Psyllid ID: psy4625

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120
Protein Sequence
PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEMEMELSLLNKANSNNQNN
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHccccHHHHHHHHccHHHHHHHHcccccHHHHHHHcccccccccccccHHHHHHHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
cccEEcccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHcccccccccHHHHHHHccccccccccccccccccccEcccccccccccc
Coil and Loop (DISEMBL)
prsrriksgkdkrskekrprtafsgeqLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNPLALQLMAQGLynhstvpmsdeEMEMELSLLNKANSNNQNN
Flexible Loop (DISEMBL)
prsrriksgkdkrskekrprtafsgeqlsrlkveftenryltERRRQELanelglneaqIKIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEMEMELSLlnkansnnqnn
Low Complexity Region (SEG)
PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPmsdeememelsllnkansnnqnn
Disordered region (IsUnstruct)
**************************************RYLT******LANELGLNEAQIKIWFQNKRA*************LQLMA**L******************************
Disordered Region (DISOPRED)
***********************SGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR****************************************************
Disordered Region (DISEMBL)
************************GEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEMEMELSLLNKANSNNQNN
Disordered Region (DISPRO)
*****I*************RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNPLALQLMAQGLYNH***************************
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEMEMELSLLNKANSNNQNN
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	120	2.2.26 [Sep-21-2011]
P09145	584	Segmentation polarity hom	N/A	N/A	0.891	0.183	0.775	8e-44
P02836	552	Segmentation polarity hom	yes	N/A	0.891	0.193	0.775	1e-43
P27610	476	Homeobox protein invected	N/A	N/A	0.891	0.224	0.770	3e-42
P09075	109	Homeobox protein E60 (Fra	no	N/A	0.866	0.954	0.777	8e-42
P27609	372	Segmentation polarity hom	N/A	N/A	0.883	0.284	0.777	2e-41
P09076	109	Homeobox protein E30 (Fra	no	N/A	0.875	0.963	0.75	1e-40
O02491	594	Segmentation polarity hom	yes	N/A	0.891	0.180	0.759	2e-40
Q05640	349	Homeobox protein engraile	N/A	N/A	0.85	0.292	0.764	5e-40
P05527	576	Homeobox protein invected	no	N/A	0.708	0.147	0.811	7e-37
P09532	154	Homeobox protein engraile	N/A	N/A	0.941	0.733	0.646	1e-34

>sp|P09145|HMEN_DROVI Segmentation polarity homeobox protein engrailed OS=Drosophila virilis GN=en PE=3 SV=1

 Score =  175 bits (443), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 83/107 (77%), Positives = 95/107 (88%)

Query: 1   PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
           PR RR K  KDK + EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQI
Sbjct: 471 PRYRRPKQPKDKTNDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQI 530

Query: 61  KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEMEMEL 107
           KIWFQNKRAKIKK++G KNPLALQLMAQGLYNH+TVP++ EE E+E+
Sbjct: 531 KIWFQNKRAKIKKSTGSKNPLALQLMAQGLYNHTTVPLTKEEEELEM 577

This protein specifies the body segmentation pattern. It is required for the development of the central nervous system. Transcriptional regulator that repress activated promoters.
Drosophila virilis (taxid: 7244)

>sp|P02836|HMEN_DROME Segmentation polarity homeobox protein engrailed OS=Drosophila melanogaster GN=en PE=1 SV=2

 Score =  174 bits (441), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 83/107 (77%), Positives = 95/107 (88%)

Query: 1   PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
           PR RR K  KDK + EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQI
Sbjct: 439 PRYRRPKQPKDKTNDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQI 498

Query: 61  KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEMEMEL 107
           KIWFQNKRAKIKK++G KNPLALQLMAQGLYNH+TVP++ EE E+E+
Sbjct: 499 KIWFQNKRAKIKKSTGSKNPLALQLMAQGLYNHTTVPLTKEEEELEM 545

This protein specifies the body segmentation pattern. It is required for the development of the central nervous system. Transcriptional regulator that represses activated promoters. Wg signaling operates by inactivating the SGG repression of EN autoactivation.

Drosophila melanogaster (taxid: 7227)

>sp|P27610|HMIN_BOMMO Homeobox protein invected OS=Bombyx mori GN=INV PE=2 SV=1

 Score =  169 bits (429), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 84/109 (77%), Positives = 92/109 (84%), Gaps = 2/109 (1%)

Query: 1   PRSRRIK--SGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEA 58
           PR+RR K   G    + EKRPRTAFSG QL+RLK EF ENRYLTERRRQ LA ELGL EA
Sbjct: 355 PRTRRPKKPPGDTASNDEKRPRTAFSGPQLARLKHEFAENRYLTERRRQSLAAELGLAEA 414

Query: 59  QIKIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEMEMEL 107
           QIKIWFQNKRAKIKKASGQ+NPLALQLMAQGLYNHSTVP++ EE E+E+
Sbjct: 415 QIKIWFQNKRAKIKKASGQRNPLALQLMAQGLYNHSTVPLTKEEEELEM 463

This protein might be involved in the compartmentalization of the silk gland.

Bombyx mori (taxid: 7091)

>sp|P09075|HME60_APIME Homeobox protein E60 (Fragment) OS=Apis mellifera PE=3 SV=3

 Score =  168 bits (426), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 84/108 (77%), Positives = 93/108 (86%), Gaps = 4/108 (3%)

Query: 1   PRSRRIKS----GKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLN 56
           PR+RR+K     G     +EKRPRTAFSGEQL+RLK EF ENRYLTERRRQ+L+ +LGLN
Sbjct: 1   PRTRRVKRSDGRGNGGTPEEKRPRTAFSGEQLARLKREFAENRYLTERRRQQLSRDLGLN 60

Query: 57  EAQIKIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEME 104
           EAQIKIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVP++ EE E
Sbjct: 61  EAQIKIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPLTKEEEE 108

Apis mellifera (taxid: 7460)

>sp|P27609|HMEN_BOMMO Segmentation polarity homeobox protein engrailed OS=Bombyx mori GN=en PE=2 SV=1

 Score =  167 bits (422), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 84/108 (77%), Positives = 92/108 (85%), Gaps = 2/108 (1%)

Query: 1   PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
           PRSRR+K  K    +EKRPRTAFSG QL+RLK EF ENRYLTERRRQ LA ELGL EAQI
Sbjct: 267 PRSRRVK--KKAAPEEKRPRTAFSGAQLARLKHEFAENRYLTERRRQSLAAELGLAEAQI 324

Query: 61  KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEMEMELS 108
           KIWFQNKRAKIKKASGQ+NPLALQLMAQGLYNHSTV  SD+E E+ ++
Sbjct: 325 KIWFQNKRAKIKKASGQRNPLALQLMAQGLYNHSTVTESDDEEEINVT 372

This protein might be involved in the compartmentalization of the silk gland.

Bombyx mori (taxid: 7091)

>sp|P09076|HME30_APIME Homeobox protein E30 (Fragment) OS=Apis mellifera PE=3 SV=3

 Score =  164 bits (416), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 81/108 (75%), Positives = 94/108 (87%), Gaps = 3/108 (2%)

Query: 1   PRSRRIK---SGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNE 57
           PR+RR+K   +GK+   +EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L+ +LGL E
Sbjct: 2   PRTRRVKRSHNGKNGSPEEKRPRTAFSAEQLARLKREFAENRYLTERRRQQLSRDLGLTE 61

Query: 58  AQIKIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEMEM 105
           AQIKIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVP+ ++  E+
Sbjct: 62  AQIKIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPVDEDGEEI 109

Apis mellifera (taxid: 7460)

>sp|O02491|HMEN_ANOGA Segmentation polarity homeobox protein engrailed OS=Anopheles gambiae GN=en PE=2 SV=3

 Score =  164 bits (414), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 82/108 (75%), Positives = 92/108 (85%), Gaps = 1/108 (0%)

Query: 1   PRSRRIKSGKDK-RSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQ 59
           PR RR K  K+K  S+EKRPRTAFS  QL RLK EF ENRYLTE+RRQ L+ ELGLNEAQ
Sbjct: 480 PRYRRTKQPKEKGDSEEKRPRTAFSNAQLQRLKNEFNENRYLTEKRRQTLSAELGLNEAQ 539

Query: 60  IKIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEMEMEL 107
           IKIWFQNKRAKIKK+S +KNPLALQLMAQGLYNHSTVP++ EE E+E+
Sbjct: 540 IKIWFQNKRAKIKKSSSEKNPLALQLMAQGLYNHSTVPLTKEEEELEM 587

This protein specifies the body segmentation pattern. It is required for the development of the central nervous system. Transcriptional regulator that repress activated promoters.

Anopheles gambiae (taxid: 7165)

>sp|Q05640|HMEN_ARTSF Homeobox protein engrailed OS=Artemia franciscana PE=2 SV=1

 Score =  162 bits (411), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 78/102 (76%), Positives = 86/102 (84%)

Query: 1   PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
           PR RR+K  K     EKRPRTAF+ EQLSRLK EF ENRYLTERRRQ+LA ELGL+E QI
Sbjct: 234 PRCRRMKKDKAITPDEKRPRTAFTAEQLSRLKHEFNENRYLTERRRQDLARELGLHENQI 293

Query: 61  KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEE 102
           KIWFQN RAK+KK+SGQKNPLALQLMAQGLYNHST+P  D+E
Sbjct: 294 KIWFQNNRAKLKKSSGQKNPLALQLMAQGLYNHSTIPTEDDE 335

Artemia franciscana (taxid: 6661)

>sp|P05527|HMIN_DROME Homeobox protein invected OS=Drosophila melanogaster GN=inv PE=1 SV=2

 Score =  152 bits (383), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 69/85 (81%), Positives = 80/85 (94%)

Query: 15  KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
           ++KRPRTAFSG QL+RLK EF ENRYLTE+RRQ+L+ ELGLNEAQIKIWFQNKRAK+KK+
Sbjct: 470 EDKRPRTAFSGTQLARLKHEFNENRYLTEKRRQQLSGELGLNEAQIKIWFQNKRAKLKKS 529

Query: 75  SGQKNPLALQLMAQGLYNHSTVPMS 99
           SG KNPLALQLMAQGLYNHST+P++
Sbjct: 530 SGTKNPLALQLMAQGLYNHSTIPLT 554

Engrailed (en) and invected (inv) are functionally redundant transcription factors in neuronal precursor cell NB5-3 specification. Inv is unable to substitute for en in other regulatory processes such as maintaining gsb expression in the neuroectoderm after stage 10 of embryogenesis. Maintenance of gsb expression in row 5 of the neuroectoderm involves an as yet unidentified short range signaling molecule.

Drosophila melanogaster (taxid: 7227)

>sp|P09532|HMEN_TRIGR Homeobox protein engrailed (Fragment) OS=Tripneustes gratilla GN=EN PE=3 SV=1

 Score =  145 bits (365), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 75/116 (64%), Positives = 92/116 (79%), Gaps = 3/116 (2%)

Query: 1   PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
           PR+R++K  ++K++ EKRPRTAFS  QL RLK EF ++ YLTE+RR+ LA EL L+E+QI
Sbjct: 23  PRTRKVKR-REKKADEKRPRTAFSASQLQRLKQEFQQSNYLTEQRRRSLAKELTLSESQI 81

Query: 61  KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEMEMELSLLNKANSN 116
           KIWFQNKRAKIKKASG KN LA QLMAQGLYNHSTVP+  E   M+  LLN  N++
Sbjct: 82  KIWFQNKRAKIKKASGLKNDLARQLMAQGLYNHSTVPL--EADSMDTKLLNGQNTS 135

Tripneustes gratilla (taxid: 7673)

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	120
84619787	287	engrailed-1 [Schistocerca gregaria]	0.858	0.358	0.855	1e-43
84619789	271	engrailed-2 [Schistocerca gregaria]	0.825	0.365	0.848	3e-42
195382828	584	engrailed [Drosophila virilis] gi|194144	0.891	0.183	0.775	3e-42
123359	584	RecName: Full=Segmentation polarity home	0.891	0.183	0.775	3e-42
195123895	596	GI21047 [Drosophila mojavensis] gi|19391	0.891	0.179	0.775	4e-42
242004267	118	Homeobox protein E30, putative [Pediculu	0.95	0.966	0.741	4e-42
194752942	562	GF12393 [Drosophila ananassae] gi|190620	0.891	0.190	0.775	5e-42
195436455	563	GK22225 [Drosophila willistoni] gi|19416	0.891	0.190	0.775	6e-42
195485703	552	GE13516 [Drosophila yakuba] gi|194177300	0.891	0.193	0.775	6e-42
194883939	553	GG22644 [Drosophila erecta] gi|190659240	0.891	0.193	0.775	6e-42

>gi|84619787|gb|ABC59240.1| engrailed-1 [Schistocerca gregaria]

 Score =  179 bits (455), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 89/104 (85%), Positives = 97/104 (93%), Gaps = 1/104 (0%)

Query: 1   PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
           PRSRR+K  KDK+ +EKRPRTAFSGEQL+RLK EFTENRYLTERRRQELA ELGLNEAQI
Sbjct: 157 PRSRRLKR-KDKKPEEKRPRTAFSGEQLARLKHEFTENRYLTERRRQELARELGLNEAQI 215

Query: 61  KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEME 104
           KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVP+ +++ E
Sbjct: 216 KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPIDEDDEE 259

Source: Schistocerca gregaria

Species: Schistocerca gregaria

Genus: Schistocerca

Family: Acrididae

Order: Orthoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|84619789|gb|ABC59241.1| engrailed-2 [Schistocerca gregaria]

 Score =  175 bits (444), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 84/99 (84%), Positives = 92/99 (92%)

Query: 10  KDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRA 69
           ++K+ +EKRPRTAFSGEQL+RLK EFTENRYLTERRRQELA ELGLNEAQIKIWFQNKRA
Sbjct: 170 RNKKPEEKRPRTAFSGEQLARLKHEFTENRYLTERRRQELARELGLNEAQIKIWFQNKRA 229

Query: 70  KIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEMEMELS 108
           KIKKASGQKNPLALQLMAQGLYNHSTVPM+ EE E  ++
Sbjct: 230 KIKKASGQKNPLALQLMAQGLYNHSTVPMTREEEEQAIA 268

Source: Schistocerca gregaria

Species: Schistocerca gregaria

Genus: Schistocerca

Family: Acrididae

Order: Orthoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195382828|ref|XP_002050130.1| engrailed [Drosophila virilis] gi|194144927|gb|EDW61323.1| engrailed [Drosophila virilis]

 Score =  175 bits (443), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 83/107 (77%), Positives = 95/107 (88%)

Query: 1   PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
           PR RR K  KDK + EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQI
Sbjct: 471 PRYRRPKQPKDKTNDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQI 530

Query: 61  KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEMEMEL 107
           KIWFQNKRAKIKK++G KNPLALQLMAQGLYNH+TVP++ EE E+E+
Sbjct: 531 KIWFQNKRAKIKKSTGSKNPLALQLMAQGLYNHTTVPLTKEEEELEM 577

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|123359|sp|P09145.1|HMEN_DROVI RecName: Full=Segmentation polarity homeobox protein engrailed gi|9174|emb|CAA28436.1| en-gene product [Drosophila virilis]

 Score =  175 bits (443), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 83/107 (77%), Positives = 95/107 (88%)

Query: 1   PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
           PR RR K  KDK + EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQI
Sbjct: 471 PRYRRPKQPKDKTNDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQI 530

Query: 61  KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEMEMEL 107
           KIWFQNKRAKIKK++G KNPLALQLMAQGLYNH+TVP++ EE E+E+
Sbjct: 531 KIWFQNKRAKIKKSTGSKNPLALQLMAQGLYNHTTVPLTKEEEELEM 577

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195123895|ref|XP_002006437.1| GI21047 [Drosophila mojavensis] gi|193911505|gb|EDW10372.1| GI21047 [Drosophila mojavensis]

 Score =  175 bits (443), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 83/107 (77%), Positives = 95/107 (88%)

Query: 1   PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
           PR RR K  KDK + EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQI
Sbjct: 483 PRYRRPKQPKDKTNDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQI 542

Query: 61  KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEMEMEL 107
           KIWFQNKRAKIKK++G KNPLALQLMAQGLYNH+TVP++ EE E+E+
Sbjct: 543 KIWFQNKRAKIKKSTGSKNPLALQLMAQGLYNHTTVPLTKEEEELEM 589

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242004267|ref|XP_002423027.1| Homeobox protein E30, putative [Pediculus humanus corporis] gi|212505958|gb|EEB10289.1| Homeobox protein E30, putative [Pediculus humanus corporis]

 Score =  174 bits (442), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 89/120 (74%), Positives = 103/120 (85%), Gaps = 6/120 (5%)

Query: 1   PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
           PRSRRIK  KDK+ +EKRPRTAFSG+QLSRLK EF ENRYLTERRRQ+LA ELGLNEAQI
Sbjct: 3   PRSRRIKR-KDKKPEEKRPRTAFSGDQLSRLKHEFAENRYLTERRRQDLAKELGLNEAQI 61

Query: 61  KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEMEMELSLLNKANSNNQNN 120
           KIWFQNKRAK+KKA G+KNPLALQLMAQGLYNHST+P+ ++E   E+     A ++NQ+N
Sbjct: 62  KIWFQNKRAKMKKAKGEKNPLALQLMAQGLYNHSTIPVDEDEYLEEM-----AAASNQSN 116

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194752942|ref|XP_001958778.1| GF12393 [Drosophila ananassae] gi|190620076|gb|EDV35600.1| GF12393 [Drosophila ananassae]

 Score =  174 bits (442), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 83/107 (77%), Positives = 95/107 (88%)

Query: 1   PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
           PR RR K  KDK + EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQI
Sbjct: 449 PRYRRPKQPKDKTNDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQI 508

Query: 61  KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEMEMEL 107
           KIWFQNKRAKIKK++G KNPLALQLMAQGLYNH+TVP++ EE E+E+
Sbjct: 509 KIWFQNKRAKIKKSTGSKNPLALQLMAQGLYNHTTVPLTKEEEELEM 555

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195436455|ref|XP_002066183.1| GK22225 [Drosophila willistoni] gi|194162268|gb|EDW77169.1| GK22225 [Drosophila willistoni]

 Score =  174 bits (441), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 83/107 (77%), Positives = 95/107 (88%)

Query: 1   PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
           PR RR K  KDK + EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQI
Sbjct: 450 PRYRRPKQPKDKTNDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQI 509

Query: 61  KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEMEMEL 107
           KIWFQNKRAKIKK++G KNPLALQLMAQGLYNH+TVP++ EE E+E+
Sbjct: 510 KIWFQNKRAKIKKSNGSKNPLALQLMAQGLYNHTTVPLTKEEEELEM 556

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195485703|ref|XP_002091199.1| GE13516 [Drosophila yakuba] gi|194177300|gb|EDW90911.1| GE13516 [Drosophila yakuba]

 Score =  174 bits (441), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 83/107 (77%), Positives = 95/107 (88%)

Query: 1   PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
           PR RR K  KDK + EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQI
Sbjct: 439 PRYRRPKQPKDKTNDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQI 498

Query: 61  KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEMEMEL 107
           KIWFQNKRAKIKK++G KNPLALQLMAQGLYNH+TVP++ EE E+E+
Sbjct: 499 KIWFQNKRAKIKKSTGSKNPLALQLMAQGLYNHTTVPLTKEEEELEM 545

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194883939|ref|XP_001976053.1| GG22644 [Drosophila erecta] gi|190659240|gb|EDV56453.1| GG22644 [Drosophila erecta]

 Score =  174 bits (441), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 83/107 (77%), Positives = 95/107 (88%)

Query: 1   PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
           PR RR K  KDK + EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQI
Sbjct: 440 PRYRRPKQPKDKTNDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQI 499

Query: 61  KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVPMSDEEMEMEL 107
           KIWFQNKRAKIKK++G KNPLALQLMAQGLYNH+TVP++ EE E+E+
Sbjct: 500 KIWFQNKRAKIKKSTGSKNPLALQLMAQGLYNHTTVPLTKEEEELEM 546

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	120
FB|FBgn0000577	552	en "engrailed" [Drosophila mel	0.808	0.175	0.814	8.9e-38
FB|FBgn0001269	576	inv "invected" [Drosophila mel	0.691	0.144	0.831	2.9e-33
ZFIN|ZDB-GENE-980526-6	274	eng1b "engrailed 1b" [Danio re	0.783	0.343	0.736	1.1e-32
UNIPROTKB|Q05917	289	EN2 "Homeobox protein engraile	0.783	0.325	0.736	2.9e-32
ZFIN|ZDB-GENE-980526-167	265	eng2a "engrailed 2a" [Danio re	0.775	0.350	0.770	4.7e-32
ZFIN|ZDB-GENE-980526-40	261	eng2b "engrailed 2b" [Danio re	0.791	0.363	0.729	9.8e-32
UNIPROTKB|F1N5R9	400	LOC529707 "Uncharacterized pro	0.783	0.235	0.715	1.3e-31
UNIPROTKB|F1PG21	327	EN2 "Uncharacterized protein"	0.783	0.287	0.726	1.3e-31
UNIPROTKB|J9NSM7	194	EN1 "Uncharacterized protein"	0.783	0.484	0.715	1.3e-31
UNIPROTKB|P19622	333	EN2 "Homeobox protein engraile	0.783	0.282	0.726	1.3e-31

FB|FBgn0000577 en "engrailed" [Drosophila melanogaster (taxid:7227)]

 Score = 405 (147.6 bits), Expect = 8.9e-38, P = 8.9e-38
 Identities = 79/97 (81%), Positives = 87/97 (89%)

Query:     1 PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
             PR RR K  KDK + EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQI
Sbjct:   439 PRYRRPKQPKDKTNDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQI 498

Query:    61 KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVP 97
             KIWFQNKRAKIKK++G KNPLALQLMAQGLYNH+TVP
Sbjct:   499 KIWFQNKRAKIKKSTGSKNPLALQLMAQGLYNHTTVP 535

GO:0005634 "nucleus" evidence=NAS;IDA

GO:0000980 "RNA polymerase II distal enhancer sequence-specific DNA binding" evidence=IDA

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

GO:0001078 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription" evidence=IDA

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

GO:0035224 "genital disc anterior/posterior pattern formation" evidence=IEP;TAS

GO:0007400 "neuroblast fate determination" evidence=IGI

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

GO:0007448 "anterior/posterior pattern specification, imaginal disc" evidence=TAS

GO:0048099 "anterior/posterior lineage restriction, imaginal disc" evidence=TAS

GO:0048100 "wing disc anterior/posterior pattern formation" evidence=TAS

GO:0007386 "compartment pattern specification" evidence=NAS;TAS

GO:0007417 "central nervous system development" evidence=NAS

GO:0007367 "segment polarity determination" evidence=NAS;TAS

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

GO:0007447 "imaginal disc pattern formation" evidence=TAS

GO:0007485 "imaginal disc-derived male genitalia development" evidence=TAS

GO:0007487 "analia development" evidence=TAS

GO:0007486 "imaginal disc-derived female genitalia development" evidence=TAS

GO:0007388 "posterior compartment specification" evidence=TAS

GO:0035288 "anterior head segmentation" evidence=TAS

GO:0035290 "trunk segmentation" evidence=TAS

GO:0035289 "posterior head segmentation" evidence=TAS

GO:0035215 "genital disc development" evidence=IMP

GO:0035277 "spiracle morphogenesis, open tracheal system" evidence=IMP

GO:0021960 "anterior commissure morphogenesis" evidence=IMP

GO:0007418 "ventral midline development" evidence=IMP

GO:0007411 "axon guidance" evidence=IMP

GO:0010629 "negative regulation of gene expression" evidence=IMP

GO:0008406 "gonad development" evidence=IMP

FB|FBgn0001269 inv "invected" [Drosophila melanogaster (taxid:7227)]

 Score = 366 (133.9 bits), Expect = 2.9e-33, P = 2.9e-33
 Identities = 69/83 (83%), Positives = 78/83 (93%)

Query:    15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
             ++KRPRTAFSG QL+RLK EF ENRYLTE+RRQ+L+ ELGLNEAQIKIWFQNKRAK+KK+
Sbjct:   470 EDKRPRTAFSGTQLARLKHEFNENRYLTEKRRQQLSGELGLNEAQIKIWFQNKRAKLKKS 529

Query:    75 SGQKNPLALQLMAQGLYNHSTVP 97
             SG KNPLALQLMAQGLYNHST+P
Sbjct:   530 SGTKNPLALQLMAQGLYNHSTIP 552

GO:0007386 "compartment pattern specification" evidence=ISS;IMP;TAS

GO:0007400 "neuroblast fate determination" evidence=IGI

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

GO:0005634 "nucleus" evidence=ISS;NAS

GO:0048100 "wing disc anterior/posterior pattern formation" evidence=TAS

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

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

GO:0007476 "imaginal disc-derived wing morphogenesis" evidence=IMP

ZFIN|ZDB-GENE-980526-6 eng1b "engrailed 1b" [Danio rerio (taxid:7955)]

 Score = 357 (130.7 bits), Expect = 1.1e-32, P = 1.1e-32
 Identities = 70/95 (73%), Positives = 81/95 (85%)

Query:     1 PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
             PR+R++K  K ++ ++KRPRTAF+ EQL RLK EF  NRY+TE+RRQ LA EL LNE+QI
Sbjct:   170 PRTRKLKKKKSEK-EDKRPRTAFTAEQLQRLKAEFQANRYITEQRRQSLAQELNLNESQI 228

Query:    61 KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHST 95
             KIWFQNKRAKIKKASG KN LALQLMAQGLYNHST
Sbjct:   229 KIWFQNKRAKIKKASGYKNGLALQLMAQGLYNHST 263

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

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

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

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

GO:0048663 "neuron fate commitment" evidence=IEP

UNIPROTKB|Q05917 EN2 "Homeobox protein engrailed-2" [Gallus gallus (taxid:9031)]

 Score = 353 (129.3 bits), Expect = 2.9e-32, P = 2.9e-32
 Identities = 70/95 (73%), Positives = 79/95 (83%)

Query:     1 PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
             PRSR+ K  K+   ++KRPRTAF+ EQL RLK EF  NRYLTE+RRQ LA ELGLNE+QI
Sbjct:   186 PRSRKPKK-KNPNKEDKRPRTAFTAEQLQRLKAEFQTNRYLTEQRRQSLAQELGLNESQI 244

Query:    61 KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHST 95
             KIWFQNKRAKIKKA+G KN LA+ LMAQGLYNHST
Sbjct:   245 KIWFQNKRAKIKKATGSKNSLAVHLMAQGLYNHST 279

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0007411 "axon guidance" evidence=IDA

GO:0030426 "growth cone" evidence=IDA

GO:0030175 "filopodium" evidence=IDA

GO:0030027 "lamellipodium" evidence=IDA

GO:0043005 "neuron projection" evidence=IDA

GO:0045727 "positive regulation of translation" evidence=IDA

GO:0042327 "positive regulation of phosphorylation" evidence=IDA

ZFIN|ZDB-GENE-980526-167 eng2a "engrailed 2a" [Danio rerio (taxid:7955)]

 Score = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 74/96 (77%), Positives = 79/96 (82%)

Query:     1 PRSRRIKSGKDKRSKE-KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQ 59
             PRSR+ K  K   SKE KRPRTAF+ EQL RLK EF  NRYLTE+RRQ LA ELGLNE+Q
Sbjct:   162 PRSRKPK--KKAASKEDKRPRTAFTAEQLQRLKAEFQTNRYLTEQRRQSLAQELGLNESQ 219

Query:    60 IKIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHST 95
             IKIWFQNKRAKIKKASG KN LA+ LMAQGLYNHST
Sbjct:   220 IKIWFQNKRAKIKKASGVKNGLAIHLMAQGLYNHST 255

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

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

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

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

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0030901 "midbrain development" evidence=IGI

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

GO:0001708 "cell fate specification" evidence=IGI

ZFIN|ZDB-GENE-980526-40 eng2b "engrailed 2b" [Danio rerio (taxid:7955)]

 Score = 348 (127.6 bits), Expect = 9.8e-32, P = 9.8e-32
 Identities = 70/96 (72%), Positives = 79/96 (82%)

Query:     1 PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
             PRSR+ K  K    ++KRPRTAF+ EQL RLK EF  NRYLTE+RRQ LA ELGLNE+QI
Sbjct:   158 PRSRKPKK-KTPTKEDKRPRTAFTAEQLQRLKNEFQNNRYLTEQRRQALAQELGLNESQI 216

Query:    61 KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTV 96
             KIWFQNKRAKIKKA+G KN LA+ LMAQGLYNH+TV
Sbjct:   217 KIWFQNKRAKIKKATGNKNALAVHLMAQGLYNHATV 252

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

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

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

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

GO:0030901 "midbrain development" evidence=IGI

GO:0001708 "cell fate specification" evidence=IGI

UNIPROTKB|F1N5R9 LOC529707 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 347 (127.2 bits), Expect = 1.3e-31, P = 1.3e-31
 Identities = 68/95 (71%), Positives = 81/95 (85%)

Query:     1 PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
             PR+R++K  K+++ ++KRPRTAF+ EQL RLK EF  NRY+TE+RRQ LA EL LNE+QI
Sbjct:   297 PRTRKLKKKKNEK-EDKRPRTAFTAEQLQRLKAEFQANRYITEQRRQTLAQELSLNESQI 355

Query:    61 KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHST 95
             KIWFQNKRAKIKKA+G KN LAL LMAQGLYNHST
Sbjct:   356 KIWFQNKRAKIKKATGIKNGLALHLMAQGLYNHST 390

GO:0005634 "nucleus" evidence=IEA

GO:0048666 "neuron development" evidence=IEA

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

GO:0043473 "pigmentation" evidence=IEA

GO:0035115 "embryonic forelimb morphogenesis" evidence=IEA

GO:0030917 "midbrain-hindbrain boundary development" evidence=IEA

GO:0030902 "hindbrain development" evidence=IEA

GO:0030901 "midbrain development" evidence=IEA

GO:0009954 "proximal/distal pattern formation" evidence=IEA

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

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

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

UNIPROTKB|F1PG21 EN2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 347 (127.2 bits), Expect = 1.3e-31, P = 1.3e-31
 Identities = 69/95 (72%), Positives = 78/95 (82%)

Query:     1 PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
             PRSR+ K  K+   ++KRPRTAF+ EQL RLK EF  NRYLTE+RRQ LA EL LNE+QI
Sbjct:   224 PRSRKPKK-KNPNKEDKRPRTAFTAEQLQRLKAEFQTNRYLTEQRRQSLAQELSLNESQI 282

Query:    61 KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHST 95
             KIWFQNKRAKIKKA+G KN LA+ LMAQGLYNHST
Sbjct:   283 KIWFQNKRAKIKKATGNKNTLAVHLMAQGLYNHST 317

GO:0005634 "nucleus" evidence=IEA

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

GO:0007275 "multicellular organismal development" evidence=IEA

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

UNIPROTKB|J9NSM7 EN1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 347 (127.2 bits), Expect = 1.3e-31, P = 1.3e-31
 Identities = 68/95 (71%), Positives = 81/95 (85%)

Query:     1 PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
             PR+R++K  K+++ ++KRPRTAF+ EQL RLK EF  NRY+TE+RRQ LA EL LNE+QI
Sbjct:    91 PRTRKLKKKKNEK-EDKRPRTAFTAEQLQRLKAEFQANRYITEQRRQTLAQELSLNESQI 149

Query:    61 KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHST 95
             KIWFQNKRAKIKKA+G KN LAL LMAQGLYNHST
Sbjct:   150 KIWFQNKRAKIKKATGIKNGLALHLMAQGLYNHST 184

GO:0005634 "nucleus" evidence=IEA

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

GO:0007275 "multicellular organismal development" evidence=IEA

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

UNIPROTKB|P19622 EN2 "Homeobox protein engrailed-2" [Homo sapiens (taxid:9606)]

 Score = 347 (127.2 bits), Expect = 1.3e-31, P = 1.3e-31
 Identities = 69/95 (72%), Positives = 78/95 (82%)

Query:     1 PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
             PRSR+ K  K+   ++KRPRTAF+ EQL RLK EF  NRYLTE+RRQ LA EL LNE+QI
Sbjct:   230 PRSRKPKK-KNPNKEDKRPRTAFTAEQLQRLKAEFQTNRYLTEQRRQSLAQELSLNESQI 288

Query:    61 KIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHST 95
             KIWFQNKRAKIKKA+G KN LA+ LMAQGLYNHST
Sbjct:   289 KIWFQNKRAKIKKATGNKNTLAVHLMAQGLYNHST 323

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

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

GO:0016020 "membrane" evidence=IEA

GO:0030901 "midbrain development" evidence=IEA

GO:0030902 "hindbrain development" evidence=IEA

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

GO:0048666 "neuron development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=TAS

---

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)
P09066	HME2_MOUSE	No assigned EC number	0.7187	0.7916	0.2932	yes	N/A
P02836	HMEN_DROME	No assigned EC number	0.7757	0.8916	0.1938	yes	N/A
P34326	HM16_CAEEL	No assigned EC number	0.6125	0.6666	0.4278	yes	N/A
P09075	HME60_APIME	No assigned EC number	0.7777	0.8666	0.9541	no	N/A
P09076	HME30_APIME	No assigned EC number	0.75	0.875	0.9633	no	N/A
P23397	HMEN_HELTR	No assigned EC number	0.8076	0.65	0.7959	N/A	N/A
O02491	HMEN_ANOGA	No assigned EC number	0.7592	0.8916	0.1801	yes	N/A
P09015	HME2A_DANRE	No assigned EC number	0.7425	0.8166	0.3698	yes	N/A
P19622	HME2_HUMAN	No assigned EC number	0.7187	0.7916	0.2852	yes	N/A
Q05917	HME2_CHICK	No assigned EC number	0.7291	0.7916	0.3287	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	120
pfam00046	57	pfam00046, Homeobox, Homeobox domain	2e-21
smart00389	57	smart00389, HOX, Homeodomain	4e-18
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	1e-17
pfam10525	32	pfam10525, Engrail_1_C_sig, Engrailed homeobox C-t	1e-15
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	6e-10

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

 Score = 79.8 bits (198), Expect = 2e-21
 Identities = 31/57 (54%), Positives = 42/57 (73%)

Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          +R RT F+ EQL  L+ EF +NRY +   R+ELA +LGL E Q+K+WFQN+RAK K+
Sbjct: 1  RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57

Length = 57

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 71.5 bits (176), Expect = 4e-18
 Identities = 30/56 (53%), Positives = 42/56 (75%)

Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK 72
          +R RT+F+ EQL  L+ EF +N Y +   R+ELA +LGL+E Q+K+WFQN+RAK K
Sbjct: 2  RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

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

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

 Score = 70.4 bits (173), Expect = 1e-17
 Identities = 32/57 (56%), Positives = 42/57 (73%)

Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          +R RT F+ EQL  L+ EF +N Y +   R+ELA ELGL E Q+KIWFQN+RAK+K+
Sbjct: 1  RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57

Length = 59

>gnl|CDD|119045 pfam10525, Engrail_1_C_sig, Engrailed homeobox C-terminal signature domain

 Score = 64.6 bits (158), Expect = 1e-15
 Identities = 24/31 (77%), Positives = 25/31 (80%)

Query: 74  ASGQKNPLALQLMAQGLYNHSTVPMSDEEME 104
           ASG KNPLALQLMAQGLYNHST P  D+E  
Sbjct: 1   ASGVKNPLALQLMAQGLYNHSTTPKDDDEDS 31

Engrailed homeobox proteins are characterized by the presence of a conserved region of some 20 amino-acid residues located at the C-terminal of the 'homeobox' domain. This domain of approximately 20 residues forms a kind of a signature pattern for this subfamily of proteins. Length = 32

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

 Score = 53.2 bits (128), Expect = 6e-10
 Identities = 26/65 (40%), Positives = 34/65 (52%)

Query: 11  DKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAK 70
           D  S  K  R   + EQL  L+ EF  N Y +   R +L+  L +    ++IWFQNKRAK
Sbjct: 46  DGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAK 105

Query: 71  IKKAS 75
            KK  
Sbjct: 106 EKKKR 110

Length = 156

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	120
KOG0493|consensus	342		99.8
KOG0850|consensus	245		99.77
KOG0488|consensus	309		99.77
KOG0484|consensus	125		99.76
KOG0489|consensus	261		99.76
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.76
KOG0843|consensus	197		99.73
KOG2251|consensus	228		99.72
KOG0842|consensus	307		99.71
KOG0485|consensus	268		99.7
KOG0494|consensus	332		99.69
KOG0487|consensus	308		99.67
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.64
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.64
KOG0492|consensus	246		99.63
KOG0848|consensus	317		99.63
COG5576	156	Homeodomain-containing transcription factor [Trans	99.61
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.6
KOG3802|consensus	398		99.59
KOG0847|consensus	288		99.54
KOG0491|consensus	194		99.54
KOG0483|consensus	198		99.52
KOG0486|consensus	351		99.47
KOG4577|consensus	383		99.45
KOG0844|consensus	408		99.37
KOG0775|consensus	304		99.27
KOG0490|consensus	235		99.23
KOG0849|consensus	354		99.18
KOG1168|consensus	385		99.18
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.83
KOG0774|consensus	334		98.71
KOG2252|consensus	558		98.67
KOG0490|consensus	235		98.24
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	97.8
KOG1146|consensus	1406		97.68
KOG3623|consensus	1007		97.2
KOG0773|consensus	342		96.75
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	95.71
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	91.11
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	87.01
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	86.04
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	83.43
PF10668	60	Phage_terminase: Phage terminase small subunit; In	82.55
KOG1146|consensus	1406		82.26

>KOG0493|consensus

Probab=99.80  E-value=1.6e-19  Score=130.41  Aligned_cols=106  Identities=70%  Similarity=1.023  Sum_probs=92.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCCh
Q psy4625           1 PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNP   80 (120)
Q Consensus         1 ~~~~~~~~~~~~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~   80 (120)
                      |+.++++..+.....-+|.||.|+.+|+..|...|+.+.|.+...|..||.+|+|.+.||+|||||+|+|.||....+..
T Consensus       231 PR~Rk~kkkk~~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn~  310 (342)
T KOG0493|consen  231 PRHRKPKKKKSSSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKNR  310 (342)
T ss_pred             cccccccccCCccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCCc
Confidence            45555555555555667889999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHhhcCCCCCCCCCCCCchHHHh
Q psy4625          81 LALQLMAQGLYNHSTVPMSDEEMEME  106 (120)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~s~~~~~~~  106 (120)
                      .+...+.++.+.+++.+....+..++
T Consensus       311 la~~lmaqglyNHst~~l~a~e~k~e  336 (342)
T KOG0493|consen  311 LALHLMAQGLYNHSTTHLMAQEAKVE  336 (342)
T ss_pred             hhhhhhccccccCccchhhhhhhhhh
Confidence            99999999999999887655544443

>KOG0850|consensus

Probab=99.77  E-value=4.9e-19  Score=125.67  Aligned_cols=70  Identities=44%  Similarity=0.692  Sum_probs=64.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCChh
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNPL   81 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~~   81 (120)
                      +.+|.|+.||.++.-||..|...|++++|..-.||.+||..|||+..||+|||||||.|.||..+.+...
T Consensus       118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~~  187 (245)
T KOG0850|consen  118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSGP  187 (245)
T ss_pred             CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCCc
Confidence            5667788999999999999999999999999999999999999999999999999999999998754433

>KOG0488|consensus

Probab=99.77  E-value=9.3e-19  Score=131.08  Aligned_cols=73  Identities=40%  Similarity=0.657  Sum_probs=65.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625           5 RIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus         5 ~~~~~~~~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      .+.......+++|+.||.|+..|+..||..|+...|.+..+|+.||..|||+..||++||||||.|||+....
T Consensus       161 ~~~~~~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~  233 (309)
T KOG0488|consen  161 NHPYQRSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE  233 (309)
T ss_pred             CCCcccCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence            3444455567888899999999999999999999999999999999999999999999999999999998654

>KOG0484|consensus

Probab=99.76  E-value=3.6e-19  Score=112.44  Aligned_cols=66  Identities=38%  Similarity=0.678  Sum_probs=62.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      ..++.||-||.|+..|+..|+..|...+||++..+++||..+.|++..|++||||||+|.||..+.
T Consensus        13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~   78 (125)
T KOG0484|consen   13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERA   78 (125)
T ss_pred             HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence            456778889999999999999999999999999999999999999999999999999999998754

>KOG0489|consensus

Probab=99.76  E-value=1.2e-18  Score=128.10  Aligned_cols=70  Identities=51%  Similarity=0.706  Sum_probs=64.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCChh
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNPL   81 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~~   81 (120)
                      ..++.||.||.|+..|+..||+.|..+.|.+...|.+||..|.|+++||+|||||||.||||..+.....
T Consensus       155 ~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~  224 (261)
T KOG0489|consen  155 TGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ  224 (261)
T ss_pred             ccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence            3456788999999999999999999999999999999999999999999999999999999998766554

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.76  E-value=4.4e-18  Score=97.94  Aligned_cols=57  Identities=56%  Similarity=0.814  Sum_probs=54.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625          17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK   73 (120)
Q Consensus        17 rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   73 (120)
                      |+.|+.|+.+|+.+|+.+|..++||+..++..||..+||+..+|.+||+|+|.++|+
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence            467899999999999999999999999999999999999999999999999999885

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

>KOG0843|consensus

Probab=99.73  E-value=5e-18  Score=116.68  Aligned_cols=64  Identities=44%  Similarity=0.741  Sum_probs=60.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCC
Q psy4625          15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQK   78 (120)
Q Consensus        15 ~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~   78 (120)
                      +.+|.||.|+.+|+..||..|+.++|....+|..||..|+|++.||+|||||||.|.||.....
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~  164 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED  164 (197)
T ss_pred             CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence            6788999999999999999999999999999999999999999999999999999999987653

>KOG2251|consensus

Probab=99.72  E-value=7.3e-18  Score=119.12  Aligned_cols=68  Identities=35%  Similarity=0.621  Sum_probs=63.8

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCC
Q psy4625          11 DKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQK   78 (120)
Q Consensus        11 ~~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~   78 (120)
                      .+.++.||+||.|+..|+.+|+..|.+.+||+...+++||.+++|.+.+|+|||+|||+|+|+.....
T Consensus        32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            35678899999999999999999999999999999999999999999999999999999999987653

>KOG0842|consensus

Probab=99.71  E-value=4.8e-18  Score=126.12  Aligned_cols=75  Identities=39%  Similarity=0.620  Sum_probs=66.3

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCChhhHHHhh
Q psy4625          13 RSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNPLALQLMA   87 (120)
Q Consensus        13 ~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~~~~~~~~   87 (120)
                      ..++||.|..|+..|+..||..|.+..|.+..||+.||..|.|++.||+|||||||-|.||....+.........
T Consensus       150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~~~~  224 (307)
T KOG0842|consen  150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALLLAS  224 (307)
T ss_pred             cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcccCCC
Confidence            456777788999999999999999999999999999999999999999999999999999998776655444333

>KOG0485|consensus

Probab=99.70  E-value=1.9e-17  Score=116.91  Aligned_cols=66  Identities=41%  Similarity=0.655  Sum_probs=62.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      ++.++|+.||+|+..|+..||..|+...|.+..+|..||..|.|++.||+|||||||.|||+....
T Consensus       100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa  165 (268)
T KOG0485|consen  100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA  165 (268)
T ss_pred             cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence            566888899999999999999999999999999999999999999999999999999999998643

>KOG0494|consensus

Probab=99.69  E-value=3.7e-17  Score=118.07  Aligned_cols=67  Identities=36%  Similarity=0.531  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCChh
Q psy4625          15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNPL   81 (120)
Q Consensus        15 ~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~~   81 (120)
                      ++|+.||.|+..|+..||+.|+...||+...++.||..+.|.+.+|++||||||+||||........
T Consensus       140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~s  206 (332)
T KOG0494|consen  140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGS  206 (332)
T ss_pred             ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcc
Confidence            3444599999999999999999999999999999999999999999999999999999998664433

>KOG0487|consensus

Probab=99.67  E-value=2.2e-17  Score=122.63  Aligned_cols=64  Identities=39%  Similarity=0.651  Sum_probs=60.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        14 ~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      +..||+|.-+|+.|+..||..|..|.|.+...|.+|+..|+|+++||+|||||||.|.||..+.
T Consensus       233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re  296 (308)
T KOG0487|consen  233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRE  296 (308)
T ss_pred             cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhh
Confidence            4567778899999999999999999999999999999999999999999999999999999853

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

Probab=99.64  E-value=1.6e-15  Score=87.39  Aligned_cols=57  Identities=56%  Similarity=0.919  Sum_probs=53.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625          18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA   74 (120)
Q Consensus        18 r~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   74 (120)
                      +.+..++..++.+|+..|..++||+..++..||..+||+..+|++||+|+|.+.++.
T Consensus         2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~   58 (59)
T cd00086           2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS   58 (59)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence            457789999999999999999999999999999999999999999999999998753

>smart00389 HOX Homeodomain

Probab=99.64  E-value=1.1e-15  Score=87.36  Aligned_cols=55  Identities=55%  Similarity=0.888  Sum_probs=51.6

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHH
Q psy4625          18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK   72 (120)
Q Consensus        18 r~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k   72 (120)
                      +.|+.|+..++.+|+..|..++||+..++..||..+||+..+|++||+|+|.+.+
T Consensus         2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~   56 (56)
T smart00389        2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK   56 (56)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence            4577899999999999999999999999999999999999999999999998753

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

>KOG0492|consensus

Probab=99.63  E-value=3.4e-16  Score=109.89  Aligned_cols=65  Identities=43%  Similarity=0.751  Sum_probs=60.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      +.+..|+.|+-|+..|+..||..|...+|.++.++.+++..|.|++.||+|||||||+|.||.+.
T Consensus       140 Khk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe  204 (246)
T KOG0492|consen  140 KHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE  204 (246)
T ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence            34456788999999999999999999999999999999999999999999999999999998864

>KOG0848|consensus

Probab=99.63  E-value=1.6e-16  Score=115.07  Aligned_cols=64  Identities=45%  Similarity=0.718  Sum_probs=59.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCChh
Q psy4625          18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNPL   81 (120)
Q Consensus        18 r~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~~   81 (120)
                      +-|.+++..|.-.||+.|..++|.++.-+.+||.-|||+++||+|||||||+|+||..+++..+
T Consensus       201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~~~  264 (317)
T KOG0848|consen  201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKRLQ  264 (317)
T ss_pred             ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHHHH
Confidence            4477899999999999999999999999999999999999999999999999999998776433

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.61  E-value=2e-15  Score=103.12  Aligned_cols=70  Identities=39%  Similarity=0.464  Sum_probs=63.3

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCCh
Q psy4625          11 DKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNP   80 (120)
Q Consensus        11 ~~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~   80 (120)
                      .++...++.|.+.+..|+.+|+..|..++||+..++..|+..++|+++-|++||||+|++.|+....+..
T Consensus        46 ~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~~  115 (156)
T COG5576          46 DGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVE  115 (156)
T ss_pred             cCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccchh
Confidence            4566778888999999999999999999999999999999999999999999999999999988655433

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.60  E-value=7.2e-16  Score=88.86  Aligned_cols=52  Identities=25%  Similarity=0.503  Sum_probs=50.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCC----CCHHHHHHHHHHhCCChhhHHHHHHHHH
Q psy4625          17 KRPRTAFSGEQLSRLKVEFTENRY----LTERRRQELANELGLNEAQIKIWFQNKR   68 (120)
Q Consensus        17 rr~R~~~~~~q~~~L~~~F~~~~~----p~~~~~~~La~~l~l~~~~V~~WFqNrR   68 (120)
                      +|.||.|+.+|+..|+.+|..++|    |+..++..||..+||++.+|++||||.+
T Consensus         2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            678999999999999999999999    9999999999999999999999999964

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

>KOG3802|consensus

Probab=99.59  E-value=3e-16  Score=119.09  Aligned_cols=64  Identities=25%  Similarity=0.447  Sum_probs=60.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          13 RSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        13 ~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      .+++||+||.|.......||.+|..|+.|+..++..||.+|+|.+.+|+|||||||+|.||...
T Consensus       291 ~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  291 QSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             cccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            3477888999999999999999999999999999999999999999999999999999999876

>KOG0847|consensus

Probab=99.54  E-value=4.5e-15  Score=105.15  Aligned_cols=66  Identities=36%  Similarity=0.720  Sum_probs=62.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      ++++++..|..|+..|+..|+..|+..+|+-..++.+||..+||++.+|++||||||.||||+...
T Consensus       163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa  228 (288)
T KOG0847|consen  163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA  228 (288)
T ss_pred             cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence            667888889999999999999999999999999999999999999999999999999999998654

>KOG0491|consensus

Probab=99.54  E-value=3.2e-15  Score=101.64  Aligned_cols=66  Identities=48%  Similarity=0.763  Sum_probs=60.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCChh
Q psy4625          16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKNPL   81 (120)
Q Consensus        16 ~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~~   81 (120)
                      +++-|++|+..|+..|++.|+...|.+..++.+||..|+|++.||+.||||||.|.||..+..+..
T Consensus       100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p~  165 (194)
T KOG0491|consen  100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQPK  165 (194)
T ss_pred             hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCCC
Confidence            356689999999999999999999999999999999999999999999999999999998776643

>KOG0483|consensus

Probab=99.52  E-value=1.4e-14  Score=102.20  Aligned_cols=58  Identities=34%  Similarity=0.635  Sum_probs=54.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625          18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS   75 (120)
Q Consensus        18 r~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   75 (120)
                      .++.+|+.+|+..|+..|+...+..+..+..||.+|||.++||.+||||||++||..+
T Consensus        52 ~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq  109 (198)
T KOG0483|consen   52 GKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ  109 (198)
T ss_pred             cccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence            4456799999999999999999999999999999999999999999999999999875

>KOG0486|consensus

Probab=99.47  E-value=2e-14  Score=106.32  Aligned_cols=65  Identities=38%  Similarity=0.690  Sum_probs=61.8

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCC
Q psy4625          15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKN   79 (120)
Q Consensus        15 ~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~   79 (120)
                      ++||.|+.|+..|+..||..|+++.||+...+++||.-++|++..|++||.|||+||||.++...
T Consensus       111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~  175 (351)
T KOG0486|consen  111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ  175 (351)
T ss_pred             hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence            67888999999999999999999999999999999999999999999999999999999987655

>KOG4577|consensus

Probab=99.45  E-value=1.5e-13  Score=100.84  Aligned_cols=66  Identities=33%  Similarity=0.590  Sum_probs=62.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      +++..+|+||.++..|+..|..+|...+.|....|+.|+.++||.-++|++||||||+|+|+..+.
T Consensus       163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD  228 (383)
T KOG4577|consen  163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD  228 (383)
T ss_pred             cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence            567789999999999999999999999999999999999999999999999999999999987554

>KOG0844|consensus

Probab=99.37  E-value=1.2e-13  Score=102.05  Aligned_cols=65  Identities=45%  Similarity=0.685  Sum_probs=59.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      .+.+-||-||.|+.+|+..||+.|-...|.+...|.+||.+|+|.+..|++||||||.|+|+...
T Consensus       177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl  241 (408)
T KOG0844|consen  177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL  241 (408)
T ss_pred             ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence            34455788999999999999999999999999999999999999999999999999999998754

>KOG0775|consensus

Probab=99.27  E-value=7.4e-12  Score=91.27  Aligned_cols=54  Identities=31%  Similarity=0.561  Sum_probs=48.4

Q ss_pred             CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      |...-..+|.+.|..++||++.++.+||.++||+..||-+||.|||+++|-...
T Consensus       183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~a  236 (304)
T KOG0775|consen  183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAAA  236 (304)
T ss_pred             hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhccc
Confidence            445557799999999999999999999999999999999999999999994443

>KOG0490|consensus

Probab=99.23  E-value=3.7e-12  Score=91.36  Aligned_cols=64  Identities=30%  Similarity=0.392  Sum_probs=60.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          13 RSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        13 ~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      ..++++.|+.|+..|++.|+..|...+||+...++.||..+++++..|++||||+|+++++...
T Consensus        57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~  120 (235)
T KOG0490|consen   57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER  120 (235)
T ss_pred             hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence            4567888999999999999999999999999999999999999999999999999999998764

>KOG0849|consensus

Probab=99.18  E-value=5.7e-11  Score=90.82  Aligned_cols=66  Identities=36%  Similarity=0.585  Sum_probs=60.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      ...+.++.|+.|+..|+..|+..|+.++||++..++.||.++++++..|++||+|+|+++++....
T Consensus       172 ~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~  237 (354)
T KOG0849|consen  172 LQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD  237 (354)
T ss_pred             ccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence            445566778999999999999999999999999999999999999999999999999999998843

>KOG1168|consensus

Probab=99.18  E-value=3e-12  Score=94.12  Aligned_cols=65  Identities=23%  Similarity=0.422  Sum_probs=59.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      ..+.++|+||.+...+...||.+|...+.|+.+.+..||.+|.|.+.+|++||||.|+|.|+...
T Consensus       305 ~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~  369 (385)
T KOG1168|consen  305 PGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR  369 (385)
T ss_pred             CccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence            35677888999999999999999999999999999999999999999999999999999988543

>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants []

Probab=98.83  E-value=6.1e-09  Score=55.73  Aligned_cols=34  Identities=38%  Similarity=0.715  Sum_probs=28.8

Q ss_pred             hCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhH
Q psy4625          37 ENRYLTERRRQELANELGLNEAQIKIWFQNKRAK   70 (120)
Q Consensus        37 ~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k   70 (120)
                      .+|||+..++..||..+||+..||..||-|.|.+
T Consensus         7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR   40 (40)
T PF05920_consen    7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR   40 (40)
T ss_dssp             TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence            4799999999999999999999999999999864

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

>KOG0774|consensus

Probab=98.71  E-value=5.9e-09  Score=75.94  Aligned_cols=64  Identities=33%  Similarity=0.546  Sum_probs=57.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHH---hCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCC
Q psy4625          16 EKRPRTAFSGEQLSRLKVEFT---ENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKN   79 (120)
Q Consensus        16 ~rr~R~~~~~~q~~~L~~~F~---~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~   79 (120)
                      .+|+|..|++....+|..+|.   .++||+...+++||.+++++..||..||.|+|-+++|......
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~~  254 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKNQ  254 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhhh
Confidence            356788899999999999995   5889999999999999999999999999999999998765433

>KOG2252|consensus

Probab=98.67  E-value=6.7e-08  Score=76.54  Aligned_cols=61  Identities=26%  Similarity=0.429  Sum_probs=56.0

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHH
Q psy4625          11 DKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI   71 (120)
Q Consensus        11 ~~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~   71 (120)
                      ...-..+|.|.+|+..|...|..+|+.+++|+..+.+.|+.+|+|....|.+||.|-|.+.
T Consensus       415 d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  415 DKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             cccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            3455667889999999999999999999999999999999999999999999999988774

>KOG0490|consensus

Probab=98.24  E-value=1.4e-06  Score=62.29  Aligned_cols=65  Identities=40%  Similarity=0.673  Sum_probs=60.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      ...+.++.++.+...++..|...|...++|+...+..|+..+|+....|++||+|+|.+.++...
T Consensus       149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            44567788999999999999999999999999999999999999999999999999999988755

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

Probab=97.80  E-value=3.3e-05  Score=43.96  Aligned_cols=42  Identities=19%  Similarity=0.413  Sum_probs=31.5

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHh
Q psy4625          28 LSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRA   69 (120)
Q Consensus        28 ~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~   69 (120)
                      ...|+.+|...+++.......|+.+.+|+..+|+.||-.+..
T Consensus        10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~   51 (56)
T PF11569_consen   10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ   51 (56)
T ss_dssp             -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred             hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence            456999999999999999999999999999999999986644

>KOG1146|consensus

Probab=97.68  E-value=4.2e-05  Score=66.12  Aligned_cols=62  Identities=35%  Similarity=0.429  Sum_probs=57.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        15 ~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      .++..|++++..|+..|..+|....+|...+.+.|...+++..+.|++||||-|++.++...
T Consensus       902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~  963 (1406)
T KOG1146|consen  902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL  963 (1406)
T ss_pred             hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence            34567899999999999999999999999999999999999999999999999999988765

>KOG3623|consensus

Probab=97.20  E-value=0.0022  Score=53.20  Aligned_cols=49  Identities=27%  Similarity=0.403  Sum_probs=45.4

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          28 LSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        28 ~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      +.+|..+|..|..|+..+...+|.+.||....|+.||.+++.......+
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~r  616 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVER  616 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhcc
Confidence            6789999999999999999999999999999999999999998777654

>KOG0773|consensus

Probab=96.75  E-value=0.0014  Score=49.97  Aligned_cols=58  Identities=28%  Similarity=0.487  Sum_probs=46.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHH-H--hCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625          16 EKRPRTAFSGEQLSRLKVEF-T--ENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK   73 (120)
Q Consensus        16 ~rr~R~~~~~~q~~~L~~~F-~--~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   73 (120)
                      ..+.+..+......+|+... +  ..+||+..++..||.++||+..||.+||-|.|.+.-+
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~  299 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWK  299 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCC
Confidence            33445578888888888663 3  2579999999999999999999999999999877443

>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere

Probab=95.71  E-value=0.055  Score=30.31  Aligned_cols=47  Identities=21%  Similarity=0.420  Sum_probs=34.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHH
Q psy4625          17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR   68 (120)
Q Consensus        17 rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR   68 (120)
                      ++.|..++-++...+-..++.+.     ....||..+|++..+|..|..|+.
T Consensus         1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~   47 (53)
T PF04218_consen    1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD   47 (53)
T ss_dssp             SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred             CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence            45678899988777777787776     477889999999999999998854

Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.

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

Probab=91.11  E-value=1.3  Score=23.91  Aligned_cols=46  Identities=11%  Similarity=0.309  Sum_probs=33.7

Q ss_pred             CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHH
Q psy4625          22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK   72 (120)
Q Consensus        22 ~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k   72 (120)
                      .+++.+..+|...|-     ......++|..+|++...|+.+...-..+.|
T Consensus         4 ~L~~~er~vi~~~y~-----~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR   49 (50)
T PF04545_consen    4 QLPPREREVIRLRYF-----EGLTLEEIAERLGISRSTVRRILKRALKKLR   49 (50)
T ss_dssp             TS-HHHHHHHHHHHT-----ST-SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHhc-----CCCCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence            467888999999992     2234677899999999999998876555443

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

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

Probab=87.01  E-value=2.5  Score=23.65  Aligned_cols=42  Identities=21%  Similarity=0.343  Sum_probs=34.0

Q ss_pred             CCHHHHHHHHHHHHhCCC--CCHHHHHHHHHHhCCChhhHHHHH
Q psy4625          23 FSGEQLSRLKVEFTENRY--LTERRRQELANELGLNEAQIKIWF   64 (120)
Q Consensus        23 ~~~~q~~~L~~~F~~~~~--p~~~~~~~La~~l~l~~~~V~~WF   64 (120)
                      ++..|..+|...|...-|  |-......||..+|++...|..-+
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~L   44 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHL   44 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHH
Confidence            467899999999988764  667778899999999987765433

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

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

Probab=86.04  E-value=1.3  Score=25.89  Aligned_cols=45  Identities=22%  Similarity=0.324  Sum_probs=29.0

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHH
Q psy4625          19 PRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNK   67 (120)
Q Consensus        19 ~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNr   67 (120)
                      .|..|+.++...+...+...    ......+|..+|+++..+..|-.--
T Consensus         3 ~r~~ys~e~K~~~v~~~~~~----g~sv~~va~~~gi~~~~l~~W~~~~   47 (76)
T PF01527_consen    3 KRRRYSPEFKLQAVREYLES----GESVSEVAREYGISPSTLYNWRKQY   47 (76)
T ss_dssp             SS----HHHHHHHHHHHHHH----HCHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHC----CCceEeeecccccccccccHHHHHH
Confidence            46779998866665555222    2567788999999999999998543

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

>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs)

Probab=83.43  E-value=3.3  Score=21.53  Aligned_cols=44  Identities=16%  Similarity=0.292  Sum_probs=31.2

Q ss_pred             CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhH
Q psy4625          22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAK   70 (120)
Q Consensus        22 ~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k   70 (120)
                      .++..+..++...|...     .....+|..+|++...|..|...-+.+
T Consensus        10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~   53 (55)
T cd06171          10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK   53 (55)
T ss_pred             hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            35667777777776432     235667999999999999998755443

A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas

>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=82.55  E-value=1.3  Score=25.49  Aligned_cols=21  Identities=29%  Similarity=0.725  Sum_probs=17.8

Q ss_pred             HHHHHHHHhCCChhhHHHHHH
Q psy4625          45 RRQELANELGLNEAQIKIWFQ   65 (120)
Q Consensus        45 ~~~~La~~l~l~~~~V~~WFq   65 (120)
                      ....||.+||+++.+|+.|=.
T Consensus        24 ~lkdIA~~Lgvs~~tIr~WK~   44 (60)
T PF10668_consen   24 KLKDIAEKLGVSESTIRKWKS   44 (60)
T ss_pred             cHHHHHHHHCCCHHHHHHHhh
Confidence            456789999999999999953

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 [].

>KOG1146|consensus

Probab=82.26  E-value=3.3  Score=37.21  Aligned_cols=60  Identities=15%  Similarity=0.215  Sum_probs=54.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625          16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS   75 (120)
Q Consensus        16 ~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   75 (120)
                      .+..+..+-.++..+|-..|-.+.-|+......|......+.+.+.+||++-+.+.++..
T Consensus       705 ~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~  764 (1406)
T KOG1146|consen  705 DKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ  764 (1406)
T ss_pred             cccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence            355677788899999999999999999999999999999999999999999999988876

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	120
3hdd_A	60	Engrailed Homeodomain Dna Complex Length = 60		8e-24
1hdd_C	61	Crystal Structure Of An Engrailed Homeodomain-Dna C		1e-23
2hdd_A	61	Engrailed Homeodomain Q50k Variant Dna Complex Leng		4e-23
1p7j_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		4e-23
1p7i_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		5e-23
1ztr_A	61	Solution Structure Of Engrailed Homeodomain L16a Mu		3e-22
2hos_A	63	Phage-selected Homeodomain Bound To Unmodified Dna		6e-22
1du0_A	57	Engrailed Homeodomain Q50a Variant Dna Complex Leng		7e-22
1enh_A	54	Structural Studies Of The Engrailed Homeodomain Len		2e-21
2p81_A	44	Engrailed Homeodomain Helix-Turn-Helix Motif Length		2e-15
2djn_A	70	The Solution Structure Of The Homeobox Domain Of Hu		2e-11
2r5y_A	88	Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO		6e-11
2m34_A	71	Nmr Structure Of The Homeodomain Transcription Fact		2e-10
1ftz_A	70	Nuclear Magnetic Resonance Solution Structure Of Th		2e-10
1b72_A	97	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		5e-10
1ahd_P	68	Determination Of The Nmr Solution Structure Of An A		5e-10
1hom_A	68	Determination Of The Three-Dimensional Structure Of		5e-10
9ant_A	62	Antennapedia Homeodomain-Dna Complex Length = 62		6e-10
1b8i_A	81	Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX		6e-10
1jgg_A	60	Even-Skipped Homeodomain Complexed To At-Rich Dna L		1e-09
2h1k_A	63	Crystal Structure Of The Pdx1 Homeodomain In Comple		2e-09
1san_A	62	The Des(1-6)antennapedia Homeodomain: Comparison Of		5e-09
1ig7_A	58	Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58		7e-09
1zq3_P	68	Nmr Solution Structure Of The Bicoid Homeodomain Bo		1e-08
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		2e-08
1fjl_A	81	Homeodomain From The Drosophila Paired Protein Boun		2e-08
2lp0_A	60	The Solution Structure Of Homeodomain-Protein Compl		3e-08
1puf_A	77	Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo		3e-08
2kt0_A	84	Solution Structure Of Human Stem Cell Transcription		6e-08
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		7e-08
3a01_A	93	Crystal Structure Of Aristaless And Clawless Homeod		8e-08
2vi6_A	62	Crystal Structure Of The Nanog Homeodomain Length =		9e-08
2dmt_A	80	Solution Structure Of The Homeobox Domain Of Homeob		1e-07
3rkq_A	58	Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Lengt		1e-07
2l7f_P	68	Solution Structure Of The Pitx2 Homeodomain Length		1e-07
2l7m_P	68	Solution Structure Of The Pitx2 Homeodomain R24h Mu		5e-07
1nk2_P	77	VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES		1e-06
1ftt_A	68	Thyroid Transcription Factor 1 Homeodomain (Rattus		1e-06
3a02_A	60	Crystal Structure Of Aristaless Homeodomain Length		2e-06
2k40_A	67	Nmr Structure Of Hesx-1 Homeodomain Double Mutant R		2e-06
2m0c_A	75	Solution Nmr Structure Of Homeobox Domain Of Human		2e-06
3cmy_A	61	Structure Of A Homeodomain In Complex With Dna Leng		2e-06
2cra_A	70	Solution Structure Of The Homeobox Domain Of Human		2e-06
1qry_A	80	Homeobox Protein Vnd (Ventral Nervous System Defect		3e-06
2dmu_A	70	Solution Structure Of The Homeobox Domain Of Homeob		4e-06
2cue_A	80	Solution Structure Of The Homeobox Domain Of The Hu		5e-06
2dms_A	80	Solution Structure Of The Homeobox Domain Of Homeob		5e-06
2l7z_A	73	Nmr Structure Of A13 Homedomain Length = 73		1e-05
2ld5_A	67	Solution Nmr-Derived Complex Structure Of Hoxa13 Dn		1e-05
2e1o_A	70	Solution Structure Of Rsgi Ruh-028, A Homeobox Doma		1e-05
2l9r_A	69	Solution Nmr Structure Of Homeobox Domain Of Homeob		2e-05
3a03_A	56	Crystal Structure Of Hox11l1 Homeodomain Length = 5		3e-05
2dmq_A	80	Solution Structure Of The Homeobox Domain Of LimHOM		5e-05
2da3_A	80	Solution Structure Of The Third Homeobox Domain Of		2e-04
1bw5_A	66	The Nmr Solution Structure Of The Homeodomain Of Th		5e-04
2da1_A	70	Solution Structure Of The First Homeobox Domain Of		8e-04

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

Iteration: 1
 Score =  105 bits (261), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 51/60 (85%), Positives = 57/60 (95%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75
          EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQIKIWFQNKRAKIKK++
Sbjct: 1  EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKST 60

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

Iteration: 1
 Score =  104 bits (260), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 51/59 (86%), Positives = 56/59 (94%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
          EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQIKIWFQNKRAKIKK+
Sbjct: 3  EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 61

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

Iteration: 1
 Score =  102 bits (255), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 50/59 (84%), Positives = 56/59 (94%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
          EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQIKIWF+NKRAKIKK+
Sbjct: 3  EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKKS 61

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

Iteration: 1
 Score =  102 bits (255), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 50/59 (84%), Positives = 56/59 (94%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
          EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQIKIWFQN+RAKIKK+
Sbjct: 1  EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKKS 59

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

Iteration: 1
 Score =  102 bits (254), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 50/59 (84%), Positives = 55/59 (93%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
          EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQIKIWFQN RAKIKK+
Sbjct: 1  EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKKS 59

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

Iteration: 1
 Score =  100 bits (248), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 48/59 (81%), Positives = 55/59 (93%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
          EKRPRTAFS EQL+R K EF ENRYLTERRRQ+L++ELGLNEAQIKIWFQNKRAKI+++
Sbjct: 3  EKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRRS 61

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

Iteration: 1
 Score = 99.0 bits (245), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 48/62 (77%), Positives = 56/62 (90%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          S EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQ+K WF+N RAKIKK
Sbjct: 2  SDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61
Query: 74 AS 75
          ++
Sbjct: 62 ST 63

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

Iteration: 1
 Score = 99.0 bits (245), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 48/57 (84%), Positives = 53/57 (92%)
Query: 18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
          RPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQIKIWF NKRAKIKK+
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKKS 57

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

Iteration: 1
 Score = 97.4 bits (241), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 47/54 (87%), Positives = 51/54 (94%)
Query: 18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71
          RPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQIKIWFQNKRAKI
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKI 54

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

Iteration: 1
 Score = 77.0 bits (188), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 37/43 (86%), Positives = 41/43 (95%)
Query: 32 KVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
          K EF ENRYLTERRRQ+L++ELGLNEAQIKIWFQNKRAKIKK+
Sbjct: 2  KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 44

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/61 (50%), Positives = 42/61 (68%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          S  ++PRT +S  QL+ L+  F + +YL    R ELA  LGL + Q+KIWFQNKR+KIKK
Sbjct: 5  SSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64
Query: 74 A 74
          +
Sbjct: 65 S 65

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

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 33/57 (57%), Positives = 40/57 (70%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          KR RT+++  Q   L+ EF  NRYLT RRR E+A+ L L E QIKIWFQN+R K KK
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 85

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

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 30/59 (50%), Positives = 42/59 (71%)
Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          K +R RTAF+ EQL  L+ EF   +YL+   R ++A+ L L+E Q+KIWFQN+RAK K+
Sbjct: 6  KSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKR 64

>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 = 60.5 bits (145), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/57 (54%), Positives = 39/57 (68%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          KR R  ++  Q   L+ EF  NRY+T RRR ++AN L L+E QIKIWFQN+R K KK
Sbjct: 4  KRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKK 60

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

Iteration: 1
 Score = 59.3 bits (142), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 30/54 (55%), Positives = 38/54 (70%)
Query: 20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          RT F+  QL+ L+ EF  N+YL+  RR E+A  L LNE Q+KIWFQN+R K KK
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91

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

Iteration: 1
 Score = 59.3 bits (142), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 33/62 (53%), Positives = 40/62 (64%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
          KR R  ++  Q   L+ EF  NRYLT RRR E+A+ L L E QIKIWFQN+R K KK + 
Sbjct: 3  KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 62
Query: 77 QK 78
           K
Sbjct: 63 TK 64

>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 = 59.3 bits (142), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 33/62 (53%), Positives = 40/62 (64%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
          KR R  ++  Q   L+ EF  NRYLT RRR E+A+ L L E QIKIWFQN+R K KK + 
Sbjct: 3  KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 62
Query: 77 QK 78
           K
Sbjct: 63 TK 64

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

Iteration: 1
 Score = 59.3 bits (142), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 32/57 (56%), Positives = 38/57 (66%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          KR R  ++  Q   L+ EF  NRYLT RRR E+A+ L L E QIKIWFQN+R K KK
Sbjct: 4  KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 60

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

Iteration: 1
 Score = 59.3 bits (142), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 30/57 (52%), Positives = 38/57 (66%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          +R R  ++  Q   L+ EF  N YLT RRR E+A+ L L E QIKIWFQN+R K+KK
Sbjct: 21 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKK 77

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/57 (50%), Positives = 41/57 (71%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          +R RTAF+ +QL RL+ EF +  Y++  RR ELA +L L E+ IK+WFQN+R K K+
Sbjct: 2  RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 58

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

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 31/57 (54%), Positives = 38/57 (66%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          KR RTA++  QL  L+ EF  N+Y++  RR ELA  L L E  IKIWFQN+R K KK
Sbjct: 4  KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60

>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 = 55.8 bits (133), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 30/57 (52%), Positives = 37/57 (64%)
Query: 22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQK 78
           ++  Q   L+ EF  NRYLT RRR E+A+ L L E QIKIWFQN+R K KK +  K
Sbjct: 2  TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTK 58

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 39/57 (68%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          ++PRT F+  QL  L+ +F + +YL+   R E ++ L L E Q+KIWFQN+RAK K+
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 26/61 (42%), Positives = 39/61 (63%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
          +R RT F+  Q++ L+  F + RYLT  R  +L+ +L L  AQ+KIWF+N+R + K  S 
Sbjct: 3  RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 62
Query: 77 Q 77
          Q
Sbjct: 63 Q 63

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 27/59 (45%), Positives = 40/59 (67%)
Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          K++R RT F+  QL  L+  F+   Y     R+ELA ++GL EA+I++WFQN+RAK +K
Sbjct: 5  KQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 63

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 38/59 (64%)
Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          K++R RT FS  QL  L+  F   +Y     R+ELA    L EA+I++WFQN+RA+++K
Sbjct: 17 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK 75

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 27/59 (45%), Positives = 37/59 (62%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75
          ++ R  ++  Q   L+ EF  N YLT  RR E+A  L L E Q+KIWFQN+R K+KK +
Sbjct: 2  RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKMN 60

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 27/62 (43%), Positives = 38/62 (61%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
          ++ R  ++  Q   L+ EF  N YLT  RR E+A  L L E Q+KIWFQN+R K+KK + 
Sbjct: 14 RKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINK 73
Query: 77 QK 78
           +
Sbjct: 74 DR 75

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 29/65 (44%), Positives = 41/65 (63%), Gaps = 2/65 (3%)
Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
          K+++ RT FS  QL  L   F   +YL+ ++ QEL+N L L+  Q+K WFQN+R K K+ 
Sbjct: 21 KKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKR- 79
Query: 75 SGQKN 79
            QKN
Sbjct: 80 -WQKN 83

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 26/56 (46%), Positives = 37/56 (66%)
Query: 18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          R RT F+  QL  L+  F+   Y     R+ELA ++GL EA+I++WFQN+RAK +K
Sbjct: 1  RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 46/77 (59%), Gaps = 2/77 (2%)
Query: 3  SRRIKSGKDKRS--KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
          +RRI      R+  K K+PRT+F+  Q++ L+  F + +YL    R  LA  L + +AQ+
Sbjct: 2  ARRIGHPYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQV 61
Query: 61 KIWFQNKRAKIKKASGQ 77
          K WFQN+R K ++ + +
Sbjct: 62 KTWFQNRRTKWRRQTAE 78

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 25/58 (43%), Positives = 39/58 (67%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          +++ RT FS  QL  LK  F + +YL+ ++ QEL++ L L+  Q+K WFQN+R K K+
Sbjct: 3  KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/63 (42%), Positives = 40/63 (63%)
Query: 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71
          K  K +R RT F+  QL  L+  F + +YL+   R +LA  LGL++ Q+K W+QN+R K 
Sbjct: 13 KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKW 72
Query: 72 KKA 74
          KK+
Sbjct: 73 KKS 75

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/56 (44%), Positives = 35/56 (62%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK 72
          ++PR  FS  Q+  L+  F + RYL+   R +LA+ L L   Q+KIWFQN+R K K
Sbjct: 3  RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 38/58 (65%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          ++R RT F+ +QL  L+  F  NRY     R+E+A    L EA++++WF+N+RAK +K
Sbjct: 3  QRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 37/58 (63%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          ++R RT F+ +QL  L+  F  N Y     R+E+A    L EA++++WF+N+RAK +K
Sbjct: 3  QRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 39/65 (60%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          +K+++ R  F+  Q   L+  F + RYL+   R+ LA+ + L   Q+KIWFQN R K K+
Sbjct: 7  NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66
Query: 74 ASGQK 78
          A  +K
Sbjct: 67 AQNEK 71

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 23/59 (38%), Positives = 35/59 (59%)
Query: 20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQK 78
          R  FS  Q+  L+  F + +YL+   R+ LA+ + L   Q+KIWFQN R K+K+ +  K
Sbjct: 6  RVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDK 64

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/52 (44%), Positives = 34/52 (65%)
Query: 22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
           F+  QL  L+  F+   Y     R+ELA ++GL EA+I++WFQN+RAK +K
Sbjct: 5  TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/58 (43%), Positives = 38/58 (65%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
          +RPRTAF+  Q+  L+  F  N Y      ++LA +L L   +I+IWFQN+RAK+K++
Sbjct: 2  RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRS 59

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 39/66 (59%)
Query: 8  SGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNK 67
          S    + K++R RT F+  QL  L+  F +  Y     R++LA    L EA++++WFQN+
Sbjct: 1  SHMSNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNR 60
Query: 68 RAKIKK 73
          RAK +K
Sbjct: 61 RAKWRK 66

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 35/58 (60%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          ++R RT F+ EQL  L+  F    Y     R+ELA    L EA++++WF N+RA+ +K
Sbjct: 2  QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRK 59

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 40/61 (65%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          S  ++ R  +S  QL  L+ E+  N+++T+ +R++++    L+E QI IWFQN+R K KK
Sbjct: 5  SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64
Query: 74 A 74
          +
Sbjct: 65 S 65

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/65 (36%), Positives = 38/65 (58%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          +K+++ R  F+  Q   L+  F + RYL+   R+ L + + L   Q+KIWFQN R K K+
Sbjct: 10 NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKR 69
Query: 74 ASGQK 78
          A  +K
Sbjct: 70 AQNEK 74

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 40/61 (65%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          S  +R RT F+ EQL  L+  F E +Y     R++LA ++ L E ++++WF+N+RAK ++
Sbjct: 5  SSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRR 64
Query: 74 A 74
          +
Sbjct: 65 S 65

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/60 (40%), Positives = 38/60 (63%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          S  +R RT+F+ EQ+  L+ EF    Y     R+ LA ++ L EA+I++WF N+RAK ++
Sbjct: 5  SSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRR 64

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          S  +R RT F+  QL  L+  F + RY     R+E+A ++ L E+++++WF+N+RAK ++
Sbjct: 5  SSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQ 64
Query: 74 A------SGQKNP 80
                  GQ  P
Sbjct: 65 QQQQQQNGGQSGP 77

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 37/58 (63%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
          ++ R  ++  QL  L+ E+  N+++T+ +R+ ++    L+E Q+ IWFQN+R K KK 
Sbjct: 8  RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKV 65

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 37/58 (63%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
          ++ R  ++  QL  L+ E+  N+++T+ +R+ ++    L+E Q+ IWFQN+R K KK 
Sbjct: 2  RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKV 59

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 34/52 (65%)
Query: 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
          FS +Q   L+ +F   +YL+   R+ LA  L L+E Q+K WFQN+RAK +++
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRS 65

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/47 (44%), Positives = 30/47 (63%)
Query: 27 QLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          Q+  L+ +F+  +YL+   R  LA  L L E Q+KIWFQN+R K K+
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/53 (39%), Positives = 31/53 (58%)
Query: 21 TAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          T+FS  Q+  L+  F   +YL    R  LA  L + +AQ+K WFQN+R K ++
Sbjct: 2  TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRR 54

>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX Protein Lhx9 Length = 80

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/60 (36%), Positives = 34/60 (56%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          S  KR RT+F   QL  +K  F  N     +  ++LA + GL +  +++WFQN RAK ++
Sbjct: 5  SSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRR 64

>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At- Binding Transcription Factor 1 (Atbf1) Length = 80

Iteration: 1
 Score = 40.4 bits (93), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 37/60 (61%)
Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
          ++KR RT  + EQL  L  ++  +   T +    +A+E+GL +  +++WFQN RA+ +K+
Sbjct: 16 RDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKS 75

>pdb|1BW5|A Chain A, The Nmr Solution Structure Of The Homeodomain Of The Rat Insulin Gene Enhancer Protein Isl-1, 50 Structures Length = 66

Iteration: 1
 Score = 39.3 bits (90), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 32/61 (52%)
Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
          K  R RT  + +QL  L+  +  N       +++L    GL+   I++WFQNKR K KK 
Sbjct: 2  KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61
Query: 75 S 75
          S
Sbjct: 62 S 62

>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At- Binding Transcription Factor 1 (Atbf1) Length = 70

Iteration: 1
 Score = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 21/53 (39%), Positives = 32/53 (60%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQN 66
          S  KRPRT  + +QL  L+  F  N   +E + +E+A++ GL +  IK WF+N
Sbjct: 5  SSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRN 57

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	120
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	2e-28
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	2e-23
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	8e-22
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	4e-21
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	4e-21
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	8e-21
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	1e-20
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	1e-20
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	3e-20
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	4e-20
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	6e-20
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	7e-20
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	9e-20
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	9e-20
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	1e-19
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	4e-19
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	8e-19
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	2e-18
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	3e-18
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	3e-18
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	3e-18
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	1e-17
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	1e-17
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	1e-17
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	8e-17
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	8e-16
1e3o_C	160	Octamer-binding transcription factor 1; transcript	1e-15
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	1e-15
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	2e-15
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	4e-15
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	6e-15
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	6e-15
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	1e-14
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	2e-14
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	6e-14
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	1e-13
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	2e-13
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	4e-13
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	4e-13
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	5e-13
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	6e-13
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	6e-13
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	1e-12
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	4e-12
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	4e-12
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	1e-11
1uhs_A	72	HOP, homeodomain only protein; structural genomics	3e-11
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	3e-10
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	3e-10
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	2e-09
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	2e-09
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	2e-08
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	7e-07
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	2e-06
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	2e-05
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	5e-05
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	9e-05
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	1e-04
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	1e-04
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	1e-04
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	2e-04
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	2e-04
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	3e-04
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	3e-04
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	5e-04
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	6e-04
2e19_A	64	Transcription factor 8; homeobox domain, structura	7e-04
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	9e-04

>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 = 97.4 bits (243), Expect = 2e-28
 Identities = 50/59 (84%), Positives = 56/59 (94%)

Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
          EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQIKIWF+NKRAKIKK+
Sbjct: 3  EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKKS 61

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

 Score = 85.1 bits (211), Expect = 2e-23
 Identities = 31/67 (46%), Positives = 42/67 (62%)

Query: 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71
            S  ++PRT +S  QL+ L+  F + +YL    R ELA  LGL + Q+KIWFQNKR+KI
Sbjct: 3  SGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKI 62

Query: 72 KKASGQK 78
          KK+    
Sbjct: 63 KKSGPSS 69

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

 Score = 81.4 bits (201), Expect = 8e-22
 Identities = 27/73 (36%), Positives = 40/73 (54%)

Query: 1  PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
            +   K       K+++ RT FS  QL  L   F   +YL+ ++ QEL+N L L+  Q+
Sbjct: 7  AENSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQV 66

Query: 61 KIWFQNKRAKIKK 73
          K WFQN+R K K+
Sbjct: 67 KTWFQNQRMKSKR 79

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

 Score = 79.0 bits (195), Expect = 4e-21
 Identities = 26/64 (40%), Positives = 39/64 (60%)

Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
          +R RT F+  Q++ L+  F + RYLT  R  +L+ +L L  AQ+KIWF+N+R + K  S 
Sbjct: 3  RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 62

Query: 77 QKNP 80
          Q   
Sbjct: 63 QHKD 66

>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 = 79.4 bits (196), Expect = 4e-21
 Identities = 27/67 (40%), Positives = 40/67 (59%)

Query: 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71
          K  K +R RT F+  QL  L+  F + +YL+   R +LA  LGL++ Q+K W+QN+R K 
Sbjct: 13 KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKW 72

Query: 72 KKASGQK 78
          KK+    
Sbjct: 73 KKSGPSS 79

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

 Score = 78.1 bits (193), Expect = 8e-21
 Identities = 26/57 (45%), Positives = 39/57 (68%)

Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          ++PRT F+  QL  L+ +F + +YL+   R E ++ L L E Q+KIWFQN+RAK K+
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

 Score = 77.6 bits (192), Expect = 1e-20
 Identities = 16/61 (26%), Positives = 35/61 (57%)

Query: 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71
          K+ K  + +++ S +  + L+  F   + L  + ++E+A + G+   Q+++WF NKR + 
Sbjct: 1  KKEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS 60

Query: 72 K 72
          K
Sbjct: 61 K 61

>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 = 77.8 bits (192), Expect = 1e-20
 Identities = 24/65 (36%), Positives = 37/65 (56%)

Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          S  K  +  FS +Q   L+ +F   +YL+   R+ LA  L L+E Q+K WFQN+RAK ++
Sbjct: 5  SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64

Query: 74 ASGQK 78
          +    
Sbjct: 65 SGPSS 69

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

 Score = 76.6 bits (189), Expect = 3e-20
 Identities = 29/57 (50%), Positives = 41/57 (71%)

Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          +R RTAF+ +QL RL+ EF +  Y++  RR ELA +L L E+ IK+WFQN+R K K+
Sbjct: 2  RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 58

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

 Score = 76.2 bits (188), Expect = 4e-20
 Identities = 25/59 (42%), Positives = 39/59 (66%)

Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
           +++ RT FS  QL  LK  F + +YL+ ++ QEL++ L L+  Q+K WFQN+R K K+
Sbjct: 2  TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60

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

 Score = 76.9 bits (189), Expect = 6e-20
 Identities = 30/65 (46%), Positives = 39/65 (60%)

Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
                RT F+  QL+ L+ EF  N+YL+  RR E+A  L LNE Q+KIWFQN+R K KK
Sbjct: 32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91

Query: 74 ASGQK 78
             + 
Sbjct: 92 REREG 96

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

 Score = 75.9 bits (187), Expect = 7e-20
 Identities = 22/66 (33%), Positives = 32/66 (48%)

Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
                 +  S  Q+  L+ +F+  +YL+   R  LA  L L E Q+KIWFQN+R K K+
Sbjct: 2  GHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61

Query: 74 ASGQKN 79
                
Sbjct: 62 KQLSSE 67

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

 Score = 75.9 bits (187), Expect = 9e-20
 Identities = 18/74 (24%), Positives = 33/74 (44%)

Query: 9  GKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR 68
          G    S     +   S EQLS LK  F  N++  +   + L    GL+  +++ WF ++R
Sbjct: 1  GSSGSSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRR 60

Query: 69 AKIKKASGQKNPLA 82
             +   G ++  +
Sbjct: 61 YHCRNLKGSRSGPS 74

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

 Score = 76.0 bits (187), Expect = 9e-20
 Identities = 25/72 (34%), Positives = 40/72 (55%)

Query: 8  SGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNK 67
          +     +K+++ R  F+  Q   L+  F + RYL+   R+ LA+ + L   Q+KIWFQN 
Sbjct: 1  ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNH 60

Query: 68 RAKIKKASGQKN 79
          R K K+A  +K 
Sbjct: 61 RYKTKRAQNEKG 72

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

 Score = 75.0 bits (185), Expect = 1e-19
 Identities = 25/56 (44%), Positives = 35/56 (62%)

Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK 72
          ++PR  FS  Q+  L+  F + RYL+   R +LA+ L L   Q+KIWFQN+R K K
Sbjct: 3  RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

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

 Score = 74.9 bits (184), Expect = 4e-19
 Identities = 25/73 (34%), Positives = 42/73 (57%)

Query: 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71
             K K+PRT+F+  Q++ L+  F + +YL    R  LA  L + +AQ+K WFQN+R K 
Sbjct: 13 TPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKW 72

Query: 72 KKASGQKNPLALQ 84
          ++ + ++     Q
Sbjct: 73 RRQTAEEREAERQ 85

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

 Score = 73.7 bits (181), Expect = 8e-19
 Identities = 35/72 (48%), Positives = 44/72 (61%)

Query: 2  RSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIK 61
          R     S  +   + KR RT+++  Q   L+ EF  NRYLT RRR E+A+ L L E QIK
Sbjct: 14 RVHLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIK 73

Query: 62 IWFQNKRAKIKK 73
          IWFQN+R K KK
Sbjct: 74 IWFQNRRMKWKK 85

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

 Score = 71.6 bits (176), Expect = 2e-18
 Identities = 21/55 (38%), Positives = 32/55 (58%)

Query: 21 TAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75
          T+FS  Q+  L+  F   +YL    R  LA  L + +AQ+K WFQN+R K ++ +
Sbjct: 2  TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQT 56

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

 Score = 71.6 bits (176), Expect = 3e-18
 Identities = 31/59 (52%), Positives = 38/59 (64%)

Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
            KR RTA++  QL  L+ EF  N+Y++  RR ELA  L L E  IKIWFQN+R K KK
Sbjct: 2  SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60

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

 Score = 72.2 bits (177), Expect = 3e-18
 Identities = 30/60 (50%), Positives = 38/60 (63%)

Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
             +R R  ++  Q   L+ EF  N YLT RRR E+A+ L L E QIKIWFQN+R K+KK
Sbjct: 18 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKK 77

>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 = 71.6 bits (176), Expect = 3e-18
 Identities = 22/60 (36%), Positives = 35/60 (58%)

Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          S  KRPRT  + +QL  L+  F  N   +E + +E+A++ GL +  IK WF+N   K ++
Sbjct: 5  SSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQ 64

>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 = 70.6 bits (173), Expect = 1e-17
 Identities = 21/66 (31%), Positives = 40/66 (60%)

Query: 8  SGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNK 67
          +G ++  ++KR RT  + EQL  L  ++  +   T +    +A+E+GL +  +++WFQN 
Sbjct: 9  TGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNT 68

Query: 68 RAKIKK 73
          RA+ +K
Sbjct: 69 RARERK 74

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

 Score = 70.1 bits (172), Expect = 1e-17
 Identities = 23/62 (37%), Positives = 37/62 (59%)

Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
          ++ R  FS  Q+  L+  F + +YL+   R+ LA+ + L   Q+KIWFQN R K+K+ + 
Sbjct: 3  RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62

Query: 77 QK 78
           K
Sbjct: 63 DK 64

>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 = 70.1 bits (172), Expect = 1e-17
 Identities = 33/65 (50%), Positives = 40/65 (61%)

Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75
           KR R  ++  Q   L+ EF  NRYLT RRR E+A+ L L E QIKIWFQN+R K KK +
Sbjct: 2  RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61

Query: 76 GQKNP 80
            K  
Sbjct: 62 KTKGE 66

>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 = 68.2 bits (167), Expect = 8e-17
 Identities = 22/60 (36%), Positives = 31/60 (51%)

Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          S  +  RT F+  QL  L+  F  N Y  +   ++L+N L L    I +WFQN R K +K
Sbjct: 5  SSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 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 = 65.6 bits (160), Expect = 8e-16
 Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 14 SKEKRPRTAFSGEQLSRLKVEFTE-NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK 72
          S   R RT  S E L  L+    +   Y  +     L+ +L L +  I  +FQN+R  +K
Sbjct: 5  SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVK 64

Query: 73 K 73
           
Sbjct: 65 H 65

>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 = 67.7 bits (165), Expect = 1e-15
 Identities = 18/67 (26%), Positives = 33/67 (49%)

Query: 7   KSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQN 66
             G +  S+ ++ RT+        L+  F EN+  T      +A +L + +  I++WF N
Sbjct: 92  SPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSN 151

Query: 67  KRAKIKK 73
           +R K K+
Sbjct: 152 RRQKEKR 158

>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 = 65.2 bits (159), Expect = 1e-15
 Identities = 23/65 (35%), Positives = 40/65 (61%)

Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          S  ++ R  +S  QL  L+ E+  N+++T+ +R++++    L+E QI IWFQN+R K KK
Sbjct: 5  SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64

Query: 74 ASGQK 78
          +    
Sbjct: 65 SGPSS 69

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

 Score = 64.5 bits (157), Expect = 2e-15
 Identities = 27/65 (41%), Positives = 38/65 (58%)

Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
             ++ R  ++  Q   L+ EF  N YLT  RR E+A  L L E Q+KIWFQN+R K+KK
Sbjct: 11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70

Query: 74 ASGQK 78
           +  +
Sbjct: 71 INKDR 75

>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 = 64.0 bits (156), Expect = 4e-15
 Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 1/81 (1%)

Query: 9  GKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR 68
          G       KR RT+F   QL  +K  F  N     +  ++LA + GL +  +++WFQN R
Sbjct: 1  GSSGS-SGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNAR 59

Query: 69 AKIKKASGQKNPLALQLMAQG 89
          AK ++   ++    +   + G
Sbjct: 60 AKFRRNLLRQENGGVSGPSSG 80

>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 = 65.4 bits (159), Expect = 6e-15
 Identities = 15/63 (23%), Positives = 31/63 (49%)

Query: 11  DKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAK 70
               ++++ RT  S      L+  F E+   + +    +A EL L +  +++WF N+R +
Sbjct: 82  GANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQR 141

Query: 71  IKK 73
            K+
Sbjct: 142 EKR 144

>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 = 63.1 bits (154), Expect = 6e-15
 Identities = 22/63 (34%), Positives = 32/63 (50%)

Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
          K  R RT  + +QL  L+  +  N       +++L    GL+   I++WFQNKR K KK 
Sbjct: 2  KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

Query: 75 SGQ 77
          S  
Sbjct: 62 SIM 64

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

 Score = 62.6 bits (152), Expect = 1e-14
 Identities = 20/69 (28%), Positives = 40/69 (57%)

Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
           + ++ R  ++  QL  L+ E+  N+++T+ +R+ ++    L+E Q+ IWFQN+R K KK
Sbjct: 5  LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64

Query: 74 ASGQKNPLA 82
             +    +
Sbjct: 65 VINKLKTTS 73

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

 Score = 64.3 bits (156), Expect = 2e-14
 Identities = 14/63 (22%), Positives = 30/63 (47%)

Query: 11  DKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAK 70
             + ++++ RT+        L+  F +    +      LA+ L L +  +++WF N+R K
Sbjct: 94  AAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQK 153

Query: 71  IKK 73
            K+
Sbjct: 154 EKR 156

>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 = 60.8 bits (148), Expect = 6e-14
 Identities = 25/63 (39%), Positives = 39/63 (61%)

Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
          +RPRTAF+  Q+  L+  F  N Y      ++LA +L L   +I+IWFQN+RAK+K++  
Sbjct: 2  RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61

Query: 77 QKN 79
          +  
Sbjct: 62 ESQ 64

>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 = 59.8 bits (145), Expect = 1e-13
 Identities = 13/64 (20%), Positives = 28/64 (43%)

Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          +         + EQ++ LK  F ++++  +     L    GL  ++IK WF + R + ++
Sbjct: 2  AHHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR 61

Query: 74 ASGQ 77
              
Sbjct: 62 GIVH 65

>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 = 61.6 bits (149), Expect = 2e-13
 Identities = 18/63 (28%), Positives = 35/63 (55%)

Query: 11  DKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAK 70
            + SK+++ RT+F+ + +  L   F +N   T +   E+A EL  +   +++WF N+R  
Sbjct: 88  GEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQT 147

Query: 71  IKK 73
           +K 
Sbjct: 148 LKN 150

>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 = 58.5 bits (142), Expect = 4e-13
 Identities = 23/65 (35%), Positives = 39/65 (60%), Gaps = 1/65 (1%)

Query: 9  GKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR 68
          G       +R RT F+ EQL  L+  F E +Y     R++LA ++ L E ++++WF+N+R
Sbjct: 1  GSSGS-SGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRR 59

Query: 69 AKIKK 73
          AK ++
Sbjct: 60 AKWRR 64

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

 Score = 58.6 bits (142), Expect = 4e-13
 Identities = 14/64 (21%), Positives = 32/64 (50%), Gaps = 1/64 (1%)

Query: 17 KRPRTAFSGEQLSRLKVEFTE-NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75
           +  +  + +Q+  L+  F + N++        +A E GL E Q + WF+ + A+ +++ 
Sbjct: 3  AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 62

Query: 76 GQKN 79
          G  +
Sbjct: 63 GLPS 66

>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 = 58.6 bits (142), Expect = 5e-13
 Identities = 24/78 (30%), Positives = 43/78 (55%)

Query: 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71
            S  +R RT F+  QL  L+  F + RY     R+E+A ++ L E+++++WF+N+RAK 
Sbjct: 3  SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKC 62

Query: 72 KKASGQKNPLALQLMAQG 89
          ++   Q+        + G
Sbjct: 63 RQQQQQQQNGGQSGPSSG 80

>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 = 58.5 bits (142), Expect = 6e-13
 Identities = 27/66 (40%), Positives = 40/66 (60%)

Query: 8  SGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNK 67
           G   + K++R RT FS  QL  L+  F   +Y     R+ELA    L EA+I++WFQN+
Sbjct: 10 PGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNR 69

Query: 68 RAKIKK 73
          RA+++K
Sbjct: 70 RARLRK 75

>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 = 58.1 bits (141), Expect = 6e-13
 Identities = 24/59 (40%), Positives = 39/59 (66%)

Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
           ++R RT F+ +QL +L+  F  NRY     R+E+A    L EA++++WF+N+RAK +K
Sbjct: 2  SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60

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

 Score = 57.4 bits (139), Expect = 1e-12
 Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 1/81 (1%)

Query: 9  GKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR 68
          G       +R RT+F+ EQ+  L+ EF    Y     R+ LA ++ L EA+I++WF N+R
Sbjct: 1  GSSGS-SGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRR 59

Query: 69 AKIKKASGQKNPLALQLMAQG 89
          AK ++    +N       + G
Sbjct: 60 AKWRREEKLRNQRRQSGPSSG 80

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

 Score = 58.6 bits (141), Expect = 4e-12
 Identities = 18/61 (29%), Positives = 34/61 (55%)

Query: 15  KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
             KR RT+        L+  F ++   + ++   +AN+LGL +  +++WF N+R K K++
Sbjct: 95  ARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS 154

Query: 75  S 75
           S
Sbjct: 155 S 155

>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 = 55.7 bits (135), Expect = 4e-12
 Identities = 23/54 (42%), Positives = 34/54 (62%)

Query: 20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
             F+  QL  L+  F+   Y     R+ELA ++GL EA+I++WFQN+RAK +K
Sbjct: 3  HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56

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

 Score = 57.2 bits (137), Expect = 1e-11
 Identities = 15/66 (22%), Positives = 31/66 (46%)

Query: 14  SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
           +  K+PR  F+  Q   L   F EN+  ++  +  ++ +LGL  + +  +F N R +   
Sbjct: 95  NTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLD 154

Query: 74  ASGQKN 79
              + +
Sbjct: 155 KWLEHH 160

>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 = 53.9 bits (130), Expect = 3e-11
 Identities = 14/63 (22%), Positives = 30/63 (47%), Gaps = 1/63 (1%)

Query: 18 RPRTAFSGEQLSRLKVEFTE-NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
                + +Q+  L+  F + N++        +A E GL E Q + WF+ + A+ +++ G
Sbjct: 3  EGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG 62

Query: 77 QKN 79
            +
Sbjct: 63 LPS 65

>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 = 51.4 bits (123), Expect = 3e-10
 Identities = 15/65 (23%), Positives = 25/65 (38%)

Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          S         + EQL  L+  F +N    +     L +E  +   +I  WF  +R K+  
Sbjct: 5  SSGPTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNA 64

Query: 74 ASGQK 78
             +K
Sbjct: 65 EETKK 69

>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 = 51.9 bits (124), Expect = 3e-10
 Identities = 11/55 (20%), Positives = 21/55 (38%)

Query: 24 SGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQK 78
          +  Q+  L+  F ++ + T+     L  E  L+  +I  WF  +R          
Sbjct: 21 TQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAV 75

>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 = 50.0 bits (119), Expect = 2e-09
 Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 15/75 (20%)

Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELG---------------LNEA 58
          S  +  R  +  E L+ ++  F EN+Y  E +R+E+AN                  +   
Sbjct: 5  SSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSL 64

Query: 59 QIKIWFQNKRAKIKK 73
          ++  WF N+R +IK+
Sbjct: 65 KVYNWFANRRKEIKR 79

>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 = 49.6 bits (118), Expect = 2e-09
 Identities = 16/63 (25%), Positives = 24/63 (38%), Gaps = 6/63 (9%)

Query: 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71
          ++ KEK        EQL  L+  F  +  LT+     L  +  L   +I  WF  K+   
Sbjct: 13 QKFKEKTA------EQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSK 66

Query: 72 KKA 74
             
Sbjct: 67 ALK 69

>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens} Length = 96

 Score = 47.9 bits (113), Expect = 2e-08
 Identities = 17/60 (28%), Positives = 23/60 (38%)

Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          S         + EQL  LK  F   ++ +     +LA E GL    I  WF + R   K 
Sbjct: 23 SGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKN 82

>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1 Length = 72

 Score = 42.5 bits (100), Expect = 7e-07
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 5/73 (6%)

Query: 8  SGKDKRSKEKRPRTAFSGEQLSRLKVEF-TENRYLTERRRQELANELGLNEAQIKIWFQN 66
          SG     K+         E    L+  F +  +Y  E+R + L+ +L  +  +I+ WF++
Sbjct: 3  SGSSGGIKDSPVNKV---EPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRH 59

Query: 67 KRAKIKKASGQKN 79
          +R + K  SG  +
Sbjct: 60 RRNQDKP-SGPSS 71

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

 Score = 41.9 bits (98), Expect = 2e-06
 Identities = 15/56 (26%), Positives = 24/56 (42%)

Query: 18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
                + EQL+ LK  F + ++      Q+L    GL   +I  WF + R  +K 
Sbjct: 5  SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH 60

>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 Length = 87

 Score = 39.5 bits (92), Expect = 2e-05
 Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 3/75 (4%)

Query: 1  PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENR---YLTERRRQELANELGLNE 57
               +      +S +      F+ E +  L+  F +N    YL  +  + L     L+ 
Sbjct: 12 LVFNVVTQDMINKSTKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSR 71

Query: 58 AQIKIWFQNKRAKIK 72
           QIK W  N+R K K
Sbjct: 72 IQIKNWVSNRRRKEK 86

>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 Length = 60

 Score = 37.3 bits (87), Expect = 5e-05
 Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 3/56 (5%)

Query: 23 FSGEQLSRLKVEFTENR---YLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75
          F+ E +  L+  F +N    YL  +  + L     L+  QIK W  N+R K K  +
Sbjct: 5  FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTIT 60

>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* Length = 83

 Score = 37.5 bits (87), Expect = 9e-05
 Identities = 17/62 (27%), Positives = 26/62 (41%), Gaps = 3/62 (4%)

Query: 17 KRPRTAFSGEQLSRLKVEFTENR---YLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
                F+ E +  L+  F +N    YL  +  + L     L+  QIK W   +RAK K 
Sbjct: 3  PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKT 62

Query: 74 AS 75
           +
Sbjct: 63 IT 64

>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1 Length = 64

 Score = 36.9 bits (86), Expect = 1e-04
 Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 3/63 (4%)

Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENR---YLTERRRQELANELGLNEAQIKIWFQNKRAK 70
          S         + +    L   F  +    Y +E  ++ELA + G+  +Q+  WF NKR +
Sbjct: 1  SSGHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR 60

Query: 71 IKK 73
           KK
Sbjct: 61 YKK 63

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

 Score = 38.7 bits (89), Expect = 1e-04
 Identities = 12/82 (14%), Positives = 24/82 (29%), Gaps = 21/82 (25%)

Query: 12  KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANEL------------------ 53
              K +R R  +       L   +   +  ++  R+ L  E                   
Sbjct: 111 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGL 170

Query: 54  ---GLNEAQIKIWFQNKRAKIK 72
               + E ++  WF N+R +  
Sbjct: 171 GSNLVTEVRVYNWFANRRKEEA 192

>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80

 Score = 36.9 bits (84), Expect = 1e-04
 Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 4/76 (5%)

Query: 9  GKDKRSKEKRPRTAFSGEQLSRLKVEF----TENRYLTERRRQELANELGLNEAQIKIWF 64
          G    S   + RT FS   L+ LK  +    T    +   + + +A EL ++   ++ W 
Sbjct: 1  GSSGSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWI 60

Query: 65 QNKRAKIKKASGQKNP 80
           N+R K +    + + 
Sbjct: 61 GNRRRKYRLMGIEVSG 76

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

 Score = 35.9 bits (83), Expect = 2e-04
 Identities = 9/40 (22%), Positives = 21/40 (52%)

Query: 36 TENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75
             ++  E+R + L+ +L  +   I+ WF+ +R + K + 
Sbjct: 21 AITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPSG 60

>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 Length = 87

 Score = 36.3 bits (84), Expect = 2e-04
 Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 3/64 (4%)

Query: 17 KRPRTAFSGEQLSRLKVEFTENR---YLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          +R R  F+ +    L   F  +    Y +E  ++ELA + G+  +Q+  WF NKR + KK
Sbjct: 2  RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61

Query: 74 ASGQ 77
            G+
Sbjct: 62 NIGK 65

>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* Length = 73

 Score = 35.8 bits (83), Expect = 3e-04
 Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 3/64 (4%)

Query: 17 KRPRTAFSGEQLSRLKVEFTENR---YLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          +R R  F+ +    L   F  +    Y +E  ++ELA + G+  +Q+  WF NKR + KK
Sbjct: 2  RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61

Query: 74 ASGQ 77
            G+
Sbjct: 62 NIGK 65

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

 Score = 37.7 bits (86), Expect = 3e-04
 Identities = 12/82 (14%), Positives = 24/82 (29%), Gaps = 21/82 (25%)

Query: 12  KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANEL------------------ 53
              K +R R  +       L   +   +  ++  R+ L  E                   
Sbjct: 138 TNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGL 197

Query: 54  ---GLNEAQIKIWFQNKRAKIK 72
               + E ++  WF N+R +  
Sbjct: 198 GSNLVTEVRVYNWFANRRKEEA 219

>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens} Length = 89

 Score = 35.5 bits (82), Expect = 5e-04
 Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 3/68 (4%)

Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENR---YLTERRRQELANELGLNEAQIKIWFQNKRAK 70
                      E +  L+    E+R   Y +E+ +  L+ +  L+  Q+  WF N R +
Sbjct: 3  HHHHHHSHMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRR 62

Query: 71 IKKASGQK 78
          +     +K
Sbjct: 63 LLPDMLRK 70

>2ys9_A Homeobox and leucine zipper protein homez; homeodomain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 70

 Score = 35.2 bits (80), Expect = 6e-04
 Identities = 10/50 (20%), Positives = 23/50 (46%)

Query: 27 QLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
           +  L+  +  ++ L E    +L+    L+  Q+  WF ++  +  + SG
Sbjct: 17 DIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSRLPQPAEVSG 66

>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 64

 Score = 34.6 bits (79), Expect = 7e-04
 Identities = 11/48 (22%), Positives = 20/48 (41%)

Query: 26 EQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
            LS LK  +  N   +     ++A+ + L    +K WF+  +A    
Sbjct: 13 NLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS 60

>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding, transcription, nucleus, phosphoprotein, DNA bindi protein; 1.95A {Homo sapiens} Length = 67

 Score = 34.2 bits (79), Expect = 9e-04
 Identities = 14/66 (21%), Positives = 30/66 (45%), Gaps = 3/66 (4%)

Query: 20 RTAFSGEQLSRLKVEFTENR---YLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
             F     + ++    ++    Y +E ++++LA + GL   Q+  WF N R +I +   
Sbjct: 2  SGIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMI 61

Query: 77 QKNPLA 82
           ++  A
Sbjct: 62 DQSNRA 67

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	120
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.86
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.86
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.86
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.86
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.86
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.85
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.85
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.85
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.85
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.85
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.85
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.85
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.85
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.85
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.85
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.85
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.84
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.84
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.84
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.83
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.83
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.83
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.83
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.83
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.83
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.83
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.83
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.83
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.83
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.83
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.82
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.82
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.82
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.82
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.82
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.82
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.81
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.81
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.81
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.81
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.81
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.81
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.81
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.81
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.81
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.8
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.8
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.8
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.8
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.8
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.79
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.79
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.78
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.77
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.77
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.77
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.76
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.76
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.76
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.75
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.75
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.75
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.75
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.75
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.75
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.75
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.73
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.73
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.72
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.72
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.71
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.67
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.6
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.6
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.52
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.52
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.39
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.64
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	97.16
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	88.14
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	87.18
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	84.73
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	83.89
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	80.08

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

Probab=99.86  E-value=1.1e-21  Score=119.75  Aligned_cols=67  Identities=34%  Similarity=0.602  Sum_probs=62.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCC
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQK   78 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~   78 (120)
                      .+++.++.|+.|+..|+.+|+.+|..++||+..++..||..++|++.+|++||||||+++|+.....
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~~   69 (80)
T 2dms_A            3 SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQ   69 (80)
T ss_dssp             CCCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCSC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHcc
Confidence            3567788899999999999999999999999999999999999999999999999999999987653

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

Probab=99.86  E-value=2.4e-21  Score=115.35  Aligned_cols=65  Identities=35%  Similarity=0.638  Sum_probs=60.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      .++..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+...
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2dmu_A            3 SGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP   67 (70)
T ss_dssp             STTSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTST
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccCC
Confidence            34567788999999999999999999999999999999999999999999999999999998764

>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=99.86  E-value=1.6e-21  Score=116.13  Aligned_cols=65  Identities=35%  Similarity=0.646  Sum_probs=60.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      ..+..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+...
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (70)
T 2cra_A            3 SGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGP   67 (70)
T ss_dssp             SSCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSCT
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccCC
Confidence            45677888999999999999999999999999999999999999999999999999999998754

>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=99.86  E-value=1.6e-21  Score=118.91  Aligned_cols=66  Identities=33%  Similarity=0.520  Sum_probs=61.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCC
Q psy4625          13 RSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQK   78 (120)
Q Consensus        13 ~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~   78 (120)
                      .+..++.|+.|+.+|+.+|+.+|..++||+..++..||..+||++.+|++||||||+++|+.....
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~   69 (80)
T 2dmq_A            4 GSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQ   69 (80)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHHH
Confidence            456788899999999999999999999999999999999999999999999999999999986543

>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=99.86  E-value=2.3e-21  Score=115.42  Aligned_cols=67  Identities=33%  Similarity=0.476  Sum_probs=61.7

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          11 DKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        11 ~~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      ...++.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+....
T Consensus         2 ~~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (70)
T 2da2_A            2 SSGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGPS   68 (70)
T ss_dssp             CCSCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCSSC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhcccc
Confidence            3456778889999999999999999999999999999999999999999999999999999987543

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

Probab=99.85  E-value=9.8e-22  Score=119.94  Aligned_cols=65  Identities=37%  Similarity=0.630  Sum_probs=61.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      .++..++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||||||+++|+...
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   67 (80)
T 2cue_A            3 SGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK   67 (80)
T ss_dssp             SCCSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhh
Confidence            35677888999999999999999999999999999999999999999999999999999999864

>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=99.85  E-value=2.7e-21  Score=115.10  Aligned_cols=66  Identities=33%  Similarity=0.490  Sum_probs=61.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      ..++.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+....
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (70)
T 2da1_A            3 SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGPS   68 (70)
T ss_dssp             SSCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhccc
Confidence            345677889999999999999999999999999999999999999999999999999999987643

>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=99.85  E-value=7.8e-21  Score=113.17  Aligned_cols=64  Identities=38%  Similarity=0.609  Sum_probs=59.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          13 RSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        13 ~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      ....++.|++|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+...
T Consensus         4 ~~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2e1o_A            4 GSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGP   67 (70)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCCC
Confidence            4466778899999999999999999999999999999999999999999999999999998765

>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=99.85  E-value=6.7e-21  Score=116.21  Aligned_cols=65  Identities=42%  Similarity=0.689  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      ...+.++.|+.|+..|+.+|+..|..++||+..++..||..|+|++.+|++||||||+++|+...
T Consensus        13 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~~   77 (80)
T 2dmt_A           13 KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGP   77 (80)
T ss_dssp             CCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCCS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcccC
Confidence            44566788999999999999999999999999999999999999999999999999999998754

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

Probab=99.85  E-value=4.2e-21  Score=112.15  Aligned_cols=61  Identities=51%  Similarity=0.746  Sum_probs=56.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625          15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS   75 (120)
Q Consensus        15 ~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   75 (120)
                      ..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+..
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   62 (63)
T 2h1k_A            2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE   62 (63)
T ss_dssp             ---CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhhc
Confidence            4677899999999999999999999999999999999999999999999999999999864

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

Probab=99.85  E-value=3.1e-21  Score=114.90  Aligned_cols=65  Identities=48%  Similarity=0.765  Sum_probs=60.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      .++..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+...
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2djn_A            3 SGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGP   67 (70)
T ss_dssp             SCCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSSS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccCC
Confidence            45677888999999999999999999999999999999999999999999999999999988654

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

Probab=99.85  E-value=6.7e-21  Score=117.13  Aligned_cols=66  Identities=39%  Similarity=0.582  Sum_probs=61.2

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          11 DKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        11 ~~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      ....+.++.|+.|+..|+.+|+.+|..++||+..++..||..+||++.+|++||||||+++|+...
T Consensus        17 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k   82 (84)
T 2kt0_A           17 KVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK   82 (84)
T ss_dssp             CCCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhh
Confidence            345677888999999999999999999999999999999999999999999999999999998754

>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=99.85  E-value=8.9e-21  Score=114.88  Aligned_cols=66  Identities=36%  Similarity=0.612  Sum_probs=61.1

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          11 DKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        11 ~~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      +...+.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+...
T Consensus         4 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~   69 (77)
T 1nk2_P            4 GLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQN   69 (77)
T ss_dssp             CCSCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhc
Confidence            345567788999999999999999999999999999999999999999999999999999998754

>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=99.85  E-value=5.5e-21  Score=116.42  Aligned_cols=65  Identities=31%  Similarity=0.528  Sum_probs=60.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      ...+.++.|+.|+.+|+.+|+..|..++||+..++..||..|||++.+|++||||||+++|+...
T Consensus        13 ~~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   77 (80)
T 2da3_A           13 EPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSGP   77 (80)
T ss_dssp             CCCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhcc
Confidence            45667888999999999999999999999999999999999999999999999999999998764

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

Probab=99.85  E-value=3.3e-21  Score=112.26  Aligned_cols=61  Identities=41%  Similarity=0.629  Sum_probs=53.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625          14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA   74 (120)
Q Consensus        14 ~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   74 (120)
                      ++.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus         1 g~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A            1 GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             -------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            3567889999999999999999999999999999999999999999999999999999985

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

Probab=99.85  E-value=8e-21  Score=114.33  Aligned_cols=68  Identities=35%  Similarity=0.587  Sum_probs=62.6

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCC
Q psy4625          11 DKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQK   78 (120)
Q Consensus        11 ~~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~   78 (120)
                      ...++.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+.....
T Consensus         4 ~~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r~~   71 (75)
T 2m0c_A            4 SNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRERFG   71 (75)
T ss_dssp             CCCSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCCCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHhhh
Confidence            34567788899999999999999999999999999999999999999999999999999999986653

>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=99.84  E-value=1.1e-20  Score=114.40  Aligned_cols=66  Identities=41%  Similarity=0.604  Sum_probs=61.4

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          11 DKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        11 ~~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      ...+..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+...
T Consensus         8 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k   73 (77)
T 1puf_A            8 LHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINK   73 (77)
T ss_dssp             CCCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhh
Confidence            445677888999999999999999999999999999999999999999999999999999998754

>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=99.84  E-value=9.9e-21  Score=109.86  Aligned_cols=58  Identities=86%  Similarity=1.248  Sum_probs=53.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625          16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK   73 (120)
Q Consensus        16 ~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   73 (120)
                      .++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            4678999999999999999999999999999999999999999999999999999986

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

Probab=99.84  E-value=1.7e-20  Score=107.78  Aligned_cols=57  Identities=46%  Similarity=0.828  Sum_probs=55.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625          17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK   73 (120)
Q Consensus        17 rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   73 (120)
                      ++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr   57 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhcc
Confidence            467899999999999999999999999999999999999999999999999999986

>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=99.83  E-value=6e-21  Score=113.06  Aligned_cols=65  Identities=37%  Similarity=0.644  Sum_probs=60.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCC
Q psy4625          14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQK   78 (120)
Q Consensus        14 ~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~   78 (120)
                      |+.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+.....
T Consensus         1 g~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~~~   65 (68)
T 1yz8_P            1 GSQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEFI   65 (68)
T ss_dssp             CCSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhhcc
Confidence            35678899999999999999999999999999999999999999999999999999999987643

>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=99.83  E-value=1.5e-20  Score=111.37  Aligned_cols=64  Identities=52%  Similarity=0.736  Sum_probs=59.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCC
Q psy4625          16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKN   79 (120)
Q Consensus        16 ~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~   79 (120)
                      .++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+......
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~~~~   65 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTKG   65 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSCCCS
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhccccC
Confidence            4678999999999999999999999999999999999999999999999999999999876543

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

Probab=99.83  E-value=5e-20  Score=115.34  Aligned_cols=68  Identities=35%  Similarity=0.691  Sum_probs=62.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCC
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKN   79 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~   79 (120)
                      ...+.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+......
T Consensus        13 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~   80 (93)
T 3a01_A           13 TPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEER   80 (93)
T ss_dssp             CCCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC-
T ss_pred             CCCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHHH
Confidence            45567788999999999999999999999999999999999999999999999999999999876543

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

Probab=99.83  E-value=1.7e-20  Score=111.08  Aligned_cols=63  Identities=41%  Similarity=0.722  Sum_probs=59.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCC
Q psy4625          16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQK   78 (120)
Q Consensus        16 ~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~   78 (120)
                      .++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+.....
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~~   64 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQH   64 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhccc
Confidence            467899999999999999999999999999999999999999999999999999999986543

>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=99.83  E-value=1.5e-20  Score=114.76  Aligned_cols=62  Identities=23%  Similarity=0.330  Sum_probs=58.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTE----NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK   73 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~----~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   73 (120)
                      ..++.++.|+.|+.+|+..|+.+|..    ++||+..++..||..|||++.+|++||||||+|+++
T Consensus        13 ~~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           13 GGGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            44567888999999999999999999    999999999999999999999999999999999774

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

Probab=99.83  E-value=1.5e-20  Score=116.58  Aligned_cols=66  Identities=50%  Similarity=0.725  Sum_probs=55.5

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625          10 KDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS   75 (120)
Q Consensus        10 ~~~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   75 (120)
                      ....+..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+..
T Consensus        22 ~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   87 (88)
T 2r5y_A           22 VNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH   87 (88)
T ss_dssp             ---------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhhc
Confidence            345667788999999999999999999999999999999999999999999999999999999864

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

Probab=99.83  E-value=3.7e-20  Score=109.68  Aligned_cols=63  Identities=37%  Similarity=0.665  Sum_probs=59.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCC
Q psy4625          16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQK   78 (120)
Q Consensus        16 ~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~   78 (120)
                      .++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+.....
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~~~   64 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDK   64 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhhHh
Confidence            467899999999999999999999999999999999999999999999999999999987654

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

Probab=99.83  E-value=2.5e-20  Score=111.84  Aligned_cols=64  Identities=31%  Similarity=0.631  Sum_probs=59.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        14 ~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      .+.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+....
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~   68 (73)
T 2l7z_A            5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINK   68 (73)
T ss_dssp             SCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSSSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHhcc
Confidence            3567789999999999999999999999999999999999999999999999999999988654

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

Probab=99.83  E-value=1.5e-20  Score=114.68  Aligned_cols=64  Identities=23%  Similarity=0.389  Sum_probs=60.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhC----CCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTEN----RYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS   75 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~----~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   75 (120)
                      ..++.++.|+.|+.+|+.+|+.+|..+    +||+..++..||..+||++.+|++||||||+++|+..
T Consensus         4 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~~   71 (80)
T 2da4_A            4 GSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMG   71 (80)
T ss_dssp             CCCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhcc
Confidence            456778889999999999999999999    9999999999999999999999999999999999864

>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=99.83  E-value=1.6e-20  Score=110.60  Aligned_cols=62  Identities=35%  Similarity=0.500  Sum_probs=58.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        15 ~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      +.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+...
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   63 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI   63 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHHhh
Confidence            35778999999999999999999999999999999999999999999999999999988653

>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=99.83  E-value=3.6e-20  Score=113.15  Aligned_cols=64  Identities=41%  Similarity=0.716  Sum_probs=58.8

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS   75 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   75 (120)
                      ..++.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+..
T Consensus        14 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~   77 (81)
T 1fjl_A           14 LKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH   77 (81)
T ss_dssp             ---CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhc
Confidence            3556788899999999999999999999999999999999999999999999999999999875

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

Probab=99.82  E-value=3.5e-20  Score=107.17  Aligned_cols=58  Identities=50%  Similarity=0.813  Sum_probs=55.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625          17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA   74 (120)
Q Consensus        17 rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   74 (120)
                      ++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||+|+++|+.
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   59 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHhHhhcc
Confidence            5779999999999999999999999999999999999999999999999999999874

>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=99.82  E-value=2.5e-20  Score=113.96  Aligned_cols=64  Identities=47%  Similarity=0.722  Sum_probs=54.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS   75 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   75 (120)
                      ..+..++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+..
T Consensus        16 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   79 (81)
T 1b8i_A           16 TNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEI   79 (81)
T ss_dssp             --------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhc
Confidence            4456778899999999999999999999999999999999999999999999999999999864

>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=99.82  E-value=2.1e-20  Score=108.43  Aligned_cols=60  Identities=25%  Similarity=0.526  Sum_probs=48.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHH
Q psy4625          13 RSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK   72 (120)
Q Consensus        13 ~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k   72 (120)
                      .++.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|||+++|
T Consensus         2 k~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            2 KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             ----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            356778899999999999999999999999999999999999999999999999999875

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

Probab=99.82  E-value=4.2e-20  Score=109.06  Aligned_cols=62  Identities=40%  Similarity=0.652  Sum_probs=58.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        16 ~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      .++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+....
T Consensus         1 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~~   62 (67)
T 2k40_A            1 GRRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRE   62 (67)
T ss_dssp             CCCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCCT
T ss_pred             CcCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhchh
Confidence            36789999999999999999999999999999999999999999999999999999987654

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

Probab=99.82  E-value=3e-20  Score=116.75  Aligned_cols=66  Identities=29%  Similarity=0.511  Sum_probs=62.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhC---------------CChhhHHHHHHHHHhHHHHhhc
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELG---------------LNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~---------------l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      ...+.++.|+.|+..|+.+|+..|..++||+..++..||..|+               |++.+|++||||||+++|+...
T Consensus         3 ~~~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~   82 (95)
T 2cuf_A            3 SGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRAN   82 (95)
T ss_dssp             SSSCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhh
Confidence            3557788999999999999999999999999999999999999               9999999999999999999876


Q ss_pred             C
Q psy4625          77 Q   77 (120)
Q Consensus        77 ~   77 (120)
                      .
T Consensus        83 ~   83 (95)
T 2cuf_A           83 I   83 (95)
T ss_dssp             C
T ss_pred             c
Confidence            5

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

Probab=99.82  E-value=5.8e-20  Score=105.32  Aligned_cols=57  Identities=44%  Similarity=0.761  Sum_probs=54.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHH
Q psy4625          16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK   72 (120)
Q Consensus        16 ~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k   72 (120)
                      .++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|
T Consensus         2 ~rr~Rt~~t~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~k   58 (58)
T 3rkq_A            2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK   58 (58)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHC
T ss_pred             cCCCCCCcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhhccCC
Confidence            456789999999999999999999999999999999999999999999999999875

>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=99.81  E-value=6e-20  Score=115.77  Aligned_cols=66  Identities=45%  Similarity=0.673  Sum_probs=57.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      +.+..++.|+.|+..|+.+|+..|..++||+..++..||..|||++.+|++||||||+++|+....
T Consensus        30 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~   95 (97)
T 1b72_A           30 GLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE   95 (97)
T ss_dssp             -------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhcc
Confidence            446778889999999999999999999999999999999999999999999999999999998654

>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=99.81  E-value=7.6e-20  Score=110.18  Aligned_cols=59  Identities=25%  Similarity=0.349  Sum_probs=55.3

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          19 PRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        19 ~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      .|..|+.+|+.+|+..|..++||+..++..||..+||++.+|++||||+|+++|+....
T Consensus         6 ~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~l~   64 (76)
T 2ecc_A            6 SGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLK   64 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCCS
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHHHH
Confidence            45679999999999999999999999999999999999999999999999999988654

>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=99.81  E-value=1.9e-19  Score=107.95  Aligned_cols=66  Identities=21%  Similarity=0.349  Sum_probs=60.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTE---NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      .+++.++.|+.|+..|+.+|+..|..   ++||+..++..||..+||++.+|++||+|+|+++++....
T Consensus         3 ~~~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~   71 (73)
T 1x2n_A            3 SGSSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSGPS   71 (73)
T ss_dssp             CCSSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhccccccc
Confidence            35567788999999999999999987   9999999999999999999999999999999999987643

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

Probab=99.81  E-value=5.8e-20  Score=106.24  Aligned_cols=57  Identities=40%  Similarity=0.686  Sum_probs=50.6

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625          19 PRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS   75 (120)
Q Consensus        19 ~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   75 (120)
                      .|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+..
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~   58 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE   58 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC---
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhc
Confidence            578999999999999999999999999999999999999999999999999999864

>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=99.81  E-value=1.5e-19  Score=108.14  Aligned_cols=61  Identities=23%  Similarity=0.412  Sum_probs=57.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          17 KRPRTAFSGEQLSRLKVEFTE-NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        17 rr~R~~~~~~q~~~L~~~F~~-~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      .+.|+.|+..|+.+|+..|.. ++||+..++..||..+||++.+|++||||||+++|+....
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~~~   63 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGL   63 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhccC
Confidence            356899999999999999996 9999999999999999999999999999999999998743

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

Probab=99.81  E-value=3.8e-20  Score=112.92  Aligned_cols=61  Identities=25%  Similarity=0.414  Sum_probs=56.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh-----CCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTE-----NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK   73 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~-----~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   73 (120)
                      ...+.+|.||.|+.+|+..|+ .|..     ++||+..++..||..++|++.+|++||||||+++++
T Consensus        13 ~~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           13 SGGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            455678889999999999999 7999     999999999999999999999999999999999875

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

Probab=99.81  E-value=8.4e-20  Score=110.32  Aligned_cols=63  Identities=25%  Similarity=0.433  Sum_probs=58.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        15 ~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      .....|++|+.+|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+....
T Consensus         7 ~~~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~~   69 (76)
T 2dn0_A            7 GASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGS   69 (76)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCSS
T ss_pred             CCCCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhccc
Confidence            444568999999999999999999999999999999999999999999999999999987654

>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=99.81  E-value=1.5e-19  Score=108.94  Aligned_cols=60  Identities=22%  Similarity=0.382  Sum_probs=56.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        18 r~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      +.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+....
T Consensus         9 ~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~~   68 (75)
T 2da5_A            9 TKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETK   68 (75)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSCS
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhhc
Confidence            456779999999999999999999999999999999999999999999999999998654

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

Probab=99.81  E-value=1.9e-19  Score=107.94  Aligned_cols=61  Identities=23%  Similarity=0.391  Sum_probs=57.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          17 KRPRTAFSGEQLSRLKVEFTE-NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        17 rr~R~~~~~~q~~~L~~~F~~-~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      ++.|+.|+..|+.+|+..|.. ++||+..++..||..+||++.+|++||||||+++|+....
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~~~   64 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGL   64 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhccC
Confidence            456899999999999999995 9999999999999999999999999999999999998753

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

Probab=99.80  E-value=1.3e-19  Score=103.48  Aligned_cols=54  Identities=39%  Similarity=0.704  Sum_probs=51.0

Q ss_pred             CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625          21 TAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA   74 (120)
Q Consensus        21 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   74 (120)
                      |.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~   55 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ   55 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhhccc
Confidence            679999999999999999999999999999999999999999999999999985

>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=99.80  E-value=1.9e-19  Score=105.37  Aligned_cols=61  Identities=28%  Similarity=0.347  Sum_probs=56.8

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHH
Q psy4625          11 DKRSKEKRPRTAFSGEQLSRLKVEFTE-NRYLTERRRQELANELGLNEAQIKIWFQNKRAKI   71 (120)
Q Consensus        11 ~~~~~~rr~R~~~~~~q~~~L~~~F~~-~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~   71 (120)
                      .+.+.++|.||.|+.+|+.+|+.+|+. ++||+...++.||.++||++++|++||||+|.-.
T Consensus         2 ~~~~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~~   63 (71)
T 1wi3_A            2 SSGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHV   63 (71)
T ss_dssp             CCCCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceeee
Confidence            345678899999999999999999999 9999999999999999999999999999999753

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

Probab=99.80  E-value=1.3e-19  Score=114.10  Aligned_cols=65  Identities=26%  Similarity=0.373  Sum_probs=56.3

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625          11 DKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS   75 (120)
Q Consensus        11 ~~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   75 (120)
                      ......++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+..
T Consensus        20 ~~~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   84 (96)
T 3nar_A           20 APKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGN   84 (96)
T ss_dssp             -------CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTC
T ss_pred             CCCCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhc
Confidence            34555667899999999999999999999999999999999999999999999999999999875

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

Probab=99.80  E-value=2.2e-19  Score=107.81  Aligned_cols=62  Identities=26%  Similarity=0.433  Sum_probs=58.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        16 ~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      .++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+....
T Consensus         6 ~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~   67 (74)
T 2ly9_A            6 SFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKSN   67 (74)
T ss_dssp             CCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTTCS
T ss_pred             CCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhCcC
Confidence            45678999999999999999999999999999999999999999999999999999987654

>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=99.80  E-value=3.5e-19  Score=106.75  Aligned_cols=63  Identities=33%  Similarity=0.557  Sum_probs=59.0

Q ss_pred             CCCCCCCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCC
Q psy4625          17 KRPRTAFSGEQLSRLKVEF---TENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKN   79 (120)
Q Consensus        17 rr~R~~~~~~q~~~L~~~F---~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~   79 (120)
                      ++.|+.|+..|+.+|+..|   ..++||+..++..||..+||++.+|++||+|+|+++|+......
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~~~   67 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQ   67 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTTTT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccccccccc
Confidence            6778999999999999999   89999999999999999999999999999999999998876544

>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=99.79  E-value=1.8e-19  Score=111.41  Aligned_cols=62  Identities=34%  Similarity=0.562  Sum_probs=57.8

Q ss_pred             CCCCCCCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCC
Q psy4625          17 KRPRTAFSGEQLSRLKVEF---TENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQK   78 (120)
Q Consensus        17 rr~R~~~~~~q~~~L~~~F---~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~   78 (120)
                      ++.|+.|+..|+.+|+..|   ..++||+..++..||..+||++.+|++||+|+|+++|+.....
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~   66 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKF   66 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGGG
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhccccc
Confidence            5778999999999999999   8999999999999999999999999999999999999987554

>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=99.79  E-value=4.1e-19  Score=109.00  Aligned_cols=66  Identities=26%  Similarity=0.347  Sum_probs=59.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCC
Q psy4625          13 RSKEKRPRTAFSGEQLSRLKVEFTE---NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQK   78 (120)
Q Consensus        13 ~~~~rr~R~~~~~~q~~~L~~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~   78 (120)
                      ..+.++.|+.|+..|+.+|+..|..   ++||+..++..||..+||++.+|++||+|+|.++++.....
T Consensus         4 ~~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~~~   72 (83)
T 2dmn_A            4 GSSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQ   72 (83)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHTCC
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHHHh
Confidence            4567778999999999999999987   59999999999999999999999999999999999876543

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

Probab=99.78  E-value=2.3e-19  Score=104.93  Aligned_cols=59  Identities=29%  Similarity=0.455  Sum_probs=55.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625          15 KEKRPRTAFSGEQLSRLKVEF---TENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK   73 (120)
Q Consensus        15 ~~rr~R~~~~~~q~~~L~~~F---~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   73 (120)
                      ..++.|+.|+..|+.+|+..|   ..++||+..++..||..+||++.+|++||+|+|+++|+
T Consensus         2 ~~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A            2 SGHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             CCCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            356778999999999999999   89999999999999999999999999999999999875

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

Probab=99.77  E-value=1.7e-18  Score=107.45  Aligned_cols=58  Identities=22%  Similarity=0.363  Sum_probs=54.4

Q ss_pred             CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCCC
Q psy4625          22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKN   79 (120)
Q Consensus        22 ~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~   79 (120)
                      .|+.+|+.+|+..|..++||+..++..||..|||++.+|++||||||+++++......
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~~~~   74 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKME   74 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCCC
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHHHhh
Confidence            7999999999999999999999999999999999999999999999999998765433

>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=99.77  E-value=1.3e-18  Score=100.52  Aligned_cols=55  Identities=31%  Similarity=0.475  Sum_probs=52.8

Q ss_pred             CCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625          20 RTAFSGEQLSRLKVEFTE---NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA   74 (120)
Q Consensus        20 R~~~~~~q~~~L~~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   74 (120)
                      |+.|+..|+.+|+..|..   ++||+..++..||..+||++.+|++||+|+|+++|+.
T Consensus         2 r~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A            2 GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             cCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            678999999999999999   9999999999999999999999999999999999864

>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=99.77  E-value=1.8e-18  Score=109.40  Aligned_cols=64  Identities=17%  Similarity=0.278  Sum_probs=59.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHh---------------------CCChhhHHHHHHHHHhHH
Q psy4625          13 RSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANEL---------------------GLNEAQIKIWFQNKRAKI   71 (120)
Q Consensus        13 ~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l---------------------~l~~~~V~~WFqNrR~k~   71 (120)
                      .++.++.|+.|++.|+.+|+..|..++||+..+++.||..|                     +|++.+|++||||||+++
T Consensus         3 ~~~~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k~   82 (102)
T 2da6_A            3 SGSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEE   82 (102)
T ss_dssp             TCCSCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHHH
Confidence            45678889999999999999999999999999999999999                     799999999999999999


Q ss_pred             HHhhc
Q psy4625          72 KKASG   76 (120)
Q Consensus        72 kk~~~   76 (120)
                      ++...
T Consensus        83 kr~~~   87 (102)
T 2da6_A           83 AFRQK   87 (102)
T ss_dssp             HHHHH
T ss_pred             HHhhH
Confidence            98754

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

Probab=99.76  E-value=6.9e-19  Score=105.33  Aligned_cols=60  Identities=22%  Similarity=0.379  Sum_probs=54.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHH-HhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625          16 EKRPRTAFSGEQLSRLKVEF-TENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS   75 (120)
Q Consensus        16 ~rr~R~~~~~~q~~~L~~~F-~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   75 (120)
                      ..+.+.+++..|+.+|+..| ..++||+..++..||..+||++.+|++||||||+++|+..
T Consensus         8 g~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~~   68 (72)
T 2cqx_A            8 GIKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSG   68 (72)
T ss_dssp             CCCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSCC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCCC
Confidence            34556678888999999999 9999999999999999999999999999999999999764

>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=99.76  E-value=2.4e-18  Score=116.30  Aligned_cols=62  Identities=29%  Similarity=0.589  Sum_probs=58.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK   73 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   73 (120)
                      ..+++++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++||
T Consensus        89 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           89 EPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             SCCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            44677888999999999999999999999999999999999999999999999999999986

>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=99.76  E-value=2.5e-18  Score=106.31  Aligned_cols=59  Identities=31%  Similarity=0.448  Sum_probs=55.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHH
Q psy4625          14 SKEKRPRTAFSGEQLSRLKVEFTE---NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK   72 (120)
Q Consensus        14 ~~~rr~R~~~~~~q~~~L~~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k   72 (120)
                      ..+++.|+.|+..|+.+|+..|..   ++||+..++..||..+||++.+|++||+|||+++|
T Consensus        25 ~~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k   86 (87)
T 1mnm_C           25 STKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK   86 (87)
T ss_dssp             ESSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcc
Confidence            455667899999999999999999   99999999999999999999999999999999987

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

Probab=99.75  E-value=3e-18  Score=100.16  Aligned_cols=52  Identities=25%  Similarity=0.512  Sum_probs=49.9

Q ss_pred             CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625          23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA   74 (120)
Q Consensus        23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   74 (120)
                      -+..|+..|+..|..++||+..++..||..+||++.+|++||||||.++|+.
T Consensus        11 ~~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg   62 (66)
T 3nau_A           11 KTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRG   62 (66)
T ss_dssp             CCHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhcc
Confidence            4689999999999999999999999999999999999999999999999975

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

Probab=99.75  E-value=1.5e-18  Score=118.82  Aligned_cols=65  Identities=22%  Similarity=0.393  Sum_probs=52.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          13 RSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        13 ~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      .++.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+....
T Consensus        96 ~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~  160 (164)
T 2xsd_C           96 QGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTPA  160 (164)
T ss_dssp             ----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC-
T ss_pred             cccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhccCC
Confidence            45677889999999999999999999999999999999999999999999999999999987653

>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=99.75  E-value=1.9e-18  Score=117.84  Aligned_cols=62  Identities=27%  Similarity=0.469  Sum_probs=54.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625          13 RSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA   74 (120)
Q Consensus        13 ~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   74 (120)
                      ..+.++.|+.|+..|+.+|+.+|..++||+..++..||..+||++.+|++||||||+++||.
T Consensus        98 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C           98 LSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            35678889999999999999999999999999999999999999999999999999999874

>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=99.75  E-value=2e-18  Score=116.09  Aligned_cols=63  Identities=24%  Similarity=0.458  Sum_probs=55.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA   74 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   74 (120)
                      ..++.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        83 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           83 ANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             ------CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            345677889999999999999999999999999999999999999999999999999999874

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

Probab=99.75  E-value=2.8e-18  Score=101.82  Aligned_cols=58  Identities=38%  Similarity=0.637  Sum_probs=54.1

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        20 R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      -..++..|+..|+..|..++||+..++..||..+||++.+|++||||||+++|+....
T Consensus         8 ~~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~~~   65 (69)
T 2l9r_A            8 HSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLS   65 (69)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSSSS
T ss_pred             CCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhhhh
Confidence            3568999999999999999999999999999999999999999999999999987654

>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=99.75  E-value=4e-18  Score=104.53  Aligned_cols=59  Identities=29%  Similarity=0.402  Sum_probs=54.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          18 RPRTAFSGEQLSRLKVEFTE---NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        18 r~R~~~~~~q~~~L~~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      +.|++|+..|+.+|+..|..   ++||+..++..||..+||++.+|++||||||+++|+...
T Consensus         4 krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~~   65 (83)
T 1le8_B            4 YRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITI   65 (83)
T ss_dssp             -CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHcccccccc
Confidence            45667999999999999999   999999999999999999999999999999999998643

>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=99.75  E-value=1.1e-17  Score=103.87  Aligned_cols=59  Identities=19%  Similarity=0.256  Sum_probs=54.5

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCC
Q psy4625          20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQK   78 (120)
Q Consensus        20 R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~   78 (120)
                      +..|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++++.....
T Consensus        17 ~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~~~   75 (89)
T 2dmp_A           17 FKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAV   75 (89)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCSCC
T ss_pred             cccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhHhh
Confidence            34599999999999999999999999999999999999999999999999999876543

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

Probab=99.73  E-value=3.6e-18  Score=107.94  Aligned_cols=64  Identities=22%  Similarity=0.384  Sum_probs=53.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHH------------------hC---CChhhHHHHHHHHHhHH
Q psy4625          13 RSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANE------------------LG---LNEAQIKIWFQNKRAKI   71 (120)
Q Consensus        13 ~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~------------------l~---l~~~~V~~WFqNrR~k~   71 (120)
                      ..+.++.|+.|+..|+.+|+..|..++||+..+++.||..                  +|   |++.+|++||||||+++
T Consensus         6 ~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k~   85 (99)
T 1lfb_A            6 TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEE   85 (99)
T ss_dssp             -------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHHH
Confidence            4467788999999999999999999999999999999999                  88   99999999999999988


Q ss_pred             HHhhc
Q psy4625          72 KKASG   76 (120)
Q Consensus        72 kk~~~   76 (120)
                      ++...
T Consensus        86 k~k~~   90 (99)
T 1lfb_A           86 AFRHK   90 (99)
T ss_dssp             SCCC-
T ss_pred             HHhch
Confidence            76654

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

Probab=99.73  E-value=1.2e-17  Score=97.81  Aligned_cols=54  Identities=20%  Similarity=0.240  Sum_probs=50.0

Q ss_pred             CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625          21 TAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA   74 (120)
Q Consensus        21 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   74 (120)
                      ..+...|+.+|+.+|..++||+..++..||..+||++.+|++||||||+|.++.
T Consensus         8 ~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~~   61 (64)
T 2e19_A            8 QPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISV   61 (64)
T ss_dssp             CCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSCS
T ss_pred             CCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCCC
Confidence            345689999999999999999999999999999999999999999999987654

>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=99.72  E-value=8.4e-18  Score=114.08  Aligned_cols=61  Identities=28%  Similarity=0.485  Sum_probs=57.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625          14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA   74 (120)
Q Consensus        14 ~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   74 (120)
                      +++++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             cCCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            5677889999999999999999999999999999999999999999999999999999874

>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=99.72  E-value=7.6e-18  Score=98.33  Aligned_cols=51  Identities=22%  Similarity=0.393  Sum_probs=46.7

Q ss_pred             HHHHHHHHHHH-HhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625          25 GEQLSRLKVEF-TENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS   75 (120)
Q Consensus        25 ~~q~~~L~~~F-~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   75 (120)
                      ..++.+||.+| ..++||+..++..||..|||+++||++||||||+++|+..
T Consensus         9 ~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~~~   60 (64)
T 1x2m_A            9 AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPSG   60 (64)
T ss_dssp             SCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCCSS
T ss_pred             chHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCCCC
Confidence            34799999999 5799999999999999999999999999999999988653

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

Probab=99.71  E-value=1.5e-17  Score=113.65  Aligned_cols=66  Identities=23%  Similarity=0.365  Sum_probs=54.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      ...+.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+++|+....
T Consensus        93 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~~  158 (164)
T 2d5v_A           93 RGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWLE  158 (164)
T ss_dssp             -------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC---
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccCCC
Confidence            445678889999999999999999999999999999999999999999999999999998876543

>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=99.67  E-value=1.5e-16  Score=93.87  Aligned_cols=56  Identities=23%  Similarity=0.408  Sum_probs=50.4

Q ss_pred             CCCHHHHHHHHHHHH---hCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          22 AFSGEQLSRLKVEFT---ENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        22 ~~~~~q~~~L~~~F~---~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      .|+.+++.+|+..|.   .++||+..++..||..+||+..+|++||+|+|.++++....
T Consensus         4 ~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~   62 (67)
T 3k2a_A            4 IFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMID   62 (67)
T ss_dssp             --CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC--
T ss_pred             cCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHHH
Confidence            689999999999999   99999999999999999999999999999999999986543

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

Probab=99.60  E-value=4.4e-16  Score=108.93  Aligned_cols=61  Identities=20%  Similarity=0.349  Sum_probs=53.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhC---------------------CChhhHHHHHHHHHhHH
Q psy4625          13 RSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELG---------------------LNEAQIKIWFQNKRAKI   71 (120)
Q Consensus        13 ~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~---------------------l~~~~V~~WFqNrR~k~   71 (120)
                      ..+.||.|+.|+..|+.+|+..|..++||+..+++.||..|+                     |++.+|++||||||++.
T Consensus       112 ~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~~  191 (194)
T 1ic8_A          112 TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEE  191 (194)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHHC
T ss_pred             cccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhhh
Confidence            356788999999999999999999999999999999999999                     99999999999999986


Q ss_pred             HH
Q psy4625          72 KK   73 (120)
Q Consensus        72 kk   73 (120)
                      +.
T Consensus       192 k~  193 (194)
T 1ic8_A          192 AF  193 (194)
T ss_dssp             C-
T ss_pred             hc
Confidence            53

>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=99.60  E-value=2.2e-15  Score=88.59  Aligned_cols=46  Identities=20%  Similarity=0.376  Sum_probs=44.2

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhH
Q psy4625          25 GEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAK   70 (120)
Q Consensus        25 ~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k   70 (120)
                      .+|+.+|+.+|..+++|+..++..||..+||..++|++||||||+.
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~   59 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVY   59 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhcccc
Confidence            5789999999999999999999999999999999999999999974

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

Probab=99.52  E-value=1.9e-14  Score=102.02  Aligned_cols=59  Identities=20%  Similarity=0.385  Sum_probs=52.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhC---------------------CChhhHHHHHHHHHhHH
Q psy4625          13 RSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELG---------------------LNEAQIKIWFQNKRAKI   71 (120)
Q Consensus        13 ~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~---------------------l~~~~V~~WFqNrR~k~   71 (120)
                      ..+.||.|+.|++.|+.+|+..|..++||+..+++.||..|+                     |++.+|++||+|||+..
T Consensus       139 ~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~~~  218 (221)
T 2h8r_A          139 NKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEE  218 (221)
T ss_dssp             ---CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHTTC
T ss_pred             cCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhhhh
Confidence            456788899999999999999999999999999999999987                     89999999999999863

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

Probab=99.52  E-value=3.8e-14  Score=87.47  Aligned_cols=55  Identities=24%  Similarity=0.358  Sum_probs=51.5

Q ss_pred             CCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625          21 TAFSGEQLSRLKVEFTE---NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS   75 (120)
Q Consensus        21 ~~~~~~q~~~L~~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   75 (120)
                      ..|+.++..+|+..|..   ++||+..++..||..+||++.||.+||+|+|.+.++..
T Consensus        10 ~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~   67 (89)
T 2lk2_A           10 HMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDM   67 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHH
Confidence            35899999999999987   99999999999999999999999999999999998764

>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=99.39  E-value=2.9e-13  Score=102.47  Aligned_cols=54  Identities=28%  Similarity=0.529  Sum_probs=50.9

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHH
Q psy4625          19 PRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK   72 (120)
Q Consensus        19 ~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k   72 (120)
                      -++.++..|+..|+..|+.++||+..++..||..+||+++||++||||||.|+|
T Consensus       368 ~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          368 AAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            356789999999999999999999999999999999999999999999999865

>2nzz_A Penetratin conjugated GAS (374-394) peptide; conformational analysis, G protein, GAS subunit, A2A adenosine receptor, cell-penetrating peptides; NMR {Synthetic} PDB: 2o00_A

Probab=98.64  E-value=2.9e-10  Score=58.89  Aligned_cols=20  Identities=60%  Similarity=0.823  Sum_probs=17.7

Q ss_pred             hhHHHHHHHHHhHHHHhhcC
Q psy4625          58 AQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        58 ~~V~~WFqNrR~k~kk~~~~   77 (120)
                      +||+|||||||+|+|+....
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~   20 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFN   20 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHH
T ss_pred             CCceeccHHHHHHHHHHhHH
Confidence            48999999999999998764

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

Probab=97.16  E-value=0.0008  Score=39.12  Aligned_cols=43  Identities=19%  Similarity=0.336  Sum_probs=38.9

Q ss_pred             CHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHH
Q psy4625          24 SGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQN   66 (120)
Q Consensus        24 ~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqN   66 (120)
                      ++.-..+|+.+|.............|+.+.+|+..+|+-||-.
T Consensus        14 ~p~~~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~   56 (70)
T 2ys9_A           14 PPPDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDS   56 (70)
T ss_dssp             CCCCCHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCCcchHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHh
Confidence            3444689999999999999999999999999999999999964

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

Probab=88.14  E-value=1  Score=24.30  Aligned_cols=46  Identities=15%  Similarity=0.286  Sum_probs=31.4

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHH
Q psy4625          20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQN   66 (120)
Q Consensus        20 R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqN   66 (120)
                      +..|+.++...+...+... .........+|..+|++...|..|...
T Consensus         3 r~~ys~efK~~~~~~~~~g-~s~~~~~~~vA~~~gIs~~tl~~W~~~   48 (59)
T 2glo_A            3 RRIFTPHFKLQVLESYRND-NDCKGNQRATARKYNIHRRQIQKWLQC   48 (59)
T ss_dssp             CCCCCHHHHHHHHHHHHHC-TTTTTCHHHHHHHTTSCHHHHHHHHTT
T ss_pred             CCcCCHHHHHHHHHHHHcC-CCcchHHHHHHHHHCcCHHHHHHHHHH
Confidence            4568888866665555433 221223568899999999999999753

>1hlv_A CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} SCOP: a.4.1.7 a.4.1.7 PDB: 1bw6_A

Probab=87.18  E-value=3.2  Score=25.66  Aligned_cols=49  Identities=27%  Similarity=0.340  Sum_probs=37.5

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhH
Q psy4625          19 PRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAK   70 (120)
Q Consensus        19 ~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k   70 (120)
                      .|..++.++...+...+..++....   ..+|..+|++...|..|..++...
T Consensus         4 ~r~~~t~e~K~~iv~~~~~~g~~~~---~~~A~~~gvs~stl~~~~~~~~~~   52 (131)
T 1hlv_A            4 KRRQLTFREKSRIIQEVEENPDLRK---GEIARRFNIPPSTLSTILKNKRAI   52 (131)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSCH---HHHHHHHTCCHHHHHHHHHTHHHH
T ss_pred             cceeCCHHHHHHHHHHHHHCCCCcH---HHHHHHhCCCHHHHHHHHhchhhh
Confidence            4678999998777777755555543   357889999999999999876654

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

Probab=84.73  E-value=3.4  Score=24.12  Aligned_cols=48  Identities=15%  Similarity=0.288  Sum_probs=35.3

Q ss_pred             CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625          23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS   75 (120)
Q Consensus        23 ~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   75 (120)
                      ++..+..+|...|-...     ....+|..+|++...|+.+...-+.+.++..
T Consensus        38 L~~~~r~vl~l~~~~g~-----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l   85 (92)
T 3hug_A           38 LSAEHRAVIQRSYYRGW-----STAQIATDLGIAEGTVKSRLHYAVRALRLTL   85 (92)
T ss_dssp             SCHHHHHHHHHHHTSCC-----CHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            56667777766553332     3567899999999999999988777776653

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=83.89  E-value=4.6  Score=23.45  Aligned_cols=44  Identities=16%  Similarity=0.385  Sum_probs=31.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHH
Q psy4625          18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQN   66 (120)
Q Consensus        18 r~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqN   66 (120)
                      +.+..|+.++.......+.. ..    ....+|..+|++...|..|...
T Consensus        18 ~~~~~ys~e~k~~~v~~~~~-g~----s~~~iA~~~gIs~sTl~rW~k~   61 (87)
T 2elh_A           18 RPLRSLTPRDKIHAIQRIHD-GE----SKASVARDIGVPESTLRGWCKN   61 (87)
T ss_dssp             SCCSSCCHHHHHHHHHHHHH-TC----CHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHC-CC----CHHHHHHHHCcCHHHHHHHHHH
Confidence            34567888886555555543 22    2557899999999999999853

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=80.08  E-value=3.9  Score=20.09  Aligned_cols=39  Identities=18%  Similarity=0.294  Sum_probs=27.6

Q ss_pred             CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHH
Q psy4625          22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQ   65 (120)
Q Consensus        22 ~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFq   65 (120)
                      .++..+...+...+... +    ....+|..+|++...|..|..
T Consensus         5 ~l~~~~~~~i~~~~~~g-~----s~~~IA~~lgis~~Tv~~~~~   43 (51)
T 1tc3_C            5 ALSDTERAQLDVMKLLN-V----SLHEMSRKISRSRHCIRVYLK   43 (51)
T ss_dssp             CCCHHHHHHHHHHHHTT-C----CHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcC-C----CHHHHHHHHCcCHHHHHHHHh
Confidence            46677665555555433 2    255789999999999999985

---

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	120
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	2e-18
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	2e-18
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	4e-18
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	4e-18
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	5e-18
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	8e-18
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	2e-17
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	7e-17
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	3e-16
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	5e-16
d1bw5a_	66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	6e-16
d1fjla_	65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	1e-15
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	2e-15
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	7e-15
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	9e-15
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	2e-14
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	4e-14
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	4e-14
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	5e-14
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	5e-13
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	9e-13
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	1e-12
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	1e-12
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	2e-12
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	2e-12
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	2e-12
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	5e-12
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	9e-12
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	3e-11
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	4e-08
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	4e-08
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	2e-06

>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 = 71.0 bits (174), Expect = 2e-18
 Identities = 24/63 (38%), Positives = 39/63 (61%)

Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
          +R RT+F+ EQ+  L+ EF    Y     R+ LA ++ L EA+I++WF N+RAK ++   
Sbjct: 2  QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 61

Query: 77 QKN 79
           +N
Sbjct: 62 LRN 64

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

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

 Score = 71.4 bits (175), Expect = 2e-18
 Identities = 27/68 (39%), Positives = 38/68 (55%)

Query: 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71
               ++ R  ++  Q   L+ EF  N YLT  RR E+A  L L E Q+KIWFQN+R K+
Sbjct: 9  HARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKM 68

Query: 72 KKASGQKN 79
          KK +  + 
Sbjct: 69 KKINKDRA 76

>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 = 70.2 bits (172), Expect = 4e-18
 Identities = 30/56 (53%), Positives = 37/56 (66%)

Query: 20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75
          R  ++  Q   L+ EF  NRYLT RRR E+A+ L L E QIKIWFQN+R K KK +
Sbjct: 1  RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 56

>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 = 70.2 bits (172), Expect = 4e-18
 Identities = 23/57 (40%), Positives = 35/57 (61%)

Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          K  +  FS +Q   L+ +F   +YL+   R+ LA  L L+E Q+K WFQN+RAK ++
Sbjct: 1  KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 57

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

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

 Score = 69.5 bits (170), Expect = 5e-18
 Identities = 45/53 (84%), Positives = 49/53 (92%)

Query: 18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAK 70
          RPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQIKIWFQN RAK
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>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 = 70.0 bits (171), Expect = 8e-18
 Identities = 31/71 (43%), Positives = 41/71 (57%)

Query: 3  SRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKI 62
           +  K  +         RT F+  QL+ L+ EF  N+YL+  RR E+A  L LNE Q+KI
Sbjct: 14 PKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKI 73

Query: 63 WFQNKRAKIKK 73
          WFQN+R K KK
Sbjct: 74 WFQNRRMKQKK 84

>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 = 68.4 bits (167), Expect = 2e-17
 Identities = 22/57 (38%), Positives = 38/57 (66%)

Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          ++ R  +S  QL  L+ E+  N+++T+ +R++++    L+E QI IWFQN+R K KK
Sbjct: 2  RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 58

>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 = 66.8 bits (163), Expect = 7e-17
 Identities = 14/50 (28%), Positives = 25/50 (50%)

Query: 19 PRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR 68
          PR  F+  Q   L   F EN+  ++  +  ++ +LGL  + +  +F N R
Sbjct: 1  PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57

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

 Score = 65.3 bits (159), Expect = 3e-16
 Identities = 29/56 (51%), Positives = 40/56 (71%)

Query: 18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          R RTAF+ +QL RL+ EF +  Y++  RR ELA +L L E+ IK+WFQN+R K K+
Sbjct: 1  RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 56

>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 = 64.6 bits (157), Expect = 5e-16
 Identities = 26/57 (45%), Positives = 39/57 (68%)

Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          ++PRT F+  QL  L+ +F + +YL+   R E ++ L L E Q+KIWFQN+RAK K+
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

>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 = 64.9 bits (158), Expect = 6e-16
 Identities = 22/61 (36%), Positives = 32/61 (52%)

Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
          K  R RT  + +QL  L+  +  N       +++L    GL+   I++WFQNKR K KK 
Sbjct: 2  KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61

Query: 75 S 75
          S
Sbjct: 62 S 62

>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 = 64.2 bits (156), Expect = 1e-15
 Identities = 26/59 (44%), Positives = 38/59 (64%)

Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          K++R RT FS  QL  L+  F   +Y     R+ELA    L EA+I++WFQN+RA+++K
Sbjct: 1  KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK 59

>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 = 63.4 bits (154), Expect = 2e-15
 Identities = 26/62 (41%), Positives = 39/62 (62%)

Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
          +R RT F+  Q++ L+  F + RYLT  R  +L+ +L L  AQ+KIWF+N+R + K  S 
Sbjct: 2  RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 61

Query: 77 QK 78
          Q 
Sbjct: 62 QH 63

>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 = 61.7 bits (150), Expect = 7e-15
 Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 3/60 (5%)

Query: 17 KRPRTAFSGEQLSRLKVEFTE---NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          K  R        + ++    +   + Y TE  ++++A +  L   Q+  WF N R +I +
Sbjct: 3  KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQ 62

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

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

 Score = 61.5 bits (149), Expect = 9e-15
 Identities = 24/57 (42%), Positives = 38/57 (66%)

Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          +R RT F+ +QL +L+  F  NRY     R+E+A    L EA++++WF+N+RAK +K
Sbjct: 2  RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 58

>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 = 60.8 bits (147), Expect = 2e-14
 Identities = 25/67 (37%), Positives = 39/67 (58%)

Query: 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71
            +K+++ R  F+  Q   L+  F + RYL+   R+ LA+ + L   Q+KIWFQN R K 
Sbjct: 5  LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKT 64

Query: 72 KKASGQK 78
          K+A  +K
Sbjct: 65 KRAQNEK 71

>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 = 59.9 bits (145), Expect = 4e-14
 Identities = 14/53 (26%), Positives = 31/53 (58%)

Query: 20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK 72
          +++ S +  + L+  F   + L  + ++E+A + G+   Q+++WF NKR + K
Sbjct: 1  KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 68

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

 Score = 60.3 bits (146), Expect = 4e-14
 Identities = 23/62 (37%), Positives = 37/62 (59%)

Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
          ++ R  FS  Q+  L+  F + +YL+   R+ LA+ + L   Q+KIWFQN R K+K+ + 
Sbjct: 3  RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62

Query: 77 QK 78
           K
Sbjct: 63 DK 64

>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 = 59.5 bits (144), Expect = 5e-14
 Identities = 15/56 (26%), Positives = 28/56 (50%)

Query: 18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          + RT  S      L+  F E+   + +    +A EL L +  +++WF N+R + K+
Sbjct: 1  KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 56

>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 = 57.7 bits (139), Expect = 5e-13
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 3/64 (4%)

Query: 17 KRPRTAFSGEQLSRLKVEFTE---NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          +R R  F+ +    L   F     N Y +E  ++ELA + G+  +Q+  WF NKR + KK
Sbjct: 2  RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61

Query: 74 ASGQ 77
            G+
Sbjct: 62 NIGK 65

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 67

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

 Score = 56.6 bits (136), Expect = 9e-13
 Identities = 18/61 (29%), Positives = 33/61 (54%)

Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
            KR RT+        L+  F +    + ++   +AN+LGL +  +++WF N+R K K++
Sbjct: 7  ARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS 66

Query: 75 S 75
          S
Sbjct: 67 S 67

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 52

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

 Score = 55.9 bits (135), Expect = 1e-12
 Identities = 12/51 (23%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 24 SGEQLSRLKVEFTE-NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          + +  + L+  FT   ++  E+R + L+ +L  +   I+ WF+ +R + K 
Sbjct: 1  TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 51

>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 = 56.6 bits (136), Expect = 1e-12
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 15/74 (20%)

Query: 18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANE---------------LGLNEAQIKI 62
            R  +  E L+ ++  F EN+Y  E +R+E+AN                  +   ++  
Sbjct: 2  GSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYN 61

Query: 63 WFQNKRAKIKKASG 76
          WF N+R +IK+ + 
Sbjct: 62 WFANRRKEIKRRAN 75

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 60

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

 Score = 55.9 bits (135), Expect = 2e-12
 Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 3/56 (5%)

Query: 23 FSGEQLSRLKVEFTENR---YLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75
          F+ E +  L+  F +N    YL  +  + L     L+  QIK W  N+R K K  +
Sbjct: 5  FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTIT 60

>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 = 56.2 bits (135), Expect = 2e-12
 Identities = 14/61 (22%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 17 KRPRTAFSGEQLSRLKVEF-TENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75
                 + +Q+  L+  F   N++        +A E GL E Q + WF+ + A+ +++ 
Sbjct: 2  SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 61

Query: 76 G 76
          G
Sbjct: 62 G 62

>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 = 55.8 bits (134), Expect = 2e-12
 Identities = 13/71 (18%), Positives = 25/71 (35%), Gaps = 4/71 (5%)

Query: 8  SGKDKRSKEKRPRTAFSGEQLSRLKVEFTE----NRYLTERRRQELANELGLNEAQIKIW 63
          +        KR RT F+ EQ  ++           +   +   ++   E G+    +KIW
Sbjct: 9  NPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIW 68

Query: 64 FQNKRAKIKKA 74
            N +     +
Sbjct: 69 MHNNKNSGPSS 79

>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 = 54.4 bits (131), Expect = 5e-12
 Identities = 13/56 (23%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 18 RPRTAFSGEQLSRLKVEF-TENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK 72
          +       E    L+  F +  +Y  E+R + L+ +L  +  +I+ WF+++R + K
Sbjct: 3  KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 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 = 54.3 bits (130), Expect = 9e-12
 Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 14 SKEKRPRTAFSGEQLSRLKVEFTE-NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK 72
          S   R RT  S E L  L+    +   Y  +     L+ +L L +  I  +FQN+R  +K
Sbjct: 5  SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVK 64

Query: 73 K 73
           
Sbjct: 65 H 65

>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 = 52.6 bits (126), Expect = 3e-11
 Identities = 16/54 (29%), Positives = 27/54 (50%)

Query: 20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
          RT+        L+  F EN+  T      +A +L + +  I++WF N+R K K+
Sbjct: 2  RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 55

>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 = 45.2 bits (106), Expect = 4e-08
 Identities = 10/75 (13%), Positives = 21/75 (28%), Gaps = 21/75 (28%)

Query: 20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANEL---------------------GLNEA 58
          R  +       L   +   +  ++  R+ L  E                       + E 
Sbjct: 1  RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 59 QIKIWFQNKRAKIKK 73
          ++  WF N+R +   
Sbjct: 61 RVYNWFANRRKEEAF 75

>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 = 44.7 bits (105), Expect = 4e-08
 Identities = 13/62 (20%), Positives = 22/62 (35%)

Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
           +     + EQL  L+  F  +  LT+     L  +  L   +I  WF  K+        
Sbjct: 5  PQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEE 64

Query: 77 QK 78
          + 
Sbjct: 65 KM 66

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

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

 Score = 40.5 bits (94), Expect = 2e-06
 Identities = 15/57 (26%), Positives = 24/57 (42%)

Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
                 + EQL+ LK  F + ++      Q+L    GL   +I  WF + R  +K 
Sbjct: 4  GSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH 60

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	120
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.88
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.88
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.87
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.87
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.87
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.87
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.87
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.87
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.86
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.86
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.86
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.86
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.85
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.85
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.84
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.84
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.83
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.83
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.83
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.83
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.81
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.81
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.79
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.77
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.77
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.77
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.76
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.73
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.72
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.71
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.69
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.68
d1hlva1	66	DNA-binding domain of centromere binding protein B	94.01
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	84.74

>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=99.88  E-value=3e-23  Score=117.97  Aligned_cols=57  Identities=39%  Similarity=0.733  Sum_probs=54.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625          17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK   73 (120)
Q Consensus        17 rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   73 (120)
                      ++.|+.|+..|+.+|+.+|..++||+..++..||..+||++.+|++||||||+++||
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            567899999999999999999999999999999999999999999999999999875

>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=99.88  E-value=1e-22  Score=115.85  Aligned_cols=57  Identities=46%  Similarity=0.828  Sum_probs=55.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625          17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK   73 (120)
Q Consensus        17 rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   73 (120)
                      |+.|+.|+..|+.+|+.+|..++||+..++..||..+||++.+|++||||+|+++||
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            467899999999999999999999999999999999999999999999999999987

>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=99.87  E-value=3.5e-22  Score=119.51  Aligned_cols=65  Identities=42%  Similarity=0.634  Sum_probs=59.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      .....++.|++|+.+|+.+|+.+|..++||+..++..||..|||++.+|++||||||+++|+...
T Consensus         9 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~   73 (77)
T d1pufa_           9 HARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINK   73 (77)
T ss_dssp             CCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHH
Confidence            44456678999999999999999999999999999999999999999999999999999998753

>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=99.87  E-value=1.9e-22  Score=114.34  Aligned_cols=57  Identities=40%  Similarity=0.681  Sum_probs=54.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625          17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK   73 (120)
Q Consensus        17 rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   73 (120)
                      ++.|++|++.|+.+|+.+|..++||+..++..||..+||++.+|++||||||+++||
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k~kk   57 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR   57 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhhccC
Confidence            467899999999999999999999999999999999999999999999999999886

>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=99.87  E-value=1.4e-22  Score=118.43  Aligned_cols=62  Identities=42%  Similarity=0.730  Sum_probs=58.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        16 ~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      +++.|++|+..|+.+|+.+|..++||+..++..||..|||++.+|++||||||+++|+....
T Consensus         1 Prr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~~   62 (67)
T d1zq3p1           1 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ   62 (67)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhhh
Confidence            35679999999999999999999999999999999999999999999999999999987643

>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=99.87  E-value=1.5e-22  Score=114.09  Aligned_cols=55  Identities=55%  Similarity=0.795  Sum_probs=53.6

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625          20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA   74 (120)
Q Consensus        20 R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   74 (120)
                      ||.|+.+|+.+|+..|..++||+..++..||..+||++++|++||||||+++|+.
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk~   55 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   55 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhhc
Confidence            6899999999999999999999999999999999999999999999999999985

>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=99.87  E-value=2.7e-22  Score=113.73  Aligned_cols=57  Identities=51%  Similarity=0.812  Sum_probs=54.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625          18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA   74 (120)
Q Consensus        18 r~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   74 (120)
                      |.|+.|+..|+.+|+.+|..++||+..++..||..+||++.+|++||||+|+++|+.
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk~   57 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   57 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhcC
Confidence            468999999999999999999999999999999999999999999999999999873

>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=99.87  E-value=4.6e-22  Score=115.54  Aligned_cols=61  Identities=43%  Similarity=0.749  Sum_probs=57.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625          15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS   75 (120)
Q Consensus        15 ~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   75 (120)
                      +.++.|+.|+.+|+.+|+.+|..++||+..++..||..+||++.+|++||||+|+++|+..
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~   61 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH   61 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhcc
Confidence            3577899999999999999999999999999999999999999999999999999999864

>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=99.86  E-value=3.8e-22  Score=122.16  Aligned_cols=65  Identities=46%  Similarity=0.675  Sum_probs=56.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      +.+.+++.|+.|+..|+.+|+.+|..++||+..+++.||..|||++.+|++||||+|+++|+...
T Consensus        23 ~~~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~~   87 (88)
T d1b72a_          23 GLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   87 (88)
T ss_dssp             -------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhcc
Confidence            44566788999999999999999999999999999999999999999999999999999998753

>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=99.86  E-value=1.9e-22  Score=120.80  Aligned_cols=66  Identities=36%  Similarity=0.620  Sum_probs=60.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      ...+.++.|++|+.+|+.+|+.+|..++||+..++..||..+||++.+|++||||+|+++|+....
T Consensus         5 ~p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   70 (77)
T d1vnda_           5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNE   70 (77)
T ss_dssp             CSSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHhhc
Confidence            345667789999999999999999999999999999999999999999999999999998876543

>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=99.86  E-value=5.6e-22  Score=110.83  Aligned_cols=53  Identities=85%  Similarity=1.243  Sum_probs=51.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhH
Q psy4625          18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAK   70 (120)
Q Consensus        18 r~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k   70 (120)
                      |.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||||||+|
T Consensus         1 R~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~lgL~~~qV~vWFqNrRaK   53 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK   53 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             CCCccCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChHHhhhcccccCCC
Confidence            46899999999999999999999999999999999999999999999999985

>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=99.86  E-value=1.3e-21  Score=114.46  Aligned_cols=62  Identities=35%  Similarity=0.658  Sum_probs=58.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        16 ~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      +++.|++|+..|+.+|+.+|..++||+..++..||..+||++.+|++||||+|+++|+....
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~~~   63 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKD   63 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhcccc
Confidence            46789999999999999999999999999999999999999999999999999999987544

>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=99.85  E-value=1.8e-21  Score=113.92  Aligned_cols=59  Identities=39%  Similarity=0.697  Sum_probs=56.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhh
Q psy4625          17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS   75 (120)
Q Consensus        17 rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~   75 (120)
                      ++.|++|+.+|+.+|+.+|..++||+..++..||..+||++.+|++||||+|+++|+..
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~   60 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREE   60 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhh
Confidence            56789999999999999999999999999999999999999999999999999999864

>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=99.85  E-value=7e-22  Score=113.09  Aligned_cols=58  Identities=41%  Similarity=0.739  Sum_probs=56.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625          17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA   74 (120)
Q Consensus        17 rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   74 (120)
                      |+.|++|+.+|+.+|+.+|..++||+..++..||..+||++.+|++||+|+|+++|+.
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1           2 RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             SCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            5779999999999999999999999999999999999999999999999999999975

>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=99.84  E-value=2e-21  Score=113.09  Aligned_cols=62  Identities=35%  Similarity=0.500  Sum_probs=58.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        15 ~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      +.+|.|+.|+.+|+.+|+.+|..++||+..++..||..+||++.+|++||||+|++.|+...
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~~~   63 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI   63 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCCC
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHHHH
Confidence            45788999999999999999999999999999999999999999999999999999987654

>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=99.84  E-value=4.4e-21  Score=113.21  Aligned_cols=60  Identities=23%  Similarity=0.427  Sum_probs=56.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          17 KRPRTAFSGEQLSRLKVEFTE-NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        17 rr~R~~~~~~q~~~L~~~F~~-~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      ++.|++|+.+|+.+|+..|.. ++||+...++.||..+||++++|++||||||+++|+...
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~~   62 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG   62 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhccC
Confidence            467899999999999999986 689999999999999999999999999999999998754

>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=99.83  E-value=2.5e-21  Score=112.94  Aligned_cols=60  Identities=28%  Similarity=0.463  Sum_probs=56.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625          15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA   74 (120)
Q Consensus        15 ~~rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   74 (120)
                      .+++.|++|+..|+.+|+.+|..++||+..++..||..+||++.+|++||||+|+++|+.
T Consensus         7 ~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_           7 ARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             CSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             ccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            346789999999999999999999999999999999999999999999999999998864

>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=99.83  E-value=5.6e-21  Score=106.67  Aligned_cols=53  Identities=26%  Similarity=0.555  Sum_probs=51.2

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHH
Q psy4625          20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK   72 (120)
Q Consensus        20 R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k   72 (120)
                      |+.|+++|+.+|+.+|..++||+..++..||..+||++.+|++||||+|++.|
T Consensus         1 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~K   53 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   53 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTTC
T ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhccC
Confidence            68999999999999999999999999999999999999999999999999864

>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=99.83  E-value=7.7e-21  Score=107.95  Aligned_cols=57  Identities=26%  Similarity=0.466  Sum_probs=54.4

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625          18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA   74 (120)
Q Consensus        18 r~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   74 (120)
                      |.|+.|+.+|+.+|+.+|..++||+..++..||..+||++.+|++||||+|+++|+.
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr~   57 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV   57 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHhc
Confidence            468999999999999999999999999999999999999999999999999998863

>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=99.83  E-value=7e-21  Score=112.32  Aligned_cols=62  Identities=29%  Similarity=0.340  Sum_probs=56.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625          13 RSKEKRPRTAFSGEQLSRLKVEFT-ENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA   74 (120)
Q Consensus        13 ~~~~rr~R~~~~~~q~~~L~~~F~-~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   74 (120)
                      ++..++.|++|+.+|+.+|+.+|. .++||+..+++.||..+||++.+|++||||+|++.|+.
T Consensus         4 ~~~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk~   66 (71)
T d1wi3a_           4 GSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS   66 (71)
T ss_dssp             CCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCSS
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhccc
Confidence            455667899999999999999997 58999999999999999999999999999999998864

>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=99.81  E-value=1.8e-20  Score=113.33  Aligned_cols=62  Identities=29%  Similarity=0.539  Sum_probs=57.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhC---------------CChhhHHHHHHHHHhHHHHhhcCC
Q psy4625          17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELG---------------LNEAQIKIWFQNKRAKIKKASGQK   78 (120)
Q Consensus        17 rr~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~---------------l~~~~V~~WFqNrR~k~kk~~~~~   78 (120)
                      |+.|++|+++|+.+|+.+|..++||+..+++.||..+|               |++.+|++||||||+++|+.....
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~~a   77 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANIA   77 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhhHH
Confidence            57899999999999999999999999999999999875               999999999999999999986543

>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=99.81  E-value=3.3e-20  Score=104.94  Aligned_cols=56  Identities=29%  Similarity=0.469  Sum_probs=53.9

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHh
Q psy4625          19 PRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA   74 (120)
Q Consensus        19 ~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~   74 (120)
                      .||.|+.+|+.+|+.+|..++||+..++..||..+||++.+|++||||+|+++|+.
T Consensus         1 kRT~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk~   56 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI   56 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHcc
Confidence            48999999999999999999999999999999999999999999999999999874

>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=99.79  E-value=2.5e-19  Score=106.86  Aligned_cols=57  Identities=26%  Similarity=0.350  Sum_probs=53.4

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhc
Q psy4625          20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG   76 (120)
Q Consensus        20 R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~   76 (120)
                      +.+++.+|+.+|+..|..++||+..++..||..+||+..+|++||+|+|+++|+...
T Consensus         7 ~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~~~   63 (76)
T d2ecca1           7 GKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQL   63 (76)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhchH
Confidence            346899999999999999999999999999999999999999999999999998654

>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=99.77  E-value=2.4e-19  Score=107.82  Aligned_cols=62  Identities=21%  Similarity=0.317  Sum_probs=55.9

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625          12 KRSKEKRPRTAFSGEQLSRLKVEFTE----NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK   73 (120)
Q Consensus        12 ~~~~~rr~R~~~~~~q~~~L~~~F~~----~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   73 (120)
                      ..++.+|.|++|+.+|+..|+.+|+.    ++||+..+++.||..+||++.+|++||||+|++.+.
T Consensus        13 ~~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          13 SGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            44566788999999999999999986    789999999999999999999999999999987653

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

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

Probab=99.77  E-value=1.1e-19  Score=100.31  Aligned_cols=50  Identities=28%  Similarity=0.478  Sum_probs=48.6

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHH
Q psy4625          19 PRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR   68 (120)
Q Consensus        19 ~R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR   68 (120)
                      +|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||||+|
T Consensus         1 PRt~ft~~Q~~~Le~~F~~n~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1           1 PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             CCSCCCHHHHHHHHHHTTSSCSSTHHHHHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhhcCCcCc
Confidence            48999999999999999999999999999999999999999999999987

>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=99.77  E-value=4e-19  Score=105.92  Aligned_cols=57  Identities=23%  Similarity=0.364  Sum_probs=52.3

Q ss_pred             CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcCC
Q psy4625          22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQK   78 (120)
Q Consensus        22 ~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~   78 (120)
                      .++.+|+.+|+.+|..++||+..++..||..+||++.+|++||||+|++.++.....
T Consensus        10 ~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~~~   66 (76)
T d2ecba1          10 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKM   66 (76)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCC
T ss_pred             CCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhHhh
Confidence            468999999999999999999999999999999999999999999999877665443

>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=99.76  E-value=1.8e-18  Score=102.35  Aligned_cols=61  Identities=34%  Similarity=0.586  Sum_probs=55.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHHhhcC
Q psy4625          17 KRPRTAFSGEQLSRLKVEFTE---NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ   77 (120)
Q Consensus        17 rr~R~~~~~~q~~~L~~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~   77 (120)
                      |+.|+.|+.+|+.+|+..|..   ++||+..+++.||..+||+..+|++||+|+|++.++....
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~~~   65 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGK   65 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccchh
Confidence            567889999999999999974   8899999999999999999999999999999999876543

>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=99.73  E-value=1.3e-18  Score=96.53  Aligned_cols=50  Identities=24%  Similarity=0.432  Sum_probs=46.2

Q ss_pred             CHHHHHHHHHHHHh-CCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625          24 SGEQLSRLKVEFTE-NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK   73 (120)
Q Consensus        24 ~~~q~~~L~~~F~~-~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   73 (120)
                      +++|..+|+.+|.. ++||+..++..||..+||++++|++||||||+++|+
T Consensus         1 T~~q~~iLE~~F~~~~~~P~~~~~~~LA~~~~ls~~qV~~WFqNrR~k~k~   51 (52)
T d1x2ma1           1 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   51 (52)
T ss_dssp             SSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             ChhHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccCc
Confidence            35689999999987 789999999999999999999999999999999874

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

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

Probab=99.72  E-value=2.6e-18  Score=102.62  Aligned_cols=55  Identities=18%  Similarity=0.330  Sum_probs=51.8

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhC---------------------CChhhHHHHHHHHHhHHHHh
Q psy4625          20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELG---------------------LNEAQIKIWFQNKRAKIKKA   74 (120)
Q Consensus        20 R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~---------------------l~~~~V~~WFqNrR~k~kk~   74 (120)
                      |++|++.|+.+|+.+|..++||+..+++.||.+|+                     |++.+|++||+|||++.|+.
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr~   76 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFR   76 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCC
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHHh
Confidence            67899999999999999999999999999999994                     89999999999999998865

>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=99.71  E-value=4.5e-18  Score=96.57  Aligned_cols=55  Identities=24%  Similarity=0.429  Sum_probs=50.4

Q ss_pred             CCCCCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHH
Q psy4625          18 RPRTAFSGEQLSRLKVEFTE-NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK   72 (120)
Q Consensus        18 r~R~~~~~~q~~~L~~~F~~-~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k   72 (120)
                      +.+.+++.++..+|+.+|.. ++||+..++..||..+||++.+|++||||||+++|
T Consensus         3 k~~~~~k~~~~~iLE~~F~~~~~yPs~~~~~~LA~~lgls~~qV~~WFqNrR~k~r   58 (59)
T d2cqxa1           3 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK   58 (59)
T ss_dssp             CCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCccccHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccC
Confidence            45677888889999999986 68999999999999999999999999999999976

>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=99.69  E-value=4.8e-17  Score=92.62  Aligned_cols=53  Identities=32%  Similarity=0.504  Sum_probs=48.9

Q ss_pred             CCCCHHHHHHHHHHHHhC---CCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHHH
Q psy4625          21 TAFSGEQLSRLKVEFTEN---RYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK   73 (120)
Q Consensus        21 ~~~~~~q~~~L~~~F~~~---~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk   73 (120)
                      .+|+.+|+.+|+..|..+   +||+..+++.||..+||++.+|++||+|+|.+.|.
T Consensus         3 ~Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~   58 (60)
T d1k61a_           3 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   58 (60)
T ss_dssp             CSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhcccccc
Confidence            349999999999999764   79999999999999999999999999999998775

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

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

Probab=99.68  E-value=1e-16  Score=91.80  Aligned_cols=56  Identities=23%  Similarity=0.398  Sum_probs=51.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhHHH
Q psy4625          17 KRPRTAFSGEQLSRLKVEFTE---NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK   72 (120)
Q Consensus        17 rr~R~~~~~~q~~~L~~~F~~---~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k   72 (120)
                      ++.|+.|+++++.+|+..|..   ++||+..++..||..+||+..+|.+||+|+|.+..
T Consensus         3 krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R~l   61 (62)
T d1x2na1           3 KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRIL   61 (62)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhc
Confidence            445778999999999999985   78999999999999999999999999999998754

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=94.01  E-value=0.15  Score=27.76  Aligned_cols=48  Identities=27%  Similarity=0.362  Sum_probs=38.9

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHHHHHHhH
Q psy4625          20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAK   70 (120)
Q Consensus        20 R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k   70 (120)
                      |..++-.+...+...|+.++...   ...+|..+|+....|..|..|+..-
T Consensus         5 Rk~LT~~eK~~ii~~~e~g~k~s---q~eIA~~fGv~~STvs~IlKnK~ki   52 (66)
T d1hlva1           5 RRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNKRAI   52 (66)
T ss_dssp             SCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTHHHH
T ss_pred             cccCCHHHHHHHHHHHHcCCcch---HHHHHHHhCCChhHHHHHHHHHHHH
Confidence            45688888888888888887655   4568999999999999999986443

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=84.74  E-value=1.4  Score=21.96  Aligned_cols=40  Identities=18%  Similarity=0.290  Sum_probs=33.1

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhhHHHHH
Q psy4625          20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWF   64 (120)
Q Consensus        20 R~~~~~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF   64 (120)
                      +..++.+|+..+...+.... +    ...+|..+|++...|-.||
T Consensus         3 ~~~lt~~q~~~a~~l~~~G~-s----~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_           3 PRAINKHEQEQISRLLEKGH-P----RQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             CCSSCHHHHHHHHHHHHTTC-C----HHHHHHHHTCCHHHHHHHS
T ss_pred             CCcCCHHHHHHHHHHHHCCC-C----HHHHHHHHCcCHHHHHhhC
Confidence            35689999999998887643 2    6778999999999999887