Psyllid ID: psy15889

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90--
Protein Sequence
MGELMALWLRVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPDTDSLYTSAYSSYNNWASKVPSPLGTIGVNDLGFQS
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MGELMALWLRVRVWFKNRRAKWRKRERNAMNAAAAAAVdfkngfstqfnglmqtfpdtdslyTSAYSSYnnwaskvpsplgtigvndlgfqs
Flexible Loop (DISEMBL)
mgelmalwLRVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPDTDSLYTSAYSSYNNWASKVPSPLGTIGVNDLGFQS
Low Complexity Region (SEG)
MGELMALWLRVRVWFKNRRAKWRKRERnamnaaaaaaVDFKNGFSTQFNGLMQTFPDTDSLYTSAYSSYNNWASKVPSPLGTIGVNDLGFQS
Disordered region (IsUnstruct)
***LMALWLRVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPDTDSLYTSAYSSYNNWASKVPSPLGTIGV*******
Disordered Region (DISOPRED)
*****ALWLRVRVWFKNRR************************************PDTDSLYTSAYSSYNNWASKV****************
Disordered Region (DISEMBL)
MGELMALWLRVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPDTDSLYTSAYSSYNNWASKVPSPLGTIGVNDLGFQS
Disordered Region (DISPRO)
MGELMALWLRVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPDTDSLYTSAYSSYNNWASKVPS**************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MGELMALWLRVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPDTDSLYTSAYSSYNNWASKVPSPLGTIGVNDLGFQS
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	92	2.2.26 [Sep-21-2011]
Q9U637	331	Pituitary homeobox x OS=B	N/A	N/A	0.75	0.208	0.578	5e-19
O18400	509	Pituitary homeobox homolo	yes	N/A	0.858	0.155	0.604	3e-16
Q6QU75	293	Pituitary homeobox 3 OS=D	yes	N/A	0.673	0.211	0.564	5e-14
Q9PWR3	326	Pituitary homeobox 2 OS=X	N/A	N/A	0.673	0.190	0.564	7e-14
Q9W5Z2	314	Pituitary homeobox 2 OS=D	no	N/A	0.673	0.197	0.551	8e-14
Q99NA7	315	Pituitary homeobox 1 OS=R	yes	N/A	0.782	0.228	0.5	9e-14
O93385	333	Pituitary homeobox 2 OS=G	yes	N/A	0.673	0.186	0.551	1e-13
Q9R0W1	324	Pituitary homeobox 2 OS=R	no	N/A	0.673	0.191	0.551	1e-13
P56673	311	Pituitary homeobox 1 OS=G	no	N/A	0.760	0.225	0.5	1e-13
Q9W751	305	Pituitary homeobox 1 OS=X	N/A	N/A	0.760	0.229	0.511	2e-13

>sp|Q9U637|PITX_BRABE Pituitary homeobox x OS=Branchiostoma belcheri GN=Ptx PE=2 SV=1

 Score = 92.8 bits (229), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 48/83 (57%), Positives = 54/83 (65%), Gaps = 14/83 (16%)

Query: 3   ELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPD 57
           E +A W      RVRVWFKNRRAKWRKRERN +        +FKNGF   FNGLMQ F  
Sbjct: 136 EEIAAWTNLTEARVRVWFKNRRAKWRKRERNQLG-------EFKNGFGPHFNGLMQPF-- 186

Query: 58  TDSLYTSAYSSYNNWASKVPSPL 80
            D LY+    +YNNWA+KVPSPL
Sbjct: 187 DDGLYSGYSPAYNNWAAKVPSPL 209

Involved in left-right asymmetry in the developing embryo.
Branchiostoma belcheri (taxid: 7741)

>sp|O18400|PITX_DROME Pituitary homeobox homolog Ptx1 OS=Drosophila melanogaster GN=Ptx1 PE=2 SV=2

 Score = 84.0 bits (206), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 58/96 (60%), Positives = 63/96 (65%), Gaps = 17/96 (17%)

Query: 3   ELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPD 57
           E +A+W      RVRVWFKNRRAKWRKRER     AA AA DFK+GF TQF   MQ F D
Sbjct: 295 EEIAMWTNLTEARVRVWFKNRRAKWRKRER-NAMNAAVAAADFKSGFGTQF---MQPFAD 350

Query: 58  TDSLYTSAYSSYNNWASKVPSPLGTI----GVNDLG 89
            DSLY+S    YNNW +KVPSPLGT      VN LG
Sbjct: 351 -DSLYSSY--PYNNW-TKVPSPLGTKPFPWPVNPLG 382

Appears to control physiological cell functions rather than pattern formation during embryogenesis.

Drosophila melanogaster (taxid: 7227)

>sp|Q6QU75|PITX3_DANRE Pituitary homeobox 3 OS=Danio rerio GN=pitx3 PE=2 SV=1

 Score = 76.3 bits (186), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 44/78 (56%), Positives = 48/78 (61%), Gaps = 16/78 (20%)

Query: 3   ELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPD 57
           E +A+W      RVRVWFKNRRAKWRKRERN        A   KNGF  QFNGLMQ + D
Sbjct: 91  EEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ------AELCKNGFGAQFNGLMQPYDD 144

Query: 58  TDSLYTSAYSSYNNWASK 75
             S Y     SYNNWA+K
Sbjct: 145 MYSGY-----SYNNWATK 157

Transcriptional regulator which may play a role in the differentiation and maintenance of meso-diencephalic dopaminergic (mdDA) neurons (By similarity). Required for lens and retinal development and for pituitary pre-placode formation and cell specification.

Danio rerio (taxid: 7955)

>sp|Q9PWR3|PITX2_XENLA Pituitary homeobox 2 OS=Xenopus laevis GN=pitx2 PE=2 SV=1

 Score = 75.9 bits (185), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 44/78 (56%), Positives = 49/78 (62%), Gaps = 16/78 (20%)

Query: 3   ELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPD 57
           E +A+W      RVRVWFKNRRAKWRKRERN        A   KNGF  QFNGLMQ +  
Sbjct: 125 EEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ------AELCKNGFGPQFNGLMQPY-- 176

Query: 58  TDSLYTSAYSSYNNWASK 75
            D +Y S   SYNNWA+K
Sbjct: 177 -DDMYPSY--SYNNWAAK 191

May play an important role in development and maintenance of anterior structures and mediate left-right asymmetry. Could play a role at the interface of lateral plate signaling and heart and gut morphogenesis.

Xenopus laevis (taxid: 8355)

>sp|Q9W5Z2|PITX2_DANRE Pituitary homeobox 2 OS=Danio rerio GN=pitx2 PE=2 SV=1

 Score = 75.5 bits (184), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 43/78 (55%), Positives = 47/78 (60%), Gaps = 16/78 (20%)

Query: 3   ELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPD 57
           E +A+W      RVRVWFKNRRAKWRKRERN        A   KNGF  QFNGLMQ + D
Sbjct: 113 EEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ------AELCKNGFGPQFNGLMQPYDD 166

Query: 58  TDSLYTSAYSSYNNWASK 75
               YT     YNNWA+K
Sbjct: 167 MYPSYT-----YNNWAAK 179

Isoform a and isoform c differentially regulate mesendoderm formation and asymmetric organ development. Both isoforms regulate left-right development, but isoform a has a stronger effect on heart laterality.

Danio rerio (taxid: 7955)

>sp|Q99NA7|PITX1_RAT Pituitary homeobox 1 OS=Rattus norvegicus GN=Pitx1 PE=2 SV=1

 Score = 75.5 bits (184), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 45/90 (50%), Positives = 56/90 (62%), Gaps = 18/90 (20%)

Query: 1   MGELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAAAVDF-KNGFSTQFNGLMQT 54
           M E +A+W      RVRVWFKNRRAKWRKRERN         +D  K G+  QF+GL+Q 
Sbjct: 118 MREEIAVWTNLTEPRVRVWFKNRRAKWRKRERNQQ-------LDLCKGGYVPQFSGLVQP 170

Query: 55  FPDTDSLYTSAYSSYNNWASK--VPSPLGT 82
           + D   +Y +A  SYNNWA+K   P+PL T
Sbjct: 171 YED---VYAAAGYSYNNWAAKSLAPAPLST 197

May play a role in the development of anterior structures, and in particular, the brain and facies and in specifying the identity or structure of hindlimb.

Rattus norvegicus (taxid: 10116)

>sp|O93385|PITX2_CHICK Pituitary homeobox 2 OS=Gallus gallus GN=PITX2 PE=2 SV=1

 Score = 75.1 bits (183), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 43/78 (55%), Positives = 47/78 (60%), Gaps = 16/78 (20%)

Query: 3   ELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPD 57
           E +A+W      RVRVWFKNRRAKWRKRERN        A   KNGF  QFNGLMQ + D
Sbjct: 132 EEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ------AELCKNGFGPQFNGLMQPYDD 185

Query: 58  TDSLYTSAYSSYNNWASK 75
               Y     SYNNWA+K
Sbjct: 186 MYPGY-----SYNNWAAK 198

May play an important role in development and maintenance of anterior structures. May play a role in determining left-right asymmetry and in vasculogenesis during avian embryogenesis.

Gallus gallus (taxid: 9031)

>sp|Q9R0W1|PITX2_RAT Pituitary homeobox 2 OS=Rattus norvegicus GN=Pitx2 PE=2 SV=1

 Score = 75.1 bits (183), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 43/78 (55%), Positives = 47/78 (60%), Gaps = 16/78 (20%)

Query: 3   ELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPD 57
           E +A+W      RVRVWFKNRRAKWRKRERN        A   KNGF  QFNGLMQ + D
Sbjct: 123 EEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ------AELCKNGFGPQFNGLMQPYDD 176

Query: 58  TDSLYTSAYSSYNNWASK 75
               Y     SYNNWA+K
Sbjct: 177 MYPGY-----SYNNWAAK 189

Controls cell proliferation in a tissue-specific manner and is involved in morphogenesis. During embryonic development, exerts a role in the expansion of muscle progenitors. May play a role in the proper localization of asymmetric organs such as the heart and stomach.

Rattus norvegicus (taxid: 10116)

>sp|P56673|PITX1_CHICK Pituitary homeobox 1 OS=Gallus gallus GN=PITX1 PE=2 SV=1

 Score = 75.1 bits (183), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 45/90 (50%), Positives = 54/90 (60%), Gaps = 20/90 (22%)

Query: 1   MGELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAAAVDF-KNGFSTQFNGLMQT 54
           M E +A+W      RVRVWFKNRRAKWRKRERN         +D  KNG+  QF+GLMQ 
Sbjct: 117 MREEIAVWTNLTEPRVRVWFKNRRAKWRKRERNQQ-------MDLCKNGYVPQFSGLMQP 169

Query: 55  FPDTDSLYTSAYSSYNNWASK--VPSPLGT 82
           + D  + Y      YNNWA+K   P+PL T
Sbjct: 170 YDDMYAGYP-----YNNWATKSLTPAPLST 194

May play a role in the development of anterior structures, and in particular, the brain and facies and in specifying the identity or structure of hindlimb. Acts as a transcriptional activator by binding to promoter sequences with a TAAT/GCC core motif.

Gallus gallus (taxid: 9031)

>sp|Q9W751|PITX1_XENLA Pituitary homeobox 1 OS=Xenopus laevis GN=pitx1 PE=2 SV=1

 Score = 74.7 bits (182), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 46/90 (51%), Positives = 55/90 (61%), Gaps = 20/90 (22%)

Query: 1   MGELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAAAVDF-KNGFSTQFNGLMQT 54
           M E +A+W      RVRVWFKNRRAKWRKRERN         +D  KNG+  QF+GLMQ 
Sbjct: 107 MREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ-------MDLCKNGYVPQFSGLMQP 159

Query: 55  FPDTDSLYTSAYSSYNNWASK--VPSPLGT 82
           +   D +Y  A   YNNWA+K   P+PL T
Sbjct: 160 Y---DEMY--AGYPYNNWATKSLTPAPLST 184

May play a role in the development of anterior structures, and in particular, the brain and facies and in specifying the identity or structure of hindlimb.

Xenopus laevis (taxid: 8355)

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	92
242017518	302	Pituitary homeobox, putative [Pediculus	0.858	0.261	0.8	6e-28
148298661	387	pituitary homeobox1 [Bombyx mori] gi|121	0.923	0.219	0.739	6e-28
357615722	377	pituitary homeobox1 [Danaus plexippus]	0.923	0.225	0.729	2e-27
193624928	429	PREDICTED: pituitary homeobox homolog Pt	0.945	0.202	0.75	3e-27
189234679	517	PREDICTED: similar to pituitary homeobox	0.836	0.148	0.729	2e-21
270002832	508	Ptx1 [Tribolium castaneum]	0.836	0.151	0.729	2e-21
170053388	644	homeobox protein [Culex quinquefasciatus	0.771	0.110	0.690	3e-20
170061749	624	homeobox protein [Culex quinquefasciatus	0.771	0.113	0.690	4e-20
347963348	493	AGAP000190-PA [Anopheles gambiae str. PE	0.771	0.144	0.666	7e-20
295798066	276	ptx protein [Tribolium castaneum]	0.836	0.278	0.658	9e-20

>gi|242017518|ref|XP_002429235.1| Pituitary homeobox, putative [Pediculus humanus corporis] gi|212514124|gb|EEB16497.1| Pituitary homeobox, putative [Pediculus humanus corporis]

 Score =  127 bits (320), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 68/85 (80%), Positives = 73/85 (85%), Gaps = 6/85 (7%)

Query: 3   ELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPD 57
           E +A+W      RVRVWFKNRRAKWRKRERNAMNAAAAAA DFKNGF TQFNGLMQ F D
Sbjct: 86  EEIAMWTNLTEARVRVWFKNRRAKWRKRERNAMNAAAAAAADFKNGFGTQFNGLMQPFTD 145

Query: 58  TDSLYTSAYSSYNNWASKVPSPLGT 82
           TDSLY S+YS+YNNWA+KVPSPLGT
Sbjct: 146 TDSLY-SSYSTYNNWAAKVPSPLGT 169

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|148298661|ref|NP_001091838.1| pituitary homeobox1 [Bombyx mori] gi|121582239|dbj|BAF44479.1| pituitary homeobox1 [Bombyx mori]

 Score =  127 bits (320), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 71/96 (73%), Positives = 76/96 (79%), Gaps = 11/96 (11%)

Query: 3   ELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPD 57
           E +A+W      RVRVWFKNRRAKWRKRERNAMNAAAAAA DFKNGFSTQFNGLMQ FPD
Sbjct: 177 EEIAMWTNLTEARVRVWFKNRRAKWRKRERNAMNAAAAAAADFKNGFSTQFNGLMQPFPD 236

Query: 58  TDSLYTSAYSSYNNWASKVPSPLGTIG----VNDLG 89
           TD+LY+S    YNNWA+KVPSPLGT      VN LG
Sbjct: 237 TDALYSSY--PYNNWAAKVPSPLGTKSFPWPVNPLG 270

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357615722|gb|EHJ69804.1| pituitary homeobox1 [Danaus plexippus]

 Score =  126 bits (316), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 70/96 (72%), Positives = 76/96 (79%), Gaps = 11/96 (11%)

Query: 3   ELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPD 57
           E +A+W      RVRVWFKNRRAKWRKRERNAMNAAAAAA DFKNGFSTQFNGLMQ FPD
Sbjct: 172 EEIAMWTNLTEARVRVWFKNRRAKWRKRERNAMNAAAAAAADFKNGFSTQFNGLMQPFPD 231

Query: 58  TDSLYTSAYSSYNNWASKVPSPLGTIG----VNDLG 89
           T++LY+S    YNNWA+KVPSPLGT      VN LG
Sbjct: 232 TEALYSSY--PYNNWAAKVPSPLGTKSFPWPVNPLG 265

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193624928|ref|XP_001949221.1| PREDICTED: pituitary homeobox homolog Ptx1-like isoform 1 [Acyrthosiphon pisum] gi|328705300|ref|XP_003242759.1| PREDICTED: pituitary homeobox homolog Ptx1-like isoform 2 [Acyrthosiphon pisum] gi|328705302|ref|XP_003242760.1| PREDICTED: pituitary homeobox homolog Ptx1-like isoform 3 [Acyrthosiphon pisum]

 Score =  125 bits (314), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 72/96 (75%), Positives = 79/96 (82%), Gaps = 9/96 (9%)

Query: 3   ELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPD 57
           E +A+W      RVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGF TQFNGLMQ F D
Sbjct: 200 EEIAMWTNLTEARVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFGTQFNGLMQPFTD 259

Query: 58  TDSLYTSAYSSYNNWASKVPSPLGTI----GVNDLG 89
           TDSLY++AY+SYNNWA+KVPSPLG+      VN LG
Sbjct: 260 TDSLYSTAYTSYNNWATKVPSPLGSKTFPWSVNPLG 295

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189234679|ref|XP_970167.2| PREDICTED: similar to pituitary homeobox1 [Tribolium castaneum]

 Score =  106 bits (264), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 62/85 (72%), Positives = 68/85 (80%), Gaps = 8/85 (9%)

Query: 3   ELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPD 57
           E +A+W      RVRVWFKNRRAKWRKRERNAMNA  AAA +FK GF TQFNGLM TF D
Sbjct: 198 EEIAMWTNLTEARVRVWFKNRRAKWRKRERNAMNAMNAAA-EFKTGFGTQFNGLMPTFGD 256

Query: 58  TDSLYTSAYSSYNNWASKVPSPLGT 82
           TD+LY+S   SYNNWA+KVPSPLGT
Sbjct: 257 TDTLYSS--YSYNNWATKVPSPLGT 279

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270002832|gb|EEZ99279.1| Ptx1 [Tribolium castaneum]

 Score =  105 bits (263), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 62/85 (72%), Positives = 68/85 (80%), Gaps = 8/85 (9%)

Query: 3   ELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPD 57
           E +A+W      RVRVWFKNRRAKWRKRERNAMNA  AAA +FK GF TQFNGLM TF D
Sbjct: 198 EEIAMWTNLTEARVRVWFKNRRAKWRKRERNAMNAMNAAA-EFKTGFGTQFNGLMPTFGD 256

Query: 58  TDSLYTSAYSSYNNWASKVPSPLGT 82
           TD+LY+S   SYNNWA+KVPSPLGT
Sbjct: 257 TDTLYSS--YSYNNWATKVPSPLGT 279

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170053388|ref|XP_001862650.1| homeobox protein [Culex quinquefasciatus] gi|167873959|gb|EDS37342.1| homeobox protein [Culex quinquefasciatus]

 Score =  102 bits (253), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 58/84 (69%), Positives = 62/84 (73%), Gaps = 13/84 (15%)

Query: 3   ELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPD 57
           E +A+W      RVRVWFKNRRAKWRKRERN MNA AAA  DFKNGF  QF   +Q F D
Sbjct: 366 EEIAMWTNLTEARVRVWFKNRRAKWRKRERNQMNAIAAA--DFKNGFGPQF---VQPFAD 420

Query: 58  TDSLYTSAYSSYNNWASKVPSPLG 81
           TDSLY+S   SYNNWA KVPSPLG
Sbjct: 421 TDSLYSSY--SYNNWA-KVPSPLG 441

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170061749|ref|XP_001866371.1| homeobox protein [Culex quinquefasciatus] gi|167879868|gb|EDS43251.1| homeobox protein [Culex quinquefasciatus]

 Score =  102 bits (253), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 58/84 (69%), Positives = 62/84 (73%), Gaps = 13/84 (15%)

Query: 3   ELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPD 57
           E +A+W      RVRVWFKNRRAKWRKRERN MNA AAA  DFKNGF  QF   +Q F D
Sbjct: 276 EEIAMWTNLTEARVRVWFKNRRAKWRKRERNQMNAIAAA--DFKNGFGPQF---VQPFAD 330

Query: 58  TDSLYTSAYSSYNNWASKVPSPLG 81
           TDSLY+S   SYNNWA KVPSPLG
Sbjct: 331 TDSLYSSY--SYNNWA-KVPSPLG 351

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347963348|ref|XP_310944.5| AGAP000190-PA [Anopheles gambiae str. PEST] gi|333467242|gb|EAA06466.6| AGAP000190-PA [Anopheles gambiae str. PEST]

 Score =  101 bits (251), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 56/84 (66%), Positives = 62/84 (73%), Gaps = 13/84 (15%)

Query: 3   ELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPD 57
           E +A+W      RVRVWFKNRRAKWRKRERN MNA AAA  DFKNGF  QF   +Q F D
Sbjct: 279 EEIAMWTNLTEARVRVWFKNRRAKWRKRERNQMNAIAAA--DFKNGFGPQF---VQPFAD 333

Query: 58  TDSLYTSAYSSYNNWASKVPSPLG 81
           TD+LY+S   +YNNWA KVPSPLG
Sbjct: 334 TDTLYSSY--TYNNWA-KVPSPLG 354

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|295798066|emb|CBL87030.1| ptx protein [Tribolium castaneum]

 Score =  100 bits (250), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 56/85 (65%), Positives = 62/85 (72%), Gaps = 8/85 (9%)

Query: 3   ELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQTFPD 57
           E +A+W      RVRVWFKNRRAKWRKR R     A  AA +FK GF TQFNGLM TF D
Sbjct: 79  EEIAMWTNLTEARVRVWFKNRRAKWRKRGR-NAMNAMNAAAEFKTGFGTQFNGLMPTFGD 137

Query: 58  TDSLYTSAYSSYNNWASKVPSPLGT 82
           TD+LY+S   SYNNWA+KVPSPLGT
Sbjct: 138 TDTLYSSY--SYNNWATKVPSPLGT 160

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

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	92
FB|FBgn0020912	509	Ptx1 "Ptx1" [Drosophila melano	0.782	0.141	0.6	1.7e-16
ZFIN|ZDB-GENE-041229-4	293	pitx3 "paired-like homeodomain	0.728	0.228	0.541	9.1e-14
UNIPROTKB|F1MU46	314	PITX1 "Uncharacterized protein	0.771	0.226	0.488	2.9e-13
RGD|69253	315	Pitx1 "paired-like homeodomain	0.782	0.228	0.488	2.9e-13
UNIPROTKB|E1C143	292	PITX3 "Uncharacterized protein	0.728	0.229	0.529	3.4e-13
UNIPROTKB|E2RRG5	313	PITX1 "Uncharacterized protein	0.771	0.226	0.488	3.7e-13
UNIPROTKB|P78337	314	PITX1 "Pituitary homeobox 1" [	0.771	0.226	0.488	3.7e-13
MGI|MGI:107374	315	Pitx1 "paired-like homeodomain	0.771	0.225	0.488	3.8e-13
UNIPROTKB|P56673	311	PITX1 "Pituitary homeobox 1" [	0.760	0.225	0.5	6e-13
UNIPROTKB|D6RFI4	290	PITX2 "Pituitary homeobox 2" [	0.673	0.213	0.538	9.7e-13

FB|FBgn0020912 Ptx1 "Ptx1" [Drosophila melanogaster (taxid:7227)]

 Score = 212 (79.7 bits), Expect = 1.7e-16, P = 1.7e-16
 Identities = 51/85 (60%), Positives = 56/85 (65%)

Query:     3 ELMALWL-----RVRVWFKNRRAKWRKRERXXXXXXXXXXVDFKNGFSTQFNGLMQTFPD 57
             E +A+W      RVRVWFKNRRAKWRKRER           DFK+GF TQF   MQ F D
Sbjct:   295 EEIAMWTNLTEARVRVWFKNRRAKWRKRERNAMNAAVAAA-DFKSGFGTQF---MQPFAD 350

Query:    58 TDSLYTSAYSSYNNWASKVPSPLGT 82
              DSLY+S Y  YNNW +KVPSPLGT
Sbjct:   351 -DSLYSS-YP-YNNW-TKVPSPLGT 371

GO:0005634 "nucleus" evidence=ISS;IDA

GO:0048813 "dendrite morphogenesis" evidence=IMP

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

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

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

GO:0005667 "transcription factor complex" evidence=ISS

ZFIN|ZDB-GENE-041229-4 pitx3 "paired-like homeodomain transcription factor 3" [Danio rerio (taxid:7955)]

 Score = 180 (68.4 bits), Expect = 9.1e-14, P = 9.1e-14
 Identities = 46/85 (54%), Positives = 51/85 (60%)

Query:     3 ELMALWL-----RVRVWFKNRRAKWRKRERXXXXXXXXXXVDFKNGFSTQFNGLMQTFPD 57
             E +A+W      RVRVWFKNRRAKWRKRER             KNGF  QFNGLMQ +  
Sbjct:    91 EEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAELC------KNGFGAQFNGLMQPY-- 142

Query:    58 TDSLYTSAYSSYNNWASK--VPSPL 80
              D +Y S YS YNNWA+K    SPL
Sbjct:   143 -DDMY-SGYS-YNNWATKSLASSPL 164

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:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0035270 "endocrine system development" evidence=IMP

GO:0021984 "adenohypophysis development" evidence=IMP

GO:0043010 "camera-type eye development" evidence=IMP

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0002088 "lens development in camera-type eye" evidence=IMP

UNIPROTKB|F1MU46 PITX1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 177 (67.4 bits), Expect = 2.9e-13, P = 2.9e-13
 Identities = 44/90 (48%), Positives = 55/90 (61%)

Query:     1 MGELMALWL-----RVRVWFKNRRAKWRKRERXXXXXXXXXXVDF-KNGFSTQFNGLMQT 54
             M E +A+W      RVRVWFKNRRAKWRKRER          +D  K G+  QF+GL+Q 
Sbjct:   118 MREEIAVWTNLTEPRVRVWFKNRRAKWRKRERNQQ-------LDLCKGGYVPQFSGLVQP 170

Query:    55 FPDTDSLYTSAYSSYNNWASK--VPSPLGT 82
             +   D +Y + YS YNNWA+K   P+PL T
Sbjct:   171 Y---DDVYAAGYS-YNNWAAKSLAPAPLST 196

GO:0051216 "cartilage development" evidence=IEA

GO:0048625 "myoblast cell fate commitment" evidence=IEA

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

GO:0035116 "embryonic hindlimb morphogenesis" evidence=IEA

GO:0021983 "pituitary gland development" evidence=IEA

GO:0014707 "branchiomeric skeletal muscle development" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

GO:0000988 "protein binding transcription factor activity" evidence=IEA

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

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

RGD|69253 Pitx1 "paired-like homeodomain 1" [Rattus norvegicus (taxid:10116)]

 Score = 177 (67.4 bits), Expect = 2.9e-13, P = 2.9e-13
 Identities = 44/90 (48%), Positives = 55/90 (61%)

Query:     1 MGELMALWL-----RVRVWFKNRRAKWRKRERXXXXXXXXXXVDF-KNGFSTQFNGLMQT 54
             M E +A+W      RVRVWFKNRRAKWRKRER          +D  K G+  QF+GL+Q 
Sbjct:   118 MREEIAVWTNLTEPRVRVWFKNRRAKWRKRERNQQ-------LDLCKGGYVPQFSGLVQP 170

Query:    55 FPDTDSLYTSAYSSYNNWASK--VPSPLGT 82
             + D   +Y +A  SYNNWA+K   P+PL T
Sbjct:   171 YED---VYAAAGYSYNNWAAKSLAPAPLST 197

GO:0000988 "protein binding transcription factor activity" evidence=IEA;ISO

GO:0001501 "skeletal system development" evidence=ISO

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

GO:0005634 "nucleus" evidence=ISO

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

GO:0005730 "nucleolus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

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

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

GO:0014707 "branchiomeric skeletal muscle development" evidence=IEA;ISO

GO:0021983 "pituitary gland development" evidence=IEA;ISO

GO:0035116 "embryonic hindlimb morphogenesis" evidence=IEA;ISO

GO:0035137 "hindlimb morphogenesis" evidence=ISO

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

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

GO:0048625 "myoblast cell fate commitment" evidence=IEA;ISO

GO:0051216 "cartilage development" evidence=IEA;ISO

UNIPROTKB|E1C143 PITX3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 175 (66.7 bits), Expect = 3.4e-13, P = 3.4e-13
 Identities = 45/85 (52%), Positives = 51/85 (60%)

Query:     3 ELMALWL-----RVRVWFKNRRAKWRKRERXXXXXXXXXXVDFKNGFSTQFNGLMQTFPD 57
             E +A+W      RVRVWFKNRRAKWRKRER             KN F  QFNGLMQ +  
Sbjct:    91 EEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAELC------KNSFGAQFNGLMQPY-- 142

Query:    58 TDSLYTSAYSSYNNWASK--VPSPL 80
              D +Y+S YS YNNWA+K    SPL
Sbjct:   143 -DDMYSS-YS-YNNWATKGLATSPL 164

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:0002089 "lens morphogenesis in camera-type eye" evidence=IEA

GO:0007626 "locomotory behavior" evidence=IEA

GO:0030901 "midbrain development" evidence=IEA

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

GO:0048666 "neuron development" evidence=IEA

GO:0070306 "lens fiber cell differentiation" evidence=IEA

GO:0071542 "dopaminergic neuron differentiation" evidence=IEA

UNIPROTKB|E2RRG5 PITX1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 176 (67.0 bits), Expect = 3.7e-13, P = 3.7e-13
 Identities = 44/90 (48%), Positives = 55/90 (61%)

Query:     1 MGELMALWL-----RVRVWFKNRRAKWRKRERXXXXXXXXXXVDF-KNGFSTQFNGLMQT 54
             M E +A+W      RVRVWFKNRRAKWRKRER          +D  K G+  QF+GL+Q 
Sbjct:   117 MREEIAVWTNLTEPRVRVWFKNRRAKWRKRERNQQ-------LDLCKGGYVPQFSGLVQP 169

Query:    55 FPDTDSLYTSAYSSYNNWASK--VPSPLGT 82
             + D   +Y + YS YNNWA+K   P+PL T
Sbjct:   170 YED---VYAAGYS-YNNWAAKSLAPAPLST 195

GO:0051216 "cartilage development" evidence=IEA

GO:0048625 "myoblast cell fate commitment" evidence=IEA

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

GO:0035116 "embryonic hindlimb morphogenesis" evidence=IEA

GO:0021983 "pituitary gland development" evidence=IEA

GO:0014707 "branchiomeric skeletal muscle development" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

GO:0000988 "protein binding transcription factor activity" evidence=IEA

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

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

UNIPROTKB|P78337 PITX1 "Pituitary homeobox 1" [Homo sapiens (taxid:9606)]

 Score = 176 (67.0 bits), Expect = 3.7e-13, P = 3.7e-13
 Identities = 44/90 (48%), Positives = 55/90 (61%)

Query:     1 MGELMALWL-----RVRVWFKNRRAKWRKRERXXXXXXXXXXVDF-KNGFSTQFNGLMQT 54
             M E +A+W      RVRVWFKNRRAKWRKRER          +D  K G+  QF+GL+Q 
Sbjct:   118 MREEIAVWTNLTEPRVRVWFKNRRAKWRKRERNQQ-------LDLCKGGYVPQFSGLVQP 170

Query:    55 FPDTDSLYTSAYSSYNNWASK--VPSPLGT 82
             + D   +Y + YS YNNWA+K   P+PL T
Sbjct:   171 YED---VYAAGYS-YNNWAAKSLAPAPLST 196

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

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

GO:0000988 "protein binding transcription factor activity" evidence=IEA

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

GO:0005667 "transcription factor complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0014707 "branchiomeric skeletal muscle development" evidence=IEA

GO:0021983 "pituitary gland development" evidence=IEA

GO:0035116 "embryonic hindlimb morphogenesis" evidence=IEA

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

GO:0048625 "myoblast cell fate commitment" evidence=IEA

GO:0051216 "cartilage development" evidence=IEA

GO:0001501 "skeletal system development" evidence=TAS

GO:0009653 "anatomical structure morphogenesis" evidence=TAS

GO:0005730 "nucleolus" evidence=IDA

MGI|MGI:107374 Pitx1 "paired-like homeodomain transcription factor 1" [Mus musculus (taxid:10090)]

 Score = 176 (67.0 bits), Expect = 3.8e-13, P = 3.8e-13
 Identities = 44/90 (48%), Positives = 55/90 (61%)

Query:     1 MGELMALWL-----RVRVWFKNRRAKWRKRERXXXXXXXXXXVDF-KNGFSTQFNGLMQT 54
             M E +A+W      RVRVWFKNRRAKWRKRER          +D  K G+  QF+GL+Q 
Sbjct:   119 MREEIAVWTNLTEPRVRVWFKNRRAKWRKRERNQQ-------LDLCKGGYVPQFSGLVQP 171

Query:    55 FPDTDSLYTSAYSSYNNWASK--VPSPLGT 82
             + D   +Y + YS YNNWA+K   P+PL T
Sbjct:   172 YED---VYAAGYS-YNNWAAKSLAPAPLST 197

GO:0000988 "protein binding transcription factor activity" evidence=IPI

GO:0001501 "skeletal system development" evidence=IMP

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IDA

GO:0005667 "transcription factor complex" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0014707 "branchiomeric skeletal muscle development" evidence=IMP

GO:0021983 "pituitary gland development" evidence=IMP

GO:0035116 "embryonic hindlimb morphogenesis" evidence=IGI

GO:0035137 "hindlimb morphogenesis" evidence=IDA;IMP

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

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

GO:0048625 "myoblast cell fate commitment" evidence=IMP

GO:0051216 "cartilage development" evidence=IMP

UNIPROTKB|P56673 PITX1 "Pituitary homeobox 1" [Gallus gallus (taxid:9031)]

 Score = 174 (66.3 bits), Expect = 6.0e-13, P = 6.0e-13
 Identities = 45/90 (50%), Positives = 55/90 (61%)

Query:     1 MGELMALWL-----RVRVWFKNRRAKWRKRERXXXXXXXXXXVDF-KNGFSTQFNGLMQT 54
             M E +A+W      RVRVWFKNRRAKWRKRER          +D  KNG+  QF+GLMQ 
Sbjct:   117 MREEIAVWTNLTEPRVRVWFKNRRAKWRKRERNQQ-------MDLCKNGYVPQFSGLMQP 169

Query:    55 FPDTDSLYTSAYSSYNNWASK--VPSPLGT 82
             +   D +Y + Y  YNNWA+K   P+PL T
Sbjct:   170 Y---DDMY-AGYP-YNNWATKSLTPAPLST 194

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

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|D6RFI4 PITX2 "Pituitary homeobox 2" [Homo sapiens (taxid:9606)]

 Score = 171 (65.3 bits), Expect = 9.7e-13, P = 9.7e-13
 Identities = 42/78 (53%), Positives = 47/78 (60%)

Query:     3 ELMALWL-----RVRVWFKNRRAKWRKRERXXXXXXXXXXVDFKNGFSTQFNGLMQTFPD 57
             E +A+W      RVRVWFKNRRAKWRKRER             KNGF  QFNGLMQ +  
Sbjct:   116 EEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAELC------KNGFGPQFNGLMQPY-- 167

Query:    58 TDSLYTSAYSSYNNWASK 75
              D +Y   YS YNNWA+K
Sbjct:   168 -DDMYPG-YS-YNNWAAK 182

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O18400	PITX_DROME	No assigned EC number	0.6041	0.8586	0.1552	yes	N/A
Q6QU75	PITX3_DANRE	No assigned EC number	0.5641	0.6739	0.2116	yes	N/A
O93385	PITX2_CHICK	No assigned EC number	0.5512	0.6739	0.1861	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	92
pfam00046	57	pfam00046, Homeobox, Homeobox domain	1e-05
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	1e-04
smart00389	57	smart00389, HOX, Homeodomain	8e-04

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

 Score = 38.6 bits (91), Expect = 1e-05
 Identities = 10/15 (66%), Positives = 15/15 (100%)

Query: 10 RVRVWFKNRRAKWRK 24
          +V+VWF+NRRAKW++
Sbjct: 43 QVKVWFQNRRAKWKR 57

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 = 36.5 bits (85), Expect = 1e-04
 Identities = 9/17 (52%), Positives = 15/17 (88%)

Query: 10 RVRVWFKNRRAKWRKRE 26
          +V++WF+NRRAK ++ E
Sbjct: 43 QVKIWFQNRRAKLKRSE 59

Length = 59

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 34.1 bits (79), Expect = 8e-04
 Identities = 10/14 (71%), Positives = 14/14 (100%)

Query: 10 RVRVWFKNRRAKWR 23
          +V+VWF+NRRAKW+
Sbjct: 44 QVKVWFQNRRAKWK 57

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	92
KOG0485|consensus	268		99.39
KOG0489|consensus	261		99.37
KOG0484|consensus	125		99.34
KOG0488|consensus	309		99.32
KOG0842|consensus	307		99.29
KOG0486|consensus	351		99.24
KOG0850|consensus	245		99.24
KOG0487|consensus	308		99.21
KOG0848|consensus	317		99.18
KOG0492|consensus	246		99.15
KOG0843|consensus	197		99.12
KOG2251|consensus	228		98.95
KOG0847|consensus	288		98.92
KOG0494|consensus	332		98.91
KOG0844|consensus	408		98.88
KOG0491|consensus	194		98.85
KOG0483|consensus	198		98.83
KOG4577|consensus	383		98.69
KOG0493|consensus	342		98.45
KOG0490|consensus	235		98.43
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	98.26
COG5576	156	Homeodomain-containing transcription factor [Trans	98.19
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	97.76
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	97.67
KOG0849|consensus	354		97.57
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	97.31
KOG3802|consensus	398		96.95
KOG0775|consensus	304		95.75
KOG0774|consensus	334		94.61
KOG0490|consensus	235		94.53
KOG1168|consensus	385		94.16
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	93.14

>KOG0485|consensus

Probab=99.39  E-value=4.2e-13  Score=96.96  Aligned_cols=34  Identities=32%  Similarity=0.670  Sum_probs=29.0

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERNAMNAAA   34 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~~~~~~   34 (92)
                      +|..||++     +||||||||||.||||+.....+...
T Consensus       133 eRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ea~s  171 (268)
T KOG0485|consen  133 ERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLEAAS  171 (268)
T ss_pred             HHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhhhhh
Confidence            57778888     99999999999999999988776543

>KOG0489|consensus

Probab=99.37  E-value=5.2e-14  Score=103.42  Aligned_cols=30  Identities=30%  Similarity=0.665  Sum_probs=26.5

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERNAM   30 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~~   30 (92)
                      +|.|||..     +|||||||||||||||.++...
T Consensus       188 RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~  222 (261)
T KOG0489|consen  188 RRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS  222 (261)
T ss_pred             HHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence            57888887     9999999999999999888663

>KOG0484|consensus

Probab=99.34  E-value=1.1e-12  Score=85.49  Aligned_cols=35  Identities=57%  Similarity=0.832  Sum_probs=30.6

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHHHHHHHHHHh
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRERNAMNAAAAA   36 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~~~~~~~~   36 (92)
                      |||||.+     ++|||||||||+|.|||++.....+...
T Consensus        47 REEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~~~~~   86 (125)
T KOG0484|consen   47 REEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAKMAAK   86 (125)
T ss_pred             HHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHHhhhh
Confidence            8999999     9999999999999999999876655543

>KOG0488|consensus

Probab=99.32  E-value=3.2e-13  Score=101.58  Aligned_cols=32  Identities=28%  Similarity=0.577  Sum_probs=28.5

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERNAMNA   32 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~~~~   32 (92)
                      +|.+||.+     +|||+|||||||||||+...+.+.
T Consensus       201 DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~~  237 (309)
T KOG0488|consen  201 DRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGEL  237 (309)
T ss_pred             HHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhcc
Confidence            58999999     999999999999999999876544

>KOG0842|consensus

Probab=99.29  E-value=7e-13  Score=99.56  Aligned_cols=30  Identities=30%  Similarity=0.597  Sum_probs=27.6

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERNAM   30 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~~   30 (92)
                      |||+||..     |||||||||||.|.||+++.+.
T Consensus       182 ERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~  216 (307)
T KOG0842|consen  182 EREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKA  216 (307)
T ss_pred             hHHHHHHhcCCCchheeeeeecchhhhhhhhhhhh
Confidence            79999999     9999999999999999988664

>KOG0486|consensus

Probab=99.24  E-value=7.2e-12  Score=94.26  Aligned_cols=72  Identities=61%  Similarity=1.005  Sum_probs=54.2

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHHHHHHHHHHhhhccCCCCCCCCC-CCCCCCCCCCCCCCccccccCCCCCC
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFN-GLMQTFPDTDSLYTSAYSSYNNWASK   75 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~p~~~~~~~~s~~~~~~~~~~~~   75 (92)
                      |||+|.+     .+|+|||.|||+||||.++..+      +..++.+|...+. ++++|+-+   .|......|++|...
T Consensus       142 rEEIavwtNlTE~rvrvwfknrrakwrkrErN~~------ae~~k~~f~~~~~t~~~~P~~~---vy~~~~y~ynnWs~~  212 (351)
T KOG0486|consen  142 REEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ------AELAKGGFGPQFLTGLMQPYFD---VYPLNPYSYNNWSAK  212 (351)
T ss_pred             hhHHHhhccccchhhhhhcccchhhhhhhhhhHH------HHhhhcCCcccccccccCchhh---hcccCCccccccchh
Confidence            8999999     9999999999999999888664      2256777887776 67777766   555222289999984


Q ss_pred             --CCCCCCC
Q psy15889         76 --VPSPLGT   82 (92)
Q Consensus        76 --~p~P~~~   82 (92)
                        .++|+++
T Consensus       213 ql~da~l~t  221 (351)
T KOG0486|consen  213 QLNDAPLGT  221 (351)
T ss_pred             hcccccccc
Confidence              3556655

>KOG0850|consensus

Probab=99.24  E-value=1.8e-12  Score=93.92  Aligned_cols=29  Identities=31%  Similarity=0.654  Sum_probs=26.5

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERNA   29 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~   29 (92)
                      ||.|||..     +||||||||||.|.||..+.+
T Consensus       151 ERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g  184 (245)
T KOG0850|consen  151 ERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQG  184 (245)
T ss_pred             HHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcC
Confidence            69999999     999999999999999988843

>KOG0487|consensus

Probab=99.21  E-value=2.7e-12  Score=96.44  Aligned_cols=29  Identities=31%  Similarity=0.494  Sum_probs=25.5

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERNA   29 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~   29 (92)
                      +|-||++.     +||||||||||||.||..++.
T Consensus       264 KR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~  297 (308)
T KOG0487|consen  264 KRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN  297 (308)
T ss_pred             HHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence            47788887     999999999999999988754

>KOG0848|consensus

Probab=99.18  E-value=2.2e-11  Score=90.24  Aligned_cols=30  Identities=37%  Similarity=0.550  Sum_probs=26.0

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRERNAMN   31 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~~~   31 (92)
                      +.|||..     +||||||||||+|.||+++.+..
T Consensus       229 KSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~~  263 (317)
T KOG0848|consen  229 KSELAATLGLSERQVKIWFQNRRAKERKDNKKKRL  263 (317)
T ss_pred             hHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHHH
Confidence            4678777     99999999999999999987753

>KOG0492|consensus

Probab=99.15  E-value=1.8e-11  Score=88.02  Aligned_cols=37  Identities=27%  Similarity=0.448  Sum_probs=30.5

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHHHHHHHHHhh
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERNAMNAAAAAA   37 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~~~~~~~~~   37 (92)
                      +|.|++..     +||||||||||+|.||.++.+.+....+.
T Consensus       173 EraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~Ek~kmaa  214 (246)
T KOG0492|consen  173 ERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELEKLKMAA  214 (246)
T ss_pred             HHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHHHhhhhh
Confidence            46676665     99999999999999999998887766543

>KOG0843|consensus

Probab=99.12  E-value=1.7e-11  Score=86.31  Aligned_cols=29  Identities=31%  Similarity=0.610  Sum_probs=26.1

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERNA   29 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~   29 (92)
                      +|++||+.     +||||||||||+|.||.....
T Consensus       131 eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~  164 (197)
T KOG0843|consen  131 ERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED  164 (197)
T ss_pred             HHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence            58999998     999999999999999977654

>KOG2251|consensus

Probab=98.95  E-value=5.1e-10  Score=80.78  Aligned_cols=29  Identities=55%  Similarity=0.867  Sum_probs=26.5

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERNA   29 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~   29 (92)
                      .|||||.+     .||||||.|||+|||++++..
T Consensus        66 ~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   66 MREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             HHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            48999999     999999999999999998864

>KOG0847|consensus

Probab=98.92  E-value=2.1e-10  Score=83.27  Aligned_cols=32  Identities=41%  Similarity=0.747  Sum_probs=26.8

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERNAMNA   32 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~~~~   32 (92)
                      +|.+||..     .+|+|||||||+||||+...++.+
T Consensus       196 ~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmas  232 (288)
T KOG0847|consen  196 DRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMAS  232 (288)
T ss_pred             hHHHhhccccccHHHHHHHHhcchhhhhhhhccchhh
Confidence            46777777     899999999999999988776544

>KOG0494|consensus

Probab=98.91  E-value=2.9e-10  Score=84.15  Aligned_cols=28  Identities=54%  Similarity=0.930  Sum_probs=24.1

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRERNA   29 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~   29 (92)
                      ||-||.+     -||+|||||||+||||.++.-
T Consensus       171 re~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w  203 (332)
T KOG0494|consen  171 REMLADKTELPEDRIQVWFQNRRAKWRKTEKRW  203 (332)
T ss_pred             HHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence            5667777     799999999999999998864

>KOG0844|consensus

Probab=98.88  E-value=5.3e-10  Score=84.41  Aligned_cols=28  Identities=29%  Similarity=0.449  Sum_probs=24.9

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERN   28 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~   28 (92)
                      +|+|||..     +.|||||||||||.|||+-.
T Consensus       210 rRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla  242 (408)
T KOG0844|consen  210 RRCELAAALNLPETTIKVWFQNRRMKDKRQRLA  242 (408)
T ss_pred             hhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence            58999888     99999999999999997653

>KOG0491|consensus

Probab=98.85  E-value=1.1e-09  Score=76.47  Aligned_cols=29  Identities=38%  Similarity=0.641  Sum_probs=25.0

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERNA   29 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~   29 (92)
                      +|.|||..     +|||.||||||||.||+.+..
T Consensus       129 e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~  162 (194)
T KOG0491|consen  129 ERQELANALSLSETQVKTWFQNRRMKHKKQQRNN  162 (194)
T ss_pred             HHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence            36788776     999999999999999988854

>KOG0483|consensus

Probab=98.83  E-value=4.5e-10  Score=80.11  Aligned_cols=27  Identities=37%  Similarity=0.783  Sum_probs=22.8

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRERN   28 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~~   28 (92)
                      +..||..     +||.|||||||||||.++..
T Consensus        80 K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE  111 (198)
T KOG0483|consen   80 KKKLAKELGLQPRQVAVWFQNRRARWKTKQLE  111 (198)
T ss_pred             HHHHHHhhCCChhHHHHHHhhccccccchhhh
Confidence            4567777     99999999999999987654

>KOG4577|consensus

Probab=98.69  E-value=3.9e-09  Score=79.26  Aligned_cols=29  Identities=38%  Similarity=0.611  Sum_probs=25.7

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERNA   29 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~   29 (92)
                      +||+|+.+     +.|||||||||||.||.++..
T Consensus       196 VREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDA  229 (383)
T KOG4577|consen  196 VREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDA  229 (383)
T ss_pred             HHHHhhhccCcceeehhhhhhhhhHHHHhhhhhc
Confidence            48999988     899999999999999987753

>KOG0493|consensus

Probab=98.45  E-value=3.5e-08  Score=73.36  Aligned_cols=27  Identities=30%  Similarity=0.570  Sum_probs=23.5

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      +|.+||.+     .||||||||.|+|.||...
T Consensus       275 RRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTg  306 (342)
T KOG0493|consen  275 RRQELAQELGLNESQIKIWFQNKRAKIKKSTG  306 (342)
T ss_pred             HHHHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence            47788888     9999999999999998554

>KOG0490|consensus

Probab=98.43  E-value=5.9e-08  Score=68.36  Aligned_cols=26  Identities=65%  Similarity=0.993  Sum_probs=23.6

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      |++||..     .+|+|||||||+||+++++
T Consensus        90 r~~la~~~~~~e~rVqvwFqnrrak~r~~~~  120 (235)
T KOG0490|consen   90 RECLALLLTGDEFRVQVWFQNRRAKDRKEER  120 (235)
T ss_pred             HHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence            6788877     9999999999999999886

>PF00046 Homeobox: Homeobox domain not present here

Probab=98.26  E-value=9.1e-08  Score=54.63  Aligned_cols=23  Identities=43%  Similarity=0.608  Sum_probs=20.3

Q ss_pred             hhhhhhh-----cccccccccchhHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRK   24 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr   24 (92)
                      +++||..     .+|++||+|||.|+||
T Consensus        30 ~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen   30 REELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             HHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccccccCHHHhHHHhCc
Confidence            5678877     9999999999999986

; 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 ....

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=98.19  E-value=4.4e-07  Score=62.64  Aligned_cols=31  Identities=29%  Similarity=0.575  Sum_probs=25.4

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRERNAMNA   32 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~~~~   32 (92)
                      |.+|+..     .-|||||||||+|.|+....+...
T Consensus        81 r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~~~  116 (156)
T COG5576          81 RIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQ  116 (156)
T ss_pred             HHHHHHhcCCChhhhhhhhchHHHHHHHhcccchhc
Confidence            5677777     789999999999999988765443

>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=97.76  E-value=2.9e-06  Score=48.05  Aligned_cols=23  Identities=43%  Similarity=0.773  Sum_probs=19.7

Q ss_pred             hhhhhhh-----cccccccccchhHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRK   24 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr   24 (92)
                      +++||..     .+|+.||+|||.+.++
T Consensus        30 ~~~la~~~~l~~~qV~~WF~nrR~~~~~   57 (59)
T cd00086          30 REELAKELGLTERQVKIWFQNRRAKLKR   57 (59)
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence            4667777     9999999999999876

>smart00389 HOX Homeodomain

Probab=97.67  E-value=3.4e-06  Score=47.56  Aligned_cols=22  Identities=55%  Similarity=1.022  Sum_probs=18.0

Q ss_pred             hhhhhhh-----cccccccccchhHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWR   23 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~r   23 (92)
                      +++||..     .+|++||+|||.+.+
T Consensus        30 ~~~la~~~~l~~~qV~~WF~nrR~~~~   56 (56)
T smart00389       30 REELAAKLGLSERQVKVWFQNRRAKWK   56 (56)
T ss_pred             HHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence            4667777     899999999998753

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

>KOG0849|consensus

Probab=97.57  E-value=1.4e-05  Score=61.34  Aligned_cols=27  Identities=56%  Similarity=1.020  Sum_probs=24.6

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRERN   28 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~~   28 (92)
                      ||+||.+     .+|+|||+|||+||+|+...
T Consensus       206 Re~La~~i~l~e~riqvwf~nrra~~rr~~~~  237 (354)
T KOG0849|consen  206 RETLAKETGLPEPRVQVWFQNRRAKWRRQHRD  237 (354)
T ss_pred             HHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence            7889988     99999999999999998853

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=97.31  E-value=5.8e-05  Score=44.27  Aligned_cols=19  Identities=16%  Similarity=0.223  Sum_probs=15.9

Q ss_pred             Chhhhhhh-----cccccccccch
Q psy15889          1 MGELMALW-----LRVRVWFKNRR   19 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRR   19 (92)
                      +|++||..     .+|||||||-+
T Consensus        34 ~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565        34 EVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             HHHHHHHHhCCCHHHeeeecccCC
Confidence            37788888     89999999964

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

>KOG3802|consensus

Probab=96.95  E-value=0.00016  Score=56.30  Aligned_cols=24  Identities=42%  Similarity=0.500  Sum_probs=19.8

Q ss_pred             hhhhh-----cccccccccchhHHHHHHH
Q psy15889          4 LMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         4 eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      +||.+     ..|+|||-|||.|.||...
T Consensus       326 ~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  326 HIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             HHHHHhccccceEEEEeeccccccccCCC
Confidence            45555     8899999999999998665

>KOG0775|consensus

Probab=95.75  E-value=0.003  Score=47.43  Aligned_cols=22  Identities=41%  Similarity=0.548  Sum_probs=18.8

Q ss_pred             hhhhhhh-----cccccccccchhHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWR   23 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~r   23 (92)
                      +.|||..     +||-.||.|||.+.|
T Consensus       206 KReLA~aTgLt~tQVsNWFKNRRQRDR  232 (304)
T KOG0775|consen  206 KRELAEATGLTITQVSNWFKNRRQRDR  232 (304)
T ss_pred             HHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence            4578888     888889999999977

>KOG0774|consensus

Probab=94.61  E-value=0.12  Score=39.03  Aligned_cols=27  Identities=30%  Similarity=0.517  Sum_probs=22.5

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRERN   28 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~~   28 (92)
                      ++|||.+     +||--||.|.|.+.+|....
T Consensus       221 K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k  252 (334)
T KOG0774|consen  221 KEELAKQCNITVSQVSNWFGNKRIRYKKNMGK  252 (334)
T ss_pred             HHHHHHHcCceehhhccccccceeehhhhhhh
Confidence            5789998     78888999999999986543

>KOG0490|consensus

Probab=94.53  E-value=0.016  Score=40.57  Aligned_cols=26  Identities=50%  Similarity=0.745  Sum_probs=21.0

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      +++|+..     ..|+|||||+|++.++...
T Consensus       183 ~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  183 REQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             HHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            4566665     7889999999999998655

>KOG1168|consensus

Probab=94.16  E-value=0.024  Score=43.19  Aligned_cols=19  Identities=47%  Similarity=0.786  Sum_probs=16.8

Q ss_pred             cccccccccchhHHHHHHH
Q psy15889          9 LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         9 ~qVkiWFQNRRaK~rr~~~   27 (92)
                      ..|+|||.|.|.|.||...
T Consensus       351 NVVRVWFCNQRQKQKRm~~  369 (385)
T KOG1168|consen  351 NVVRVWFCNQRQKQKRMKR  369 (385)
T ss_pred             ceEEEEeeccHHHHHHhhh
Confidence            8899999999999988554

>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=93.14  E-value=0.0098  Score=32.20  Aligned_cols=20  Identities=30%  Similarity=0.489  Sum_probs=16.1

Q ss_pred             hhhhhhh-----cccccccccchhH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAK   21 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK   21 (92)
                      +++||..     .||..||-|.|.+
T Consensus        16 k~~L~~~tgls~~Qi~~WF~NaRrR   40 (40)
T PF05920_consen   16 KEELAKQTGLSRKQISNWFINARRR   40 (40)
T ss_dssp             HHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHhHcc
Confidence            5678777     8999999998854

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	92
2l7m_P	68	Solution Structure Of The Pitx2 Homeodomain R24h Mu		3e-04
2l7f_P	68	Solution Structure Of The Pitx2 Homeodomain Length		3e-04

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/29 (68%), Positives = 22/29 (75%), Gaps = 5/29 (17%)
Query: 3  ELMALWL-----RVRVWFKNRRAKWRKRE 26
          E +A+W      RVRVWFKNRRAKWRKRE
Sbjct: 34 EEIAVWTNLTEARVRVWFKNRRAKWRKRE 62

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

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/29 (68%), Positives = 22/29 (75%), Gaps = 5/29 (17%)
Query: 3  ELMALWL-----RVRVWFKNRRAKWRKRE 26
          E +A+W      RVRVWFKNRRAKWRKRE
Sbjct: 34 EEIAVWTNLTEARVRVWFKNRRAKWRKRE 62

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	92
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	6e-11
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	3e-10
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	6e-10
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	6e-10
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	2e-09
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	2e-09
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	3e-09
1uhs_A	72	HOP, homeodomain only protein; structural genomics	5e-09
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	1e-08
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	2e-08
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	3e-08
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	8e-08
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	1e-07
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	2e-07
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	3e-07
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	1e-06
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	7e-06
1lfb_A	99	Liver transcription factor (LFB1); transcription r	1e-05
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	2e-05
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	4e-05
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	9e-05
1e3o_C	160	Octamer-binding transcription factor 1; transcript	1e-04
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	2e-04
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	7e-04

>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 = 52.3 bits (126), Expect = 6e-11
 Identities = 20/36 (55%), Positives = 23/36 (63%), Gaps = 5/36 (13%)

Query: 1  MGELMALWL-----RVRVWFKNRRAKWRKRERNAMN 31
            E +A+W      RVRVWFKNRRAKWRKRE   + 
Sbjct: 32 TREEIAVWTNLTEARVRVWFKNRRAKWRKREEFIVT 67

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

 Score = 50.8 bits (122), Expect = 3e-10
 Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 5/33 (15%)

Query: 1  MGELMALWL-----RVRVWFKNRRAKWRKRERN 28
            E +A        R++VWF+NRRA+ RK+  +
Sbjct: 47 TREELAQRTNLTEARIQVWFQNRRARLRKQHTS 79

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

 Score = 49.2 bits (118), Expect = 6e-10
 Identities = 15/30 (50%), Positives = 23/30 (76%), Gaps = 5/30 (16%)

Query: 3  ELMALWL-----RVRVWFKNRRAKWRKRER 27
          E +A+ +     R++VWF+NRRAKWRK+E+
Sbjct: 30 EELAMKIGLTEARIQVWFQNRRAKWRKQEK 59

>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 = 49.7 bits (119), Expect = 6e-10
 Identities = 17/41 (41%), Positives = 25/41 (60%), Gaps = 5/41 (12%)

Query: 1  MGELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAA 36
          M E +AL +     RV+VWFKNRRAK R++++   N   + 
Sbjct: 36 MREEVALKINLPESRVQVWFKNRRAKCRQQQQQQQNGGQSG 76

>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 = 48.5 bits (116), Expect = 2e-09
 Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 5/34 (14%)

Query: 1  MGELMALWL-----RVRVWFKNRRAKWRKRERNA 29
            E +A  +     +V VWFKNRRAKWR+   ++
Sbjct: 36 TREQLARKVHLREEKVEVWFKNRRAKWRRSGPSS 69

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

 Score = 48.5 bits (116), Expect = 2e-09
 Identities = 12/28 (42%), Positives = 17/28 (60%)

Query: 10 RVRVWFKNRRAKWRKRERNAMNAAAAAA 37
          R++VWF NRRAKWR+ E+       +  
Sbjct: 50 RIQVWFSNRRAKWRREEKLRNQRRQSGP 77

>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 = 48.1 bits (115), Expect = 3e-09
 Identities = 9/20 (45%), Positives = 16/20 (80%)

Query: 10 RVRVWFKNRRAKWRKRERNA 29
          R+++WF+NRRAK ++  R +
Sbjct: 44 RIQIWFQNRRAKLKRSHRES 63

>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 = 47.4 bits (113), Expect = 5e-09
 Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 5/30 (16%)

Query: 3  ELMALWL-----RVRVWFKNRRAKWRKRER 27
           L+A        + + WFK R A+WR+ E 
Sbjct: 33 CLIAAEAGLTEEQTQKWFKQRLAEWRRSEG 62

>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 = 46.2 bits (110), Expect = 1e-08
 Identities = 9/18 (50%), Positives = 13/18 (72%)

Query: 10 RVRVWFKNRRAKWRKRER 27
           +RVWF+N+R K +KR  
Sbjct: 46 VIRVWFQNKRCKDKKRSI 63

>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 = 45.9 bits (109), Expect = 2e-08
 Identities = 9/27 (33%), Positives = 15/27 (55%)

Query: 10 RVRVWFKNRRAKWRKRERNAMNAAAAA 36
           ++VWF+N RAK+R+      N   + 
Sbjct: 50 VLQVWFQNARAKFRRNLLRQENGGVSG 76

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

 Score = 45.5 bits (108), Expect = 3e-08
 Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 5/30 (16%)

Query: 3  ELMALWL-----RVRVWFKNRRAKWRKRER 27
           L+A        + + WFK R A+WR+ E 
Sbjct: 34 CLIAAEAGLTEEQTQKWFKQRLAEWRRSEG 63

>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 = 44.3 bits (105), Expect = 8e-08
 Identities = 8/20 (40%), Positives = 12/20 (60%)

Query: 10 RVRVWFKNRRAKWRKRERNA 29
           + VWF+N R K RK   ++
Sbjct: 50 VIVVWFQNARQKARKSGPSS 69

>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 = 44.0 bits (104), Expect = 1e-07
 Identities = 9/20 (45%), Positives = 14/20 (70%)

Query: 10 RVRVWFKNRRAKWRKRERNA 29
           V+VWF+N RA+ RK   ++
Sbjct: 60 VVQVWFQNTRARERKSGPSS 79

>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 = 43.1 bits (102), Expect = 2e-07
 Identities = 5/20 (25%), Positives = 11/20 (55%)

Query: 10 RVRVWFKNRRAKWRKRERNA 29
           ++ WF+N   K R+   ++
Sbjct: 50 VIKHWFRNTLFKERQSGPSS 69

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

 Score = 43.5 bits (102), Expect = 3e-07
 Identities = 8/25 (32%), Positives = 13/25 (52%)

Query: 10 RVRVWFKNRRAKWRKRERNAMNAAA 34
          +V  WF NRR + ++R   A    +
Sbjct: 65 KVYNWFANRRKEIKRRANIAAILES 89

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

 Score = 41.3 bits (97), Expect = 1e-06
 Identities = 7/26 (26%), Positives = 12/26 (46%)

Query: 10 RVRVWFKNRRAKWRKRERNAMNAAAA 35
           VR WF +RR   R  + +    ++ 
Sbjct: 51 EVRKWFSDRRYHCRNLKGSRSGPSSG 76

>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 = 40.8 bits (95), Expect = 7e-06
 Identities = 8/15 (53%), Positives = 9/15 (60%)

Query: 10  RVRVWFKNRRAKWRK 24
            VRVWF NRR   + 
Sbjct: 136 VVRVWFSNRRQTLKN 150

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

 Score = 39.0 bits (90), Expect = 1e-05
 Identities = 10/24 (41%), Positives = 14/24 (58%)

Query: 9  LRVRVWFKNRRAKWRKRERNAMNA 32
          +RV  WF NRR +   R + AM+ 
Sbjct: 72 VRVYNWFANRRKEEAFRHKLAMDT 95

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

 Score = 39.6 bits (92), Expect = 2e-05
 Identities = 10/20 (50%), Positives = 12/20 (60%)

Query: 10  RVRVWFKNRRAKWRKRERNA 29
            VRVWF NRR K ++    A
Sbjct: 142 VVRVWFCNRRQKEKRMTPAA 161

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

 Score = 38.4 bits (89), Expect = 4e-05
 Identities = 8/15 (53%), Positives = 11/15 (73%)

Query: 10  RVRVWFKNRRAKWRK 24
            VRVWF NRR + ++
Sbjct: 130 VVRVWFCNRRQREKR 144

>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 = 37.8 bits (87), Expect = 9e-05
 Identities = 9/15 (60%), Positives = 11/15 (73%)

Query: 10  RVRVWFKNRRAKWRK 24
            VRVWF NRR K ++
Sbjct: 139 VVRVWFSNRRQKGKR 153

>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 = 37.3 bits (86), Expect = 1e-04
 Identities = 8/15 (53%), Positives = 11/15 (73%)

Query: 10  RVRVWFKNRRAKWRK 24
            +RVWF NRR K ++
Sbjct: 144 VIRVWFSNRRQKEKR 158

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

 Score = 36.0 bits (83), Expect = 2e-04
 Identities = 12/27 (44%), Positives = 16/27 (59%)

Query: 11 VRVWFKNRRAKWRKRERNAMNAAAAAA 37
          V+ WF+NRR KWR++      A   AA
Sbjct: 61 VKTWFQNRRTKWRRQTAEEREAERQAA 87

>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 = 34.0 bits (78), Expect = 7e-04
 Identities = 3/19 (15%), Positives = 10/19 (52%)

Query: 10 RVRVWFKNRRAKWRKRERN 28
           ++ WF + R + ++   +
Sbjct: 47 EIKKWFSDHRYRCQRGIVH 65

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	92
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	99.41
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.11
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.1
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.1
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.08
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.05
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.05
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.04
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.03
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.03
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.03
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.02
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.01
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.0
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.0
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.0
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	98.99
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	98.98
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	98.97
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	98.97
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	98.97
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	98.96
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	98.96
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	98.96
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	98.96
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	98.95
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	98.95
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	98.94
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	98.94
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	98.93
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	98.93
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	98.93
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	98.93
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	98.91
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	98.91
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	98.9
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	98.89
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	98.88
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	98.88
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	98.88
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	98.88
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	98.87
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	98.87
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	98.85
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	98.84
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	98.83
2e19_A	64	Transcription factor 8; homeobox domain, structura	98.83
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	98.83
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	98.82
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	98.81
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	98.8
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	98.78
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	98.78
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	98.75
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	98.74
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	98.74
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	98.73
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	98.72
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	98.71
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	98.69
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	98.61
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	98.5
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	98.44
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	98.21
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	98.07
1lfb_A	99	Liver transcription factor (LFB1); transcription r	98.02

>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=99.41  E-value=5.9e-14  Score=74.96  Aligned_cols=21  Identities=48%  Similarity=1.107  Sum_probs=18.8

Q ss_pred             cccccccccchhHHHHHHHHH
Q psy15889          9 LRVRVWFKNRRAKWRKRERNA   29 (92)
Q Consensus         9 ~qVkiWFQNRRaK~rr~~~~~   29 (92)
                      +||+||||||||||||.+...
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~   21 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFND   21 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHH
T ss_pred             CCceeccHHHHHHHHHHhHHH
Confidence            589999999999999988764

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

Probab=99.11  E-value=4.1e-12  Score=72.47  Aligned_cols=25  Identities=40%  Similarity=0.860  Sum_probs=22.4

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKR   25 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~   25 (92)
                      +|++||..     .+|+|||||||+||||+
T Consensus        26 ~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~   55 (56)
T 3a03_A           26 ERAALAKALRMTDAQVKTWFQNRRTKWRRQ   55 (56)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCcCHHHhhHhhHHhhhhhccc
Confidence            36788888     99999999999999985

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

Probab=99.10  E-value=2.6e-13  Score=84.93  Aligned_cols=29  Identities=10%  Similarity=0.227  Sum_probs=24.7

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERNA   29 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~   29 (92)
                      +|++||..     +||+|||||||+|||+.++..
T Consensus        40 ~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~~~   73 (89)
T 2ecb_A           40 ELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKM   73 (89)
T ss_dssp             HHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCC
T ss_pred             HHHHHHHHhCcChHHCeecccccchHHHHHHHHh
Confidence            47888888     999999999999999866543

>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=99.10  E-value=1.4e-12  Score=77.17  Aligned_cols=24  Identities=21%  Similarity=0.354  Sum_probs=21.7

Q ss_pred             Chhhhhhh-----cccccccccchhHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRK   24 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr   24 (92)
                      +|++||.+     +||||||||||+|+|+
T Consensus        30 ~r~~LA~~l~LterQVkvWFqNRR~k~k~   58 (64)
T 1x2m_A           30 RLEGLSKQLDWDVRSIQRWFRQRRNQEKP   58 (64)
T ss_dssp             HHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHhccCC
Confidence            37889988     9999999999999886

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

Probab=99.08  E-value=1.2e-11  Score=75.16  Aligned_cols=28  Identities=50%  Similarity=0.919  Sum_probs=25.2

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRERNA   29 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~   29 (92)
                      |++||..     .+|+|||||||+||||+.+..
T Consensus        37 r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~   69 (80)
T 2cue_A           37 RERLAAKIDLPEARIQVWFSNRRAKWRREEKLR   69 (80)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhh
Confidence            6788888     999999999999999988765

>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=99.05  E-value=1.5e-11  Score=74.22  Aligned_cols=27  Identities=33%  Similarity=0.615  Sum_probs=24.3

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRERN   28 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~~   28 (92)
                      |++||..     .+|+|||||||+|||+..+.
T Consensus        43 r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k~   74 (77)
T 1puf_A           43 RYEVARLLNLTERQVKIWFQNRRMKMKKINKD   74 (77)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHHHHHHhhhh
Confidence            6788888     99999999999999998764

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

Probab=99.05  E-value=8.3e-12  Score=78.02  Aligned_cols=32  Identities=34%  Similarity=0.686  Sum_probs=25.5

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERNAMNA   32 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~~~~   32 (92)
                      +|++||..     .+|+|||||||+|||++.....+.
T Consensus        46 ~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~~~   82 (93)
T 3a01_A           46 ERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEEREA   82 (93)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC---
T ss_pred             HHHHHHHHhCCChhhcccccHhhhhhhhhhhHHHHHH
Confidence            37788888     999999999999999988765443

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

Probab=99.04  E-value=1.4e-11  Score=73.33  Aligned_cols=25  Identities=12%  Similarity=0.272  Sum_probs=22.6

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKR   25 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~   25 (92)
                      +|++||..     ++|+|||||||+|||+.
T Consensus        33 er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg   62 (66)
T 3nau_A           33 EVYRLIEVTGLARSEIKKWFSDHRYRCQRG   62 (66)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCcCHHHhhHhcccchhhhhcc
Confidence            47889988     99999999999999974

>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=99.03  E-value=1.2e-11  Score=73.66  Aligned_cols=26  Identities=38%  Similarity=0.638  Sum_probs=23.4

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      |++||..     .+|+|||||||+||||..+
T Consensus        32 r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~~   62 (72)
T 1uhs_A           32 LCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   62 (72)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHCcCHHHhhHHhHHHHHHHhhhcc
Confidence            6788888     9999999999999999764

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

Probab=99.03  E-value=7.3e-12  Score=72.16  Aligned_cols=26  Identities=58%  Similarity=1.117  Sum_probs=20.5

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      |++||..     .+|+|||||||+||||+++
T Consensus        29 r~~La~~l~l~~~qV~~WFqNrR~k~rk~~k   59 (60)
T 3a02_A           29 REELAMKIGLTEARIQVWFQNRRAKWRKQEK   59 (60)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHHHHHHC----
T ss_pred             HHHHHHHHCcCHHHHHHHhhhhhhhhHhhcc
Confidence            6788888     9999999999999999765

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

Probab=99.03  E-value=1.5e-11  Score=73.45  Aligned_cols=26  Identities=38%  Similarity=0.638  Sum_probs=23.5

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      |++||..     .+|+|||||||+||||..+
T Consensus        33 r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~~   63 (73)
T 2hi3_A           33 LCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   63 (73)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHHHHHHhcc
Confidence            6788888     9999999999999999775

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

Probab=99.02  E-value=7.3e-12  Score=75.14  Aligned_cols=25  Identities=16%  Similarity=0.365  Sum_probs=22.1

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKR   25 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~   25 (92)
                      +|++||.+     ++|+|||||||+|||+.
T Consensus        38 ~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~   67 (72)
T 2cqx_A           38 RLKGLSKQLDWSVRKIQCWFRHRRNQDKPS   67 (72)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHhCCChhhcchhhhhcccCCCCC
Confidence            37889888     99999999999999863

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

Probab=99.01  E-value=1.4e-11  Score=71.60  Aligned_cols=25  Identities=40%  Similarity=0.934  Sum_probs=22.3

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRE   26 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~   26 (92)
                      |++||..     .+|+|||||||+||||.+
T Consensus        33 r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   62 (63)
T 2h1k_A           33 RVELAVMLNLTERHIKIWFQNRRMKWKKEE   62 (63)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHhCcCHHHhhHHHHhhhhhhhhhc
Confidence            6788888     999999999999999863

>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=99.00  E-value=2.2e-11  Score=71.78  Aligned_cols=28  Identities=71%  Similarity=1.260  Sum_probs=24.4

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERN   28 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~   28 (92)
                      +|++||..     .+|+|||||||+|||+.++.
T Consensus        32 ~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~~   64 (68)
T 1yz8_P           32 TREEIAVWTNLTEARVRVWFKNRRAKWRKREEF   64 (68)
T ss_dssp             TTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhhc
Confidence            47788888     99999999999999997763

>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=99.00  E-value=2.6e-11  Score=73.11  Aligned_cols=27  Identities=30%  Similarity=0.612  Sum_probs=23.8

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRERN   28 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~~   28 (92)
                      |++||..     .+|+|||||||+|+|+....
T Consensus        39 r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~   70 (77)
T 1nk2_P           39 REHLASLIRLTPTQVKIWFQNHRYKTKRAQNE   70 (77)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCHHHHHHHhHHhhcchhhhhcc
Confidence            6788888     99999999999999997664

>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=99.00  E-value=1.4e-11  Score=72.75  Aligned_cols=26  Identities=35%  Similarity=0.815  Sum_probs=23.3

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      |++||..     .+|+|||||||+|||+..+
T Consensus        32 r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~   62 (68)
T 1ahd_P           32 RIEIAHALSLTERQIKIWFQNRRMKWKKENK   62 (68)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHCcCHhhhhHHhHHHHhHHhHhcc
Confidence            6788888     9999999999999999765

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

Probab=98.99  E-value=7.2e-12  Score=74.88  Aligned_cols=27  Identities=30%  Similarity=0.556  Sum_probs=23.4

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      +|++||.+     ++|+|||||||+||||+..
T Consensus        33 ~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~~   64 (69)
T 2l9r_A           33 ERAHLAKNLKLTETQVKIWFQNRRYKTKRKQL   64 (69)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHSCCSSS
T ss_pred             HHHHHHHHhCCChhheeecchhhhhhhhhhhh
Confidence            37788888     9999999999999998654

>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=98.98  E-value=2.9e-11  Score=73.67  Aligned_cols=27  Identities=11%  Similarity=0.182  Sum_probs=23.7

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      +|++||..     +||+|||||||+|||+..-
T Consensus        32 er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~l   63 (76)
T 2ecc_A           32 DYQKLEQITGLPRPEIIQWFGDTRYALKHGQL   63 (76)
T ss_dssp             HHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHCcCHHHhhHHhHhhHHHHHHHHH
Confidence            47889988     9999999999999998643

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

Probab=98.97  E-value=4.3e-11  Score=72.71  Aligned_cols=26  Identities=46%  Similarity=0.810  Sum_probs=23.4

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      |++||..     .+|+|||||||+||||+.+
T Consensus        48 r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~   78 (81)
T 1fjl_A           48 REELAQRTNLTEARIQVWFQNRRARLRKQHT   78 (81)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHhhhhhhhcc
Confidence            6788888     9999999999999999765

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

Probab=98.97  E-value=3.4e-11  Score=72.97  Aligned_cols=25  Identities=40%  Similarity=0.437  Sum_probs=22.2

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKR   25 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~   25 (92)
                      +|++||.+     .+|+|||||||+|||+.
T Consensus        41 ~r~~La~~lgL~~~qV~vWFqNrR~k~rk~   70 (80)
T 2da4_A           41 KIEAVATELNVDCEIVRTWIGNRRRKYRLM   70 (80)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCHHHhhHhHHHHHHHHhhc
Confidence            36788888     99999999999999984

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

Probab=98.97  E-value=4.4e-11  Score=72.36  Aligned_cols=27  Identities=33%  Similarity=0.502  Sum_probs=23.8

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRERN   28 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~~   28 (92)
                      |++||..     .+|+|||||||+||||+...
T Consensus        37 r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (80)
T 2dmq_A           37 LKQLAQKTGLTKRVLQVWFQNARAKFRRNLLR   68 (80)
T ss_dssp             HHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHhCCCHHHhhHccHHHHHHHHHHHHH
Confidence            6788888     99999999999999997653

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

Probab=98.96  E-value=1.8e-11  Score=74.22  Aligned_cols=27  Identities=56%  Similarity=0.852  Sum_probs=23.9

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRERN   28 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~~   28 (92)
                      |++||..     .+|+|||||||+|||++.+.
T Consensus        37 r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~   68 (80)
T 2dms_A           37 REEVALKINLPESRVQVWFKNRRAKCRQQQQQ   68 (80)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCS
T ss_pred             HHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHc
Confidence            6788888     99999999999999997653

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

Probab=98.96  E-value=4.4e-11  Score=70.55  Aligned_cols=27  Identities=26%  Similarity=0.518  Sum_probs=23.9

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRERN   28 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~~   28 (92)
                      |++||..     .+|+|||||||+|+|++...
T Consensus        32 r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~   63 (68)
T 1zq3_P           32 LADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ   63 (68)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHhCcCHHHhhHhhHHHHHHHHHHhcc
Confidence            6788888     99999999999999997764

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

Probab=98.96  E-value=1.7e-11  Score=74.69  Aligned_cols=27  Identities=33%  Similarity=0.544  Sum_probs=22.9

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      +|++||..     .+|+|||||||+||||+.+
T Consensus        49 ~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   80 (81)
T 1b8i_A           49 RRIEMAHALSLTERQIKIWFQNRRMKLKKEIQ   80 (81)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC-
T ss_pred             HHHHHHHHhCCCHHHHHHHhHHhhhhhhhhcc
Confidence            37788888     9999999999999998643

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

Probab=98.96  E-value=2.2e-12  Score=80.17  Aligned_cols=29  Identities=17%  Similarity=0.281  Sum_probs=24.6

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERNA   29 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~   29 (92)
                      +|++||..     ++|+|||||||+|||+.++..
T Consensus        42 ~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~~~   75 (89)
T 2dmp_A           42 ELDRLRVETKLSRREIDSWFSERRKLRDSMEQAV   75 (89)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCSCC
T ss_pred             HHHHHHHHhCCCHHhccHhhHhHHHHHHHHhHhh
Confidence            37788888     999999999999999876643

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

Probab=98.95  E-value=1.7e-11  Score=73.72  Aligned_cols=26  Identities=23%  Similarity=0.353  Sum_probs=23.3

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      |++||..     ++|+|||||||+|||++.+
T Consensus        37 r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (75)
T 2da5_A           37 LDRLRSETKMTRREIDSWFSERRKKVNAEET   67 (75)
T ss_dssp             HHHHHHHHCCCHHHHHHHHHHHTTHHHHSSC
T ss_pred             HHHHHHHhCCCHHHhhHhhHHHHHHHHHhhh
Confidence            6788888     9999999999999999665

>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=98.95  E-value=3.2e-11  Score=69.64  Aligned_cols=23  Identities=35%  Similarity=0.741  Sum_probs=21.1

Q ss_pred             hhhhhhh-----cccccccccchhHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRK   24 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr   24 (92)
                      |++||..     .+|+|||||||+||||
T Consensus        33 r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A           33 RQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            6788888     9999999999999987

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

Probab=98.94  E-value=4.7e-11  Score=68.14  Aligned_cols=23  Identities=35%  Similarity=0.670  Sum_probs=21.1

Q ss_pred             hhhhhhh-----cccccccccchhHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRK   24 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr   24 (92)
                      |++||..     .+|+|||||||+|+||
T Consensus        30 r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A           30 RAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            6788888     9999999999999997

>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=98.94  E-value=2.3e-11  Score=73.82  Aligned_cols=26  Identities=38%  Similarity=0.713  Sum_probs=22.7

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRE   26 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~   26 (92)
                      +|++||..     .+|+|||||||+||||..
T Consensus        46 ~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   76 (80)
T 2dmt_A           46 DRIDLAESLGLSQLQVKTWYQNRRMKWKKSG   76 (80)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHHHHHHHHSCCC
T ss_pred             HHHHHHHHhCCCHHHeeeccHHHHHHhhccc
Confidence            37788888     999999999999999854

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

Probab=98.93  E-value=3e-11  Score=71.25  Aligned_cols=27  Identities=30%  Similarity=0.689  Sum_probs=23.8

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRERN   28 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~~   28 (92)
                      |++||..     .+|+|||||||+|||+..+.
T Consensus        32 r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~~   63 (68)
T 1ftt_A           32 REHLASMIHLTPTQVKIWFQNHRYKMKRQAKD   63 (68)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSC
T ss_pred             HHHHHHHhCCCHHHhHHHhHHHhhhhhhhhhH
Confidence            6788888     99999999999999997653

>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=98.93  E-value=6e-11  Score=70.25  Aligned_cols=26  Identities=42%  Similarity=0.855  Sum_probs=22.9

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      |++||..     .+|+|||||||+|||+...
T Consensus        37 r~~La~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2e1o_A           37 RKRLAKMLQLSERQVKTWFQNRRAKWRRSGP   67 (70)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHCCCHHHhhHhhHhhHhhcCCCCC
Confidence            6788888     9999999999999999653

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

Probab=98.93  E-value=8.7e-12  Score=76.11  Aligned_cols=26  Identities=23%  Similarity=0.515  Sum_probs=22.9

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      |++||..     .+|+|||||||+||||..+
T Consensus        52 r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k   82 (84)
T 2kt0_A           52 MQELSNILNLSYKQVKTWFQNQRMKSKRWQK   82 (84)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHTTTSCCC
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHHHHHHhh
Confidence            6788888     9999999999999998653

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

Probab=98.93  E-value=5.5e-11  Score=70.32  Aligned_cols=26  Identities=54%  Similarity=0.903  Sum_probs=22.8

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      |++||..     .+|+|||||||+||||...
T Consensus        37 r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2dmu_A           37 REQLARKVHLREEKVEVWFKNRRAKWRRSGP   67 (70)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHHHHHTST
T ss_pred             HHHHHHHHCCCHHHeehccccccccccccCC
Confidence            6788888     9999999999999998543

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

Probab=98.91  E-value=2.2e-11  Score=70.54  Aligned_cols=24  Identities=25%  Similarity=0.541  Sum_probs=21.7

Q ss_pred             hhhhhhh-----cccccccccchhHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKR   25 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~   25 (92)
                      |++||..     .+|+|||||||+||||.
T Consensus        33 r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A           33 MQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             HHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            6788888     99999999999999984

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

Probab=98.91  E-value=5.1e-11  Score=68.55  Aligned_cols=24  Identities=33%  Similarity=0.577  Sum_probs=21.7

Q ss_pred             hhhhhhh-----cccccccccchhHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKR   25 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~   25 (92)
                      |++||..     .+|+|||||||+|+||+
T Consensus        31 r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (60)
T 1jgg_A           31 RCELAAQLNLPESTIKVWFQNRRMKDKRQ   59 (60)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHCcCHHHHHHhhHHHHhHhhcc
Confidence            6788888     99999999999999985

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

Probab=98.90  E-value=5.4e-11  Score=71.79  Aligned_cols=25  Identities=40%  Similarity=0.506  Sum_probs=22.3

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRE   26 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~   26 (92)
                      |++||..     .+|+|||||||+||||+.
T Consensus        47 r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   76 (80)
T 2da3_A           47 LDHIAHEVGLKKRVVQVWFQNTRARERKSG   76 (80)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHCcCHHHhHHHhHHHHHhHhhhc
Confidence            6788888     999999999999999854

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

Probab=98.89  E-value=2.9e-11  Score=72.19  Aligned_cols=26  Identities=15%  Similarity=0.247  Sum_probs=23.0

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      |++||..     .+|+|||||||+||||.+.
T Consensus        36 r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   66 (74)
T 2ly9_A           36 IIRLMKITGLTKGEIKKWFSDTRYNQRNSKS   66 (74)
T ss_dssp             HHHHHHHHCCCHHHHHHHHHHHHHHTTTTTC
T ss_pred             HHHHHHHhCcCHHHeeeCChhHhHHHHhhCc
Confidence            6788888     9999999999999998654

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

Probab=98.88  E-value=6.8e-11  Score=74.10  Aligned_cols=30  Identities=17%  Similarity=0.318  Sum_probs=24.7

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERNAM   30 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~~   30 (92)
                      +|++||..     .+|+|||||||+||||+...-.
T Consensus        54 ~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~lk~~   88 (96)
T 3nar_A           54 EYDKLAKESGLARTDIVSWFGDTRYAWKNGNLKWY   88 (96)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHHHHHHHHTTTCCHHH
T ss_pred             HHHHHHHHhCCCHHHeeecchhhhhHhhhhcccHH
Confidence            36788888     9999999999999999764433

>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=98.88  E-value=3.6e-11  Score=71.23  Aligned_cols=25  Identities=28%  Similarity=0.550  Sum_probs=22.3

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRE   26 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~   26 (92)
                      |++||..     .+|+|||||||+||||..
T Consensus        37 r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~   66 (70)
T 2cra_A           37 RRKISAATSLSERQITIWFQNRRVKEKKSG   66 (70)
T ss_dssp             HHHHHHHTCCCHHHHHHHHHHHHHTTTSSC
T ss_pred             HHHHHHHHCCCHHHhhHhhHhHHHHhcccC
Confidence            6788888     999999999999999854

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

Probab=98.88  E-value=6.5e-11  Score=70.74  Aligned_cols=27  Identities=30%  Similarity=0.454  Sum_probs=23.1

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      +|++||..     .+|+|||||||+||||...
T Consensus        36 ~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   67 (73)
T 2l7z_A           36 KRRRISATTNLSERQVTIWFQNRRVKEKKVIN   67 (73)
T ss_dssp             HHHHHHHHHTSCSHHHHHHHHHHHHHHTTSSS
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHhHHHHHHhc
Confidence            36788888     9999999999999998543

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

Probab=98.88  E-value=1.2e-10  Score=71.45  Aligned_cols=30  Identities=27%  Similarity=0.405  Sum_probs=25.4

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERNAM   30 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~~   30 (92)
                      +|++||..     .||+|||||||+|+|+......
T Consensus        33 ~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~~   67 (87)
T 1b72_B           33 AKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQ   67 (87)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGGGH
T ss_pred             HHHHHHHHHCcCHHHHHHHHHHHHHHhhhcccccc
Confidence            36788888     9999999999999999776543

>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=98.87  E-value=8.2e-11  Score=69.50  Aligned_cols=26  Identities=27%  Similarity=0.245  Sum_probs=22.8

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      |++||..     .+|+|||||||+||||..+
T Consensus        37 r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2da1_A           37 IKEMADKSGLPQKVIKHWFRNTLFKERQSGP   67 (70)
T ss_dssp             HHHHHHHHCCCHHHHHHHHHHHHHHHHCCCC
T ss_pred             HHHHHHHhCCCHHHHHHHhhhhhHHHhhhcc
Confidence            6788888     9999999999999998643

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

Probab=98.87  E-value=2.9e-11  Score=72.11  Aligned_cols=27  Identities=67%  Similarity=1.143  Sum_probs=23.5

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRERN   28 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~~   28 (92)
                      |++||..     .+|+|||||||+||||.++.
T Consensus        39 r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r~   70 (75)
T 2m0c_A           39 REQLAMRTDLTEARVQVWFQNRRAKWRKRERF   70 (75)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHHHTCCCCC
T ss_pred             HHHHHHHhCCCHHHHHHHhHHHHHHHHHHHhh
Confidence            6788887     99999999999999996653

>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=98.85  E-value=6.5e-11  Score=69.95  Aligned_cols=25  Identities=36%  Similarity=0.457  Sum_probs=22.2

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRE   26 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~   26 (92)
                      |++||..     .+|+|||||||+||||..
T Consensus        37 r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2da2_A           37 FEQLSNLLNLPTRVIVVWFQNARQKARKSG   66 (70)
T ss_dssp             HHHHHHHSCCCHHHHHHHHHHHHHHHCCCS
T ss_pred             HHHHHHHhCCCHHHhHHhhHhhhHHHhhcc
Confidence            6788888     999999999999999854

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

Probab=98.84  E-value=1.1e-10  Score=67.09  Aligned_cols=24  Identities=25%  Similarity=0.374  Sum_probs=21.4

Q ss_pred             hhhhhhh-----cccccccccchhHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKR   25 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~   25 (92)
                      |++||..     .+|+|||||||+|+|+.
T Consensus        31 r~~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A           31 LENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             HHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            6788888     99999999999999873

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

Probab=98.83  E-value=1.1e-10  Score=66.20  Aligned_cols=22  Identities=36%  Similarity=0.702  Sum_probs=19.7

Q ss_pred             hhhhhhh-----cccccccccchhHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWR   23 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~r   23 (92)
                      |++||..     .+|+|||||||+|+|
T Consensus        32 r~~La~~l~l~~~qV~~WFqNrR~k~k   58 (58)
T 3rkq_A           32 RDQLASVLKLTSTQVKIWFQNRRYKSK   58 (58)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHhCcCHHHHHHhhHHhhccCC
Confidence            6788888     999999999999985

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

Probab=98.83  E-value=5.2e-11  Score=69.94  Aligned_cols=24  Identities=21%  Similarity=0.099  Sum_probs=20.6

Q ss_pred             Chhhhhhh-----cccccccccchhHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRK   24 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr   24 (92)
                      +|++||.+     ++|+|||||||+|.++
T Consensus        32 ~r~~LA~~l~L~e~qVqvWFqNRRak~~~   60 (64)
T 2e19_A           32 ELSKIADSVNLPLDVVKKWFEKMQAGQIS   60 (64)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHTCSC
T ss_pred             HHHHHHHHhCcChhhcCcchhcccCCCCC
Confidence            37788888     9999999999998654

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

Probab=98.83  E-value=5.6e-11  Score=70.36  Aligned_cols=25  Identities=32%  Similarity=0.635  Sum_probs=22.1

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRE   26 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~   26 (92)
                      |++||..     .+|+|||||||+||||..
T Consensus        37 r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   66 (70)
T 2djn_A           37 RAELAASLGLTQTQVKIWFQNKRSKIKKSG   66 (70)
T ss_dssp             HHHHHHHSSCCHHHHHHHHHHHHHTCSSSS
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHhhhhcccC
Confidence            6788888     999999999999998853

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

Probab=98.82  E-value=7.8e-11  Score=70.83  Aligned_cols=27  Identities=30%  Similarity=0.415  Sum_probs=23.5

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      +|++||..     .+|+|||||||+||||..+
T Consensus        37 ~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~   68 (76)
T 2dn0_A           37 EVEHLTKVTGLSTREVRKWFSDRRYHCRNLKG   68 (76)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCS
T ss_pred             HHHHHHHHhCCChHHhhHHhHHHhHHHHHhcc
Confidence            37788888     9999999999999998654

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

Probab=98.81  E-value=2.5e-10  Score=67.95  Aligned_cols=26  Identities=27%  Similarity=0.387  Sum_probs=22.7

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRE   26 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~   26 (92)
                      +|++||..     .||+|||||||+|+|+..
T Consensus        39 ~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~   69 (73)
T 1x2n_A           39 EKKQIAAQTNLTLLQVNNWFINARRRILQSG   69 (73)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHCcCHHHHHHHhHHHHhhccccc
Confidence            36788888     999999999999999854

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

Probab=98.80  E-value=1.8e-10  Score=67.51  Aligned_cols=26  Identities=42%  Similarity=0.703  Sum_probs=22.8

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      |++||..     .+|+|||||||+|+|+..+
T Consensus        31 r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~   61 (67)
T 2k40_A           31 LEDLAQKLNLELDRIQIWFQNRRAKLKRSHR   61 (67)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHHHHCSCC
T ss_pred             HHHHHHHHCcCHHHhhHhhHhHHHHHhHhch
Confidence            6788888     9999999999999998654

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

Probab=98.78  E-value=3.8e-10  Score=67.14  Aligned_cols=27  Identities=30%  Similarity=0.498  Sum_probs=23.5

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRERN   28 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~~~   28 (92)
                      |++||..     .+|+|||||||+|+|+....
T Consensus        34 r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~   65 (73)
T 1puf_B           34 KEELAKKCGITVSQVSNWFGNKRIRYKKNIGK   65 (73)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTT
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHhhccccccc
Confidence            6788888     99999999999999986654

>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=98.78  E-value=1.2e-10  Score=68.13  Aligned_cols=25  Identities=40%  Similarity=0.670  Sum_probs=21.9

Q ss_pred             hhhhhhh-----cccccccccchhHHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKRE   26 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~~   26 (92)
                      |++||..     .+|+|||||||+|||+..
T Consensus        33 r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   62 (66)
T 1bw5_A           33 KEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             HHHHHHHHCcCHHHHHHHhHHHHHHHhHHh
Confidence            6788888     999999999999998853

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

Probab=98.75  E-value=3.2e-10  Score=69.31  Aligned_cols=27  Identities=22%  Similarity=0.239  Sum_probs=23.3

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      +|++||..     .||+|||||||+|||+...
T Consensus        34 ~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~~   65 (83)
T 1le8_B           34 GLENLMKNTSLSRIQIKNWVAARRAKEKTITI   65 (83)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHHHHHHHHTTSCC
T ss_pred             HHHHHHHHHCCCHHHcccccHHHHcccccccc
Confidence            36788888     9999999999999998654

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

Probab=98.74  E-value=5.1e-10  Score=68.48  Aligned_cols=27  Identities=19%  Similarity=0.313  Sum_probs=23.3

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      +|++||..     .||+|||||||+|+|+...
T Consensus        39 ~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~   70 (83)
T 2dmn_A           39 EKQMLSEKTNLSLLQISNWFINARRRILPDML   70 (83)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHT
T ss_pred             HHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHH
Confidence            37888888     9999999999999988654

>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=98.74  E-value=3.3e-10  Score=65.15  Aligned_cols=22  Identities=45%  Similarity=0.709  Sum_probs=19.1

Q ss_pred             hhhhhhh-----cccccccccchhHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWR   23 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~r   23 (92)
                      |++||..     .+|+|||||||+|+|
T Consensus        35 r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A           35 KEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            6788888     999999999999986

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

Probab=98.73  E-value=1.6e-10  Score=67.14  Aligned_cols=24  Identities=33%  Similarity=0.587  Sum_probs=21.1

Q ss_pred             Chhhhhhh-----cccccccccchhHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRK   24 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr   24 (92)
                      +|++||..     .||+|||||||+|+||
T Consensus        35 ~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A           35 AKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             HHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            36788888     9999999999999886

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

Probab=98.72  E-value=1.2e-09  Score=69.80  Aligned_cols=21  Identities=43%  Similarity=0.651  Sum_probs=18.3

Q ss_pred             cccccccccchhHHHHHHHHH
Q psy15889          9 LRVRVWFKNRRAKWRKRERNA   29 (92)
Q Consensus         9 ~qVkiWFQNRRaK~rr~~~~~   29 (92)
                      ++|+|||||||+|+|++.+..
T Consensus        69 ~~V~~WFqNRR~k~kr~~~~~   89 (102)
T 2da6_A           69 VRVYNWFANRRKEEAFRQKLA   89 (102)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             cceeeeecchHHHHHHhhHhh
Confidence            389999999999999987755

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

Probab=98.71  E-value=4.5e-10  Score=76.61  Aligned_cols=27  Identities=37%  Similarity=0.330  Sum_probs=23.8

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      +|++||..     ++|+|||||||+||||+.+
T Consensus       128 ~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~  159 (164)
T 2xsd_C          128 EITGLADSLQLEKEVVRVWFCNRRQKEKRMTP  159 (164)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC
T ss_pred             HHHHHHHHHCCChhhhhhhhHHhhHHHhhccC
Confidence            37788888     9999999999999999665

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

Probab=98.69  E-value=7.1e-10  Score=65.41  Aligned_cols=27  Identities=26%  Similarity=0.303  Sum_probs=22.7

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      +|++||..     .||+|||||||+|+|+...
T Consensus        30 ~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~   61 (67)
T 3k2a_A           30 QKKQLAQDTGLTILQVNNWFINARRRIVQPMI   61 (67)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC-
T ss_pred             HHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHH
Confidence            37788888     9999999999999998544

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

Probab=98.61  E-value=3.3e-09  Score=66.12  Aligned_cols=20  Identities=40%  Similarity=0.778  Sum_probs=17.9

Q ss_pred             cccccccccchhHHHHHHHH
Q psy15889          9 LRVRVWFKNRRAKWRKRERN   28 (92)
Q Consensus         9 ~qVkiWFQNRRaK~rr~~~~   28 (92)
                      .+|+|||||||+|+|++.+.
T Consensus        64 ~qV~~WFqNRR~k~kr~~~~   83 (95)
T 2cuf_A           64 LKVYNWFANRRKEIKRRANI   83 (95)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHhhc
Confidence            67999999999999997764

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

Probab=98.50  E-value=1.2e-08  Score=63.78  Aligned_cols=27  Identities=26%  Similarity=0.324  Sum_probs=23.3

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      +|++||..     +||++||||||+|+++...
T Consensus        37 ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~   68 (89)
T 2lk2_A           37 EKALLSQQTHLSTLQVCNWFINARRRLLPDML   68 (89)
T ss_dssp             HHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHH
Confidence            47788888     8999999999999988654

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

Probab=98.44  E-value=4.4e-09  Score=71.14  Aligned_cols=28  Identities=14%  Similarity=0.087  Sum_probs=22.3

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERN   28 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~   28 (92)
                      +|++||..     ++|+|||||||+|+|+....
T Consensus       126 ~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~~  158 (164)
T 2d5v_A          126 LQITISQQLGLELSTVSNFFMNARRRSLDKWLE  158 (164)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHTSSCC---
T ss_pred             HHHHHHHHHCcCHHHhhhcChhhhccccccCCC
Confidence            37788888     99999999999999986553

>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=98.21  E-value=5.8e-08  Score=58.13  Aligned_cols=21  Identities=14%  Similarity=0.181  Sum_probs=18.1

Q ss_pred             Chhhhhhh-----cccccccccchhH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAK   21 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK   21 (92)
                      +|++||.+     .+|||||||||.-
T Consensus        37 ~r~~La~~tGL~~~~IqVWFQNrR~~   62 (71)
T 1wi3_A           37 AIHTLSAQLDLPKHTIIKFFQNQRYH   62 (71)
T ss_dssp             HHHHHHHHSCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCHHHHHHhhccceee
Confidence            37889888     9999999999964

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

Probab=98.07  E-value=2e-07  Score=55.94  Aligned_cols=19  Identities=21%  Similarity=0.392  Sum_probs=16.2

Q ss_pred             hhhhhhh-----cccccccccchh
Q psy15889          2 GELMALW-----LRVRVWFKNRRA   20 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRa   20 (92)
                      +++||..     ..|||||||||+
T Consensus        35 i~~LA~~lgL~~~VVrVWFqNrRa   58 (71)
T 2da7_A           35 LLKISIAVGLPQEFVKEWFEQRKV   58 (71)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCHHHHHHHHhhccc
Confidence            5667777     999999999997

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

Probab=98.02  E-value=6.8e-08  Score=61.10  Aligned_cols=21  Identities=43%  Similarity=0.631  Sum_probs=16.2

Q ss_pred             cccccccccchhHHHHHHHHH
Q psy15889          9 LRVRVWFKNRRAKWRKRERNA   29 (92)
Q Consensus         9 ~qVkiWFQNRRaK~rr~~~~~   29 (92)
                      ++|+|||||||+|+++..+.+
T Consensus        72 ~qV~vWFqNRR~k~k~k~~~~   92 (99)
T 1lfb_A           72 VRVYNWFANRRKEEAFRHKLA   92 (99)
T ss_dssp             HHHHHHHHHHHHTTSCCC---
T ss_pred             ceeeeccHHHHHHHHHhchhh
Confidence            789999999999988766544

---

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	92
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	1e-06
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	1e-06
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	2e-06
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	3e-06
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	4e-06
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	6e-06
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	1e-05
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	2e-05
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	2e-05
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	2e-05
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	3e-05
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	3e-05
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	3e-05
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	3e-05
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	4e-05
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	5e-05
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	1e-04
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	2e-04
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	0.001
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	0.001
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	0.001
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	0.001
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	0.003
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	0.004
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	0.004
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	0.004

>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 = 40.2 bits (94), Expect = 1e-06
 Identities = 12/18 (66%), Positives = 16/18 (88%)

Query: 10 RVRVWFKNRRAKWRKRER 27
          R++VWF NRRAKWR+ E+
Sbjct: 44 RIQVWFSNRRAKWRREEK 61

>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 = 39.8 bits (93), Expect = 1e-06
 Identities = 9/18 (50%), Positives = 13/18 (72%)

Query: 10 RVRVWFKNRRAKWRKRER 27
           +RVWF+N+R K +KR  
Sbjct: 46 VIRVWFQNKRCKDKKRSI 63

>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 = 39.6 bits (92), Expect = 2e-06
 Identities = 11/18 (61%), Positives = 16/18 (88%)

Query: 10 RVRVWFKNRRAKWRKRER 27
          +V++WF+NRR K +KRER
Sbjct: 70 QVKIWFQNRRMKQKKRER 87

>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 = 39.0 bits (91), Expect = 3e-06
 Identities = 8/19 (42%), Positives = 15/19 (78%)

Query: 10 RVRVWFKNRRAKWRKRERN 28
          +V++WF+NRR K +K  ++
Sbjct: 56 QVKIWFQNRRMKMKKINKD 74

>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 = 38.9 bits (90), Expect = 4e-06
 Identities = 8/21 (38%), Positives = 12/21 (57%)

Query: 10 RVRVWFKNRRAKWRKRERNAM 30
          +V  WF NRR + ++R   A 
Sbjct: 58 KVYNWFANRRKEIKRRANIAA 78

>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 = 38.0 bits (88), Expect = 6e-06
 Identities = 7/22 (31%), Positives = 14/22 (63%)

Query: 10 RVRVWFKNRRAKWRKRERNAMN 31
          +V++WFKNRR + + +     +
Sbjct: 44 QVKIWFKNRRRRHKIQSDQHKD 65

>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 = 37.6 bits (87), Expect = 1e-05
 Identities = 6/19 (31%), Positives = 15/19 (78%)

Query: 10 RVRVWFKNRRAKWRKRERN 28
          +V++WF+N R K +++ ++
Sbjct: 45 QVKIWFQNHRYKMKRQAKD 63

>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 = 36.7 bits (85), Expect = 2e-05
 Identities = 8/15 (53%), Positives = 14/15 (93%)

Query: 10 RVRVWFKNRRAKWRK 24
          ++++WF+NRR KW+K
Sbjct: 40 QIKIWFQNRRMKWKK 54

>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 = 36.4 bits (84), Expect = 2e-05
 Identities = 7/16 (43%), Positives = 13/16 (81%)

Query: 10 RVRVWFKNRRAKWRKR 25
           ++VWF+NRR K +++
Sbjct: 42 TIKVWFQNRRMKDKRQ 57

>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 = 36.4 bits (84), Expect = 2e-05
 Identities = 7/15 (46%), Positives = 12/15 (80%)

Query: 10 RVRVWFKNRRAKWRK 24
          ++ +WF+NRR K +K
Sbjct: 44 QITIWFQNRRVKEKK 58

>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 = 36.4 bits (84), Expect = 3e-05
 Identities = 10/18 (55%), Positives = 15/18 (83%)

Query: 10 RVRVWFKNRRAKWRKRER 27
          R++VWF+NRRA+ RK+  
Sbjct: 45 RIQVWFQNRRARLRKQHT 62

>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 = 36.0 bits (83), Expect = 3e-05
 Identities = 10/15 (66%), Positives = 14/15 (93%)

Query: 10 RVRVWFKNRRAKWRK 24
          +V+ WF+NRRAKWR+
Sbjct: 43 QVKTWFQNRRAKWRR 57

>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 = 36.5 bits (84), Expect = 3e-05
 Identities = 8/19 (42%), Positives = 12/19 (63%)

Query: 10 RVRVWFKNRRAKWRKRERN 28
          + + WFK R A+WR+ E  
Sbjct: 45 QTQKWFKQRLAEWRRSEGL 63

>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 = 36.1 bits (83), Expect = 3e-05
 Identities = 17/17 (100%), Positives = 17/17 (100%)

Query: 10 RVRVWFKNRRAKWRKRE 26
          RVRVWFKNRRAKWRKRE
Sbjct: 44 RVRVWFKNRRAKWRKRE 60

>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 = 36.0 bits (83), Expect = 4e-05
 Identities = 8/15 (53%), Positives = 14/15 (93%)

Query: 10 RVRVWFKNRRAKWRK 24
          +V++WF+NRRAK ++
Sbjct: 43 QVKIWFQNRRAKAKR 57

>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 = 35.5 bits (82), Expect = 5e-05
 Identities = 4/15 (26%), Positives = 9/15 (60%)

Query: 10 RVRVWFKNRRAKWRK 24
           ++ WF+ RR + + 
Sbjct: 37 SIQRWFRQRRNQEKP 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 = 35.1 bits (80), Expect = 1e-04
 Identities = 8/18 (44%), Positives = 10/18 (55%)

Query: 10 RVRVWFKNRRAKWRKRER 27
          RV  WF NRR +   R +
Sbjct: 61 RVYNWFANRRKEEAFRHK 78

>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 = 34.6 bits (79), Expect = 2e-04
 Identities = 7/24 (29%), Positives = 12/24 (50%)

Query: 10 RVRVWFKNRRAKWRKRERNAMNAA 33
          +V  WF N+R +++K        A
Sbjct: 47 QVSNWFGNKRIRYKKNIGKFQEEA 70

>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 = 32.7 bits (74), Expect = 0.001
 Identities = 6/18 (33%), Positives = 13/18 (72%)

Query: 10 RVRVWFKNRRAKWRKRER 27
          +V++WF+N R K ++ + 
Sbjct: 52 QVKIWFQNHRYKTKRAQN 69

>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 = 32.4 bits (74), Expect = 0.001
 Identities = 4/14 (28%), Positives = 11/14 (78%)

Query: 10 RVRVWFKNRRAKWR 23
          +++ WF++RR + +
Sbjct: 45 KIQCWFRHRRNQDK 58

>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 = 31.8 bits (72), Expect = 0.001
 Identities = 7/14 (50%), Positives = 11/14 (78%)

Query: 10 RVRVWFKNRRAKWR 23
          +VRVWF N+R + +
Sbjct: 40 QVRVWFINKRMRSK 53

>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 = 31.7 bits (72), Expect = 0.001
 Identities = 5/15 (33%), Positives = 9/15 (60%)

Query: 10 RVRVWFKNRRAKWRK 24
          +++ W  NRR K + 
Sbjct: 44 QIKNWVSNRRRKEKT 58

>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 = 31.0 bits (70), Expect = 0.003
 Identities = 8/17 (47%), Positives = 12/17 (70%)

Query: 10 RVRVWFKNRRAKWRKRE 26
           VRVWF NRR + ++ +
Sbjct: 42 VVRVWFCNRRQREKRVK 58

>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 = 31.1 bits (70), Expect = 0.004
 Identities = 9/16 (56%), Positives = 11/16 (68%)

Query: 10 RVRVWFKNRRAKWRKR 25
           VRVWF NRR K ++ 
Sbjct: 51 VVRVWFCNRRQKGKRS 66

>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 = 30.6 bits (69), Expect = 0.004
 Identities = 6/12 (50%), Positives = 11/12 (91%)

Query: 10 RVRVWFKNRRAK 21
          ++++WF+N RAK
Sbjct: 42 QIKIWFQNARAK 53

>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 = 30.9 bits (69), Expect = 0.004
 Identities = 3/25 (12%), Positives = 8/25 (32%)

Query: 3  ELMALWLRVRVWFKNRRAKWRKRER 27
          +       +  WF  ++     +E 
Sbjct: 40 QTKLTRREIDAWFTEKKKSKALKEE 64

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	92
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.16
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.11
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.07
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.06
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.05
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.03
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.02
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.0
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	98.94
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	98.93
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	98.91
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	98.89
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	98.8
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	98.79
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	98.78
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	98.76
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	98.74
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	98.68
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	98.67
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	98.65
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	98.62
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	98.61
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	98.61
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	98.57
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	98.54
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	98.47
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	98.43
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	98.28
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	98.14
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	97.96

>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=99.16  E-value=5.1e-13  Score=75.78  Aligned_cols=25  Identities=36%  Similarity=0.777  Sum_probs=22.5

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKR   25 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~   25 (92)
                      +|++||..     .+|+|||||||+|+||+
T Consensus        26 ~r~~LA~~l~l~~~~V~iWFQNrRak~kk~   55 (56)
T d9anta_          26 RRIEIAHALSLTERQIKIWFQNRRMKWKKE   55 (56)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHhCCChhHeeeccccchhhhhhc
Confidence            37889988     99999999999999984

>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=99.11  E-value=2.3e-12  Score=76.36  Aligned_cols=27  Identities=37%  Similarity=0.607  Sum_probs=23.7

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      +|++||..     .+|+|||||||+|+||+..
T Consensus        31 ~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~~   62 (72)
T d1uhsa_          31 TLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   62 (72)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHHHHHhccC
Confidence            37889988     9999999999999998654

>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=99.07  E-value=4.5e-12  Score=73.94  Aligned_cols=28  Identities=25%  Similarity=0.480  Sum_probs=24.1

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERN   28 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~   28 (92)
                      +|++||..     .+|+|||||||+|+|++...
T Consensus        30 ~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~~   62 (67)
T d1zq3p1          30 RLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ   62 (67)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhCCCccceeeccccHHHhHhhhhhh
Confidence            37788888     99999999999999986653

>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=99.06  E-value=2.8e-12  Score=72.69  Aligned_cols=25  Identities=32%  Similarity=0.532  Sum_probs=22.3

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKR   25 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~   25 (92)
                      +|++||.+     .+|+|||||||+|+||+
T Consensus        28 ~r~~LA~~lgl~~~qV~vWFqNrR~k~kk~   57 (57)
T d1jgga_          28 RRCELAAQLNLPESTIKVWFQNRRMKDKRQ   57 (57)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHhCCChhHhhhcchhhhhhhhcC
Confidence            37889988     99999999999999973

>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=99.05  E-value=1.5e-12  Score=74.17  Aligned_cols=24  Identities=29%  Similarity=0.567  Sum_probs=21.5

Q ss_pred             Chhhhhhh-----cccccccccchhHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRK   24 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr   24 (92)
                      +|++||..     .+|+|||||||+|+||
T Consensus        30 ~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1          30 KRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             HHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             HHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            37889988     9999999999999875

>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=99.03  E-value=1.2e-11  Score=73.96  Aligned_cols=29  Identities=31%  Similarity=0.547  Sum_probs=25.0

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERNA   29 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~   29 (92)
                      +|++||..     .+|+|||||||+|+|+..+..
T Consensus        42 ~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~~   75 (77)
T d1pufa_          42 RRYEVARLLNLTERQVKIWFQNRRMKMKKINKDR   75 (77)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHHh
Confidence            37889888     999999999999999977643

>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=99.02  E-value=7.3e-12  Score=70.89  Aligned_cols=23  Identities=48%  Similarity=0.993  Sum_probs=21.2

Q ss_pred             hhhhhhh-----cccccccccchhHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRK   24 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr   24 (92)
                      |++||..     .+|+|||||||+|+||
T Consensus        30 r~~LA~~l~L~~~qV~~WFqNrR~k~kk   57 (57)
T d2e1oa1          30 RKRLAKMLQLSERQVKTWFQNRRAKWRR   57 (57)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCHHHhhHhhhhhhhhccC
Confidence            6788888     9999999999999987

>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=99.00  E-value=1e-11  Score=70.46  Aligned_cols=24  Identities=33%  Similarity=0.614  Sum_probs=21.8

Q ss_pred             Chhhhhhh-----cccccccccchhHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRK   24 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr   24 (92)
                      +|++||..     .+|+|||||||+|+||
T Consensus        29 ~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_          29 ERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            37889988     8999999999999997

>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=98.94  E-value=3.3e-11  Score=69.76  Aligned_cols=27  Identities=44%  Similarity=0.773  Sum_probs=23.7

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      +|++||..     .+|+|||||||+|+|++.+
T Consensus        31 ~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~   62 (65)
T d1fjla_          31 TREELAQRTNLTEARIQVWFQNRRARLRKQHT   62 (65)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCHHHhhHhhhhHHHHHHhccc
Confidence            36788888     9999999999999999765

>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=98.93  E-value=1.4e-11  Score=68.72  Aligned_cols=21  Identities=29%  Similarity=0.640  Sum_probs=19.0

Q ss_pred             Chhhhhhh-----cccccccccchhH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAK   21 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK   21 (92)
                      +|++||..     .+|+|||||||+|
T Consensus        28 ~r~~LA~~lgL~~~qV~vWFqNrRaK   53 (53)
T d1p7ia_          28 RRQQLSSELGLNEAQIKIWFQNARAK   53 (53)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHhCCChHHhhhcccccCCC
Confidence            47889998     9999999999997

>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=98.91  E-value=3.9e-11  Score=68.37  Aligned_cols=25  Identities=76%  Similarity=1.399  Sum_probs=22.7

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKR   25 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~   25 (92)
                      +|++||.+     .+|+|||||||+|+||+
T Consensus        30 ~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1          30 TREEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             TTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            47889988     99999999999999986

>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=98.89  E-value=1.1e-10  Score=67.98  Aligned_cols=29  Identities=48%  Similarity=0.879  Sum_probs=25.4

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRERNA   29 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~~~   29 (92)
                      +|++||..     .+|+|||||||+|+|+..+..
T Consensus        30 ~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~~   63 (68)
T d2cuea1          30 ARERLAAKIDLPEARIQVWFSNRRAKWRREEKLR   63 (68)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCcChhheeecCcchhHHHHhhhhhh
Confidence            37889988     999999999999999977654

>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=98.80  E-value=1.4e-10  Score=67.65  Aligned_cols=27  Identities=30%  Similarity=0.638  Sum_probs=23.3

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      +|++||..     .+|+|||||||+|+|+..+
T Consensus        31 ~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~~   62 (68)
T d1ftta_          31 EREHLASMIHLTPTQVKIWFQNHRYKMKRQAK   62 (68)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHhCCCccceeeecccHHHHHhhccc
Confidence            37888888     9999999999999998643

>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=98.79  E-value=3.6e-11  Score=71.76  Aligned_cols=26  Identities=31%  Similarity=0.594  Sum_probs=22.6

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRE   26 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~   26 (92)
                      +|++||..     .+|+|||||||+|+|+..
T Consensus        38 ~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~   68 (77)
T d1vnda_          38 EREHLASLIRLTPTQVKIWFQNHRYKTKRAQ   68 (77)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHSSSSCSSSC
T ss_pred             HHHHHHHHhCCChhhhhhcchhHHHHHHHHh
Confidence            37889988     999999999999988744

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-containing protein 1, HMBOX1 (Flj21616)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.78  E-value=2.3e-10  Score=68.81  Aligned_cols=19  Identities=42%  Similarity=0.868  Sum_probs=17.1

Q ss_pred             cccccccccchhHHHHHHH
Q psy15889          9 LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         9 ~qVkiWFQNRRaK~rr~~~   27 (92)
                      .+|+|||||||+|+||+..
T Consensus        57 ~~V~vWFqNRR~k~kk~~~   75 (82)
T d2cufa1          57 LKVYNWFANRRKEIKRRAN   75 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhHHHHHHhhh
Confidence            5899999999999999765

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.76  E-value=8.3e-11  Score=65.38  Aligned_cols=23  Identities=22%  Similarity=0.394  Sum_probs=20.4

Q ss_pred             hhhhhhh-----cccccccccchhHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRK   24 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr   24 (92)
                      |++||..     .+|+|||||||+|.|+
T Consensus        24 ~~~LA~~~~ls~~qV~~WFqNrR~k~k~   51 (52)
T d1x2ma1          24 LEGLSKQLDWDVRSIQRWFRQRRNQEKP   51 (52)
T ss_dssp             HHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHCcCHHHHHHHHHhhhcccCc
Confidence            6788888     9999999999999764

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.74  E-value=1.4e-10  Score=65.55  Aligned_cols=23  Identities=43%  Similarity=0.635  Sum_probs=20.9

Q ss_pred             hhhhhhh-----cccccccccchhHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRK   24 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr   24 (92)
                      +++||.+     .+|+|||||||+|+||
T Consensus        28 ~~~LA~~lgL~~~qV~~WFqNrR~k~kk   55 (57)
T d1e3oc1          28 ITLIAEQLNMEKEVIRVWFSNRRQKEKR   55 (57)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHc
Confidence            6788888     9999999999999987

>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=98.68  E-value=2e-10  Score=63.95  Aligned_cols=23  Identities=43%  Similarity=0.650  Sum_probs=19.8

Q ss_pred             Chhhhhhh-----cccccccccchhHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWR   23 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~r   23 (92)
                      +|++||.+     .+|+|||||||+|.|
T Consensus        26 ~~~~LA~~lgl~~~qV~~WFqNrR~k~K   53 (53)
T d1le8a_          26 EKEEVAKKCGITPLQVRVWFINKRMRSK   53 (53)
T ss_dssp             HHHHHHHHTTSCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHCCCHHHHHHHHHhhhhccC
Confidence            36788888     999999999999864

>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=98.67  E-value=1.3e-10  Score=67.64  Aligned_cols=24  Identities=42%  Similarity=0.462  Sum_probs=21.5

Q ss_pred             Chhhhhhh-----cccccccccchhHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRK   24 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr   24 (92)
                      +|++||..     .+|+|||||||+|+||
T Consensus        37 ~r~~La~~~~l~~~~V~~WFqNrR~k~Kk   65 (67)
T d1ocpa_          37 QITHIANQLGLEKDVVRVWFCNRRQKGKR   65 (67)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHSSSSS
T ss_pred             HHHHHHHHHcCCHHHHHHHhHHHHHHHhc
Confidence            37889988     9999999999999886

>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=98.65  E-value=3e-10  Score=64.26  Aligned_cols=24  Identities=42%  Similarity=0.429  Sum_probs=21.1

Q ss_pred             hhhhhhh-----cccccccccchhHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKR   25 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~   25 (92)
                      |++||..     .+|+|||||||+|+|+.
T Consensus        29 ~~~La~~l~l~~~~V~~WFqNrR~k~kr~   57 (58)
T d1au7a1          29 IMRMAEELNLEKEVVRVWFCNRRQREKRV   57 (58)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHhHHHHhc
Confidence            6778888     99999999999998863

>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=98.62  E-value=3.2e-10  Score=66.40  Aligned_cols=23  Identities=13%  Similarity=0.186  Sum_probs=20.7

Q ss_pred             hhhhhhh-----cccccccccchhHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRK   24 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr   24 (92)
                      |++||..     .+|+|||||||+|+|+
T Consensus        38 ~~~La~~lgl~~~qV~~WFqNrR~k~kk   65 (71)
T d1wi3a_          38 IHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             HHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             HHHHHHHhCCCHHHHHHHhHhhHhhhcc
Confidence            6788888     9999999999999876

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Zinc fingers and homeoboxes protein 1, ZHX1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.61  E-value=7.7e-10  Score=65.51  Aligned_cols=27  Identities=11%  Similarity=0.243  Sum_probs=22.4

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRER   27 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~~   27 (92)
                      +|++||..     .+|+|||||||+|.|+..+
T Consensus        33 ~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~   64 (76)
T d2ecba1          33 ELNRLRAQTKLTRREIDAWFTEKKKSKALKEE   64 (76)
T ss_dssp             HHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCS
T ss_pred             HHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhH
Confidence            37889988     9999999999998766443

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: LAG1 longevity assurance homolog 5, LASS5
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.61  E-value=6.8e-10  Score=63.02  Aligned_cols=22  Identities=18%  Similarity=0.453  Sum_probs=19.7

Q ss_pred             hhhhhhh-----cccccccccchhHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWR   23 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~r   23 (92)
                      |++||.+     .+|+|||||||+|.|
T Consensus        32 ~~~LA~~lgls~~qV~~WFqNrR~k~r   58 (59)
T d2cqxa1          32 LKGLSKQLDWSVRKIQCWFRHRRNQDK   58 (59)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHCcCHHHHHHHHHhhhcccC
Confidence            6788888     999999999999975

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

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

Probab=98.57  E-value=1.8e-09  Score=63.84  Aligned_cols=24  Identities=13%  Similarity=0.253  Sum_probs=21.3

Q ss_pred             hhhhhhh-----cccccccccchhHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKR   25 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~   25 (92)
                      +++||..     .+|+|||||||+|+|+.
T Consensus        33 ~~~La~~~gL~~~qV~~WF~NrR~k~k~~   61 (76)
T d2ecca1          33 YQKLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             HHHHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHHHHhc
Confidence            6778888     99999999999999974

>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=98.54  E-value=7.2e-10  Score=64.15  Aligned_cols=24  Identities=42%  Similarity=0.695  Sum_probs=21.2

Q ss_pred             hhhhhhh-----cccccccccchhHHHHH
Q psy15889          2 GELMALW-----LRVRVWFKNRRAKWRKR   25 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRRaK~rr~   25 (92)
                      |++||.+     .+|+|||||||+|.|+.
T Consensus        33 ~~~LA~~l~l~~~~V~~WFqNrR~k~kk~   61 (66)
T d1bw5a_          33 KEQLVEMTGLSPRVIRVWFQNKRCKDKKR   61 (66)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHHHHHCSSC
T ss_pred             HHHHHHHcCcCHHHhhhhhHhHHHHHHHH
Confidence            6788888     99999999999998764

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.47  E-value=4.5e-09  Score=61.61  Aligned_cols=26  Identities=31%  Similarity=0.511  Sum_probs=22.4

Q ss_pred             Chhhhhhh-----cccccccccchhHHHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRKRE   26 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr~~   26 (92)
                      +|++||.+     .||+|||||+|+|+|+..
T Consensus        33 ~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~   63 (73)
T d1pufb_          33 AKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (73)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHCcCHHHhHHHHHHHHHHhcccc
Confidence            36788888     999999999999988744

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.43  E-value=6e-09  Score=59.02  Aligned_cols=24  Identities=25%  Similarity=0.358  Sum_probs=20.6

Q ss_pred             Chhhhhhh-----cccccccccchhHHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWRK   24 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~rr   24 (92)
                      +|++||..     .+|++||||+|+|.|+
T Consensus        30 e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_          30 GLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            36788888     9999999999998764

>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=98.28  E-value=1.6e-08  Score=55.10  Aligned_cols=18  Identities=22%  Similarity=0.189  Sum_probs=16.5

Q ss_pred             hhhhhhh-----cccccccccch
Q psy15889          2 GELMALW-----LRVRVWFKNRR   19 (92)
Q Consensus         2 R~eLA~~-----~qVkiWFQNRR   19 (92)
                      |++||.+     .+|+|||||||
T Consensus        28 ~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1          28 QITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             HHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             HHHHHHHHCcCHHHhhhcCCcCc
Confidence            6788888     99999999998

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Rat (Rattus rattus) [TaxId: 10117]

Probab=98.14  E-value=1.4e-08  Score=60.44  Aligned_cols=17  Identities=47%  Similarity=0.730  Sum_probs=14.3

Q ss_pred             cccccccccchhHHHHH
Q psy15889          9 LRVRVWFKNRRAKWRKR   25 (92)
Q Consensus         9 ~qVkiWFQNRRaK~rr~   25 (92)
                      .+|++||||||+|.|++
T Consensus        60 ~~V~~WF~NRR~~~kr~   76 (78)
T d1lfba_          60 VRVYNWFANRRKEEAFR   76 (78)
T ss_dssp             HHHHHHHHHHHHTTSCC
T ss_pred             HHHHHHHHHHHHHHHHh
Confidence            36999999999998764

>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=97.96  E-value=2.7e-07  Score=52.34  Aligned_cols=23  Identities=30%  Similarity=0.430  Sum_probs=19.2

Q ss_pred             Chhhhhhh-----cccccccccchhHHH
Q psy15889          1 MGELMALW-----LRVRVWFKNRRAKWR   23 (92)
Q Consensus         1 ~R~eLA~~-----~qVkiWFQNRRaK~r   23 (92)
                      ++++||..     .||++||+|+|.|..
T Consensus        34 e~~~La~~~~l~~~qI~~WF~N~R~R~l   61 (62)
T d1x2na1          34 EKKQIAAQTNLTLLQVNNWFINARRRIL   61 (62)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCcCHHHhHHHHHHHHHHhc
Confidence            36778888     999999999998753