Psyllid ID: psy16797

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------10
Protein Sequence
MDRVQKYLDDSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNLEYKLHYTTHSHLAA
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHccccHHHHHHHHcccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHccHHHHccccccccccccccccccc
Coil and Loop (DISEMBL)
MDRVQKYLDDSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRrmkkkkgktpednleyklhytthshlaa
Flexible Loop (DISEMBL)
mdrvqkylddsliadekkgkkrarTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIkiwfqnrrmkkkkgktpednleyklhytthshlaa
Low Complexity Region (SEG)
MDRVQKYLDDSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNLEYKLHYTTHSHLAA
Disordered region (IsUnstruct)
****************************SNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWF*******************************
Disordered Region (DISOPRED)
***************************TSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRR***************************
Disordered Region (DISEMBL)
MDRVQKYLDDSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNR**********EDNLEYKLHYTTHSHLAA
Disordered Region (DISPRO)
***********************RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG*********************
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDRVQKYLDDSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNLEYKLHYTTHSHLAA
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	99	2.2.26 [Sep-21-2011]
P02831	443	Homeobox protein Hox-A3 O	yes	N/A	0.616	0.137	0.639	3e-16
O43365	443	Homeobox protein Hox-A3 O	yes	N/A	0.616	0.137	0.639	3e-16
Q08DG7	442	Homeobox protein Hox-A3 O	yes	N/A	0.616	0.138	0.639	3e-16
P09026	433	Homeobox protein Hox-B3 O	no	N/A	0.575	0.131	0.684	3e-16
P14651	431	Homeobox protein Hox-B3 O	no	N/A	0.575	0.132	0.684	3e-16
Q1KKX7	474	Homeobox protein Hox-B3a	N/A	N/A	0.575	0.120	0.684	7e-16
P31249	432	Homeobox protein Hox-D3 O	no	N/A	0.575	0.131	0.666	9e-16
O93353	413	Homeobox protein Hox-A3 O	yes	N/A	0.616	0.147	0.639	1e-15
P09027	433	Homeobox protein Hox-D3 O	no	N/A	0.575	0.131	0.666	1e-15
Q9IA21	410	Homeobox protein Hox-A3 O	N/A	N/A	0.575	0.139	0.684	1e-15

>sp|P02831|HXA3_MOUSE Homeobox protein Hox-A3 OS=Mus musculus GN=Hoxa3 PE=1 SV=2

 Score = 84.0 bits (206), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 39/61 (63%), Positives = 46/61 (75%)

Query: 17  KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
           +   KRARTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQNRRMK K
Sbjct: 189 QASSKRARTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLTERQIKIWFQNRRMKYK 248

Query: 77  K 77
           K
Sbjct: 249 K 249

Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Binds 5' to its own homeobox.
Mus musculus (taxid: 10090)

>sp|O43365|HXA3_HUMAN Homeobox protein Hox-A3 OS=Homo sapiens GN=HOXA3 PE=2 SV=1

 Score = 84.0 bits (206), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 39/61 (63%), Positives = 46/61 (75%)

Query: 17  KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
           +   KRARTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQNRRMK K
Sbjct: 188 QASSKRARTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLTERQIKIWFQNRRMKYK 247

Query: 77  K 77
           K
Sbjct: 248 K 248

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

Homo sapiens (taxid: 9606)

>sp|Q08DG7|HXA3_BOVIN Homeobox protein Hox-A3 OS=Bos taurus GN=HOXA3 PE=2 SV=1

 Score = 84.0 bits (206), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 39/61 (63%), Positives = 46/61 (75%)

Query: 17  KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
           +   KRARTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQNRRMK K
Sbjct: 188 QASSKRARTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLTERQIKIWFQNRRMKYK 247

Query: 77  K 77
           K
Sbjct: 248 K 248

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

Bos taurus (taxid: 9913)

>sp|P09026|HXB3_MOUSE Homeobox protein Hox-B3 OS=Mus musculus GN=Hoxb3 PE=2 SV=4

 Score = 84.0 bits (206), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 39/57 (68%), Positives = 45/57 (78%)

Query: 21  KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
           KRARTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQNRRMK KK
Sbjct: 192 KRARTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLSERQIKIWFQNRRMKYKK 248

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

Mus musculus (taxid: 10090)

>sp|P14651|HXB3_HUMAN Homeobox protein Hox-B3 OS=Homo sapiens GN=HOXB3 PE=1 SV=2

 Score = 84.0 bits (206), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 39/57 (68%), Positives = 45/57 (78%)

Query: 21  KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
           KRARTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQNRRMK KK
Sbjct: 189 KRARTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLSERQIKIWFQNRRMKYKK 245

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

Homo sapiens (taxid: 9606)

>sp|Q1KKX7|HXB3A_TAKRU Homeobox protein Hox-B3a OS=Takifugu rubripes GN=hoxb3a PE=3 SV=1

 Score = 82.4 bits (202), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 39/57 (68%), Positives = 45/57 (78%)

Query: 21  KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
           KRARTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQNRRMK KK
Sbjct: 213 KRARTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLSERQIKIWFQNRRMKYKK 269

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

Takifugu rubripes (taxid: 31033)

>sp|P31249|HXD3_HUMAN Homeobox protein Hox-D3 OS=Homo sapiens GN=HOXD3 PE=1 SV=3

 Score = 82.0 bits (201), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 38/57 (66%), Positives = 44/57 (77%)

Query: 21  KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
           KR RTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQNRRMK KK
Sbjct: 195 KRVRTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLTERQIKIWFQNRRMKYKK 251

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

Homo sapiens (taxid: 9606)

>sp|O93353|HXA3_CHICK Homeobox protein Hox-A3 OS=Gallus gallus GN=HOXA3 PE=2 SV=2

 Score = 82.0 bits (201), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 39/61 (63%), Positives = 46/61 (75%)

Query: 17  KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
           +   KRARTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQNRRMK K
Sbjct: 170 QTSSKRARTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLTERQIKIWFQNRRMKYK 229

Query: 77  K 77
           K
Sbjct: 230 K 230

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

Gallus gallus (taxid: 9031)

>sp|P09027|HXD3_MOUSE Homeobox protein Hox-D3 OS=Mus musculus GN=Hoxd3 PE=2 SV=4

 Score = 82.0 bits (201), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 38/57 (66%), Positives = 44/57 (77%)

Query: 21  KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
           KR RTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQNRRMK KK
Sbjct: 196 KRVRTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLTERQIKIWFQNRRMKYKK 252

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

Mus musculus (taxid: 10090)

>sp|Q9IA21|HXA3_HETFR Homeobox protein Hox-A3 OS=Heterodontus francisci GN=HOXA3 PE=3 SV=1

 Score = 81.6 bits (200), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 39/57 (68%), Positives = 45/57 (78%)

Query: 21  KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
           KRARTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQNRRMK KK
Sbjct: 169 KRARTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLTERQIKIWFQNRRMKYKK 225

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

Heterodontus francisci (taxid: 7792)

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	99
387598534	351	homeodomain transcription factor 3, part	0.808	0.227	0.55	3e-16
350410207	324	PREDICTED: homeobox protein Hox-A3-like	0.717	0.219	0.605	3e-15
358341731	531	homeobox protein Hox-B3 [Clonorchis sine	0.717	0.133	0.563	8e-15
74096123	349	Gsx [Ciona intestinalis] gi|12584104|gb|	0.686	0.194	0.573	9e-15
17384023	435	zerknuellt protein [Haematopota pluviali	0.666	0.151	0.621	1e-14
70569805	287	transcription factor protein [Ciona inte	0.686	0.236	0.573	1e-14
426355738	443	PREDICTED: homeobox protein Hox-A3 isofo	0.616	0.137	0.639	1e-14
426228410	492	PREDICTED: LOW QUALITY PROTEIN: homeobox	0.616	0.123	0.639	1e-14
30585409	444	Homo sapiens homeo box A3 [synthetic con	0.616	0.137	0.639	1e-14
46275824	443	homeobox protein Hox-A3 [Mus musculus] g	0.616	0.137	0.639	1e-14

>gi|387598534|gb|AFJ91923.1| homeodomain transcription factor 3, partial [Platynereis dumerilii]

 Score = 89.4 bits (220), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 44/80 (55%), Positives = 55/80 (68%)

Query: 10  DSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQ 69
           DS   + +K  KRARTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQ
Sbjct: 167 DSTSGESEKPSKRARTAYTSAQLVELEKEFHFNRYLCRPRRIEMAALLNLSERQIKIWFQ 226

Query: 70  NRRMKKKKGKTPEDNLEYKL 89
           NRRMK KK    + N E ++
Sbjct: 227 NRRMKYKKDSRLKPNSEKEM 246

Source: Platynereis dumerilii

Species: Platynereis dumerilii

Genus: Platynereis

Family: Nereididae

Order: Phyllodocida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|350410207|ref|XP_003488980.1| PREDICTED: homeobox protein Hox-A3-like [Bombus impatiens]

 Score = 85.9 bits (211), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 43/71 (60%), Positives = 52/71 (73%)

Query: 9   DDSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWF 68
           D  LI+  +K  KR RTAYTS QL+ LEKEFN+  Y+ R +R +LA  L+L ERQIKIWF
Sbjct: 44  DTFLISGAEKKTKRTRTAYTSAQLVELEKEFNRTRYLCRPRRIELAAALSLTERQIKIWF 103

Query: 69  QNRRMKKKKGK 79
           QNRRMK KK +
Sbjct: 104 QNRRMKYKKDQ 114

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|358341731|dbj|GAA49331.1| homeobox protein Hox-B3 [Clonorchis sinensis]

 Score = 84.3 bits (207), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 40/71 (56%), Positives = 53/71 (74%)

Query: 7   YLDDSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKI 66
           +L D+  A      KR R+AYT+ QL+ LEKEF+  NY+++ +R +LAK+L L ERQIKI
Sbjct: 315 HLTDTGCATVTSTSKRPRSAYTNQQLVELEKEFHYSNYLVQPRRVELAKQLGLSERQIKI 374

Query: 67  WFQNRRMKKKK 77
           WFQNRRMK+KK
Sbjct: 375 WFQNRRMKQKK 385

Source: Clonorchis sinensis

Species: Clonorchis sinensis

Genus: Clonorchis

Family: Opisthorchiidae

Order: Opisthorchiida

Class: Trematoda

Phylum: Platyhelminthes

Superkingdom: Eukaryota

>gi|74096123|ref|NP_001027663.1| Gsx [Ciona intestinalis] gi|12584104|gb|AAG59803.1|AF305500_1 Gsx [Ciona intestinalis]

 Score = 84.3 bits (207), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 39/68 (57%), Positives = 54/68 (79%)

Query: 15  DEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74
           DE+  +KR RTA+T +QLL LE+EF+   Y+ R +R ++A+ LNL E+QIKIWFQNRR+K
Sbjct: 275 DEQGDRKRMRTAFTGSQLLELEREFHSDMYLTRLRRIRIAQMLNLSEKQIKIWFQNRRVK 334

Query: 75  KKKGKTPE 82
           KKKG+ P+
Sbjct: 335 KKKGEKPQ 342

Source: Ciona intestinalis

Species: Ciona intestinalis

Genus: Ciona

Family: Cionidae

Order: Enterogona

Class: Ascidiacea

Phylum: Chordata

Superkingdom: Eukaryota

>gi|17384023|emb|CAD11912.1| zerknuellt protein [Haematopota pluvialis]

 Score = 84.0 bits (206), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 41/66 (62%), Positives = 49/66 (74%)

Query: 21  KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80
           KRARTAY+S QL+ LEKEFN  +Y+ R +R +LA +L L ERQIKIWFQNRRMK KK K 
Sbjct: 137 KRARTAYSSVQLMELEKEFNMGSYLCRPRRIELANKLKLNERQIKIWFQNRRMKHKKSKK 196

Query: 81  PEDNLE 86
              N +
Sbjct: 197 QNGNTD 202

Source: Haematopota pluvialis

Species: Haematopota pluvialis

Genus: Haematopota

Family: Tabanidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|70569805|dbj|BAE06480.1| transcription factor protein [Ciona intestinalis]

 Score = 84.0 bits (206), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 39/68 (57%), Positives = 54/68 (79%)

Query: 15  DEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74
           DE+  +KR RTA+T +QLL LE+EF+   Y+ R +R ++A+ LNL E+QIKIWFQNRR+K
Sbjct: 213 DEQGDRKRMRTAFTGSQLLELEREFHSDMYLTRLRRIRIAQMLNLSEKQIKIWFQNRRVK 272

Query: 75  KKKGKTPE 82
           KKKG+ P+
Sbjct: 273 KKKGEKPQ 280

Source: Ciona intestinalis

Species: Ciona intestinalis

Genus: Ciona

Family: Cionidae

Order: Enterogona

Class: Ascidiacea

Phylum: Chordata

Superkingdom: Eukaryota

>gi|426355738|ref|XP_004045265.1| PREDICTED: homeobox protein Hox-A3 isoform 1 [Gorilla gorilla gorilla] gi|426355740|ref|XP_004045266.1| PREDICTED: homeobox protein Hox-A3 isoform 2 [Gorilla gorilla gorilla]

 Score = 84.0 bits (206), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 39/61 (63%), Positives = 46/61 (75%)

Query: 17  KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
           +   KRARTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQNRRMK K
Sbjct: 188 QASSKRARTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLTERQIKIWFQNRRMKYK 247

Query: 77  K 77
           K
Sbjct: 248 K 248

Source: Gorilla gorilla gorilla

Species: Gorilla gorilla

Genus: Gorilla

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|426228410|ref|XP_004008302.1| PREDICTED: LOW QUALITY PROTEIN: homeobox protein Hox-A3 [Ovis aries]

 Score = 84.0 bits (206), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 39/61 (63%), Positives = 46/61 (75%)

Query: 17  KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
           +   KRARTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQNRRMK K
Sbjct: 167 QASSKRARTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLTERQIKIWFQNRRMKYK 226

Query: 77  K 77
           K
Sbjct: 227 K 227

Source: Ovis aries

Species: Ovis aries

Genus: Ovis

Family: Bovidae

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|30585409|gb|AAP36977.1| Homo sapiens homeo box A3 [synthetic construct] gi|61370826|gb|AAX43558.1| homeobox A3 [synthetic construct] gi|61370831|gb|AAX43559.1| homeobox A3 [synthetic construct]

 Score = 84.0 bits (206), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 39/61 (63%), Positives = 46/61 (75%)

Query: 17  KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
           +   KRARTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQNRRMK K
Sbjct: 188 QASSKRARTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLTERQIKIWFQNRRMKYK 247

Query: 77  K 77
           K
Sbjct: 248 K 248

Source: synthetic construct

Species: synthetic construct

Genus: N/A

Family: N/A

Order: N/A

Class: N/A

Phylum: N/A

>gi|46275824|ref|NP_034582.1| homeobox protein Hox-A3 [Mus musculus] gi|2811092|sp|P02831.2|HXA3_MOUSE RecName: Full=Homeobox protein Hox-A3; AltName: Full=Homeobox protein Hox-1.5; AltName: Full=Homeobox protein MO-10 gi|1888441|emb|CAA72404.1| homeobox-containing transcription factor [Mus musculus] gi|66794501|gb|AAH96612.1| Homeo box A3 [Mus musculus] gi|148666235|gb|EDK98651.1| homeobox A3, isoform CRA_a [Mus musculus] gi|148666236|gb|EDK98652.1| homeobox A3, isoform CRA_a [Mus musculus]

 Score = 84.0 bits (206), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 39/61 (63%), Positives = 46/61 (75%)

Query: 17  KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
           +   KRARTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQNRRMK K
Sbjct: 189 QASSKRARTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLTERQIKIWFQNRRMKYK 248

Query: 77  K 77
           K
Sbjct: 249 K 249

Source: Mus musculus

Species: Mus musculus

Genus: Mus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

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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	99
WB|WBGene00003024	253	lin-39 [Caenorhabditis elegans	0.606	0.237	0.616	2e-15
UNIPROTKB|F8VXG0	297	HOXB3 "Homeobox protein Hox-B3	0.575	0.191	0.684	3.6e-15
UNIPROTKB|B7Z5N8	299	HOXB3 "cDNA FLJ51054, highly s	0.575	0.190	0.684	3.8e-15
FB|FBgn0025776	391	ind "intermediate neuroblasts	0.747	0.189	0.526	6e-15
UNIPROTKB|B7ZAD0	358	HOXB3 "cDNA, FLJ79144, highly	0.575	0.159	0.684	9.7e-15
UNIPROTKB|E2QT60	310	HOXB2 "Uncharacterized protein	0.707	0.225	0.528	1.1e-14
UNIPROTKB|F1NH10	377	HOXB3 "Homeobox protein Hox-B3	0.575	0.151	0.684	1.2e-14
UNIPROTKB|P23682	399	HOXB3 "Homeobox protein Hox-B3	0.575	0.142	0.684	1.4e-14
ZFIN|ZDB-GENE-000823-3	410	hoxa3a "homeo box A3a" [Danio	0.575	0.139	0.684	1.5e-14
UNIPROTKB|O93353	413	HOXA3 "Homeobox protein Hox-A3	0.575	0.138	0.684	1.5e-14

WB|WBGene00003024 lin-39 [Caenorhabditis elegans (taxid:6239)]

 Score = 194 (73.4 bits), Expect = 2.0e-15, P = 2.0e-15
 Identities = 37/60 (61%), Positives = 46/60 (76%)

Query:    18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
             +G+KR RTAYT NQ+L LEKEF+   Y+ R +R ++A  L L ERQ+KIWFQNRRMK KK
Sbjct:   163 RGEKRQRTAYTRNQVLELEKEFHTHKYLTRKRRIEVAHSLMLTERQVKIWFQNRRMKHKK 222

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

GO:0005634 "nucleus" evidence=IEA;IDA

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

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

GO:0003677 "DNA binding" evidence=IEA

GO:0018991 "oviposition" evidence=IMP

GO:0040026 "positive regulation of vulval development" evidence=IGI;IMP

GO:0040027 "negative regulation of vulval development" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0016477 "cell migration" evidence=IMP

GO:0007411 "axon guidance" evidence=IMP

GO:0040025 "vulval development" evidence=IEP

GO:0042659 "regulation of cell fate specification" evidence=IMP

GO:0051302 "regulation of cell division" evidence=IMP

GO:0045026 "plasma membrane fusion" evidence=IMP

GO:0007265 "Ras protein signal transduction" evidence=IEP

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

UNIPROTKB|F8VXG0 HOXB3 "Homeobox protein Hox-B3" [Homo sapiens (taxid:9606)]

 Score = 192 (72.6 bits), Expect = 3.6e-15, P = 3.6e-15
 Identities = 39/57 (68%), Positives = 45/57 (78%)

Query:    21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
             KRARTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQNRRMK KK
Sbjct:    55 KRARTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLSERQIKIWFQNRRMKYKK 111

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

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

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|B7Z5N8 HOXB3 "cDNA FLJ51054, highly similar to Homeobox protein Hox-B3" [Homo sapiens (taxid:9606)]

 Score = 192 (72.6 bits), Expect = 3.8e-15, P = 3.8e-15
 Identities = 39/57 (68%), Positives = 45/57 (78%)

Query:    21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
             KRARTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQNRRMK KK
Sbjct:    57 KRARTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLSERQIKIWFQNRRMKYKK 113

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

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

GO:0000979 "RNA polymerase II core promoter sequence-specific DNA binding" evidence=IEA

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

GO:0021546 "rhombomere development" evidence=IEA

GO:0021615 "glossopharyngeal nerve morphogenesis" evidence=IEA

GO:0030878 "thyroid gland development" evidence=IEA

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

GO:0050767 "regulation of neurogenesis" evidence=IEA

GO:0051216 "cartilage development" evidence=IEA

GO:0060216 "definitive hemopoiesis" evidence=IEA

GO:0060324 "face development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

FB|FBgn0025776 ind "intermediate neuroblasts defective" [Drosophila melanogaster (taxid:7227)]

 Score = 195 (73.7 bits), Expect = 6.0e-15, P = 6.0e-15
 Identities = 40/76 (52%), Positives = 53/76 (69%)

Query:    12 LIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNR 71
             LI D     KR RTA+TS QLL LE+EF+   Y+ R +R ++A  L L E+Q+KIWFQNR
Sbjct:   290 LINDYADSSKRIRTAFTSTQLLELEREFSHNAYLSRLRRIEIANRLRLSEKQVKIWFQNR 349

Query:    72 RMKKKKG--KTPEDNL 85
             R+K+KKG  ++P  NL
Sbjct:   350 RVKQKKGGSESPTFNL 365

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

GO:0005634 "nucleus" evidence=ISS;IDA

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

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

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

GO:0007419 "ventral cord development" evidence=NAS;TAS

GO:0007400 "neuroblast fate determination" evidence=TAS

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

GO:0007398 "ectoderm development" evidence=TAS

GO:0007420 "brain development" evidence=TAS

GO:0007389 "pattern specification process" evidence=NAS

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

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

GO:0008134 "transcription factor binding" evidence=IPI

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

UNIPROTKB|B7ZAD0 HOXB3 "cDNA, FLJ79144, highly similar to Homeobox protein Hox-B3" [Homo sapiens (taxid:9606)]

 Score = 192 (72.6 bits), Expect = 9.7e-15, P = 9.7e-15
 Identities = 39/57 (68%), Positives = 45/57 (78%)

Query:    21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
             KRARTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQNRRMK KK
Sbjct:   116 KRARTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLSERQIKIWFQNRRMKYKK 172

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

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

GO:0000979 "RNA polymerase II core promoter sequence-specific DNA binding" evidence=IEA

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

GO:0021546 "rhombomere development" evidence=IEA

GO:0021615 "glossopharyngeal nerve morphogenesis" evidence=IEA

GO:0030878 "thyroid gland development" evidence=IEA

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

GO:0050767 "regulation of neurogenesis" evidence=IEA

GO:0051216 "cartilage development" evidence=IEA

GO:0060216 "definitive hemopoiesis" evidence=IEA

GO:0060324 "face development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|E2QT60 HOXB2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 189 (71.6 bits), Expect = 1.1e-14, P = 1.1e-14
 Identities = 37/70 (52%), Positives = 49/70 (70%)

Query:     8 LDDSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIW 67
             L  S  +  +KG  R RTAYT+ QLL LEKEF+   Y+ R +R ++A  L+L ERQ+K+W
Sbjct:   119 LGKSFFSARRKGLDRLRTAYTNTQLLELEKEFHFNKYLCRPRRVEIAALLDLTERQVKVW 178

Query:    68 FQNRRMKKKK 77
             FQNRRMK K+
Sbjct:   179 FQNRRMKHKR 188

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

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

UNIPROTKB|F1NH10 HOXB3 "Homeobox protein Hox-B3" [Gallus gallus (taxid:9031)]

 Score = 192 (72.6 bits), Expect = 1.2e-14, P = 1.2e-14
 Identities = 39/57 (68%), Positives = 45/57 (78%)

Query:    21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
             KRARTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQNRRMK KK
Sbjct:   159 KRARTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLSERQIKIWFQNRRMKYKK 215

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0000979 "RNA polymerase II core promoter sequence-specific DNA binding" evidence=IEA

GO:0001525 "angiogenesis" evidence=IEA

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

GO:0021546 "rhombomere development" evidence=IEA

GO:0021615 "glossopharyngeal nerve morphogenesis" evidence=IEA

GO:0030878 "thyroid gland development" evidence=IEA

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

GO:0050767 "regulation of neurogenesis" evidence=IEA

GO:0051216 "cartilage development" evidence=IEA

GO:0060216 "definitive hemopoiesis" evidence=IEA

GO:0060324 "face development" evidence=IEA

UNIPROTKB|P23682 HOXB3 "Homeobox protein Hox-B3" [Gallus gallus (taxid:9031)]

 Score = 192 (72.6 bits), Expect = 1.4e-14, P = 1.4e-14
 Identities = 39/57 (68%), Positives = 45/57 (78%)

Query:    21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
             KRARTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQNRRMK KK
Sbjct:   160 KRARTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLSERQIKIWFQNRRMKYKK 216

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

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

ZFIN|ZDB-GENE-000823-3 hoxa3a "homeo box A3a" [Danio rerio (taxid:7955)]

 Score = 192 (72.6 bits), Expect = 1.5e-14, P = 1.5e-14
 Identities = 39/57 (68%), Positives = 45/57 (78%)

Query:    21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
             KRARTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQNRRMK KK
Sbjct:   164 KRARTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLTERQIKIWFQNRRMKYKK 220

GO:0003677 "DNA binding" evidence=IEA;IDA

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

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0048538 "thymus development" evidence=IMP

GO:0060017 "parathyroid gland development" evidence=IMP

GO:0007275 "multicellular organismal development" evidence=IEA

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

UNIPROTKB|O93353 HOXA3 "Homeobox protein Hox-A3" [Gallus gallus (taxid:9031)]

 Score = 192 (72.6 bits), Expect = 1.5e-14, P = 1.5e-14
 Identities = 39/57 (68%), Positives = 45/57 (78%)

Query:    21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
             KRARTAYTS QL+ LEKEF+   Y+ R +R ++A  LNL ERQIKIWFQNRRMK KK
Sbjct:   174 KRARTAYTSAQLVELEKEFHFNRYLCRPRRVEMANLLNLTERQIKIWFQNRRMKYKK 230

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

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0001525 "angiogenesis" evidence=IEA

GO:0001974 "blood vessel remodeling" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

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

GO:0010159 "specification of organ position" evidence=IEA

GO:0021615 "glossopharyngeal nerve morphogenesis" evidence=IEA

GO:0030878 "thyroid gland development" evidence=IEA

GO:0048538 "thymus development" evidence=IEA

GO:0048645 "organ formation" evidence=IEA

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

GO:0051216 "cartilage development" evidence=IEA

GO:0060017 "parathyroid gland development" evidence=IEA

GO:0071837 "HMG box domain binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O43365	HXA3_HUMAN	No assigned EC number	0.6393	0.6161	0.1376	yes	N/A
O42367	HXB2A_DANRE	No assigned EC number	0.5454	0.6666	0.1692	yes	N/A
P02831	HXA3_MOUSE	No assigned EC number	0.6393	0.6161	0.1376	yes	N/A
Q08DG7	HXA3_BOVIN	No assigned EC number	0.6393	0.6161	0.1380	yes	N/A
P34684	LIN39_CAEEL	No assigned EC number	0.6065	0.6161	0.2411	yes	N/A
O93353	HXA3_CHICK	No assigned EC number	0.6393	0.6161	0.1476	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	99
pfam00046	57	pfam00046, Homeobox, Homeobox domain	2e-21
smart00389	57	smart00389, HOX, Homeodomain	3e-19
cd00086	59	cd00086, homeodomain, Homeodomain; DNA binding dom	1e-17
COG5576	156	COG5576, COG5576, Homeodomain-containing transcrip	4e-07

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

 Score = 79.4 bits (197), Expect = 2e-21
 Identities = 30/57 (52%), Positives = 39/57 (68%)

Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          +R RT +T  QL  LEKEF +  Y    +R +LAK+L L ERQ+K+WFQNRR K K+
Sbjct: 1  RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57

Length = 57

>gnl|CDD|197696 smart00389, HOX, Homeodomain

 Score = 73.8 bits (182), Expect = 3e-19
 Identities = 32/57 (56%), Positives = 41/57 (71%)

Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
          K+R RT++T  QL  LEKEF +  Y  R +R +LAK+L L ERQ+K+WFQNRR K K
Sbjct: 1  KRRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57

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

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

 Score = 70.0 bits (172), Expect = 1e-17
 Identities = 33/59 (55%), Positives = 41/59 (69%)

Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79
          +R RT +T  QL  LEKEF +  Y  R +R +LAKEL L ERQ+KIWFQNRR K K+ +
Sbjct: 1  RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59

Length = 59

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

 Score = 44.7 bits (106), Expect = 4e-07
 Identities = 23/60 (38%), Positives = 34/60 (56%)

Query: 20  KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79
            K  R   T  QL+ LE+EF    Y     R +L+  LN+  + ++IWFQN+R K+KK +
Sbjct: 51  PKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKR 110

Length = 156

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	99
KOG0488|consensus	309		99.78
KOG0842|consensus	307		99.78
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.78
KOG0494|consensus	332		99.77
KOG0489|consensus	261		99.77
KOG0484|consensus	125		99.76
KOG0487|consensus	308		99.75
KOG0850|consensus	245		99.74
KOG0843|consensus	197		99.74
KOG0485|consensus	268		99.73
KOG2251|consensus	228		99.68
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.67
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.67
COG5576	156	Homeodomain-containing transcription factor [Trans	99.67
KOG0492|consensus	246		99.66
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.65
KOG0493|consensus	342		99.64
KOG3802|consensus	398		99.62
KOG0483|consensus	198		99.62
KOG0491|consensus	194		99.61
KOG0848|consensus	317		99.58
KOG0486|consensus	351		99.52
KOG0847|consensus	288		99.5
KOG4577|consensus	383		99.47
KOG0844|consensus	408		99.33
KOG0490|consensus	235		99.29
KOG0775|consensus	304		99.21
KOG0849|consensus	354		99.19
KOG1168|consensus	385		99.14
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	99.01
KOG2252|consensus	558		98.96
KOG0774|consensus	334		98.85
KOG0490|consensus	235		98.27
KOG1146|consensus	1406		98.02
PF11569	56	Homez: Homeodomain leucine-zipper encoding, Homez;	97.94
KOG0773|consensus	342		97.42
KOG3623|consensus	1007		96.51
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	95.8
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	93.9
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	89.84
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	89.57
PF10668	60	Phage_terminase: Phage terminase small subunit; In	89.05
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	88.39
PRK03975	141	tfx putative transcriptional regulator; Provisiona	87.34
PRK10072	96	putative transcriptional regulator; Provisional	85.48
PF09607	58	BrkDBD: Brinker DNA-binding domain; InterPro: IPR0	84.95
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	84.94
PRK09413	121	IS2 repressor TnpA; Reviewed	84.82
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	84.67
PRK06759	154	RNA polymerase factor sigma-70; Validated	82.54
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	82.02
PF13518	52	HTH_28: Helix-turn-helix domain	81.17
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	81.05
COG3413	215	Predicted DNA binding protein [General function pr	80.78

>KOG0488|consensus

Probab=99.78  E-value=2.3e-19  Score=127.14  Aligned_cols=66  Identities=42%  Similarity=0.708  Sum_probs=61.6

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCC
Q psy16797         17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPE   82 (99)
Q Consensus        17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~   82 (99)
                      .+|+++.|+.||..|+..||+.|+...|++..+|++||..|||+..||++||||||+|||+.....
T Consensus       169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g  234 (309)
T KOG0488|consen  169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEG  234 (309)
T ss_pred             CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhh
Confidence            366677899999999999999999999999999999999999999999999999999999977663

>KOG0842|consensus

Probab=99.78  E-value=6.1e-20  Score=129.03  Aligned_cols=73  Identities=36%  Similarity=0.602  Sum_probs=65.7

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCchhhc
Q psy16797         16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNLEYK   88 (99)
Q Consensus        16 ~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~~~~~   88 (99)
                      ...++||.|..||..|..+||+.|..+.|++..+|+.||..|+||+.||+|||||+|-|.||...........
T Consensus       149 ~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~  221 (307)
T KOG0842|consen  149 GKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALL  221 (307)
T ss_pred             ccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhccc
Confidence            3557777889999999999999999999999999999999999999999999999999999988776654433

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.78  E-value=1.5e-18  Score=95.00  Aligned_cols=57  Identities=54%  Similarity=0.809  Sum_probs=54.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797         21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK   77 (99)
Q Consensus        21 ~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr   77 (99)
                      ++.|+.|+.+|+..|+.+|..++||+..++..||..+||+..+|.+||+|+|.++|+
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            468899999999999999999999999999999999999999999999999999885

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

>KOG0494|consensus

Probab=99.77  E-value=5.2e-19  Score=121.22  Aligned_cols=75  Identities=35%  Similarity=0.438  Sum_probs=71.4

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCchhhccccCCCcCC
Q psy16797         23 ARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNLEYKLHYTTHSHL   97 (99)
Q Consensus        23 ~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~~~~~~~~~~~~~~   97 (99)
                      .|+.||..|+..||+.|++.+||+...|+.||..+.|.+..|++||||||+||||.++.++.......|+..+.|
T Consensus       144 ~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~sT~maeyglyGam  218 (332)
T KOG0494|consen  144 FRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGSTIMAEYGLYGAM  218 (332)
T ss_pred             ccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcchhhhhhcccchh
Confidence            499999999999999999999999999999999999999999999999999999999999999988888887755

>KOG0489|consensus

Probab=99.77  E-value=5.2e-19  Score=122.97  Aligned_cols=68  Identities=54%  Similarity=0.800  Sum_probs=63.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCch
Q psy16797         18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNL   85 (99)
Q Consensus        18 ~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~~   85 (99)
                      ++.+|.|+.||..|+..||+.|..|.|++...|.+||..|.|+++||+|||||||+||||..+.....
T Consensus       157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~  224 (261)
T KOG0489|consen  157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ  224 (261)
T ss_pred             CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence            45788999999999999999999999999999999999999999999999999999999988776655

>KOG0484|consensus

Probab=99.76  E-value=4.5e-19  Score=106.69  Aligned_cols=73  Identities=40%  Similarity=0.634  Sum_probs=65.6

Q ss_pred             hhhhhhhccccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797          7 YLDDSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK   79 (99)
Q Consensus         7 ~~~~~~~~~~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~   79 (99)
                      +-++...+..+++.+|-|+.|+..|+..|+..|-+.+||++..|++||..+.|++..|++||||||+|.++..
T Consensus         4 ~~~~~~~l~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE   76 (125)
T KOG0484|consen    4 YGDDPLGLTEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE   76 (125)
T ss_pred             cCCCCCChhHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence            3345555666778888999999999999999999999999999999999999999999999999999998864

>KOG0487|consensus

Probab=99.75  E-value=6.8e-19  Score=123.81  Aligned_cols=68  Identities=49%  Similarity=0.721  Sum_probs=62.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCch
Q psy16797         18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNL   85 (99)
Q Consensus        18 ~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~~   85 (99)
                      +..||+|+.+|+.|+..||+.|-.|.|++.+.|.+|+..|+||++||+|||||||.|+||+..+....
T Consensus       233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r~~  300 (308)
T KOG0487|consen  233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENRLK  300 (308)
T ss_pred             cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhhcc
Confidence            56678899999999999999999999999999999999999999999999999999999998654443

>KOG0850|consensus

Probab=99.74  E-value=2e-18  Score=116.36  Aligned_cols=64  Identities=47%  Similarity=0.684  Sum_probs=59.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797         18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP   81 (99)
Q Consensus        18 ~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~   81 (99)
                      +|-|+.||-++..||..|+..|+.++|+.-.+|.+||..|||+..||+|||||||.|.||..+.
T Consensus       120 KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~  183 (245)
T KOG0850|consen  120 KKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQ  183 (245)
T ss_pred             ccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhc
Confidence            3445689999999999999999999999999999999999999999999999999999998873

>KOG0843|consensus

Probab=99.74  E-value=2.5e-18  Score=112.28  Aligned_cols=63  Identities=49%  Similarity=0.796  Sum_probs=60.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797         19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP   81 (99)
Q Consensus        19 ~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~   81 (99)
                      +-+|.||.|+.+|+..||..|+.++|-...+|..||..|+|++.||+|||||||.|.||....
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e  163 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE  163 (197)
T ss_pred             CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence            667789999999999999999999999999999999999999999999999999999998766

>KOG0485|consensus

Probab=99.73  E-value=2e-18  Score=115.78  Aligned_cols=74  Identities=36%  Similarity=0.544  Sum_probs=65.2

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCchhhcc
Q psy16797         16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNLEYKL   89 (99)
Q Consensus        16 ~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~~~~~~   89 (99)
                      .+.+|+|.|++|+..|+..||..|+...|++..+|..||.+|.|++.||++||||||.||||............
T Consensus       100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ea~sl~  173 (268)
T KOG0485|consen  100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLEAASLH  173 (268)
T ss_pred             cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhhhhhcc
Confidence            44578889999999999999999999999999999999999999999999999999999999765544333333

>KOG2251|consensus

Probab=99.68  E-value=3.5e-17  Score=109.82  Aligned_cols=68  Identities=34%  Similarity=0.564  Sum_probs=63.6

Q ss_pred             cccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCC
Q psy16797         15 DEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPE   82 (99)
Q Consensus        15 ~~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~   82 (99)
                      ...++.+|.||.|+-.|+++||..|.+..||+...+++||..|+|.+.+|+|||+|||+|+|+.+..+
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            45677788999999999999999999999999999999999999999999999999999999987754

>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=99.67  E-value=4.5e-16  Score=85.25  Aligned_cols=57  Identities=58%  Similarity=0.873  Sum_probs=53.8

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        22 r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      +.+..++..++..|+.+|..++||+..++..||..+||+..+|++||+|+|.+.++.
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            567789999999999999999999999999999999999999999999999998763

>smart00389 HOX Homeodomain

Probab=99.67  E-value=3e-16  Score=85.33  Aligned_cols=55  Identities=55%  Similarity=0.848  Sum_probs=51.6

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797         22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK   76 (99)
Q Consensus        22 r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k   76 (99)
                      +.|+.+++.++..|+..|..++||+..++..||..+||+..+|++||+|+|.+.+
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            5677899999999999999999999999999999999999999999999998753

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

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.67  E-value=1.1e-16  Score=103.67  Aligned_cols=71  Identities=34%  Similarity=0.505  Sum_probs=63.9

Q ss_pred             hccccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCC
Q psy16797         13 IADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPED   83 (99)
Q Consensus        13 ~~~~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~   83 (99)
                      ..+.+...+++|.+.+..|+.+|+..|..++||+...+..|+..++|+++.|++||||+|++.|+......
T Consensus        44 ~~~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~  114 (156)
T COG5576          44 KQDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKV  114 (156)
T ss_pred             cccCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccch
Confidence            34566677788999999999999999999999999999999999999999999999999999988766533

>KOG0492|consensus

Probab=99.66  E-value=1e-16  Score=106.88  Aligned_cols=63  Identities=44%  Similarity=0.777  Sum_probs=58.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797         18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT   80 (99)
Q Consensus        18 ~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~   80 (99)
                      +.-|+.|+.||..|+..||+-|...+|++++++.+++..|.|++.||+|||||||+|.||-+.
T Consensus       142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe  204 (246)
T KOG0492|consen  142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE  204 (246)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence            344568999999999999999999999999999999999999999999999999999988653

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.65  E-value=1.4e-16  Score=87.51  Aligned_cols=53  Identities=23%  Similarity=0.463  Sum_probs=50.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCC----CCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy16797         20 KKRARTAYTSNQLLALEKEFNQQNY----ILRAKRHQLAKELNLCERQIKIWFQNRR   72 (99)
Q Consensus        20 ~~r~r~~~s~~q~~~L~~~f~~~~~----p~~~~~~~la~~l~l~~~~V~~WFqNrR   72 (99)
                      ++|.||.||.+|+..|+.+|..++|    |+...+.+||..+||+..+|++||||.+
T Consensus         1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            4789999999999999999999999    9999999999999999999999999965

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

>KOG0493|consensus

Probab=99.64  E-value=5.2e-16  Score=106.72  Aligned_cols=67  Identities=48%  Similarity=0.773  Sum_probs=60.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCchhh
Q psy16797         21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNLEY   87 (99)
Q Consensus        21 ~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~~~~   87 (99)
                      +|.|+.|+.+|+..|...|+.|.|++...|.+||.+|+|.+.||+|||||+|+|.||.........+
T Consensus       247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn~la~  313 (342)
T KOG0493|consen  247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKNRLAL  313 (342)
T ss_pred             cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCCchhh
Confidence            4679999999999999999999999999999999999999999999999999999997766555443

>KOG3802|consensus

Probab=99.62  E-value=2.1e-16  Score=113.63  Aligned_cols=78  Identities=27%  Similarity=0.409  Sum_probs=68.4

Q ss_pred             hhhhhhhhhhhc------------cccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHH
Q psy16797          3 RVQKYLDDSLIA------------DEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQN   70 (99)
Q Consensus         3 ~~~~~~~~~~~~------------~~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqN   70 (99)
                      .+.+|+++....            ....+|||+||.|.......||.+|.+|+.|+..++..||.+|+|....|+|||||
T Consensus       265 LL~KWLeEAes~~~~~~~~~~e~i~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCN  344 (398)
T KOG3802|consen  265 LLEKWLEEAESRESTGSPNSIEKIGAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCN  344 (398)
T ss_pred             HHHHHHHHHhcccccCCCCCHHHhhccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeec
Confidence            456677665551            23346788999999999999999999999999999999999999999999999999


Q ss_pred             HHhHHhhcCC
Q psy16797         71 RRMKKKKGKT   80 (99)
Q Consensus        71 rR~k~kr~~~   80 (99)
                      ||.|.||...
T Consensus       345 RRQkeKR~~~  354 (398)
T KOG3802|consen  345 RRQKEKRITP  354 (398)
T ss_pred             cccccccCCC
Confidence            9999999877

>KOG0483|consensus

Probab=99.62  E-value=2.9e-16  Score=105.00  Aligned_cols=72  Identities=35%  Similarity=0.500  Sum_probs=64.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCchhhcccc
Q psy16797         20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNLEYKLHY   91 (99)
Q Consensus        20 ~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~~~~~~~~   91 (99)
                      ..+++.+++.+|...|+..|..+.++.+..+..||..|||.++||.+||||||++||.++...+...+...+
T Consensus        50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~  121 (198)
T KOG0483|consen   50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQL  121 (198)
T ss_pred             cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHH
Confidence            344566799999999999999999999999999999999999999999999999999999888776665544

>KOG0491|consensus

Probab=99.61  E-value=4.2e-16  Score=100.72  Aligned_cols=64  Identities=45%  Similarity=0.786  Sum_probs=59.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCC
Q psy16797         20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPED   83 (99)
Q Consensus        20 ~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~   83 (99)
                      +++.|++|+..|+..|++.|+...|++..++.+||..|+|++.||+.||||+|.|.||......
T Consensus       100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~  163 (194)
T KOG0491|consen  100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ  163 (194)
T ss_pred             hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence            4567999999999999999999999999999999999999999999999999999999776544

>KOG0848|consensus

Probab=99.58  E-value=6.3e-16  Score=106.43  Aligned_cols=60  Identities=48%  Similarity=0.781  Sum_probs=56.1

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCC
Q psy16797         23 ARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPE   82 (99)
Q Consensus        23 ~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~   82 (99)
                      =|.++|..|..+||+.|..++|.++..+-+||.-|||+++||+|||||||+|+||..+..
T Consensus       202 YRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk  261 (317)
T KOG0848|consen  202 YRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK  261 (317)
T ss_pred             eeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence            477899999999999999999999999999999999999999999999999999877654

>KOG0486|consensus

Probab=99.52  E-value=3.9e-15  Score=104.37  Aligned_cols=73  Identities=33%  Similarity=0.503  Sum_probs=64.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCchhhcccc
Q psy16797         19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNLEYKLHY   91 (99)
Q Consensus        19 ~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~~~~~~~~   91 (99)
                      |++|.|+.|+..|+..||..|..|.||+...+++||...++++..|++||.|||+||++++.-+.....+..+
T Consensus       111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ae~~k~~f  183 (351)
T KOG0486|consen  111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAELAKGGF  183 (351)
T ss_pred             hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHHHHhhhcCC
Confidence            4566899999999999999999999999999999999999999999999999999999988766633344433

>KOG0847|consensus

Probab=99.50  E-value=1.7e-14  Score=97.16  Aligned_cols=66  Identities=42%  Similarity=0.740  Sum_probs=60.8

Q ss_pred             cccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797         15 DEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT   80 (99)
Q Consensus        15 ~~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~   80 (99)
                      ..+++++-.|..|+..|+..|+..|+...|+..+++.++|..+|++..+|++||||||+|||++..
T Consensus       162 ~kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA  227 (288)
T KOG0847|consen  162 NLNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA  227 (288)
T ss_pred             CcCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence            345667778899999999999999999999999999999999999999999999999999999753

>KOG4577|consensus

Probab=99.47  E-value=5e-14  Score=98.18  Aligned_cols=71  Identities=35%  Similarity=0.494  Sum_probs=64.8

Q ss_pred             hccccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCC
Q psy16797         13 IADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPED   83 (99)
Q Consensus        13 ~~~~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~   83 (99)
                      ..+++...+|.|+.+|..|++.|...|+..+.|....|+.|+.++||..+.|++||||||+|+||-++..+
T Consensus       160 ~l~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAG  230 (383)
T KOG4577|consen  160 ELEGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAG  230 (383)
T ss_pred             ccccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcc
Confidence            34567788899999999999999999999999999999999999999999999999999999998766544

>KOG0844|consensus

Probab=99.33  E-value=2.9e-13  Score=95.05  Aligned_cols=64  Identities=50%  Similarity=0.800  Sum_probs=58.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797         18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP   81 (99)
Q Consensus        18 ~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~   81 (99)
                      ..-+|=|+.||-+|+..||+.|....|-+...|.+||..|+|.+..|++||||||.|+||+..-
T Consensus       179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla  242 (408)
T KOG0844|consen  179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA  242 (408)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence            3446678999999999999999999999999999999999999999999999999999997643

>KOG0490|consensus

Probab=99.29  E-value=2.1e-12  Score=87.51  Aligned_cols=64  Identities=38%  Similarity=0.460  Sum_probs=60.1

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797         17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT   80 (99)
Q Consensus        17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~   80 (99)
                      ..++++.|+.|+..|++.|+..|+..+||+...++.+|..+++++..|++||||+|+++++...
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            4567789999999999999999999999999999999999999999999999999999998774

>KOG0775|consensus

Probab=99.21  E-value=3.5e-11  Score=83.35  Aligned_cols=54  Identities=22%  Similarity=0.409  Sum_probs=48.9

Q ss_pred             CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797         27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT   80 (99)
Q Consensus        27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~   80 (99)
                      |...-...|..+|..++||++.++.+||..+||+..||.+||+|||+++|....
T Consensus       183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~a  236 (304)
T KOG0775|consen  183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAAA  236 (304)
T ss_pred             hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhccc
Confidence            555567899999999999999999999999999999999999999999995544

>KOG0849|consensus

Probab=99.19  E-value=2.6e-11  Score=87.67  Aligned_cols=66  Identities=38%  Similarity=0.603  Sum_probs=60.4

Q ss_pred             cccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797         15 DEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT   80 (99)
Q Consensus        15 ~~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~   80 (99)
                      ...++.++.|+.|+..|++.|+..|..++||+...++.||..++++...|.+||+|+|+++++...
T Consensus       171 ~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~  236 (354)
T KOG0849|consen  171 ALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR  236 (354)
T ss_pred             cccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence            344556677899999999999999999999999999999999999999999999999999999773

>KOG1168|consensus

Probab=99.14  E-value=4.4e-12  Score=88.62  Aligned_cols=63  Identities=32%  Similarity=0.427  Sum_probs=58.3

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797         17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK   79 (99)
Q Consensus        17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~   79 (99)
                      -+.++|+|+.+-..+...||.+|...+.|+.+.+..||+.|.|....|++||+|.|+|.||+.
T Consensus       306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~  368 (385)
T KOG1168|consen  306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK  368 (385)
T ss_pred             ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence            345678899999999999999999999999999999999999999999999999999998854

>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=99.01  E-value=6.8e-10  Score=56.67  Aligned_cols=35  Identities=31%  Similarity=0.568  Sum_probs=29.4

Q ss_pred             hhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhH
Q psy16797         40 NQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK   74 (99)
Q Consensus        40 ~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k   74 (99)
                      ..+|||+.+++..||..+|++..||..||-|.|.+
T Consensus         6 ~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR   40 (40)
T PF05920_consen    6 LHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR   40 (40)
T ss_dssp             TTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence            35799999999999999999999999999999864

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

>KOG2252|consensus

Probab=98.96  E-value=3.6e-09  Score=79.21  Aligned_cols=58  Identities=22%  Similarity=0.306  Sum_probs=54.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHH
Q psy16797         18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKK   75 (99)
Q Consensus        18 ~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~   75 (99)
                      -+.+|.|.+|+..|.+-|...|+.+++|+.+..+.|+..|+|....|.+||.|.|.+.
T Consensus       418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            3456679999999999999999999999999999999999999999999999999875

>KOG0774|consensus

Probab=98.85  E-value=1.3e-09  Score=75.42  Aligned_cols=60  Identities=27%  Similarity=0.483  Sum_probs=54.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797         20 KKRARTAYTSNQLLALEKEFN---QQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK   79 (99)
Q Consensus        20 ~~r~r~~~s~~q~~~L~~~f~---~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~   79 (99)
                      .+|+|..|++...++|..+|.   .|+||+.+.+++||.+++++..||.+||.|+|-+.++-.
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~  250 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM  250 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence            456778899999999999995   689999999999999999999999999999998877744

>KOG0490|consensus

Probab=98.27  E-value=1.2e-06  Score=59.30  Aligned_cols=64  Identities=45%  Similarity=0.620  Sum_probs=58.7

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797         17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT   80 (99)
Q Consensus        17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~   80 (99)
                      ..+.++.++.+...++..+...|...++|+...+..|+..+|++...+++||+|+|.+.++...
T Consensus       150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR  213 (235)
T ss_pred             ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence            4556678899999999999999999999999999999999999999999999999999988655

>KOG1146|consensus

Probab=98.02  E-value=7.8e-06  Score=66.74  Aligned_cols=63  Identities=29%  Similarity=0.385  Sum_probs=58.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCC
Q psy16797         20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPE   82 (99)
Q Consensus        20 ~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~   82 (99)
                      ++..|+.++..|+..+...|....||...+.+.+...+++..+.|.+||+|.|.+.++.....
T Consensus       903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~  965 (1406)
T KOG1146|consen  903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG  965 (1406)
T ss_pred             hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence            345789999999999999999999999999999999999999999999999999999877744

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

Probab=97.94  E-value=1.8e-05  Score=42.96  Aligned_cols=41  Identities=17%  Similarity=0.396  Sum_probs=31.3

Q ss_pred             HHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy16797         32 LLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRR   72 (99)
Q Consensus        32 ~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR   72 (99)
                      +..|+.+|...+++.......|....+|+..+|+.||-.+.
T Consensus        10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~   50 (56)
T PF11569_consen   10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM   50 (56)
T ss_dssp             -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred             hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence            45699999999999999999999999999999999997654

>KOG0773|consensus

Probab=97.42  E-value=9.4e-05  Score=53.27  Aligned_cols=57  Identities=25%  Similarity=0.347  Sum_probs=47.5

Q ss_pred             CCCCCCCCCHHHHHHHHHH-Hh--hcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797         20 KKRARTAYTSNQLLALEKE-FN--QQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK   76 (99)
Q Consensus        20 ~~r~r~~~s~~q~~~L~~~-f~--~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k   76 (99)
                      +.+.+..+.+....+|..+ |.  ..+||+..++..|+.++|++..||.+||.|.|.+.-
T Consensus       239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w  298 (342)
T KOG0773|consen  239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLW  298 (342)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccC
Confidence            4455667888888888877 33  368999999999999999999999999999997643

>KOG3623|consensus

Probab=96.51  E-value=0.01  Score=47.01  Aligned_cols=48  Identities=13%  Similarity=0.231  Sum_probs=44.7

Q ss_pred             HHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797         32 LLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK   79 (99)
Q Consensus        32 ~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~   79 (99)
                      ..+|..+|..|..|+..+...+|.+.|+....|+.||.+.++......
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~  615 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE  615 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence            678999999999999999999999999999999999999999877655

>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=95.80  E-value=0.045  Score=29.17  Aligned_cols=47  Identities=19%  Similarity=0.408  Sum_probs=34.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy16797         21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRR   72 (99)
Q Consensus        21 ~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR   72 (99)
                      ++.|..+|-++...+-..++...     ....||..+|++..+|..|..|+.
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            46778899998777777777655     477899999999999999998854

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=93.90  E-value=0.4  Score=24.72  Aligned_cols=46  Identities=7%  Similarity=0.145  Sum_probs=35.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797         26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK   76 (99)
Q Consensus        26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k   76 (99)
                      .+++.+..++...|..     .....++|..+|++...|+.+...-..+.|
T Consensus         4 ~L~~~er~vi~~~y~~-----~~t~~eIa~~lg~s~~~V~~~~~~al~kLR   49 (50)
T PF04545_consen    4 QLPPREREVIRLRYFE-----GLTLEEIAERLGISRSTVRRILKRALKKLR   49 (50)
T ss_dssp             TS-HHHHHHHHHHHTS-----T-SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHhcC-----CCCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence            4678888999988832     234677899999999999999887766655

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=89.84  E-value=1.9  Score=22.99  Aligned_cols=43  Identities=19%  Similarity=0.264  Sum_probs=34.6

Q ss_pred             CCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHhCCChHHHHHHHH
Q psy16797         27 YTSNQLLALEKEFNQQNY--ILRAKRHQLAKELNLCERQIKIWFQ   69 (99)
Q Consensus        27 ~s~~q~~~L~~~f~~~~~--p~~~~~~~la~~l~l~~~~V~~WFq   69 (99)
                      +|+.|..+|...|...-|  |-.....+||..+|++...+..-..
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LR   45 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLR   45 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHH
Confidence            478899999999886544  6667778899999999998876553

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=89.57  E-value=0.71  Score=25.62  Aligned_cols=47  Identities=19%  Similarity=0.345  Sum_probs=29.1

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy16797         22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRR   72 (99)
Q Consensus        22 r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR   72 (99)
                      +.|..||+++...+-..+..    .......+|..+|+++.++..|-.--+
T Consensus         2 ~~r~~ys~e~K~~~v~~~~~----~g~sv~~va~~~gi~~~~l~~W~~~~~   48 (76)
T PF01527_consen    2 RKRRRYSPEFKLQAVREYLE----SGESVSEVAREYGISPSTLYNWRKQYR   48 (76)
T ss_dssp             -SS----HHHHHHHHHHHHH----HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHH----CCCceEeeecccccccccccHHHHHHh
Confidence            35677999986655555421    225577889999999999999986544

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.

>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=89.05  E-value=0.44  Score=26.20  Aligned_cols=22  Identities=27%  Similarity=0.543  Sum_probs=18.6

Q ss_pred             HHHHHHHHhCCChHHHHHHHHH
Q psy16797         49 KRHQLAKELNLCERQIKIWFQN   70 (99)
Q Consensus        49 ~~~~la~~l~l~~~~V~~WFqN   70 (99)
                      .-..||..||+++.+|+.|=..
T Consensus        24 ~lkdIA~~Lgvs~~tIr~WK~~   45 (60)
T PF10668_consen   24 KLKDIAEKLGVSESTIRKWKSR   45 (60)
T ss_pred             cHHHHHHHHCCCHHHHHHHhhh
Confidence            3567899999999999999643

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 [].

>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=88.39  E-value=1.7  Score=21.57  Aligned_cols=43  Identities=9%  Similarity=0.149  Sum_probs=30.9

Q ss_pred             CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhH
Q psy16797         27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK   74 (99)
Q Consensus        27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k   74 (99)
                      +++.+..++...|...     .....+|..+|++...|..|...-+.+
T Consensus        11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~   53 (55)
T cd06171          11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK   53 (55)
T ss_pred             CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            5666777776666322     235667999999999999999765544

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

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=87.34  E-value=4.5  Score=25.93  Aligned_cols=50  Identities=14%  Similarity=0.141  Sum_probs=38.8

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797         24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK   79 (99)
Q Consensus        24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~   79 (99)
                      ...+++.|..+|...+.  .    ....++|..+|++...|..|..+.+.+.++..
T Consensus         4 ~~~Lt~rqreVL~lr~~--G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~   53 (141)
T PRK03975          4 ESFLTERQIEVLRLRER--G----LTQQEIADILGTSRANVSSIEKRARENIEKAR   53 (141)
T ss_pred             ccCCCHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            35688999999977432  2    33568999999999999999998888766643

>PRK10072 putative transcriptional regulator; Provisional

Probab=85.48  E-value=2.8  Score=25.07  Aligned_cols=40  Identities=20%  Similarity=0.245  Sum_probs=29.3

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy16797         26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRR   72 (99)
Q Consensus        26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR   72 (99)
                      +.+...+..|...-..       ...++|..+|++...|..|...++
T Consensus        32 ~~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r   71 (96)
T PRK10072         32 TTSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRV   71 (96)
T ss_pred             cCChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCC
Confidence            4566666666544322       257789999999999999998665

>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx

Probab=84.95  E-value=4.6  Score=22.03  Aligned_cols=46  Identities=24%  Similarity=0.414  Sum_probs=23.8

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHH
Q psy16797         24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQN   70 (99)
Q Consensus        24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqN   70 (99)
                      |..|+.......-.+|....---...|. .|..+|++..+|+-|-+-
T Consensus         3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RA-aarkf~V~r~~Vr~W~kq   48 (58)
T PF09607_consen    3 RRSYTAEFKLKVVEYAEKDNNCKGNQRA-AARKFNVSRRQVRKWRKQ   48 (58)
T ss_dssp             -----HHHHHHHHHHHHH-TTTTT-HHH-HHHHTTS-HHHHHHHHTT
T ss_pred             ccccChHHHHHHHHHHHHccchhhhHHH-HHHHhCccHHHHHHHHHH
Confidence            4567777644444444433322223333 499999999999999853

100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.

>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators

Probab=84.94  E-value=4.1  Score=21.47  Aligned_cols=45  Identities=20%  Similarity=0.197  Sum_probs=34.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797         26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK   76 (99)
Q Consensus        26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k   76 (99)
                      .+|+.+..+|.-...-      ....++|..+|+++..|..+..+=+.|..
T Consensus         3 ~LT~~E~~vl~~l~~G------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~   47 (58)
T PF00196_consen    3 SLTERELEVLRLLAQG------MSNKEIAEELGISEKTVKSHRRRIMKKLG   47 (58)
T ss_dssp             SS-HHHHHHHHHHHTT------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred             ccCHHHHHHHHHHHhc------CCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence            5788888888776543      33678999999999999999988776654

The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=84.82  E-value=4.4  Score=24.92  Aligned_cols=45  Identities=13%  Similarity=0.242  Sum_probs=30.2

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHH
Q psy16797         23 ARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNR   71 (99)
Q Consensus        23 ~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNr   71 (99)
                      .+.+++.++....-.....+.    .....+|..+|+++.+|..|..--
T Consensus         9 ~rr~ys~EfK~~aV~~~~~~g----~sv~evA~e~gIs~~tl~~W~r~y   53 (121)
T PRK09413          9 KRRRRTTQEKIAIVQQSFEPG----MTVSLVARQHGVAASQLFLWRKQY   53 (121)
T ss_pred             CCCCCCHHHHHHHHHHHHcCC----CCHHHHHHHHCcCHHHHHHHHHHH
Confidence            356688887554433333333    235678999999999999997543

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

Probab=84.67  E-value=3.9  Score=21.05  Aligned_cols=43  Identities=19%  Similarity=0.185  Sum_probs=27.9

Q ss_pred             CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhH
Q psy16797         27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK   74 (99)
Q Consensus        27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k   74 (99)
                      +++.+..++...|-.     .-...++|..+|++...|+.|....+.+
T Consensus        11 L~~~~r~i~~l~~~~-----g~s~~eIa~~l~~s~~~v~~~l~ra~~~   53 (54)
T PF08281_consen   11 LPERQREIFLLRYFQ-----GMSYAEIAEILGISESTVKRRLRRARKK   53 (54)
T ss_dssp             S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHH-----CcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence            455555555555432     3456789999999999999999876643

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

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=82.54  E-value=9.3  Score=23.71  Aligned_cols=29  Identities=14%  Similarity=0.180  Sum_probs=24.7

Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797         49 KRHQLAKELNLCERQIKIWFQNRRMKKKK   77 (99)
Q Consensus        49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr   77 (99)
                      ...+||..+|++...|+.+...-+.+.|+
T Consensus       124 s~~EIA~~l~is~~tV~~~~~ra~~~Lr~  152 (154)
T PRK06759        124 TMGEIALETEMTYYQVRWIYRQALEKMRN  152 (154)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence            36788999999999999999887777665

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=82.02  E-value=4.5  Score=20.38  Aligned_cols=40  Identities=15%  Similarity=0.150  Sum_probs=21.1

Q ss_pred             CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHH
Q psy16797         25 TAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQ   69 (99)
Q Consensus        25 ~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFq   69 (99)
                      ..+|..+...++..+..     .....+||..+|++...|..+..
T Consensus         3 ~~Lt~~eR~~I~~l~~~-----G~s~~~IA~~lg~s~sTV~relk   42 (44)
T PF13936_consen    3 KHLTPEERNQIEALLEQ-----GMSIREIAKRLGRSRSTVSRELK   42 (44)
T ss_dssp             ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred             cchhhhHHHHHHHHHHc-----CCCHHHHHHHHCcCcHHHHHHHh
Confidence            35777887888777653     24466799999999999998875

>PF13518 HTH_28: Helix-turn-helix domain

Probab=81.17  E-value=2.9  Score=21.22  Aligned_cols=25  Identities=16%  Similarity=0.453  Sum_probs=20.3

Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHh
Q psy16797         49 KRHQLAKELNLCERQIKIWFQNRRM   73 (99)
Q Consensus        49 ~~~~la~~l~l~~~~V~~WFqNrR~   73 (99)
                      ...++|..+|++..+|..|.+.-+.
T Consensus        14 s~~~~a~~~gis~~tv~~w~~~y~~   38 (52)
T PF13518_consen   14 SVREIAREFGISRSTVYRWIKRYRE   38 (52)
T ss_pred             CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence            3556899999999999999975443

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=81.05  E-value=2.2  Score=21.65  Aligned_cols=23  Identities=17%  Similarity=0.397  Sum_probs=17.3

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHH
Q psy16797         48 AKRHQLAKELNLCERQIKIWFQN   70 (99)
Q Consensus        48 ~~~~~la~~l~l~~~~V~~WFqN   70 (99)
                      ....++|..+|++...|..|...
T Consensus        18 ~s~~~ia~~lgvs~~Tv~~w~kr   40 (50)
T PF13384_consen   18 WSIREIAKRLGVSRSTVYRWIKR   40 (50)
T ss_dssp             --HHHHHHHHTS-HHHHHHHHT-
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHH
Confidence            44677899999999999999854

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

Probab=80.78  E-value=6.1  Score=26.60  Aligned_cols=44  Identities=25%  Similarity=0.330  Sum_probs=36.2

Q ss_pred             CCCHHHHHHHHHHHhhcC--CCCHHHHHHHHHHhCCChHHHHHHHH
Q psy16797         26 AYTSNQLLALEKEFNQQN--YILRAKRHQLAKELNLCERQIKIWFQ   69 (99)
Q Consensus        26 ~~s~~q~~~L~~~f~~~~--~p~~~~~~~la~~l~l~~~~V~~WFq   69 (99)
                      .+|+.|+.+|...|...=  +|-......||..+|+++..+..-.+
T Consensus       155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLR  200 (215)
T COG3413         155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLR  200 (215)
T ss_pred             cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHH
Confidence            699999999999998654  37777778899999999988766443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	99
2h1k_A	63	Crystal Structure Of The Pdx1 Homeodomain In Comple		8e-14
1ftz_A	70	Nuclear Magnetic Resonance Solution Structure Of Th		2e-13
1jgg_A	60	Even-Skipped Homeodomain Complexed To At-Rich Dna L		6e-13
1b8i_A	81	Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX		1e-12
2r5y_A	88	Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO		2e-12
1ahd_P	68	Determination Of The Nmr Solution Structure Of An A		7e-12
9ant_A	62	Antennapedia Homeodomain-Dna Complex Length = 62		9e-12
1hdd_C	61	Crystal Structure Of An Engrailed Homeodomain-Dna C		1e-11
3hdd_A	60	Engrailed Homeodomain Dna Complex Length = 60		1e-11
1puf_A	77	Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo		1e-11
2lp0_A	60	The Solution Structure Of Homeodomain-Protein Compl		2e-11
1b72_A	97	Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le		2e-11
1p7j_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		2e-11
1hom_A	68	Determination Of The Three-Dimensional Structure Of		2e-11
1p7i_A	59	Crystal Structure Of Engrailed Homeodomain Mutant K		3e-11
2m34_A	71	Nmr Structure Of The Homeodomain Transcription Fact		3e-11
2hdd_A	61	Engrailed Homeodomain Q50k Variant Dna Complex Leng		3e-11
1ig7_A	58	Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58		4e-11
1ztr_A	61	Solution Structure Of Engrailed Homeodomain L16a Mu		1e-10
1du0_A	57	Engrailed Homeodomain Q50a Variant Dna Complex Leng		2e-10
1enh_A	54	Structural Studies Of The Engrailed Homeodomain Len		2e-10
2dmt_A	80	Solution Structure Of The Homeobox Domain Of Homeob		2e-10
1san_A	62	The Des(1-6)antennapedia Homeodomain: Comparison Of		2e-10
2hos_A	63	Phage-selected Homeodomain Bound To Unmodified Dna		6e-10
2djn_A	70	The Solution Structure Of The Homeobox Domain Of Hu		3e-09
2ld5_A	67	Solution Nmr-Derived Complex Structure Of Hoxa13 Dn		4e-09
2l7z_A	73	Nmr Structure Of A13 Homedomain Length = 73		4e-09
3rkq_A	58	Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Lengt		5e-09
2cra_A	70	Solution Structure Of The Homeobox Domain Of Human		6e-09
3a01_A	93	Crystal Structure Of Aristaless And Clawless Homeod		2e-08
2e1o_A	70	Solution Structure Of Rsgi Ruh-028, A Homeobox Doma		4e-08
3a01_B	67	Crystal Structure Of Aristaless And Clawless Homeod		1e-07
1fjl_A	81	Homeodomain From The Drosophila Paired Protein Boun		1e-07
3a03_A	56	Crystal Structure Of Hox11l1 Homeodomain Length = 5		1e-07
2l9r_A	69	Solution Nmr Structure Of Homeobox Domain Of Homeob		1e-07
1zq3_P	68	Nmr Solution Structure Of The Bicoid Homeodomain Bo		1e-07
2kt0_A	84	Solution Structure Of Human Stem Cell Transcription		1e-07
2m0c_A	75	Solution Nmr Structure Of Homeobox Domain Of Human		2e-07
3lnq_A	58	Structure Of Aristaless Homeodomain In Complex With		3e-07
2cue_A	80	Solution Structure Of The Homeobox Domain Of The Hu		3e-07
2vi6_A	62	Crystal Structure Of The Nanog Homeodomain Length =		7e-07
1nk2_P	77	VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES		8e-07
2dmu_A	70	Solution Structure Of The Homeobox Domain Of Homeob		1e-06
3cmy_A	61	Structure Of A Homeodomain In Complex With Dna Leng		1e-06
2p81_A	44	Engrailed Homeodomain Helix-Turn-Helix Motif Length		1e-06
2l7m_P	68	Solution Structure Of The Pitx2 Homeodomain R24h Mu		2e-06
1qry_A	80	Homeobox Protein Vnd (Ventral Nervous System Defect		2e-06
1ftt_A	68	Thyroid Transcription Factor 1 Homeodomain (Rattus		3e-06
2l7f_P	68	Solution Structure Of The Pitx2 Homeodomain Length		3e-06
3a02_A	60	Crystal Structure Of Aristaless Homeodomain Length		6e-06
2k40_A	67	Nmr Structure Of Hesx-1 Homeodomain Double Mutant R		1e-05
2dms_A	80	Solution Structure Of The Homeobox Domain Of Homeob		5e-05

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

Iteration: 1
 Score = 72.0 bits (175), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 39/57 (68%), Positives = 41/57 (71%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          KR RTAYT  QLL LEKEF    YI R +R +LA  LNL ER IKIWFQNRRMK KK
Sbjct: 4  KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60

>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 = 70.9 bits (172), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 37/67 (55%), Positives = 45/67 (67%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80
          KR R  YT  Q L LEKEF+   YI R +R  +A  L+L ERQIKIWFQNRRMK KK +T
Sbjct: 4  KRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKDRT 63
Query: 81 PEDNLEY 87
           + + E+
Sbjct: 64 LDSSPEH 70

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 33/57 (57%), Positives = 44/57 (77%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          +R RTA+T +QL  LEKEF ++NY+ R +R +LA +LNL E  IK+WFQNRRMK K+
Sbjct: 2  RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 58

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

Iteration: 1
 Score = 67.8 bits (164), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 35/65 (53%), Positives = 44/65 (67%)
Query: 13 IADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRR 72
          IA     ++R R  YT  Q L LEKEF+  +Y+ R +R ++A  L+L ERQIKIWFQNRR
Sbjct: 13 IAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRR 72
Query: 73 MKKKK 77
          MK KK
Sbjct: 73 MKLKK 77

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

Iteration: 1
 Score = 67.8 bits (164), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 35/57 (61%), Positives = 42/57 (73%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          KR RT+YT  Q L LEKEF+   Y+ R +R ++A  L+L ERQIKIWFQNRRMK KK
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 85

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

Iteration: 1
 Score = 65.5 bits (158), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 34/58 (58%), Positives = 41/58 (70%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          +KR R  YT  Q L LEKEF+   Y+ R +R ++A  L+L ERQIKIWFQNRRMK KK
Sbjct: 2  RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 59

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

Iteration: 1
 Score = 65.1 bits (157), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 34/58 (58%), Positives = 41/58 (70%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          +KR R  YT  Q L LEKEF+   Y+ R +R ++A  L+L ERQIKIWFQNRRMK KK
Sbjct: 3  RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 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 = 65.1 bits (157), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 32/58 (55%), Positives = 41/58 (70%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78
          KR RTA++S QL  L++EFN+  Y+   +R QL+ EL L E QIKIWFQN+R K KK 
Sbjct: 4  KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 61

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

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 32/58 (55%), Positives = 41/58 (70%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78
          KR RTA++S QL  L++EFN+  Y+   +R QL+ EL L E QIKIWFQN+R K KK 
Sbjct: 2  KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 59

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

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 32/60 (53%), Positives = 43/60 (71%)
Query: 18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          +  ++ R  YT +Q L LEKEF    Y+ R +R+++A+ LNL ERQ+KIWFQNRRMK KK
Sbjct: 11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/57 (56%), Positives = 41/57 (71%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          ++ R  YT  Q L LEKEF    Y+ R +R+++A+ LNL ERQ+KIWFQNRRMK KK
Sbjct: 2  RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/54 (57%), Positives = 40/54 (74%)
Query: 24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          RT +T+ QL  LEKEF+   Y+ RA+R ++A  L L E Q+KIWFQNRRMK+KK
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91

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

Iteration: 1
 Score = 63.9 bits (154), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/58 (55%), Positives = 40/58 (68%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78
          KR RTA++S QL  L++EFN+  Y+   +R QL+ EL L E QIKIWFQN R K KK 
Sbjct: 2  KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKKS 59

>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 = 63.9 bits (154), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/58 (58%), Positives = 40/58 (68%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          +KR R  YT  Q L LEKEF+   Y+ R +R ++A  L L ERQIKIWFQNRRMK KK
Sbjct: 2  RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 59

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

Iteration: 1
 Score = 63.5 bits (153), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 32/58 (55%), Positives = 40/58 (68%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78
          KR RTA++S QL  L++EFN+  Y+   +R QL+ EL L E QIKIWFQN R K KK 
Sbjct: 2  KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKKS 59

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

Iteration: 1
 Score = 63.2 bits (152), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 33/60 (55%), Positives = 42/60 (70%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80
          +R RTA+TS QLL LEKEF+ + Y+   +R Q+A  L L E Q+KIWFQNRR K K+ K 
Sbjct: 8  RRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKRIKA 67

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

Iteration: 1
 Score = 63.2 bits (152), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 42/60 (70%)
Query: 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78
           +KR RTA++S QL  L++EFN+  Y+   +R QL+ EL L E QIKIWF+N+R K KK 
Sbjct: 2  AEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKKS 61

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

Iteration: 1
 Score = 63.2 bits (152), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 42/57 (73%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          ++ RT +T+ QLLALE++F Q+ Y+  A+R + +  L+L E Q+KIWFQNRR K K+
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

Iteration: 1
 Score = 61.2 bits (147), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 29/55 (52%), Positives = 39/55 (70%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74
          +KR RTA++S QL   ++EFN+  Y+   +R QL+ EL L E QIKIWFQN+R K
Sbjct: 3  EKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 57

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

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 30/57 (52%), Positives = 39/57 (68%)
Query: 22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78
          R RTA++S QL  L++EFN+  Y+   +R QL+ EL L E QIKIWF N+R K KK 
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKKS 57

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

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 29/53 (54%), Positives = 38/53 (71%)
Query: 22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74
          R RTA++S QL  L++EFN+  Y+   +R QL+ EL L E QIKIWFQN+R K
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53

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

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/61 (50%), Positives = 41/61 (67%), Gaps = 1/61 (1%)
Query: 17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
          KKG+ R+RT +T  QL+ LEK F +Q Y+    R  LA+ L L + Q+K W+QNRRMK K
Sbjct: 15 KKGR-RSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWK 73
Query: 77 K 77
          K
Sbjct: 74 K 74

>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 = 60.5 bits (145), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/52 (59%), Positives = 37/52 (71%)
Query: 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
           YT  Q L LEKEF+   Y+ R +R ++A  L+L ERQIKIWFQNRRMK KK
Sbjct: 2  TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 53

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 29/57 (50%), Positives = 39/57 (68%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          KR RTA++S QL  L++EFN+  Y+   +R QL+ EL L E Q+K WF+N R K KK
Sbjct: 5  KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 38/57 (66%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          ++ RT Y+S QL AL++ F +  Y+   +R +LA  L L + Q+KIWFQN+R K KK
Sbjct: 8  RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 28/59 (47%), Positives = 40/59 (67%), Gaps = 1/59 (1%)
Query: 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          G+K+ R  YT  QL  LE+E+    +I + KR +++   NL ERQ+ IWFQNRR+K+KK
Sbjct: 1  GRKK-RVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 28/59 (47%), Positives = 40/59 (67%), Gaps = 1/59 (1%)
Query: 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          G+K+ R  YT  QL  LE+E+    +I + KR +++   NL ERQ+ IWFQNRR+K+KK
Sbjct: 7  GRKK-RVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 26/58 (44%), Positives = 36/58 (62%)
Query: 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
          G+++ R  ++  Q+  LE+ F QQ Y+   +R QLA  L L   Q+KIWFQNRR K K
Sbjct: 1  GRRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 36/54 (66%)
Query: 24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          R  Y+  QL  LE+E+    +I + KR +++   +L ERQI IWFQNRR+K+KK
Sbjct: 11 RIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 27/67 (40%), Positives = 42/67 (62%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79
          +K+ RT++T  Q+  LEK F++Q Y+  A+R  LA+ L + + Q+K WFQNRR K ++  
Sbjct: 17 RKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQT 76
Query: 80 TPEDNLE 86
            E   E
Sbjct: 77 AEEREAE 83

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 24/48 (50%), Positives = 34/48 (70%)
Query: 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74
          ++++Q + LEK+F  Q Y+   +R +LAK L L ERQ+K WFQNRR K
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAK 61

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/61 (44%), Positives = 41/61 (67%)
Query: 17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
          K+ ++R RT +TS QL  LEK F++ +Y     R +LA ++ L E +I++WFQNRR K +
Sbjct: 3  KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 62
Query: 77 K 77
          K
Sbjct: 63 K 63

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/64 (39%), Positives = 42/64 (65%)
Query: 17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
          K+ ++R+RT ++++QL  LE+ F +  Y     R +LA+  NL E +I++WFQNRR + +
Sbjct: 15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLR 74
Query: 77 KGKT 80
          K  T
Sbjct: 75 KQHT 78

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

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 23/53 (43%), Positives = 37/53 (69%)
Query: 25 TAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          T+++ +Q+L LE+ F +Q Y+  A+R  LAK L + + Q+K WFQNRR K ++
Sbjct: 2  TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRR 54

>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 = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/48 (50%), Positives = 33/48 (68%)
Query: 30 NQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
           Q++ LE++F+ Q Y+   +R  LAK L L E Q+KIWFQNRR K K+
Sbjct: 14 TQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61

>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 = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 36/58 (62%)
Query: 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
          G +R RT +TS+Q+  LE+ F Q  Y+   +   L+ +L L   Q+KIWF+NRR + K
Sbjct: 1  GPRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 37/58 (63%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          K++ RT ++S QL  L   F +Q Y+   +  +L+  LNL  +Q+K WFQN+RMK K+
Sbjct: 22 KQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKR 79

>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 = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/61 (49%), Positives = 39/61 (63%), Gaps = 1/61 (1%)
Query: 18 KGKKRA-RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
          KGKKR  RT +TS QL  LEK F + +Y     R QLA   +L E ++++WFQNRR K +
Sbjct: 6  KGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWR 65
Query: 77 K 77
          K
Sbjct: 66 K 66

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

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/56 (46%), Positives = 37/56 (66%)
Query: 22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          R RT +TS QL  LEK F++ +Y     R +LA ++ L E +I++WFQNRR K +K
Sbjct: 1  RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56

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

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 39/57 (68%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          +R RT++T  Q+ ALEKEF + +Y     R +LA +++L E +I++WF NRR K ++
Sbjct: 8  QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRR 64

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 24/58 (41%), Positives = 38/58 (65%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          K++ RT ++  QL AL+  F +Q Y+   +  +L+  LNL  +Q+K WFQN+RMK K+
Sbjct: 3  KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 24/60 (40%), Positives = 34/60 (56%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79
          K++ R  +T  Q   LE+ F QQ Y+   +R  LA  + L   Q+KIWFQN R K K+ +
Sbjct: 9  KRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ 68

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 23/57 (40%), Positives = 37/57 (64%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          +R RT +T  QL ALE  F +  Y     R QLA++++L E ++++WF+NRR K ++
Sbjct: 8  RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRR 64

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 38/59 (64%)
Query: 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          G++R+RT +T+ QL  LE+ F + +Y     R +LA+   L E ++++WF NRR + +K
Sbjct: 1  GQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRK 59

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 23/42 (54%), Positives = 29/42 (69%)
Query: 37 KEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78
          +EFN+  Y+   +R QL+ EL L E QIKIWFQN+R K KK 
Sbjct: 3  REFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 44

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/59 (38%), Positives = 37/59 (62%)
Query: 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
           ++R RT +TS QL  LE  F + +Y   + R ++A   NL E ++++WF+NRR K +K
Sbjct: 2  SQRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60

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

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/71 (38%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 10 DSLIADEKKGKKRARTA-YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWF 68
           S ++D    KKR R   +T  Q   LE+ F QQ Y+   +R  L   + L   Q+KIWF
Sbjct: 1  GSHMSDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWF 60
Query: 69 QNRRMKKKKGK 79
          QN R K K+ +
Sbjct: 61 QNHRYKTKRAQ 71

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 35/58 (60%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          +++ R  ++  Q+  LE+ F QQ Y+   +R  LA  ++L   Q+KIWFQN R K K+
Sbjct: 2  RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKR 59

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 23/59 (38%), Positives = 36/59 (61%)
Query: 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
           ++R RT +TS QL  LE  F +  Y   + R ++A   NL E ++++WF+NRR K +K
Sbjct: 2  SQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 23/52 (44%), Positives = 34/52 (65%)
Query: 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
           +TS QL  LEK F++ +Y     R +LA ++ L E +I++WFQNRR K +K
Sbjct: 5  TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/58 (44%), Positives = 34/58 (58%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78
          +R RTA+T NQ+  LE  F    Y        LA++LNL   +I+IWFQNRR K K+ 
Sbjct: 2  RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRS 59

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/54 (38%), Positives = 33/54 (61%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74
          +R RT +T  QL  LE  F +  Y     R ++A ++NL E ++++WF+NRR K
Sbjct: 8  RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAK 61

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	99
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	7e-25
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	3e-24
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	3e-24
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	5e-24
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	6e-24
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	8e-24
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	2e-23
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	2e-23
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	4e-23
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	6e-23
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	9e-23
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	1e-22
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	1e-22
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	2e-22
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	2e-22
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	3e-22
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	6e-22
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	6e-22
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	9e-22
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	8e-21
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	1e-20
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	2e-20
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	3e-20
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	1e-19
1e3o_C	160	Octamer-binding transcription factor 1; transcript	4e-19
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	2e-17
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	3e-17
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	6e-17
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	7e-17
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	2e-16
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	6e-16
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	7e-15
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	9e-15
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	5e-14
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	5e-14
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	9e-14
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	1e-12
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	2e-12
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	2e-12
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	3e-12
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	3e-12
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	3e-12
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	3e-12
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	3e-12
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	5e-12
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	9e-12
1uhs_A	72	HOP, homeodomain only protein; structural genomics	1e-11
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	2e-11
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	3e-11
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	8e-11
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	2e-09
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	1e-08
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	5e-08
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	1e-06
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	2e-06
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	2e-06
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	2e-06
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	1e-05
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	5e-05
2e19_A	64	Transcription factor 8; homeobox domain, structura	1e-04
1lfb_A	99	Liver transcription factor (LFB1); transcription r	3e-04

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

 Score = 87.9 bits (218), Expect = 7e-25
 Identities = 29/64 (45%), Positives = 40/64 (62%)

Query: 14 ADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRM 73
            + K  +R+RT +T  QL+ LEK F +Q Y+    R  LA+ L L + Q+K W+QNRRM
Sbjct: 11 GTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRM 70

Query: 74 KKKK 77
          K KK
Sbjct: 71 KWKK 74

>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 = 85.9 bits (213), Expect = 3e-24
 Identities = 24/59 (40%), Positives = 36/59 (61%)

Query: 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          G +R RT +TS+Q+  LE+ F Q  Y+   +   L+ +L L   Q+KIWF+NRR + K 
Sbjct: 1  GPRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKI 59

>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 = 85.8 bits (213), Expect = 3e-24
 Identities = 31/59 (52%), Positives = 42/59 (71%)

Query: 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
           +KR RTA++S QL  L++EFN+  Y+   +R QL+ EL L E QIKIWF+N+R K KK
Sbjct: 2  AEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 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 = 86.5 bits (214), Expect = 5e-24
 Identities = 31/59 (52%), Positives = 40/59 (67%)

Query: 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
               RT +T+ QL  LEKEF+   Y+ RA+R ++A  L L E Q+KIWFQNRRMK+KK
Sbjct: 33 SPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91

>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 = 85.1 bits (211), Expect = 6e-24
 Identities = 33/59 (55%), Positives = 45/59 (76%)

Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79
          +R RTA+T +QL  LEKEF ++NY+ R +R +LA +LNL E  IK+WFQNRRMK K+ +
Sbjct: 2  RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQR 60

>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 = 8e-24
 Identities = 26/60 (43%), Positives = 38/60 (63%)

Query: 18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
             ++ RT Y+S QL AL++ F +  Y+   +R +LA  L L + Q+KIWFQN+R K KK
Sbjct: 5  SSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64

>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 = 84.0 bits (208), Expect = 2e-23
 Identities = 25/64 (39%), Positives = 38/64 (59%)

Query: 14 ADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRM 73
                 K  +  ++++Q + LEK+F  Q Y+   +R +LAK L L ERQ+K WFQNRR 
Sbjct: 1  GSSGSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRA 60

Query: 74 KKKK 77
          K ++
Sbjct: 61 KWRR 64

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

 Score = 83.5 bits (207), Expect = 2e-23
 Identities = 28/57 (49%), Positives = 42/57 (73%)

Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          ++ RT +T+ QLLALE++F Q+ Y+  A+R + +  L+L E Q+KIWFQNRR K K+
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

 Score = 83.2 bits (206), Expect = 4e-23
 Identities = 39/59 (66%), Positives = 42/59 (71%)

Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79
          KR RTAYT  QLL LEKEF    YI R +R +LA  LNL ER IKIWFQNRRMK KK +
Sbjct: 4  KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE 62

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

 Score = 83.3 bits (206), Expect = 6e-23
 Identities = 33/58 (56%), Positives = 42/58 (72%)

Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          ++R R  YT  Q L LEKEF+  +Y+ R +R ++A  L+L ERQIKIWFQNRRMK KK
Sbjct: 20 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKK 77

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

 Score = 82.9 bits (205), Expect = 9e-23
 Identities = 24/61 (39%), Positives = 37/61 (60%)

Query: 17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
             K++ RT ++S QL  L   F +Q Y+   +  +L+  LNL  +Q+K WFQN+RMK K
Sbjct: 19 PVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSK 78

Query: 77 K 77
          +
Sbjct: 79 R 79

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

 Score = 82.0 bits (203), Expect = 1e-22
 Identities = 24/64 (37%), Positives = 37/64 (57%)

Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79
               +  +  Q++ LE++F+ Q Y+   +R  LAK L L E Q+KIWFQNRR K K+ +
Sbjct: 4  HHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 63

Query: 80 TPED 83
             +
Sbjct: 64 LSSE 67

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

 Score = 82.6 bits (204), Expect = 1e-22
 Identities = 35/64 (54%), Positives = 43/64 (67%)

Query: 14 ADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRM 73
           +     KR RT+YT  Q L LEKEF+   Y+ R +R ++A  L+L ERQIKIWFQNRRM
Sbjct: 22 VNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRM 81

Query: 74 KKKK 77
          K KK
Sbjct: 82 KWKK 85

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

 Score = 81.1 bits (201), Expect = 2e-22
 Identities = 26/58 (44%), Positives = 36/58 (62%)

Query: 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
          G+++ R  ++  Q+  LE+ F QQ Y+   +R QLA  L L   Q+KIWFQNRR K K
Sbjct: 1  GRRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 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 = 81.2 bits (201), Expect = 2e-22
 Identities = 24/58 (41%), Positives = 38/58 (65%)

Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          K++ RT ++  QL AL+  F +Q Y+   +  +L+  LNL  +Q+K WFQN+RMK K+
Sbjct: 3  KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60

>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 = 80.9 bits (200), Expect = 3e-22
 Identities = 34/58 (58%), Positives = 41/58 (70%)

Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          +KR R  YT  Q L LEKEF+   Y+ R +R ++A  L+L ERQIKIWFQNRRMK KK
Sbjct: 2  RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 59

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

 Score = 81.1 bits (200), Expect = 6e-22
 Identities = 25/60 (41%), Positives = 40/60 (66%)

Query: 18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
            +K+ RT++T  Q+  LEK F++Q Y+  A+R  LA+ L + + Q+K WFQNRR K ++
Sbjct: 15 PKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRR 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 = 80.6 bits (199), Expect = 6e-22
 Identities = 24/66 (36%), Positives = 35/66 (53%)

Query: 18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
            K++ R  +T  Q   LE+ F QQ Y+   +R  LA  + L   Q+KIWFQN R K K+
Sbjct: 7  NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66

Query: 78 GKTPED 83
           +  + 
Sbjct: 67 AQNEKG 72

>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 = 79.5 bits (197), Expect = 9e-22
 Identities = 13/61 (21%), Positives = 35/61 (57%)

Query: 16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKK 75
          +K+   + +++ +      LE+ F ++  +   ++ ++AK+  +   Q+++WF N+RM+ 
Sbjct: 1  KKEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS 60

Query: 76 K 76
          K
Sbjct: 61 K 61

>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 = 77.6 bits (191), Expect = 8e-21
 Identities = 32/60 (53%), Positives = 43/60 (71%)

Query: 18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          +  ++ R  YT +Q L LEKEF    Y+ R +R+++A+ LNL ERQ+KIWFQNRRMK KK
Sbjct: 11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70

>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 = 77.2 bits (190), Expect = 1e-20
 Identities = 25/60 (41%), Positives = 38/60 (63%)

Query: 18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
             ++ R  Y+  QL  LE+E+    +I + KR +++   +L ERQI IWFQNRR+K+KK
Sbjct: 5  SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64

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

 Score = 76.2 bits (188), Expect = 2e-20
 Identities = 23/53 (43%), Positives = 37/53 (69%)

Query: 25 TAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          T+++ +Q+L LE+ F +Q Y+  A+R  LAK L + + Q+K WFQNRR K ++
Sbjct: 2  TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRR 54

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

 Score = 76.2 bits (188), Expect = 3e-20
 Identities = 22/58 (37%), Positives = 35/58 (60%)

Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          +++ R  ++  Q+  LE+ F QQ Y+   +R  LA  ++L   Q+KIWFQN R K K+
Sbjct: 2  RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKR 59

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

 Score = 74.9 bits (184), Expect = 1e-19
 Identities = 26/57 (45%), Positives = 38/57 (66%)

Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          ++ R  YT  QL  LE+E+    +I + KR +++   NL ERQ+ IWFQNRR+K+KK
Sbjct: 8  RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64

>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 = 75.8 bits (186), Expect = 4e-19
 Identities = 19/58 (32%), Positives = 35/58 (60%)

Query: 20  KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
           +++ RT+  +N  +ALEK F +           +A++LN+ +  I++WF NRR K+K+
Sbjct: 101 RRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 158

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

 Score = 69.0 bits (169), Expect = 2e-17
 Identities = 15/64 (23%), Positives = 28/64 (43%)

Query: 17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
            G    +   +  QL AL+  F +  +  +++   L K   L  R+++ WF +RR   +
Sbjct: 5  SSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCR 64

Query: 77 KGKT 80
            K 
Sbjct: 65 NLKG 68

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

 Score = 70.8 bits (173), Expect = 3e-17
 Identities = 19/81 (23%), Positives = 32/81 (39%)

Query: 1   MDRVQKYLDDSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLC 60
            D       +      +  K++ RT+       ALE  F +       +   LA  L L 
Sbjct: 80  TDSSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLE 139

Query: 61  ERQIKIWFQNRRMKKKKGKTP 81
           +  +++WF NRR K+K+    
Sbjct: 140 KEVVRVWFCNRRQKEKRMTPA 160

>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 = 67.9 bits (166), Expect = 6e-17
 Identities = 20/65 (30%), Positives = 35/65 (53%)

Query: 15 DEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74
          +E +  KR RT  T  QL  L +++   +   R     +A E+ L +R +++WFQN R +
Sbjct: 12 EEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRAR 71

Query: 75 KKKGK 79
          ++K  
Sbjct: 72 ERKSG 76

>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 = 69.6 bits (170), Expect = 7e-17
 Identities = 19/65 (29%), Positives = 37/65 (56%)

Query: 15  DEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74
              + K++ RT  +     ALE+ F + +     +  ++A+ELNL +  +++WF NRR +
Sbjct: 82  GANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQR 141

Query: 75  KKKGK 79
           +K+ K
Sbjct: 142 EKRVK 146

>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 = 66.2 bits (162), Expect = 2e-16
 Identities = 22/61 (36%), Positives = 31/61 (50%)

Query: 17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
              + +RT +T  QL  L+  F+   Y    +  QL+  LNL  R I +WFQN R K +
Sbjct: 4  GSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKAR 63

Query: 77 K 77
          K
Sbjct: 64 K 64

>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 = 65.1 bits (159), Expect = 6e-16
 Identities = 18/66 (27%), Positives = 31/66 (46%)

Query: 14 ADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRM 73
                 KR RT  T +QL  L + F+  N     +  ++A +  L ++ IK WF+N   
Sbjct: 1  GSSGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLF 60

Query: 74 KKKKGK 79
          K+++  
Sbjct: 61 KERQSG 66

>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 = 64.7 bits (157), Expect = 7e-15
 Identities = 19/69 (27%), Positives = 32/69 (46%)

Query: 9   DDSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWF 68
               +  E   K++ RT++T   + AL   F +       +  ++AKELN     +++WF
Sbjct: 82  LMEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWF 141

Query: 69  QNRRMKKKK 77
            NRR   K 
Sbjct: 142 SNRRQTLKN 150

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

 Score = 62.5 bits (152), Expect = 9e-15
 Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 2/65 (3%)

Query: 21 KRARTAYTSNQLLALEKEFNQQN-YILRAKRHQLAKELNLCERQIKIWFQNRRMK-KKKG 78
           +  +  T +Q+  LE  FN+ N +        +A E  L E Q + WF+ R  + ++  
Sbjct: 3  AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 62

Query: 79 KTPED 83
            P +
Sbjct: 63 GLPSE 67

>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 = 60.5 bits (147), Expect = 5e-14
 Identities = 19/69 (27%), Positives = 35/69 (50%)

Query: 16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKK 75
               KR RT++  +QL  ++  F   +        QLA++  L +R +++WFQN R K 
Sbjct: 3  SGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKF 62

Query: 76 KKGKTPEDN 84
          ++    ++N
Sbjct: 63 RRNLLRQEN 71

>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 = 60.2 bits (146), Expect = 5e-14
 Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAK-RHQLAKELNLCERQIKIWFQNRRMKKKK 77
            R+RT  +   L  L+   +        +  H L+ +L+L +  I  +FQN+R   K 
Sbjct: 7  GPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH 65

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

 Score = 61.7 bits (149), Expect = 9e-14
 Identities = 19/77 (24%), Positives = 35/77 (45%)

Query: 1   MDRVQKYLDDSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLC 60
            D  +   + S      + +KR RT+  +    +LE  F +       +   +A +L L 
Sbjct: 77  ADNNENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLE 136

Query: 61  ERQIKIWFQNRRMKKKK 77
           +  +++WF NRR K K+
Sbjct: 137 KDVVRVWFSNRRQKGKR 153

>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 = 57.3 bits (138), Expect = 1e-12
 Identities = 13/59 (22%), Positives = 26/59 (44%)

Query: 28 TSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNLE 86
          T+ QL  L+  F   + +   + ++L  +  L  R+I  WF  ++  K   +   +  E
Sbjct: 19 TAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEIDE 77

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

 Score = 56.2 bits (136), Expect = 2e-12
 Identities = 26/57 (45%), Positives = 34/57 (59%)

Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          +R RTA+T NQ+  LE  F    Y        LA++LNL   +I+IWFQNRR K K+
Sbjct: 2  RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKR 58

>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 = 56.5 bits (136), Expect = 2e-12
 Identities = 15/57 (26%), Positives = 26/57 (45%)

Query: 28 TSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDN 84
          T  Q+  LE  F + ++  +A+  +L  E  L  R+I  WF  RR  +   +    +
Sbjct: 21 TQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAVLD 77

>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 = 55.8 bits (135), Expect = 3e-12
 Identities = 19/58 (32%), Positives = 25/58 (43%)

Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
            R RT     QL  L   +          + QL +   L  R I++WFQN+R K KK
Sbjct: 3  TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKK 60

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

 Score = 55.8 bits (135), Expect = 3e-12
 Identities = 23/62 (37%), Positives = 37/62 (59%)

Query: 16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKK 75
               +R RT +T  QL ALE  F +  Y     R QLA++++L E ++++WF+NRR K 
Sbjct: 3  SGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKW 62

Query: 76 KK 77
          ++
Sbjct: 63 RR 64

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

 Score = 55.9 bits (135), Expect = 3e-12
 Identities = 21/62 (33%), Positives = 35/62 (56%)

Query: 16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKK 75
               +R RT +T  QL  LE  F +  Y     R ++A ++NL E ++++WF+NRR K 
Sbjct: 3  SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKC 62

Query: 76 KK 77
          ++
Sbjct: 63 RQ 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 = 55.6 bits (134), Expect = 3e-12
 Identities = 14/60 (23%), Positives = 26/60 (43%)

Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80
                 T  Q+  L+  F Q  +   A+ ++L +   L   +IK WF + R + ++G  
Sbjct: 5  HHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGIV 64

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

 Score = 55.9 bits (135), Expect = 3e-12
 Identities = 24/62 (38%), Positives = 39/62 (62%)

Query: 16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKK 75
               +R RT++T  Q+ ALEKEF + +Y     R +LA +++L E +I++WF NRR K 
Sbjct: 3  SGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKW 62

Query: 76 KK 77
          ++
Sbjct: 63 RR 64

>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 = 55.3 bits (133), Expect = 5e-12
 Identities = 18/57 (31%), Positives = 24/57 (42%)

Query: 28 TSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDN 84
             QL ALE  F Q    L  +  +L  E  +  R+I  WF  RR K    +T +  
Sbjct: 15 APEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETKKSG 71

>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 = 54.7 bits (132), Expect = 9e-12
 Identities = 24/69 (34%), Positives = 42/69 (60%)

Query: 9  DDSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWF 68
          +       K+ ++R+RT ++++QL  LE+ F +  Y     R +LA+  NL E +I++WF
Sbjct: 7  ESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWF 66

Query: 69 QNRRMKKKK 77
          QNRR + +K
Sbjct: 67 QNRRARLRK 75

>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 = 1e-11
 Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 1/54 (1%)

Query: 22 RARTAYTSNQLLALEKEFNQQN-YILRAKRHQLAKELNLCERQIKIWFQNRRMK 74
                T +Q+  LE  FN+ N +        +A E  L E Q + WF+ R  +
Sbjct: 3  EGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAE 56

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

 Score = 53.5 bits (129), Expect = 2e-11
 Identities = 23/58 (39%), Positives = 36/58 (62%)

Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          ++R RT +TS QL  LE  F +  Y   + R ++A   NL E ++++WF+NRR K +K
Sbjct: 3  QRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60

>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 = 53.0 bits (128), Expect = 3e-11
 Identities = 23/54 (42%), Positives = 34/54 (62%)

Query: 24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
             +TS QL  LEK F++ +Y     R +LA ++ L E +I++WFQNRR K +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 = 54.5 bits (130), Expect = 8e-11
 Identities = 12/70 (17%), Positives = 25/70 (35%)

Query: 15  DEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74
           D     K+ R  +T  Q   L   F +     +  +  ++++L L    +  +F N R +
Sbjct: 92  DRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRR 151

Query: 75  KKKGKTPEDN 84
                    +
Sbjct: 152 SLDKWLEHHH 161

>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 = 49.3 bits (117), Expect = 2e-09
 Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 15/79 (18%)

Query: 14 ADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELN--------------- 58
                 + +R  +    L  +E  FN+  Y   AKR ++A   N               
Sbjct: 1  GSSGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLER 60

Query: 59 LCERQIKIWFQNRRMKKKK 77
          +   ++  WF NRR + K+
Sbjct: 61 VTSLKVYNWFANRRKEIKR 79

>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 = 46.7 bits (111), Expect = 1e-08
 Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 3/59 (5%)

Query: 20 KKRARTAYTSNQLLALEKEFNQQN-YILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          K         N  L  EK F     Y    +   L+K+L+   R+I+ WF++RR + K 
Sbjct: 10 KDSPVNKVEPNDTL--EKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKP 66

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

 Score = 45.6 bits (107), Expect = 5e-08
 Identities = 18/63 (28%), Positives = 24/63 (38%)

Query: 17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
          K G        T  QL  L+  F +  +    +  +LAKE  L    I  WF + R   K
Sbjct: 22 KSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWK 81

Query: 77 KGK 79
           G 
Sbjct: 82 NGN 84

>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 = 41.3 bits (97), Expect = 1e-06
 Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 35 LEKEFNQQN-YILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          LEK F     +    +   L+K+L+   R I+ WF+ RR ++K 
Sbjct: 15 LEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 58

>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 = 41.1 bits (96), Expect = 2e-06
 Identities = 15/60 (25%), Positives = 23/60 (38%)

Query: 22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP 81
           +    T  QL  L+  F Q  +  R    +L +   L   +I  WF + R   K G+  
Sbjct: 5  SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLK 64

>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 = 41.5 bits (96), Expect = 2e-06
 Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 4/68 (5%)

Query: 14 ADEKKGKKRARTAYTSNQLLALEKEF----NQQNYILRAKRHQLAKELNLCERQIKIWFQ 69
          +    G  + RT ++   L  L+K +         + R K   +A ELN+    ++ W  
Sbjct: 2  SSGSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIG 61

Query: 70 NRRMKKKK 77
          NRR K + 
Sbjct: 62 NRRRKYRL 69

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

 Score = 43.1 bits (100), Expect = 2e-06
 Identities = 17/89 (19%), Positives = 32/89 (35%), Gaps = 21/89 (23%)

Query: 9   DDSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELN---------- 58
           DD+      K  +R R  +       L + +++Q    + +R  L +E N          
Sbjct: 131 DDACSEPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVS 190

Query: 59  -----------LCERQIKIWFQNRRMKKK 76
                      + E ++  WF NRR ++ 
Sbjct: 191 PSKAHGLGSNLVTEVRVYNWFANRRKEEA 219

>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 = 40.6 bits (94), Expect = 1e-05
 Identities = 15/89 (16%), Positives = 30/89 (33%), Gaps = 21/89 (23%)

Query: 9   DDSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELN---------- 58
           + +      K  +R R  +       L + + +Q    + +R  L +E N          
Sbjct: 104 EPTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVS 163

Query: 59  -----------LCERQIKIWFQNRRMKKK 76
                      + E ++  WF NRR ++ 
Sbjct: 164 PSQAQGLGSNLVTEVRVYNWFANRRKEEA 192

>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 = 37.5 bits (86), Expect = 5e-05
 Identities = 10/60 (16%), Positives = 21/60 (35%)

Query: 22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP 81
                    +  LE+ +     +      QL++   L  +Q+  WF +R  +  +   P
Sbjct: 8  PLPIPPPPPDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSRLPQPAEVSGP 67

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

 Score = 36.2 bits (83), Expect = 1e-04
 Identities = 9/50 (18%), Positives = 20/50 (40%)

Query: 30 NQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79
          N L  L+  +         +  ++A  +NL    +K WF+  +  +   +
Sbjct: 13 NLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISVQ 62

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

 Score = 36.0 bits (82), Expect = 3e-04
 Identities = 16/84 (19%), Positives = 29/84 (34%), Gaps = 21/84 (25%)

Query: 15 DEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELN---------------- 58
          D  K  +R R  +       L + + +Q    + +R  L +E N                
Sbjct: 4  DPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQG 63

Query: 59 -----LCERQIKIWFQNRRMKKKK 77
               + E ++  WF NRR ++  
Sbjct: 64 LGSNLVTEVRVYNWFANRRKEEAF 87

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	99
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.87
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.87
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.87
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.87
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.87
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.86
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.86
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.86
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.86
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.86
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.86
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.86
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.86
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.86
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.85
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.85
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.85
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.85
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.85
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.85
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.85
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.85
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.85
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.85
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.85
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.84
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.84
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.84
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.84
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.84
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.84
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.84
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.84
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.84
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.84
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.84
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.83
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.83
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.83
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.83
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.83
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.83
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.83
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.83
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.83
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.82
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.82
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.82
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.82
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.82
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.81
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.81
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.81
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.8
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.8
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.8
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.8
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.8
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.79
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.79
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.79
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.79
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.79
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.77
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.77
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.77
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.77
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.77
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.76
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.75
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.75
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.73
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.63
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	99.58
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.58
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.56
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.44
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	98.69
2ys9_A	70	Homeobox and leucine zipper protein homez; homeodo	97.34
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	93.13
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	92.92
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	90.12
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	88.62
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	88.43
3c57_A	95	Two component transcriptional regulatory protein;	86.91
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	86.76
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	86.53
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	86.12
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	84.47
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	84.1
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	83.9
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	83.25
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	82.2
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	82.14
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	81.7
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	81.03
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	80.74
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	80.73
2rn7_A	108	IS629 ORFA; helix, all alpha, unknown function, st	80.56
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	80.28

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

Probab=99.87  E-value=1.1e-21  Score=113.72  Aligned_cols=69  Identities=32%  Similarity=0.502  Sum_probs=63.3

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCch
Q psy16797         17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNL   85 (99)
Q Consensus        17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~~   85 (99)
                      .++.++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+........
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~~~~~   72 (80)
T 2dms_A            4 GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQQNG   72 (80)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCSCCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHccCCC
Confidence            456778999999999999999999999999999999999999999999999999999999987665443

>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=99.87  E-value=9.1e-22  Score=111.41  Aligned_cols=65  Identities=38%  Similarity=0.706  Sum_probs=60.7

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797         16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT   80 (99)
Q Consensus        16 ~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~   80 (99)
                      ..+..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+...
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            35667788999999999999999999999999999999999999999999999999999998664

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

Probab=99.87  E-value=1.4e-21  Score=110.62  Aligned_cols=65  Identities=35%  Similarity=0.606  Sum_probs=60.6

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797         17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP   81 (99)
Q Consensus        17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~   81 (99)
                      .+..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+....
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~~   68 (70)
T 2dmu_A            4 GSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGPS   68 (70)
T ss_dssp             TTSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTSTT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccCCC
Confidence            45667889999999999999999999999999999999999999999999999999999997653

>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=99.87  E-value=1.1e-21  Score=110.95  Aligned_cols=66  Identities=33%  Similarity=0.480  Sum_probs=61.3

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797         16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP   81 (99)
Q Consensus        16 ~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~   81 (99)
                      ..++.++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+....
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (70)
T 2da2_A            3 SGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGPS   68 (70)
T ss_dssp             CSCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCSSC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhcccc
Confidence            356677899999999999999999999999999999999999999999999999999999997654

>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=99.87  E-value=1.3e-21  Score=113.46  Aligned_cols=65  Identities=45%  Similarity=0.709  Sum_probs=60.5

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797         16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT   80 (99)
Q Consensus        16 ~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~   80 (99)
                      ..++.++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||+|+++|+...
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            34566778999999999999999999999999999999999999999999999999999999765

>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=99.86  E-value=1.3e-21  Score=110.75  Aligned_cols=66  Identities=27%  Similarity=0.409  Sum_probs=61.1

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797         16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP   81 (99)
Q Consensus        16 ~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~   81 (99)
                      ..++.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|+|+++|+....
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            345677899999999999999999999999999999999999999999999999999999997654

>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=99.86  E-value=7.8e-22  Score=114.17  Aligned_cols=68  Identities=29%  Similarity=0.477  Sum_probs=62.3

Q ss_pred             ccccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797         14 ADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP   81 (99)
Q Consensus        14 ~~~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~   81 (99)
                      .....+.++.|+.|+.+|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+....
T Consensus        11 ~~~~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~   78 (80)
T 2da3_A           11 GEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSGPS   78 (80)
T ss_dssp             CCCCCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSCCC
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhccC
Confidence            34456677899999999999999999999999999999999999999999999999999999997654

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

Probab=99.86  E-value=8.2e-22  Score=109.17  Aligned_cols=61  Identities=39%  Similarity=0.653  Sum_probs=53.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797         19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK   79 (99)
Q Consensus        19 ~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~   79 (99)
                      +.++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.+
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~q   62 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRWQ   62 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGGC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhcC
Confidence            5677899999999999999999999999999999999999999999999999999999853

>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=1.2e-21  Score=113.48  Aligned_cols=68  Identities=28%  Similarity=0.442  Sum_probs=62.0

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCc
Q psy16797         17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDN   84 (99)
Q Consensus        17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~   84 (99)
                      ..+.++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.......
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~~   71 (80)
T 2dmq_A            4 GSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQEN   71 (80)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHSSCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHHHhc
Confidence            45667889999999999999999999999999999999999999999999999999999997655443

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

Probab=99.86  E-value=1.5e-21  Score=108.43  Aligned_cols=61  Identities=64%  Similarity=0.882  Sum_probs=56.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797         19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK   79 (99)
Q Consensus        19 ~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~   79 (99)
                      ..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+..
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            4577899999999999999999999999999999999999999999999999999999864

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

Probab=99.86  E-value=1.9e-21  Score=110.11  Aligned_cols=65  Identities=40%  Similarity=0.662  Sum_probs=60.5

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797         16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT   80 (99)
Q Consensus        16 ~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~   80 (99)
                      ..++.++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+...
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            35567789999999999999999999999999999999999999999999999999999998654

>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=99.86  E-value=4.2e-21  Score=108.65  Aligned_cols=65  Identities=38%  Similarity=0.664  Sum_probs=60.0

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797         17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP   81 (99)
Q Consensus        17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~   81 (99)
                      ....++.|++|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+....
T Consensus         4 ~~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~~~   68 (70)
T 2e1o_A            4 GSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGPS   68 (70)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHSCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCCCC
Confidence            34566788999999999999999999999999999999999999999999999999999987653

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

Probab=99.86  E-value=2.4e-21  Score=113.12  Aligned_cols=66  Identities=36%  Similarity=0.611  Sum_probs=61.1

Q ss_pred             cccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797         15 DEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT   80 (99)
Q Consensus        15 ~~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~   80 (99)
                      ...++.++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||+|+++|+...
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            345567788999999999999999999999999999999999999999999999999999998764

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

Probab=99.86  E-value=4.9e-21  Score=109.52  Aligned_cols=68  Identities=41%  Similarity=0.569  Sum_probs=62.5

Q ss_pred             cccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCC
Q psy16797         15 DEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPE   82 (99)
Q Consensus        15 ~~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~   82 (99)
                      +..+++++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.....
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            34567778999999999999999999999999999999999999999999999999999999976553

>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=99.85  E-value=3e-21  Score=106.54  Aligned_cols=58  Identities=53%  Similarity=0.873  Sum_probs=53.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797         20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK   77 (99)
Q Consensus        20 ~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr   77 (99)
                      .++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+
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            4678999999999999999999999999999999999999999999999999999987

>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=99.85  E-value=3.5e-21  Score=107.84  Aligned_cols=62  Identities=31%  Similarity=0.431  Sum_probs=58.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797         19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT   80 (99)
Q Consensus        19 ~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~   80 (99)
                      +.++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+...
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            35678999999999999999999999999999999999999999999999999999998653

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

Probab=99.85  E-value=5.6e-21  Score=109.01  Aligned_cols=66  Identities=39%  Similarity=0.643  Sum_probs=61.0

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCC
Q psy16797         17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPE   82 (99)
Q Consensus        17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~   82 (99)
                      ..+.++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.....
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~   69 (73)
T 2l7z_A            4 MLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINKL   69 (73)
T ss_dssp             SSCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSSSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHhccc
Confidence            345677899999999999999999999999999999999999999999999999999999976554

>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=99.85  E-value=2.9e-21  Score=108.84  Aligned_cols=64  Identities=53%  Similarity=0.819  Sum_probs=60.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCC
Q psy16797         20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPED   83 (99)
Q Consensus        20 ~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~   83 (99)
                      +++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+......
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            4678999999999999999999999999999999999999999999999999999999876544

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

Probab=99.85  E-value=4.8e-21  Score=104.69  Aligned_cols=58  Identities=48%  Similarity=0.822  Sum_probs=55.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        21 ~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      ++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   58 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL   58 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhccC
Confidence            4688999999999999999999999999999999999999999999999999999873

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

Probab=99.85  E-value=7.6e-21  Score=107.07  Aligned_cols=63  Identities=35%  Similarity=0.669  Sum_probs=59.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCC
Q psy16797         20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPE   82 (99)
Q Consensus        20 ~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~   82 (99)
                      +++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.....
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            567899999999999999999999999999999999999999999999999999999977654

>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=5.9e-21  Score=109.91  Aligned_cols=66  Identities=36%  Similarity=0.620  Sum_probs=60.4

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797         16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP   81 (99)
Q Consensus        16 ~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~   81 (99)
                      ..+++++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||+|+++|+....
T Consensus         5 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~   70 (77)
T 1nk2_P            5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNE   70 (77)
T ss_dssp             CSCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhcc
Confidence            345667789999999999999999999999999999999999999999999999999999986543

>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=5.9e-21  Score=110.63  Aligned_cols=64  Identities=38%  Similarity=0.626  Sum_probs=59.9

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797         17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT   80 (99)
Q Consensus        17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~   80 (99)
                      .+..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+...
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   67 (80)
T 2cue_A            4 GSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK   67 (80)
T ss_dssp             CCSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhh
Confidence            4567788999999999999999999999999999999999999999999999999999998653

>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=99.85  E-value=5.6e-21  Score=110.92  Aligned_cols=65  Identities=37%  Similarity=0.639  Sum_probs=58.3

Q ss_pred             cccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797         15 DEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK   79 (99)
Q Consensus        15 ~~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~   79 (99)
                      ...++.++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+..
T Consensus        13 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~   77 (81)
T 1fjl_A           13 ALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH   77 (81)
T ss_dssp             ----CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             cccCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhc
Confidence            34566778999999999999999999999999999999999999999999999999999999853

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

Probab=99.85  E-value=3.7e-21  Score=114.41  Aligned_cols=73  Identities=37%  Similarity=0.623  Sum_probs=63.3

Q ss_pred             ccccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCchh
Q psy16797         14 ADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNLE   86 (99)
Q Consensus        14 ~~~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~~~   86 (99)
                      ....++.++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||+|+++|+........+
T Consensus        11 ~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~~~~   83 (93)
T 3a01_A           11 NRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEEREAE   83 (93)
T ss_dssp             TSCCCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC----
T ss_pred             CCCCCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHHHHHH
Confidence            3445667789999999999999999999999999999999999999999999999999999999876654433

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

Probab=99.85  E-value=3.2e-21  Score=111.71  Aligned_cols=66  Identities=26%  Similarity=0.391  Sum_probs=61.1

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhhc----CCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797         16 EKKGKKRARTAYTSNQLLALEKEFNQQ----NYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP   81 (99)
Q Consensus        16 ~~~~~~r~r~~~s~~q~~~L~~~f~~~----~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~   81 (99)
                      ..++.++.|+.|+.+|+.+|+..|..+    +||+..++..||..+||++.+|++||||+|+++|+....
T Consensus         4 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~~~~   73 (80)
T 2da4_A            4 GSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMGIE   73 (80)
T ss_dssp             CCCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhccCC
Confidence            456677899999999999999999999    999999999999999999999999999999999996543

>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=99.84  E-value=2.2e-21  Score=109.26  Aligned_cols=65  Identities=35%  Similarity=0.553  Sum_probs=60.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCC
Q psy16797         18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPE   82 (99)
Q Consensus        18 ~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~   82 (99)
                      ++.++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.....
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            35678899999999999999999999999999999999999999999999999999999977643

>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=108.74  Aligned_cols=64  Identities=50%  Similarity=0.767  Sum_probs=59.7

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797         16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK   79 (99)
Q Consensus        16 ~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~   79 (99)
                      ..+..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||+|+++|+..
T Consensus         9 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~   72 (77)
T 1puf_A            9 HARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKIN   72 (77)
T ss_dssp             CCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhh
Confidence            4556677899999999999999999999999999999999999999999999999999999854

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

Probab=99.84  E-value=1.1e-20  Score=104.00  Aligned_cols=58  Identities=57%  Similarity=0.889  Sum_probs=55.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        21 ~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      ++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.
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            5689999999999999999999999999999999999999999999999999999874

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

Probab=99.84  E-value=1.6e-20  Score=105.43  Aligned_cols=61  Identities=43%  Similarity=0.588  Sum_probs=58.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797         21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP   81 (99)
Q Consensus        21 ~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~   81 (99)
                      ++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+....
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~~   62 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRE   62 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCCT
T ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhchh
Confidence            6789999999999999999999999999999999999999999999999999999987654

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

Probab=99.84  E-value=7.1e-21  Score=107.20  Aligned_cols=62  Identities=37%  Similarity=0.628  Sum_probs=58.2

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797         20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP   81 (99)
Q Consensus        20 ~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~   81 (99)
                      .++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+....
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~   63 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ   63 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhcc
Confidence            46789999999999999999999999999999999999999999999999999999986544

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

Probab=99.84  E-value=1.4e-20  Score=102.69  Aligned_cols=57  Identities=44%  Similarity=0.781  Sum_probs=54.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797         20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK   76 (99)
Q Consensus        20 ~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k   76 (99)
                      +++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|
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            457899999999999999999999999999999999999999999999999999875

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

Probab=99.84  E-value=1.1e-20  Score=111.18  Aligned_cols=64  Identities=55%  Similarity=0.802  Sum_probs=55.5

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797         16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK   79 (99)
Q Consensus        16 ~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~   79 (99)
                      ..+..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||+|+++|+..
T Consensus        24 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   87 (88)
T 2r5y_A           24 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH   87 (88)
T ss_dssp             -------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhhc
Confidence            4556778999999999999999999999999999999999999999999999999999999864

>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=99.84  E-value=7e-21  Score=105.01  Aligned_cols=59  Identities=20%  Similarity=0.480  Sum_probs=48.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797         18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK   76 (99)
Q Consensus        18 ~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k   76 (99)
                      ++.++.|+.|+..|+.+|+..|..++||+..++..||..+||++.+|++||+|+|+++|
T Consensus         3 ~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            3 EKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             ---------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            45667899999999999999999999999999999999999999999999999999875

>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=99.84  E-value=3.1e-20  Score=105.83  Aligned_cols=67  Identities=19%  Similarity=0.257  Sum_probs=60.9

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCC
Q psy16797         16 EKKGKKRARTAYTSNQLLALEKEFNQ---QNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPE   82 (99)
Q Consensus        16 ~~~~~~r~r~~~s~~q~~~L~~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~   82 (99)
                      ..++.++.|+.|+..|+.+|+.+|..   ++||+..++..||..+||+..+|++||+|+|+++++.....
T Consensus         3 ~~~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~~   72 (73)
T 1x2n_A            3 SGSSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSGPSS   72 (73)
T ss_dssp             CCSSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTTSC
T ss_pred             CCCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhcccccccc
Confidence            34567778999999999999999976   99999999999999999999999999999999999976543

>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=99.84  E-value=1.3e-20  Score=109.47  Aligned_cols=64  Identities=52%  Similarity=0.794  Sum_probs=54.6

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797         16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK   79 (99)
Q Consensus        16 ~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~   79 (99)
                      ..+..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+..
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            3456677899999999999999999999999999999999999999999999999999999864

>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=99.84  E-value=7.4e-21  Score=110.32  Aligned_cols=61  Identities=16%  Similarity=0.217  Sum_probs=57.3

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhh----cCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797         17 KKGKKRARTAYTSNQLLALEKEFNQ----QNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK   77 (99)
Q Consensus        17 ~~~~~r~r~~~s~~q~~~L~~~f~~----~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr   77 (99)
                      .++++|.|+.|+.+|+..|+..|..    ++||+..++.+||..+||++.+|++||||+|+|+|+
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           14 GGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            4466788999999999999999999    999999999999999999999999999999999876

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

Probab=99.83  E-value=1.7e-20  Score=112.13  Aligned_cols=66  Identities=27%  Similarity=0.370  Sum_probs=56.8

Q ss_pred             cccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797         15 DEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT   80 (99)
Q Consensus        15 ~~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~   80 (99)
                      ...+..++.|+.|+..|+.+|+..|..++||+..++..||..+||+..+|++||||+|+++|+...
T Consensus        20 ~~~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~l   85 (96)
T 3nar_A           20 APKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNL   85 (96)
T ss_dssp             -------CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTCC
T ss_pred             CCCCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhcc
Confidence            344556678999999999999999999999999999999999999999999999999999999654

>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=99.83  E-value=3.5e-20  Score=106.23  Aligned_cols=63  Identities=29%  Similarity=0.418  Sum_probs=57.9

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCc
Q psy16797         22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDN   84 (99)
Q Consensus        22 r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~   84 (99)
                      +.|..||..|+..|+..|..++||+..++..||..+||+..+|++||+|+|+++|+.......
T Consensus         9 ~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~~~~~   71 (75)
T 2da5_A            9 TKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETKKSG   71 (75)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSCSSCC
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhhcccC
Confidence            456779999999999999999999999999999999999999999999999999998765443

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

Probab=99.83  E-value=1.5e-20  Score=103.40  Aligned_cols=57  Identities=40%  Similarity=0.619  Sum_probs=50.6

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797         23 ARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK   79 (99)
Q Consensus        23 ~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~   79 (99)
                      .|+.||..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+..
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            578999999999999999999999999999999999999999999999999999865

>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=99.83  E-value=2.6e-20  Score=105.90  Aligned_cols=62  Identities=23%  Similarity=0.302  Sum_probs=57.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHhh-cCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCC
Q psy16797         21 KRARTAYTSNQLLALEKEFNQ-QNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPE   82 (99)
Q Consensus        21 ~r~r~~~s~~q~~~L~~~f~~-~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~   82 (99)
                      .+.|+.|+..|+..|+..|.. ++||+..++..||..+||++.+|++||+|+|+++|+.....
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~~~~   64 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLP   64 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhccCC
Confidence            467889999999999999996 99999999999999999999999999999999999976443

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

Probab=99.83  E-value=3.1e-20  Score=105.88  Aligned_cols=62  Identities=23%  Similarity=0.287  Sum_probs=57.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHhh-cCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCC
Q psy16797         21 KRARTAYTSNQLLALEKEFNQ-QNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPE   82 (99)
Q Consensus        21 ~r~r~~~s~~q~~~L~~~f~~-~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~   82 (99)
                      .+.|+.|+..|+..|+..|.. ++||+..++..||..+||++.+|++||+|+|+++|+.....
T Consensus         3 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~~~~   65 (73)
T 2hi3_A            3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLP   65 (73)
T ss_dssp             CSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhccCC
Confidence            467899999999999999995 99999999999999999999999999999999999977543

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

Probab=99.83  E-value=1.6e-20  Score=111.98  Aligned_cols=68  Identities=25%  Similarity=0.407  Sum_probs=62.6

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhC---------------CChHHHHHHHHHHHhHHhhcCC
Q psy16797         16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELN---------------LCERQIKIWFQNRRMKKKKGKT   80 (99)
Q Consensus        16 ~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~---------------l~~~~V~~WFqNrR~k~kr~~~   80 (99)
                      ..+++++.|+.|++.|+.+|+..|..++||+..++..||..++               |++.+|++||||+|+++|+...
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            3566778999999999999999999999999999999999999               9999999999999999999876


Q ss_pred             CCC
Q psy16797         81 PED   83 (99)
Q Consensus        81 ~~~   83 (99)
                      ...
T Consensus        83 ~~~   85 (95)
T 2cuf_A           83 IAA   85 (95)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            543

>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=99.83  E-value=6.6e-20  Score=105.04  Aligned_cols=61  Identities=25%  Similarity=0.291  Sum_probs=56.5

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCC
Q psy16797         22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPE   82 (99)
Q Consensus        22 r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~   82 (99)
                      ..|..||.+|+.+|+..|..++||+..++.+||..+||+..+|++||+|+|+++|+.....
T Consensus         5 ~~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~l~w   65 (76)
T 2ecc_A            5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLKW   65 (76)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCCSS
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHHHHH
Confidence            3556799999999999999999999999999999999999999999999999999976554

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

Probab=99.83  E-value=6.9e-20  Score=108.04  Aligned_cols=65  Identities=20%  Similarity=0.301  Sum_probs=58.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCchhhccc
Q psy16797         26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNLEYKLH   90 (99)
Q Consensus        26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~~~~~~~   90 (99)
                      .||.+|+..|+..|..++||+..++.+||..+||++.+|++||||||+++++.............
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~~~~~~~~~~~   81 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEIDESNAG   81 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCCCCCCCCCC
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHHHhhcccCCCC
Confidence            79999999999999999999999999999999999999999999999999997766654444333

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

Probab=99.83  E-value=3.3e-20  Score=106.54  Aligned_cols=64  Identities=22%  Similarity=0.372  Sum_probs=58.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCC
Q psy16797         20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPED   83 (99)
Q Consensus        20 ~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~   83 (99)
                      ..+.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+......
T Consensus         8 ~~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~~~~   71 (76)
T 2dn0_A            8 ASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGSRS   71 (76)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCSSSC
T ss_pred             CCCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhcccCC
Confidence            3446889999999999999999999999999999999999999999999999999999766544

>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=99.82  E-value=2.4e-20  Score=111.63  Aligned_cols=66  Identities=47%  Similarity=0.706  Sum_probs=56.5

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797         16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP   81 (99)
Q Consensus        16 ~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~   81 (99)
                      ..+..++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||+|+++|+....
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            345667789999999999999999999999999999999999999999999999999999987543

>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=99.82  E-value=8.3e-20  Score=104.01  Aligned_cols=64  Identities=23%  Similarity=0.398  Sum_probs=59.3

Q ss_pred             CCCCCCCCHHHHHHHHHHH---hhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCc
Q psy16797         21 KRARTAYTSNQLLALEKEF---NQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDN   84 (99)
Q Consensus        21 ~r~r~~~s~~q~~~L~~~f---~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~   84 (99)
                      ++.|+.|+..|+.+|+.+|   ..++||+..++..||..+||+..+|++||+|+|+++|+.......
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~~~~   68 (73)
T 1puf_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQE   68 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTTTTT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhcccccccccc
Confidence            5788999999999999999   899999999999999999999999999999999999997765443

>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=99.82  E-value=1.1e-20  Score=109.63  Aligned_cols=62  Identities=21%  Similarity=0.277  Sum_probs=57.2

Q ss_pred             cccCCCCCCCCCCCHHHHHHHHHHHhh-----cCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797         15 DEKKGKKRARTAYTSNQLLALEKEFNQ-----QNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK   77 (99)
Q Consensus        15 ~~~~~~~r~r~~~s~~q~~~L~~~f~~-----~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr   77 (99)
                      ...++++|.|+.|+.+|+..|+ .|..     ++||+..++.+||..+||++.+|++||||+|+++++
T Consensus        12 ~~~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           12 SSGGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            3455677899999999999999 7999     999999999999999999999999999999999876

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

Probab=99.82  E-value=1e-19  Score=103.86  Aligned_cols=63  Identities=22%  Similarity=0.361  Sum_probs=58.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCC
Q psy16797         20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPE   82 (99)
Q Consensus        20 ~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~   82 (99)
                      .++.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||+|+++|+.....
T Consensus         6 ~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~   68 (74)
T 2ly9_A            6 SFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKSNQ   68 (74)
T ss_dssp             CCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTTCSC
T ss_pred             CCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhCcCC
Confidence            456889999999999999999999999999999999999999999999999999999876543

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

Probab=99.82  E-value=5.1e-20  Score=100.05  Aligned_cols=54  Identities=43%  Similarity=0.759  Sum_probs=50.8

Q ss_pred             CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         25 TAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        25 ~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      +.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.
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            579999999999999999999999999999999999999999999999999984

>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=99.81  E-value=1.3e-19  Score=105.64  Aligned_cols=68  Identities=18%  Similarity=0.260  Sum_probs=60.7

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCc
Q psy16797         17 KKGKKRARTAYTSNQLLALEKEFNQ---QNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDN   84 (99)
Q Consensus        17 ~~~~~r~r~~~s~~q~~~L~~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~   84 (99)
                      ..++++.|+.|+..|+.+|+.+|..   ++||+..++..||..+||+..+|++||+|+|+++++.......
T Consensus         4 ~~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~~~~~   74 (83)
T 2dmn_A            4 GSSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQRR   74 (83)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHTCCCC
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHHHhcc
Confidence            4466778999999999999999987   5999999999999999999999999999999999887655544

>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=99.81  E-value=1.2e-19  Score=105.82  Aligned_cols=62  Identities=27%  Similarity=0.342  Sum_probs=55.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797         20 KKRARTAYTSNQLLALEKEFNQ---QNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP   81 (99)
Q Consensus        20 ~~r~r~~~s~~q~~~L~~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~   81 (99)
                      +++.+++|+..|+.+|+.+|..   ++||+..++..||..+||+..+|++||+|+|+++|+....
T Consensus         2 K~krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~~~   66 (83)
T 1le8_B            2 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITIA   66 (83)
T ss_dssp             ---CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSCCC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHccccccccC
Confidence            3455667999999999999999   9999999999999999999999999999999999997554

>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=99.81  E-value=7.7e-20  Score=107.33  Aligned_cols=64  Identities=23%  Similarity=0.398  Sum_probs=58.6

Q ss_pred             CCCCCCCCHHHHHHHHHHH---hhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCc
Q psy16797         21 KRARTAYTSNQLLALEKEF---NQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDN   84 (99)
Q Consensus        21 ~r~r~~~s~~q~~~L~~~f---~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~   84 (99)
                      +|.|+.|+..|+.+|+.+|   ..++||+..++..||..+||+..+|++||+|+|+++|+.......
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~~~   68 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQE   68 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGGGHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhccccccc
Confidence            5788999999999999999   899999999999999999999999999999999999997655443

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

Probab=99.80  E-value=7.9e-20  Score=101.67  Aligned_cols=58  Identities=22%  Similarity=0.348  Sum_probs=55.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHH---hhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797         20 KKRARTAYTSNQLLALEKEF---NQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK   77 (99)
Q Consensus        20 ~~r~r~~~s~~q~~~L~~~f---~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr   77 (99)
                      .++.|+.|+..|+.+|+.+|   ..++||+..++..||..+||+..+|++||+|+|+++|+
T Consensus         3 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A            3 GHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             CCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            46788999999999999999   89999999999999999999999999999999999886

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

Probab=99.80  E-value=1.2e-19  Score=117.74  Aligned_cols=65  Identities=28%  Similarity=0.353  Sum_probs=52.8

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797         17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP   81 (99)
Q Consensus        17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~   81 (99)
                      .++++|.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+++|+....
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            45667789999999999999999999999999999999999999999999999999999997754

>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=99.80  E-value=1.6e-19  Score=116.65  Aligned_cols=62  Identities=31%  Similarity=0.493  Sum_probs=54.9

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      .++++|.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+++|+.
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            34667799999999999999999999999999999999999999999999999999999985

>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=99.80  E-value=2.8e-19  Score=98.24  Aligned_cols=55  Identities=31%  Similarity=0.406  Sum_probs=52.9

Q ss_pred             CCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         24 RTAYTSNQLLALEKEFNQ---QNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        24 r~~~s~~q~~~L~~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      +++|+..|+.+|+..|..   ++||+..++..||..+||+..+|++||+|+|+++|+.
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   9999999999999999999999999999999999874

>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=99.80  E-value=8.3e-19  Score=103.48  Aligned_cols=62  Identities=24%  Similarity=0.347  Sum_probs=56.2

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCc
Q psy16797         23 ARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDN   84 (99)
Q Consensus        23 ~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~   84 (99)
                      .+..+|..|+.+|+..|..++||+..++..||..+||+..+|++||+|+|+++++.......
T Consensus        16 k~k~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~~~~~   77 (89)
T 2dmp_A           16 KFKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAVLD   77 (89)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCSCCCC
T ss_pred             ccccCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhHhhhc
Confidence            34459999999999999999999999999999999999999999999999999987766543

>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=99.79  E-value=3.8e-19  Score=113.88  Aligned_cols=62  Identities=31%  Similarity=0.515  Sum_probs=58.5

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797         16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK   77 (99)
Q Consensus        16 ~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr   77 (99)
                      ..++++|.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||+|+++|+
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            44567778999999999999999999999999999999999999999999999999999986

>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=99.79  E-value=3.9e-19  Score=104.37  Aligned_cols=61  Identities=31%  Similarity=0.404  Sum_probs=56.4

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797         17 KKGKKRARTAYTSNQLLALEKEFNQ---QNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK   77 (99)
Q Consensus        17 ~~~~~r~r~~~s~~q~~~L~~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr   77 (99)
                      ..++++.|+.|+..|+.+|+.+|..   ++||+..++..||..+||+..+|++||+|+|+++|.
T Consensus        24 ~~~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k~   87 (87)
T 1mnm_C           24 KSTKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   87 (87)
T ss_dssp             EESSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTC
T ss_pred             cCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccC
Confidence            3456667899999999999999999   999999999999999999999999999999999873

>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=99.79  E-value=3.2e-19  Score=113.79  Aligned_cols=62  Identities=29%  Similarity=0.488  Sum_probs=55.6

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      .++++|.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+++|+.
T Consensus        84 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           84 NERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             -----CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            34566789999999999999999999999999999999999999999999999999999985

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

Probab=99.79  E-value=2e-19  Score=102.37  Aligned_cols=61  Identities=25%  Similarity=0.373  Sum_probs=55.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHH-hhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797         20 KKRARTAYTSNQLLALEKEF-NQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT   80 (99)
Q Consensus        20 ~~r~r~~~s~~q~~~L~~~f-~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~   80 (99)
                      ..+.+.+++..|+..|+..| ..++||+..++..||..+||++.+|++||||||+++|+...
T Consensus         8 g~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~~~   69 (72)
T 2cqx_A            8 GIKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSGP   69 (72)
T ss_dssp             CCCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSCCC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCCCC
Confidence            34566678888999999999 99999999999999999999999999999999999998654

>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=99.79  E-value=5.9e-19  Score=98.38  Aligned_cols=61  Identities=26%  Similarity=0.307  Sum_probs=56.2

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhh-cCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797         16 EKKGKKRARTAYTSNQLLALEKEFNQ-QNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK   76 (99)
Q Consensus        16 ~~~~~~r~r~~~s~~q~~~L~~~f~~-~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k   76 (99)
                      ..+.++|.|+.|+.+|+.+|+..|.. ++||+...+..||..+||++.+|++||||+|--.+
T Consensus         3 ~~~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~~~   64 (71)
T 1wi3_A            3 SGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVK   64 (71)
T ss_dssp             CCCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCC
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceeeec
Confidence            34577889999999999999999999 99999999999999999999999999999997543

>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=1.4e-18  Score=104.42  Aligned_cols=64  Identities=20%  Similarity=0.320  Sum_probs=59.5

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHh---------------------CCChHHHHHHHHHHHhHH
Q psy16797         17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKEL---------------------NLCERQIKIWFQNRRMKK   75 (99)
Q Consensus        17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l---------------------~l~~~~V~~WFqNrR~k~   75 (99)
                      .++++|.|+.|++.|+.+|+..|..++||+..++.+||..+                     ++++.+|++||+|||+++
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            45677899999999999999999999999999999999999                     799999999999999999


Q ss_pred             hhcCC
Q psy16797         76 KKGKT   80 (99)
Q Consensus        76 kr~~~   80 (99)
                      ++...
T Consensus        83 kr~~~   87 (102)
T 2da6_A           83 AFRQK   87 (102)
T ss_dssp             HHHHH
T ss_pred             HHhhH
Confidence            88643

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

Probab=99.77  E-value=6.2e-19  Score=105.83  Aligned_cols=66  Identities=23%  Similarity=0.352  Sum_probs=54.0

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHH------------------hC---CChHHHHHHHHHHHhH
Q psy16797         16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKE------------------LN---LCERQIKIWFQNRRMK   74 (99)
Q Consensus        16 ~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~------------------l~---l~~~~V~~WFqNrR~k   74 (99)
                      ..++.++.|+.|+..|+.+|+..|..++||+...+.+||..                  +|   |++.+|++||||+|++
T Consensus         5 ~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~k   84 (99)
T 1lfb_A            5 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE   84 (99)
T ss_dssp             --------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHHH
Confidence            34566779999999999999999999999999999999999                  88   9999999999999999


Q ss_pred             HhhcCCC
Q psy16797         75 KKKGKTP   81 (99)
Q Consensus        75 ~kr~~~~   81 (99)
                      ++++...
T Consensus        85 ~k~k~~~   91 (99)
T 1lfb_A           85 EAFRHKL   91 (99)
T ss_dssp             TSCCC--
T ss_pred             HHHhchh
Confidence            8876644

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

Probab=99.77  E-value=1e-18  Score=97.22  Aligned_cols=52  Identities=27%  Similarity=0.444  Sum_probs=50.0

Q ss_pred             CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      .+..|+..|+..|..++||+..++.+||..+||+..+|++||+|+|.++|+.
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            5799999999999999999999999999999999999999999999999874

>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=99.77  E-value=8.6e-19  Score=112.75  Aligned_cols=61  Identities=28%  Similarity=0.451  Sum_probs=57.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        18 ~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      ++++|.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||||||+++|+.
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            4667789999999999999999999999999999999999999999999999999999984

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

Probab=99.77  E-value=1.3e-18  Score=98.15  Aligned_cols=57  Identities=42%  Similarity=0.754  Sum_probs=53.5

Q ss_pred             CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797         25 TAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP   81 (99)
Q Consensus        25 ~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~   81 (99)
                      ...+..|+..|+..|..++||+..++..||..+||++.+|++||||||+++|+....
T Consensus         9 ~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~~~   65 (69)
T 2l9r_A            9 SHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLS   65 (69)
T ss_dssp             CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSSSS
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhhhh
Confidence            457899999999999999999999999999999999999999999999999987654

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

Probab=99.76  E-value=2.8e-18  Score=95.51  Aligned_cols=56  Identities=16%  Similarity=0.170  Sum_probs=51.3

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797         24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK   79 (99)
Q Consensus        24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~   79 (99)
                      +..++..|+..|+..|..++||+..++..||..+||++.+|++||||||+|.++.+
T Consensus         7 ~~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~~~   62 (64)
T 2e19_A            7 GQPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISVQ   62 (64)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSCSS
T ss_pred             CCCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCCCC
Confidence            34567999999999999999999999999999999999999999999999877643

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

Probab=99.75  E-value=1.9e-18  Score=111.92  Aligned_cols=66  Identities=17%  Similarity=0.199  Sum_probs=54.9

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCC
Q psy16797         17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPE   82 (99)
Q Consensus        17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~   82 (99)
                      ..+.+|.|+.|+..|+..|+..|..++||+...+..||..+||++.+|++||||+|+++|+.....
T Consensus        94 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~~~  159 (164)
T 2d5v_A           94 GNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWLEH  159 (164)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC----
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccCCCC
Confidence            345677999999999999999999999999999999999999999999999999999998865543

>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=99.75  E-value=2.9e-18  Score=95.28  Aligned_cols=51  Identities=27%  Similarity=0.366  Sum_probs=47.1

Q ss_pred             HHHHHHHHHHH-hhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797         29 SNQLLALEKEF-NQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK   79 (99)
Q Consensus        29 ~~q~~~L~~~f-~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~   79 (99)
                      +.++..||..| ..++||+..++.+||..+||++++|++||||||+++|+..
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            45799999999 6799999999999999999999999999999999998754

>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=99.73  E-value=1.6e-17  Score=93.25  Aligned_cols=59  Identities=17%  Similarity=0.231  Sum_probs=50.8

Q ss_pred             CCCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCC
Q psy16797         25 TAYTSNQLLALEKEFN---QQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPED   83 (99)
Q Consensus        25 ~~~s~~q~~~L~~~f~---~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~   83 (99)
                      ..|+++++.+|+.+|.   .++||+..++..||..+||+..+|++||+|+|+++++....+.
T Consensus         3 g~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~~   64 (67)
T 3k2a_A            3 GIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQS   64 (67)
T ss_dssp             ---CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC----
T ss_pred             CcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHHHHh
Confidence            3699999999999999   9999999999999999999999999999999999998765543

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

Probab=99.63  E-value=1.8e-16  Score=105.15  Aligned_cols=61  Identities=25%  Similarity=0.386  Sum_probs=53.4

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhC---------------------CChHHHHHHHHHHHhHH
Q psy16797         17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELN---------------------LCERQIKIWFQNRRMKK   75 (99)
Q Consensus        17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~---------------------l~~~~V~~WFqNrR~k~   75 (99)
                      .++.+|.|+.|++.|+..|+..|..++||+...+.+||..++                     +++.+|++||+|||+++
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            345677899999999999999999999999999999999999                     99999999999999987


Q ss_pred             hh
Q psy16797         76 KK   77 (99)
Q Consensus        76 kr   77 (99)
                      +.
T Consensus       192 k~  193 (194)
T 1ic8_A          192 AF  193 (194)
T ss_dssp             C-
T ss_pred             hc
Confidence            64

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

Probab=99.58  E-value=5.2e-15  Score=86.87  Aligned_cols=55  Identities=16%  Similarity=0.245  Sum_probs=51.1

Q ss_pred             CCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797         25 TAYTSNQLLALEKEFNQ---QNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK   79 (99)
Q Consensus        25 ~~~s~~q~~~L~~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~   79 (99)
                      .-|++.+..+|+.+|..   ++||+..++..||..+||+..||.+||+|+|.+.++..
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            35889999999999987   99999999999999999999999999999999988754

>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=99.58  E-value=4.7e-15  Score=83.02  Aligned_cols=47  Identities=13%  Similarity=0.275  Sum_probs=44.5

Q ss_pred             HHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHH
Q psy16797         29 SNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKK   75 (99)
Q Consensus        29 ~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~   75 (99)
                      +.|+..|+.+|..|++|+.+++..||..+||+...|++||+|+|+.-
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~~   60 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVYQ   60 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhccccc
Confidence            57899999999999999999999999999999999999999999743

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

Probab=99.56  E-value=7.7e-15  Score=98.59  Aligned_cols=59  Identities=25%  Similarity=0.435  Sum_probs=52.4

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhC---------------------CChHHHHHHHHHHHhHH
Q psy16797         17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELN---------------------LCERQIKIWFQNRRMKK   75 (99)
Q Consensus        17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~---------------------l~~~~V~~WFqNrR~k~   75 (99)
                      .++.+|.|+.|++.|+.+|+..|..++||+..+|.+||..+|                     |++.+|++||+|||+..
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            445677899999999999999999999999999999999987                     89999999999999753

>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=99.44  E-value=1.1e-13  Score=98.87  Aligned_cols=55  Identities=25%  Similarity=0.493  Sum_probs=51.5

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797         22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK   76 (99)
Q Consensus        22 r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k   76 (99)
                      +.+..++..++..|+..|..++||+..+|.+||..+||+.+||++||||||.|+|
T Consensus       367 ~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          367 AAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            3466799999999999999999999999999999999999999999999998865

>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=98.69  E-value=1.8e-10  Score=56.95  Aligned_cols=23  Identities=65%  Similarity=0.913  Sum_probs=19.0

Q ss_pred             HHHHHHHHHHHhHHhhcCCCCCc
Q psy16797         62 RQIKIWFQNRRMKKKKGKTPEDN   84 (99)
Q Consensus        62 ~~V~~WFqNrR~k~kr~~~~~~~   84 (99)
                      +||+|||||||+|||+.......
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~~~   23 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFNDAR   23 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHHTT
T ss_pred             CCceeccHHHHHHHHHHhHHHHH
Confidence            47999999999999998766433

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

Probab=97.34  E-value=0.00048  Score=38.16  Aligned_cols=45  Identities=20%  Similarity=0.364  Sum_probs=40.1

Q ss_pred             CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHH
Q psy16797         27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNR   71 (99)
Q Consensus        27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNr   71 (99)
                      .++.....|+.+|.....+.......|+.+.+|+..+|+-||-.+
T Consensus        13 ~~p~~~e~L~~Yy~~hk~L~EeDl~~L~~kskms~qqvkdwFa~k   57 (70)
T 2ys9_A           13 PPPPDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSR   57 (70)
T ss_dssp             CCCCCCHHHHHHHHHTCCCCTTHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             CCCCcchHHHHHHHHhcccchhhHHHHHHHhCCCHHHHHHHHHhc
Confidence            444556899999999999999999999999999999999999653

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

Probab=93.13  E-value=0.25  Score=25.55  Aligned_cols=46  Identities=22%  Similarity=0.425  Sum_probs=31.9

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHH
Q psy16797         24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQN   70 (99)
Q Consensus        24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqN   70 (99)
                      +..|+.++.......+.. ..+.......+|..+|++...|..|...
T Consensus         3 r~~ys~efK~~~~~~~~~-g~s~~~~~~~vA~~~gIs~~tl~~W~~~   48 (59)
T 2glo_A            3 RRIFTPHFKLQVLESYRN-DNDCKGNQRATARKYNIHRRQIQKWLQC   48 (59)
T ss_dssp             CCCCCHHHHHHHHHHHHH-CTTTTTCHHHHHHHTTSCHHHHHHHHTT
T ss_pred             CCcCCHHHHHHHHHHHHc-CCCcchHHHHHHHHHCcCHHHHHHHHHH
Confidence            456888887666555443 3321223568899999999999999753

>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=92.92  E-value=0.65  Score=27.51  Aligned_cols=48  Identities=15%  Similarity=0.258  Sum_probs=37.4

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHh
Q psy16797         23 ARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRM   73 (99)
Q Consensus        23 ~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~   73 (99)
                      .|..+|.++...+-..+..++.+..   ..+|..+|++...|..|..++..
T Consensus         4 ~r~~~t~e~K~~iv~~~~~~g~~~~---~~~A~~~gvs~stl~~~~~~~~~   51 (131)
T 1hlv_A            4 KRRQLTFREKSRIIQEVEENPDLRK---GEIARRFNIPPSTLSTILKNKRA   51 (131)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSCH---HHHHHHHTCCHHHHHHHHHTHHH
T ss_pred             cceeCCHHHHHHHHHHHHHCCCCcH---HHHHHHhCCCHHHHHHHHhchhh
Confidence            5678999998777777755655542   35789999999999999987665

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=90.12  E-value=1.5  Score=24.38  Aligned_cols=47  Identities=15%  Similarity=0.332  Sum_probs=33.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy16797         21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRR   72 (99)
Q Consensus        21 ~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR   72 (99)
                      ++.+..++.++....-..+. ...    ...++|..+|++...|..|...-.
T Consensus        17 ~~~~~~ys~e~k~~~v~~~~-~g~----s~~~iA~~~gIs~sTl~rW~k~~~   63 (87)
T 2elh_A           17 KRPLRSLTPRDKIHAIQRIH-DGE----SKASVARDIGVPESTLRGWCKNED   63 (87)
T ss_dssp             SSCCSSCCHHHHHHHHHHHH-HTC----CHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHH-CCC----CHHHHHHHHCcCHHHHHHHHHHHH
Confidence            34566789988655555554 332    255789999999999999985433

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=88.62  E-value=1  Score=23.36  Aligned_cols=50  Identities=14%  Similarity=-0.107  Sum_probs=37.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797         26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT   80 (99)
Q Consensus        26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~   80 (99)
                      .+++.+..++...|-..     ....++|..+|++...|+.+...-+.+.++...
T Consensus        15 ~L~~~~r~il~l~~~~g-----~s~~eIA~~lgis~~tv~~~~~ra~~~l~~~l~   64 (70)
T 2o8x_A           15 DLTTDQREALLLTQLLG-----LSYADAAAVCGCPVGTIRSRVARARDALLADAE   64 (70)
T ss_dssp             SSCHHHHHHHHHHHTSC-----CCHHHHHHHHTSCHHHHHHHHHHHHHHHHC---
T ss_pred             hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence            47788888888765432     225678999999999999999988888776543

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

Probab=88.43  E-value=1.9  Score=23.95  Aligned_cols=47  Identities=11%  Similarity=0.193  Sum_probs=35.6

Q ss_pred             CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      +++.+..+|...|-..     ....+||..+|++...|+.+...-+.+.++.
T Consensus        38 L~~~~r~vl~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~   84 (92)
T 3hug_A           38 LSAEHRAVIQRSYYRG-----WSTAQIATDLGIAEGTVKSRLHYAVRALRLT   84 (92)
T ss_dssp             SCHHHHHHHHHHHTSC-----CCHHHHHHHHTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            6677777776654322     2356789999999999999999888887764

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=86.91  E-value=2.8  Score=23.61  Aligned_cols=50  Identities=16%  Similarity=0.147  Sum_probs=38.7

Q ss_pred             CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797         25 TAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT   80 (99)
Q Consensus        25 ~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~   80 (99)
                      ..+++.+..+|...+.-  +    ...+||..+|++...|+.+..+-+.+.+....
T Consensus        26 ~~Lt~~e~~vl~l~~~g--~----s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~   75 (95)
T 3c57_A           26 SGLTDQERTLLGLLSEG--L----TNKQIADRMFLAEKTVKNYVSRLLAKLGMERR   75 (95)
T ss_dssp             -CCCHHHHHHHHHHHTT--C----CHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCC
T ss_pred             hcCCHHHHHHHHHHHcC--C----CHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCH
Confidence            45899999998886432  2    24678999999999999999988888776543

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=86.76  E-value=2.2  Score=22.28  Aligned_cols=52  Identities=12%  Similarity=0.100  Sum_probs=38.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      .+++.+..++...|..+.+.. ....++|..+|++...|+.+...-+.+.+..
T Consensus         5 ~L~~~er~il~l~~~l~~~~g-~s~~eIA~~lgis~~tV~~~~~ra~~kLr~~   56 (68)
T 2p7v_B            5 GLTAREAKVLRMRFGIDMNTD-YTLEEVGKQFDVTRERIRQIEAKALRKLRHP   56 (68)
T ss_dssp             CCCHHHHHHHHHHTTTTSSSC-CCHHHHHHHHTCCHHHHHHHHHHHHHGGGSC
T ss_pred             cCCHHHHHHHHHHHccCCCCC-CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            478888899988883321111 2356789999999999999998887777654

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=86.53  E-value=2.9  Score=23.38  Aligned_cols=43  Identities=16%  Similarity=0.302  Sum_probs=30.3

Q ss_pred             CCCCCHHHHHHHHHHHhhc-CCCCHHHHHHHHHHhCCChHHHHHHHHH
Q psy16797         24 RTAYTSNQLLALEKEFNQQ-NYILRAKRHQLAKELNLCERQIKIWFQN   70 (99)
Q Consensus        24 r~~~s~~q~~~L~~~f~~~-~~p~~~~~~~la~~l~l~~~~V~~WFqN   70 (99)
                      |..++.++....-..+... .    .....+|..+|++...|..|...
T Consensus         3 r~~ys~e~k~~~v~~~~~~~g----~s~~~ia~~~gIs~~tl~rW~~~   46 (97)
T 2jn6_A            3 TKTYSEEFKRDAVALYENSDG----ASLQQIANDLGINRVTLKNWIIK   46 (97)
T ss_dssp             CCCCCHHHHHHHHHHHTTGGG----SCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHcCC----ChHHHHHHHHCcCHHHHHHHHHH
Confidence            3568888765555444322 2    23567899999999999999864

>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A

Probab=86.12  E-value=2.8  Score=22.90  Aligned_cols=48  Identities=17%  Similarity=0.160  Sum_probs=36.7

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797         24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK   77 (99)
Q Consensus        24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr   77 (99)
                      -..+++.+..+|..++.  .    ....+||..+|++...|+.+..+-+.+.+.
T Consensus        19 ~~~Lt~~e~~vl~l~~~--g----~s~~eIA~~l~is~~tV~~~l~r~~~kL~~   66 (82)
T 1je8_A           19 VNQLTPRERDILKLIAQ--G----LPNKMIARRLDITESTVKVHVKHMLKKMKL   66 (82)
T ss_dssp             GGGSCHHHHHHHHHHTT--T----CCHHHHHHHHTSCHHHHHHHHHHHHHHTTC
T ss_pred             HccCCHHHHHHHHHHHc--C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHcC
Confidence            34689999999888532  2    235678999999999999999877766544

>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp}

Probab=84.47  E-value=4.2  Score=24.14  Aligned_cols=47  Identities=15%  Similarity=0.033  Sum_probs=33.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      .+++.+..++. .|-     ......+||..+|++...|+.+...-+.+.++.
T Consensus       109 ~L~~~~r~v~~-~~~-----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~  155 (164)
T 3mzy_A          109 NFSKFEKEVLT-YLI-----RGYSYREIATILSKNLKSIDNTIQRIRKKSEEW  155 (164)
T ss_dssp             HSCHHHHHHHH-HHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHH-HHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            35556656665 322     222456789999999999999998888877764

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=84.10  E-value=3.3  Score=21.96  Aligned_cols=45  Identities=16%  Similarity=0.216  Sum_probs=32.9

Q ss_pred             CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797         27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK   77 (99)
Q Consensus        27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr   77 (99)
                      +++.+..++.-++.  .+    ...++|..+|++...|+.+..+-+.+.+.
T Consensus        17 L~~~e~~vl~l~~~--g~----s~~eIA~~l~is~~tV~~~~~r~~~kl~~   61 (79)
T 1x3u_A           17 LSERERQVLSAVVA--GL----PNKSIAYDLDISPRTVEVHRANVMAKMKA   61 (79)
T ss_dssp             HCHHHHHHHHHHTT--TC----CHHHHHHHTTSCHHHHHHHHHHHHHHTTC
T ss_pred             CCHHHHHHHHHHHc--CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHcC
Confidence            56777777776432  22    24579999999999999999877766554

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

Probab=83.90  E-value=2.3  Score=25.90  Aligned_cols=51  Identities=10%  Similarity=-0.063  Sum_probs=36.9

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797         26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP   81 (99)
Q Consensus        26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~   81 (99)
                      .+++.+..++.-.|-     ......+||..+|++...|+......|.+.++....
T Consensus        93 ~Lp~~~r~vl~L~~~-----~g~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~~  143 (157)
T 2lfw_A           93 RMTPLSRQALLLTAM-----EGFSPEDAAYLIEVDTSEVETLVTEALAEIEKQTRA  143 (157)
T ss_dssp             TSCTTHHHHHTTTSS-----SCCCHHHHHHTTTSCHHHHHHHHHHHHHHHHTTSSC
T ss_pred             hCCHHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence            456666666644332     223357899999999999999999988888876543

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=83.25  E-value=4.7  Score=23.08  Aligned_cols=47  Identities=17%  Similarity=0.041  Sum_probs=36.5

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797         24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK   76 (99)
Q Consensus        24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k   76 (99)
                      ...+++.+..+|.-.+.--      ...+||..+|++...|+.+..+-+.+..
T Consensus        32 ~~~Lt~re~~Vl~l~~~G~------s~~EIA~~L~iS~~TV~~~l~ri~~KLg   78 (99)
T 1p4w_A           32 DKRLSPKESEVLRLFAEGF------LVTEIAKKLNRSIKTISSQKKSAMMKLG   78 (99)
T ss_dssp             SSSCCHHHHHHHHHHHHTC------CHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             cCCCCHHHHHHHHHHHcCC------CHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence            4569999999997765422      2478999999999999999987666544

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=82.20  E-value=3  Score=23.09  Aligned_cols=47  Identities=15%  Similarity=0.129  Sum_probs=35.4

Q ss_pred             CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797         25 TAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK   77 (99)
Q Consensus        25 ~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr   77 (99)
                      ..+++.+..+|.-++.  .+.    ..+||..+|++...|+.+..+-+.+.+.
T Consensus        28 ~~Lt~~e~~vl~l~~~--g~s----~~eIA~~l~is~~tV~~~l~r~~~kL~~   74 (91)
T 2rnj_A           28 EMLTEREMEILLLIAK--GYS----NQEIASASHITIKTVKTHVSNILSKLEV   74 (91)
T ss_dssp             GGCCSHHHHHHHHHHT--TCC----TTHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             hcCCHHHHHHHHHHHc--CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            4588888888877543  322    3468999999999999999877766554

>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=82.14  E-value=2.8  Score=19.65  Aligned_cols=40  Identities=13%  Similarity=0.285  Sum_probs=28.0

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHH
Q psy16797         26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQN   70 (99)
Q Consensus        26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqN   70 (99)
                      .++..+...+...+.. ..    ...++|..+|++...|..|...
T Consensus         5 ~l~~~~~~~i~~~~~~-g~----s~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C            5 ALSDTERAQLDVMKLL-NV----SLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             CCCHHHHHHHHHHHHT-TC----CHHHHHHHHTCCHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHc-CC----CHHHHHHHHCcCHHHHHHHHhh
Confidence            4677766555455542 22    2567899999999999999853

>1s7o_A Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SPS1042/SPYM18_1152; putative DNA binding protein, structural genomics; 2.31A {Streptococcus pyogenes serotype M3} SCOP: a.4.13.3

Probab=81.70  E-value=5.9  Score=23.18  Aligned_cols=48  Identities=10%  Similarity=0.086  Sum_probs=37.2

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      .+++.+..++...|...-     ...++|..+|++...|+.+...-+.+.+..
T Consensus        22 ~L~~~~r~vl~l~y~~g~-----s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~   69 (113)
T 1s7o_A           22 LLTDKQMNYIELYYADDY-----SLAEIADEFGVSRQAVYDNIKRTEKILETY   69 (113)
T ss_dssp             GSCHHHHHHHHHHHHTCC-----CHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            367888888877654321     256789999999999999999888877654

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=81.03  E-value=4.3  Score=21.10  Aligned_cols=49  Identities=18%  Similarity=0.202  Sum_probs=36.8

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797         23 ARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK   77 (99)
Q Consensus        23 ~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr   77 (99)
                      .-..+++.+..+|..++  ..+    ...++|..+|++...|..+...-+.+.+.
T Consensus         8 ~~~~L~~~e~~il~~~~--~g~----s~~eIA~~l~is~~tV~~~~~~~~~kl~~   56 (74)
T 1fse_A            8 SKPLLTKREREVFELLV--QDK----TTKEIASELFISEKTVRNHISNAMQKLGV   56 (74)
T ss_dssp             CCCCCCHHHHHHHHHHT--TTC----CHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCHHHHHHHHHHH--cCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence            34568899999988853  232    35678999999999999999876666544

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

Probab=80.74  E-value=0.96  Score=21.79  Aligned_cols=39  Identities=13%  Similarity=0.201  Sum_probs=26.2

Q ss_pred             CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHH
Q psy16797         27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQN   70 (99)
Q Consensus        27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqN   70 (99)
                      ++.++...+...+.. . .   ...++|..+|++...|..|+..
T Consensus         6 ~~~~~~~~i~~l~~~-g-~---s~~~ia~~lgvs~~Tv~r~l~~   44 (52)
T 1jko_C            6 INKHEQEQISRLLEK-G-H---PRQQLAIIFGIGVSTLYRYFPA   44 (52)
T ss_dssp             SCTTHHHHHHHHHHT-T-C---CHHHHHHTTSCCHHHHHHHSCT
T ss_pred             CCHHHHHHHHHHHHc-C-C---CHHHHHHHHCCCHHHHHHHHHH
Confidence            445554444444543 2 2   3567899999999999999854

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*

Probab=80.73  E-value=4.6  Score=21.28  Aligned_cols=50  Identities=8%  Similarity=0.029  Sum_probs=37.5

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797         26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK   76 (99)
Q Consensus        26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k   76 (99)
                      .+++.+..++...|..... ......++|..+|++...|+.+...-+.+.+
T Consensus        10 ~L~~~er~il~l~~~l~~~-~~~s~~eIA~~l~is~~tV~~~~~ra~~kLr   59 (73)
T 1ku3_A           10 KLSEREAMVLKMRKGLIDG-REHTLEEVGAYFGVTRERIRQIENKALRKLK   59 (73)
T ss_dssp             TSCHHHHHHHHHHHTTTTS-SCCCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHHhcccC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            4788888999888752110 0122457899999999999999988888877

>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri}

Probab=80.56  E-value=5.9  Score=22.45  Aligned_cols=47  Identities=13%  Similarity=0.270  Sum_probs=31.3

Q ss_pred             CCCCCHHHHHHHHHHH-hhc-CCCC-HHHHHHHHHHhCCChHHHHHHHHH
Q psy16797         24 RTAYTSNQLLALEKEF-NQQ-NYIL-RAKRHQLAKELNLCERQIKIWFQN   70 (99)
Q Consensus        24 r~~~s~~q~~~L~~~f-~~~-~~p~-~~~~~~la~~l~l~~~~V~~WFqN   70 (99)
                      +..|+.++....-..+ ... .+.+ ......+|..+|+++.+|..|..-
T Consensus         4 ~~~ys~e~K~~~v~~~~~~~~~~~s~g~s~~~va~~~gIs~~tl~~W~~~   53 (108)
T 2rn7_A            4 NTRFSPEVRQRAVRMVLESQGEYDSQWATICSIAPKIGCTPETLRVWVRQ   53 (108)
T ss_dssp             SCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHhcccccccccccHHHHHHHHCcCHHHHHHHHHH
Confidence            3468888865444433 321 1222 245677999999999999999864

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=80.28  E-value=5.5  Score=21.87  Aligned_cols=53  Identities=8%  Similarity=0.090  Sum_probs=38.4

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797         26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK   79 (99)
Q Consensus        26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~   79 (99)
                      .+++.+..++...|-...- ......+||..+|++...|+.+...-+.+.+...
T Consensus        18 ~L~~~er~vl~l~~~l~~~-~~~s~~EIA~~lgis~~tV~~~~~ra~~kLr~~l   70 (87)
T 1tty_A           18 TLSPREAMVLRMRYGLLDG-KPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPS   70 (87)
T ss_dssp             TSCHHHHHHHHHHHTTTTS-SCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBTTB
T ss_pred             hCCHHHHHHHHHHHccCCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            3678888888888752100 0123567899999999999999988887777644

---

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	99
d9anta_	56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	8e-19
d1pufa_	77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	2e-18
d1p7ia_	53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	3e-18
d2cuea1	68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	4e-18
d2e1oa1	57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	5e-18
d2craa1	58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	1e-17
d1jgga_	57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	7e-17
d1b72a_	88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	1e-16
d1ig7a_	58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	2e-16
d1s7ea1	50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	2e-16
d1zq3p1	67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	4e-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	4e-15
d1vnda_	77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	5e-15
d1ftta_	68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	1e-14
d1au7a1	58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	2e-14
d1x2ma1	52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	2e-14
d1le8a_	53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	3e-14
d1yz8p1	60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	4e-14
d1uhsa_	72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	1e-13
d1ocpa_	67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	1e-13
d2cufa1	82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	3e-13
d1wh7a_	80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	1e-12
d1x2na1	62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	1e-12
d1wi3a_	71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	2e-12
d2cqxa1	59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	3e-12
d1e3oc1	57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	1e-11
d1k61a_	60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	1e-11
d1pufb_	73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	2e-11
d2ecba1	76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	1e-10
d1lfba_	78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	2e-09
d2ecca1	76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	2e-08

>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 = 71.0 bits (174), Expect = 8e-19
 Identities = 32/54 (59%), Positives = 38/54 (70%)

Query: 24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          R  YT  Q L LEKEF+   Y+ R +R ++A  L+L ERQIKIWFQNRRMK KK
Sbjct: 1  RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 54

>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 = 70.6 bits (173), Expect = 2e-18
 Identities = 32/60 (53%), Positives = 43/60 (71%)

Query: 18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          +  ++ R  YT +Q L LEKEF    Y+ R +R+++A+ LNL ERQ+KIWFQNRRMK KK
Sbjct: 11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70

>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 = 3e-18
 Identities = 29/53 (54%), Positives = 37/53 (69%)

Query: 22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74
          R RTA++S QL  L++EFN+  Y+   +R QL+ EL L E QIKIWFQN R K
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 53

>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 = 69.4 bits (170), Expect = 4e-18
 Identities = 24/57 (42%), Positives = 39/57 (68%)

Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          +R RT++T  Q+ ALEKEF + +Y     R +LA +++L E +I++WF NRR K ++
Sbjct: 2  QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRR 58

>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 = 68.7 bits (168), Expect = 5e-18
 Identities = 25/57 (43%), Positives = 38/57 (66%)

Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          K  +  ++++Q + LEK+F  Q Y+   +R +LAK L L ERQ+K WFQNRR K ++
Sbjct: 1  KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 57

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.4 bits (167), Expect = 1e-17
 Identities = 25/57 (43%), Positives = 38/57 (66%)

Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          ++ R  Y+  QL  LE+E+    +I + KR +++   +L ERQI IWFQNRR+K+KK
Sbjct: 2  RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 58

>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 = 66.1 bits (161), Expect = 7e-17
 Identities = 33/56 (58%), Positives = 43/56 (76%)

Query: 22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          R RTA+T +QL  LEKEF ++NY+ R +R +LA +LNL E  IK+WFQNRRMK K+
Sbjct: 1  RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 56

>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 = 66.2 bits (161), Expect = 1e-16
 Identities = 31/58 (53%), Positives = 40/58 (68%)

Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
              RT +T+ QL  LEKEF+   Y+ RA+R ++A  L L E Q+KIWFQNRRMK+KK
Sbjct: 27 PSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 84

>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 = 64.9 bits (158), Expect = 2e-16
 Identities = 28/57 (49%), Positives = 42/57 (73%)

Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          ++ RT +T+ QLLALE++F Q+ Y+  A+R + +  L+L E Q+KIWFQNRR K K+
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57

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

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

 Score = 64.5 bits (157), Expect = 2e-16
 Identities = 10/49 (20%), Positives = 20/49 (40%)

Query: 24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRR 72
          R  +T  Q   L   F +     +  +  ++++L L    +  +F N R
Sbjct: 2  RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 50

>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 = 64.2 bits (156), Expect = 4e-16
 Identities = 23/64 (35%), Positives = 36/64 (56%)

Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80
          +R RT +TS+Q+  LE+ F Q  Y+   +   L+ +L L   Q+KIWF+NRR + K    
Sbjct: 2  RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 61

Query: 81 PEDN 84
             +
Sbjct: 62 QHKD 65

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 66

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 64.1 bits (156), Expect = 6e-16
 Identities = 19/58 (32%), Positives = 25/58 (43%)

Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
            R RT     QL  L   +          + QL +   L  R I++WFQN+R K KK
Sbjct: 3  TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKK 60

>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 = 61.9 bits (150), Expect = 4e-15
 Identities = 23/58 (39%), Positives = 39/58 (67%)

Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          ++R+RT ++++QL  LE+ F +  Y     R +LA+  NL E +I++WFQNRR + +K
Sbjct: 2  QRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK 59

>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 = 62.0 bits (150), Expect = 5e-15
 Identities = 24/64 (37%), Positives = 35/64 (54%)

Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79
          K++ R  +T  Q   LE+ F QQ Y+   +R  LA  + L   Q+KIWFQN R K K+ +
Sbjct: 9  KRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ 68

Query: 80 TPED 83
            + 
Sbjct: 69 NEKG 72

>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 = 60.7 bits (147), Expect = 1e-14
 Identities = 22/58 (37%), Positives = 35/58 (60%)

Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          +++ R  ++  Q+  LE+ F QQ Y+   +R  LA  ++L   Q+KIWFQN R K K+
Sbjct: 2  RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKR 59

>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 = 59.9 bits (145), Expect = 2e-14
 Identities = 18/58 (31%), Positives = 34/58 (58%)

Query: 22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79
          + RT  +     ALE+ F + +     +  ++A+ELNL +  +++WF NRR ++K+ K
Sbjct: 1  KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRVK 58

>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 = 59.3 bits (144), Expect = 2e-14
 Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 28 TSNQLLALEKEFNQQN-YILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          T+     LEK F     +    +   L+K+L+   R I+ WF+ RR ++K 
Sbjct: 1  TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 51

>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 = 59.1 bits (143), Expect = 3e-14
 Identities = 12/53 (22%), Positives = 31/53 (58%)

Query: 24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
          +++ +      LE+ F ++  +   ++ ++AK+  +   Q+++WF N+RM+ K
Sbjct: 1  KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53

>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 = 59.2 bits (143), Expect = 4e-14
 Identities = 23/57 (40%), Positives = 35/57 (61%)

Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          +R RT +TS QL  LE  F +  Y   + R ++A   NL E ++++WF+NRR K +K
Sbjct: 2  RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 58

>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 = 58.5 bits (141), Expect = 1e-13
 Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 1/58 (1%)

Query: 21 KRARTAYTSNQLLALEKEFNQ-QNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
                 T +Q+  LE  FN+   +        +A E  L E Q + WF+ R  + ++
Sbjct: 2  SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRR 59

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 67

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

 Score = 58.1 bits (140), Expect = 1e-13
 Identities = 17/61 (27%), Positives = 31/61 (50%)

Query: 17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
           + +KR RT+  +    +LE  F +       +   +A +L L +  +++WF NRR K K
Sbjct: 5  VQARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGK 64

Query: 77 K 77
          +
Sbjct: 65 R 65

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

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

 Score = 57.4 bits (138), Expect = 3e-13
 Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 15/71 (21%)

Query: 22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELN---------------LCERQIKI 66
           +R  +    L  +E  FN+  Y   AKR ++A   N               +   ++  
Sbjct: 2  GSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYN 61

Query: 67 WFQNRRMKKKK 77
          WF NRR + K+
Sbjct: 62 WFANRRKEIKR 72

>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 = 56.2 bits (135), Expect = 1e-12
 Identities = 12/67 (17%), Positives = 20/67 (29%), Gaps = 4/67 (5%)

Query: 15 DEKKGKKRARTAYTSNQLLALEKEFNQQ----NYILRAKRHQLAKELNLCERQIKIWFQN 70
                KR RT +T+ Q   +     +              Q   E  +  + +KIW  N
Sbjct: 12 SSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHN 71

Query: 71 RRMKKKK 77
           +     
Sbjct: 72 NKNSGPS 78

>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 = 55.5 bits (134), Expect = 1e-12
 Identities = 13/61 (21%), Positives = 22/61 (36%), Gaps = 3/61 (4%)

Query: 20 KKRARTAYTSNQLLALEKEFNQQ---NYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
           K  R     +    +     Q     Y    ++ Q+A + NL   Q+  WF N R +  
Sbjct: 2  GKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRIL 61

Query: 77 K 77
          +
Sbjct: 62 Q 62

>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 = 55.1 bits (132), Expect = 2e-12
 Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 18 KGKKRARTAYTSNQLLALEKEFNQQN-YILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
              R+RT  +   L  L+   +    Y  +   H L+ +L+L +  I  +FQN+R   K
Sbjct: 5  SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVK 64

Query: 77 K 77
           
Sbjct: 65 H 65

>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 = 54.0 bits (130), Expect = 3e-12
 Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 22 RARTAYTSNQLLALEKEFNQQN-YILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
          +            LEK F     Y    +   L+K+L+   R+I+ WF++RR + K
Sbjct: 3  KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 58

>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 = 1e-11
 Identities = 19/54 (35%), Positives = 32/54 (59%)

Query: 24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          RT+  +N  +ALEK F +           +A++LN+ +  I++WF NRR K+K+
Sbjct: 2  RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 55

>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 = 52.9 bits (127), Expect = 1e-11
 Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 3/54 (5%)

Query: 27 YTSNQLLALEKEFNQQN---YILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          +T   +  LE  F +     Y+       L K  +L   QIK W  NRR K+K 
Sbjct: 5  FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58

>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 = 52.7 bits (126), Expect = 2e-11
 Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 3/60 (5%)

Query: 21 KRARTAYTSNQLLALEKEFNQQN---YILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
          +R R  +       L + F       Y     + +LAK+  +   Q+  WF N+R++ KK
Sbjct: 2  RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61

>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 = 50.9 bits (121), Expect = 1e-10
 Identities = 12/58 (20%), Positives = 24/58 (41%)

Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
            +     T+ QL  L+  F   + +   + ++L  +  L  R+I  WF  ++  K  
Sbjct: 4  TPQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKAL 61

>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 = 47.9 bits (113), Expect = 2e-09
 Identities = 13/75 (17%), Positives = 25/75 (33%), Gaps = 21/75 (28%)

Query: 24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELN---------------------LCER 62
          R  +       L + + +Q    + +R  L +E N                     + E 
Sbjct: 1  RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 60

Query: 63 QIKIWFQNRRMKKKK 77
          ++  WF NRR ++  
Sbjct: 61 RVYNWFANRRKEEAF 75

>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 = 44.7 bits (105), Expect = 2e-08
 Identities = 15/59 (25%), Positives = 23/59 (38%)

Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79
            +    T  QL  L+  F Q  +  R    +L +   L   +I  WF + R   K G+
Sbjct: 4  GSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ 62

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	99
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.9
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.89
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.89
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.89
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.89
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.88
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.88
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.88
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.88
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.87
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.87
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.87
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.86
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.86
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.86
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.86
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.86
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.86
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.85
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.83
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.83
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.83
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.83
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.8
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.79
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.79
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.79
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.76
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.75
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.74
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.73
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.72
d1hlva1	66	DNA-binding domain of centromere binding protein B	95.12
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	89.07
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	87.81
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	87.76
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	86.32
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	84.24
d1j9ia_	68	Terminase gpNU1 subunit domain {Bacteriophage lamb	82.77

>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=99.90  E-value=9.6e-24  Score=114.25  Aligned_cols=57  Identities=44%  Similarity=0.817  Sum_probs=54.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797         21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK   77 (99)
Q Consensus        21 ~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr   77 (99)
                      ++.|+.||..|+.+|+..|..++||+..++..||..+||++.+|++||||+|+++|+
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=99.89  E-value=2e-23  Score=113.12  Aligned_cols=58  Identities=48%  Similarity=0.822  Sum_probs=55.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        21 ~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      +|.|+.||+.|+.+|+..|..++||+..++..||..+||++.+|++||||+|+++|+.
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   58 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL   58 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhccC
Confidence            4678999999999999999999999999999999999999999999999999999974

>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=99.89  E-value=3.5e-23  Score=111.77  Aligned_cols=57  Identities=44%  Similarity=0.768  Sum_probs=54.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797         21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK   77 (99)
Q Consensus        21 ~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr   77 (99)
                      ++.|++||+.|+..|+..|..++||+..++..||..+||++.+|++||||+|+++|+
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            467899999999999999999999999999999999999999999999999999986

>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=99.89  E-value=4.4e-23  Score=110.76  Aligned_cols=55  Identities=58%  Similarity=0.871  Sum_probs=53.5

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      |+.||+.|+..|+..|..++||+...+.+||..+||++.+|++||||+|+++|+.
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

>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=99.89  E-value=6.5e-23  Score=116.70  Aligned_cols=65  Identities=49%  Similarity=0.734  Sum_probs=59.7

Q ss_pred             cccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797         15 DEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK   79 (99)
Q Consensus        15 ~~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~   79 (99)
                      ...+..++.|++|++.|+.+|+..|..++||+..++..||..+||++.+|++||||+|+++|+..
T Consensus         8 ~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~   72 (77)
T d1pufa_           8 LHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKIN   72 (77)
T ss_dssp             CCCCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CccCcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHH
Confidence            34555677899999999999999999999999999999999999999999999999999999753

>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=99.88  E-value=6.8e-23  Score=110.59  Aligned_cols=57  Identities=58%  Similarity=0.889  Sum_probs=54.8

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        22 r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      |.|+.||+.|+..|+..|..++||+..++..||..+||++.+|++||||+|+++|+.
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            578999999999999999999999999999999999999999999999999999873

>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=99.88  E-value=5e-23  Score=114.46  Aligned_cols=61  Identities=38%  Similarity=0.641  Sum_probs=57.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797         21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP   81 (99)
Q Consensus        21 ~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~   81 (99)
                      +|.|++||+.|+..|+..|..++||+..++..||..+||++.+|++||||+|+++|+....
T Consensus         2 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~~   62 (67)
T d1zq3p1           2 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ   62 (67)
T ss_dssp             SCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhhh
Confidence            4578999999999999999999999999999999999999999999999999999986543

>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=99.88  E-value=1.3e-22  Score=112.18  Aligned_cols=60  Identities=38%  Similarity=0.674  Sum_probs=57.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        19 ~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      ++++.|+.|++.|+.+|+..|..++||+..++..||..+||++.+|++||||+|+++|+.
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~   60 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ   60 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhc
Confidence            456789999999999999999999999999999999999999999999999999999974

>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=99.88  E-value=1.7e-22  Score=112.56  Aligned_cols=64  Identities=34%  Similarity=0.657  Sum_probs=59.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCC
Q psy16797         20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPED   83 (99)
Q Consensus        20 ~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~   83 (99)
                      ++|.|+.||+.|+..|+..|..++||+...+..||..+||++.+|++||+|+|+++|+......
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~~~~~   65 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDKA   65 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSCCS
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhcccchh
Confidence            4678999999999999999999999999999999999999999999999999999998765543

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

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

Probab=99.87  E-value=5.4e-23  Score=117.11  Aligned_cols=66  Identities=36%  Similarity=0.640  Sum_probs=60.3

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCC
Q psy16797         17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPE   82 (99)
Q Consensus        17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~   82 (99)
                      ..++++.|++||++|+.+|+..|..++||+..++..||..+||++.+|++||||+|++.|+.....
T Consensus         6 p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~   71 (77)
T d1vnda_           6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEK   71 (77)
T ss_dssp             SSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSCCCS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHhhcc
Confidence            345667899999999999999999999999999999999999999999999999999998866544

>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=99.87  E-value=1.3e-22  Score=108.07  Aligned_cols=53  Identities=55%  Similarity=0.888  Sum_probs=51.2

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhH
Q psy16797         22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK   74 (99)
Q Consensus        22 r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k   74 (99)
                      |.|+.||+.|+..|+..|..++||+..++.+||..+||++.+|++||||+|+|
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            57899999999999999999999999999999999999999999999999985

>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=99.87  E-value=1.7e-22  Score=117.62  Aligned_cols=64  Identities=48%  Similarity=0.732  Sum_probs=55.3

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797         16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK   79 (99)
Q Consensus        16 ~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~   79 (99)
                      +.+..++.|+.|++.|+.+|+..|..++||+..++..||..+||++.+|++||||+|+++|+..
T Consensus        23 ~~~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~   86 (88)
T d1b72a_          23 GLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRE   86 (88)
T ss_dssp             -------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhc
Confidence            3445567899999999999999999999999999999999999999999999999999999854

>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=99.86  E-value=7.6e-22  Score=109.30  Aligned_cols=62  Identities=31%  Similarity=0.431  Sum_probs=58.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797         19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT   80 (99)
Q Consensus        19 ~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~   80 (99)
                      +.+|.|+.|+++|+.+|+..|..|+||+..++..||..+||++.+|++||+|+|++.|+...
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            45778999999999999999999999999999999999999999999999999999988654

>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=99.86  E-value=7.2e-22  Score=109.97  Aligned_cols=58  Identities=41%  Similarity=0.693  Sum_probs=55.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        21 ~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      +|.|+.||+.|+.+|+..|..++||+...+..||..+||++.+|++||+|+|+++|+.
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~   59 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE   59 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhh
Confidence            5678999999999999999999999999999999999999999999999999999874

>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=99.86  E-value=2e-22  Score=109.83  Aligned_cols=58  Identities=40%  Similarity=0.645  Sum_probs=55.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        21 ~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      +|.|+.||++|+.+|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.
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            5678999999999999999999999999999999999999999999999999999875

>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=99.86  E-value=5.8e-22  Score=110.04  Aligned_cols=61  Identities=28%  Similarity=0.422  Sum_probs=57.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        18 ~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      ..++|.|+.|++.|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.
T Consensus         6 ~~~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_           6 QARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             CCSSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             hccCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            3456789999999999999999999999999999999999999999999999999998874

>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=99.86  E-value=1.1e-21  Score=110.14  Aligned_cols=60  Identities=23%  Similarity=0.328  Sum_probs=56.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHhh-cCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797         21 KRARTAYTSNQLLALEKEFNQ-QNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT   80 (99)
Q Consensus        21 ~r~r~~~s~~q~~~L~~~f~~-~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~   80 (99)
                      ++.|++||..|+.+|+..|.. ++||+...+..||..+||++.+|++||||+|+++|+...
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            567899999999999999986 789999999999999999999999999999999998654

>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=99.86  E-value=1.2e-21  Score=106.04  Aligned_cols=57  Identities=30%  Similarity=0.490  Sum_probs=54.9

Q ss_pred             CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        22 r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      |.|+.|+.+|+.+|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.
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            578999999999999999999999999999999999999999999999999999875

>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=99.85  E-value=1.3e-21  Score=104.07  Aligned_cols=53  Identities=23%  Similarity=0.518  Sum_probs=51.2

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797         24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK   76 (99)
Q Consensus        24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k   76 (99)
                      |++||++|+.+|+..|..++||+..++..||..+||++.+|++||+|+|++.|
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            68899999999999999999999999999999999999999999999999865

>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=8e-21  Score=106.53  Aligned_cols=61  Identities=26%  Similarity=0.304  Sum_probs=56.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHh-hcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         18 KGKKRARTAYTSNQLLALEKEFN-QQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        18 ~~~~r~r~~~s~~q~~~L~~~f~-~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      ...++.|++|+++|+.+|+.+|. .++||+..++..||..+||++.+|++||+|+|++.|+.
T Consensus         5 ~~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk~   66 (71)
T d1wi3a_           5 SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS   66 (71)
T ss_dssp             CCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCSS
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhccc
Confidence            44567899999999999999997 58999999999999999999999999999999998873

>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=99.83  E-value=3.3e-21  Score=110.87  Aligned_cols=63  Identities=27%  Similarity=0.447  Sum_probs=57.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhC---------------CChHHHHHHHHHHHhHHhhcCCCCC
Q psy16797         21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELN---------------LCERQIKIWFQNRRMKKKKGKTPED   83 (99)
Q Consensus        21 ~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~---------------l~~~~V~~WFqNrR~k~kr~~~~~~   83 (99)
                      ++.|+.|++.|+.+|+.+|..++||+..++.+||..+|               |++.+|++||||+|+++|+......
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~~a~   78 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANIAA   78 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhhHHH
Confidence            57899999999999999999999999999999999875               9999999999999999999655443

>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=99.83  E-value=1.1e-20  Score=101.84  Aligned_cols=56  Identities=34%  Similarity=0.515  Sum_probs=54.0

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         23 ARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        23 ~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      .|+.|+++|+..|+..|..++||+..++..||..+||++.+|++||+|+|+++|+.
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            48899999999999999999999999999999999999999999999999999875

>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=99.83  E-value=2.7e-20  Score=105.62  Aligned_cols=64  Identities=20%  Similarity=0.313  Sum_probs=56.8

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCchhhcc
Q psy16797         26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNLEYKL   89 (99)
Q Consensus        26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~~~~~~   89 (99)
                      .+|++|+.+|+..|..++||+..++..||..+||++.+|++||+|+|++.++........+..+
T Consensus        10 ~~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~~~~~~~~~s   73 (76)
T d2ecba1          10 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEIDESNA   73 (76)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCCCCCCCCC
T ss_pred             CCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhHhhhcccCCC
Confidence            3589999999999999999999999999999999999999999999999888776665544433

>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=99.80  E-value=2.3e-19  Score=101.71  Aligned_cols=59  Identities=25%  Similarity=0.326  Sum_probs=54.6

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797         23 ARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP   81 (99)
Q Consensus        23 ~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~   81 (99)
                      .+.++|.+|+.+|+..|..++||+..++..||..+||+..+|++||+|+|+++|+....
T Consensus         6 ~~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~~~~   64 (76)
T d2ecca1           6 SGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLK   64 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCCS
T ss_pred             CCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhchHH
Confidence            34568999999999999999999999999999999999999999999999999986554

>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=99.79  E-value=3.4e-19  Score=100.26  Aligned_cols=61  Identities=25%  Similarity=0.438  Sum_probs=56.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797         21 KRARTAYTSNQLLALEKEFN---QQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP   81 (99)
Q Consensus        21 ~r~r~~~s~~q~~~L~~~f~---~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~   81 (99)
                      +|.|+.|+++|+.+|+.+|.   .++||+..++..||..+||+..+|++||+|+|++.++....
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            56788999999999999997   48899999999999999999999999999999999986543

>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=99.79  E-value=4e-20  Score=97.13  Aligned_cols=50  Identities=20%  Similarity=0.280  Sum_probs=48.6

Q ss_pred             CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy16797         23 ARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRR   72 (99)
Q Consensus        23 ~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR   72 (99)
                      +|+.||+.|+.+|+..|..++||+..++..||..+||++.+|++||||+|
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

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

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

Probab=99.79  E-value=5e-20  Score=105.40  Aligned_cols=63  Identities=19%  Similarity=0.206  Sum_probs=56.2

Q ss_pred             cccCCCCCCCCCCCHHHHHHHHHHHhh----cCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797         15 DEKKGKKRARTAYTSNQLLALEKEFNQ----QNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK   77 (99)
Q Consensus        15 ~~~~~~~r~r~~~s~~q~~~L~~~f~~----~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr   77 (99)
                      ....+++|.|+.||.+|+..|+.+|+.    ++||+..++..||..+||++.+|++||||+|.+.+.
T Consensus        12 ~~~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          12 SSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            334556678999999999999999986    789999999999999999999999999999987654

>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=99.76  E-value=8.6e-19  Score=99.59  Aligned_cols=56  Identities=23%  Similarity=0.369  Sum_probs=52.4

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhC---------------------CChHHHHHHHHHHHhHHhhcC
Q psy16797         24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELN---------------------LCERQIKIWFQNRRMKKKKGK   79 (99)
Q Consensus        24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~---------------------l~~~~V~~WFqNrR~k~kr~~   79 (99)
                      |.+|++.|+.+|+.+|..++||+...+..||..++                     |++.+|++||+|||++.|++.
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr~~   77 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFRH   77 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCCC
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHHhc
Confidence            67899999999999999999999999999999994                     899999999999999988754

>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=99.75  E-value=4.9e-19  Score=93.52  Aligned_cols=50  Identities=30%  Similarity=0.411  Sum_probs=46.4

Q ss_pred             CHHHHHHHHHHHhh-cCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797         28 TSNQLLALEKEFNQ-QNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK   77 (99)
Q Consensus        28 s~~q~~~L~~~f~~-~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr   77 (99)
                      |++|..+|+.+|.. ++||+..++..||..+||+..+|++||+|+|++.|+
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            45789999999986 789999999999999999999999999999999875

>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=99.74  E-value=6.2e-18  Score=91.68  Aligned_cols=54  Identities=31%  Similarity=0.420  Sum_probs=49.5

Q ss_pred             CCCCHHHHHHHHHHHhhc---CCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         25 TAYTSNQLLALEKEFNQQ---NYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        25 ~~~s~~q~~~L~~~f~~~---~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      .+|+++|+.+|+.+|..+   |||+..++..||..+||++.+|++||+|+|.+.|..
T Consensus         3 ~Rft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~~   59 (60)
T d1k61a_           3 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhccccccC
Confidence            349999999999999764   799999999999999999999999999999988763

>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=99.73  E-value=1.9e-18  Score=93.44  Aligned_cols=55  Identities=27%  Similarity=0.431  Sum_probs=50.1

Q ss_pred             CCCCCCCHHHHHHHHHHHhh-cCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797         22 RARTAYTSNQLLALEKEFNQ-QNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK   76 (99)
Q Consensus        22 r~r~~~s~~q~~~L~~~f~~-~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k   76 (99)
                      +.+.+++.++..+|+.+|.. ++||+..++..||..+||++.+|++||+|+|+++|
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            45667888888999999976 68999999999999999999999999999999876

>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=99.72  E-value=2.6e-17  Score=89.74  Aligned_cols=56  Identities=23%  Similarity=0.306  Sum_probs=51.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797         21 KRARTAYTSNQLLALEKEFNQ---QNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK   76 (99)
Q Consensus        21 ~r~r~~~s~~q~~~L~~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k   76 (99)
                      ++.|+.|++++..+|+.+|..   +|||+..++..||..+||+..+|++||+|+|.+..
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            345678999999999999985   79999999999999999999999999999998753

>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=95.12  E-value=0.073  Score=27.69  Aligned_cols=47  Identities=15%  Similarity=0.266  Sum_probs=38.6

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHh
Q psy16797         24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRM   73 (99)
Q Consensus        24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~   73 (99)
                      |..+|-.+...+-..|+.++...   ..+||..+|+...+|..|..|+..
T Consensus         5 Rk~LT~~eK~~ii~~~e~g~k~s---q~eIA~~fGv~~STvs~IlKnK~k   51 (66)
T d1hlva1           5 RRQLTFREKSRIIQEVEENPDLR---KGEIARRFNIPPSTLSTILKNKRA   51 (66)
T ss_dssp             SCCCCHHHHHHHHHHHHHCTTSC---HHHHHHHHTCCHHHHHHHHHTHHH
T ss_pred             cccCCHHHHHHHHHHHHcCCcch---HHHHHHHhCCChhHHHHHHHHHHH
Confidence            44589999888888888877555   457899999999999999998653

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=89.07  E-value=0.67  Score=23.30  Aligned_cols=47  Identities=6%  Similarity=-0.027  Sum_probs=34.8

Q ss_pred             CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797         27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG   78 (99)
Q Consensus        27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~   78 (99)
                      +++.+..++.-.|-..-     ...++|..+|++...|+......|.+.+..
T Consensus        19 Lp~~~r~v~~l~~~~~~-----s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~   65 (68)
T d1or7a1          19 LPEDLRMAITLRELDGL-----SYEEIAAIMDCPVGTVRSRIFRAREAIDNK   65 (68)
T ss_dssp             SCHHHHHHHHHHHTTCC-----CHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            45666666666654322     256789999999999999999888877654

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=87.81  E-value=0.77  Score=21.90  Aligned_cols=40  Identities=15%  Similarity=0.211  Sum_probs=33.3

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHH
Q psy16797         24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWF   68 (99)
Q Consensus        24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF   68 (99)
                      +..+|++|+......+.. ..    ...++|..+|++...|-.||
T Consensus         3 ~~~lt~~q~~~a~~l~~~-G~----s~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_           3 PRAINKHEQEQISRLLEK-GH----PRQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             CCSSCHHHHHHHHHHHHT-TC----CHHHHHHHHTCCHHHHHHHS
T ss_pred             CCcCCHHHHHHHHHHHHC-CC----CHHHHHHHHCcCHHHHHhhC
Confidence            456899999999999874 33    26789999999999999988

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=87.76  E-value=0.98  Score=23.99  Aligned_cols=44  Identities=16%  Similarity=0.301  Sum_probs=30.1

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHH
Q psy16797         24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQN   70 (99)
Q Consensus        24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqN   70 (99)
                      |..|+++.....-..+....   ......+|..+|+++.+|..|.+.
T Consensus         3 rk~Ys~EfK~~aV~l~~~~~---g~s~~~vA~~lGIs~~tl~~W~k~   46 (89)
T d2jn6a1           3 TKTYSEEFKRDAVALYENSD---GASLQQIANDLGINRVTLKNWIIK   46 (89)
T ss_dssp             CCCCCHHHHHHHHHHHTTGG---GSCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHcC---CCcHHHHHHHHCCCHHHHHHHHHH
Confidence            44689987665544443221   122566899999999999999864

>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Germination protein GerE
species: Bacillus subtilis [TaxId: 1423]

Probab=86.32  E-value=1.1  Score=22.44  Aligned_cols=46  Identities=17%  Similarity=0.225  Sum_probs=34.3

Q ss_pred             CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHH
Q psy16797         24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKK   75 (99)
Q Consensus        24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~   75 (99)
                      +..+|+.|..+|.-.-.  .    ..-.++|..+|+++..|+....+=..|.
T Consensus         2 ~p~LT~rE~~vl~l~~~--G----~s~~eIA~~L~is~~TV~~~~~~i~~Kl   47 (67)
T d1fsea_           2 KPLLTKREREVFELLVQ--D----KTTKEIASELFISEKTVRNHISNAMQKL   47 (67)
T ss_dssp             CCCCCHHHHHHHHHHTT--T----CCHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHc--c----CCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence            44689999999966532  2    2356789999999999999887665553

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=84.24  E-value=1.5  Score=21.87  Aligned_cols=47  Identities=11%  Similarity=0.129  Sum_probs=36.1

Q ss_pred             CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797         26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK   77 (99)
Q Consensus        26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr   77 (99)
                      .+++.+..++..+|-..     -...++|..+|++...|+......+.+.|+
T Consensus        21 ~L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~~~ra~~~Lr~   67 (71)
T d1rp3a2          21 KLPEREKLVIQLIFYEE-----LPAKEVAKILETSVSRVSQLKAKALERLRE   67 (71)
T ss_dssp             TSCHHHHHHHHHHHTSC-----CCHHHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhHh-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            36777777777766432     236788999999999999999888877665

>d1j9ia_ a.6.1.5 (A:) Terminase gpNU1 subunit domain {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: Terminase gpNU1 subunit domain
domain: Terminase gpNU1 subunit domain
species: Bacteriophage lambda [TaxId: 10710]

Probab=82.77  E-value=0.55  Score=24.33  Aligned_cols=19  Identities=32%  Similarity=0.489  Sum_probs=17.4

Q ss_pred             HHHHHHHhCCChHHHHHHH
Q psy16797         50 RHQLAKELNLCERQIKIWF   68 (99)
Q Consensus        50 ~~~la~~l~l~~~~V~~WF   68 (99)
                      +.+||..+|+++..|..|-
T Consensus         5 k~~lA~iFGVS~~TI~~W~   23 (68)
T d1j9ia_           5 KKQLADIFGASIRTIQNWQ   23 (68)
T ss_dssp             HHHHHHHTTCCHHHHHHHT
T ss_pred             HHHHHHHhCCCHHHHHHHH
Confidence            5789999999999999995