-value=2.8e-16  Score=95.00  Aligned_cols=55  Identities=20%  Similarity=0.314  Sum_probs=50.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHh-cCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHH
Q psy10638         37 RVRTIFTPEQLERLEAEFER-QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR   91 (140)
Q Consensus        37 r~Rt~~s~~q~~~Le~~F~~-~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~k   91 (140)
                      +.+..++.++..+|+.+|.. ++||+..++..||..|||++++|++||+|||+++|
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            45667888888999999986 68999999999999999999999999999999986

>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=99.52  E-value=6.1e-15  Score=89.28  Aligned_cols=52  Identities=31%  Similarity=0.430  Sum_probs=48.5

Q ss_pred             CCCHHHHHHHHHHHHhc---CCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638         41 IFTPEQLERLEAEFERQ---QYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK   92 (140)
Q Consensus        41 ~~s~~q~~~Le~~F~~~---~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk   92 (140)
                      .|+.+++.+|+.+|..+   +||+..+++.||..+||++.+|++||+|+|.+.|+
T Consensus         4 Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           4 RFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             SCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            48999999999999865   69999999999999999999999999999998875

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=1.1e-14  Score=88.73  Aligned_cols=56  Identities=25%  Similarity=0.313  Sum_probs=50.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHH
Q psy10638         36 KRVRTIFTPEQLERLEAEFER---QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR   91 (140)
Q Consensus        36 rr~Rt~~s~~q~~~Le~~F~~---~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~k   91 (140)
                      ++.|+.|+.+++.+|+.+|..   ++||+..++..||..+||+..+|.+||+|+|.|..
T Consensus         3 krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R~l   61 (62)
T d1x2na1           3 KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRIL   61 (62)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhc
Confidence            455678999999999999985   78999999999999999999999999999997754

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.45  E-value=0.42  Score=27.64  Aligned_cols=45  Identities=18%  Similarity=0.260  Sum_probs=36.8

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccch
Q psy10638         39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNR   86 (140)
Q Consensus        39 Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNr   86 (140)
                      |..++..+...+-..|+.++...   ...||..+|+....|..|..|+
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            44689988888888888887554   4568999999999999999873