Psyllid ID: psy12003

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60-
Protein Sequence
MNLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHLAT
Secondary Structure (PSIPRED)
cccccccccccccHHHHHHHHHHcHHHHHHHHHcccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccHHHHHHHHHHHHHcHccHHHccccccccccccccccccccHHHHHccc
Coil and Loop (DISEMBL)
mnllrdknpprgterQIKIWFQNRRMKWKKEHKMASmnvipyhyhmsqpygnpyqfthlat
Flexible Loop (DISEMBL)
mnllrdknpprgterqikiwfqnrrMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHLAT
Low Complexity Region (SEG)
MNLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHLAT
Disordered region (IsUnstruct)
****************IKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQF*****
Disordered Region (DISOPRED)
*******NPPRGTERQIKIWFQNRR************************************
Disordered Region (DISEMBL)
MNLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHLAT
Disordered Region (DISPRO)
******KNPPRGTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHLAT
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MNLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHLAT
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	61	2.2.26 [Sep-21-2011]
P09077	417	Homeotic protein Sex comb	yes	N/A	0.754	0.110	0.666	2e-14
P15859	86	Homeobox protein H55 (Fra	no	N/A	0.639	0.453	0.857	2e-13
Q9IA11	252	Homeobox protein Hox-D5 O	N/A	N/A	0.475	0.115	0.793	1e-07
Q1KKX0	280	Homeobox protein Hox-B5b	N/A	N/A	0.459	0.1	0.714	1e-06
Q9PWD3	281	Homeobox protein Hox-A5 O	N/A	N/A	0.442	0.096	0.777	1e-06
Q9YGT6	265	Homeobox protein Hox-A5a	yes	N/A	0.459	0.105	0.75	1e-06
Q1KL14	274	Homeobox protein Hox-A5a	N/A	N/A	0.442	0.098	0.777	2e-06
Q1KKX9	319	Homeobox protein Hox-B5a	N/A	N/A	0.442	0.084	0.777	2e-06
Q9IA23	275	Homeobox protein Hox-A5 O	N/A	N/A	0.459	0.101	0.75	2e-06
P24061	242	Homeobox protein Hox-A7 O	N/A	N/A	0.442	0.111	0.814	2e-06

>sp|P09077|SCR_DROME Homeotic protein Sex combs reduced OS=Drosophila melanogaster GN=Scr PE=1 SV=5

 Score = 77.4 bits (189), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 38/57 (66%), Positives = 42/57 (73%), Gaps = 11/57 (19%)

Query: 13  TERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPY--------QFTHLAT 61
           TERQIKIWFQNRRMKWKKEHKMASMN++PYH     PYG+PY        QF HL+ 
Sbjct: 364 TERQIKIWFQNRRMKWKKEHKMASMNIVPYHM---GPYGHPYHQFDIHPSQFAHLSA 417

Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Controls the segmental transformation of the first to the second thoracic segment (prothorax to mesothorax) and of the labial palps into maxillary palps. In embryo, required for fusion of labial lobes and development of the T1 denticle belt. In adult, expression in the head is necessary for proper development of the labium. In the first thoracic segment of the adult, required for proper development of the sex comb and to suppress improper prothoracic wing development.
Drosophila melanogaster (taxid: 7227)

>sp|P15859|SCR_APIME Homeobox protein H55 (Fragment) OS=Apis mellifera PE=3 SV=1

 Score = 74.7 bits (182), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 36/42 (85%), Positives = 39/42 (92%), Gaps = 3/42 (7%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPY 54
          TERQIKIWFQNRRMKWKKEHKMASMN++P  YHMS PYG+PY
Sbjct: 48 TERQIKIWFQNRRMKWKKEHKMASMNIVP--YHMS-PYGHPY 86

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

Apis mellifera (taxid: 7460)

>sp|Q9IA11|HXD5_HETFR Homeobox protein Hox-D5 OS=Heterodontus francisci GN=HOXD5 PE=3 SV=1

 Score = 54.7 bits (130), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 23/29 (79%), Positives = 27/29 (93%)

Query: 13  TERQIKIWFQNRRMKWKKEHKMASMNVIP 41
           TERQIKIWFQNRRMKWKK++K+ S+NV P
Sbjct: 217 TERQIKIWFQNRRMKWKKDNKLKSINVSP 245

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

Heterodontus francisci (taxid: 7792)

>sp|Q1KKX0|HXB5B_TAKRU Homeobox protein Hox-B5b OS=Takifugu rubripes GN=hoxb5b PE=3 SV=1

 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 20/28 (71%), Positives = 27/28 (96%)

Query: 13  TERQIKIWFQNRRMKWKKEHKMASMNVI 40
           +ERQIKIWFQNRRMKWKK++K+ SM+++
Sbjct: 245 SERQIKIWFQNRRMKWKKDNKLKSMSLV 272

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

Takifugu rubripes (taxid: 31033)

>sp|Q9PWD3|HXA5_MORSA Homeobox protein Hox-A5 OS=Morone saxatilis GN=hoxa5 PE=3 SV=1

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 21/27 (77%), Positives = 26/27 (96%)

Query: 13  TERQIKIWFQNRRMKWKKEHKMASMNV 39
           +ERQIKIWFQNRRMKWKK++K+ SMN+
Sbjct: 245 SERQIKIWFQNRRMKWKKDNKLKSMNM 271

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

Morone saxatilis (taxid: 34816)

>sp|Q9YGT6|HXA5A_DANRE Homeobox protein Hox-A5a OS=Danio rerio GN=hoxa5a PE=2 SV=2

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 21/28 (75%), Positives = 26/28 (92%)

Query: 13  TERQIKIWFQNRRMKWKKEHKMASMNVI 40
           +ERQIKIWFQNRRMKWKK++K+ SMN+ 
Sbjct: 230 SERQIKIWFQNRRMKWKKDNKLKSMNMA 257

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

Danio rerio (taxid: 7955)

>sp|Q1KL14|HXA5A_TAKRU Homeobox protein Hox-A5a OS=Takifugu rubripes GN=hoxa5a PE=3 SV=1

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/27 (77%), Positives = 26/27 (96%)

Query: 13  TERQIKIWFQNRRMKWKKEHKMASMNV 39
           +ERQIKIWFQNRRMKWKK++K+ SMN+
Sbjct: 238 SERQIKIWFQNRRMKWKKDNKLKSMNM 264

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

Takifugu rubripes (taxid: 31033)

>sp|Q1KKX9|HXB5A_TAKRU Homeobox protein Hox-B5a OS=Takifugu rubripes GN=hoxb5a PE=3 SV=1

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 21/27 (77%), Positives = 26/27 (96%)

Query: 13  TERQIKIWFQNRRMKWKKEHKMASMNV 39
           TERQIKIWFQNRRMKWKK++K+ SM++
Sbjct: 284 TERQIKIWFQNRRMKWKKDNKLKSMSL 310

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

Takifugu rubripes (taxid: 31033)

>sp|Q9IA23|HXA5_HETFR Homeobox protein Hox-A5 OS=Heterodontus francisci GN=HOXA5 PE=3 SV=1

 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/28 (75%), Positives = 26/28 (92%)

Query: 13  TERQIKIWFQNRRMKWKKEHKMASMNVI 40
           TERQIKIWFQNRRMKWKK++K+ SM++ 
Sbjct: 240 TERQIKIWFQNRRMKWKKDNKLKSMSMA 267

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

Heterodontus francisci (taxid: 7792)

>sp|P24061|HXA7_COTJA Homeobox protein Hox-A7 OS=Coturnix coturnix japonica GN=HOXA7 PE=2 SV=1

 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/27 (81%), Positives = 23/27 (85%)

Query: 13  TERQIKIWFQNRRMKWKKEHKMASMNV 39
           TERQIKIWFQNRRMKWKKEHK  S + 
Sbjct: 169 TERQIKIWFQNRRMKWKKEHKEESSST 195

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

Coturnix coturnix japonica (taxid: 93934)

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	61
326370247	329	sex combs reduced [Publilia modesta]	0.803	0.148	0.979	6e-22
270065291	302	sex combs reduced [Oncopeltus fasciatus]	0.803	0.162	0.979	8e-22
224460203	338	sex combs reduced [Rhodnius prolixus]	0.803	0.144	0.938	2e-20
328778440	380	PREDICTED: homeotic protein Sex combs re	0.754	0.121	0.75	4e-14
383849607	373	PREDICTED: homeobox protein Hox-A5a-like	0.754	0.123	0.75	4e-14
7229537	312	sex combs reduced Scr [Tribolium castane	0.754	0.147	0.75	5e-14
350405517	372	PREDICTED: hypothetical protein LOC10074	0.754	0.123	0.75	5e-14
340727747	372	PREDICTED: hypothetical protein LOC10064	0.754	0.123	0.75	5e-14
86515396	312	cephalothorax [Tribolium castaneum] gi|1	0.754	0.147	0.75	5e-14
54607270	312	cephalothorax [Tribolium castaneum]	0.754	0.147	0.75	5e-14

>gi|326370247|gb|ADZ56089.1| sex combs reduced [Publilia modesta]

 Score =  108 bits (269), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 48/49 (97%), Positives = 48/49 (97%)

Query: 13  TERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHLAT 61
           TERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHL T
Sbjct: 281 TERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHLTT 329

Source: Publilia modesta

Species: Publilia modesta

Genus: Publilia

Family: Membracidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270065291|gb|ACZ60640.1| sex combs reduced [Oncopeltus fasciatus]

 Score =  107 bits (267), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 48/49 (97%), Positives = 48/49 (97%)

Query: 13  TERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHLAT 61
           TERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHL T
Sbjct: 254 TERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHLTT 302

Source: Oncopeltus fasciatus

Species: Oncopeltus fasciatus

Genus: Oncopeltus

Family: Lygaeidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|224460203|gb|ACN43631.1| sex combs reduced [Rhodnius prolixus]

 Score =  102 bits (255), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 46/49 (93%), Positives = 47/49 (95%)

Query: 13  TERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQFTHLAT 61
           TERQIKIWFQNRRMKWKKE+KMASMNVIPYHYHMSQPY NPYQFTHL T
Sbjct: 290 TERQIKIWFQNRRMKWKKENKMASMNVIPYHYHMSQPYANPYQFTHLTT 338

Source: Rhodnius prolixus

Species: Rhodnius prolixus

Genus: Rhodnius

Family: Reduviidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328778440|ref|XP_623903.2| PREDICTED: homeotic protein Sex combs reduced [Apis mellifera]

 Score = 82.0 bits (201), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 42/56 (75%), Positives = 45/56 (80%), Gaps = 10/56 (17%)

Query: 13  TERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPY-------QFTHLAT 61
           TERQIKIWFQNRRMKWKKEHKMASMN++P  YHMS PYG+PY       QF HLAT
Sbjct: 328 TERQIKIWFQNRRMKWKKEHKMASMNIVP--YHMS-PYGHPYQFAPHPGQFAHLAT 380

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383849607|ref|XP_003700436.1| PREDICTED: homeobox protein Hox-A5a-like [Megachile rotundata]

 Score = 82.0 bits (201), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 42/56 (75%), Positives = 45/56 (80%), Gaps = 10/56 (17%)

Query: 13  TERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPY-------QFTHLAT 61
           TERQIKIWFQNRRMKWKKEHKMASMN++P  YHMS PYG+PY       QF HLAT
Sbjct: 321 TERQIKIWFQNRRMKWKKEHKMASMNIVP--YHMS-PYGHPYQFAPHPGQFAHLAT 373

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|7229537|gb|AAF42868.1|AF227628_1 sex combs reduced Scr [Tribolium castaneum] gi|54607266|gb|AAL26542.2| cephalothorax [Tribolium castaneum] gi|54607268|gb|AAL27023.2| cephalothorax [Tribolium castaneum]

 Score = 82.0 bits (201), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 42/56 (75%), Positives = 45/56 (80%), Gaps = 10/56 (17%)

Query: 13  TERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPY-------QFTHLAT 61
           TERQIKIWFQNRRMKWKKEHKMASMN++P  YHMS PYG+PY       QF HLAT
Sbjct: 260 TERQIKIWFQNRRMKWKKEHKMASMNIVP--YHMS-PYGHPYQFDLHPSQFAHLAT 312

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350405517|ref|XP_003487459.1| PREDICTED: hypothetical protein LOC100747162 [Bombus impatiens]

 Score = 81.6 bits (200), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 42/56 (75%), Positives = 45/56 (80%), Gaps = 10/56 (17%)

Query: 13  TERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPY-------QFTHLAT 61
           TERQIKIWFQNRRMKWKKEHKMASMN++P  YHMS PYG+PY       QF HLAT
Sbjct: 320 TERQIKIWFQNRRMKWKKEHKMASMNIVP--YHMS-PYGHPYQFAPHPGQFAHLAT 372

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340727747|ref|XP_003402198.1| PREDICTED: hypothetical protein LOC100643224 [Bombus terrestris]

 Score = 81.6 bits (200), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 42/56 (75%), Positives = 45/56 (80%), Gaps = 10/56 (17%)

Query: 13  TERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPY-------QFTHLAT 61
           TERQIKIWFQNRRMKWKKEHKMASMN++P  YHMS PYG+PY       QF HLAT
Sbjct: 320 TERQIKIWFQNRRMKWKKEHKMASMNIVP--YHMS-PYGHPYQFAPHPGQFAHLAT 372

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|86515396|ref|NP_001034523.1| cephalothorax [Tribolium castaneum] gi|13241681|gb|AAK16422.1|AF321227_2 Scr [Tribolium castaneum] gi|270002805|gb|EEZ99252.1| sex combs reduced [Tribolium castaneum]

 Score = 81.6 bits (200), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 42/56 (75%), Positives = 45/56 (80%), Gaps = 10/56 (17%)

Query: 13  TERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPY-------QFTHLAT 61
           TERQIKIWFQNRRMKWKKEHKMASMN++P  YHMS PYG+PY       QF HLAT
Sbjct: 260 TERQIKIWFQNRRMKWKKEHKMASMNIVP--YHMS-PYGHPYQFDLHPSQFAHLAT 312

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|54607270|gb|AAL23667.2| cephalothorax [Tribolium castaneum]

 Score = 81.6 bits (200), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 42/56 (75%), Positives = 45/56 (80%), Gaps = 10/56 (17%)

Query: 13  TERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPY-------QFTHLAT 61
           TERQIKIWFQNRRMKWKKEHKMASMN++P  YHMS PYG+PY       QF HLAT
Sbjct: 260 TERQIKIWFQNRRMKWKKEHKMASMNIVP--YHMS-PYGHPYQFDLHPSQFAHLAT 312

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	61
FB|FBgn0003339	417	Scr "Sex combs reduced" [Droso	0.672	0.098	0.822	9.4e-15
UNIPROTKB|P09016	255	HOXD4 "Homeobox protein Hox-D4	0.360	0.086	0.863	6e-08
MGI|MGI:96208	250	Hoxd4 "homeobox D4" [Mus muscu	0.360	0.088	0.863	6.9e-08
RGD|1309690	251	Hoxd4 "homeo box D4" [Rattus n	0.360	0.087	0.863	7e-08
UNIPROTKB|F1RZG0	257	HOXD4 "Uncharacterized protein	0.360	0.085	0.863	7.9e-08
UNIPROTKB|A7MBD6	258	HOXD4 "Uncharacterized protein	0.360	0.085	0.863	8.1e-08
UNIPROTKB|F1NLW0	187	LOC100858514 "Uncharacterized	0.393	0.128	0.916	1.1e-07
RGD|1587253	105	Hoxa7 "homeobox A7" [Rattus no	0.344	0.2	1.0	1.4e-07
UNIPROTKB|P09634	105	Hoxa7 "Homeobox protein Hox-A7	0.344	0.2	1.0	1.4e-07
UNIPROTKB|Q90VZ9	219	HOXA7 "Homeobox protein Hox-A7	0.393	0.109	0.916	1.8e-07

FB|FBgn0003339 Scr "Sex combs reduced" [Drosophila melanogaster (taxid:7227)]

 Score = 194 (73.4 bits), Expect = 9.4e-15, P = 9.4e-15
 Identities = 37/45 (82%), Positives = 40/45 (88%)

Query:    13 TERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPY-QF 56
             TERQIKIWFQNRRMKWKKEHKMASMN++PYH  M  PYG+PY QF
Sbjct:   364 TERQIKIWFQNRRMKWKKEHKMASMNIVPYH--MG-PYGHPYHQF 405

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

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

GO:0005634 "nucleus" evidence=ISS;NAS

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

GO:0007494 "midgut development" evidence=TAS

GO:0007379 "segment specification" evidence=NAS

GO:0007381 "specification of segmental identity, labial segment" evidence=TAS

GO:0045498 "sex comb development" evidence=IMP;NAS

GO:0007548 "sex differentiation" evidence=TAS

GO:0007432 "salivary gland boundary specification" evidence=NAS;TAS

GO:0000977 "RNA polymerase II regulatory region sequence-specific DNA binding" evidence=IDA

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

GO:0042803 "protein homodimerization activity" evidence=IDA

UNIPROTKB|P09016 HOXD4 "Homeobox protein Hox-D4" [Homo sapiens (taxid:9606)]

 Score = 115 (45.5 bits), Expect = 6.0e-08, Sum P(2) = 6.0e-08
 Identities = 19/22 (86%), Positives = 22/22 (100%)

Query:    13 TERQIKIWFQNRRMKWKKEHKM 34
             +ERQIKIWFQNRRMKWKK+HK+
Sbjct:   194 SERQIKIWFQNRRMKWKKDHKL 215

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

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

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

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

GO:0048863 "stem cell differentiation" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=NAS

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

GO:0005634 "nucleus" evidence=NAS

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

MGI|MGI:96208 Hoxd4 "homeobox D4" [Mus musculus (taxid:10090)]

 Score = 115 (45.5 bits), Expect = 6.9e-08, Sum P(2) = 6.9e-08
 Identities = 19/22 (86%), Positives = 22/22 (100%)

Query:    13 TERQIKIWFQNRRMKWKKEHKM 34
             +ERQIKIWFQNRRMKWKK+HK+
Sbjct:   192 SERQIKIWFQNRRMKWKKDHKL 213

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

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

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

GO:0048704 "embryonic skeletal system morphogenesis" evidence=IGI;IMP

GO:0048863 "stem cell differentiation" evidence=IDA

RGD|1309690 Hoxd4 "homeo box D4" [Rattus norvegicus (taxid:10116)]

 Score = 115 (45.5 bits), Expect = 7.0e-08, Sum P(2) = 7.0e-08
 Identities = 19/22 (86%), Positives = 22/22 (100%)

Query:    13 TERQIKIWFQNRRMKWKKEHKM 34
             +ERQIKIWFQNRRMKWKK+HK+
Sbjct:   192 SERQIKIWFQNRRMKWKKDHKL 213

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

GO:0005634 "nucleus" evidence=IEA

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

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

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

GO:0048863 "stem cell differentiation" evidence=IEA;ISO

UNIPROTKB|F1RZG0 HOXD4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 115 (45.5 bits), Expect = 7.9e-08, Sum P(2) = 7.9e-08
 Identities = 19/22 (86%), Positives = 22/22 (100%)

Query:    13 TERQIKIWFQNRRMKWKKEHKM 34
             +ERQIKIWFQNRRMKWKK+HK+
Sbjct:   195 SERQIKIWFQNRRMKWKKDHKL 216

GO:0005634 "nucleus" evidence=IEA

GO:0048863 "stem cell differentiation" evidence=IEA

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

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

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

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

UNIPROTKB|A7MBD6 HOXD4 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 115 (45.5 bits), Expect = 8.1e-08, Sum P(2) = 8.1e-08
 Identities = 19/22 (86%), Positives = 22/22 (100%)

Query:    13 TERQIKIWFQNRRMKWKKEHKM 34
             +ERQIKIWFQNRRMKWKK+HK+
Sbjct:   197 SERQIKIWFQNRRMKWKKDHKL 218

GO:0005634 "nucleus" evidence=IEA

GO:0048863 "stem cell differentiation" evidence=IEA

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

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

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

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

UNIPROTKB|F1NLW0 LOC100858514 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 121 (47.7 bits), Expect = 1.1e-07, P = 1.1e-07
 Identities = 22/24 (91%), Positives = 22/24 (91%)

Query:    13 TERQIKIWFQNRRMKWKKEHKMAS 36
             TERQIKIWFQNRRMKWKKEHK  S
Sbjct:   137 TERQIKIWFQNRRMKWKKEHKEES 160

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

RGD|1587253 Hoxa7 "homeobox A7" [Rattus norvegicus (taxid:10116)]

 Score = 120 (47.3 bits), Expect = 1.4e-07, P = 1.4e-07
 Identities = 21/21 (100%), Positives = 21/21 (100%)

Query:    13 TERQIKIWFQNRRMKWKKEHK 33
             TERQIKIWFQNRRMKWKKEHK
Sbjct:    45 TERQIKIWFQNRRMKWKKEHK 65

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

GO:0001525 "angiogenesis" evidence=ISO

GO:0001953 "negative regulation of cell-matrix adhesion" evidence=ISO

GO:0002686 "negative regulation of leukocyte migration" evidence=ISO

GO:0003677 "DNA binding" evidence=ISO

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

GO:0005634 "nucleus" evidence=IEA;ISO

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0008134 "transcription factor binding" evidence=ISO

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

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

GO:0045617 "negative regulation of keratinocyte differentiation" evidence=ISO

GO:0045656 "negative regulation of monocyte differentiation" evidence=ISO

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

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

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

GO:0048863 "stem cell differentiation" evidence=ISO

UNIPROTKB|P09634 Hoxa7 "Homeobox protein Hox-A7" [Rattus norvegicus (taxid:10116)]

 Score = 120 (47.3 bits), Expect = 1.4e-07, P = 1.4e-07
 Identities = 21/21 (100%), Positives = 21/21 (100%)

Query:    13 TERQIKIWFQNRRMKWKKEHK 33
             TERQIKIWFQNRRMKWKKEHK
Sbjct:    45 TERQIKIWFQNRRMKWKKEHK 65

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

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

UNIPROTKB|Q90VZ9 HOXA7 "Homeobox protein Hox-A7" [Gallus gallus (taxid:9031)]

 Score = 121 (47.7 bits), Expect = 1.8e-07, P = 1.8e-07
 Identities = 22/24 (91%), Positives = 22/24 (91%)

Query:    13 TERQIKIWFQNRRMKWKKEHKMAS 36
             TERQIKIWFQNRRMKWKKEHK  S
Sbjct:   169 TERQIKIWFQNRRMKWKKEHKEES 192

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

---

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)
P09067	HXB5_HUMAN	No assigned EC number	0.7142	0.4590	0.1040	yes	N/A
P09077	SCR_DROME	No assigned EC number	0.6666	0.7540	0.1103	yes	N/A
Q90VZ9	HXA7_CHICK	No assigned EC number	0.8148	0.4426	0.1232	yes	N/A
Q9YGT6	HXA5A_DANRE	No assigned EC number	0.75	0.4590	0.1056	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	61
pfam00046	57	pfam00046, Homeobox, Homeobox domain	1e-08
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	3e-07
smart00389	57	smart00389, HOX, Homeodomain	9e-07

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

 Score = 45.2 bits (108), Expect = 1e-08
 Identities = 14/18 (77%), Positives = 17/18 (94%)

Query: 13 TERQIKIWFQNRRMKWKK 30
          TERQ+K+WFQNRR KWK+
Sbjct: 40 TERQVKVWFQNRRAKWKR 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 = 41.8 bits (99), Expect = 3e-07
 Identities = 14/20 (70%), Positives = 16/20 (80%)

Query: 13 TERQIKIWFQNRRMKWKKEH 32
          TERQ+KIWFQNRR K K+  
Sbjct: 40 TERQVKIWFQNRRAKLKRSE 59

Length = 59

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 40.7 bits (96), Expect = 9e-07
 Identities = 13/17 (76%), Positives = 16/17 (94%)

Query: 13 TERQIKIWFQNRRMKWK 29
          +ERQ+K+WFQNRR KWK
Sbjct: 41 SERQVKVWFQNRRAKWK 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	61
KOG0489|consensus	261		99.66
KOG0487|consensus	308		99.62
KOG0848|consensus	317		99.6
KOG0850|consensus	245		99.59
KOG0488|consensus	309		99.59
KOG0844|consensus	408		99.58
KOG0842|consensus	307		99.57
KOG0485|consensus	268		99.5
KOG0484|consensus	125		99.5
KOG0843|consensus	197		99.47
KOG0492|consensus	246		99.47
KOG0491|consensus	194		99.45
KOG0483|consensus	198		99.39
KOG2251|consensus	228		99.39
KOG0494|consensus	332		99.34
KOG0847|consensus	288		99.27
KOG4577|consensus	383		99.17
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.16
KOG0493|consensus	342		99.07
KOG0486|consensus	351		99.06
KOG3802|consensus	398		99.0
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	98.99
COG5576	156	Homeodomain-containing transcription factor [Trans	98.97
KOG0490|consensus	235		98.94
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	98.89
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	98.82
KOG0849|consensus	354		98.46
KOG0775|consensus	304		98.23
KOG1168|consensus	385		98.17
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	97.75
KOG0490|consensus	235		97.41
KOG0774|consensus	334		96.46
KOG1146|consensus	1406		95.86
PF10668	60	Phage_terminase: Phage terminase small subunit; In	94.54
KOG3623|consensus	1007		94.14
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	93.87
KOG0773|consensus	342		92.06
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	89.94
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	87.48
COG5484	279	Uncharacterized conserved protein [Function unknow	86.28
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	85.86
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	85.57
KOG2252|consensus	558		83.1
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	82.04
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	81.88
cd04763	68	HTH_MlrA-like Helix-Turn-Helix DNA binding domain	80.88
cd04764	67	HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding dom	80.41

>KOG0489|consensus

Probab=99.66  E-value=1.9e-17  Score=106.23  Aligned_cols=35  Identities=60%  Similarity=0.880  Sum_probs=31.7

Q ss_pred             hhhhcCCCCCccceeeccccchhHHHHHhhhhccC
Q psy12003          4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHKMASMN   38 (61)
Q Consensus         4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~~~   38 (61)
                      .|||..|+|+|+|||||||||||||||..+.....
T Consensus       190 iEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~  224 (261)
T KOG0489|consen  190 IEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ  224 (261)
T ss_pred             HHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence            48999999999999999999999999998866654

>KOG0487|consensus

Probab=99.62  E-value=7.9e-17  Score=105.49  Aligned_cols=32  Identities=53%  Similarity=0.674  Sum_probs=29.3

Q ss_pred             hhhhcCCCCCccceeeccccchhHHHHHhhhh
Q psy12003          4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHKMA   35 (61)
Q Consensus         4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~   35 (61)
                      .|||+.|||||+||||||||||+|.||..+..
T Consensus       266 ~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~  297 (308)
T KOG0487|consen  266 LELSRTLNLTERQVKIWFQNRRMKEKKVNREN  297 (308)
T ss_pred             HHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence            48999999999999999999999999998633

>KOG0848|consensus

Probab=99.60  E-value=1.8e-16  Score=102.39  Aligned_cols=32  Identities=44%  Similarity=0.577  Sum_probs=29.3

Q ss_pred             hhhhcCCCCCccceeeccccchhHHHHHhhhh
Q psy12003          4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHKMA   35 (61)
Q Consensus         4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~   35 (61)
                      .|||..|+|+|+||||||||||||.||..+.+
T Consensus       230 SELA~~LgLsERQVKIWFQNRRAKERK~nKKk  261 (317)
T KOG0848|consen  230 SELAATLGLSERQVKIWFQNRRAKERKDNKKK  261 (317)
T ss_pred             HHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence            58999999999999999999999999986654

>KOG0850|consensus

Probab=99.59  E-value=5e-16  Score=98.38  Aligned_cols=36  Identities=42%  Similarity=0.473  Sum_probs=32.3

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhhcc
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMASM   37 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~~   37 (61)
                      |=+|||+.||||.+||||||||||.|.||..+.+..
T Consensus       151 ERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~  186 (245)
T KOG0850|consen  151 ERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSG  186 (245)
T ss_pred             HHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCC
Confidence            568999999999999999999999999999885443

>KOG0488|consensus

Probab=99.59  E-value=4.7e-16  Score=101.97  Aligned_cols=31  Identities=39%  Similarity=0.678  Sum_probs=29.0

Q ss_pred             hhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003          4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHKM   34 (61)
Q Consensus         4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~   34 (61)
                      ++||+.||||++|||+||||||+||||+...
T Consensus       203 ~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~  233 (309)
T KOG0488|consen  203 IELAASLGLTDAQVKTWFQNRRTKWKRQTAE  233 (309)
T ss_pred             HHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence            6899999999999999999999999999654

>KOG0844|consensus

Probab=99.58  E-value=8.3e-17  Score=105.79  Aligned_cols=34  Identities=35%  Similarity=0.453  Sum_probs=30.3

Q ss_pred             hhhhcCCCCCccceeeccccchhHHHHHhhhhcc
Q psy12003          4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHKMASM   37 (61)
Q Consensus         4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~~   37 (61)
                      -|||.+|||+|++|||||||||+|.|||.....+
T Consensus       212 cELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaW  245 (408)
T KOG0844|consen  212 CELAAALNLPETTIKVWFQNRRMKDKRQRLAMAW  245 (408)
T ss_pred             hhHHHhhCCCcceeehhhhhchhhhhhhhhhccC
Confidence            3899999999999999999999999999765444

>KOG0842|consensus

Probab=99.57  E-value=1.1e-15  Score=100.19  Aligned_cols=40  Identities=35%  Similarity=0.474  Sum_probs=34.6

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhhccCccC
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMASMNVIP   41 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~~~~~~   41 (61)
                      |=.+||..|+||++||||||||||.|.||++..+......
T Consensus       182 ERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~  221 (307)
T KOG0842|consen  182 EREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALL  221 (307)
T ss_pred             hHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhccc
Confidence            3468999999999999999999999999998877665533

>KOG0485|consensus

Probab=99.50  E-value=2.7e-15  Score=94.96  Aligned_cols=32  Identities=44%  Similarity=0.659  Sum_probs=28.9

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      |=+.||++|.|||+||||||||||.||||+-.
T Consensus       133 eRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a  164 (268)
T KOG0485|consen  133 ERAGLAASLQLTETQVKIWFQNRRNKWKRQYA  164 (268)
T ss_pred             HHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence            44679999999999999999999999999944

>KOG0484|consensus

Probab=99.50  E-value=2.4e-15  Score=86.15  Aligned_cols=32  Identities=34%  Similarity=0.551  Sum_probs=29.4

Q ss_pred             hhhhcCCCCCccceeeccccchhHHHHHhhhh
Q psy12003          4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHKMA   35 (61)
Q Consensus         4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~   35 (61)
                      .|||.+++|||.+|||||||||+|.||+++..
T Consensus        48 EEiA~kidLTEARVQVWFQNRRAKfRKQEr~a   79 (125)
T KOG0484|consen   48 EEIALKIDLTEARVQVWFQNRRAKFRKQERAA   79 (125)
T ss_pred             HHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHH
Confidence            58999999999999999999999999997743

>KOG0843|consensus

Probab=99.47  E-value=9.7e-15  Score=89.96  Aligned_cols=33  Identities=33%  Similarity=0.490  Sum_probs=29.9

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKM   34 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~   34 (61)
                      |=.+||+.|+|+|+||||||||||.|.||....
T Consensus       131 eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e  163 (197)
T KOG0843|consen  131 ERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE  163 (197)
T ss_pred             HHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence            446899999999999999999999999998664

>KOG0492|consensus

Probab=99.47  E-value=1.3e-14  Score=91.25  Aligned_cols=33  Identities=39%  Similarity=0.488  Sum_probs=30.0

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKM   34 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~   34 (61)
                      |=+|++..|.|||+||||||||||+|.||.+..
T Consensus       173 EraefSsSL~LTeTqVKIWFQNRRAKaKRlQea  205 (246)
T KOG0492|consen  173 ERAEFSSSLELTETQVKIWFQNRRAKAKRLQEA  205 (246)
T ss_pred             HHHhhhhhhhhhhhheehhhhhhhHHHHHHHHH
Confidence            457899999999999999999999999998663

>KOG0491|consensus

Probab=99.45  E-value=2e-14  Score=87.76  Aligned_cols=35  Identities=40%  Similarity=0.545  Sum_probs=32.2

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhhc
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMAS   36 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~   36 (61)
                      |+.|||..|+|+|+|||.||||||+|.||+.+...
T Consensus       129 e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~  163 (194)
T KOG0491|consen  129 ERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ  163 (194)
T ss_pred             HHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence            67899999999999999999999999999987544

>KOG0483|consensus

Probab=99.39  E-value=2.7e-14  Score=89.07  Aligned_cols=32  Identities=31%  Similarity=0.590  Sum_probs=28.7

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +...||..|||.++||.||||||||+||.++.
T Consensus        79 ~K~~LAk~LgL~pRQVavWFQNRRARwK~kql  110 (198)
T KOG0483|consen   79 RKKKLAKELGLQPRQVAVWFQNRRARWKTKQL  110 (198)
T ss_pred             HHHHHHHhhCCChhHHHHHHhhccccccchhh
Confidence            34689999999999999999999999998843

>KOG2251|consensus

Probab=99.39  E-value=1.8e-13  Score=86.32  Aligned_cols=32  Identities=22%  Similarity=0.437  Sum_probs=29.8

Q ss_pred             hhhhcCCCCCccceeeccccchhHHHHHhhhh
Q psy12003          4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHKMA   35 (61)
Q Consensus         4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~   35 (61)
                      .|||.+|||+|.+|||||+|||+|+|++++..
T Consensus        68 EelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   68 EELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             HHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            58999999999999999999999999998864

>KOG0494|consensus

Probab=99.34  E-value=1.9e-13  Score=88.48  Aligned_cols=32  Identities=38%  Similarity=0.642  Sum_probs=28.7

Q ss_pred             hhcCCCCCccceeeccccchhHHHHHhhhhcc
Q psy12003          6 DKNPPRGTERQIKIWFQNRRMKWKKEHKMASM   37 (61)
Q Consensus         6 LA~~l~Lte~~VqvWFqNrRak~kr~~~~~~~   37 (61)
                      ||.++.|+|.+|+|||||||+||||.++.-..
T Consensus       174 la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~  205 (332)
T KOG0494|consen  174 LADKTELPEDRIQVWFQNRRAKWRKTEKRWGG  205 (332)
T ss_pred             HhhhccCchhhhhHHhhhhhHHhhhhhhhcCc
Confidence            68899999999999999999999999886443

>KOG0847|consensus

Probab=99.27  E-value=7.9e-13  Score=84.07  Aligned_cols=32  Identities=44%  Similarity=0.783  Sum_probs=29.4

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      |-++||..+|++|.+|+|||||||.||||+..
T Consensus       196 ~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA  227 (288)
T KOG0847|consen  196 DRAQLAQELNMTESQVKVWFQNRRTKWRKKHA  227 (288)
T ss_pred             hHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence            45789999999999999999999999999854

>KOG4577|consensus

Probab=99.17  E-value=7.4e-12  Score=82.19  Aligned_cols=34  Identities=32%  Similarity=0.385  Sum_probs=29.8

Q ss_pred             hhhhcCCCCCccceeeccccchhHHHHHhhhhcc
Q psy12003          4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHKMASM   37 (61)
Q Consensus         4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~~   37 (61)
                      ..|+.++||+.++|||||||||||.||..+..+.
T Consensus       198 EQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR  231 (383)
T KOG4577|consen  198 EQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGR  231 (383)
T ss_pred             HHhhhccCcceeehhhhhhhhhHHHHhhhhhcch
Confidence            3689999999999999999999999999775443

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.16  E-value=1.2e-12  Score=66.48  Aligned_cols=29  Identities=48%  Similarity=0.486  Sum_probs=27.3

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK   30 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr   30 (61)
                      ++.+||..|||++.+|++||+|||.++|+
T Consensus        29 ~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen   29 EREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             HHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             ccccccccccccccccccCHHHhHHHhCc
Confidence            57899999999999999999999999986

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

>KOG0493|consensus

Probab=99.07  E-value=1.8e-11  Score=79.53  Aligned_cols=30  Identities=43%  Similarity=0.509  Sum_probs=27.3

Q ss_pred             hhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      .+||.+|+|.|.||||||||+|+|.||--.
T Consensus       277 Q~La~ELgLNEsQIKIWFQNKRAKiKKsTg  306 (342)
T KOG0493|consen  277 QELAQELGLNESQIKIWFQNKRAKIKKSTG  306 (342)
T ss_pred             HHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence            479999999999999999999999998644

>KOG0486|consensus

Probab=99.06  E-value=7.4e-11  Score=77.81  Aligned_cols=33  Identities=30%  Similarity=0.585  Sum_probs=30.0

Q ss_pred             hhhhcCCCCCccceeeccccchhHHHHHhhhhc
Q psy12003          4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHKMAS   36 (61)
Q Consensus         4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~   36 (61)
                      .|||..++|||.+|+|||.|||+||||.++...
T Consensus       143 EEIavwtNlTE~rvrvwfknrrakwrkrErN~~  175 (351)
T KOG0486|consen  143 EEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ  175 (351)
T ss_pred             hHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence            488999999999999999999999999987544

>KOG3802|consensus

Probab=99.00  E-value=1.6e-10  Score=77.89  Aligned_cols=32  Identities=22%  Similarity=0.376  Sum_probs=30.8

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      ||.+||.+|+|...+|+|||+|||.|.||...
T Consensus       323 EIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  323 EITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             HHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            89999999999999999999999999999876

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

Probab=98.99  E-value=2e-11  Score=61.79  Aligned_cols=30  Identities=47%  Similarity=0.593  Sum_probs=27.7

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE   31 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~   31 (61)
                      ++.+||..+||++.+|++||+|||.+.++.
T Consensus        29 ~~~~la~~~~l~~~qV~~WF~nrR~~~~~~   58 (59)
T cd00086          29 EREELAKELGLTERQVKIWFQNRRAKLKRS   58 (59)
T ss_pred             HHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence            678999999999999999999999998763

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=98.97  E-value=1.4e-10  Score=70.21  Aligned_cols=32  Identities=28%  Similarity=0.395  Sum_probs=28.8

Q ss_pred             hhhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003          3 LLRDKNPPRGTERQIKIWFQNRRMKWKKEHKM   34 (61)
Q Consensus         3 ~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~   34 (61)
                      -.+|+..||++++-|||||||||++.|+....
T Consensus        81 r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~  112 (156)
T COG5576          81 RIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG  112 (156)
T ss_pred             HHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence            35799999999999999999999999998654

>KOG0490|consensus

Probab=98.94  E-value=5.4e-10  Score=69.11  Aligned_cols=30  Identities=37%  Similarity=0.512  Sum_probs=27.9

Q ss_pred             hhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      .+||..++++|.+|||||||||+||+++..
T Consensus        91 ~~la~~~~~~e~rVqvwFqnrrak~r~~~~  120 (235)
T KOG0490|consen   91 ECLALLLTGDEFRVQVWFQNRRAKDRKEER  120 (235)
T ss_pred             HHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence            368999999999999999999999999875

>smart00389 HOX Homeodomain

Probab=98.89  E-value=5.3e-11  Score=59.90  Aligned_cols=28  Identities=46%  Similarity=0.741  Sum_probs=25.6

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWK   29 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~k   29 (61)
                      ++.+||..+||+..+|+.||+|||++.+
T Consensus        29 ~~~~la~~~~l~~~qV~~WF~nrR~~~~   56 (56)
T smart00389       29 EREELAAKLGLSERQVKVWFQNRRAKWK   56 (56)
T ss_pred             HHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence            5789999999999999999999998753

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

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=98.82  E-value=7.3e-10  Score=57.47  Aligned_cols=24  Identities=17%  Similarity=0.311  Sum_probs=22.1

Q ss_pred             chhhhhcCCCCCccceeeccccch
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRR   25 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrR   25 (61)
                      +..+||..|||++.+|||||||.+
T Consensus        34 ~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565        34 EVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             HHHHHHHHhCCCHHHeeeecccCC
Confidence            578999999999999999999975

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.

>KOG0849|consensus

Probab=98.46  E-value=6.7e-08  Score=64.60  Aligned_cols=30  Identities=33%  Similarity=0.769  Sum_probs=28.3

Q ss_pred             hhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      .+||.+++|+|.+|+|||+|||++|+|+..
T Consensus       207 e~La~~i~l~e~riqvwf~nrra~~rr~~~  236 (354)
T KOG0849|consen  207 ETLAKETGLPEPRVQVWFQNRRAKWRRQHR  236 (354)
T ss_pred             HHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence            579999999999999999999999999984

>KOG0775|consensus

Probab=98.23  E-value=6.7e-07  Score=58.47  Aligned_cols=31  Identities=23%  Similarity=0.258  Sum_probs=27.2

Q ss_pred             hhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          3 LLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         3 ~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      =-|||.++||+.+||-.||+|||.+.|-...
T Consensus       206 KReLA~aTgLt~tQVsNWFKNRRQRDRa~~a  236 (304)
T KOG0775|consen  206 KRELAEATGLTITQVSNWFKNRRQRDRAAAA  236 (304)
T ss_pred             HHHHHHHhCCchhhhhhhhhhhhhhhhhccc
Confidence            3589999999999999999999999985433

>KOG1168|consensus

Probab=98.17  E-value=7.8e-07  Score=58.88  Aligned_cols=34  Identities=21%  Similarity=0.358  Sum_probs=30.4

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMA   35 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~   35 (61)
                      .|+-+|.+|+|...+|+|||+|.|.|.||.....
T Consensus       338 kIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa  371 (385)
T KOG1168|consen  338 KIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSA  371 (385)
T ss_pred             HHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhh
Confidence            4788999999999999999999999999976543

>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=97.75  E-value=8.9e-07  Score=42.70  Aligned_cols=26  Identities=23%  Similarity=0.311  Sum_probs=22.6

Q ss_pred             chhhhhcCCCCCccceeeccccchhH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMK   27 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak   27 (61)
                      |..+||..+||+..||..||-|.|.+
T Consensus        15 ek~~L~~~tgls~~Qi~~WF~NaRrR   40 (40)
T PF05920_consen   15 EKEELAKQTGLSRKQISNWFINARRR   40 (40)
T ss_dssp             HHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence            56789999999999999999998864

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

>KOG0490|consensus

Probab=97.41  E-value=5.1e-05  Score=46.84  Aligned_cols=30  Identities=37%  Similarity=0.609  Sum_probs=27.5

Q ss_pred             hhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          4 LRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         4 ~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      .+|+..+++++..|+|||||+|++.++...
T Consensus       184 ~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  184 EQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             HHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            578999999999999999999999998765

>KOG0774|consensus

Probab=96.46  E-value=0.0024  Score=42.06  Aligned_cols=30  Identities=27%  Similarity=0.386  Sum_probs=27.6

Q ss_pred             hhhhhcCCCCCccceeeccccchhHHHHHh
Q psy12003          3 LLRDKNPPRGTERQIKIWFQNRRMKWKKEH   32 (61)
Q Consensus         3 ~~eLA~~l~Lte~~VqvWFqNrRak~kr~~   32 (61)
                      =.|||.+.|++-.||-.||.|.|-++||..
T Consensus       221 K~eLAkqCnItvsQvsnwfgnkrIrykK~~  250 (334)
T KOG0774|consen  221 KEELAKQCNITVSQVSNWFGNKRIRYKKNM  250 (334)
T ss_pred             HHHHHHHcCceehhhccccccceeehhhhh
Confidence            368999999999999999999999999873

>KOG1146|consensus

Probab=95.86  E-value=0.0059  Score=46.96  Aligned_cols=34  Identities=32%  Similarity=0.389  Sum_probs=29.2

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMA   35 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~   35 (61)
                      ++..|-..++|+.+.|+|||||-|+|.++.....
T Consensus       932 ~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~  965 (1406)
T KOG1146|consen  932 ECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG  965 (1406)
T ss_pred             HHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence            4667788899999999999999999999986633

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

Probab=94.54  E-value=0.0048  Score=32.12  Aligned_cols=28  Identities=25%  Similarity=0.471  Sum_probs=21.6

Q ss_pred             CchhhhhcCCCCCccceeeccccchhHHHH
Q psy12003          1 MNLLRDKNPPRGTERQIKIWFQNRRMKWKK   30 (61)
Q Consensus         1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~kr   30 (61)
                      |.+.+||.+||+++.+|+.|  -.+.+|..
T Consensus        23 i~lkdIA~~Lgvs~~tIr~W--K~~dkW~~   50 (60)
T PF10668_consen   23 IKLKDIAEKLGVSESTIRKW--KSRDKWDE   50 (60)
T ss_pred             ccHHHHHHHHCCCHHHHHHH--hhhcchhh
Confidence            45789999999999999998  33444544

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

>KOG3623|consensus

Probab=94.14  E-value=0.012  Score=43.46  Aligned_cols=33  Identities=12%  Similarity=0.152  Sum_probs=29.5

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKM   34 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~   34 (61)
                      ||..+|.+.||+...|++||++++++...-++.
T Consensus       585 elskia~qvglp~~vvk~wfE~~~a~e~sv~rs  617 (1007)
T KOG3623|consen  585 ELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERS  617 (1007)
T ss_pred             HHHHHHHHhcccHHHHHHHHHhhhhhhhhhccC
Confidence            688899999999999999999999998876653

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

Probab=93.87  E-value=0.0049  Score=31.72  Aligned_cols=24  Identities=25%  Similarity=0.403  Sum_probs=18.8

Q ss_pred             chhhhhcCCCCCccceeeccccch
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRR   25 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrR   25 (61)
                      .|-+|..+.+|+..+|+.||-.|.
T Consensus        27 DL~~L~~kS~ms~qqVr~WFa~~~   50 (56)
T PF11569_consen   27 DLDELCDKSRMSYQQVRDWFAERM   50 (56)
T ss_dssp             HHHHHHHHTT--HHHHHHHHHHHS
T ss_pred             hHHHHHHHHCCCHHHHHHHHHHhc
Confidence            477899999999999999997553

>KOG0773|consensus

Probab=92.06  E-value=0.051  Score=35.90  Aligned_cols=28  Identities=21%  Similarity=0.264  Sum_probs=24.3

Q ss_pred             hhhcCCCCCccceeeccccchhHHHHHh
Q psy12003          5 RDKNPPRGTERQIKIWFQNRRMKWKKEH   32 (61)
Q Consensus         5 eLA~~l~Lte~~VqvWFqNrRak~kr~~   32 (61)
                      .||.++||+-.+|-.||-|.|-+..+..
T Consensus       274 ~La~~TGLs~~Qv~NWFINaR~R~w~p~  301 (342)
T KOG0773|consen  274 MLAKQTGLSRPQVSNWFINARVRLWKPM  301 (342)
T ss_pred             ccchhcCCCcccCCchhhhcccccCCch
Confidence            5899999999999999999988765543

>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily

Probab=89.94  E-value=0.035  Score=26.43  Aligned_cols=24  Identities=0%  Similarity=-0.101  Sum_probs=20.2

Q ss_pred             CchhhhhcCCCCCccceeeccccc
Q psy12003          1 MNLLRDKNPPRGTERQIKIWFQNR   24 (61)
Q Consensus         1 ~~~~eLA~~l~Lte~~VqvWFqNr   24 (61)
                      |-+.|+|..+|+++.+|+.|.++.
T Consensus         1 ~~~~e~a~~~gv~~~tlr~~~~~g   24 (49)
T cd04761           1 YTIGELAKLTGVSPSTLRYYERIG   24 (49)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHCC
Confidence            457899999999999999996543

Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B

Probab=87.48  E-value=0.058  Score=27.50  Aligned_cols=21  Identities=0%  Similarity=-0.064  Sum_probs=18.6

Q ss_pred             CchhhhhcCCCCCccceeecc
Q psy12003          1 MNLLRDKNPPRGTERQIKIWF   21 (61)
Q Consensus         1 ~~~~eLA~~l~Lte~~VqvWF   21 (61)
                      |.+.|+|..+|++..+|+.|-
T Consensus         1 yti~eva~~~gvs~~tlr~y~   21 (69)
T PF13411_consen    1 YTIKEVAKLLGVSPSTLRYYE   21 (69)
T ss_dssp             EEHHHHHHHTTTTHHHHHHHH
T ss_pred             CcHHHHHHHHCcCHHHHHHHH
Confidence            467899999999999999983

>COG5484 Uncharacterized conserved protein [Function unknown]

Probab=86.28  E-value=0.1  Score=34.30  Aligned_cols=27  Identities=30%  Similarity=0.464  Sum_probs=23.8

Q ss_pred             CchhhhhcCCCCCccceeeccccchhHHH
Q psy12003          1 MNLLRDKNPPRGTERQIKIWFQNRRMKWK   29 (61)
Q Consensus         1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~k   29 (61)
                      |-+.+||.++|+++.+|+-|  -||..|.
T Consensus        20 mk~~dIAeklGvspntiksW--Krr~gWs   46 (279)
T COG5484          20 MKLKDIAEKLGVSPNTIKSW--KRRDGWS   46 (279)
T ss_pred             ccHHHHHHHhCCChHHHHHH--HHhcCCC
Confidence            66899999999999999999  5688883

>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []

Probab=85.86  E-value=0.11  Score=26.64  Aligned_cols=28  Identities=14%  Similarity=0.284  Sum_probs=21.7

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE   31 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~   31 (61)
                      -+.|+|..||++..+|.-|-+  |.+|...
T Consensus        15 ~~~eIA~~Lg~~~~TV~~W~~--r~~W~~~   42 (58)
T PF06056_consen   15 SIKEIAEELGVPRSTVYSWKD--RYKWDEL   42 (58)
T ss_pred             CHHHHHHHHCCChHHHHHHHH--hhCcccc
Confidence            468999999999999999943  5555443

Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly

>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins

Probab=85.57  E-value=0.094  Score=24.37  Aligned_cols=26  Identities=4%  Similarity=0.216  Sum_probs=21.4

Q ss_pred             CchhhhhcCCCCCccceeeccccchh
Q psy12003          1 MNLLRDKNPPRGTERQIKIWFQNRRM   26 (61)
Q Consensus         1 ~~~~eLA~~l~Lte~~VqvWFqNrRa   26 (61)
                      +.+.|+|..+|++..+|.-|.++...
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~g~~   26 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKEGKL   26 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence            45789999999999999999775543

Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.

>KOG2252|consensus

Probab=83.10  E-value=0.18  Score=36.05  Aligned_cols=25  Identities=12%  Similarity=-0.028  Sum_probs=21.9

Q ss_pred             hhhhcCCCCCccceeeccccchhHH
Q psy12003          4 LRDKNPPRGTERQIKIWFQNRRMKW   28 (61)
Q Consensus         4 ~eLA~~l~Lte~~VqvWFqNrRak~   28 (61)
                      .-|+.+|||.-++|..||-|-|.+.
T Consensus       451 ~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  451 ETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             HHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            3579999999999999999987764

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=82.04  E-value=0.19  Score=27.04  Aligned_cols=23  Identities=9%  Similarity=0.029  Sum_probs=19.8

Q ss_pred             CchhhhhcCCCCCccceeecccc
Q psy12003          1 MNLLRDKNPPRGTERQIKIWFQN   23 (61)
Q Consensus         1 ~~~~eLA~~l~Lte~~VqvWFqN   23 (61)
                      |...|+|..+|+|+..|+.|+.+
T Consensus        33 lS~kEIAe~LGIS~~TVk~~l~~   55 (73)
T TIGR03879        33 KTASEIAEELGRTEQTVRNHLKG   55 (73)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHhc
Confidence            34679999999999999998774

This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=81.88  E-value=0.13  Score=25.14  Aligned_cols=22  Identities=9%  Similarity=-0.037  Sum_probs=17.4

Q ss_pred             chhhhhcCCCCCccceeecccc
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQN   23 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqN   23 (61)
                      ...|+|..+|+++..|+.|.+.
T Consensus        28 s~~eIa~~l~~s~~~v~~~l~r   49 (54)
T PF08281_consen   28 SYAEIAEILGISESTVKRRLRR   49 (54)
T ss_dssp             -HHHHHHHCTS-HHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHHH
Confidence            4679999999999999988763

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.

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

Probab=80.88  E-value=0.19  Score=25.74  Aligned_cols=22  Identities=5%  Similarity=0.007  Sum_probs=19.1

Q ss_pred             CchhhhhcCCCCCccceeeccc
Q psy12003          1 MNLLRDKNPPRGTERQIKIWFQ   22 (61)
Q Consensus         1 ~~~~eLA~~l~Lte~~VqvWFq   22 (61)
                      +.+.|+|+.+|++..+++-|.+
T Consensus         1 ~~i~e~A~~~gVs~~tlr~ye~   22 (68)
T cd04763           1 YTIGEVALLTGIKPHVLRAWER   22 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            3578999999999999998855

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

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

Probab=80.41  E-value=0.24  Score=25.24  Aligned_cols=22  Identities=0%  Similarity=-0.047  Sum_probs=19.1

Q ss_pred             CchhhhhcCCCCCccceeeccc
Q psy12003          1 MNLLRDKNPPRGTERQIKIWFQ   22 (61)
Q Consensus         1 ~~~~eLA~~l~Lte~~VqvWFq   22 (61)
                      +.+.|+|..+|++..+++-|-+
T Consensus         1 ~~i~evA~~~gvs~~tlR~~~~   22 (67)
T cd04764           1 YTIKEVSEIIGVKPHTLRYYEK   22 (67)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            4578999999999999998855

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	61
2r5y_A	88	Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO		2e-06
1san_A	62	The Des(1-6)antennapedia Homeodomain: Comparison Of		1e-05
1ahd_P	68	Determination Of The Nmr Solution Structure Of An A		1e-05
1hom_A	68	Determination Of The Three-Dimensional Structure Of		1e-05
9ant_A	62	Antennapedia Homeodomain-Dna Complex Length = 62		4e-05
2h1k_A	63	Crystal Structure Of The Pdx1 Homeodomain In Comple		1e-04
1b8i_A	81	Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX		4e-04
1ftz_A	70	Nuclear Magnetic Resonance Solution Structure Of Th		7e-04

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/21 (100%), Positives = 21/21 (100%)
Query: 13 TERQIKIWFQNRRMKWKKEHK 33
          TERQIKIWFQNRRMKWKKEHK
Sbjct: 68 TERQIKIWFQNRRMKWKKEHK 88

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 20/21 (95%), Positives = 21/21 (100%)
Query: 13 TERQIKIWFQNRRMKWKKEHK 33
          TERQIKIWFQNRRMKWKKE+K
Sbjct: 36 TERQIKIWFQNRRMKWKKENK 56

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 20/21 (95%), Positives = 21/21 (100%)
Query: 13 TERQIKIWFQNRRMKWKKEHK 33
          TERQIKIWFQNRRMKWKKE+K
Sbjct: 42 TERQIKIWFQNRRMKWKKENK 62

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 20/21 (95%), Positives = 21/21 (100%)
Query: 13 TERQIKIWFQNRRMKWKKEHK 33
          TERQIKIWFQNRRMKWKKE+K
Sbjct: 42 TERQIKIWFQNRRMKWKKENK 62

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 19/19 (100%), Positives = 19/19 (100%)
Query: 13 TERQIKIWFQNRRMKWKKE 31
          TERQIKIWFQNRRMKWKKE
Sbjct: 43 TERQIKIWFQNRRMKWKKE 61

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/20 (90%), Positives = 18/20 (90%)
Query: 13 TERQIKIWFQNRRMKWKKEH 32
          TER IKIWFQNRRMKWKKE 
Sbjct: 43 TERHIKIWFQNRRMKWKKEE 62

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

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 18/19 (94%), Positives = 18/19 (94%)
Query: 13 TERQIKIWFQNRRMKWKKE 31
          TERQIKIWFQNRRMK KKE
Sbjct: 60 TERQIKIWFQNRRMKLKKE 78

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

Iteration: 1
 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 17/24 (70%), Positives = 20/24 (83%)
Query: 13 TERQIKIWFQNRRMKWKKEHKMAS 36
          +ERQIKIWFQNRRMK KK+  + S
Sbjct: 43 SERQIKIWFQNRRMKSKKDRTLDS 66

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

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

>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 54.8 bits (132), Expect = 2e-12
 Identities = 12/21 (57%), Positives = 16/21 (76%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
          ++ Q+K W+QNRRMKWKK   
Sbjct: 57 SQLQVKTWYQNRRMKWKKSGP 77

>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 70

 Score = 54.0 bits (130), Expect = 4e-12
 Identities = 12/21 (57%), Positives = 16/21 (76%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
          +ERQ+K WFQNRR KW++   
Sbjct: 47 SERQVKTWFQNRRAKWRRSGP 67

>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A 1hom_A 1ftz_A Length = 68

 Score = 52.8 bits (127), Expect = 1e-11
 Identities = 20/21 (95%), Positives = 21/21 (100%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
          TERQIKIWFQNRRMKWKKE+K
Sbjct: 42 TERQIKIWFQNRRMKWKKENK 62

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

 Score = 52.0 bits (125), Expect = 2e-11
 Identities = 9/21 (42%), Positives = 13/21 (61%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
             Q+KIWF+NRR + K +  
Sbjct: 42 GTAQVKIWFKNRRRRHKIQSD 62

>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA binding, homeodomain, homeotic proteins, development, specificity; HET: DNA; 2.40A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 9ant_A* Length = 81

 Score = 52.1 bits (125), Expect = 3e-11
 Identities = 18/21 (85%), Positives = 19/21 (90%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
          TERQIKIWFQNRRMK KKE +
Sbjct: 60 TERQIKIWFQNRRMKLKKEIQ 80

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

 Score = 51.6 bits (124), Expect = 3e-11
 Identities = 18/20 (90%), Positives = 18/20 (90%)

Query: 13 TERQIKIWFQNRRMKWKKEH 32
          TER IKIWFQNRRMKWKKE 
Sbjct: 43 TERHIKIWFQNRRMKWKKEE 62

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

 Score = 51.6 bits (124), Expect = 3e-11
 Identities = 13/25 (52%), Positives = 18/25 (72%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMASM 37
          TE Q+KIWFQNRR K K++   + +
Sbjct: 44 TETQVKIWFQNRRYKTKRKQLSSEL 68

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

 Score = 51.2 bits (123), Expect = 4e-11
 Identities = 12/21 (57%), Positives = 15/21 (71%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
          T+ Q+KIWFQN+R K KK   
Sbjct: 47 TQTQVKIWFQNKRSKIKKSGP 67

>1b72_A Protein (homeobox protein HOX-B1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1 Length = 97

 Score = 51.8 bits (124), Expect = 5e-11
 Identities = 14/21 (66%), Positives = 16/21 (76%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
           E Q+KIWFQNRRMK KK  +
Sbjct: 74 NETQVKIWFQNRRMKQKKRER 94

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

 Score = 51.0 bits (122), Expect = 6e-11
 Identities = 14/21 (66%), Positives = 16/21 (76%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
          +ERQI IWFQNRR+K KK   
Sbjct: 47 SERQITIWFQNRRVKEKKSGP 67

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

 Score = 51.0 bits (122), Expect = 8e-11
 Identities = 21/21 (100%), Positives = 21/21 (100%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
          TERQIKIWFQNRRMKWKKEHK
Sbjct: 68 TERQIKIWFQNRRMKWKKEHK 88

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

 Score = 50.0 bits (120), Expect = 1e-10
 Identities = 12/19 (63%), Positives = 15/19 (78%)

Query: 13 TERQIKIWFQNRRMKWKKE 31
           E  IK+WFQNRRMK K++
Sbjct: 41 PESTIKVWFQNRRMKDKRQ 59

>1puf_A HOX-1.7, homeobox protein HOX-A9; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Mus musculus} SCOP: a.4.1.1 PDB: 1san_A Length = 77

 Score = 50.2 bits (120), Expect = 1e-10
 Identities = 17/21 (80%), Positives = 19/21 (90%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
          TERQ+KIWFQNRRMK KK +K
Sbjct: 53 TERQVKIWFQNRRMKMKKINK 73

>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA binding protein/DNA), transcription/DNA complex; HET: DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A 1du0_A* 1ztr_A 1enh_A 2p81_A Length = 61

 Score = 49.6 bits (119), Expect = 1e-10
 Identities = 12/18 (66%), Positives = 14/18 (77%)

Query: 13 TERQIKIWFQNRRMKWKK 30
           E QIKIWF+N+R K KK
Sbjct: 43 NEAQIKIWFKNKRAKIKK 60

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

 Score = 50.2 bits (120), Expect = 2e-10
 Identities = 11/21 (52%), Positives = 16/21 (76%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
          T+ Q+K WFQNRR KW+++  
Sbjct: 57 TDAQVKTWFQNRRTKWRRQTA 77

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

 Score = 49.2 bits (118), Expect = 2e-10
 Identities = 11/19 (57%), Positives = 16/19 (84%)

Query: 13 TERQIKIWFQNRRMKWKKE 31
          T+ Q+K WFQNRR KW+++
Sbjct: 37 TDAQVKTWFQNRRTKWRRQ 55

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

 Score = 49.2 bits (118), Expect = 3e-10
 Identities = 13/18 (72%), Positives = 15/18 (83%)

Query: 13 TERQIKIWFQNRRMKWKK 30
          TE Q+KIWFQNRR K K+
Sbjct: 40 TETQVKIWFQNRRAKAKR 57

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

 Score = 49.5 bits (118), Expect = 3e-10
 Identities = 13/21 (61%), Positives = 16/21 (76%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
          +ERQ+ IWFQNRR+K KK   
Sbjct: 47 SERQVTIWFQNRRVKEKKVIN 67

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

 Score = 49.4 bits (118), Expect = 4e-10
 Identities = 11/21 (52%), Positives = 16/21 (76%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
          + +Q+K WFQN+RMK K+  K
Sbjct: 62 SYKQVKTWFQNQRMKSKRWQK 82

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

 Score = 48.6 bits (116), Expect = 5e-10
 Identities = 12/29 (41%), Positives = 14/29 (48%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMASMNVIP 41
          T  Q+KIWFQN R K K+          P
Sbjct: 49 TPTQVKIWFQNHRYKTKRAQNEKGYEGHP 77

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

 Score = 47.7 bits (114), Expect = 9e-10
 Identities = 10/19 (52%), Positives = 15/19 (78%)

Query: 13 TERQIKIWFQNRRMKWKKE 31
          + +Q+K WFQN+RMK K+ 
Sbjct: 43 SYKQVKTWFQNQRMKCKRW 61

>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding proteins/DNA), complex, DNA- binding protein, DNA; HET: DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1f43_A 1yrn_A* Length = 61

 Score = 47.2 bits (113), Expect = 1e-09
 Identities = 8/17 (47%), Positives = 13/17 (76%)

Query: 13 TERQIKIWFQNRRMKWK 29
          T  Q+++WF N+RM+ K
Sbjct: 45 TPLQVRVWFINKRMRSK 61

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

 Score = 46.6 bits (111), Expect = 3e-09
 Identities = 12/25 (48%), Positives = 16/25 (64%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMASM 37
          T  Q+KIWFQN R K K++ K  + 
Sbjct: 42 TPTQVKIWFQNHRYKMKRQAKDKAA 66

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

 Score = 46.1 bits (110), Expect = 4e-09
 Identities = 12/17 (70%), Positives = 13/17 (76%)

Query: 13 TERQIKIWFQNRRMKWK 29
          T  Q+KIWFQNRR K K
Sbjct: 42 TSTQVKIWFQNRRYKSK 58

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

 Score = 43.2 bits (102), Expect = 8e-08
 Identities = 8/24 (33%), Positives = 14/24 (58%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMAS 36
          TE Q + WF+ R  +W++   + S
Sbjct: 43 TEEQTQKWFKQRLAEWRRSEGLPS 66

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

 Score = 44.2 bits (104), Expect = 1e-07
 Identities = 8/25 (32%), Positives = 13/25 (52%)

Query: 13  TERQIKIWFQNRRMKWKKEHKMASM 37
            +  +++WF NRR K K+    A  
Sbjct: 139 EKEVVRVWFCNRRQKEKRMTPAAGA 163

>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 = 44.2 bits (104), Expect = 1e-07
 Identities = 8/18 (44%), Positives = 12/18 (66%)

Query: 13  TERQIKIWFQNRRMKWKK 30
            +  I++WF NRR K K+
Sbjct: 141 EKEVIRVWFSNRRQKEKR 158

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

 Score = 42.0 bits (99), Expect = 2e-07
 Identities = 6/24 (25%), Positives = 12/24 (50%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMAS 36
          + R+++ WF +RR   +      S
Sbjct: 48 STREVRKWFSDRRYHCRNLKGSRS 71

>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 = 40.8 bits (96), Expect = 5e-07
 Identities = 9/21 (42%), Positives = 11/21 (52%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
            R I +WFQN R K +K   
Sbjct: 47 PTRVIVVWFQNARQKARKSGP 67

>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 = 40.5 bits (95), Expect = 9e-07
 Identities = 7/23 (30%), Positives = 14/23 (60%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMA 35
           +R +++WFQN R + +K    +
Sbjct: 57 KKRVVQVWFQNTRARERKSGPSS 79

>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 = 39.7 bits (93), Expect = 2e-06
 Identities = 8/24 (33%), Positives = 14/24 (58%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMAS 36
          TE Q + WF+ R  +W++   + S
Sbjct: 42 TEEQTQKWFKQRLAEWRRSEGLPS 65

>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 = 39.2 bits (92), Expect = 2e-06
 Identities = 11/25 (44%), Positives = 16/25 (64%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMASM 37
             +I+IWFQNRR K K+ H+ +  
Sbjct: 41 ELDRIQIWFQNRRAKLKRSHRESQF 65

>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 = 38.4 bits (90), Expect = 5e-06
 Identities = 13/22 (59%), Positives = 19/22 (86%)

Query: 13 TERQIKIWFQNRRMKWKKEHKM 34
          TE +I++WFQNRR KW+K+ K+
Sbjct: 39 TEARIQVWFQNRRAKWRKQEKV 60

>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 = 38.1 bits (89), Expect = 6e-06
 Identities = 6/21 (28%), Positives = 11/21 (52%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
           ++ IK WF+N   K ++   
Sbjct: 47 PQKVIKHWFRNTLFKERQSGP 67

>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 = 39.2 bits (91), Expect = 9e-06
 Identities = 6/18 (33%), Positives = 12/18 (66%)

Query: 13  TERQIKIWFQNRRMKWKK 30
            +  +++WF NRR + K+
Sbjct: 127 EKEVVRVWFCNRRQREKR 144

>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 = 37.7 bits (88), Expect = 1e-05
 Identities = 12/24 (50%), Positives = 18/24 (75%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMAS 36
          TE +I++WFQNRR + +K+H   S
Sbjct: 58 TEARIQVWFQNRRARLRKQHTSVS 81

>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 = 37.7 bits (87), Expect = 2e-05
 Identities = 8/25 (32%), Positives = 15/25 (60%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMASM 37
          T  ++  WF NRR + K+   +A++
Sbjct: 62 TSLKVYNWFANRRKEIKRRANIAAI 86

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

 Score = 36.9 bits (86), Expect = 2e-05
 Identities = 11/22 (50%), Positives = 15/22 (68%)

Query: 13 TERQIKIWFQNRRMKWKKEHKM 34
          + R I++WFQN+R K KK   M
Sbjct: 43 SPRVIRVWFQNKRCKDKKRSIM 64

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

 Score = 37.3 bits (86), Expect = 2e-05
 Identities = 6/24 (25%), Positives = 9/24 (37%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMAS 36
          + R+I  WF  RR       +   
Sbjct: 53 SRREIDSWFSERRKLRDSMEQAVL 76

>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 = 36.5 bits (85), Expect = 2e-05
 Identities = 10/26 (38%), Positives = 18/26 (69%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMASMN 38
          TE ++++WF+NRR KW+K  +    +
Sbjct: 43 TEARVRVWFKNRRAKWRKREEFIVTD 68

>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 = 37.7 bits (87), Expect = 3e-05
 Identities = 6/18 (33%), Positives = 9/18 (50%)

Query: 13  TERQIKIWFQNRRMKWKK 30
               +++WF NRR   K 
Sbjct: 133 DREVVRVWFSNRRQTLKN 150

>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 = 36.6 bits (85), Expect = 3e-05
 Identities = 7/24 (29%), Positives = 16/24 (66%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMAS 36
           E ++++WF+NRR K +++ +   
Sbjct: 47 PESRVQVWFKNRRAKCRQQQQQQQ 70

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

 Score = 36.9 bits (85), Expect = 4e-05
 Identities = 5/26 (19%), Positives = 12/26 (46%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMASMN 38
          T R+I  WF  ++     + +   ++
Sbjct: 51 TRREIDAWFTEKKKSKALKEEKMEID 76

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

 Score = 36.4 bits (84), Expect = 4e-05
 Identities = 10/24 (41%), Positives = 11/24 (45%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMAS 36
          T R+I  WF  RR K   E    S
Sbjct: 47 TRREIDSWFSERRKKVNAEETKKS 70

>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 = 36.3 bits (84), Expect = 4e-05
 Identities = 8/22 (36%), Positives = 15/22 (68%)

Query: 13 TERQIKIWFQNRRMKWKKEHKM 34
          T+R +++WFQN R K+++    
Sbjct: 47 TKRVLQVWFQNARAKFRRNLLR 68

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

 Score = 36.2 bits (84), Expect = 4e-05
 Identities = 11/29 (37%), Positives = 18/29 (62%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMASMNVIP 41
           E +I++WF NRR KW++E K+ +     
Sbjct: 47 PEARIQVWFSNRRAKWRREEKLRNQRRQS 75

>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 = 35.8 bits (83), Expect = 6e-05
 Identities = 8/23 (34%), Positives = 16/23 (69%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMA 35
           E ++++WF+NRR KW++    +
Sbjct: 47 REEKVEVWFKNRRAKWRRSGPSS 69

>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 = 34.8 bits (80), Expect = 1e-04
 Identities = 5/21 (23%), Positives = 10/21 (47%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
             +IK WF + R + ++   
Sbjct: 44 ARSEIKKWFSDHRYRCQRGIV 64

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

 Score = 34.8 bits (80), Expect = 1e-04
 Identities = 6/18 (33%), Positives = 9/18 (50%)

Query: 13 TERQIKIWFQNRRMKWKK 30
           +  I  +FQN+R   K 
Sbjct: 48 PKHTIIKFFQNQRYHVKH 65

>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 = 35.9 bits (82), Expect = 2e-04
 Identities = 7/18 (38%), Positives = 12/18 (66%)

Query: 13  TERQIKIWFQNRRMKWKK 30
            +  +++WF NRR K K+
Sbjct: 136 EKDVVRVWFSNRRQKGKR 153

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	61
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.64
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.58
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.55
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.55
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.54
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.54
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.53
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.53
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.53
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.52
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.52
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.52
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.52
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.52
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.51
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.51
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.51
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.5
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.5
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.5
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.5
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.5
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.5
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.49
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.49
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.48
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.48
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.48
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.48
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.48
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.48
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.48
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.48
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.48
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.47
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.47
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.47
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.47
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.46
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.46
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.45
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.45
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.45
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.44
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.44
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.44
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.44
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.44
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.43
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.43
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.42
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	99.42
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.41
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.39
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.39
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.39
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.39
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.39
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.36
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.36
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.35
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.34
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.34
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.32
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.3
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.3
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.3
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.28
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.27
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.27
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.17
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.15
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.15
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.11
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.07
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.05
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	98.76
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	98.29
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	88.12
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	88.03
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	85.37
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	82.04

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

Probab=99.64  E-value=5.7e-18  Score=93.51  Aligned_cols=36  Identities=19%  Similarity=0.370  Sum_probs=31.5

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhhcc
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMASM   37 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~~   37 (61)
                      +..+||..|||+|++|+|||||||+|||+.+.....
T Consensus        40 ~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~~~~~   75 (89)
T 2ecb_A           40 ELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEI   75 (89)
T ss_dssp             HHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCCCC
T ss_pred             HHHHHHHHhCcChHHCeecccccchHHHHHHHHhhc
Confidence            457899999999999999999999999997765444

>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=99.58  E-value=1.1e-17  Score=87.62  Aligned_cols=30  Identities=27%  Similarity=0.305  Sum_probs=27.6

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE   31 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~   31 (61)
                      +..+||..|||+|+||+|||||||+|+|+.
T Consensus        30 ~r~~LA~~l~LterQVkvWFqNRR~k~k~~   59 (64)
T 1x2m_A           30 RLEGLSKQLDWDVRSIQRWFRQRRNQEKPS   59 (64)
T ss_dssp             HHHHHHHHHCSCHHHHHHHHHHHHHHSCCS
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHhccCCC
Confidence            468999999999999999999999999863

>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=99.55  E-value=2.4e-16  Score=84.28  Aligned_cols=36  Identities=33%  Similarity=0.385  Sum_probs=31.9

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhhcc
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMASM   37 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~~   37 (61)
                      +..+||..|||++.+|+|||||||+|+|+.......
T Consensus        38 ~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~~~~   73 (77)
T 1nk2_P           38 EREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGY   73 (77)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhCCCHHHHHHHhHHhhcchhhhhccccC
Confidence            467899999999999999999999999998775544

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

Probab=99.55  E-value=9.9e-17  Score=81.29  Aligned_cols=30  Identities=40%  Similarity=0.739  Sum_probs=27.9

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE   31 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~   31 (61)
                      +..+||..+||++.+|+|||||||+|+|++
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            457899999999999999999999999985

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

Probab=99.54  E-value=3.3e-16  Score=84.23  Aligned_cols=36  Identities=33%  Similarity=0.612  Sum_probs=32.0

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhhcc
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMASM   37 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~~   37 (61)
                      +..+||..|+|++.+|+|||||||+|+|+..+....
T Consensus        36 ~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~~~   71 (80)
T 2cue_A           36 ARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQ   71 (80)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhhhc
Confidence            467899999999999999999999999999875543

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

Probab=99.54  E-value=2.9e-16  Score=84.39  Aligned_cols=35  Identities=20%  Similarity=0.356  Sum_probs=31.1

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhhc
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMAS   36 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~   36 (61)
                      +..+||..|+|++.+|+|||||||+|+|+......
T Consensus        36 ~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~~~   70 (80)
T 2dms_A           36 MREEVALKINLPESRVQVWFKNRRAKCRQQQQQQQ   70 (80)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCSCC
T ss_pred             HHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHccC
Confidence            46789999999999999999999999999876443

>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=99.53  E-value=2.5e-16  Score=83.24  Aligned_cols=32  Identities=25%  Similarity=0.461  Sum_probs=29.6

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..|||++.+|+|||||||+|+|+..+
T Consensus        31 ~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~~   62 (72)
T 1uhs_A           31 TLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   62 (72)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHCcCHHHhhHHhHHHHHHHhhhcc
Confidence            46789999999999999999999999999875

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

Probab=99.53  E-value=2e-16  Score=83.20  Aligned_cols=31  Identities=19%  Similarity=0.370  Sum_probs=28.7

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEH   32 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~   32 (61)
                      |..+||..||||+++|+|||||||+|||+..
T Consensus        33 er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg~   63 (66)
T 3nau_A           33 EVYRLIEVTGLARSEIKKWFSDHRYRCQRGI   63 (66)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCcCHHHhhHhcccchhhhhccC
Confidence            5789999999999999999999999999854

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

Probab=99.53  E-value=2.9e-16  Score=83.21  Aligned_cols=33  Identities=24%  Similarity=0.476  Sum_probs=30.1

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKM   34 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~   34 (61)
                      +..+||..+||++.+|+|||||||+|+|+..+.
T Consensus        32 ~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~~~   64 (73)
T 2hi3_A           32 TLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGL   64 (73)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHCcCHHHHHHHHHHHHHHHHHhccC
Confidence            467899999999999999999999999998753

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

Probab=99.52  E-value=7.7e-16  Score=82.59  Aligned_cols=34  Identities=26%  Similarity=0.477  Sum_probs=30.7

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMA   35 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~   35 (61)
                      +..+||..|+|++.+|+|||||||+|+|+.....
T Consensus        36 ~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~   69 (80)
T 2dmq_A           36 DLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQ   69 (80)
T ss_dssp             HHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHHH
Confidence            5679999999999999999999999999987643

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

Probab=99.52  E-value=6.9e-17  Score=85.47  Aligned_cols=32  Identities=41%  Similarity=0.535  Sum_probs=28.9

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..|||+|++|+|||||||+|+|+...
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            45789999999999999999999999998654

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

Probab=99.52  E-value=1.7e-16  Score=84.31  Aligned_cols=30  Identities=27%  Similarity=0.354  Sum_probs=27.5

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE   31 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~   31 (61)
                      +..+||..|||+|++|+|||||||+|||+.
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            457899999999999999999999999974

>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=99.52  E-value=3.6e-16  Score=83.56  Aligned_cols=34  Identities=50%  Similarity=0.576  Sum_probs=30.8

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMA   35 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~   35 (61)
                      +..+||..|||++.+|+|||||||+|+|+..+..
T Consensus        42 ~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k~~   75 (77)
T 1puf_A           42 RRYEVARLLNLTERQVKIWFQNRRMKMKKINKDR   75 (77)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhhhc
Confidence            4678999999999999999999999999987653

>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=99.52  E-value=2.4e-16  Score=82.65  Aligned_cols=34  Identities=59%  Similarity=0.868  Sum_probs=30.5

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMA   35 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~   35 (61)
                      +..+||..|||++.+|+|||||||+|+|+..+..
T Consensus        31 ~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~~~   64 (68)
T 1ahd_P           31 RRIEIAHALSLTERQIKIWFQNRRMKWKKENKTK   64 (68)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSCCC
T ss_pred             HHHHHHHHHCcCHhhhhHHhHHHHhHHhHhcccc
Confidence            4678999999999999999999999999987643

>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=99.51  E-value=5.3e-16  Score=81.18  Aligned_cols=33  Identities=30%  Similarity=0.591  Sum_probs=30.3

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKM   34 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~   34 (61)
                      +..+||..|||++.+|+|||||||+|+|+..+.
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            567899999999999999999999999998764

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

Probab=99.51  E-value=3.2e-16  Score=86.03  Aligned_cols=36  Identities=22%  Similarity=0.302  Sum_probs=31.3

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhhcc
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMASM   37 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~~   37 (61)
                      +..+||..|||++.+|+|||||||+|+|+.......
T Consensus        42 ~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~~~~~   77 (89)
T 2dmp_A           42 ELDRLRVETKLSRREIDSWFSERRKLRDSMEQAVLD   77 (89)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCSCCCC
T ss_pred             HHHHHHHHhCCCHHhccHhhHhHHHHHHHHhHhhhc
Confidence            457899999999999999999999999998765433

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

Probab=99.51  E-value=1.9e-16  Score=81.09  Aligned_cols=32  Identities=41%  Similarity=0.639  Sum_probs=26.5

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..+||++.+|+|||||||+|+|+..+
T Consensus        28 ~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~k   59 (60)
T 3a02_A           28 TREELAMKIGLTEARIQVWFQNRRAKWRKQEK   59 (60)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHHC----
T ss_pred             HHHHHHHHHCcCHHHHHHHhhhhhhhhHhhcc
Confidence            46789999999999999999999999998764

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

Probab=99.50  E-value=3.8e-16  Score=80.68  Aligned_cols=31  Identities=58%  Similarity=0.831  Sum_probs=28.5

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEH   32 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~   32 (61)
                      +..+||..|||++.+|+|||||||+|+|+.+
T Consensus        32 ~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   62 (63)
T 2h1k_A           32 RRVELAVMLNLTERHIKIWFQNRRMKWKKEE   62 (63)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHhCcCHHHhhHHHHhhhhhhhhhc
Confidence            4578999999999999999999999999864

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

Probab=99.50  E-value=5.7e-16  Score=83.39  Aligned_cols=32  Identities=16%  Similarity=0.234  Sum_probs=29.1

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      |..+||..|||+|++|+|||||||+|+|+...
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            56799999999999999999999999998643

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

Probab=99.50  E-value=3.4e-16  Score=82.25  Aligned_cols=32  Identities=25%  Similarity=0.580  Sum_probs=29.4

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..|||++.+|+|||||||+|+|+...
T Consensus        36 ~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2dmu_A           36 TREQLARKVHLREEKVEVWFKNRRAKWRRSGP   67 (70)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHHTST
T ss_pred             HHHHHHHHHCCCHHHeehccccccccccccCC
Confidence            46789999999999999999999999999765

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

Probab=99.50  E-value=3.7e-16  Score=81.82  Aligned_cols=35  Identities=34%  Similarity=0.398  Sum_probs=31.0

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhhc
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMAS   36 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~   36 (61)
                      +..+||..|||++.+|+|||||||+|+|+..+...
T Consensus        31 ~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~~~~   65 (68)
T 1ftt_A           31 EREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDKA   65 (68)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSCCS
T ss_pred             HHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhhHhh
Confidence            46789999999999999999999999999876443

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

Probab=99.50  E-value=6.6e-16  Score=78.43  Aligned_cols=29  Identities=45%  Similarity=0.560  Sum_probs=27.2

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK   30 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr   30 (61)
                      +..+||..+||++.+|+|||||||+|+|+
T Consensus        29 ~r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A           29 ERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            46789999999999999999999999997

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

Probab=99.50  E-value=5.4e-16  Score=81.53  Aligned_cols=32  Identities=41%  Similarity=0.685  Sum_probs=29.4

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..|+|++.+|+|||||||+|+|+...
T Consensus        36 ~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2e1o_A           36 ERKRLAKMLQLSERQVKTWFQNRRAKWRRSGP   67 (70)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHCCCHHHhhHhhHhhHhhcCCCCC
Confidence            46789999999999999999999999999765

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

Probab=99.49  E-value=1.3e-15  Score=84.12  Aligned_cols=33  Identities=33%  Similarity=0.601  Sum_probs=30.1

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKM   34 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~   34 (61)
                      +..+||..|||++.+|+|||||||+|||+....
T Consensus        46 ~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~   78 (93)
T 3a01_A           46 ERAALARGLKMTDAQVKTWFQNRRTKWRRQTAE   78 (93)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHhCCChhhcccccHhhhhhhhhhhHH
Confidence            467899999999999999999999999998664

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

Probab=99.49  E-value=1.9e-16  Score=83.30  Aligned_cols=32  Identities=44%  Similarity=0.560  Sum_probs=29.1

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..|||++.+|+|||||||+|+|+...
T Consensus        36 ~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (70)
T 2cra_A           36 KRRKISAATSLSERQITIWFQNRRVKEKKSGP   67 (70)
T ss_dssp             HHHHHHHHTCCCHHHHHHHHHHHHHTTTSSCT
T ss_pred             HHHHHHHHHCCCHHHhhHhhHhHHHHhcccCC
Confidence            46789999999999999999999999998654

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

Probab=99.48  E-value=7.6e-16  Score=85.43  Aligned_cols=33  Identities=42%  Similarity=0.569  Sum_probs=30.1

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKM   34 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~   34 (61)
                      +..+||..|||++.+|+|||||||+|+|+..+.
T Consensus        63 ~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~   95 (97)
T 1b72_A           63 RRVEIAATLELNETQVKIWFQNRRMKQKKRERE   95 (97)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhcc
Confidence            467899999999999999999999999998764

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

Probab=99.48  E-value=7.7e-16  Score=82.73  Aligned_cols=31  Identities=16%  Similarity=0.244  Sum_probs=28.6

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEH   32 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~   32 (61)
                      +..+||..|||++.+|+|||||||+|+|+..
T Consensus        41 ~r~~La~~lgL~~~qV~vWFqNrR~k~rk~~   71 (80)
T 2da4_A           41 KIEAVATELNVDCEIVRTWIGNRRRKYRLMG   71 (80)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhCCCHHHhhHhHHHHHHHHhhcc
Confidence            5679999999999999999999999999954

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

Probab=99.48  E-value=1e-15  Score=80.10  Aligned_cols=34  Identities=29%  Similarity=0.387  Sum_probs=30.6

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMA   35 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~   35 (61)
                      +..+||..|||++.+|+|||||||+|+|+.....
T Consensus        31 ~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~~   64 (68)
T 1zq3_P           31 RLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQH   64 (68)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhccc
Confidence            4578999999999999999999999999987643

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

Probab=99.48  E-value=5.8e-16  Score=84.55  Aligned_cols=31  Identities=65%  Similarity=0.980  Sum_probs=28.5

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEH   32 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~   32 (61)
                      +..+||..|||++.+|+|||||||+|+|+..
T Consensus        57 ~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   87 (88)
T 2r5y_A           57 RRIEIAHALSLTERQIKIWFQNRRMKWKKEH   87 (88)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhCcCHHHhhHHhHHHHHHhHhhc
Confidence            4678999999999999999999999999864

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

Probab=99.48  E-value=1.9e-16  Score=85.22  Aligned_cols=32  Identities=38%  Similarity=0.652  Sum_probs=29.1

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..|+|++.+|+|||||||+|+|+...
T Consensus        46 ~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~~   77 (80)
T 2dmt_A           46 DRIDLAESLGLSQLQVKTWYQNRRMKWKKSGP   77 (80)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHHHHHHHHSCCCS
T ss_pred             HHHHHHHHhCCCHHHeeeccHHHHHHhhcccC
Confidence            46789999999999999999999999998654

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

Probab=99.48  E-value=2.2e-16  Score=85.36  Aligned_cols=32  Identities=38%  Similarity=0.493  Sum_probs=29.1

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..|||++.+|+|||||||+|+|+..+
T Consensus        51 ~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k   82 (84)
T 2kt0_A           51 QMQELSNILNLSYKQVKTWFQNQRMKSKRWQK   82 (84)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCC
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhh
Confidence            46789999999999999999999999998654

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

Probab=99.48  E-value=5.4e-16  Score=79.59  Aligned_cols=29  Identities=41%  Similarity=0.520  Sum_probs=27.1

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK   30 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr   30 (61)
                      +..+||..+||++.+|+|||||||+|+|+
T Consensus        32 ~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A           32 RRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            46789999999999999999999999986

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

Probab=99.48  E-value=2.8e-16  Score=82.48  Aligned_cols=32  Identities=19%  Similarity=0.314  Sum_probs=29.5

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..|||++.+|+|||||||+|+|+..+
T Consensus        36 ~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2da1_A           36 QIKEMADKSGLPQKVIKHWFRNTLFKERQSGP   67 (70)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCC
T ss_pred             HHHHHHHHhCCCHHHHHHHhhhhhHHHhhhcc
Confidence            56799999999999999999999999998754

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

Probab=99.48  E-value=2.5e-16  Score=81.07  Aligned_cols=30  Identities=33%  Similarity=0.470  Sum_probs=27.8

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE   31 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~   31 (61)
                      +..+||..|||++.+|+|||||||+|+|+.
T Consensus        32 ~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A           32 QMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             HHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            467899999999999999999999999985

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

Probab=99.47  E-value=3.5e-16  Score=83.77  Aligned_cols=32  Identities=25%  Similarity=0.355  Sum_probs=29.1

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..|+|++.+|+|||||||+|+|+...
T Consensus        46 ~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   77 (80)
T 2da3_A           46 MLDHIAHEVGLKKRVVQVWFQNTRARERKSGP   77 (80)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHHHSSCC
T ss_pred             HHHHHHHHHCcCHHHhHHHhHHHHHhHhhhcc
Confidence            46789999999999999999999999998654

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

Probab=99.47  E-value=1.3e-15  Score=82.05  Aligned_cols=33  Identities=33%  Similarity=0.542  Sum_probs=30.0

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKM   34 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~   34 (61)
                      +..+||..|||++.+|+|||||||+|+|++...
T Consensus        47 ~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~~   79 (81)
T 1fjl_A           47 TREELAQRTNLTEARIQVWFQNRRARLRKQHTS   79 (81)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCcCHHHHHHHHHHHhhhhhhhccc
Confidence            467899999999999999999999999998753

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

Probab=99.47  E-value=3.1e-16  Score=82.31  Aligned_cols=32  Identities=31%  Similarity=0.375  Sum_probs=29.1

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..|||++.+|+|||||||+|+|+...
T Consensus        36 ~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2da2_A           36 EFEQLSNLLNLPTRVIVVWFQNARQKARKSGP   67 (70)
T ss_dssp             HHHHHHHHSCCCHHHHHHHHHHHHHHHCCCSS
T ss_pred             HHHHHHHHhCCCHHHhHHhhHhhhHHHhhccc
Confidence            46789999999999999999999999998654

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

Probab=99.47  E-value=6.1e-16  Score=82.46  Aligned_cols=32  Identities=34%  Similarity=0.536  Sum_probs=29.5

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..|||++.+|+|||||||+|+|+..+
T Consensus        36 ~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (75)
T 2da5_A           36 ELDRLRSETKMTRREIDSWFSERRKKVNAEET   67 (75)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSC
T ss_pred             HHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhh
Confidence            46789999999999999999999999999765

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

Probab=99.46  E-value=7e-16  Score=83.25  Aligned_cols=32  Identities=56%  Similarity=0.733  Sum_probs=28.6

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..|||++.+|+|||||||+|+|+..+
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            46789999999999999999999999998643

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

Probab=99.46  E-value=9.8e-16  Score=78.39  Aligned_cols=30  Identities=40%  Similarity=0.518  Sum_probs=27.8

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE   31 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~   31 (61)
                      +..+||..|||++.+|+|||||||+|+|++
T Consensus        30 ~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (60)
T 1jgg_A           30 RRCELAAQLNLPESTIKVWFQNRRMKDKRQ   59 (60)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHCcCHHHHHHhhHHHHhHhhcc
Confidence            467899999999999999999999999985

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

Probab=99.45  E-value=5.1e-16  Score=82.18  Aligned_cols=35  Identities=31%  Similarity=0.613  Sum_probs=30.8

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhhc
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMAS   36 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~   36 (61)
                      +..+||..|||++.+|+|||||||+|+|+..+.+.
T Consensus        38 ~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r~~q   72 (75)
T 2m0c_A           38 AREQLAMRTDLTEARVQVWFQNRRAKWRKRERFGQ   72 (75)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCCCCS
T ss_pred             HHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHhhhh
Confidence            46789999999999999999999999999766433

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

Probab=99.45  E-value=4.2e-16  Score=81.95  Aligned_cols=32  Identities=38%  Similarity=0.445  Sum_probs=28.9

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..|+|++.+|+|||||||+|+|+...
T Consensus        36 ~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2djn_A           36 ERAELAASLGLTQTQVKIWFQNKRSKIKKSGP   67 (70)
T ss_dssp             HHHHHHHHSSCCHHHHHHHHHHHHHTCSSSSS
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHhhhhcccCC
Confidence            46789999999999999999999999998653

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

Probab=99.45  E-value=7.5e-16  Score=81.58  Aligned_cols=34  Identities=21%  Similarity=0.356  Sum_probs=30.2

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMA   35 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~   35 (61)
                      +..+||..+||++.+|+|||||||+|+|+.....
T Consensus        35 ~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~   68 (74)
T 2ly9_A           35 EIIRLMKITGLTKGEIKKWFSDTRYNQRNSKSNQ   68 (74)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHHHHHHHTTTTTCSC
T ss_pred             HHHHHHHHhCcCHHHeeeCChhHhHHHHhhCcCC
Confidence            4678999999999999999999999999976543

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

Probab=99.44  E-value=5.4e-16  Score=82.71  Aligned_cols=34  Identities=15%  Similarity=0.319  Sum_probs=30.3

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMA   35 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~   35 (61)
                      +..+||..|||++.+|+|||||||+|+|+..+..
T Consensus        37 ~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~~~   70 (76)
T 2dn0_A           37 EVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGSR   70 (76)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCSSS
T ss_pred             HHHHHHHHhCCChHHhhHHhHHHhHHHHHhcccC
Confidence            4678999999999999999999999999976643

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

Probab=99.44  E-value=1.3e-15  Score=82.81  Aligned_cols=34  Identities=24%  Similarity=0.265  Sum_probs=30.5

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMA   35 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~   35 (61)
                      +..+||..+||++.+|+|||||||+|+|+.....
T Consensus        33 ~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~   66 (87)
T 1b72_B           33 AKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKF   66 (87)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGGG
T ss_pred             HHHHHHHHHCcCHHHHHHHHHHHHHHhhhccccc
Confidence            4678999999999999999999999999986543

>1wh5_A ZF-HD homeobox family protein; structural genomics, zinc finger homeobox family protein, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} SCOP: a.4.1.1

Probab=99.44  E-value=7.4e-16  Score=83.25  Aligned_cols=29  Identities=14%  Similarity=0.237  Sum_probs=26.6

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK   30 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr   30 (61)
                      +..+||..|+|+|.+|+|||||||+|+|+
T Consensus        50 ~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           50 VIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             HHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             HHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            45789999999999999999999999875

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

Probab=99.44  E-value=9.8e-16  Score=82.90  Aligned_cols=29  Identities=14%  Similarity=0.178  Sum_probs=26.6

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK   30 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr   30 (61)
                      +..+||..|+|+|.+|||||||||+|+|+
T Consensus        50 ~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           50 AVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             HHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             HHHHHHHHhCcCcCcccccccccccCCCC
Confidence            45789999999999999999999999875

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

Probab=99.44  E-value=1.7e-15  Score=80.33  Aligned_cols=32  Identities=44%  Similarity=0.559  Sum_probs=29.0

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..+||++.+|+|||||||+|+|+...
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            46789999999999999999999999998654

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

Probab=99.43  E-value=1.2e-15  Score=79.56  Aligned_cols=33  Identities=36%  Similarity=0.475  Sum_probs=29.7

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKM   34 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~   34 (61)
                      +..+||..+||++.+|+|||||||+|+|+....
T Consensus        30 ~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~~   62 (67)
T 2k40_A           30 ILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRE   62 (67)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCCT
T ss_pred             HHHHHHHHHCcCHHHhhHhhHhHHHHHhHhchh
Confidence            467899999999999999999999999987653

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

Probab=99.43  E-value=6.8e-16  Score=80.42  Aligned_cols=29  Identities=14%  Similarity=0.171  Sum_probs=26.5

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK   30 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr   30 (61)
                      +..+||..|||++++|+|||||||+|.++
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            46789999999999999999999998765

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

Probab=99.42  E-value=1.8e-15  Score=76.46  Aligned_cols=28  Identities=43%  Similarity=0.506  Sum_probs=25.9

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWK   29 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~k   29 (61)
                      +..+||..|||++.+|+|||||||+|+|
T Consensus        31 ~r~~La~~l~l~~~qV~~WFqNrR~k~k   58 (58)
T 3rkq_A           31 ERDQLASVLKLTSTQVKIWFQNRRYKSK   58 (58)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHhCcCHHHHHHhhHHhhccCC
Confidence            4678999999999999999999999975

>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=99.42  E-value=4.3e-14  Score=66.83  Aligned_cols=23  Identities=70%  Similarity=1.097  Sum_probs=19.8

Q ss_pred             cceeeccccchhHHHHHhhhhcc
Q psy12003         15 RQIKIWFQNRRMKWKKEHKMASM   37 (61)
Q Consensus        15 ~~VqvWFqNrRak~kr~~~~~~~   37 (61)
                      +||+|||||||||||+.......
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~~~   23 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFNDAR   23 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHHTT
T ss_pred             CCceeccHHHHHHHHHHhHHHHH
Confidence            48999999999999999886544

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

Probab=99.41  E-value=2.6e-15  Score=76.73  Aligned_cols=30  Identities=33%  Similarity=0.268  Sum_probs=27.5

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE   31 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~   31 (61)
                      |..+||..+||++.+|+|||||||+|+|+.
T Consensus        30 ~r~~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A           30 GLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            467899999999999999999999999873

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

Probab=99.39  E-value=2.3e-15  Score=78.28  Aligned_cols=31  Identities=32%  Similarity=0.374  Sum_probs=28.3

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEH   32 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~   32 (61)
                      +..+||..+||++.+|+|||||||+|+|+..
T Consensus        32 ~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   62 (66)
T 1bw5_A           32 MKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             HHHHHHHHHCcCHHHHHHHhHHHHHHHhHHh
Confidence            4678999999999999999999999998864

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

Probab=99.39  E-value=6.4e-15  Score=77.86  Aligned_cols=33  Identities=24%  Similarity=0.296  Sum_probs=29.7

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKM   34 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~   34 (61)
                      +..+||..+||++.+|+|||||||+|+|+....
T Consensus        33 ~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~   65 (73)
T 1puf_B           33 AKEELAKKCGITVSQVSNWFGNKRIRYKKNIGK   65 (73)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTT
T ss_pred             HHHHHHHHHCcCHHHHHHHHHHHHhhccccccc
Confidence            467899999999999999999999999997654

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

Probab=99.39  E-value=6.1e-15  Score=77.94  Aligned_cols=32  Identities=19%  Similarity=0.156  Sum_probs=29.0

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..+||++.+|+|||||||+|+|+...
T Consensus        39 ~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~   70 (73)
T 1x2n_A           39 EKKQIAAQTNLTLLQVNNWFINARRRILQSGP   70 (73)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHCcCHHHHHHHhHHHHhhcccccc
Confidence            45789999999999999999999999998654

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

Probab=99.39  E-value=4.3e-15  Score=82.30  Aligned_cols=31  Identities=19%  Similarity=0.406  Sum_probs=28.5

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEH   32 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~   32 (61)
                      +..+||..|||++.+|+|||||||+|+|+..
T Consensus        54 ~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   84 (96)
T 3nar_A           54 EYDKLAKESGLARTDIVSWFGDTRYAWKNGN   84 (96)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHhCCCHHHeeecchhhhhHhhhhc
Confidence            4678999999999999999999999999864

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

Probab=99.39  E-value=4.7e-15  Score=75.90  Aligned_cols=28  Identities=29%  Similarity=0.400  Sum_probs=25.4

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWK   29 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~k   29 (61)
                      +..+||..|||++.+|+|||||||+|+|
T Consensus        34 ~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A           34 EKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            4678999999999999999999999986

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

Probab=99.36  E-value=2.5e-14  Score=77.52  Aligned_cols=34  Identities=18%  Similarity=0.102  Sum_probs=29.9

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMA   35 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~   35 (61)
                      |..+||..+||++.+|+|||||||+|+++.....
T Consensus        39 ~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~~~   72 (83)
T 2dmn_A           39 EKQMLSEKTNLSLLQISNWFINARRRILPDMLQQ   72 (83)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHTCC
T ss_pred             HHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHHHh
Confidence            4578999999999999999999999999876543

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

Probab=99.36  E-value=3.6e-15  Score=77.02  Aligned_cols=29  Identities=28%  Similarity=0.381  Sum_probs=26.9

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK   30 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr   30 (61)
                      +..+||..+||++.+|+|||||||+|+|+
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            46789999999999999999999999876

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

Probab=99.35  E-value=2.6e-14  Score=78.94  Aligned_cols=34  Identities=26%  Similarity=0.331  Sum_probs=30.5

Q ss_pred             chhhhhcCCC---------------CCccceeeccccchhHHHHHhhhh
Q psy12003          2 NLLRDKNPPR---------------GTERQIKIWFQNRRMKWKKEHKMA   35 (61)
Q Consensus         2 ~~~eLA~~l~---------------Lte~~VqvWFqNrRak~kr~~~~~   35 (61)
                      +..+||..|+               |++.+|+|||||||+|+|+.....
T Consensus        36 ~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~~~   84 (95)
T 2cuf_A           36 KREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANIA   84 (95)
T ss_dssp             HHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhhcc
Confidence            4578999999               999999999999999999988753

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

Probab=99.34  E-value=1.2e-14  Score=78.63  Aligned_cols=32  Identities=28%  Similarity=0.191  Sum_probs=29.0

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..+||++.+|+|||||||+|+|+...
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            46789999999999999999999999999754

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

Probab=99.34  E-value=9.5e-15  Score=87.64  Aligned_cols=33  Identities=21%  Similarity=0.360  Sum_probs=29.5

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKM   34 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~   34 (61)
                      +..+||..|+|++++|+|||||||+|+||..+.
T Consensus       128 ~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~  160 (164)
T 2xsd_C          128 EITGLADSLQLEKEVVRVWFCNRRQKEKRMTPA  160 (164)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC-
T ss_pred             HHHHHHHHHCCChhhhhhhhHHhhHHHhhccCC
Confidence            467899999999999999999999999997653

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

Probab=99.32  E-value=1.8e-14  Score=85.97  Aligned_cols=30  Identities=27%  Similarity=0.423  Sum_probs=27.8

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE   31 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~   31 (61)
                      +..+||..|||++.+|+|||||||+|+||.
T Consensus       130 ~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C          130 DITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             HHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            467899999999999999999999999974

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

Probab=99.30  E-value=2.1e-14  Score=84.71  Aligned_cols=30  Identities=23%  Similarity=0.491  Sum_probs=27.7

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE   31 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~   31 (61)
                      +..+||..|||++++|+|||||||+|+||+
T Consensus       116 ~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A          116 EIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             HHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            467899999999999999999999999974

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

Probab=99.30  E-value=3.9e-14  Score=77.10  Aligned_cols=28  Identities=36%  Similarity=0.318  Sum_probs=26.2

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWK   29 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~k   29 (61)
                      |..+||..+||++.+|+|||||||+|+|
T Consensus        59 ~r~~La~~~gL~~~qV~~WFqNrR~r~k   86 (87)
T 1mnm_C           59 GLENLMKNTSLSRIQIKNWVSNRRRKEK   86 (87)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHCcCHHHHHHHHHHHHhhcc
Confidence            4678999999999999999999999987

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

Probab=99.30  E-value=6.4e-14  Score=83.24  Aligned_cols=30  Identities=27%  Similarity=0.463  Sum_probs=27.3

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE   31 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~   31 (61)
                      +..+||..+||++.+|+|||||||+|+||.
T Consensus       125 ~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A          125 QITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHcCCChhheeeccccccccccCC
Confidence            467899999999999999999999999974

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

Probab=99.28  E-value=4.5e-14  Score=83.40  Aligned_cols=29  Identities=21%  Similarity=0.448  Sum_probs=27.1

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK   30 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr   30 (61)
                      +..+||..|||++.+|+|||||||+|+||
T Consensus       122 ~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I          122 EITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            46789999999999999999999999986

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

Probab=99.27  E-value=2.9e-13  Score=76.22  Aligned_cols=27  Identities=33%  Similarity=0.371  Sum_probs=24.0

Q ss_pred             CCCccceeeccccchhHHHHHhhhhcc
Q psy12003         11 RGTERQIKIWFQNRRMKWKKEHKMASM   37 (61)
Q Consensus        11 ~Lte~~VqvWFqNrRak~kr~~~~~~~   37 (61)
                      .|+|.+|+|||||||+++|+..+....
T Consensus        65 ~lte~~V~~WFqNRR~k~kr~~~~~~~   91 (102)
T 2da6_A           65 LVTEVRVYNWFANRRKEEAFRQKLAMD   91 (102)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             cccccceeeeecchHHHHHHhhHhhhc
Confidence            799999999999999999998776544

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

Probab=99.27  E-value=7e-14  Score=73.16  Aligned_cols=32  Identities=19%  Similarity=0.127  Sum_probs=28.1

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..+||++.+|++||||||+|+|+...
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            45689999999999999999999999998643

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

Probab=99.17  E-value=4.4e-12  Score=69.90  Aligned_cols=35  Identities=14%  Similarity=0.099  Sum_probs=30.2

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhhc
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMAS   36 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~~   36 (61)
                      |-.+||..+||++.||++||+|+|+|+++......
T Consensus        37 ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~~~~   71 (89)
T 2lk2_A           37 EKALLSQQTHLSTLQVCNWFINARRRLLPDMLRKD   71 (89)
T ss_dssp             HHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHHHhc
Confidence            34689999999999999999999999998765443

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

Probab=99.15  E-value=2.4e-13  Score=80.98  Aligned_cols=33  Identities=9%  Similarity=-0.055  Sum_probs=27.8

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKM   34 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~   34 (61)
                      +..+||..|||++.+|+|||||||+|+|+....
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            456899999999999999999999999987653

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

Probab=99.15  E-value=6.5e-13  Score=70.45  Aligned_cols=26  Identities=23%  Similarity=0.410  Sum_probs=24.4

Q ss_pred             chhhhhcCCCCCccceeeccccchhH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMK   27 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak   27 (61)
                      ||.+||..+||++.+|||||||||++
T Consensus        34 ei~~LA~~lgL~~~VVrVWFqNrRa~   59 (71)
T 2da7_A           34 ELLKISIAVGLPQEFVKEWFEQRKVY   59 (71)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCHHHHHHHHhhcccc
Confidence            78999999999999999999999973

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

Probab=99.11  E-value=1.7e-12  Score=68.66  Aligned_cols=27  Identities=19%  Similarity=0.148  Sum_probs=23.9

Q ss_pred             chhhhhcCCCCCccceeeccccchhHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKW   28 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~   28 (61)
                      .+-+||++|||++++|||||||||.--
T Consensus        37 ~r~~La~~tGL~~~~IqVWFQNrR~~~   63 (71)
T 1wi3_A           37 AIHTLSAQLDLPKHTIIKFFQNQRYHV   63 (71)
T ss_dssp             HHHHHHHHSCCCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHhCCCHHHHHHhhccceeee
Confidence            356899999999999999999999753

>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding cooperativity, maltose binding protein, MBP, sugar binding, DNA binding protein; 2.10A {Escherichia coli} SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A

Probab=99.07  E-value=1.5e-12  Score=84.19  Aligned_cols=28  Identities=29%  Similarity=0.400  Sum_probs=25.8

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWK   29 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~k   29 (61)
                      +..+||.+|||+++||+|||||||+|+|
T Consensus       394 ~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          394 EKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             HHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            4578999999999999999999999975

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

Probab=99.05  E-value=1.4e-12  Score=72.88  Aligned_cols=25  Identities=36%  Similarity=0.476  Sum_probs=21.3

Q ss_pred             CC---CCccceeeccccchhHHHHHhhh
Q psy12003         10 PR---GTERQIKIWFQNRRMKWKKEHKM   34 (61)
Q Consensus        10 l~---Lte~~VqvWFqNrRak~kr~~~~   34 (61)
                      ||   |+|.+|+|||||||+++|+....
T Consensus        64 lg~~~lse~qV~vWFqNRR~k~k~k~~~   91 (99)
T 1lfb_A           64 LGSNLVTEVRVYNWFANRRKEEAFRHKL   91 (99)
T ss_dssp             TGGGCCCHHHHHHHHHHHHHTTSCCC--
T ss_pred             cCccccCcceeeeccHHHHHHHHHhchh
Confidence            88   99999999999999998876553

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

Probab=98.76  E-value=9.3e-11  Score=72.06  Aligned_cols=28  Identities=25%  Similarity=0.159  Sum_probs=24.3

Q ss_pred             hhhhhcCCC---------------------CCccceeeccccchhHHHH
Q psy12003          3 LLRDKNPPR---------------------GTERQIKIWFQNRRMKWKK   30 (61)
Q Consensus         3 ~~eLA~~l~---------------------Lte~~VqvWFqNrRak~kr   30 (61)
                      -.+||..+|                     |||.+|+|||||||++.|.
T Consensus       145 Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~~k~  193 (194)
T 1ic8_A          145 RETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAF  193 (194)
T ss_dssp             THHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHHCC-
T ss_pred             HHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhhhhc
Confidence            457888888                     9999999999999999764

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

Probab=98.29  E-value=1.3e-08  Score=63.69  Aligned_cols=17  Identities=41%  Similarity=0.593  Sum_probs=15.6

Q ss_pred             CCccceeeccccchhHH
Q psy12003         12 GTERQIKIWFQNRRMKW   28 (61)
Q Consensus        12 Lte~~VqvWFqNrRak~   28 (61)
                      |||.+|+|||||||++.
T Consensus       202 lte~~V~~WFqNRR~~~  218 (221)
T 2h8r_A          202 VTEVRVYNWFANRRKEE  218 (221)
T ss_dssp             CCHHHHHHHHHHHHTTC
T ss_pred             cCHHHHHHHhHHhhhhh
Confidence            89999999999999863

>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C

Probab=88.12  E-value=0.08  Score=24.09  Aligned_cols=25  Identities=8%  Similarity=-0.136  Sum_probs=19.8

Q ss_pred             hhhhhcCCCCCccceeeccccchhH
Q psy12003          3 LLRDKNPPRGTERQIKIWFQNRRMK   27 (61)
Q Consensus         3 ~~eLA~~l~Lte~~VqvWFqNrRak   27 (61)
                      +.++|..+|++..+|.-|+.....+
T Consensus        24 ~~~ia~~lgvs~~Tv~r~l~~~~~~   48 (52)
T 1jko_C           24 RQQLAIIFGIGVSTLYRYFPASSIK   48 (52)
T ss_dssp             HHHHHHTTSCCHHHHHHHSCTTC--
T ss_pred             HHHHHHHHCCCHHHHHHHHHHcccc
Confidence            5789999999999999998765443

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=88.03  E-value=0.073  Score=30.23  Aligned_cols=28  Identities=0%  Similarity=-0.139  Sum_probs=21.0

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWK   29 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~k   29 (61)
                      ...|+|..+|+++.+|+.....-|.+-|
T Consensus       111 s~~EIA~~lgis~~tV~~~l~rar~~Lr  138 (157)
T 2lfw_A          111 SPEDAAYLIEVDTSEVETLVTEALAEIE  138 (157)
T ss_dssp             CHHHHHHTTTSCHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence            4679999999999999977653333333

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

Probab=85.37  E-value=0.058  Score=28.14  Aligned_cols=21  Identities=19%  Similarity=0.428  Sum_probs=19.0

Q ss_pred             chhhhhcCCCCCccceeeccc
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQ   22 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFq   22 (61)
                      +|-+|+.+..|+..+|+-||-
T Consensus        35 Dl~~L~~kskms~qqvkdwFa   55 (70)
T 2ys9_A           35 DIPQLSQASRLSTQQVLDWFD   55 (70)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHH
T ss_pred             hHHHHHHHhCCCHHHHHHHHH
Confidence            477899999999999999995

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=82.04  E-value=0.13  Score=26.80  Aligned_cols=31  Identities=6%  Similarity=-0.117  Sum_probs=24.1

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEH   32 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~   32 (61)
                      -..|+|..+|+++.+|+.....=|.|.|+.-
T Consensus        55 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l   85 (92)
T 3hug_A           55 STAQIATDLGIAEGTVKSRLHYAVRALRLTL   85 (92)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            4679999999999999988776565555543

---

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	61
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	5e-09
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	3e-08
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	3e-08
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	3e-08
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	9e-08
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	1e-07
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	2e-07
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	2e-07
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	4e-07
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	5e-07
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	5e-07
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	6e-07
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	9e-07
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	9e-07
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	1e-06
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	2e-06
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	4e-06
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	1e-05
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	2e-05
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	2e-05
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	2e-05
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	3e-05
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	4e-05
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	5e-05
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	8e-05
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	1e-04
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	1e-04
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	2e-04
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	3e-04
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	3e-04
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	3e-04

>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 = 44.8 bits (106), Expect = 5e-09
 Identities = 19/20 (95%), Positives = 20/20 (100%)

Query: 13 TERQIKIWFQNRRMKWKKEH 32
          TERQIKIWFQNRRMKWKKE+
Sbjct: 37 TERQIKIWFQNRRMKWKKEN 56

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.2 bits (102), Expect = 3e-08
 Identities = 11/22 (50%), Positives = 17/22 (77%)

Query: 13 TERQIKIWFQNRRMKWKKEHKM 34
           E +I++WF NRR KW++E K+
Sbjct: 41 PEARIQVWFSNRRAKWRREEKL 62

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-a9
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.9 bits (101), Expect = 3e-08
 Identities = 17/21 (80%), Positives = 19/21 (90%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
          TERQ+KIWFQNRRMK KK +K
Sbjct: 53 TERQVKIWFQNRRMKMKKINK 73

>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 = 43.1 bits (101), Expect = 3e-08
 Identities = 8/25 (32%), Positives = 15/25 (60%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMASM 37
          T  ++  WF NRR + K+   +A++
Sbjct: 55 TSLKVYNWFANRRKEIKRRANIAAI 79

>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 = 41.4 bits (97), Expect = 9e-08
 Identities = 14/18 (77%), Positives = 16/18 (88%)

Query: 13 TERQIKIWFQNRRMKWKK 30
          +ERQI IWFQNRR+K KK
Sbjct: 41 SERQITIWFQNRRVKEKK 58

>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 = 41.5 bits (97), Expect = 1e-07
 Identities = 14/21 (66%), Positives = 16/21 (76%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
           E Q+KIWFQNRRMK KK  +
Sbjct: 67 NETQVKIWFQNRRMKQKKRER 87

>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 = 40.6 bits (95), Expect = 2e-07
 Identities = 12/18 (66%), Positives = 16/18 (88%)

Query: 13 TERQIKIWFQNRRMKWKK 30
          +ERQ+K WFQNRR KW++
Sbjct: 40 SERQVKTWFQNRRAKWRR 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 = 40.1 bits (94), Expect = 2e-07
 Identities = 7/18 (38%), Positives = 10/18 (55%)

Query: 13 TERQIKIWFQNRRMKWKK 30
            R I+ WF+ RR + K 
Sbjct: 34 DVRSIQRWFRQRRNQEKP 51

>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 = 39.9 bits (93), Expect = 4e-07
 Identities = 12/24 (50%), Positives = 18/24 (75%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMAS 36
          TE +I++WFQNRR + +K+H   S
Sbjct: 42 TEARIQVWFQNRRARLRKQHTSVS 65

>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 = 5e-07
 Identities = 11/22 (50%), Positives = 15/22 (68%)

Query: 13 TERQIKIWFQNRRMKWKKEHKM 34
          + R I++WFQN+R K KK   M
Sbjct: 43 SPRVIRVWFQNKRCKDKKRSIM 64

>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 = 40.1 bits (93), Expect = 5e-07
 Identities = 9/21 (42%), Positives = 12/21 (57%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
          TE ++  WF NRR +    HK
Sbjct: 58 TEVRVYNWFANRRKEEAFRHK 78

>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 = 39.5 bits (92), Expect = 6e-07
 Identities = 12/19 (63%), Positives = 15/19 (78%)

Query: 13 TERQIKIWFQNRRMKWKKE 31
           E  IK+WFQNRRMK K++
Sbjct: 39 PESTIKVWFQNRRMKDKRQ 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 = 39.2 bits (91), Expect = 9e-07
 Identities = 8/24 (33%), Positives = 14/24 (58%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMAS 36
          TE Q + WF+ R  +W++   + S
Sbjct: 42 TEEQTQKWFKQRLAEWRRSEGLPS 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 = 39.1 bits (91), Expect = 9e-07
 Identities = 12/21 (57%), Positives = 15/21 (71%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
          T  Q+KIWFQN R K K++ K
Sbjct: 42 TPTQVKIWFQNHRYKMKRQAK 62

>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 = 38.8 bits (90), Expect = 1e-06
 Identities = 9/21 (42%), Positives = 13/21 (61%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
             Q+KIWF+NRR + K +  
Sbjct: 41 GTAQVKIWFKNRRRRHKIQSD 61

>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 = 38.0 bits (88), Expect = 2e-06
 Identities = 13/18 (72%), Positives = 15/18 (83%)

Query: 13 TERQIKIWFQNRRMKWKK 30
          TE Q+KIWFQNRR K K+
Sbjct: 40 TETQVKIWFQNRRAKAKR 57

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 53

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

 Score = 37.1 bits (86), Expect = 4e-06
 Identities = 11/15 (73%), Positives = 11/15 (73%)

Query: 13 TERQIKIWFQNRRMK 27
           E QIKIWFQN R K
Sbjct: 39 NEAQIKIWFQNARAK 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 = 36.3 bits (84), Expect = 1e-05
 Identities = 9/18 (50%), Positives = 10/18 (55%)

Query: 13 TERQIKIWFQNRRMKWKK 30
          +  QIK W  NRR K K 
Sbjct: 41 SRIQIKNWVSNRRRKEKT 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 = 35.6 bits (82), Expect = 2e-05
 Identities = 8/17 (47%), Positives = 13/17 (76%)

Query: 13 TERQIKIWFQNRRMKWK 29
          T  Q+++WF N+RM+ K
Sbjct: 37 TPLQVRVWFINKRMRSK 53

>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 = 36.2 bits (83), Expect = 2e-05
 Identities = 12/29 (41%), Positives = 14/29 (48%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMASMNVIP 41
          T  Q+KIWFQN R K K+          P
Sbjct: 49 TPTQVKIWFQNHRYKTKRAQNEKGYEGHP 77

>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 = 35.7 bits (82), Expect = 2e-05
 Identities = 8/21 (38%), Positives = 13/21 (61%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
          T  Q+  WF N+R+++KK   
Sbjct: 44 TVSQVSNWFGNKRIRYKKNIG 64

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 80

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 35.4 bits (81), Expect = 3e-05
 Identities = 4/19 (21%), Positives = 7/19 (36%)

Query: 13 TERQIKIWFQNRRMKWKKE 31
            + +KIW  N +      
Sbjct: 61 RRQVLKIWMHNNKNSGPSS 79

>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 = 34.9 bits (80), Expect = 4e-05
 Identities = 6/18 (33%), Positives = 12/18 (66%)

Query: 13 TERQIKIWFQNRRMKWKK 30
           +  +++WF NRR + K+
Sbjct: 39 EKEVVRVWFCNRRQREKR 56

>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 = 34.4 bits (79), Expect = 5e-05
 Identities = 7/17 (41%), Positives = 13/17 (76%)

Query: 13 TERQIKIWFQNRRMKWK 29
          + R+I+ WF++RR + K
Sbjct: 42 SVRKIQCWFRHRRNQDK 58

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.3 bits (78), Expect = 8e-05
 Identities = 6/21 (28%), Positives = 9/21 (42%)

Query: 13 TERQIKIWFQNRRMKWKKEHK 33
           +  I  +FQN+R   K    
Sbjct: 48 PKHTIIKFFQNQRYHVKHSGP 68

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Length = 62

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.9 bits (78), Expect = 1e-04
 Identities = 6/18 (33%), Positives = 9/18 (50%)

Query: 13 TERQIKIWFQNRRMKWKK 30
          T  Q+  WF N R +  +
Sbjct: 45 TLLQVNNWFINARRRILQ 62

>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 = 33.9 bits (77), Expect = 1e-04
 Identities = 5/26 (19%), Positives = 12/26 (46%)

Query: 13 TERQIKIWFQNRRMKWKKEHKMASMN 38
          T R+I  WF  ++     + +   ++
Sbjct: 44 TRREIDAWFTEKKKSKALKEEKMEID 69

>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 = 33.0 bits (75), Expect = 2e-04
 Identities = 10/19 (52%), Positives = 16/19 (84%)

Query: 13 TERQIKIWFQNRRMKWKKE 31
          TE ++++WF+NRR KW+K 
Sbjct: 41 TEARVRVWFKNRRAKWRKR 59

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 57

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

 Score = 32.6 bits (74), Expect = 3e-04
 Identities = 8/20 (40%), Positives = 13/20 (65%)

Query: 13 TERQIKIWFQNRRMKWKKEH 32
           +  I++WF NRR K K+ +
Sbjct: 38 EKEVIRVWFSNRRQKEKRIN 57

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 50

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 32.5 bits (74), Expect = 3e-04
 Identities = 3/13 (23%), Positives = 5/13 (38%)

Query: 13 TERQIKIWFQNRR 25
              +  +F N R
Sbjct: 38 ELSTVSNFFMNAR 50

>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 = 32.7 bits (74), Expect = 3e-04
 Identities = 7/18 (38%), Positives = 12/18 (66%)

Query: 13 TERQIKIWFQNRRMKWKK 30
           +  +++WF NRR K K+
Sbjct: 48 EKDVVRVWFCNRRQKGKR 65

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	61
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.59
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.55
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.54
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.54
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.54
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.53
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.52
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.5
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.49
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.49
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.48
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.48
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.47
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.43
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.43
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.41
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.41
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.4
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.38
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.38
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.38
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.34
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.33
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.33
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.29
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.25
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.25
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.24
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.21
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.2
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	98.96
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	98.89
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	83.68
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	80.31

>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=99.59  E-value=9.7e-18  Score=84.57  Aligned_cols=30  Identities=63%  Similarity=0.946  Sum_probs=27.9

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE   31 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~   31 (61)
                      +..+||..|||++.+|+|||||||+|+||+
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            467999999999999999999999999985

>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=99.55  E-value=1.9e-17  Score=83.96  Aligned_cols=29  Identities=48%  Similarity=0.638  Sum_probs=26.9

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK   30 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr   30 (61)
                      +..+||..|||++.+|+|||||||+|+||
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            46799999999999999999999999875

>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=99.54  E-value=4.2e-17  Score=82.28  Aligned_cols=30  Identities=40%  Similarity=0.518  Sum_probs=27.6

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE   31 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~   31 (61)
                      +..+||..|||++.+|+|||||||+|+||+
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            457899999999999999999999999974

>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=99.54  E-value=8.6e-17  Score=81.12  Aligned_cols=29  Identities=45%  Similarity=0.776  Sum_probs=27.2

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK   30 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr   30 (61)
                      +..+||..|||++.+|+|||||||+|+||
T Consensus        29 ~r~~LA~~l~L~~~qV~~WFqNrR~k~kk   57 (57)
T d2e1oa1          29 ERKRLAKMLQLSERQVKTWFQNRRAKWRR   57 (57)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCHHHhhHhhhhhhhhccC
Confidence            46789999999999999999999999986

>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=99.54  E-value=6.3e-17  Score=85.06  Aligned_cols=32  Identities=25%  Similarity=0.461  Sum_probs=29.2

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..+||++.+|+|||||||+|+|+...
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            46789999999999999999999999999764

>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=99.53  E-value=1.1e-16  Score=82.98  Aligned_cols=33  Identities=30%  Similarity=0.406  Sum_probs=29.8

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKM   34 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~   34 (61)
                      +..+||..|||++.+|+|||||||+|+|+....
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            467899999999999999999999999997654

>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=99.52  E-value=1.5e-16  Score=80.44  Aligned_cols=29  Identities=45%  Similarity=0.560  Sum_probs=27.2

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK   30 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr   30 (61)
                      +..+||..|||++.+|+|||||||+|+||
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            45789999999999999999999999997

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=2.2e-16  Score=85.63  Aligned_cols=32  Identities=44%  Similarity=0.608  Sum_probs=29.5

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..|||++.+|+|||||||+|+|+..+
T Consensus        56 ~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~~   87 (88)
T d1b72a_          56 RRVEIAATLELNETQVKIWFQNRRMKQKKRER   87 (88)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCCHHHeeeccHhHHHHHHHhcc
Confidence            56899999999999999999999999999764

>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=99.49  E-value=3.3e-16  Score=83.11  Aligned_cols=34  Identities=50%  Similarity=0.576  Sum_probs=30.3

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKMA   35 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~~   35 (61)
                      +..+||..|||++.+|+|||||||+|+|+..+..
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            3568999999999999999999999999987643

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

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

Probab=99.49  E-value=3.7e-16  Score=80.56  Aligned_cols=33  Identities=33%  Similarity=0.542  Sum_probs=30.2

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKM   34 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~   34 (61)
                      +..+||..|||++.+|+|||||||+|+|+....
T Consensus        31 ~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~~   63 (65)
T d1fjla_          31 TREELAQRTNLTEARIQVWFQNRRARLRKQHTS   63 (65)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCHHHhhHhhhhHHHHHHhcccc
Confidence            578999999999999999999999999997653

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.48  E-value=1.5e-16  Score=79.16  Aligned_cols=26  Identities=42%  Similarity=0.494  Sum_probs=24.3

Q ss_pred             chhhhhcCCCCCccceeeccccchhH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMK   27 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak   27 (61)
                      +..+||..|||++.+|+|||||||+|
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            46799999999999999999999996

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

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

Probab=99.48  E-value=5.6e-16  Score=78.69  Aligned_cols=31  Identities=32%  Similarity=0.599  Sum_probs=28.7

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEH   32 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~   32 (61)
                      +..+||..+||++.+|+|||||||+|+|+.+
T Consensus        30 ~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~~   60 (60)
T d1yz8p1          30 TREEIAVWTNLTEARVRVWFKNRRAKWRKRE   60 (60)
T ss_dssp             TTTHHHHHTTSCHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHCCChHHHHHHhHHHHHHHHhcC
Confidence            5789999999999999999999999999863

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.47  E-value=9.7e-17  Score=85.18  Aligned_cols=32  Identities=38%  Similarity=0.455  Sum_probs=28.9

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..|||++.+|+|||||||+|.|+...
T Consensus        38 ~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~   69 (77)
T d1vnda_          38 EREHLASLIRLTPTQVKIWFQNHRYKTKRAQN   69 (77)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHSSSSCSSSCC
T ss_pred             HHHHHHHHhCCChhhhhhcchhHHHHHHHHhh
Confidence            56899999999999999999999999987654

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.43  E-value=2.4e-15  Score=78.02  Aligned_cols=33  Identities=36%  Similarity=0.674  Sum_probs=29.9

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKM   34 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~   34 (61)
                      +..+||..|||++.+|+|||||+|+|+|+..+.
T Consensus        30 ~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~   62 (68)
T d2cuea1          30 ARERLAAKIDLPEARIQVWFSNRRAKWRREEKL   62 (68)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCcChhheeecCcchhHHHHhhhhh
Confidence            457899999999999999999999999998664

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

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

Probab=99.43  E-value=3.8e-16  Score=77.51  Aligned_cols=29  Identities=28%  Similarity=0.313  Sum_probs=26.7

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK   30 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr   30 (61)
                      ++.+||..|||++.+|+|||||||+|.|+
T Consensus        23 ~~~~LA~~~~ls~~qV~~WFqNrR~k~k~   51 (52)
T d1x2ma1          23 RLEGLSKQLDWDVRSIQRWFRQRRNQEKP   51 (52)
T ss_dssp             HHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHCcCHHHHHHHHHhhhcccCc
Confidence            57899999999999999999999999864

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

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

Probab=99.41  E-value=1.6e-15  Score=78.77  Aligned_cols=32  Identities=38%  Similarity=0.459  Sum_probs=29.0

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..|||++.+|+|||||||+|+|+...
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            45789999999999999999999999998754

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

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

Probab=99.41  E-value=9.9e-16  Score=77.15  Aligned_cols=30  Identities=27%  Similarity=0.423  Sum_probs=27.9

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE   31 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~   31 (61)
                      ++.+||..+||++.+|+|||||||+|+|+.
T Consensus        27 ~~~~LA~~lgL~~~qV~~WFqNrR~k~kk~   56 (57)
T d1e3oc1          27 DITLIAEQLNMEKEVIRVWFSNRRQKEKRI   56 (57)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHcc
Confidence            578999999999999999999999999874

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

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

Probab=99.40  E-value=1.6e-15  Score=75.41  Aligned_cols=28  Identities=29%  Similarity=0.400  Sum_probs=25.7

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWK   29 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~k   29 (61)
                      +..+||..+||++.+|++||||||+|.|
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            5679999999999999999999999864

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

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

Probab=99.38  E-value=4.2e-15  Score=78.43  Aligned_cols=33  Identities=21%  Similarity=0.383  Sum_probs=28.9

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHKM   34 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~~   34 (61)
                      +..+||..|||++.+|+|||||||++.|+....
T Consensus        33 ~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~~   65 (76)
T d2ecba1          33 ELNRLRAQTKLTRREIDAWFTEKKKSKALKEEK   65 (76)
T ss_dssp             HHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSC
T ss_pred             HHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhHh
Confidence            568999999999999999999999987776543

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

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

Probab=99.38  E-value=3.5e-15  Score=75.59  Aligned_cols=28  Identities=29%  Similarity=0.383  Sum_probs=26.2

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWK   29 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~k   29 (61)
                      ++.+||..+||++.+|+|||||||++.|
T Consensus        31 ~~~~LA~~lgls~~qV~~WFqNrR~k~r   58 (59)
T d2cqxa1          31 RLKGLSKQLDWSVRKIQCWFRHRRNQDK   58 (59)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHCcCHHHHHHHHHhhhcccC
Confidence            5789999999999999999999999975

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

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

Probab=99.38  E-value=1.6e-15  Score=76.56  Aligned_cols=30  Identities=23%  Similarity=0.491  Sum_probs=27.7

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE   31 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~   31 (61)
                      ++.+||..|||++.+|+|||||||+++|+.
T Consensus        28 ~~~~La~~l~l~~~~V~~WFqNrR~k~kr~   57 (58)
T d1au7a1          28 EIMRMAEELNLEKEVVRVWFCNRRQREKRV   57 (58)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHhHHHHhc
Confidence            578999999999999999999999998863

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=5.2e-15  Score=77.18  Aligned_cols=29  Identities=21%  Similarity=0.181  Sum_probs=27.1

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK   30 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr   30 (61)
                      ++.+||..|||++.+|+|||||||+|.|+
T Consensus        37 ~~~~La~~lgl~~~qV~~WFqNrR~k~kk   65 (71)
T d1wi3a_          37 AIHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             HHHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             HHHHHHHHhCCCHHHHHHHhHhhHhhhcc
Confidence            56789999999999999999999999886

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

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

Probab=99.33  E-value=2.5e-14  Score=75.36  Aligned_cols=31  Identities=16%  Similarity=0.264  Sum_probs=28.7

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEH   32 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~   32 (61)
                      ++.+||..|||++.+|++||||||+|+|+..
T Consensus        32 ~~~~La~~~gL~~~qV~~WF~NrR~k~k~~~   62 (76)
T d2ecca1          32 DYQKLEQITGLPRPEIIQWFGDTRYALKHGQ   62 (76)
T ss_dssp             HHHHHHHHTCCCHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHHHhch
Confidence            5789999999999999999999999999854

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=99.33  E-value=3.1e-15  Score=77.48  Aligned_cols=30  Identities=27%  Similarity=0.434  Sum_probs=27.5

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKE   31 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~   31 (61)
                      ++.+||..+||++.+|+|||||+|+++|+.
T Consensus        37 ~r~~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_          37 QITHIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             HHHHHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            578999999999999999999999998863

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.29  E-value=1e-14  Score=75.19  Aligned_cols=31  Identities=32%  Similarity=0.374  Sum_probs=28.0

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEH   32 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~   32 (61)
                      +..+||..+||++.+|+|||||||+|.|+..
T Consensus        32 ~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~~   62 (66)
T d1bw5a_          32 MKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             HHHHHHHHcCcCHHHhhhhhHhHHHHHHHHH
Confidence            5678999999999999999999999988754

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.25  E-value=1.6e-13  Score=67.11  Aligned_cols=24  Identities=13%  Similarity=0.029  Sum_probs=22.6

Q ss_pred             chhhhhcCCCCCccceeeccccch
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRR   25 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrR   25 (61)
                      ++.+||..|||++.+|+|||||||
T Consensus        27 ~~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1          27 LQITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             HHHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             HHHHHHHHHCcCHHHhhhcCCcCc
Confidence            568999999999999999999998

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

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

Probab=99.25  E-value=6.9e-14  Score=74.62  Aligned_cols=30  Identities=30%  Similarity=0.508  Sum_probs=25.0

Q ss_pred             hcCCCCCccceeeccccchhHHHHHhhhhc
Q psy12003          7 KNPPRGTERQIKIWFQNRRMKWKKEHKMAS   36 (61)
Q Consensus         7 A~~l~Lte~~VqvWFqNrRak~kr~~~~~~   36 (61)
                      +..++|++.+|+|||||||+|+|++.....
T Consensus        49 ~~~~~l~~~~V~vWFqNRR~k~kk~~~~a~   78 (82)
T d2cufa1          49 SDLERVTSLKVYNWFANRRKEIKRRANIAA   78 (82)
T ss_dssp             CTTTCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             hhccCCCHHHHHHHHhhhHHHHHHhhhHHH
Confidence            345579999999999999999999876543

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.24  E-value=4.9e-14  Score=74.92  Aligned_cols=29  Identities=14%  Similarity=0.178  Sum_probs=26.4

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK   30 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr   30 (61)
                      ++.+||..|||++.+|+|||||+|.++|+
T Consensus        50 ~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          50 AVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             HHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             HHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            57899999999999999999999987654

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

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

Probab=99.21  E-value=1.4e-13  Score=71.94  Aligned_cols=32  Identities=25%  Similarity=0.320  Sum_probs=28.7

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHHHhh
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKKEHK   33 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr~~~   33 (61)
                      +..+||..+||++.+|++||||+|+|.|+...
T Consensus        33 ~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~~   64 (73)
T d1pufb_          33 AKEELAKKCGITVSQVSNWFGNKRIRYKKNIG   64 (73)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHCcCHHHhHHHHHHHHHHhcccch
Confidence            46799999999999999999999999997543

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

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

Probab=99.20  E-value=1.5e-13  Score=69.58  Aligned_cols=29  Identities=34%  Similarity=0.308  Sum_probs=26.7

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWKK   30 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~kr   30 (61)
                      |..+||..+||++.+|++||||+|+|.|.
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            57899999999999999999999998774

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.96  E-value=7.5e-12  Score=63.53  Aligned_cols=28  Identities=21%  Similarity=0.182  Sum_probs=25.6

Q ss_pred             chhhhhcCCCCCccceeeccccchhHHH
Q psy12003          2 NLLRDKNPPRGTERQIKIWFQNRRMKWK   29 (61)
Q Consensus         2 ~~~eLA~~l~Lte~~VqvWFqNrRak~k   29 (61)
                      |..+||..+||++.+|++||+|+|.|..
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            6789999999999999999999998754

>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=98.89  E-value=7.1e-12  Score=66.25  Aligned_cols=25  Identities=32%  Similarity=0.409  Sum_probs=20.6

Q ss_pred             cCCCCCccceeeccccchhHHHHHh
Q psy12003          8 NPPRGTERQIKIWFQNRRMKWKKEH   32 (61)
Q Consensus         8 ~~l~Lte~~VqvWFqNrRak~kr~~   32 (61)
                      ...+|||.+|++||||||++.|+..
T Consensus        53 ~~~~vt~~~V~~WF~NRR~~~kr~~   77 (78)
T d1lfba_          53 GSNLVTEVRVYNWFANRRKEEAFRH   77 (78)
T ss_dssp             GGGCCCHHHHHHHHHHHHHTTSCCC
T ss_pred             cccCCCHHHHHHHHHHHHHHHHHhc
Confidence            3346999999999999999988653

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=83.68  E-value=0.054  Score=25.89  Aligned_cols=30  Identities=3%  Similarity=-0.119  Sum_probs=22.7

Q ss_pred             CchhhhhcCCCCCccceeeccccchhHHHH
Q psy12003          1 MNLLRDKNPPRGTERQIKIWFQNRRMKWKK   30 (61)
Q Consensus         1 ~~~~eLA~~l~Lte~~VqvWFqNrRak~kr   30 (61)
                      |...|+|..+|+++..|++..+.-|.+-|.
T Consensus        35 ~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~   64 (68)
T d1or7a1          35 LSYEEIAAIMDCPVGTVRSRIFRAREAIDN   64 (68)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            346799999999999999877655544443

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=80.31  E-value=0.086  Score=25.06  Aligned_cols=25  Identities=0%  Similarity=-0.172  Sum_probs=19.1

Q ss_pred             CchhhhhcCCCCCccceeeccccch
Q psy12003          1 MNLLRDKNPPRGTERQIKIWFQNRR   25 (61)
Q Consensus         1 ~~~~eLA~~l~Lte~~VqvWFqNrR   25 (61)
                      |...|+|..+|+++.+|+.....=+
T Consensus        38 ~s~~eIA~~lgis~~tv~~~~~ra~   62 (71)
T d1rp3a2          38 LPAKEVAKILETSVSRVSQLKAKAL   62 (71)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3568999999999999986544333